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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Authors Journal PubMedID Publication Date
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Sanborn, Adrian L; Rao, Suhas S P; Huang, Su-Chen; Durand, Neva C; Huntley, Miriam H; Jewett, Andrew I; Bochkov, Ivan D; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher P; Gnirke, Andreas; Melnikov, Alexandre; McKenna, Doug; Stamenova, Elena K; Lander, Eric S; Aiden, Erez Lieberman Proceedings of the National Academy of Sciences of the United States of America 26499245 2015 Nov 24
Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nagano, Takashi; Lubling, Yaniv; Yaffe, Eitan; Wingett, Steven W; Dean, Wendy; Tanay, Amos; Fraser, Peter Nature protocols. 26540590 2015 Dec;
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun Bioinformatics (Oxford, England). 26543175 2016 03 01;
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun Cell. 26686651 2015 Dec 17
TopDom: an efficient and deterministic method for identifying topological domains in genomes. Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine Nucleic acids research 26704975 2016 Apr 20
The redundancy of the mammalian heterochromatic compartment. Politz, Joan C Ritland; Scalzo, David; Groudine, Mark Curr Opin Genet Dev 26706451 2015 Dec 16
Imaging Transcription: Past, Present, and Future. Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée Cold Spring Harbor symposia on quantitative biology. 26763984 2016 Jan 13
Chemically activatable viral capsid functionalized for cancer targeting. Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland Nanomedicine 26786134 2016 Feb
Understanding Spatial Genome Organization: Methods and Insights. Ramani, Vijay; Shendure, Jay; Duan, Zhijun Genomics Proteomics Bioinformatics 26876719 2016 Feb
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting G3 (Bethesda) 26888867 2016
Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor Nucleus 26900797 2016 Mar
Activation of proto-oncogenes by disruption of chromosome neighborhoods. Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S; Valton, Anne-Laure; Bak, Rasmus O; Li, Charles H; Goldmann, Johanna; Lajoie, Bryan R; Fan, Zi Peng; Sigova, Alla A; Reddy, Jessica; Borges-Rivera, Diego; Lee, Tong Ihn; Jaenisch, Rudolf; Porteus, Matthew H; Dekker, Job; Young, Richard A Science 26940867 2016 Mar 25
Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun Genes & development. 26944681 2016 Mar 1;
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank Proceedings of the National Academy of Sciences of the United States of America 26951677 2016 Mar 22
The 3D Genome as Moderator of Chromosomal Communication. Dekker, Job; Mirny, Leonid Cell 26967279 2016 Mar 10
HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming BMC research notes 26969411 2016 Mar 11
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A J Bioinform Comput Biol 27021249 2016 Apr
A Guide to Packing Your DNA. Dekker, Job; Guttman, Mitchell; Lomvardas, Stavros Cell 27058655 2016 Apr 07
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. Molecular Cell 27067601 2016 April 5
Evolution of Epigenetic Regulation in Vertebrate Genomes. Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting Trends Genet 27080453 2016 May
Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. Nature Biotechnology 27088723 2016 April 18
Jointly characterizing epigenetic dynamics across multiple human cell types. Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C Nucleic acids research. 27095202 2016 08 19;
TAD disruption as oncogenic driver. Valton, Anne-Laure; Dekker, Job Curr Opin Genet Dev 27111891 2016 Feb
Dosage compensation of the sex chromosomes and autosomes. Disteche, Christine M Semin Cell Dev Biol 27112542 2016 Apr 22
Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 27145786 2016 Sep;
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E Cell Stem Cell 27152443 2016 May 5
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming Bioinformatics (Oxford, England). 27153668 2016 09 01;
Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M Disaster medicine and public health preparedness. 27174171 2016 06;
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Proserpio, Valentina; Piccolo, Andrea; Haim-Vilmovsky, Liora; Kar, Gozde; Lönnberg, Tapio; Svensson, Valentine; Pramanik, Jhuma; Natarajan, Kedar Nath; Zhai, Weichao; Zhang, Xiuwei; Donati, Giacomo; Kayikci, Melis; Kotar, Jurij; McKenzie, Andrew N J; Montandon, Ruddy; Billker, Oliver; Woodhouse, Steven; Cicuta, Pietro; Nicodemi, Mario; Teichmann, Sarah A Genome biology 27176874 2016 May 12
Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. Banigan, Edward J; Marko, John F Physical review. E. 27182590 2016 Apr;
Compaction and segregation of sister chromatids via active loop extrusion. Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid eLife. 27192037 2016 May 18;
Formation of Chromosomal Domains by Loop Extrusion. Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A Cell Rep 27210764 2016 May 19
CRISPR/Cas9 for Human Genome Engineering and Disease Research. Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S Annual review of genomics and human genetics. 27216776 2016 Aug 31;
Chromosome Compaction by Active Loop Extrusion. Goloborodko, Anton; Marko, John F; Mirny, Leonid A Biophysical journal. 27224481 2016 May 24;
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol A Cell. 27238023 2016 Jun 2;
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong Nature communications 27240697 2016 May 31
Use of genome-editing tools to treat sickle cell disease. Tasan, Ipek; Jain, Surbhi; Zhao, Huimin Human genetics. 27250347 2016 Jun 1;
Chromatin Domains: The Unit of Chromosome Organization. Dixon, Jesse R; Gorkin, David U; Ren, Bing Molecular cell. 27259200 2016 Jun 2;
What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. Symmons, Orsolya; Raj, Arjun Molecular cell. 27259209 2016 Jun 2;
CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop. Beagan, Jonathan A; Phillips-Cremins, Jennifer E Wiley interdisciplinary reviews. Systems biology and medicine. 27265842 2016 Jul;
RTFBSDB: an integrated framework for transcription factor binding site analysis. Wang, Zhong; Martins, André L; Danko, Charles G Bioinformatics (Oxford, England). 27288497 2016 Oct 01;
Enhancer Control of Transcriptional Bursting. Fukaya, Takashi; Lim, Bomyi; Levine, Michael Cell. 27293191 2016 Jul 14;
A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A Genes & development. 27340175 2016 Jun 15;
Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. McGeachie, Michael J; Yates, Katherine P; Zhou, Xiaobo; Guo, Feng; Sternberg, Alice L; Van Natta, Mark L; Wise, Robert A; Szefler, Stanley J; Sharma, Sunita; Kho, Alvin T; Cho, Michael H; Croteau-Chonka, Damien C; Castaldi, Peter J; Jain, Gaurav; Sanyal, American journal of respiratory and critical care medicine. 27367781 2016 Dec 15;
Nanoscale imaging of RNA with expansion microscopy. Chen, Fei; Wassie, Asmamaw T; Cote, Allison J; Sinha, Anubhav; Alon, Shahar; Asano, Shoh; Daugharthy, Evan R; Chang, Jae-Byum; Marblestone, Adam; Church, George M; Raj, Arjun; Boyden, Edward S Nature methods. 27376770 2016 Aug;
Identifying gene regulatory network rewiring using latent differential graphical models. Tian, Dechao; Gu, Quanquan; Ma, Jian Nucleic acids research. 27378774 2016 Sep 30;
Polymer physics of chromosome large-scale 3D organisation. Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario Scientific reports. 27405443 2016 Jul 13;
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman Proceedings of the National Academy of Sciences of the United States of America. 27432957 2016 Aug 02;
Structural organization of the inactive X chromosome in the mouse. Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job Nature. 27437574 2016 Jul 28;
Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. Beagrie, Robert A; Pombo, Ana BioEssays : news and reviews in molecular, cellular and developmental biology. 27452946 2016 09;
Allele-Specific Quantification of Structural Variations in Cancer Genomes. Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian Cell systems. 27453446 2016 Jul;
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez Lieberman Cell systems. 27467249 2016 Jul;
Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, Hiroko Scientific reports. 27516062 2016 Aug 12;
Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions. Shenoy, Shailesh M Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 27516727 2016 Jul;
A new correlation clustering method for cancer mutation analysis. Hou, Jack P; Emad, Amin; Puleo, Gregory J; Ma, Jian; Milenkovic, Olgica Bioinformatics (Oxford, England). 27540270 2016 Aug 18;
CRISPR-Cas9 nuclear dynamics and target recognition in living cells. Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Huisman, Maximiliaan; Zhang, Shaojie; Grunwald, David; Pederson, Thoru The Journal of cell biology. 27551060 2016 Aug 29;
Genome-wide mapping and analysis of chromosome architecture. Schmitt, Anthony D; Hu, Ming; Ren, Bing Nature reviews. Molecular cell biology. 27580841 2016 12;
Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. Stark, Marie; Cheng, R Holland Pharmaceutical patent analyst. 27610752 2016 Sep;
Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng PloS one. 27618313 2016;
Mapping 3D genome architecture through in situ DNase Hi-C. Ramani, Vijay; Cusanovich, Darren A; Hause, Ronald J; Ma, Wenxiu; Qiu, Ruolan; Deng, Xinxian; Blau, C Anthony; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun Nature protocols. 27685100 2016 Nov;
Transferable model for chromosome architecture. Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José N Proceedings of the National Academy of Sciences of the United States of America. 27688758 2016 Oct 25;
ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y Nature methods. 27749837 ;
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S Nature methods. 27776111 2016 Dec;
High-throughput assessment of context-dependent effects of chromatin proteins. Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas Epigenetics & chromatin. 27777628 2016;
An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Micha?; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz Genome research. 27789526 2016 Dec;
The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. Matheson, Timothy D; Kaufman, Paul D Molecular biology of the cell. 27807046 2017 Jan 01;
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, Bing Cell reports. 27851967 2016 Nov 15;
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn A Cell reports. 27851973 2016 Nov 15;
A dynamic mode of mitotic bookmarking by transcription factors. Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert eLife. 27855781 2016 Nov 19;
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Fang, Rongxin; Yu, Miao; Li, Guoqiang; Chee, Sora; Liu, Tristin; Schmitt, Anthony D; Ren, Bing Cell research. 27886167 2016 Dec;
Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Shin, Yongdae; Berry, Joel; Pannucci, Nicole; Haataja, Mikko P; Toettcher, Jared E; Brangwynne, Clifford P Cell. 28041848 2017 Jan 12;
Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan Genome research. 28049628 2017 Mar;
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F Molecular biology of the cell. 28057760 2017 Jan 05;
Predicting chromatin architecture from models of polymer physics. Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 28070687 2017 03
A New Era of Genome Integration-Simply Cut and Paste! Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, Huimin ACS synthetic biology. 28073246 2017 04 21;
Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, Ting Neoplasia (New York, N.Y.). 28088687 2017 Feb;
Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. Chao, Ran; Liang, Jing; Tasan, Ipek; Si, Tong; Ju, Linyang; Zhao, Huimin ACS synthetic biology. 28103009 2017 Apr 21;
Single-cell mRNA quantification and differential analysis with Census. Qiu, Xiaojie; Hill, Andrew; Packer, Jonathan; Lin, Dejun; Ma, Yi-An; Trapnell, Cole Nature methods. 28114287 2017 Mar;
ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis. Li, Zhaomin; Zhang, Peng; Yan, Aimin; Guo, Zhengyu; Ban, Yuguang; Li, Jin; Chen, Shi; Yang, Hui; He, Yongzheng; Li, Jianping; Guo, Ying; Zhang, Wen; Hajiramezanali, Ehsan; An, Huangda; Fajardo, Darlene; Harbour, J William; Ruan, Yijun; Nimer, Stephen D; Yu, Peng; Chen, Xi; Xu, Mingjiang; Yang, Feng-Chun Science advances. 28116354 2017 Jan;
High-throughput automated microfluidic sample preparation for accurate microbial genomics. Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C Nature communications. 28128213 2017 Jan 27;
Massively multiplex single-cell Hi-C. Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Gunderson, Kevin L; Steemers, Frank J; Disteche, Christine M; Noble, William S; Duan, Zhijun; Shendure, Jay Nature methods. 28135255 2017 Mar;
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E Molecular cell. 28157505 2017 Feb 02;
Software tools for visualizing Hi-C data. Yard?mc?, Galip Gürkan; Noble, William Stafford Genome biology. 28159004 2017 Feb 03;
Comprehensive characterization of neutrophil genome topology. Zhu, Yina; Gong, Ke; Denholtz, Matthew; Chandra, Vivek; Kamps, Mark P; Alber, Frank; Murre, Cornelis Genes & development. 28167501 2017 Jan 15;
Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. Finn, Elizabeth H; Pegoraro, Gianluca; Shachar, Sigal; Misteli, Tom Methods (San Diego, Calif.). 28179124 2017 Jul 01;
A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, Huimin ACS synthetic biology. 28215080 2017 Mar 07;
Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Oomen, Marlies E; Dekker, Job Critical reviews in biochemistry and molecular biology. 28228067 2017 Apr;
Multivalent Small-Molecule Pan-RAS Inhibitors. Welsch, Matthew E; Kaplan, Anna; Chambers, Jennifer M; Stokes, Michael E; Bos, Pieter H; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A; Huang, Christine S; Tran, Timothy H; Akkiraju, Hemanth; Brown, Lewis M; Nandakumar, Renu; Cremers, Serge; Yang, Wan Seok; Tong, Liang; Olive, Kenneth P; Ferrando, Adolfo; Stockwell, Brent R Cell. 28235199 ;
Unearthing worm replication origins. Sasaki, Takayo; Gilbert, David M Nature structural & molecular biology. 28257138 2017 03 03;
Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem; Bandaria, Jigar; Mir, Mustafa; Szlachta, Karol; Singh, Ritambhara; Darzacq, Xavier; Yildiz, Ahmet; Adli, Mazhar Nature communications. 28290446 2017 Mar 14;
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. Lowdon, Rebecca F; Wang, Ting PloS one. 28333948 2017;
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman Science (New York, N.Y.). 28336562 2017 Apr 07;
Form and function of topologically associating genomic domains in budding yeast. Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M Proceedings of the National Academy of Sciences of the United States of America. 28348222 2017 Apr 11;
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting Nature communications. 28348391 2017 Mar 28;
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë Nature. 28355183 2017 04 06;
FISHing Out the Details of CRISPR Genome Tracks. Coté, Allison J; Raj, Arjun Biophysical journal. 28355532 2017 Mar 28;
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun Nature protocols. 28358394 2017 May;
Facilitated dissociation of transcription factors from single DNA binding sites. Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F Proceedings of the National Academy of Sciences of the United States of America. 28364020 2017 Apr 18;
The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu, Sarah C; Gilgenast, Thomas G; Bartman, Caroline R; Edwards, Christopher R; Stonestrom, Aaron J; Huang, Peng; Emerson, Daniel J; Evans, Perry; Werner, Michael T; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Phillips-Cremins, Jenn Molecular cell. 28388437 2017 Apr 06;
Causes and consequences of nuclear gene positioning. Shachar, Sigal; Misteli, Tom Journal of cell science. 28404786 2017 May 01;
An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso Nature structural & molecular biology. 28414321 2017 May;
p53 dynamically directs TFIID assembly on target gene promoters. Coleman, R A; Qiao, Z; Singh, S K; Peng, C S; Cianfrocco, M; Zhang, Z; Piasecka, A; Aldeborgh, H; Basishvili, G; Liu, W L Molecular and cellular biology. 28416636 2017 Apr 17;
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long Biophysical journal. 28427715 2017 May 09;
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Belaghzal, Houda; Dekker, Job; Gibcus, Johan H Methods (San Diego, Calif.). 28435001 2017 Apr 18;
Rapid Rates of Pol II Elongation in the Drosophila Embryo. Fukaya, Takashi; Lim, Bomyi; Levine, Michael Current biology : CB. 28457866 2017 May 08;
ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee The Journal of experimental medicine. 28461595 2017 May 01;
CTCF and cohesin regulate chromatin loop stability with distinct dynamics. Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier eLife. 28467304 2017 May 03;
Genetic interaction mapping in mammalian cells using CRISPR interference. Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan J Nature methods. 28481362 2017 Jun;
Combinatorial chemistry in drug discovery. Liu, Ruiwu; Li, Xiaocen; Lam, Kit S Current opinion in chemical biology. 28494316 2017 Jun;
Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. van Steensel, Bas; Belmont, Andrew S Cell. 28525751 2017 May 18;
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G Cell. 28525758 2017 May 18;
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Beagan, Jonathan A; Duong, Michael T; Titus, Katelyn R; Zhou, Linda; Cao, Zhendong; Ma, Jingjing; Lachanski, Caroline V; Gillis, Daniel R; Phillips-Cremins, Jennifer E Genome research. 28536180 2017 07;
The dynamic three-dimensional organization of the diploid yeast genome. Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya J eLife. 28537556 2017 May 24;
HUGIn: Hi-C Unifying Genomic Interrogator. Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, Yun Bioinformatics (Oxford, England). 28582503 2017 Dec 01;
Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, Ting BMC genomics. 28583088 2017 Jun 05;
Engineering biological systems using automated biofoundries. Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin Metabolic engineering. 28602523 2017 Jul;
FISH-ing for captured contacts: towards reconciling FISH and 3C. Fudenberg, Geoffrey; Imakaev, Maxim Nature methods. 28604723 2017 Jul;
Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H Nature methods. 28604724 2017 Jun 12;
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Nature genetics. 28604729 2017 Jul;
EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. He, Yu; Wang, Ting Bioinformatics (Oxford, England). 28605501 2017 Jun 09;
DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis J JCI insight. 28614801 2017 Jun 15;
Torque and buckling in stretched intertwined double-helix DNAs. Brahmachari, Sumitabha; Marko, John F Physical review. E. 28618488 2017 May;
Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. Sun, Xiaoming; Bizhanova, Aizhan; Matheson, Timothy D; Yu, Jun; Zhu, Julie L; Kaufman, Paul D Molecular and cellular biology. 28630280 2017 Jun 19;
Phase separation drives heterochromatin domain formation. Strom, Amy R; Emelyanov, Alexander V; Mir, Mustafa; Fyodorov, Dmitry V; Darzacq, Xavier; Karpen, Gary H Nature. 28636597 2017 07 13;
Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, Amos Nature. 28682332 2017 07 05;
Integrative modelling of cellular assemblies. Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, Maya Current opinion in structural biology. 28735107 2017 Jul 20;
Genome Organization Drives Chromosome Fragility. Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André Cell. 28735753 2017 Jul 27;
ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Ou, Horng D; Phan, Sébastien; Deerinck, Thomas J; Thor, Andrea; Ellisman, Mark H; O'Shea, Clodagh C Science (New York, N.Y.). 28751582 2017 07 28;
The three-dimensional genome organization of Drosophila melanogaster through data integration. Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank Genome biology. 28760140 2017 Jul 31;
Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger D Proceedings of the National Academy of Sciences of the United States of America. 28765367 2017 Aug 15;
The Three-Dimensional Organization of Mammalian Genomes. Yu, Miao; Ren, Bing Annual review of cell and developmental biology. 28783961 2017 Oct 06;
A new era of studying p53-mediated transcription activation. Liu, Wei-Li; Coleman, Robert A; Singh, Sameer K Transcription. 28795863 2018;
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P; Xu, Jianliang; Jung, Seolkyoung; Pekowska, Aleksandra; Dose, Marei; Stevens, Evan; Mathe, Ewy; Dong, Peng; Huang, Su-Chen; Ricci, Maria Aurelia; Baranello, Laura; Zheng, Ying; Tomassoni Ardori, Francesco; Resch, Wolfgang; Stavreva, Diana; Nelson, Steevenson; McAndrew, Michael; Casellas, Adriel; Finn, Elizabeth; Gregory, Charles; St Hilaire, Brian Glenn; Johnson, Steven M; Dubois, Wendy; Cosma, Maria Pia; Batchelor, Eric; Levens, David; Phair, Robert D; Misteli, Tom; Tessarollo, Lino; Hager, Gordon; Lakadamyali, Melike; Liu, Zhe; Floer, Monique; Shroff, Hari; Aiden, Erez Lieberman; Casellas, Rafael Molecular cell. 28803781 ;
A magnetic micropore chip for rapid ( Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, David Lab on a chip. 28809985 2017 Sep 12;
Comprehensive single-cell transcriptional profiling of a multicellular organism. Cao, Junyue; Packer, Jonathan S; Ramani, Vijay; Cusanovich, Darren A; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N; Steemers, Frank J; Adey, Andrew; Waterston, Robert H; Trapnell, Cole; Shendure, Jay Science (New York, N.Y.). 28818938 2017 08 18;
SMC complexes differentially compact mitotic chromosomes according to genomic context. Schalbetter, Stephanie Andrea; Goloborodko, Anton; Fudenberg, Geoffrey; Belton, Jon-Matthew; Miles, Catrina; Yu, Miao; Dekker, Job; Mirny, Leonid; Baxter, Jonathan Nature cell biology. 28825700 2017 Sep;
Reversed graph embedding resolves complex single-cell trajectories. Qiu, Xiaojie; Mao, Qi; Tang, Ying; Wang, Li; Chawla, Raghav; Pliner, Hannah A; Trapnell, Cole Nature methods. 28825705 2017 Oct;
Evolutionarily Conserved Principles Predict 3D Chromatin Organization. Rowley, M Jordan; Nichols, Michael H; Lyu, Xiaowen; Ando-Kuri, Masami; Rivera, I Sarahi M; Hermetz, Karen; Wang, Ping; Ruan, Yijun; Corces, Victor G Molecular cell. 28826674 2017 Sep 07;
Crossed wires: 3D genome misfolding in human disease. Norton, Heidi K; Phillips-Cremins, Jennifer E The Journal of cell biology. 28855250 2017 11 06;
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Yang, Tao; Zhang, Feipeng; Yard?mc?, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua Genome research. 28855260 2017 Nov;
The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality? Bach, Benjamin; Sicat, Ronell; Beyer, Johanna; Cordeil, Maxime; Pfister, Hanspeter IEEE transactions on visualization and computer graphics. 28866590 2018 01;
HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter IEEE transactions on visualization and computer graphics. 28866592 2018 Jan;
LAIT: a local ancestry inference toolkit. Hui, Daniel; Fang, Zhou; Lin, Jerome; Duan, Qing; Li, Yun; Hu, Ming; Chen, Wei BMC genetics. 28877673 2017 09 06;
Exploiting sequence-based features for predicting enhancer-promoter interactions. Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, Jian Bioinformatics (Oxford, England). 28881991 2017 Jul 15;
MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew S Cell stem cell. 28886366 2017 Sep 07;
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P Molecular cell. 28890333 2017 Sep 21;
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting BMC genomics. 28899353 2017 Sep 12;
The 4D nucleome project. Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network Nature. 28905911 2017 Sep 13;
Targeting Specificity of the CRISPR/Cas9 System. Tasan, Ipek; Zhao, Huimin ACS synthetic biology. 28911233 2017 09 15;
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Huang, Peng; Keller, Cheryl A; Giardine, Belinda; Grevet, Jeremy D; Davies, James O J; Hughes, Jim R; Kurita, Ryo; Nakamura, Yukio; Hardison, Ross C; Blobel, Gerd A Genes & development. 28916711 2017 Aug 15;
Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, Stavros eLife. 28933695 2017 Sep 21;
Liquid phase condensation in cell physiology and disease. Shin, Yongdae; Brangwynne, Clifford P Science (New York, N.Y.). 28935776 2017 09 22;
Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. Rege, Mayuri; Phillips-Cremins, Jennifer E Molecular cell. 28938095 2017 Sep 21;
Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. Isoda, Takeshi; Moore, Amanda J; He, Zhaoren; Chandra, Vivek; Aida, Masatoshi; Denholtz, Matthew; Piet van Hamburg, Jan; Fisch, Kathleen M; Chang, Aaron N; Fahl, Shawn P; Wiest, David L; Murre, Cornelis Cell. 28938112 2017 Sep 21;
Structural aspects of the inactive X chromosome. Bonora, Giancarlo; Disteche, Christine M Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 28947656 2017 Nov 05;
From structure to function, how bioinformatics help to reveal functions of our genomes. Zheng, Xiaoqi; Zhong, Sheng Genome biology. 28950915 2017 Sep 26;
Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. Germier, Thomas; Kocanova, Silvia; Walther, Nike; Bancaud, Aurélien; Shaban, Haitham Ahmed; Sellou, Hafida; Politi, Antonio Zaccaria; Ellenberg, Jan; Gallardo, Franck; Bystricky, Kerstin Biophysical journal. 28978433 2017 Oct 03;
Dense Bicoid hubs accentuate binding along the morphogen gradient. Mir, Mustafa; Reimer, Armando; Haines, Jenna E; Li, Xiao-Yong; Stadler, Michael; Garcia, Hernan; Eisen, Michael B; Darzacq, Xavier Genes & development. 28982761 2017 Sep 01;
Cohesin Loss Eliminates All Loop Domains. Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian; Engreitz, Jesse M; Perez, Elizabeth M; Kieffer-Kwon, Kyong-Rim; Sanborn, Adrian L; Johnstone, Sarah E; Bascom, Gavin D; Bochkov, Ivan D; Huang, Xingfan; Shamim, Muhammad S; Shin, Jaeweon; Turner, Douglass; Ye, Ziyi; Omer, Arina D; Robinson, James T; Schlick, Tamar; Bernstein, Bradley E; Casellas, Rafael; Lander, Eric S; Aiden, Erez Lieberman Cell. 28985562 2017 Oct 05;
Transvection. Fukaya, Takashi; Levine, Michael Current biology : CB. 29017034 2017 Oct 09;
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. Sun, Zhe; Wang, Ting; Deng, Ke; Wang, Xiao-Feng; Lafyatis, Robert; Ding, Ying; Hu, Ming; Chen, Wei Bioinformatics (Oxford, England). 29036318 2018 01 01;
RNA structure interactions and ribonucleoprotein processes of the influenza A virus. Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz Briefings in functional genomics. 29040388 2018 11 26;
Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. Banigan, Edward J; Stephens, Andrew D; Marko, John F Biophysical journal. 29045860 2017 Oct 17;
Supercoiling DNA Locates Mismatches. Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir C Physical review letters. 29053317 2017 Oct 06;
A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. Gallagher, Michael D; Posavi, Marijan; Huang, Peng; Unger, Travis L; Berlyand, Yosef; Gruenewald, Analise L; Chesi, Alessandra; Manduchi, Elisabetta; Wells, Andrew D; Grant, Struan F A; Blobel, Gerd A; Brown, Christopher D; Chen-Plotkin, Alice S American journal of human genetics. 29056226 2017 Nov 02;
Recent evidence that TADs and chromatin loops are dynamic structures. Hansen, Anders S; Cattoglio, Claudia; Darzacq, Xavier; Tjian, Robert Nucleus (Austin, Tex.). 29077530 2018 01 01;
STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus. Li, Peng; Mitra, Suman; Spolski, Rosanne; Oh, Jangsuk; Liao, Wei; Tang, Zhonghui; Mo, Fei; Li, Xingwang; West, Erin E; Gromer, Daniel; Lin, Jian-Xin; Liu, Chengyu; Ruan, Yijun; Leonard, Warren J Proceedings of the National Academy of Sciences of the United States of America. 29078395 2017 11 14;
Oligomerization and ATP stimulate condensin-mediated DNA compaction. Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John F Scientific reports. 29079757 2017 Oct 27;
De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez; Wolynes, Peter G; Onuchic, José N Proceedings of the National Academy of Sciences of the United States of America. 29087948 2017 Nov 14;
Simultaneous measurement of emission color and 3D position of single molecules. Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, Sjoerd Optics express. 29092328 2016 Mar 07;
Two independent modes of chromatin organization revealed by cohesin removal. Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois Nature. 29094699 2017 Nov 02;
Nuclear microenvironments modulate transcription from low-affinity enhancers. Tsai, Albert; Muthusamy, Anand K; Alves, Mariana Rp; Lavis, Luke D; Singer, Robert H; Stern, David L; Crocker, Justin eLife. 29095143 2017 Nov 02;
Genome-wide association study identifies a novel locus for cannabis dependence. Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E C Molecular psychiatry. 29112194 2017 Nov 07;
Single mRNA Molecule Detection in Drosophila. Little, Shawn C; Gregor, Thomas Methods in molecular biology (Clifton, N.J.). 29130194 2018;
Live Imaging of mRNA Synthesis in Drosophila. Garcia, Hernan G; Gregor, Thomas Methods in molecular biology (Clifton, N.J.). 29130209 2018;
Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J; Almassalha, Luay M; Backman, Vadim; Adam, Stephen A; Goldman, Robert D; Marko, John F Molecular biology of the cell. 29142071 2018 Jan 15;
Corrigendum: The 4D nucleome project. Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network Nature. 29168505 2017 12 14;
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. Sundaram, Vasavi; Wang, Ting BioEssays : news and reviews in molecular, cellular and developmental biology. 29206283 2018 Jan;
A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. Gassler, Johanna; Brandão, Hugo B; Imakaev, Maxim; Flyamer, Ilya M; Ladstätter, Sabrina; Bickmore, Wendy A; Peters, Jan-Michael; Mirny, Leonid A; Tachibana, Kikuë The EMBO journal. 29217590 2017 12 15;
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. Wutz, Gordana; Várnai, Csilla; Nagasaka, Kota; Cisneros, David A; Stocsits, Roman R; Tang, Wen; Schoenfelder, Stefan; Jessberger, Gregor; Muhar, Matthias; Hossain, M Julius; Walther, Nike; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Zuber, Johannes; The EMBO journal. 29217591 2017 12 15;
Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D; Mondragón, Alfonso; Marko, John F Physical review letters. 29219598 2017 Nov 03;
Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, Ting Methods in molecular biology (Clifton, N.J.). 29224147 2018;
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. Kaewsapsak, Pornchai; Shechner, David Michael; Mallard, William; Rinn, John L; Ting, Alice Y eLife. 29239719 2017 Dec 14;
Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. Mukund, Kavitha; Subramaniam, Shankar Frontiers in physiology. 29249983 2017;
The structural variability of the influenza A hemagglutinin receptor-binding site. Lazniewski, Michal; Dawson, Wayne K; Szczepinska, Teresa; Plewczynski, Dariusz Briefings in functional genomics. 29253080 2018 11 26;
Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Baddeley, David; Bewersdorf, Joerg Annual review of biochemistry. 29272143 2018 06 20;
A mixed-scale dense convolutional neural network for image analysis. Pelt, Daniël M; Sethian, James A Proceedings of the National Academy of Sciences of the United States of America. 29279403 2018 Jan 09;
Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions. Shechtman, Yoav; Gustavsson, Anna-Karin; Petrov, Petar N; Dultz, Elisa; Lee, Maurice Y; Weis, Karsten; Moerner, W E Biomedical optics express. 29296501 2017 Dec 01;
Extrusion without a motor: a new take on the loop extrusion model of genome organization. Brackley, C A; Johnson, J; Michieletto, D; Morozov, A N; Nicodemi, M; Cook, P R; Marenduzzo, D Nucleus (Austin, Tex.). 29300120 2018 01 01;
Robust model-based analysis of single-particle tracking experiments with Spot-On. Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier eLife. 29300163 2018 Jan 04;
Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. Gerace, Larry; Tapia, Olga Current opinion in cell biology. 29306725 2018 Jun;
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Yan, Jian; Chen, Shi-An A; Local, Andrea; Liu, Tristin; Qiu, Yunjiang; Dorighi, Kristel M; Preissl, Sebastian; Rivera, Chloe M; Wang, Chaochen; Ye, Zhen; Ge, Kai; Hu, Ming; Wysocka, Joanna; Ren, Bing Cell research. 29313530 2018 Feb;
3D single-molecule super-resolution microscopy with a tilted light sheet. Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E Nature communications. 29317629 2018 Jan 09;
Ki-67: more than a proliferation marker. Sun, Xiaoming; Kaufman, Paul D Chromosoma. 29322240 2018 Jan 10;
Detecting hierarchical genome folding with network modularity. Norton, Heidi K; Emerson, Daniel J; Huang, Harvey; Kim, Jesi; Titus, Katelyn R; Gu, Shi; Bassett, Danielle S; Phillips-Cremins, Jennifer E Nature methods. 29334377 2018 Feb;
High-throughput identification of RNA nuclear enrichment sequences. Shukla, Chinmay J; McCorkindale, Alexandra L; Gerhardinger, Chiara; Korthauer, Keegan D; Cabili, Moran N; Shechner, David M; Irizarry, Rafael A; Maass, Philipp G; Rinn, John L The EMBO journal. 29335281 2018 Mar 15;
Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). Maass, Philipp G; Barutcu, A Rasim; Shechner, David M; Weiner, Catherine L; Melé, Marta; Rinn, John L Nature structural & molecular biology. 29343869 2018 Feb;
A pathway for mitotic chromosome formation. Gibcus, Johan H; Samejima, Kumiko; Goloborodko, Anton; Samejima, Itaru; Naumova, Natalia; Nuebler, Johannes; Kanemaki, Masato T; Xie, Linfeng; Paulson, James R; Earnshaw, William C; Mirny, Leonid A; Dekker, Job Science (New York, N.Y.). 29348367 2018 02 09;
Dynamic evolution of regulatory element ensembles in primate CD4+T cells. Danko, Charles G; Choate, Lauren A; Marks, Brooke A; Rice, Edward J; Wang, Zhong; Chu, Tinyi; Martins, Andre L; Dukler, Noah; Coonrod, Scott A; Tait Wojno, Elia D; Lis, John T; Kraus, W Lee; Siepel, Adam Nature ecology & evolution. 29379187 2018 Mar;
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun Methods (San Diego, Calif.). 29382556 2018 Jan 31;
Single-cell replication profiling to measure stochastic variation in mammalian replication timing. Dileep, Vishnu; Gilbert, David M Nature communications. 29382831 2018 Jan 30;
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Robinson, James T; Turner, Douglass; Durand, Neva C; Thorvaldsdóttir, Helga; Mesirov, Jill P; Aiden, Erez Lieberman Cell systems. 29428417 2018 Feb 28;
Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun Cell systems. 29454938 2018 Feb 28;
Quantitative 3-D morphometric analysis of individual dendritic spines. Basu, Subhadip; Saha, Punam Kumar; Roszkowska, Matylda; Magnowska, Marta; Baczynska, Ewa; Das, Nirmal; Plewczynski, Dariusz; Wlodarczyk, Jakub Scientific reports. 29476060 2018 Feb 23;
Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. Patriarchi, Tommaso; Shen, Ao; He, Wei; Baikoghli, Mo; Cheng, R Holland; Xiang, Yang K; Coleman, Matthew A; Tian, Lin Scientific reports. 29476125 2018 Feb 23;
Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations. Stevens, Kelly R; Murry, Charles E Cell stem cell. 29499147 2018 Mar 01;
dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Tsui, Chiahao; Inouye, Carla; Levy, Michaella; Lu, Andrew; Florens, Laurence; Washburn, Michael P; Tjian, Robert Proceedings of the National Academy of Sciences of the United States of America. 29507191 2018 03 20;
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. Barton, Carl; Morganella, Sandro; Ødegård-Fougner, Øyvind; Alexander, Stephanie; Ries, Jonas; Fitzgerald, Tomas; Ellenberg, Jan; Birney, Ewan PLoS computational biology. 29522506 2018 Mar;
Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin. Annunziatella, Carlo; Chiariello, Andrea M; Esposito, Andrea; Bianco, Simona; Fiorillo, Luca; Nicodemi, Mario Methods (San Diego, Calif.). 29522804 2018 06 01;
Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto; Hopp, Hannah; Das, Devika; Alber, Frank; Chiolo, Irene Methods in enzymology. 29523239 ;
Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L Molecular cell. 29526697 2018 Mar 15;
Integrative structure and functional anatomy of a nuclear pore complex. Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P Nature. 29539637 2018 Mar 22;
Defect-facilitated buckling in supercoiled double-helix DNA. Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu; Neuman, Keir C; Marko, John F Physical review. E. 29548184 2018 Feb;
Effects of electrostatic interactions on ligand dissociation kinetics. Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F Physical review. E. 29548245 2018 Feb;
Three-dimensional organization and dynamics of the genome. Szalaj, Przemyslaw; Plewczynski, Dariusz Cell biology and toxicology. 29568981 2018 Oct;
Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan The Journal of cell biology. 29572382 2018 Jun 04;
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. NULL Scientific reports. 29581440 2018 Mar 26;
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M Nature protocols. 29599440 2018 May;
Visualization of Transvection in Living Drosophila Embryos. Lim, Bomyi; Heist, Tyler; Levine, Michael; Fukaya, Takashi Molecular cell. 29606591 2018 Apr 19;
Producing genome structure populations with the dynamic and automated PGS software. Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank Nature protocols. 29622804 2018 May;
Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L Molecular cell. 29625035 2018 Apr 05;
Real-time 3D single-molecule localization using experimental point spread functions. Li, Yiming; Mund, Markus; Hoess, Philipp; Deschamps, Joran; Matti, Ulf; Nijmeijer, Bianca; Sabinina, Vilma Jimenez; Ellenberg, Jan; Schoen, Ingmar; Ries, Jonas Nature methods. 29630062 2018 May;
A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. Walther, Nike; Hossain, M Julius; Politi, Antonio Z; Koch, Birgit; Kueblbeck, Moritz; Ødegård-Fougner, Øyvind; Lampe, Marko; Ellenberg, Jan The Journal of cell biology. 29632028 2018 Apr 09;
Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia. Carvajal, Luis A; Neriah, Daniela Ben; Senecal, Adrien; Benard, Lumie; Thiruthuvanathan, Victor; Yatsenko, Tatyana; Narayanagari, Swathi-Rao; Wheat, Justin C; Todorova, Tihomira I; Mitchell, Kelly; Kenworthy, Charles; Guerlavais, Vincent; Annis, D Allen; Bartholdy, Boris; Will, Britta; Anampa, Jesus D; Mantzaris, Ioannis; Aivado, Manuel; Singer, Robert H; Coleman, Robert A; Verma, Amit; Steidl, Ulrich Science translational medicine. 29643228 2018 Apr 11;
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Bonora, G; Deng, X; Fang, H; Ramani, V; Qiu, R; Berletch, J B; Filippova, G N; Duan, Z; Shendure, J; Noble, W S; Disteche, C M Nature communications. 29654302 2018 Apr 13;
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Barutcu, A Rasim; Maass, Philipp G; Lewandowski, Jordan P; Weiner, Catherine L; Rinn, John L Nature communications 29654311 2018 04 13
Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes. Tsai, Albert; Singer, Robert H; Crocker, Justin Molecular cell. 29677489 2018 Apr 19;
Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E Proceedings of SPIE--the International Society for Optical Engineering. 29681676 2018 Feb;
The Energetics and Physiological Impact of Cohesin Extrusion. Vian, Laura; P?kowska, Aleksandra; Rao, Suhas S P; Kieffer-Kwon, Kyong-Rim; Jung, Seolkyoung; Baranello, Laura; Huang, Su-Chen; El Khattabi, Laila; Dose, Marei; Pruett, Nathanael; Sanborn, Adrian L; Canela, Andres; Maman, Yaakov; Oksanen, Anna; Resch, Wolfgang; Li, Xingwang; Lee, Byoungkoo; Kovalchuk, Alexander L; Tang, Zhonghui; Nelson, Steevenson; Di Pierro, Michele; Cheng, Ryan R; Machol, Ido; St Hilaire, Brian Glenn; Durand, Neva C; Shamim, Muhammad S; Stamenova, Elena K; Onuchic, José N; Ruan, Yijun; Nussenzweig, Andre; Levens, David; Aiden, Erez Lieberman; Casellas, Rafael Cell. 29706548 2018 May 17;
Emerging Evidence of Chromosome Folding by Loop Extrusion. Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; Goloborodko, Anton; Mirny, Leonid A Cold Spring Harbor symposia on quantitative biology. 29728444 2017;
Allele-specific control of replication timing and genome organization during development. Rivera-Mulia, Juan Carlos; Dimond, Andrew; Vera, Daniel; Trevilla-Garcia, Claudia; Sasaki, Takayo; Zimmerman, Jared; Dupont, Catherine; Gribnau, Joost; Fraser, Peter; Gilbert, David M Genome research. 29735606 2018 06;
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Gao, Xin D; Tu, Li-Chun; Mir, Aamir; Rodriguez, Tomás; Ding, Yuehe; Leszyk, John; Dekker, Job; Shaffer, Scott A; Zhu, Lihua Julie; Wolfe, Scot A; Sontheimer, Erik J Nature methods. 29735996 2018 May 07;
qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I Scientific reports. 29743503 ;
Gene regulation in the 3D genome. Li, Yun; Hu, Ming; Shen, Yin Human molecular genetics. 29767704 2018 08 01;
Quantitative imaging of chromatin decompaction in living cells. Dultz, Elisa; Mancini, Roberta; Polles, Guido; Vallotton, Pascal; Alber, Frank; Weis, Karsten Molecular biology of the cell. 29771637 ;
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E Methods (San Diego, Calif.). 29772275 ;
Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Jarvis, James N Journal of reproductive immunology. 29800761 2018 Aug;
Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. Gustavsson, Anna-Karin; Petrov, Petar N; Moerner, W E Optics express. 29801343 2018 May 14;
Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods. Chen, Chun Chieh; Stark, Marie; Baikoghli, Mo; Cheng, R Holland Journal of visualized experiments : JoVE. 29806824 2018 05 11;
Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. Koch, Birgit; Nijmeijer, Bianca; Kueblbeck, Moritz; Cai, Yin; Walther, Nike; Ellenberg, Jan Nature protocols. 29844520 2018 06;
Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging. Politi, Antonio Z; Cai, Yin; Walther, Nike; Hossain, M Julius; Koch, Birgit; Wachsmuth, Malte; Ellenberg, Jan Nature protocols. 29844523 2018 06;
Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Lu, Huasong; Yu, Dan; Hansen, Anders S; Ganguly, Sourav; Liu, Rongdiao; Heckert, Alec; Darzacq, Xavier; Zhou, Qiang Nature. 29849146 2018 06;
Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. Dine, Elliot; Gil, Agnieszka A; Uribe, Giselle; Brangwynne, Clifford P; Toettcher, Jared E Cell systems. 29859829 2018 Jun 27;
Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers. Bardales, Jorge A; Wieser, Evin; Kawaji, Hideya; Murakawa, Yasuhiro; Darzacq, Xavier Genes. 29882899 2018 May 23;
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Quinodoz, Sofia A; Ollikainen, Noah; Tabak, Barbara; Palla, Ali; Schmidt, Jan Marten; Detmar, Elizabeth; Lai, Mason M; Shishkin, Alexander A; Bhat, Prashant; Takei, Yodai; Trinh, Vickie; Aznauryan, Erik; Russell, Pamela; Cheng, Christine; Jovanovic, Marko; Chow, Amy; Cai, Long; McDonel, Patrick; Garber, Manuel; Guttman, Mitchell Cell. 29887377 2018 Jun 04;
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. Shah, Sheel; Takei, Yodai; Zhou, Wen; Lubeck, Eric; Yun, Jina; Eng, Chee-Huat Linus; Koulena, Noushin; Cronin, Christopher; Karp, Christoph; Liaw, Eric J; Amin, Mina; Cai, Long Cell. 29887381 2018 May 31;
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Tasan, Ipek; Sustackova, Gabriela; Zhang, Liguo; Kim, Jiah; Sivaguru, Mayandi; HamediRad, Mohammad; Wang, Yuchuan; Genova, Justin; Ma, Jian; Belmont, Andrew S; Zhao, Huimin Nucleic acids research. 29912475 2018 Jun 15;
Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe; Dong, Peng; Dailey, Gina M; Cattoglio, Claudia; Heckert, Alec; Banala, Sambashiva; Lavis, Luke; Darzacq, Xavier; Tjian, Robert Science (New York, N.Y.). 29930090 2018 07 27;
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. Yang, Yang; Gu, Quanquan; Zhang, Yang; Sasaki, Takayo; Crivello, Julianna; O'Neill, Rachel J; Gilbert, David M; Ma, Jian Cell systems. 29936186 2018 Jun 18;
A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. Teves, Sheila S; An, Luye; Bhargava-Shah, Aarohi; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert eLife. 29939130 2018 06 25;
SAVER: gene expression recovery for single-cell RNA sequencing. Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I; Raj, Arjun; Li, Mingyao; Zhang, Nancy R Nature methods. 29941873 2018 Jul;
Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction. Lei, Xiao; Shi, Haoran; Kou, Yi; Rajashekar, Niroop; Wu, Fang; Sen, Chandani; Xu, Jiang; Chen, Lin Biochemistry. 29944822 2018 07 17;
Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. Sabath, Niv; Vilborg, Anna; Steitz, Joan A; Shalgi, Reut Human genomics. 29945683 2018 06 27;
Predicting CTCF-mediated chromatin loops using CTCF-MP. Zhang, Ruochi; Wang, Yuchuan; Yang, Yang; Zhang, Yang; Ma, Jian Bioinformatics (Oxford, England). 29949986 2018 Jul 01;
Unsupervised embedding of single-cell Hi-C data. Liu, Jie; Lin, Dejun; Yardimci, Galip Gürkan; Noble, William Stafford Bioinformatics (Oxford, England). 29950005 2018 07 01;
Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Mir, Mustafa; Reimer, Armando; Stadler, Michael; Tangara, Astou; Hansen, Anders S; Hockemeyer, Dirk; Eisen, Michael B; Garcia, Hernan; Darzacq, Xavier Methods in molecular biology (Clifton, N.J.). 29956254 2018;
Quantitative live and super-resolution microscopy of mitotic chromosomes. Walther, Nike; Ellenberg, Jan Methods in cell biology. 29957216 2018;
Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. Limi, Saima; Senecal, Adrien; Coleman, Robert; Lopez-Jones, Melissa; Guo, Peng; Polumbo, Christina; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales The Journal of biological chemistry. 29959226 2018 Aug 24;
Chromatin organization by an interplay of loop extrusion and compartmental segregation. Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Abdennur, Nezar; Mirny, Leonid A Proceedings of the National Academy of Sciences of the United States of America. 29967174 2018 07 17;
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E Molecular cell. 29979966 2018 Jul 05;
Enhancer hubs and loop collisions identified from single-allele topologies. Allahyar, Amin; Vermeulen, Carlo; Bouwman, Britta A M; Krijger, Peter H L; Verstegen, Marjon J A M; Geeven, Geert; van Kranenburg, Melissa; Pieterse, Mark; Straver, Roy; Haarhuis, Judith H I; Jalink, Kees; Teunissen, Hans; Renkens, Ivo J; Kloosterman, Wigard P; Rowland, Benjamin D; de Wit, Elzo; de Ridder, Jeroen; de Laat, Wouter Nature genetics 29988121 2018 08
Understanding the 3D genome: Emerging impacts on human disease. Krumm, Anton; Duan, Zhijun Seminars in cell & developmental biology. 29990539 2019 Jun;
Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. Packer, Jonathan; Trapnell, Cole Trends in genetics : TIG. 30007833 ;
GIVE: portable genome browsers for personal websites. Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng Genome biology. 30016975 2018 07 18;
The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. Menghi, Francesca; Barthel, Floris P; Yadav, Vinod; Tang, Ming; Ji, Bo; Tang, Zhonghui; Carter, Gregory W; Ruan, Yijun; Scully, Ralph; Verhaak, Roel G W; Jonkers, Jos; Liu, Edison T Cancer cell. 30017478 2018 08 13;
Computational methods for analyzing and modeling genome structure and organization. Lin, Dejun; Bonora, Giancarlo; Yard?mc?, Galip Gürkan; Noble, William S Wiley interdisciplinary reviews. Systems biology and medicine. 30022617 2018 Jul 18;
The three-dimensional organization of the genome in cellular senescence and age-associated diseases. Evans, Shane A; Horrell, Jeremy; Neretti, Nicola Seminars in cell & developmental biology. 30031215 2019 Jun;
Comparison of OCT Angiography Review Strategies to Identify Vascular Abnormalities in the AVATAR Study. Babiuch, Amy S; Khan, Mehnaz; Hu, Ming; Kaiser, Peter K; Srivastava, Sunil K; Singh, Rishi P; Watts, Allison; Reese, Jamie L; Ehlers, Justis P Ophthalmology. Retina. 30035246 2018 Jun;
Dynamic interplay between enhancer-promoter topology and gene activity. Chen, Hongtao; Levo, Michal; Barinov, Lev; Fujioka, Miki; Jaynes, James B; Gregor, Thomas Nature genetics. 30038397 2018 Sep;
Temporal dynamics of pair-rule stripes in living Drosophila embryos. Lim, Bomyi; Fukaya, Takashi; Heist, Tyler; Levine, Michael Proceedings of the National Academy of Sciences of the United States of America. 30061421 2018 08 14;
Protein motion in the nucleus: from anomalous diffusion to weak interactions. Woringer, Maxime; Darzacq, Xavier Biochemical Society transactions. 30065106 2018 Aug 20;
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cusanovich, Darren A; Hill, Andrew J; Aghamirzaie, Delasa; Daza, Riza M; Pliner, Hannah A; Berletch, Joel B; Filippova, Galina N; Huang, Xingfan; Christiansen, Lena; DeWitt, William S; Lee, Choli; Regalado, Samuel G; Read, David F; Steemers, Frank J; Dist Cell. 30078704 2018 Aug 23;
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Pliner, Hannah A; Packer, Jonathan S; McFaline-Figueroa, José L; Cusanovich, Darren A; Daza, Riza M; Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana; Minkina, Anna; Adey, Andrew C; Steemers, Frank J; Shendure, Jay; Trapnell, Cole Molecular cell. 30078726 2018 09 06;
One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. Lazniewski, Michal; Dawson, Wayne K; Rusek, Anna Maria; Plewczynski, Dariusz Seminars in cell & developmental biology. 30096365 2018 Oct 11;
Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model. Zhang, Rongrong; Hu, Ming; Zhu, Yu; Qin, Zhaohui; Deng, Ke; Liu, Jun S IEEE/ACM transactions on computational biology and bioinformatics. 30113897 2020 Mar-Apr;
Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. Wray-Dutra, Michelle N; Chawla, Raghav; Thomas, Kerri R; Seymour, Brenda J; Arkatkar, Tanvi; Sommer, Karen M; Khim, Socheath; Trapnell, Cole; James, Richard G; Rawlings, David J The Journal of experimental medicine. 30127060 2018 Sep 03;
Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan The Journal of cell biology. 30135095 2018 Sep 03;
DXR: A Toolkit for Building Immersive Data Visualizations. Sicat, Ronell; Li, Jiabao; Choi, Junyoung; Cordeil, Maxime; Jeong, Won-Ki; Bach, Benjamin; Pfister, Hanspeter IEEE transactions on visualization and computer graphics. 30136991 2019 01;
HiGlass: web-based visual exploration and analysis of genome interaction maps. Kerpedjiev, Peter; Abdennur, Nezar; Lekschas, Fritz; McCallum, Chuck; Dinkla, Kasper; Strobelt, Hendrik; Luber, Jacob M; Ouellette, Scott B; Azhir, Alaleh; Kumar, Nikhil; Hwang, Jeewon; Lee, Soohyun; Alver, Burak H; Pfister, Hanspeter; Mirny, Leonid A; Pa Genome biology. 30143029 2018 08 24;
Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. Sun, Mingxuan; Biggs, Ronald; Hornick, Jessica; Marko, John F Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 30143891 2018 Dec;
Emerging Roles of Non-Coding RNA Transcription. Kaikkonen, Minna U; Adelman, Karen Trends in biochemical sciences. 30145998 2018 09;
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Munschauer, Mathias; Nguyen, Celina T; Sirokman, Klara; Hartigan, Christina R; Hogstrom, Larson; Engreitz, Jesse M; Ulirsch, Jacob C; Fulco, Charles P; Subramanian, Vidya; Chen, Jenny; Schenone, Monica; Guttman, Mitchell; Carr, Steven A; Lander, Eric S Nature. 30150775 2018 09;
Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. Chen, Yu; Zhang, Yang; Wang, Yuchuan; Zhang, Liguo; Brinkman, Eva K; Adam, Stephen A; Goldman, Robert; van Steensel, Bas; Ma, Jian; Belmont, Andrew S The Journal of cell biology. 30154186 2018 Aug 28;
Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. van Steensel, Bas EMBO reports. 30158143 2018 Oct;
Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. Sun, James H; Zhou, Linda; Emerson, Daniel J; Phyo, Sai A; Titus, Katelyn R; Gong, Wanfeng; Gilgenast, Thomas G; Beagan, Jonathan A; Davidson, Beverly L; Tassone, Flora; Phillips-Cremins, Jennifer E Cell. 30173918 2018 Aug 27;
RNA, Action through Interactions. Nguyen, Tri C; Zaleta-Rivera, Kathia; Huang, Xuerui; Dai, Xiaofeng; Zhong, Sheng Trends in genetics : TIG. 30177410 2018 Aug 31;
Interchromosomal interactions: A genomic love story of kissing chromosomes. Maass, Philipp G; Barutcu, A Rasim; Rinn, John L The Journal of cell biology. 30181316 2019 Jan 07;
Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. Zhu, Liangliang; Yan, Feihu; Wang, Zhen; Dong, Haiyan; Bian, Chengling; Wang, Ting; Yu, Enda; Li, Jing International journal of cancer. 30183087 2018 Nov 15;
Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F; Carlon, Enrico Physical review letters. 30192578 2018 Aug 24;
Integrative detection and analysis of structural variation in cancer genomes. Dixon, Jesse R; Xu, Jie; Dileep, Vishnu; Zhan, Ye; Song, Fan; Le, Victoria T; Yard?mc?, Galip Gürkan; Chakraborty, Abhijit; Bann, Darrin V; Wang, Yanli; Clark, Royden; Zhang, Lijun; Yang, Hongbo; Liu, Tingting; Iyyanki, Sriranga; An, Lin; Pool, Christophe Nature genetics. 30202056 2018 Sep 10;
Experimental and computational framework for a dynamic protein atlas of human cell division. Cai, Yin; Hossain, M Julius; Hériché, Jean-Karim; Politi, Antonio Z; Walther, Nike; Koch, Birgit; Wachsmuth, Malte; Nijmeijer, Bianca; Kueblbeck, Moritz; Martinic-Kavur, Marina; Ladurner, Rene; Alexander, Stephanie; Peters, Jan-Michael; Ellenberg, Jan Nature. 30202089 2018 09;
X-Chromosome Inactivation and Escape from X Inactivation in Mouse. Ma, Wenxiu; Bonora, Giancarlo; Berletch, Joel B; Deng, Xinxian; Noble, William S; Disteche, Christine M Methods in molecular biology (Clifton, N.J.). 30218369 2018;
Blank spots on the map: some current questions on nuclear organization and genome architecture. Adriaens, Carmen; Serebryannyy, Leonid A; Feric, Marina; Schibler, Andria; Meaburn, Karen J; Kubben, Nard; Trzaskoma, Pawel; Shachar, Sigal; Vidak, Sandra; Finn, Elizabeth H; Sood, Varun; Pegoraro, Gianluca; Misteli, Tom Histochemistry and cell biology. 30238154 2018 Dec;
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. Chen, Weizhong; Yan, Zhangming; Li, Simin; Huang, Norman; Huang, Xuerui; Zhang, Jin; Zhong, Sheng iScience. 30240742 2018 Jun 29;
PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. Kordon, Magdalena M; Szczurek, Aleksander; Berniak, Krzysztof; Szelest, Oskar; Solarczyk, Kamil; Tworzyd?o, Magdalena; Wachsmann-Hogiu, Sebastian; Vaahtokari, Anne; Cremer, Christoph; Pederson, Thoru; Dobrucki, Jurek W FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 30260704 2019 02;
Developmental enhancers and chromosome topology. Furlong, Eileen E M; Levine, Michael Science (New York, N.Y.). 30262496 2018 09 28;
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Kragesteen, Bjørt K; Spielmann, Malte; Paliou, Christina; Heinrich, Verena; Schöpflin, Robert; Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Chiariello, Andrea M; Jerković, Ivana; Harabula, Izabela; Guckelberger, Philine; Pechstein, Michael; Wit Nature genetics 30262816 2018 Oct
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N K; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, Feng Genome biology. 30286773 2018 10 04;
CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. Daley, Timothy P; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei S Genome biology. 30296940 2018 10 08;
Understanding molecular mechanisms of disease through spatial proteomics. Pankow, Sandra; Martínez-Bartolomé, Salvador; Bamberger, Casimir; Yates, John R Current opinion in chemical biology. 30308467 2019 Feb;
The adult human testis transcriptional cell atlas. Guo, Jingtao; Grow, Edward J; Mlcochova, Hana; Maher, Geoffrey J; Lindskog, Cecilia; Nie, Xichen; Guo, Yixuan; Takei, Yodai; Yun, Jina; Cai, Long; Kim, Robin; Carrell, Douglas T; Goriely, Anne; Hotaling, James M; Cairns, Bradley R Cell research. 30315278 2018 Dec;
CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. Wang, Haifeng; Xu, Xiaoshu; Nguyen, Cindy M; Liu, Yanxia; Gao, Yuchen; Lin, Xueqiu; Daley, Timothy; Kipniss, Nathan H; La Russa, Marie; Qi, Lei S Cell. 30318144 2018 Nov 15;
CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. Liu, Yanxia; Yu, Chen; Daley, Timothy Patrick; Wang, Fangyuan; Cao, William S; Bhate, Salil; Lin, Xueqiu; Still 2nd, Chris; Liu, Honglei; Zhao, Dehua; Wang, Haifeng; Xie, Xinmin S; Ding, Sheng; Wong, Wing Hung; Wernig, Marius; Qi, Lei S Cell stem cell. 30318302 2018 Nov 01;
Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling. Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura; Wang, Ruipeng; McQuiston, Travis J; Challberg, Sharon S; Pollok, Brian A; Wang, Ting Cell reports. 30332641 2018 Oct 16;
Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Zoller, Benjamin; Little, Shawn C; Gregor, Thomas Cell. 30340044 2018 Oct 18;
Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas Cell systems. 30342881 2018 Oct 24;
CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Chung, Yu-Chieh; Grunwald, David; Zhang, Shaojie; Pederson, Thoru Nature methods. 30377374 2018 Nov;
A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. Dai, Xiaoyu; Lin, Nan; Li, Daofeng; Wang, Ting Biometrics. 30387496 2018 Nov 02;
Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho; Yuede, Carla; Li, Daofeng; Rensing, Nicholas; Huang, Ju; Baldridge, Dustin; Maloney, Susan E; Dougherty, Joseph D; Constantino, John; Jahani-Asl, Arezu; Wong, Michael; Wozniak, David F; Wang, Ting; Klyachko, Vitaly A; Bonni, Azad Cell reports. 30403997 2018 Nov 06;
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. P?kowska, Aleksandra; Klaus, Bernd; Xiang, Wanqing; Severino, Jacqueline; Daigle, Nathalie; Klein, Felix A; Ole?, Ma?gorzata; Casellas, Rafael; Ellenberg, Jan; Steinmetz, Lars M; Bertone, Paul; Huber, Wolfgang Cell systems. 30414923 2018 Nov 28;
Higher-Order Organization Principles of Pre-translational mRNPs. Metkar, Mihir; Ozadam, Hakan; Lajoie, Bryan R; Imakaev, Maxim; Mirny, Leonid A; Dekker, Job; Moore, Melissa J Molecular cell. 30415953 2018 11 15;
ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, Arjun Nature biotechnology. 30418432 2018 Nov 12;
Improved reference genome of Aedes aegypti informs arbovirus vector control. Matthews, Benjamin J; Dudchenko, Olga; Kingan, Sarah B; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E; Glassford, William J; Herre, Margaret; Redmond, Seth N; Rose, Noah H; Weedall, Gareth D; Wu, Yang; Batra, Sanjit S; Brito-Sierra, Carlos A; Bucki Nature. 30429615 2018 11;
The interdependence of gene-regulatory elements and the 3D genome. Vermunt, Marit W; Zhang, Di; Blobel, Gerd A The Journal of cell biology. 30442643 2019 01 07;
CHRAC/ACF contribute to the repressive ground state of chromatin. Scacchetti, Alessandro; Brueckner, Laura; Jain, Dhawal; Schauer, Tamas; Zhang, Xu; Schnorrer, Frank; van Steensel, Bas; Straub, Tobias; Becker, Peter B Life science alliance. 30456345 2018 Jan;
Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Peng, Qin; Lu, Shaoying; Shi, Yuxin; Pan, Yijia; Limsakul, Praopim; Chernov, Andrei V; Qiu, Juhui; Chai, Xiaoqi; Shi, Yiwen; Wang, Pengzhi; Ji, Yanmin; Li, Yi-Shuan J; Strongin, Alex Y; Verkhusha, Vladislav V; Izpisua Belmonte, Juan Carlos; Ren, Bing; Wang, Yuanliang; Chien, Shu; Wang, Yingxiao Proceedings of the National Academy of Sciences of the United States of America. 30478057 2018 12 11;
Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. Bracha, Dan; Walls, Mackenzie T; Wei, Ming-Tzo; Zhu, Lian; Kurian, Martin; Avalos, José L; Toettcher, Jared E; Brangwynne, Clifford P Cell. 30500534 2018 Nov 29;
Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. Shin, Yongdae; Chang, Yi-Che; Lee, Daniel S W; Berry, Joel; Sanders, David W; Ronceray, Pierre; Wingreen, Ned S; Haataja, Mikko; Brangwynne, Clifford P Cell. 30500535 2018 Nov 29;
Impact of optical aberrations on axial position determination by photometry. Thorsen, Rasmus Ø; Hulleman, Christiaan N; Hammer, Mathias; Grünwald, David; Stallinga, Sjoerd; Rieger, Bernd Nature methods. 30504865 2018 Dec;
Deconstructing transport-distribution reconstruction in the nuclear-pore complex. Tu, Li-Chun; Huisman, Maximiliaan; Chung, Yu-Chieh; Smith, Carlas Sierd; Grunwald, David Nature structural & molecular biology. 30518848 2018 Dec;
A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. Keleher, Madeline Rose; Zaidi, Rabab; Hicks, Lauren; Shah, Shyam; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Cheverud, James M BMC genomics. 30526554 2018 Dec 07;
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Calandrelli, Riccardo; Wu, Qiuyang; Guan, Jihong; Zhong, Sheng Genomics, proteomics & bioinformatics. 30553884 2018 Dec 13;
RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. Brahma, Sandipan; Henikoff, Steven Molecular cell. 30554944 2019 Jan 17;
Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. Bartman, Caroline R; Hamagami, Nicole; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A; Raj, Arjun Molecular cell. 30554946 2018 Dec 06;
Models of polymer physics for the architecture of the cell nucleus. Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Chiariello, Andrea M; Fiorillo, Luca; Nicodemi, Mario Wiley interdisciplinary reviews. Systems biology and medicine. 30566285 2018 Dec 19;
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. Nir, Guy; Farabella, Irene; Pérez Estrada, Cynthia; Ebeling, Carl G; Beliveau, Brian J; Sasaki, Hiroshi M; Lee, S Dean; Nguyen, Son C; McCole, Ruth B; Chattoraj, Shyamtanu; Erceg, Jelena; AlHaj Abed, Jumana; Martins, Nuno M C; Nguyen, Huy Q; Hannan, Mohammed A; Russell, Sheikh; Durand, Neva C; Rao, Suhas S P; Kishi, Jocelyn Y; Soler-Vila, Paula; Di Pierro, Michele; Onuchic, José N; Callahan, Steven P; Schreiner, John M; Stuckey, Jeff A; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A; Wu, C-Ting PLoS genetics. 30586358 2018 12;
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. Lu, Jia; Cao, Xiaoyi; Zhong, Sheng PLoS computational biology. 30586383 2018 Dec;
Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. Mir, Mustafa; Stadler, Michael R; Ortiz, Stephan A; Hannon, Colleen E; Harrison, Melissa M; Darzacq, Xavier; Eisen, Michael B eLife. 30589412 2018 12 27;
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Sima, Jiao; Chakraborty, Abhijit; Dileep, Vishnu; Michalski, Marco; Klein, Kyle N; Holcomb, Nicolas P; Turner, Jesse L; Paulsen, Michelle T; Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Bartlett, Daniel A; Zhao, Peiyao A; Washburn, Brian K; Nora, Cell. 30595451 2019 Feb 07;
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Zhang, Zhizhuo; Chng, Kern Rei; Lingadahalli, Shreyas; Chen, Zikai; Liu, Mei Hui; Do, Huy Hoang; Cai, Shaojiang; Rinaldi, Nicola; Poh, Huay Mei; Li, Guoliang; Sung, Ying Ying; Heng, Charlie L; Core, Leighton J; Tan, Si Kee; Ruan, Xiaoan; Lis, John T; Kellis, Manolis; Ruan, Yijun; Sung, Wing-Kin; Cheung, Edwin Genome research. 30606742 2019 02;
Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics. Biggs, Ronald; Liu, Patrick Z; Stephens, Andrew D; Marko, John F Molecular biology of the cell. 30625026 2019 03 21;
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, Arjun PLoS genetics. 30625149 2019 01;
LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Monahan, Kevin; Horta, Adan; Lomvardas, Stavros Nature. 30626972 2019 01;
Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers. Limi, Saima; Zhao, Yilin; Guo, Peng; Lopez-Jones, Melissa; Zheng, Deyou; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales Investigative ophthalmology & visual science. 30646012 2019 Jan 02;
Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic ? Cell Identity and Function. Lawlor, Nathan; Márquez, Eladio J; Orchard, Peter; Narisu, Narisu; Shamim, Muhammad Saad; Thibodeau, Asa; Varshney, Arushi; Kursawe, Romy; Erdos, Michael R; Kanke, Matt; Gu, Huiya; Pak, Evgenia; Dutra, Amalia; Russell, Sheikh; Li, Xingwang; Piecuch, Emaly; Luo, Oscar; Chines, Peter S; Fuchbserger, Christian; NIH Intramural Sequencing Center; Sethupathy, Praveen; Aiden, Aviva Presser; Ruan, Yijun; Aiden, Erez Lieberman; Collins, Francis S; Ucar, Duygu; Parker, Stephen C J; Stitzel, Michael L Cell reports. 30650367 2019 Jan 15;
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. Oomen, Marlies E; Hansen, Anders S; Liu, Yu; Darzacq, Xavier; Dekker, Job Genome research. 30655336 2019 02;
An automated Bayesian pipeline for rapid analysis of single-molecule binding data. Smith, Carlas S; Jouravleva, Karina; Huisman, Maximiliaan; Jolly, Samson M; Zamore, Phillip D; Grunwald, David Nature communications. 30655518 2019 01 17;
A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. Sharon, Nadav; Chawla, Raghav; Mueller, Jonas; Vanderhooft, Jordan; Whitehorn, Luke James; Rosenthal, Benjamin; Gürtler, Mads; Estanboulieh, Ralph R; Shvartsman, Dmitry; Gifford, David K; Trapnell, Cole; Melton, Doug Cell. 30661759 2019 Feb 07;
Adapting dCas9-APEX2 for subnuclear proteomic profiling. Gao, Xin D; Rodríguez, Tomás C; Sontheimer, Erik J Methods in enzymology. 30691651 2019;
Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. Chapski, Douglas J; Rosa-Garrido, Manuel; Hua, Nan; Alber, Frank; Vondriska, Thomas M Frontiers in cardiovascular medicine. 30697540 2018;
Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. Yan, Zhangming; Huang, Norman; Wu, Weixin; Chen, Weizhong; Jiang, Yiqun; Chen, Jingyao; Huang, Xuerui; Wen, Xingzhao; Xu, Jie; Jin, Qiushi; Zhang, Kang; Chen, Zhen; Chien, Shu; Zhong, Sheng Proceedings of the National Academy of Sciences of the United States of America. 30718424 2019 Feb 19;
Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. Hollerer, Ina; Barker, Juliet C; Jorgensen, Victoria; Tresenrider, Amy; Dugast-Darzacq, Claire; Chan, Leon Y; Darzacq, Xavier; Tjian, Robert; Ünal, Elçin; Brar, Gloria A G3 (Bethesda, Md.). 30723103 2019 04 09;
Replication Timing Becomes Intertwined with 3D Genome Organization. Ma, Jian; Duan, Zhijun Cell. 30735630 2019 Feb 07;
Multiplex chromatin interactions with single-molecule precision. Zheng, Meizhen; Tian, Simon Zhongyuan; Capurso, Daniel; Kim, Minji; Maurya, Rahul; Lee, Byoungkoo; Piecuch, Emaly; Gong, Liang; Zhu, Jacqueline Jufen; Li, Zhihui; Wong, Chee Hong; Ngan, Chew Yee; Wang, Ping; Ruan, Xiaoan; Wei, Chia-Lin; Ruan, Yijun Nature. 30778195 2019 02;
The single-cell transcriptional landscape of mammalian organogenesis. Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay Nature. 30787437 2019 02;
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Finn, Elizabeth H; Pegoraro, Gianluca; Brandão, Hugo B; Valton, Anne-Laure; Oomen, Marlies E; Dekker, Job; Mirny, Leonid; Misteli, Tom Cell. 30799036 2019 Mar 07;
Dendritic Spines Taxonomy: The Functional and Structural Classification ? Time-Dependent Probabilistic Model of Neuronal Activation. Urban, Paulina; Rezaei, Vahid; Bokota, Grzegorz; Denkiewicz, Micha?; Basu, Subhadip; Plewczy?ski, Dariusz Journal of computational biology : a journal of computational molecular cell biology. 30810368 2019 Apr;
Intermingling of chromosome territories. Szczepińska, Teresa; Rusek, Anna Maria; Plewczynski, Dariusz Genes, chromosomes & cancer 30828902 2019 07
Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. Ma, Hanhui; Tu, Li-Chun; Chung, Yu-Chieh; Naseri, Ardalan; Grunwald, David; Zhang, Shaojie; Pederson, Thoru The Journal of cell biology. 30846483 2019 Mar 07;
Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance. Bertolini, Jessica A; Favaro, Rebecca; Zhu, Yanfen; Pagin, Miriam; Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Vermunt, Marit W; Martynoga, Ben; Barone, Cristiana; Mariani, Jessica; Cardozo, Marcos Julián; Tabanera, Noemi; Zambelli, Federico; Mercurio, Sara; Ottolenghi, Sergio; Robson, Paul; Creyghton, Menno P; Bovolenta, Paola; Pavesi, Giulio; Guillemot, Francois; Nicolis, Silvia K; Wei, Chia-Lin Cell stem cell. 30849367 2019 Mar 07;
Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells. Al Bkhetan, Ziad; Kadlof, Michal; Kraft, Agnieszka; Plewczynski, Dariusz Methods (San Diego, Calif.). 30853548 2019 Aug 15;
Chromatin's physical properties shape the nucleus and its functions. Stephens, Andrew D; Banigan, Edward J; Marko, John F Current opinion in cell biology. 30889417 2019 06;
Measuring the reproducibility and quality of Hi-C data. Yard?mc?, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E G; Ursu, Oana; Yan, Koon-Kiu; Yang, Tao; Chakraborty, Abhijit; Kaul, Arya; Lajoie, Bryan R; Song, Fan; Zhan, Ye; Ay, Ferhat; Gerstein, Mark; Kundaje, Anshul; Li, Qunhua; Taylor, James; Yue, Feng; Dekker, Job; Noble, William S Genome biology. 30890172 2019 03 19;
Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. Gilgenast, Thomas G; Phillips-Cremins, Jennifer E Cell systems. 30904376 2019 Mar 27;
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long Nature. 30911168 2019 Apr;
Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications. He, Ming; Huang, Tse-Shun; Li, Shuai; Hong, Hsiao-Chin; Chen, Zhen; Martin, Marcy; Zhou, Xin; Huang, Hsi-Yuan; Su, Shu-Han; Zhang, Jiao; Wang, Wei-Ting; Kang, Jian; Huang, Hsien-Da; Zhang, Jin; Chien, Shu; Shyy, John Y-J Arteriosclerosis, thrombosis, and vascular biology. 30917677 2019 May;
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. Jean-Baptiste, Ken; McFaline-Figueroa, José L; Alexandre, Cristina M; Dorrity, Michael W; Saunders, Lauren; Bubb, Kerry L; Trapnell, Cole; Fields, Stanley; Queitsch, Christine; Cuperus, Josh T The Plant cell. 30923229 2019 05;
Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Boeynaems, Steven; Holehouse, Alex S; Weinhardt, Venera; Kovacs, Denes; Van Lindt, Joris; Larabell, Carolyn; Van Den Bosch, Ludo; Das, Rhiju; Tompa, Peter S; Pappu, Rohit V; Gitler, Aaron D Proceedings of the National Academy of Sciences of the United States of America. 30926670 2019 Apr 16;
Transposable elements drive widespread expression of oncogenes in human cancers. Jang, Hyo Sik; Shah, Nakul M; Du, Alan Y; Dailey, Zea Z; Pehrsson, Erica C; Godoy, Paula M; Zhang, David; Li, Daofeng; Xing, Xiaoyun; Kim, Sungsu; O'Donnell, David; Gordon, Jeffrey I; Wang, Ting Nature genetics. 30926969 2019 04;
The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Sinnamon, John R; Torkenczy, Kristof A; Linhoff, Michael W; Vitak, Sarah A; Mulqueen, Ryan M; Pliner, Hannah A; Trapnell, Cole; Steemers, Frank J; Mandel, Gail; Adey, Andrew C Genome research. 30936163 2019 05;
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Bertero, Alessandro; Fields, Paul A; Ramani, Vijay; Bonora, Giancarlo; Yardimci, Galip G; Reinecke, Hans; Pabon, Lil; Noble, William S; Shendure, Jay; Murry, Charles E Nature communications. 30948719 2019 04 04;
Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Leemans, Christ; van der Zwalm, Marloes C H; Brueckner, Laura; Comoglio, Federico; van Schaik, Tom; Pagie, Ludo; van Arensbergen, Joris; van Steensel, Bas Cell. 30982597 2019 May 02;
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. Juric, Ivan; Yu, Miao; Abnousi, Armen; Raviram, Ramya; Fang, Rongxin; Zhao, Yuan; Zhang, Yanxiao; Qiu, Yunjiang; Yang, Yuchen; Li, Yun; Ren, Bing; Hu, Ming PLoS computational biology. 30986246 2019 04;
Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. Nomidis, Stefanos K; Skoruppa, Enrico; Carlon, Enrico; Marko, John F Physical review. E. 30999490 2019 Mar;
FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. Ma, Chun-Yu; Madden, Pamela; Gontarz, Paul; Wang, Ting; Zhang, Bo Frontiers in genetics. 31001319 2019;
Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. Kim, Jung-Sik; He, Xiaoyuan; Liu, Jie; Duan, Zhijun; Kim, Taeyeon; Gerard, Julia; Kim, Brian; Pillai, Manoj M; Lane, William S; Noble, William S; Budnik, Bogdan; Waldman, Todd The Journal of biological chemistry. 31010829 2019 May 31;
Topological and functional comparison of community detection algorithms in biological networks. Rahiminejad, Sara; Maurya, Mano R; Subramaniam, Shankar BMC bioinformatics. 31029085 2019 Apr 27;
Receptor-Ligand Rebinding Kinetics in Confinement. Erba?, Aykut; Olvera de la Cruz, Monica; Marko, John F Biophysical journal. 31029377 2019 May 07;
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. McSwiggen, David Trombley; Hansen, Anders S; Teves, Sheila S; Marie-Nelly, Hervé; Hao, Yvonne; Heckert, Alec Basil; Umemoto, Kayla K; Dugast-Darzacq, Claire; Tjian, Robert; Darzacq, Xavier eLife 31038454 2019 05 07
Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. Yu, Jingting; Hu, Ming; Li, Chun BMC genetics. 31039743 2019 Apr 30;
Sensory experience remodels genome architecture in neural circuit to drive motor learning. Yamada, Tomoko; Yang, Yue; Valnegri, Pamela; Juric, Ivan; Abnousi, Armen; Markwalter, Kelly H; Guthrie, Arden N; Godec, Abigail; Oldenborg, Anna; Hu, Ming; Holy, Timothy E; Bonni, Azad Nature. 31068695 2019 May;
Tibanna: software for scalable execution of portable pipelines on the cloud. Lee, Soohyun; Johnson, Jeremy; Vitzthum, Carl; K?rl?, Koray; Alver, Burak H; Park, Peter J Bioinformatics (Oxford, England). 31077294 2019 May 11;
A combination of transcription factors mediates inducible interchromosomal contacts. Kim, Seungsoo; Dunham, Maitreya J; Shendure, Jay eLife 31081754 2019 05 13
Long-range enhancer-promoter contacts in gene expression control. Schoenfelder, Stefan; Fraser, Peter Nature reviews. Genetics. 31086298 2019 08;
Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx. Möckl, Leonhard; Pedram, Kayvon; Roy, Anish R; Krishnan, Venkatesh; Gustavsson, Anna-Karin; Dorigo, Oliver; Bertozzi, Carolyn R; Moerner, W E Developmental cell. 31105009 2019 Jul 01;
Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. Sato, Hanae; Wu, Bin; Delahaye, Fabien; Singer, Robert H; Greally, John M The Journal of cell biology. 31110057 2019 Jun 03;
Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. Li, Peipei; Marshall, Lee; Oh, Gabriel; Jakubowski, Jennifer L; Groot, Daniel; He, Yu; Wang, Ting; Petronis, Arturas; Labrie, Viviane Nature communications. 31113950 2019 05 21;
EpiAlignment: alignment with both DNA sequence and epigenomic data. Lu, Jia; Cao, Xiaoyi; Zhong, Sheng Nucleic acids research. 31114924 2019 Jul 02;
The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. Salvarani, Nicolò; Crasto, Silvia; Miragoli, Michele; Bertero, Alessandro; Paulis, Marianna; Kunderfranco, Paolo; Serio, Simone; Forni, Alberto; Lucarelli, Carla; Dal Ferro, Matteo; Larcher, Veronica; Sinagra, Gianfranco; Vezzoni, Paolo; Murry, Charles E; Faggian, Giuseppe; Condorelli, Gianluigi; Di Pasquale, Elisa Nature communications. 31118417 2019 05 22;
Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. Cheng, Li-Chun; Baboo, Sabyasachi; Lindsay, Cory; Brusman, Liza; Martinez-Bartolomé, Salvador; Tapia, Olga; Zhang, Xi; Yates 3rd, John R; Gerace, Larry Nucleus (Austin, Tex.). 31142202 2019 Dec;
Time varying causal network reconstruction of a mouse cell cycle. Masnadi-Shirazi, Maryam; Maurya, Mano R; Pao, Gerald; Ke, Eugene; Verma, Inder M; Subramaniam, Shankar BMC bioinformatics. 31142274 2019 May 29;
Preformed chromatin topology assists transcriptional robustness of Shh during limb development. Paliou, Christina; Guckelberger, Philine; Schöpflin, Robert; Heinrich, Verena; Esposito, Andrea; Chiariello, Andrea M; Bianco, Simona; Annunziatella, Carlo; Helmuth, Johannes; Haas, Stefan; Jerkovi?, Ivana; Brieske, Norbert; Wittler, Lars; Timmermann, Ber Proceedings of the National Academy of Sciences of the United States of America. 31147463 2019 Jun 18;
Principles for Integrative Structural Biology Studies. Rout, Michael P; Sali, Andrej Cell. 31150619 2019 May 30;
WashU Epigenome Browser update 2019. Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Sears, Renee L; Wang, Ting Nucleic acids research. 31165883 2019 Jul 02;
Heterochromatin drives compartmentalization of inverted and conventional nuclei. Falk, Martin; Feodorova, Yana; Naumova, Natalia; Imakaev, Maxim; Lajoie, Bryan R; Leonhardt, Heinrich; Joffe, Boris; Dekker, Job; Fudenberg, Geoffrey; Solovei, Irina; Mirny, Leonid A Nature. 31168090 2019 Jun;
FunPred 3.0: improved protein function prediction using protein interaction network. Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Nasipuri, Mita; Plewczynski, Dariusz PeerJ. 31198622 2019;
Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. Vertii, Anastassiia; Ou, Jianhong; Yu, Jun; Yan, Aimin; Pagès, Hervé; Liu, Haibo; Zhu, Lihua Julie; Kaufman, Paul D Genome research. 31201210 2019 Jun 14;
Absolute quantification of cohesin, CTCF and their regulators in human cells. Holzmann, Johann; Politi, Antonio Z; Nagasaka, Kota; Hantsche-Grininger, Merle; Walther, Nike; Koch, Birgit; Fuchs, Johannes; Dürnberger, Gerhard; Tang, Wen; Ladurner, Rene; Stocsits, Roman R; Busslinger, Georg A; Novák, Béla; Mechtler, Karl; Davidson, Ia eLife. 31204999 2019 06 17;
Determining cellular CTCF and cohesin abundances to constrain 3D genome models. Cattoglio, Claudia; Pustova, Iryna; Walther, Nike; Ho, Jaclyn J; Hantsche-Grininger, Merle; Inouye, Carla J; Hossain, M Julius; Dailey, Gina M; Ellenberg, Jan; Darzacq, Xavier; Tjian, Robert; Hansen, Anders S eLife. 31205001 2019 Jun 17;
Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data. Rosenthal, Michael; Bryner, Darshan; Huffer, Fred; Evans, Shane; Srivastava, Anuj; Neretti, Nicola Journal of computational biology : a journal of computational molecular cell biology. 31211598 2019 Nov;
Two major mechanisms of chromosome organization. Mirny, Leonid A; Imakaev, Maxim; Abdennur, Nezar Current opinion in cell biology. 31228682 2019 Jun;
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Yang, Yang; Zhang, Yang; Ren, Bing; Dixon, Jesse R; Ma, Jian Cell systems. 31229558 2019 Jun 26;
Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Khanna, Nimish; Zhang, Yaojun; Lucas, Joseph S; Dudko, Olga K; Murre, Cornelis Nature communications. 31235807 2019 06 24;
LADL: light-activated dynamic looping for endogenous gene expression control. Kim, Ji Hun; Rege, Mayuri; Valeri, Jacqueline; Dunagin, Margaret C; Metzger, Aryeh; Titus, Katelyn R; Gilgenast, Thomas G; Gong, Wanfeng; Beagan, Jonathan A; Raj, Arjun; Phillips-Cremins, Jennifer E Nature methods. 31235883 2019 07;
Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures. Hulleman, Christiaan N; Huisman, Maximiliaan; Moerland, Robert J; Grünwald, David; Stallinga, Sjoerd; Rieger, Bernd Small methods. 31240238 2018 Sep 11;
A subset of topologically associating domains fold into mesoscale core-periphery networks. Huang, Harvey; Chen, Sunnia T; Titus, Katelyn R; Emerson, Daniel J; Bassett, Danielle S; Phillips-Cremins, Jennifer E Scientific reports. 31266973 2019 Jul 02;
Archiving and disseminating integrative structure models. Vallat, Brinda; Webb, Benjamin; Westbrook, John; Sali, Andrej; Berman, Helen M Journal of biomolecular NMR. 31278630 2019 Jul;
Large distances separate coregulated genes in living Drosophila embryos. Heist, Tyler; Fukaya, Takashi; Levine, Michael Proceedings of the National Academy of Sciences of the United States of America. 31285341 2019 07 23;
Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene. Lalonde, Simon; Codina-Fauteux, Valérie-Anne; de Bellefon, Sébastian Méric; Leblanc, Francis; Beaudoin, Mélissa; Simon, Marie-Michelle; Dali, Rola; Kwan, Tony; Lo, Ken Sin; Pastinen, Tomi; Lettre, Guillaume Genome biology 31287004 2019 07 08
Cooler: scalable storage for Hi-C data and other genomically-labeled arrays. Abdennur, Nezar; Mirny, Leonid Bioinformatics (Oxford, England). 31290943 2019 Jul 10;
Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT. Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Auer, Alexander; Nijmeijer, Bianca; Kueblbeck, Moritz; Jimenez Sabinina, Vilma; Thevathasan, Jervis V; Ries, Jonas; Ellenberg, Jan; Jungmann, Ralf Angewandte Chemie (International ed. in English). 31314157 2019 09 09;
Spatial chromatin architecture alteration by structural variations in human genomes at the population scale. Sadowski, Michal; Kraft, Agnieszka; Szalaj, Przemyslaw; Wlasnowolski, Michal; Tang, Zhonghui; Ruan, Yijun; Plewczynski, Dariusz Genome biology 31362752 2019 07 30
Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. Stephens, Andrew D; Liu, Patrick Z; Kandula, Viswajit; Chen, Haimei; Almassalha, Luay M; Herman, Cameron; Backman, Vadim; O'Halloran, Thomas; Adam, Stephen A; Goldman, Robert D; Banigan, Edward J; Marko, John F Molecular biology of the cell. 31365328 2019 Aug 01;
Joint profiling of DNA methylation and chromatin architecture in single cells. Li, Guoqiang; Liu, Yaping; Zhang, Yanxiao; Kubo, Naoki; Yu, Miao; Fang, Rongxin; Kellis, Manolis; Ren, Bing Nature methods. 31384045 2019 Oct;
Learn from Your Elders: Developmental Biology Lessons to Guide Maturation of Stem Cell-Derived Cardiomyocytes. Marchianò, Silvia; Bertero, Alessandro; Murry, Charles E Pediatric cardiology. 31388700 2019 Oct;
Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells. Bianco, Simona; Annunziatella, Carlo; Andrey, Guillaume; Chiariello, Andrea M; Esposito, Andrea; Fiorillo, Luca; Prisco, Antonella; Conte, Mattia; Campanile, Raffaele; Nicodemi, Mario Cell reports. 31390570 2019 08 06;
Genome organization around nuclear speckles. Chen, Yu; Belmont, Andrew S Current opinion in genetics & development. 31394307 2019 Apr;
Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. Bertero, Alessandro; Fields, Paul A; Smith, Alec S T; Leonard, Andrea; Beussman, Kevin; Sniadecki, Nathan J; Kim, Deok-Ho; Tse, Hung-Fat; Pabon, Lil; Shendure, Jay; Noble, William S; Murry, Charles E The Journal of cell biology. 31395619 2019 Sep 02;
Visual Pattern-Driven Exploration of Big Data. Behrisch, Michael; Schreck, Tobias; Krüger, Robert; Gehlenborg, Nils; Lekschas, Fritz; Pfister, Hanspeter 2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany). 31396383 2018 Oct;
Controlling the material properties and rRNA processing function of the nucleolus using light. Zhu, Lian; Richardson, Tiffany M; Wacheul, Ludivine; Wei, Ming-Tzo; Feric, Marina; Whitney, Gena; Lafontaine, Denis L J; Brangwynne, Clifford P Proceedings of the National Academy of Sciences of the United States of America. 31399547 2019 Aug 09;
Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. Lari, Azra; Farzam, Farzin; Bensidoun, Pierre; Oeffinger, Marlene; Zenklusen, Daniel; Grunwald, David; Montpetit, Ben Methods in molecular biology (Clifton, N.J.). 31407282 2019;
Skeletal muscle: A review of molecular structure and function, in health and disease. Mukund, Kavitha; Subramaniam, Shankar Wiley interdisciplinary reviews. Systems biology and medicine 31407867 2020 01
Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Dahlke, Katelyn; Zhao, Jing; Sing, Charles E; Banigan, Edward J Biophysical journal. 31427067 2019 Sep 17;
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Zhang, Yanxiao; Li, Ting; Preissl, Sebastian; Amaral, Maria Luisa; Grinstein, Jonathan D; Farah, Elie N; Destici, Eugin; Qiu, Yunjiang; Hu, Rong; Lee, Ah Young; Chee, Sora; Ma, Kaiyue; Ye, Zhen; Zhu, Quan; Huang, Hui; Fang, Rongxin; Yu, Leqian; Izpisua Belmonte, Juan Carlos; Wu, Jun; Evans, Sylvia M; Chi, Neil C; Ren, Bing Nature genetics. 31427791 2019 Sep;
Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. Wei, Chia-Lin; Nicolis, Silvia K; Zhu, Yanfen; Pagin, Miriam Journal of experimental neuroscience. 31431802 2019;
Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets. Lekschas, Fritz; Behrisch, Michael; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter IEEE transactions on visualization and computer graphics. 31442989 2020 Jan;
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole Nature genetics. 31477929 2019 Sep;
Molecular basis and biological function of variability in spatial genome organization. Finn, Elizabeth H; Misteli, Tom Science (New York, N.Y.). 31488662 2019 09 06;
CRISPR-mediated live imaging of genome editing and transcription. Wang, Haifeng; Nakamura, Muneaki; Abbott, Timothy R; Zhao, Dehua; Luo, Kaiwen; Yu, Cordelia; Nguyen, Cindy M; Lo, Albert; Daley, Timothy P; La Russa, Marie; Liu, Yanxia; Qi, Lei S Science (New York, N.Y.). 31488703 2019 09 20;
Olfactory receptor genes make the case for inter-chromosomal interactions. Bashkirova, Elizaveta; Lomvardas, Stavros Current opinion in genetics & development. 31491591 2019 Apr;
High-Throughput Single-Cell Sequencing with Linear Amplification. Yin, Yi; Jiang, Yue; Lam, Kwan-Wood Gabriel; Berletch, Joel B; Disteche, Christine M; Noble, William S; Steemers, Frank J; Camerini-Otero, R Daniel; Adey, Andrew C; Shendure, Jay Molecular cell. 31495564 2019 Aug 28;
Supervised classification enables rapid annotation of cell atlases. Pliner, Hannah A; Shendure, Jay; Trapnell, Cole Nature methods. 31501545 2019 Oct;
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. Ray, Judhajeet; Munn, Paul R; Vihervaara, Anniina; Lewis, James J; Ozer, Abdullah; Danko, Charles G; Lis, John T Proceedings of the National Academy of Sciences of the United States of America. 31506350 2019 Sep 24;
The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. Zhang, Yu; Zhang, Xuefei; Ba, Zhaoqing; Liang, Zhuoyi; Dring, Edward W; Hu, Hongli; Lou, Jiangman; Kyritsis, Nia; Zurita, Jeffrey; Shamim, Muhammad S; Presser Aiden, Aviva; Lieberman Aiden, Erez; Alt, Frederick W Nature. 31511698 2019 Sep;
Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Hansen, Anders S; Hsieh, Tsung-Han S; Cattoglio, Claudia; Pustova, Iryna; Saldaña-Meyer, Ricardo; Reinberg, Danny; Darzacq, Xavier; Tjian, Robert Molecular cell. 31522987 2019 11 07;
Jonathan R. Warner (1936-2019)-pioneer of ribosome biosynthesis. Pederson, Thoru RNA (New York, N.Y.). 31534010 2019 Dec;
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Lee, Choli; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun Methods (San Diego, Calif.). 31536770 2019 Sep 16;
Nuclear pores as versatile reference standards for quantitative superresolution microscopy. Thevathasan, Jervis Vermal; Kahnwald, Maurice; Cie?li?ski, Konstanty; Hoess, Philipp; Peneti, Sudheer Kumar; Reitberger, Manuel; Heid, Daniel; Kasuba, Krishna Chaitanya; Hoerner, Sarah Janice; Li, Yiming; Wu, Yu-Le; Mund, Markus; Matti, Ulf; Pereira, Pedro Matos; Henriques, Ricardo; Nijmeijer, Bianca; Kueblbeck, Moritz; Sabinina, Vilma Jimenez; Ellenberg, Jan; Ries, Jonas Nature methods. 31562488 2019 Oct;
Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells. Yang, Xiulan; Rodriguez, Marita L; Leonard, Andrea; Sun, Lihua; Fischer, Karin A; Wang, Yuliang; Ritterhoff, Julia; Zhao, Limei; Kolwicz Jr, Stephen C; Pabon, Lil; Reinecke, Hans; Sniadecki, Nathan J; Tian, Rong; Ruohola-Baker, Hannele; Xu, Haodong; Murry Stem cell reports. 31564645 2019 10 08;
Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging. Zheng, Qinsi; Ayala, Anthony X; Chung, Inhee; Weigel, Aubrey V; Ranjan, Anand; Falco, Natalie; Grimm, Jonathan B; Tkachuk, Ariana N; Wu, Carl; Lippincott-Schwartz, Jennifer; Singer, Robert H; Lavis, Luke D ACS central science. 31572787 2019 Sep 25;
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Erceg, Jelena; AlHaj Abed, Jumana; Goloborodko, Anton; Lajoie, Bryan R; Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; McCole, Ruth B; Nguyen, Son C; Saylor, Wren; Joyce, Eric F; Senaratne, T Niroshini; Hannan, Mohammed A; Nir, Guy; Dekker, Job; Mirny, Leonid A; Wu, C-Ting Nature communications. 31582744 2019 Oct 03;
Highly structured homolog pairing reflects functional organization of the Drosophila genome. AlHaj Abed, Jumana; Erceg, Jelena; Goloborodko, Anton; Nguyen, Son C; McCole, Ruth B; Saylor, Wren; Fudenberg, Geoffrey; Lajoie, Bryan R; Dekker, Job; Mirny, Leonid A; Wu, C-Ting Nature communications. 31582763 2019 Oct 03;
How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. Erba?, Aykut; Marko, John F Current opinion in chemical biology. 31586479 2019 Oct 02;
Cronos Titin Is Expressed in Human Cardiomyocytes and Necessary for Normal Sarcomere Function. Zaunbrecher, Rebecca J; Abel, Ashley N; Beussman, Kevin; Leonard, Andrea; von Frieling-Salewsky, Marion; Fields, Paul A; Pabon, Lil; Reinecke, Hans; Yang, Xiulan; Macadangdang, Jesse; Kim, Deok-Ho; Linke, Wolfgang A; Sniadecki, Nathan J; Regnier, Michael; Murry, Charles E Circulation. 31587567 2019 Nov 12;
Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. McSwiggen, David T; Mir, Mustafa; Darzacq, Xavier; Tjian, Robert Genes & development. 31594803 2019 12 01;
Photoactivation of silicon rhodamines via a light-induced protonation. Frei, Michelle S; Hoess, Philipp; Lampe, Marko; Nijmeijer, Bianca; Kueblbeck, Moritz; Ellenberg, Jan; Wadepohl, Hubert; Ries, Jonas; Pitsch, Stefan; Reymond, Luc; Johnsson, Kai Nature communications. 31594948 2019 Oct 08;
Inference of chromosome 3D structures from GAM data by a physics computational approach. Fiorillo, Luca; Bianco, Simona; Chiariello, Andrea M; Barbieri, Mariano; Esposito, Andrea; Annunziatella, Carlo; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario Methods (San Diego, Calif.). 31604121 2020 10 01;
Mapping RNA-chromatin interactions by sequencing with iMARGI. Wu, Weixin; Yan, Zhangming; Nguyen, Tri C; Bouman Chen, Zhen; Chien, Shu; Zhong, Sheng Nature protocols. 31619811 2019 Nov;
Methods for comparative ChIA-PET and Hi-C data analysis. Capurso, Dan; Tang, Zhonghui; Ruan, Yijun Methods (San Diego, Calif.). 31629084 2020 01 01;
X Inactivation and Escape: Epigenetic and Structural Features. Fang, He; Disteche, Christine M; Berletch, Joel B Frontiers in cell and developmental biology. 31632970 2019;
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Abramo, Kristin; Valton, Anne-Laure; Venev, Sergey V; Ozadam, Hakan; Fox, A Nicole; Dekker, Job Nature cell biology. 31685986 2019 Nov;
A Proteomic Perspective on Cardiomyocyte Maturation. Muraoka, Naoto; Sun, Bingyun; Murry, Charles E Circulation research. 31697629 2019 11 08;
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Xiong, Kyle; Ma, Jian Nature communications. 31699985 2019 11 07;
Aggregated network centrality shows non-random structure of genomic and proteomic networks. Halder, Anup Kumar; Denkiewicz, Micha?; Sengupta, Kaustav; Basu, Subhadip; Plewczynski, Dariusz Methods (San Diego, Calif.). 31740366 2020 10 01;
The liquid nucleome - phase transitions in the nucleus at a glance. Strom, Amy R; Brangwynne, Clifford P Journal of cell science. 31754043 2019 11 21;
Gene expression amplification by nuclear speckle association. Kim, Jiah; Venkata, Neha Chivukula; Hernandez Gonzalez, Gabriela Andrea; Khanna, Nimish; Belmont, Andrew S The Journal of cell biology. 31757787 2020 Jan 06;
Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. Brahmachari, Sumitabha; Marko, John F Proceedings of the National Academy of Sciences of the United States of America. 31757850 2019 12 10;
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms. Kim, Minji; Zheng, Meizhen; Tian, Simon Zhongyuan; Lee, Byoungkoo; Chuang, Jeffrey H; Ruan, Yijun Genome biology 31767038 2019 11 25
Tasks, Techniques, and Tools for Genomic Data Visualization. Nusrat, S; Harbig, T; Gehlenborg, N Computer graphics forum : journal of the European Association for Computer Graphics. 31768085 2019 Jun;
Chromatin structure dynamics during the mitosis-to-G1 phase transition. Zhang, Haoyue; Emerson, Daniel J; Gilgenast, Thomas G; Titus, Katelyn R; Lan, Yemin; Huang, Peng; Zhang, Di; Wang, Hongxin; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Phillips-Cremins, Jennifer E; Blobel, Gerd A Nature. 31776509 2019 12;
Common DNA sequence variation influences 3-dimensional conformation of the human genome. Gorkin, David U; Qiu, Yunjiang; Hu, Ming; Fletez-Brant, Kipper; Liu, Tristin; Schmitt, Anthony D; Noor, Amina; Chiou, Joshua; Gaulton, Kyle J; Sebat, Jonathan; Li, Yun; Hansen, Kasper D; Ren, Bing Genome biology 31779666 2019 11 28
Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Fulco, Charles P; Nasser, Joseph; Jones, Thouis R; Munson, Glen; Bergman, Drew T; Subramanian, Vidya; Grossman, Sharon R; Anyoha, Rockwell; Doughty, Benjamin R; Patwardhan, Tejal A; Nguyen, Tung H; Kane, Michael; Perez, Elizabeth M; Durand, Neva C; Lareau Nature genetics. 31784727 2019 12;
Editorial: Neural epigenetics. Greenberg, Michael E; Lomvardas, Stavros Current opinion in neurobiology 31787169 2019 Dec
Spring Model - Chromatin Modeling Tool Based on OpenMM. Kadlof, Michal; Rozycka, Julia; Plewczynski, Dariusz Methods (San Diego, Calif.). 31790732 2020 10 01;
Probing and engineering liquid-phase organelles. Bracha, Dan; Walls, Mackenzie T; Brangwynne, Clifford P Nature biotechnology. 31792412 2019 12;
Guided nuclear exploration increases CTCF target search efficiency. Hansen, Anders S; Amitai, Assaf; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier Nature chemical biology. 31792445 2019 Dec 02;
Chromatin Is Frequently Unknotted at the Megabase Scale. Goundaroulis, Dimos; Lieberman Aiden, Erez; Stasiak, Andrzej Biophysical journal. 31818464 2020 May 05;
Localization microscopy at doubled precision with patterned illumination. Cnossen, Jelmer; Hinsdale, Taylor; Thorsen, Rasmus Ø; Siemons, Marijn; Schueder, Florian; Jungmann, Ralf; Smith, Carlas S; Rieger, Bernd; Stallinga, Sjoerd Nature methods. 31819263 2020 Jan;
The epigenomic landscape of transposable elements across normal human development and anatomy. Pehrsson, Erica C; Choudhary, Mayank N K; Sundaram, Vasavi; Wang, Ting Nature communications. 31822674 2019 Dec 10;
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. An, Lin; Yang, Tao; Yang, Jiahao; Nuebler, Johannes; Xiang, Guanjue; Hardison, Ross C; Li, Qunhua; Zhang, Yu Genome biology. 31847870 2019 12 18;
Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells. Chen, Changya; Yu, Wenbao; Tober, Joanna; Gao, Peng; He, Bing; Lee, Kiwon; Trieu, Tuan; Blobel, Gerd A; Speck, Nancy A; Tan, Kai Cell reports. 31851943 2019 12 17;
Physics and Biology (of Chromosomes). Marko, John F Journal of molecular biology. 31866291 2020 Jan 17;
An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms. Yu, Yi; Guo, Yijun; Tian, Qiqi; Lan, Yuanqing; Yeh, Hugh; Zhang, Meng; Tasan, Ipek; Jain, Surbhi; Zhao, Huimin Nature chemical biology. 31873222 2020 04;
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Tian, Dechao; Zhang, Ruochi; Zhang, Yang; Zhu, Xiaopeng; Ma, Jian Genome research. 31907193 2020 Jan 06;
On the existence and functionality of topologically associating domains. Beagan, Jonathan A; Phillips-Cremins, Jennifer E Nature genetics. 31925403 2020 01;
Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts. Weyers, Jill J; Gunaje, Jagadambika J; Van Biber, Benjamin; Martinson, Amy; Reinecke, Hans; Mahoney, William M; Schwartz, Stephen M; Cox, Timothy C; Murry, Charles E PloS one. 31945113 2020;
Co-opted transposons help perpetuate conserved higher-order chromosomal structures. Choudhary, Mayank Nk; Friedman, Ryan Z; Wang, Julia T; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, Ting Genome biology. 31973766 2020 01 24;
Switchable resolution in soft x-ray tomography of single cells. Weinhardt, Venera; Chen, Jian-Hua; Ekman, Axel A; Guo, Jessica; Remesh, Soumya G; Hammel, Michal; McDermott, Gerry; Chao, Weilun; Oh, Sharon; Le Gros, Mark A; Larabell, Carolyn A PloS one. 31978064 2020;
Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. Feodorova, Yana; Falk, Martin; Mirny, Leonid A; Solovei, Irina Trends in cell biology. 31980345 2020 Apr;
GiniQC: a measure for quantifying noise in single-cell Hi-C data. Horton, Connor A; Alver, Burak H; Park, Peter J Bioinformatics (Oxford, England). 32003786 2020 05 01;
Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine. Karbassi, Elaheh; Fenix, Aidan; Marchiano, Silvia; Muraoka, Naoto; Nakamura, Kenta; Yang, Xiulan; Murry, Charles E Nature reviews. Cardiology. 32015528 2020 Feb 03;
Dynamic Assembly and Disassembly of the Human DNA Polymerase ? Holoenzyme on the Genome In Vivo. Drosopoulos, William C; Vierra, David A; Kenworthy, Charles A; Coleman, Robert A; Schildkraut, Carl L Cell reports. 32023453 2020 02 04;
pyBedGraph: a python package for fast operations on 1D genomic signal tracks. Zhang, Henry B; Kim, Minji; Chuang, Jeffrey H; Ruan, Yijun Bioinformatics (Oxford, England). 32044918 2020 05 01;
Computational approaches from polymer physics to investigate chromatin folding. Bianco, Simona; Chiariello, Andrea M; Conte, Mattia; Esposito, Andrea; Fiorillo, Luca; Musella, Francesco; Nicodemi, Mario Current opinion in cell biology. 32045823 2020 06;
Derivation of trophoblast stem cells from naïve human pluripotent stem cells. Dong, Chen; Beltcheva, Mariana; Gontarz, Paul; Zhang, Bo; Popli, Pooja; Fischer, Laura A; Khan, Shafqat A; Park, Kyoung-Mi; Yoon, Eun-Ja; Xing, Xiaoyun; Kommagani, Ramakrishna; Wang, Ting; Solnica-Krezel, Lilianna; Theunissen, Thorold W eLife. 32048992 2020 Feb 12;
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL. Wutz, Gordana; Ladurner, Rene; St Hilaire, Brian Glenn; Stocsits, Roman R; Nagasaka, Kota; Pignard, Benoit; Sanborn, Adrian; Tang, Wen; Várnai, Csilla; Ivanov, Miroslav P; Schoenfelder, Stefan; van der Lelij, Petra; Huang, Xingfan; Dürnberger, Gerhard; Roitinger, Elisabeth; Mechtler, Karl; Davidson, Iain Finley; Fraser, Peter; Lieberman-Aiden, Erez; Peters, Jan-Michael eLife. 32065581 2020 Feb 17;
Chemogenetic Control of Nanobodies. Farrants, Helen; Tarnawski, Miroslaw; Müller, Thorsten G; Otsuka, Shotaro; Hiblot, Julien; Koch, Birgit; Kueblbeck, Moritz; Kräusslich, Hans-Georg; Ellenberg, Jan; Johnsson, Kai Nature methods. 32066961 2020 03;
An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. Kim, Arthur S; Zimmerman, Ofer; Fox, Julie M; Nelson, Christopher A; Basore, Katherine; Zhang, Rong; Durnell, Lorellin; Desai, Chandni; Bullock, Christopher; Deem, Sharon L; Oppenheimer, Jonas; Shapiro, Beth; Wang, Ting; Cherry, Sara; Coyne, Carolyn B; Ha Cell host & microbe. 32075743 2020 03 11;
A Dynamic Folded Hairpin Conformation Is Associated with ?-Globin Activation in Erythroid Cells. Chiariello, Andrea M; Bianco, Simona; Oudelaar, A Marieke; Esposito, Andrea; Annunziatella, Carlo; Fiorillo, Luca; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Larke, Martin S C; Telenius, Jelena M; Sciarretta, Renato; Musella, Francesco; Buckle, V Cell reports. 32075757 2020 02 18;
Local rewiring of genome-nuclear lamina interactions by transcription. Brueckner, Laura; Zhao, Peiyao A; van Schaik, Tom; Leemans, Christ; Sima, Jiao; Peric-Hupkes, Daniel; Gilbert, David M; van Steensel, Bas The EMBO journal. 32080885 2020 Mar 16;
Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation. Biswas, Jeetayu; Nunez, Leti; Das, Sulagna; Yoon, Young J; Eliscovich, Carolina; Singer, Robert H Cold Spring Harbor symposia on quantitative biology. 32086331 2020 Feb 21;
Therapeutic genome editing in cardiovascular diseases. Nishiga, Masataka; Qi, Lei S; Wu, Joseph C Advanced drug delivery reviews. 32092381 2020 Feb 21;
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Wang, Wenbo; Goldfeder, Rachel L; Choi, Cindy; He, Hao; Gong, Liang; Lin, Junyan; Urban, Barbara; Chow, Julianna; Li, Meihong; Lim, Joanne; Philip, Vivek; Murray, Stephen A; Wang, Haoyi; Wei, Chia-Lin Nature genetics. 32094912 2020 03;
Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Lee, Hyung Joo; Hou, Yiran; Chen, Yujie; Dailey, Zea Z; Riddihough, Aiyana; Jang, Hyo Sik; Wang, Ting; Johnson, Stephen L Genome biology. 32106888 2020 02 27;
Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems. Masnadi-Shirazi, Maryam; Subramaniam, Shankar Scientific reports. 32123218 2020 Mar 02;
Advanced 3D Analysis and Optimization of Single-Molecule FISH in Drosophila Muscle. Noma, Akiko; Smith, Carlas S; Huisman, Maximiliaan; Martin, Robert M; Moore, Melissa J; Grunwald, David Small methods. 32158910 2018 Sep 11;
The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process. Urban, Paulina; Rezaei Tabar, Vahid; Denkiewicz, Michał; Bokota, Grzegorz; Das, Nirmal; Basu, Subhadip; Plewczynski, Dariusz Journal of computational biology : a journal of computational molecular cell biology 32175768 2020 09
Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Sato, Hanae; Das, Sulagna; Singer, Robert H; Vera, Maria Annual review of biochemistry. 32176523 2020 06 20;
Evaluating Enhancer Function and Transcription. Field, Andrew; Adelman, Karen Annual review of biochemistry. 32197056 2020 06 20;
Cost-efficient open source laser engine for microscopy. Schröder, Daniel; Deschamps, Joran; Dasgupta, Anindita; Matti, Ulf; Ries, Jonas Biomedical optics express. 32206389 2020 Feb 01;
High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Zhao, Peiyao A; Sasaki, Takayo; Gilbert, David M Genome biology. 32209126 2020 03 24;
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Hsieh, Tsung-Han S; Cattoglio, Claudia; Slobodyanyuk, Elena; Hansen, Anders S; Rando, Oliver J; Tjian, Robert; Darzacq, Xavier Molecular cell. 32213323 2020 05 07;
Ultrastructural Details of Mammalian Chromosome Architecture. Krietenstein, Nils; Abraham, Sameer; Venev, Sergey V; Abdennur, Nezar; Gibcus, Johan; Hsieh, Tsung-Han S; Parsi, Krishna Mohan; Yang, Liyan; Maehr, René; Mirny, Leonid A; Dekker, Job; Rando, Oliver J Molecular cell. 32213324 2020 Mar 14;
Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. Zhao, Binhui; Chaturvedi, Pankaj; Zimmerman, David L; Belmont, Andrew S ACS synthetic biology. 32216371 2020 05 15;
Distinct features of nucleolus-associated domains in mouse embryonic stem cells. Bizhanova, Aizhan; Yan, Aimin; Yu, Jun; Zhu, Lihua Julie; Kaufman, Paul D Chromosoma. 32219510 2020 Mar 26;
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. Schreiber, Jacob; Durham, Timothy; Bilmes, Jeffrey; Noble, William Stafford Genome biology. 32228704 2020 03 30;
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Field, Matt A; Rosen, Benjamin D; Dudchenko, Olga; Chan, Eva K F; Minoche, Andre E; Edwards, Richard J; Barton, Kirston; Lyons, Ruth J; Tuipulotu, Daniel Enosi; Hayes, Vanessa M; D Omer, Arina; Colaric, Zane; Keilwagen, Jens; Skvortsova, Ksenia; Bogdanovi GigaScience. 32236524 2020 04 01;
Chromosome organization by one-sided and two-sided loop extrusion. Banigan, Edward J; van den Berg, Aafke A; Brandão, Hugo B; Marko, John F; Mirny, Leonid A eLife 32250245 2020 04 06
Sci-fate characterizes the dynamics of gene expression in single cells. Cao, Junyue; Zhou, Wei; Steemers, Frank; Trapnell, Cole; Shendure, Jay Nature biotechnology. 32284584 2020 Aug;
Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. Sanders, David W; Kedersha, Nancy; Lee, Daniel S W; Strom, Amy R; Drake, Victoria; Riback, Joshua A; Bracha, Dan; Eeftens, Jorine M; Iwanicki, Allana; Wang, Alicia; Wei, Ming-Tzo; Whitney, Gena; Lyons, Shawn M; Anderson, Paul; Jacobs, William M; Ivanov, P Cell. 32302570 2020 04 16;
Chromatin Viscoelasticity Measured by Local Dynamic Analysis. Vivante, Anat; Bronshtein, Irena; Garini, Yuval Biophysical journal. 32320676 2020 05 05;
Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. Schuh, Lea; Saint-Antoine, Michael; Sanford, Eric M; Emert, Benjamin L; Singh, Abhyudai; Marr, Carsten; Raj, Arjun; Goyal, Yogesh Cell systems. 32325034 2020 Apr 22;
The gene-rich genome of the scallop Pecten maximus. Kenny, Nathan J; McCarthy, Shane A; Dudchenko, Olga; James, Katherine; Betteridge, Emma; Corton, Craig; Dolucan, Jale; Mead, Dan; Oliver, Karen; Omer, Arina D; Pelan, Sarah; Ryan, Yan; Sims, Ying; Skelton, Jason; Smith, Michelle; Torrance, James; Weisz, D GigaScience 32352532 2020 05 01
Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. Trzaskoma, Pawe?; Ruszczycki, B?a?ej; Lee, Byoungkoo; Pels, Katarzyna K; Krawczyk, Katarzyna; Bokota, Grzegorz; Szczepankiewicz, Andrzej A; Aaron, Jesse; Walczak, Agnieszka; ?liwi?ska, Ma?gorzata A; Magalska, Adriana; Kadlof, Michal; Wolny, Artur; Parteka Nature communications. 32358536 2020 05 01;
Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild. Humble, Emily; Dobrynin, Pavel; Senn, Helen; Chuven, Justin; Scott, Alan F; Mohr, David W; Dudchenko, Olga; Omer, Arina D; Colaric, Zane; Lieberman Aiden, Erez; Al Dhaheri, Shaikha Salem; Wildt, David; Oliaji, Shireen; Tamazian, Gaik; Pukazhenthi, Budhan; Ogden, Rob; Koepfli, Klaus-Peter Molecular ecology resources 32365406 2020 Nov
Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. Zhang, Xiaotian; Jeong, Mira; Huang, Xingfan; Wang, Xue Qing; Wang, Xinyu; Zhou, Wanding; Shamim, Muhammad S; Gore, Haley; Himadewi, Pamela; Liu, Yushuai; Bochkov, Ivan D; Reyes, Jaime; Doty, Madison; Huang, Yung-Hsin; Jung, Haiyoung; Heikamp, Emily; Aide Molecular cell. 32386543 2020 05 07;
Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. Wang, Ping; Tang, Zhonghui; Lee, Byoungkoo; Zhu, Jacqueline Jufen; Cai, Liuyang; Szalaj, Przemyslaw; Tian, Simon Zhongyuan; Zheng, Meizhen; Plewczynski, Dariusz; Ruan, Xiaoan; Liu, Edison T; Wei, Chia-Lin; Ruan, Yijun Genome biology 32393309 2020 05 11
Composition-dependent thermodynamics of intracellular phase separation. Riback, Joshua A; Zhu, Lian; Ferrolino, Mylene C; Tolbert, Michele; Mitrea, Diana M; Sanders, David W; Wei, Ming-Tzo; Kriwacki, Richard W; Brangwynne, Clifford P Nature. 32405004 2020 05;
Histone Signatures Predict Therapeutic Efficacy in Breast Cancer. Mollah, Shamim A; Subramaniam, Shankar IEEE open journal of engineering in medicine and biology 32412527 2020
Delta-1 Functionalized Hydrogel Promotes hESC-Cardiomyocyte Graft Proliferation and Maintains Heart Function Post-Injury. Gerbin, Kaytlyn A; Mitzelfelt, Katie A; Guan, Xuan; Martinson, Amy M; Murry, Charles E Molecular therapy. Methods & clinical development. 32426414 2020 Jun 12;
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. Wlasnowolski, Michal; Sadowski, Michal; Czarnota, Tymon; Jodkowska, Karolina; Szalaj, Przemyslaw; Tang, Zhonghui; Ruan, Yijun; Plewczynski, Dariusz Nucleic acids research. 32442297 2020 07 02;
Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. Beagan, Jonathan A; Pastuzyn, Elissa D; Fernandez, Lindsey R; Guo, Michael H; Feng, Kelly; Titus, Katelyn R; Chandrashekar, Harshini; Shepherd, Jason D; Phillips-Cremins, Jennifer E Nature neuroscience. 32451484 2020 06;
Evolving methodologies and concepts in 4D nucleome research. Sparks, Thomas M; Harabula, Izabela; Pombo, Ana Current opinion in cell biology. 32473574 2020 May 27;
Biosystems Design by Machine Learning. Volk, Michael Jeffrey; Lourentzou, Ismini; Mishra, Shekhar; Vo, Lam Tung; Zhai, Chengxiang; Zhao, Huimin ACS synthetic biology. 32485108 2020 07 17;
Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy. Liu, Chia-Feng; Abnousi, Armen; Bazeley, Peter; Ni, Ying; Morley, Michael; Moravec, Christine S; Hu, Ming; Tang, W H Wilson Journal of molecular and cellular cardiology 32533974 2020 08
Loop extrusion: theory meets single-molecule experiments. Banigan, Edward J; Mirny, Leonid A Current opinion in cell biology. 32534241 2020 06;
Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Strehle, Mackenzie; Guttman, Mitchell Current opinion in cell biology. 32535328 2020 06;
MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. Zhang, Ruochi; Ma, Jian Cell systems. 32550271 2020 May 20;
Long Noncoding RNAs: Molecular Modalities to Organismal Functions. Rinn, John L; Chang, Howard Y Annual review of biochemistry. 32569523 2020 06 20;
Comparison of differential accessibility analysis strategies for ATAC-seq data. Gontarz, Paul; Fu, Shuhua; Xing, Xiaoyun; Liu, Shaopeng; Miao, Benpeng; Bazylianska, Viktoriia; Sharma, Akhil; Madden, Pamela; Cates, Kitra; Yoo, Andrew; Moszczynska, Anna; Wang, Ting; Zhang, Bo Scientific reports. 32576878 2020 Jun 23;
Single-molecule imaging of transcription dynamics in somatic stem cells. Wheat, Justin C; Sella, Yehonatan; Willcockson, Michael; Skoultchi, Arthur I; Bergman, Aviv; Singer, Robert H; Steidl, Ulrich Nature. 32581360 2020 07;
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. Chen, Xiaoying; Zhang, Bo; Wang, Ting; Bonni, Azad; Zhao, Guoyan BMC bioinformatics. 32600248 2020 Jun 29;
The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. Wang, Alan S; Chen, Leo C; Wu, R Alex; Hao, Yvonne; McSwiggen, David T; Heckert, Alec B; Richardson, Christopher D; Gowen, Benjamin G; Kazane, Katelynn R; Vu, Jonathan T; Wyman, Stacia K; Shin, Jiyung J; Darzacq, Xavier; Walter, Johannes C; Corn, Jacob E Molecular cell. 32603710 2020 07 16;
A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. El-Nachef, Danny; Shi, Kevin; Beussman, Kevin M; Martinez, Refugio; Regier, Mary C; Everett, Guy W; Murry, Charles E; Stevens, Kelly R; Young, Jessica E; Sniadecki, Nathan J; Davis, Jennifer Stem cell reports. 32619493 2020 07 14;
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. Liu, Shuli; Yu, Ying; Zhang, Shengli; Cole, John B; Tenesa, Albert; Wang, Ting; McDaneld, Tara G; Ma, Li; Liu, George E; Fang, Lingzhao BMC biology. 32620158 2020 Jul 03;
Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation. Conte, Mattia; Fiorillo, Luca; Bianco, Simona; Chiariello, Andrea M; Esposito, Andrea; Nicodemi, Mario Nature communications. 32620890 2020 07 03;
Free energy-based model of CTCF-mediated chromatin looping in the human genome. Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz Methods (San Diego, Calif.). 32645447 2020 10 01;
A supervised learning framework for chromatin loop detection in genome-wide contact maps. Salameh, Tarik J; Wang, Xiaotao; Song, Fan; Zhang, Bo; Wright, Sage M; Khunsriraksakul, Chachrit; Ruan, Yijun; Yue, Feng Nature communications. 32647330 2020 Jul 09;
MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing. Biswas, Jeetayu; Rahman, Reazur; Gupta, Varun; Rosbash, Michael; Singer, Robert H iScience. 32674054 2020 Jul 24;
Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. Lei, Xiao; Zhao, Jun; Sagendorf, Jared M; Rajashekar, Niroop; Xu, Jiang; Dantas Machado, Ana Carolina; Sen, Chandani; Rohs, Remo; Feng, Pinghui; Chen, Lin Journal of molecular biology 32681840 2020 09 04
Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Chen, Hongtao; Gregor, Thomas Methods in molecular biology (Clifton, N.J.) 32710421 2020
An integrative ENCODE resource for cancer genomics. Zhang, Jing; Lee, Donghoon; Dhiman, Vineet; Jiang, Peng; Xu, Jie; McGillivray, Patrick; Yang, Hongbo; Liu, Jason; Meyerson, William; Clarke, Declan; Gu, Mengting; Li, Shantao; Lou, Shaoke; Xu, Jinrui; Lochovsky, Lucas; Ung, Matthew; Ma, Lijia; Yu, Shan; C Nature communications. 32728046 2020 07 29;
Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. Shaffer, Sydney M; Emert, Benjamin L; Reyes Hueros, Raúl A; Cote, Christopher; Harmange, Guillaume; Schaff, Dylan L; Sizemore, Ann E; Gupte, Rohit; Torre, Eduardo; Singh, Abhyudai; Bassett, Danielle S; Raj, Arjun Cell. 32735851 2020 Aug 20;
Optimizing imaging speed and excitation intensity for single-molecule localization microscopy. Diekmann, Robin; Kahnwald, Maurice; Schoenit, Andreas; Deschamps, Joran; Matti, Ulf; Ries, Jonas Nature methods. 32807954 2020 Sep;
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments. Chen, Zhijie; Shaw, Alan; Wilson, Hugh; Woringer, Maxime; Darzacq, Xavier; Marqusee, Susan; Wang, Quan; Bustamante, Carlos Proceedings of the National Academy of Sciences of the United States of America. 32817484 2020 Sep 01;
Targeted DNase Hi-C. Duan, Zhijun Methods in molecular biology (Clifton, N.J.). 32820399 2021;
Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. Tasan, Ipek; Su, Christina Jean; Enghiad, Behnam; Zhang, Meng; Mishra, Shekhar; Zhao, Huimin ACS synthetic biology. 32822529 2020 09 18;
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Lee, Byoungkoo; Wang, Jiahui; Cai, Liuyang; Kim, Minji; Namburi, Sandeep; Tjong, Harianto; Feng, Yuliang; Wang, Ping; Tang, Zhonghui; Abbas, Ahmed; Wei, Chia-Lin; Ruan, Yijun; Li, Sheng Science advances 32832596 2020 07
Cellular diversity of the regenerating caudal fin. Hou, Yiran; Lee, Hyung Joo; Chen, Yujie; Ge, Jiaxin; Osman, Fujr Osman Ibrahim; McAdow, Anthony R; Mokalled, Mayssa H; Johnson, Stephen L; Zhao, Guoyan; Wang, Ting Science advances. 32851162 2020 Aug;
3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. Fernandez, Lindsey R; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E Genome biology. 32859248 2020 Aug 28;
Alteration of genome folding via contact domain boundary insertion. Zhang, Di; Huang, Peng; Sharma, Malini; Keller, Cheryl A; Giardine, Belinda; Zhang, Haoyue; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E; Hardison, Ross C; Blobel, Gerd A Nature genetics. 32868908 2020 Aug 31;
The nucleolus as a multiphase liquid condensate. Lafontaine, Denis L J; Riback, Joshua A; Bascetin, Rümeyza; Brangwynne, Clifford P Nature reviews. Molecular cell biology 32873929 2021 03
Cell cycle dynamics of lamina-associated DNA. van Schaik, Tom; Vos, Mabel; Peric-Hupkes, Daan; Hn Celie, Patrick; van Steensel, Bas EMBO reports. 32893442 2020 Nov 05;
Exploring the coronavirus pandemic with the WashU Virus Genome Browser. Flynn, Jennifer A; Purushotham, Deepak; Choudhary, Mayank N K; Zhuo, Xiaoyu; Fan, Changxu; Matt, Gavriel; Li, Daofeng; Wang, Ting Nature genetics. 32908257 2020 10;
Concerted localization-resets precede YAP-dependent transcription. Franklin, J Matthew; Ghosh, Rajarshi P; Shi, Quanming; Reddick, Michael P; Liphardt, Jan T Nature communications. 32917893 2020 09 11;
NuSeT: A deep learning tool for reliably separating and analyzing crowded cells. Yang, Linfeng; Ghosh, Rajarshi P; Franklin, J Matthew; Chen, Simon; You, Chenyu; Narayan, Raja R; Melcher, Marc L; Liphardt, Jan T PLoS computational biology. 32925919 2020 09;
Nucleated transcriptional condensates amplify gene expression. Wei, Ming-Tzo; Chang, Yi-Che; Shimobayashi, Shunsuke F; Shin, Yongdae; Strom, Amy R; Brangwynne, Clifford P Nature cell biology. 32929202 2020 Oct;
Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Tavares-Cadete, Filipe; Norouzi, Davood; Dekker, Bastiaan; Liu, Yu; Dekker, Job Nature structural & molecular biology. 32929283 2020 Sep 14;
DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods. He, Yu; Jang, Hyo Sik; Xing, Xiaoyun; Li, Daofeng; Vasek, Michael J; Dougherty, Joseph D; Wang, Ting Science advances. 32937429 2020 Jul;
The qBED track: a novel genome browser visualization for point processes. Moudgil, Arnav; Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Wang, Ting; Mitra, Robi D Bioinformatics (Oxford, England). 32941613 2020 Sep 17;
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. Kim, Hyeon-Jin; Yard?mc?, Galip Gürkan; Bonora, Giancarlo; Ramani, Vijay; Liu, Jie; Qiu, Ruolan; Lee, Choli; Hesson, Jennifer; Ware, Carol B; Shendure, Jay; Duan, Zhijun; Noble, William Stafford PLoS computational biology. 32946435 2020 09;
Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. Lewis, James J; Van Belleghem, Steven M; Papa, Riccardo; Danko, Charles G; Reed, Robert D Science advances. 32978147 2020 Sep;
Tissue-specific usage of transposable element-derived promoters in mouse development. Miao, Benpeng; Fu, Shuhua; Lyu, Cheng; Gontarz, Paul; Wang, Ting; Zhang, Bo Genome biology. 32988383 2020 Sep 28;
TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data. Van Buren, Eric; Hu, Ming; Weng, Chen; Jin, Fulai; Li, Yan; Wu, Di; Li, Yun Genetic epidemiology. 32989764 2020 Sep 29;
High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. Vangala, Pranitha; Murphy, Rachel; Quinodoz, Sofia A; Gellatly, Kyle; McDonel, Patrick; Guttman, Mitchell; Garber, Manuel Molecular cell. 32991830 2020 10 15;
Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. Biggs, Ronald J; Liu, Ning; Peng, Yiheng; Marko, John F; Qiao, Huanyu Communications biology. 32999386 2020 Sep 30;
A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. Lekschas, Fritz; Zhou, Xinyi; Chen, Wei; Gehlenborg, Nils; Bach, Benjamin; Pfister, Hanspeter IEEE transactions on visualization and computer graphics 33026994 2021 02
De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. Chen, Siwei; Wang, Jiebiao; Cicek, Ercument; Roeder, Kathryn; Yu, Haiyuan; Devlin, Bernie Molecular autism 33032641 2020 Oct 08
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Desai, Parth Rakesh; Brahmachari, Sumitabha; Marko, John F; Das, Siddhartha; Neuman, Keir C Nucleic acids research. 33045724 2020 11 04;
Exploring chromosomal structural heterogeneity across multiple cell lines. Cheng, Ryan R; Contessoto, Vinicius G; Lieberman Aiden, Erez; Wolynes, Peter G; Di Pierro, Michele; Onuchic, Jose N eLife. 33047670 2020 Oct 13;
Cell-type-specific 3D epigenomes in the developing human cortex. Song, Michael; Pebworth, Mark-Phillip; Yang, Xiaoyu; Abnousi, Armen; Fan, Changxu; Wen, Jia; Rosen, Jonathan D; Choudhary, Mayank N K; Cui, Xiekui; Jones, Ian R; Bergenholtz, Seth; Eze, Ugomma C; Juric, Ivan; Li, Bingkun; Maliskova, Lenka; Lee, Jerry; Liu Nature. 33057195 2020 Oct 14;
EMU: reconfigurable graphical user interfaces for Micro-Manager. Deschamps, Joran; Ries, Jonas BMC bioinformatics. 33059591 2020 Oct 15;
Stress-induced RNA-chromatin interactions promote endothelial dysfunction. Calandrelli, Riccardo; Xu, Lixia; Luo, Yingjun; Wu, Weixin; Fan, Xiaochen; Nguyen, Tri; Chen, Chien-Ju; Sriram, Kiran; Tang, Xiaofang; Burns, Andrew B; Natarajan, Rama; Chen, Zhen Bouman; Zhong, Sheng Nature communications. 33060583 2020 10 15;
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. Banerjee, Abhik K; Blanco, Mario R; Bruce, Emily A; Honson, Drew D; Chen, Linlin M; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A; Loney, Colin; Thai, Jasmine; Miller, Zachary D; Lin, Aaron E; Schmidt, Madaline M; Stewart, Douglas G; Gold Cell. 33080218 2020 11 25;
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. Jain, Dhawal; Chu, Chong; Alver, Burak Han; Lee, Soohyun; Lee, Eunjung Alice; Park, Peter J Bioinformatics (Oxford, England) 33136153 2021 05 23
Molecular basis of CTCF binding polarity in genome folding. Nora, Elphège P; Caccianini, Laura; Fudenberg, Geoffrey; So, Kevin; Kameswaran, Vasumathi; Nagle, Abigail; Uebersohn, Alec; Hajj, Bassam; Saux, Agnès Le; Coulon, Antoine; Mirny, Leonid A; Pollard, Katherine S; Dahan, Maxime; Bruneau, Benoit G Nature communications 33154377 2020 11 05
X-chromosome regulation and sex differences in brain anatomy. Raznahan, Armin; Disteche, Christine M Neuroscience and biobehavioral reviews 33171144 2021 01
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. Ma, Jingwei; Do, Myan; Le Gros, Mark A; Peskin, Charles S; Larabell, Carolyn A; Mori, Yoichiro; Isaacson, Samuel A PLoS computational biology 33196636 2020 11
Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Wu, Jun; Krchma, Karen; Lee, Hyung Joo; Prabhakar, Sairam; Wang, Xiaoli; Zhao, Haiyong; Xing, Xiaoyun; Seong, Rho H; Fremont, Daved H; Artyomov, Maxim N; Wang, Ting; Choi, Kyunghee Cell reports. 33207205 2020 Nov 17;
A map of cis-regulatory elements and 3D genome structures in zebrafish. Yang, Hongbo; Luan, Yu; Liu, Tingting; Lee, Hyung Joo; Fang, Li; Wang, Yanli; Wang, Xiaotao; Zhang, Bo; Jin, Qiushi; Ang, Khai Chung; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Sriranga, Iyyanki; Khunsriraksakul, Chachrit; Salameh, Tarik; Li, Daofeng; Nature. 33239788 2020 Dec;
Three-dimensional chromatin organization in cardiac development and disease. Bertero, Alessandro; Rosa-Garrido, Manuel Journal of molecular and cellular cardiology 33242466 2021 02
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Fang, He; Bonora, Giancarlo; Lewandowski, Jordan P; Thakur, Jitendra; Filippova, Galina N; Henikoff, Steven; Shendure, Jay; Duan, Zhijun; Rinn, John L; Deng, Xinxian; Noble, William S; Disteche, Christine M Nature communications 33247132 2020 11 27
Genome architecture and expression 2019-2020: the transition phase. Pederson, Thoru Current opinion in genetics & development 33279815 2021 04
Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. Sanford, Eric M; Emert, Benjamin L; Coté, Allison; Raj, Arjun eLife 33284110 2020 12 07
Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Feng, Ying; Wang, Yao; Wang, Xiangnan; He, Xiaohui; Yang, Chen; Naseri, Ardalan; Pederson, Thoru; Zheng, Jing; Zhang, Shaojie; Xiao, Xiao; Xie, Wei; Ma, Hanhui Genome biology 33292531 2020 12 08
The interplay between asymmetric and symmetric DNA loop extrusion. Banigan, Edward J; Mirny, Leonid A eLife 33295869 2020 12 09
The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. Serrano, Diego; Cordero, Gustavo; Kawamura, Ryo; Sverzhinsky, Aleksandr; Sarker, Muzaddid; Roy, Shamayita; Malo, Catherine; Pascal, John M; Marko, John F; D'Amours, Damien Molecular cell 33301731 2020 12 17
Epigenomic differences in the human and chimpanzee genomes are associated with structural variation. Zhuo, Xiaoyu; Du, Alan Y; Pehrsson, Erica C; Li, Daofeng; Wang, Ting Genome research 33303495 2020 Dec 10
Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. Bizhanova, Aizhan; Kaufman, Paul D Biochimica et biophysica acta. Gene regulatory mechanisms. 33307247 2020 Dec 08;
Generalized multi-SNP mediation intersection-union test. Zhong, Wujuan; Darville, Toni; Zheng, Xiaojing; Fine, Jason; Li, Yun Biometrics 33316078 2022 Mar
ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. Hu, Mengwei; Yang, Bing; Cheng, Yubao; Radda, Jonathan S D; Chen, Yanbo; Liu, Miao; Wang, Siyuan Scientific reports 33328483 2020 12 16
Implementation of a 4Pi-SMS super-resolution microscope. Wang, Jingyu; Allgeyer, Edward S; Sirinakis, George; Zhang, Yongdeng; Hu, Kevin; Lessard, Mark D; Li, Yiming; Diekmann, Robin; Phillips, Michael A; Dobbie, Ian M; Ries, Jonas; Booth, Martin J; Bewersdorf, Joerg Nature protocols 33328610 2021 02
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. Shao, Wanqing; Wang, Ting Genome research 33355230 2021 Jan
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. Zhang, Liguo; Zhang, Yang; Chen, Yu; Gholamalamdari, Omid; Wang, Yuchuan; Ma, Jian; Belmont, Andrew S Genome research 33355299 2020 Dec 18
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Kubo, Naoki; Ishii, Haruhiko; Xiong, Xiong; Bianco, Simona; Meitinger, Franz; Hu, Rong; Hocker, James D; Conte, Mattia; Gorkin, David; Yu, Miao; Li, Bin; Dixon, Jesse R; Hu, Ming; Nicodemi, Mario; Zhao, Huimin; Ren, Bing Nature structural & molecular biology 33398174 2021 Feb
Genetic screening for single-cell variability modulators driving therapy resistance. Torre, Eduardo A; Arai, Eri; Bayatpour, Sareh; Jiang, Connie L; Beck, Lauren E; Emert, Benjamin L; Shaffer, Sydney M; Mellis, Ian A; Fane, Mitchell E; Alicea, Gretchen M; Budinich, Krista A; Weeraratna, Ashani T; Shi, Junwei; Raj, Arjun Nature genetics 33398196 2021 01
Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Rosa-Mercado, Nicolle A; Zimmer, Joshua T; Apostolidi, Maria; Rinehart, Jesse; Simon, Matthew D; Steitz, Joan A Molecular cell 33400923 2021 02 04
CRISPR technologies for precise epigenome editing. Nakamura, Muneaki; Gao, Yuchen; Dominguez, Antonia A; Qi, Lei S Nature cell biology 33420494 2021 Jan
The dynamics of chromatin architecture in brain development and function. Harabula, Izabela; Pombo, Ana Current opinion in genetics & development 33421764 2021 04
SPIN reveals genome-wide landscape of nuclear compartmentalization. Wang, Yuchuan; Zhang, Yang; Zhang, Ruochi; van Schaik, Tom; Zhang, Liguo; Sasaki, Takayo; Peric-Hupkes, Daniel; Chen, Yu; Gilbert, David M; van Steensel, Bas; Belmont, Andrew S; Ma, Jian Genome biology 33446254 2021 Jan 14
Resources and challenges for integrative analysis of nuclear architecture data. Jung, Youngsook L; Kirli, Koray; Alver, Burak H; Park, Peter J Current opinion in genetics & development 33450522 2021 Apr
Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. Vahedi, Golnaz Immunological reviews 33452686 2021 Mar
Determining of canine position by multiple facial landmarks to achieve natural esthetics in complete denture treatment. Srimaneekarn, Natchalee; Arayapisit, Tawepong; Pooktuantong, Ornnicha; Cheng, Holland R; Soonsawad, Pan The Journal of prosthetic dentistry 33468316 2021 Jan 16
TALEN outperforms Cas9 in editing heterochromatin target sites. Jain, Surbhi; Shukla, Saurabh; Yang, Che; Zhang, Meng; Fatma, Zia; Lingamaneni, Manasi; Abesteh, Shireen; Lane, Stephan Thomas; Xiong, Xiong; Wang, Yuchuan; Schroeder, Charles M; Selvin, Paul R; Zhao, Huimin Nature communications 33504770 2021 01 27
Integrated spatial genomics reveals global architecture of single nuclei. Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long Nature 33505024 2021 02
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. Miko, Henriette; Qiu, Yunjiang; Gaertner, Bjoern; Sander, Maike; Ohler, Uwe BMC genomics 33509077 2021 Jan 28
SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber medRxiv : the preprint server for health sciences 33532791 2021 Jan 26
HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test. Lagler, Taylor M; Abnousi, Armen; Hu, Ming; Yang, Yuchen; Li, Yun American journal of human genetics 33545029 2021 02 04
Mammalian DNA Replication Timing. Vouzas, Athanasios E; Gilbert, David M Cold Spring Harbor perspectives in biology 33558366 2021 Jul 01
Engineering 3D genome organization. Wang, Haifeng; Han, Mengting; Qi, Lei S Nature reviews. Genetics 33558716 2021 06
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Belaghzal, Houda; Borrman, Tyler; Stephens, Andrew D; Lafontaine, Denis L; Venev, Sergey V; Weng, Zhiping; Marko, John F; Dekker, Job Nature genetics 33574602 2021 03
HiCRep.py : Fast comparison of Hi-C contact matrices in Python. Lin, Dejun; Sanders, Justin; Noble, William Stafford Bioinformatics (Oxford, England) 33576390 2021 02 11
Physical mechanisms of chromatin spatial organization. Chiariello, Andrea M; Bianco, Simona; Esposito, Andrea; Fiorillo, Luca; Conte, Mattia; Irani, Ehsan; Musella, Francesco; Abraham, Alex; Prisco, Antonella; Nicodemi, Mario The FEBS journal 33583147 2022 03
Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Fullard, John F; Shayya, Hani; Omer, Arina; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Roussos, Panos; tenOever, Benjamin R; Overdevest, Jonathan B; Lomvardas, Stavros bioRxiv : the preprint server for biology 33594368 2021 Feb 09
Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. Zhang, Meng; Yang, Che; Tasan, Ipek; Zhao, Huimin ACS synthetic biology 33596056 2021 03 19
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. Bokota, Grzegorz; Sroka, Jacek; Basu, Subhadip; Das, Nirmal; Trzaskoma, Pawel; Yushkevich, Yana; Grabowska, Agnieszka; Magalska, Adriana; Plewczynski, Dariusz BMC bioinformatics 33596823 2021 Feb 17
Direct supercritical angle localization microscopy for nanometer 3D superresolution. Dasgupta, Anindita; Deschamps, Joran; Matti, Ulf; Hübner, Uwe; Becker, Jan; Strauss, Sebastian; Jungmann, Ralf; Heintzmann, Rainer; Ries, Jonas Nature communications 33608524 2021 02 19
Variability within rare cell states enables multiple paths toward drug resistance. Emert, Benjamin L; Cote, Christopher J; Torre, Eduardo A; Dardani, Ian P; Jiang, Connie L; Jain, Naveen; Shaffer, Sydney M; Raj, Arjun Nature biotechnology 33619394 2021 Feb 22
Heterogeneity of fetal hemoglobin production in adult red blood cells. Khandros, Eugene; Blobel, Gerd A Current opinion in hematology 33631783 2021 05 01
Genome oligopaint via local denaturation fluorescence in situ hybridization. Wang, Yanbo; Cottle, Wayne Taylor; Wang, Haobo; Feng, Xinyu Ashlee; Mallon, John; Gavrilov, Momcilo; Bailey, Scott; Ha, Taekjip Molecular cell 33657402 2021 04 01
Cas9 deactivation with photocleavable guide RNAs. Zou, Roger S; Liu, Yang; Wu, Bin; Ha, Taekjip Molecular cell 33662274 2021 04 01
Properties of repression condensates in living Ciona embryos. Treen, Nicholas; Shimobayashi, Shunsuke F; Eeftens, Jorine; Brangwynne, Clifford P; Levine, Michael Nature communications 33692345 2021 03 10
Toward a Three-Dimensional Chromosome Shape Alphabet. Soto, Carlos; Bryner, Darshan; Neretti, Nicola; Srivastava, Anuj Journal of computational biology : a journal of computational molecular cell biology 33720766 2021 06
RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. Bertero, Alessandro Frontiers in genetics 33732290 2021
Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation. Makhija, Suraj; Brown, David; Rudlaff, Rachel M; Doh, Julia K; Bourke, Struan; Wang, Yina; Zhou, Shuqin; Cheloor-Kovilakam, Rasmi; Huang, Bo ACS chemical biology 33734687 2021 04 16
See(quence) and ye shall find: higher-order genome folding in intact single cells. Pham, Kenneth; Nikish, Alexandria; Phillips-Cremins, Jennifer E Molecular cell 33740473 2021 03 18
Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention. Hogan, Ann K; Foltz, Daniel R Molecular and cellular biology 33753462 2021 05 21
Phase separation in genome organization across evolution. Feric, Marina; Misteli, Tom Trends in cell biology 33771451 2021 08
Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions. Vihervaara, Anniina; Mahat, Dig Bijay; Himanen, Samu V; Blom, Malin A H; Lis, John T; Sistonen, Lea Molecular cell 33784494 2021 Apr 15
Interrogating immune cells and cancer with CRISPR-Cas9. Buquicchio, Frank A; Satpathy, Ansuman T Trends in immunology 33812776 2021 05
p53 mediates target gene association with nuclear speckles for amplified RNA expression. Alexander, Katherine A; Coté, Allison; Nguyen, Son C; Zhang, Liguo; Gholamalamdari, Omid; Agudelo-Garcia, Paula; Lin-Shiao, Enrique; Tanim, K M A; Lim, Joan; Biddle, Nicolas; Dunagin, Margaret C; Good, Charly R; Mendoza, Mariel R; Little, Shawn C; Belmont, Andrew; Joyce, Eric F; Raj, Arjun; Berger, Shelley L Molecular cell 33823140 2021 04 15
Genome-wide enhancer maps link risk variants to disease genes. Nasser, Joseph; Bergman, Drew T; Fulco, Charles P; Guckelberger, Philine; Doughty, Benjamin R; Patwardhan, Tejal A; Jones, Thouis R; Nguyen, Tung H; Ulirsch, Jacob C; Lekschas, Fritz; Mualim, Kristy; Natri, Heini M; Weeks, Elle M; Munson, Glen; Kane, Mich Nature 33828297 2021 05
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. Markowski, Julia; Kempfer, Rieke; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Loof, Gesa; Kehr, Birte; Pombo, Ana; Rahmann, Sven; Schwarz, Roland F Bioinformatics (Oxford, England) 33830196 2021 Apr 08
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Zhu, Yanfen; Gujar, Amit D; Wong, Chee-Hong; Tjong, Harianto; Ngan, Chew Yee; Gong, Liang; Chen, Yi-An; Kim, Hoon; Liu, Jihe; Li, Meihong; Mil-Homens, Adam; Maurya, Rahul; Kuhlberg, Chris; Sun, Fanyue; Yi, Eunhee; deCarvalho, Ana C; Ruan, Yijun; Verhaak, Roel G W; Wei, Chia-Lin Cancer cell 33836152 2021 May 10
Single-molecule micromanipulation studies of methylated DNA. Zaichuk, Tetiana; Marko, John F Biophysical journal 33838135 2021 06 01
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. Schep, Ruben; Brinkman, Eva K; Leemans, Christ; Vergara, Xabier; van der Weide, Robin H; Morris, Ben; van Schaik, Tom; Manzo, Stefano G; Peric-Hupkes, Daniel; van den Berg, Jeroen; Beijersbergen, Roderick L; Medema, René H; van Steensel, Bas Molecular cell 33848455 2021 05 20
Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. Iyyanki, Tejaswi; Zhang, Baozhen; Wang, Qixuan; Hou, Ye; Jin, Qiushi; Xu, Jie; Yang, Hongbo; Liu, Tingting; Wang, Xiaotao; Song, Fan; Luan, Yu; Yamashita, Hironobu; Chien, Ruby; Lyu, Huijue; Zhang, Lijun; Wang, Lu; Warrick, Joshua; Raman, Jay D; Meeks, Joshua J; DeGraff, David J; Yue, Feng Genome biology 33858483 2021 Apr 15
Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo. El-Nachef, Danny; Bugg, Darrian; Beussman, Kevin M; Steczina, Sonette; Martinson, Amy M; Murry, Charles E; Sniadecki, Nathan J; Davis, Jennifer Circulation 33872080 2021 04 20
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan J Developmental cell 33891899 2021 May 03
Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. Liu, Miao; Yang, Bing; Hu, Mengwei; Radda, Jonathan S D; Chen, Yanbo; Jin, Shengyan; Cheng, Yubao; Wang, Siyuan Nature protocols 33903756 2021 May
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. Sanborn, Adrian L; Yeh, Benjamin T; Feigerle, Jordan T; Hao, Cynthia V; Townshend, Raphael Jl; Lieberman Aiden, Erez; Dror, Ron O; Kornberg, Roger D eLife 33904398 2021 Apr 27
Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. Kaur, Parwinder; Lui, Christopher; Dudchenko, Olga; Nandety, Raja Sekhar; Hurgobin, Bhavna; Pham, Melanie; Lieberman Aiden, Erez; Wen, Jiangqi; Mysore, Kirankumar International journal of molecular sciences 33919286 2021 Apr 21
The Need for a Human Pangenome Reference Sequence. Miga, Karen H; Wang, Ting Annual review of genomics and human genetics 33929893 2021 08 31
Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. Pettinato, Anthony M; Yoo, Dasom; VanOudenhove, Jennifer; Chen, Yu-Sheng; Cohn, Rachel; Ladha, Feria A; Yang, Xiulan; Thakar, Ketan; Romano, Robert; Legere, Nicolas; Meredith, Emily; Robson, Paul; Regnier, Michael; Cotney, Justin L; Murry, Charles E; Hins Cell reports 33951429 2021 May 04
Unsupervised manifold alignment for single-cell multi-omics data. Singh, Ritambhara; Demetci, Pinar; Bonora, Giancarlo; Ramani, Vijay; Lee, Choli; Fang, He; Duan, Zhijun; Deng, Xinxian; Shendure, Jay; Disteche, Christine; Noble, William Stafford ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine 33954299 2020 Sep
From integrative structural biology to cell biology. Sali, Andrej The Journal of biological chemistry 33957123 2021 Jan-Jun
Determination of complete chromosomal haplotypes by bulk DNA sequencing. Tourdot, Richard W; Brunette, Gregory J; Pinto, Ricardo A; Zhang, Cheng-Zhong Genome biology 33957932 2021 May 06
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin. Fiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario Nature methods 33963348 2021 05
Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber Med (New York, N.Y.) 33969332 2021 May 14
PYMEVisualize: an open-source tool for exploring 3D super-resolution data. Marin, Zach; Graff, Michael; Barentine, Andrew E S; Soeller, Christian; Chung, Kenny Kwok Hin; Fuentes, Lukas A; Baddeley, David Nature methods 34002092 2021 Jun
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains. Huang, Hui; Zhu, Quan; Jussila, Adam; Han, Yuanyuan; Bintu, Bogdan; Kern, Colin; Conte, Mattia; Zhang, Yanxiao; Bianco, Simona; Chiariello, Andrea M; Yu, Miao; Hu, Rong; Tastemel, Melodi; Juric, Ivan; Hu, Ming; Nicodemi, Mario; Zhuang, Xiaowei; Ren, Bing Nature genetics 34002095 2021 May 17
Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. Huang, Xiao; Ferris, Stephen T; Kim, Sunkyung; Choudhary, Mayank N K; Belk, Julia A; Fan, Changxu; Qi, Yanyan; Sudan, Raki; Xia, Yu; Desai, Pritesh; Chen, Jing; Ly, Nghi; Shi, Quanming; Bagadia, Prachi; Liu, Tiantian; Guilliams, Martin; Egawa, Takeshi; Co Immunity 34004142 2021 May 11
Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers. Jain, Surbhi; Xun, Guanhua; Abesteh, Shireen; Ho, Sherri; Lingamaneni, Manasi; Martin, Teresa A; Tasan, Ipek; Yang, Che; Zhao, Huimin ACS synthetic biology 34006094 2021 06 18
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. Karlow, Jennifer A; Miao, Benpeng; Xing, Xiaoyun; Wang, Ting; Zhang, Bo Communications biology 34021236 2021 May 21
QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. Boehm, Ulrike; Nelson, Glyn; Brown, Claire M; Bagley, Steve; Bajcsy, Peter; Bischof, Johanna; Dauphin, Aurelien; Dobbie, Ian M; Eriksson, John E; Faklaris, Orestis; Fernandez-Rodriguez, Julia; Ferrand, Alexia; Gelman, Laurent; Gheisari, Ali; Hartmann, Hel Nature methods 34021279 2021 12
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Sarkans, Ugis; Chiu, Wah; Collinson, Lucy; Darrow, Michele C; Ellenberg, Jan; Grunwald, David; Hériché, Jean-Karim; Iudin, Andrii; Martins, Gabriel G; Meehan, Terry; Narayan, Kedar; Patwardhan, Ardan; Russell, Matthew Robert Geoffrey; Saibil, Helen R; Str Nature methods 34021280 2021 May 21
Enhancer release and retargeting activates disease-susceptibility genes. Oh, Soohwan; Shao, Jiaofang; Mitra, Joydeep; Xiong, Feng; D'Antonio, Matteo; Wang, Ruoyu; Garcia-Bassets, Ivan; Ma, Qi; Zhu, Xiaoyu; Lee, Joo-Hyung; Nair, Sreejith J; Yang, Feng; Ohgi, Kenneth; Frazer, Kelly A; Zhang, Zhengdong D; Li, Wenbo; Rosenfeld, Mi Nature 34040254 2021 May 26
3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Hoencamp, Claire; Dudchenko, Olga; Elbatsh, Ahmed M O; Brahmachari, Sumitabha; Raaijmakers, Jonne A; van Schaik, Tom; Sedeño Cacciatore, Ángela; Contessoto, Vinícius G; van Heesbeen, Roy G H P; van den Broek, Bram; Mhaskar, Aditya N; Teunissen, Hans; St H Science (New York, N.Y.) 34045355 2021 05 28
Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Scourzic, Laurianne; Salataj, Eralda; Apostolou, Effie Frontiers in immunology 34054841 2021
Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. Lin, Yen-Chen; Kumar, Meenakshi Sundaram; Ramesh, Nandini; Anderson, Eric N; Nguyen, Aivi T; Kim, Boram; Cheung, Simon; McDonough, Justin A; Skarnes, William C; Lopez-Gonzalez, Rodrigo; Landers, John E; Fawzi, Nicolas L; Mackenzie, Ian R A; Lee, Edward B; Nature neuroscience 34059832 2021 08
HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. Sahin, Merve; Wong, Wilfred; Zhan, Yingqian; Van Deynze, Kinsey; Koche, Richard; Leslie, Christina S Nature communications 34099725 2021 06 07
Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. Rajpurkar, Aparna R; Mateo, Leslie J; Murphy, Sedona E; Boettiger, Alistair N Nature communications 34103507 2021 06 08
HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. Strom, Amy R; Biggs, Ronald J; Banigan, Edward J; Wang, Xiaotao; Chiu, Katherine; Herman, Cameron; Collado, Jimena; Yue, Feng; Ritland Politz, Joan C; Tait, Leah J; Scalzo, David; Telling, Agnes; Groudine, Mark; Brangwynne, Clifford P; Marko, John F; Step eLife 34106828 2021 06 09
RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Xiong, Feng; Wang, Ruoyu; Lee, Joo-Hyung; Li, Shenglan; Chen, Shin-Fu; Liao, Zian; Hasani, Lana Al; Nguyen, Phuoc T; Zhu, Xiaoyu; Krakowiak, Joanna; Lee, Dung-Fang; Han, Leng; Tsai, Kuang-Lei; Liu, Ying; Li, Wenbo Cell research 34108665 2021 Jun 09
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, Jian Quantitative biology (Beijing, China) 34113473 2019 Jun
DMA-tudor interaction modules control the specificity of in vivo condensates. Courchaine, Edward M; Barentine, Andrew E S; Straube, Korinna; Lee, Dong-Ryoung; Bewersdorf, Joerg; Neugebauer, Karla M Cell 34115980 2021 Jul 08
Imaging Organization of RNA Processing within the Nucleus. Biswas, Jeetayu; Li, Weihan; Singer, Robert H; Coleman, Robert A Cold Spring Harbor perspectives in biology 34127450 2021 12 01
Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. Wang, Jiarui; Han, Mengting; Wang, Haifeng; Möckl, Leonhard; Zeng, Leiping; Moerner, W E; Qi, Lei S bioRxiv : the preprint server for biology 34127974 2021 Jun 09
Three-dimensional superresolution fluorescence microscopy maps the variable molecular architecture of the nuclear pore complex. Sabinina, Vilma Jimenez; Hossain, M Julius; Hériché, Jean-Karim; Hoess, Philipp; Nijmeijer, Bianca; Mosalaganti, Shyamal; Kueblbeck, Moritz; Callegari, Andrea; Szymborska, Anna; Beck, Martin; Ries, Jonas; Ellenberg, Jan Molecular biology of the cell 34191541 2021 08 15
Embryo-scale, single-cell spatial transcriptomics. Srivatsan, Sanjay R; Regier, Mary C; Barkan, Eliza; Franks, Jennifer M; Packer, Jonathan S; Grosjean, Parker; Duran, Madeleine; Saxton, Sarah; Ladd, Jon J; Spielmann, Malte; Lois, Carlos; Lampe, Paul D; Shendure, Jay; Stevens, Kelly R; Trapnell, Cole Science (New York, N.Y.) 34210887 2021 07 02
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Nelson, Glyn; Boehm, Ulrike; Bagley, Steve; Bajcsy, Peter; Bischof, Johanna; Brown, Claire M; Dauphin, Aurélien; Dobbie, Ian M; Eriksson, John E; Faklaris, Orestis; Fernandez-Rodriguez, Julia; Ferrand, Alexia; Gelman, Laurent; Gheisari, Ali; Hartmann, Hella; Kukat, Christian; Laude, Alex; Mitkovski, Miso; Munck, Sebastian; North, Alison J; Rasse, Tobias M; Resch-Genger, Ute; Schuetz, Lucas C; Seitz, Arne; Strambio-De-Castillia, Caterina; Swedlow, Jason R; Alexopoulos, Ioannis; Aumayr, Karin; Avilov, Sergiy; Bakker, Gert-Jan; Bammann, Rodrigo R; Bassi, Andrea; Beckert, Hannes; Beer, Sebastian; Belyaev, Yury; Bierwagen, Jakob; Birngruber, Konstantin A; Bosch, Manel; Breitlow, Juergen; Cameron, Lisa A; Chalfoun, Joe; Chambers, James J; Chen, Chieh-Li; Conde-Sousa, Eduardo; Corbett, Alexander D; Cordelieres, Fabrice P; Nery, Elaine Del; Dietzel, Ralf; Eismann, Frank; Fazeli, Elnaz; Felscher, Andreas; Fried, Hans; Gaudreault, Nathalie; Goh, Wah Ing; Guilbert, Thomas; Hadleigh, Roland; Hemmerich, Peter; Holst, Gerhard A; Itano, Michelle S; Jaffe, Claudia B; Jambor, Helena K; Jarvis, Stuart C; Keppler, Antje; Kirchenbuechler, David; Kirchner, Marcel; Kobayashi, Norio; Krens, Gabriel; Kunis, Susanne; Lacoste, Judith; Marcello, Marco; Martins, Gabriel G; Metcalf, Daniel J; Mitchell, Claire A; Moore, Joshua; Mueller, Tobias; Nelson, Michael S; Ogg, Stephen; Onami, Shuichi; Palmer, Alexandra L; Paul-Gilloteaux, Perrine; Pimentel, Jaime A; Plantard, Laure; Podder, Santosh; Rexhepaj, Elton; Royon, Arnaud; Saari, Markku A; Schapman, Damien; Schoonderwoert, Vincent; Schroth-Diez, Britta; Schwartz, Stanley; Shaw, Michael; Spitaler, Martin; Stoeckl, Martin T; Sudar, Damir; Teillon, Jeremie; Terjung, Stefan; Thuenauer, Roland; Wilms, Christian D; Wright, Graham D; Nitschke, Roland Journal of microscopy 34214188 2021 10
The Impact of Space and Time on the Functional Output of the Genome. Nollmann, Marcelo; Bennabi, Isma; Götz, Markus; Gregor, Thomas Cold Spring Harbor perspectives in biology 34230036 2021 Jul 06
How subtle changes in 3D structure can create large changes in transcription. Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair N eLife 34240703 2021 07 09
Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin. Zhang, Yaojun; Lee, Daniel S W; Meir, Yigal; Brangwynne, Clifford P; Wingreen, Ned S Physical review letters 34241518 2021 Jun 25
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. Liu, Shaopeng; Li, Daofeng; Lyu, Cheng; Gontarz, Paul M; Miao, Benpeng; Madden, Pamela A F; Wang, Ting; Zhang, Bo Genomics, proteomics & bioinformatics 34273560 2021 Jul 14
High-resolution, genome-wide mapping of positive supercoiling in chromosomes. Guo, Monica S; Kawamura, Ryo; Littlehale, Megan L; Marko, John F; Laub, Michael T eLife 34279217 2021 07 19
Polymer models are a versatile tool to study chromatin 3D organization. Esposito, Andrea; Bianco, Simona; Fiorillo, Luca; Conte, Mattia; Abraham, Alex; Musella, Francesco; Nicodemi, Mario; Prisco, Antonella; Chiariello, Andrea M Biochemical Society transactions 34282837 2021 08 27
Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan H Current protocols 34286910 2021 Jul
CRISPRi/a Screening with Human iPSCs. Nishiga, Masataka; Qi, Lei S; Wu, Joseph C Methods in molecular biology (Clifton, N.J.) 34302664 2021
DNA-loop-extruding SMC complexes can traverse one another in vivo. Brandão, Hugo B; Ren, Zhongqing; Karaboja, Xheni; Mirny, Leonid A; Wang, Xindan Nature structural & molecular biology 34312537 2021 08
SARS-CoV-2 Restructures the Host Chromatin Architecture. Wang, Ruoyu; Lee, Joo-Hyung; Xiong, Feng; Kim, Jieun; Hasani, Lana Al; Yuan, Xiaoyi; Shivshankar, Pooja; Krakowiak, Joanna; Qi, Chuangye; Wang, Yanyu; Eltzschig, Holger K; Li, Wenbo bioRxiv : the preprint server for biology 34312624 2021 Jul 21
Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter Computer graphics forum : journal of the European Association for Computer Graphics 34334852 2020 Jun
Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Mellis, Ian A; Edelstein, Hailey I; Truitt, Rachel; Goyal, Yogesh; Beck, Lauren E; Symmons, Orsolya; Dunagin, Margaret C; Linares Saldana, Ricardo A; Shah, Parisha P; Pérez-Bermejo, Juan A; Padmanabhan, Arun; Yang, Wenli; Jain, Rajan; Raj, Arjun Cell systems 34352221 2021 Sep 22
Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. Hanmandlu, Ankit; Zhu, Lisha; Mertens, Tinne C J; Collum, Scott; Bi, Weizhen; Xiong, Feng; Wang, Ruoyu; Amirthalingam, Rajarajan T; Ren, Dewei; Han, Leng; Jyothula, Soma S S K; Li, Wenbo; Zheng, W Jim; Karmouty-Quintana, Harry American journal of respiratory cell and molecular biology 34370624 2022 01
Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Lee, Joo-Hyung; Wang, Ruoyu; Xiong, Feng; Krakowiak, Joanna; Liao, Zian; Nguyen, Phuoc T; Moroz-Omori, Elena V; Shao, Jiaofang; Zhu, Xiaoyu; Bolt, Michael J; Wu, Haoyi; Singh, Pankaj K; Bi, Mingjun; Shi, Caleb J; Jamal, Naadir; Li, Guojie; Mistry, Ragini; Molecular cell 34375583 2021 08 19
Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, Bing Methods in molecular biology (Clifton, N.J.) 34382190 2021
X-factors in human disease: impact of gene content and dosage regulation. Fang, He; Deng, Xinxian; Disteche, Christine M Human molecular genetics 34387327 2021 Oct 01
Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. Yildirim, Asli; Boninsegna, Lorenzo; Zhan, Yuxiang; Alber, Frank Cold Spring Harbor perspectives in biology 34400556 2021 Aug 16
Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. Belmont, Andrew S Cold Spring Harbor perspectives in biology 34400557 2022 Jul 01
Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. Song, Fan; Xu, Jie; Dixon, Jesse; Yue, Feng Methods in molecular biology (Clifton, N.J.) 34415534 2022
Single-cell measurement of higher-order 3D genome organization with scSPRITE. Arrastia, Mary V; Jachowicz, Joanna W; Ollikainen, Noah; Curtis, Matthew S; Lai, Charlotte; Quinodoz, Sofia A; Selck, David A; Ismagilov, Rustem F; Guttman, Mitchell Nature biotechnology 34426703 2021 Aug 23
Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9. Gao, Yuchen; Han, Mengting; Shang, Stephen; Wang, Haifeng; Qi, Lei S Molecular cell 34428454 2021 Aug 13
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. Yu, Miao; Abnousi, Armen; Zhang, Yanxiao; Li, Guoqiang; Lee, Lindsay; Chen, Ziyin; Fang, Rongxin; Lagler, Taylor M; Yang, Yuchen; Wen, Jia; Sun, Quan; Li, Yun; Ren, Bing; Hu, Ming Nature methods 34446921 2021 09
CTCF and transcription influence chromatin structure re-configuration after mitosis. Zhang, Haoyue; Lam, Jessica; Zhang, Di; Lan, Yemin; Vermunt, Marit W; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A Nature communications 34453048 2021 Aug 27
The 3D Genome Structure of Single Cells. Zhou, Tianming; Zhang, Ruochi; Ma, Jian Annual review of biomedical data science 34465168 2021 07 20
Systematic evaluation of chromosome conformation capture assays. Akgol Oksuz, Betul; Yang, Liyan; Abraham, Sameer; Venev, Sergey V; Krietenstein, Nils; Parsi, Krishna Mohan; Ozadam, Hakan; Oomen, Marlies E; Nand, Ankita; Mao, Hui; Genga, Ryan M J; Maehr, Rene; Rando, Oliver J; Mirny, Leonid A; Gibcus, Johan H; Dekker, Nature methods 34480151 2021 09
Deep learning enables fast and dense single-molecule localization with high accuracy. Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C Nature methods 34480155 2021 09
MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples. Liu, Weifang; Yang, Yuchen; Abnousi, Armen; Zhang, Qian; Kubo, Naoki; Beem, Joshua S Martin; Li, Yun; Hu, Ming HGG advances 34485947 2021 Jul 08
Enhanced Cas12a multi-gene regulation using a CRISPR array separator. Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei S eLife 34499031 2021 09 09
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Mirny, Leonid; Dekker, Job Cold Spring Harbor perspectives in biology 34518339 2022 07 01
STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Zimmer, Joshua T; Rosa-Mercado, Nicolle A; Canzio, Daniele; Steitz, Joan A; Simon, Matthew D Molecular cell 34520723 2021 11 04
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Ren, Xingjie; Wang, Mengchi; Li, Bingkun; Jamieson, Kirsty; Zheng, Lina; Jones, Ian R; Li, Bin; Takagi, Maya Asami; Lee, Jerry; Maliskova, Lenka; Tam, Tsz Wai; Yu, Miao; Hu, Rong; Lee, Lindsay; Abnousi, Armen; Li, Gang; Li, Yun; Hu, Ming; Ren, Bing; Wang, Science advances 34524848 2021 Sep 17
The maternal blood lipidome is indicative of the pathogenesis of severe preeclampsia. He, Bing; Liu, Yu; Maurya, Mano R; Benny, Paula; Lassiter, Cameron; Li, Hui; Subramaniam, Shankar; Garmire, Lana X Journal of lipid research 34547287 2021 Sep 20
Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy. Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C Nature methods 34548656 2021 Sep 21
HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets. Rosen, Jonathan D; Yang, Yuchen; Abnousi, Armen; Chen, Jiawen; Song, Michael; Jones, Ian R; Shen, Yin; Hu, Ming; Li, Yun Current issues in molecular biology 34563051 2021 Sep 17
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Bonora, Giancarlo; Ramani, Vijay; Singh, Ritambhara; Fang, He; Jackson, Dana L; Srivatsan, Sanjay; Qiu, Ruolan; Lee, Choli; Trapnell, Cole; Shendure, Jay; Duan, Zhijun; Deng, Xinxian; Noble, William S; Disteche, Christine M Genome biology 34579774 2021 09 27
Single-cell nuclear architecture across cell types in the mouse brain. Takei, Yodai; Zheng, Shiwei; Yun, Jina; Shah, Sheel; Pierson, Nico; White, Jonathan; Schindler, Simone; Tischbirek, Carsten H; Yuan, Guo-Cheng; Cai, Long Science (New York, N.Y.) 34591592 2021 10 29
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. L'Yi, Sehi; Wang, Qianwen; Lekschas, Fritz; Gehlenborg, Nils IEEE transactions on visualization and computer graphics 34596551 2022 01
BRD4 orchestrates genome folding to promote neural crest differentiation. Linares-Saldana, Ricardo; Kim, Wonho; Bolar, Nikhita A; Zhang, Haoyue; Koch-Bojalad, Bailey A; Yoon, Sora; Shah, Parisha P; Karnay, Ashley; Park, Daniel S; Luppino, Jennifer M; Nguyen, Son C; Padmanabhan, Arun; Smith, Cheryl L; Poleshko, Andrey; Wang, Qia Nature genetics 34611363 2021 Oct
Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction. Eeftens, Jorine M; Kapoor, Manya; Michieletto, Davide; Brangwynne, Clifford P Nature communications 34620850 2021 10 07
Jointly Embedding Multiple Single-Cell Omics Measurements. Liu, Jie; Huang, Yuanhao; Singh, Ritambhara; Vert, Jean-Philippe; Noble, William Stafford Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) 34632462 2019 Sep 03
Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Hulleman, Christiaan N; Thorsen, Rasmus Ø; Kim, Eugene; Dekker, Cees; Stallinga, Sjoerd; Rieger, Bernd Nature communications 34635658 2021 10 11
Multiscale and integrative single-cell Hi-C analysis with Higashi. Zhang, Ruochi; Zhou, Tianming; Ma, Jian Nature biotechnology 34635838 2021 Oct 11
MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community. Kunis, Susanne; Hänsch, Sebastian; Schmidt, Christian; Wong, Frances; Strambio-De-Castillia, Caterina; Weidtkamp-Peters, Stefanie Nature methods 34635849 2021 12
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Modzelewski, Andrew J; Shao, Wanqing; Chen, Jingqi; Lee, Angus; Qi, Xin; Noon, Mackenzie; Tjokro, Kristy; Sales, Gabriele; Biton, Anne; Anand, Aparna; Speed, Terence P; Xuan, Zhenyu; Wang, Ting; Risso, Davide; He, Lin Cell 34644528 2021 10 28
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. Ryan, Joel; Pengo, Thomas; Rigano, Alex; Llopis, Paula Montero; Itano, Michelle S; Cameron, Lisa A; Marqués, Guillermo; Strambio-De-Castillia, Caterina; Sanders, Mark A; Brown, Claire M Nature methods 34654919 2021 12
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. Fenix, Aidan M; Miyaoka, Yuichiro; Bertero, Alessandro; Blue, Steven M; Spindler, Matthew J; Tan, Kenneth K B; Perez-Bermejo, Juan A; Chan, Amanda H; Mayerl, Steven J; Nguyen, Trieu D; Russell, Caitlin R; Lizarraga, Paweena P; Truong, Annie; So, Po-Lin; Kulkarni, Aishwarya; Chetal, Kashish; Sathe, Shashank; Sniadecki, Nathan J; Yeo, Gene W; Murry, Charles E; Conklin, Bruce R; Salomonis, Nathan Nature communications 34732726 2021 11 03
Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. Swygert, Sarah G; Lin, Dejun; Portillo-Ledesma, Stephanie; Lin, Po-Yen; Hunt, Dakota R; Kao, Cheng-Fu; Schlick, Tamar; Noble, William S; Tsukiyama, Toshio eLife 34734806 2021 Nov 04
RNA promotes the formation of spatial compartments in the nucleus. Quinodoz, Sofia A; Jachowicz, Joanna W; Bhat, Prashant; Ollikainen, Noah; Banerjee, Abhik K; Goronzy, Isabel N; Blanco, Mario R; Chovanec, Peter; Chow, Amy; Markaki, Yolanda; Thai, Jasmine; Plath, Kathrin; Guttman, Mitchell Cell 34739832 2021 11 11
Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. Wang, Jiaxi; Lareau, Caleb A; Bautista, Jhoanne L; Gupta, Alexander R; Sandor, Katalin; Germino, Joe; Yin, Yajie; Arvedson, Matthew P; Reeder, Gabriella C; Cramer, Nathan T; Xie, Fang; Ntranos, Vasilis; Satpathy, Ansuman T; Anderson, Mark S; Gardner, Jame Science immunology 34767455 2021 11 12
Trading bits in the readout from a genetic network. Bauer, Marianne; Petkova, Mariela D; Gregor, Thomas; Wieschaus, Eric F; Bialek, William Proceedings of the National Academy of Sciences of the United States of America 34772813 2021 11 16
Light activation and deactivation of Cas9 for DNA repair studies. Zou, Roger S; Ha, Taekjip Methods in enzymology 34776214 2021
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. Geusz, Ryan J; Wang, Allen; Lam, Dieter K; Vinckier, Nicholas K; Alysandratos, Konstantinos-Dionysios; Roberts, David A; Wang, Jinzhao; Kefalopoulou, Samy; Ramirez, Araceli; Qiu, Yunjiang; Chiou, Joshua; Gaulton, Kyle J; Ren, Bing; Kotton, Darrell N; Sand Nature communications 34789735 2021 11 17
Cell-type specialization is encoded by specific chromatin topologies. Winick-Ng, Warren; Kukalev, Alexander; Harabula, Izabela; Zea-Redondo, Luna; Szabó, Dominik; Meijer, Mandy; Serebreni, Leonid; Zhang, Yingnan; Bianco, Simona; Chiariello, Andrea M; Irastorza-Azcarate, Ibai; Thieme, Christoph J; Sparks, Thomas M; Carvalho, Nature 34789882 2021 11
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Hammer, Mathias; Huisman, Maximiliaan; Rigano, Alessandro; Boehm, Ulrike; Chambers, James J; Gaudreault, Nathalie; North, Alison J; Pimentel, Jaime A; Sudar, Damir; Bajcsy, Peter; Brown, Claire M; Corbett, Alexander D; Faklaris, Orestis; Lacoste, Judith; Nature methods 34862501 2021 12
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Rigano, Alessandro; Ehmsen, Shannon; Öztürk, Serkan Utku; Ryan, Joel; Balashov, Alexander; Hammer, Mathias; Kirli, Koray; Boehm, Ulrike; Brown, Claire M; Bellve, Karl; Chambers, James J; Cosolo, Andrea; Coleman, Robert A; Faklaris, Orestis; Fogarty, Kevin Nature methods 34862503 2021 12
Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. Pourmorady, Ariel; Lomvardas, Stavros Current opinion in genetics & development 34896807 2022 02
Transcriptional network orchestrating regional patterning of cortical progenitors. Ypsilanti, Athéna R; Pattabiraman, Kartik; Catta-Preta, Rinaldo; Golonzhka, Olga; Lindtner, Susan; Tang, Ke; Jones, Ian R; Abnousi, Armen; Juric, Ivan; Hu, Ming; Shen, Yin; Dickel, Diane E; Visel, Axel; Pennachio, Len A; Hawrylycz, Michael; Thompson, Caro Proceedings of the National Academy of Sciences of the United States of America 34921112 2021 12 21
Epigenome rewiring in human pluripotent stem cells. Yan, Jielin; Huangfu, Danwei Trends in cell biology 34955367 2021 Dec 23
Integrative approaches in genome structure analysis. Structure (London, England : 1993) 34963059 2022 01 06
Stress as a Chromatin Landscape Architect. Vertii, Anastassiia Frontiers in cell and developmental biology 34970548 2021
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. Lee, Soohyun; Bakker, Clara R; Vitzthum, Carl; Alver, Burak H; Park, Peter J Bioinformatics (Oxford, England) 34978573 2022 Mar 04
Single-Cell Multiomics Integration by SCOT. Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, Ritambhara Journal of computational biology : a journal of computational molecular cell biology 34985990 2022 01
Mapping Replication Timing in Single Mammalian Cells. Bartlett, Daniel A; Dileep, Vishnu; Baslan, Timour; Gilbert, David M Current protocols 34986273 2022 Jan
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Quinodoz, Sofia A; Bhat, Prashant; Chovanec, Peter; Jachowicz, Joanna W; Ollikainen, Noah; Detmar, Elizabeth; Soehalim, Elizabeth; Guttman, Mitchell Nature protocols 35013617 2022 Jan
Single nucleosome tracking to study chromatin plasticity. Lakadamyali, Melike Current opinion in cell biology 35033775 2022 Jan 13
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, Ritambhara Journal of computational biology : a journal of computational molecular cell biology 35050714 2022 01
Technological advances in super-resolution microscopy to study cellular processes. Bond, Charles; Santiago-Ruiz, Adriana N; Tang, Qing; Lakadamyali, Melike Molecular cell 35063099 2022 01 20
A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. Knoedler, Joseph R; Inoue, Sayaka; Bayless, Daniel W; Yang, Taehong; Tantry, Adarsh; Davis, Chung-Ha; Leung, Nicole Y; Parthasarathy, Srinivas; Wang, Grace; Alvarado, Maricruz; Rizvi, Abbas H; Fenno, Lief E; Ramakrishnan, Charu; Deisseroth, Karl; Shah, Ni Cell 35065713 2022 02 17
Compartmentalization of telomeres through DNA-scaffolded phase separation. Developmental cell 35077681 2022 01 24
A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis. Jha, Asmita; Hansen, Anders S Methods in molecular biology (Clifton, N.J.) 35103967 2022
Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. Yang, Hongbo; Zhang, Hui; Luan, Yu; Liu, Tingting; Yang, Wentao; Roberts, Kathryn G; Qian, Mao-Xiang; Zhang, Bo; Yang, Wenjian; Perez-Andreu, Virginia; Xu, Jie; Iyyanki, Sriranga; Kuang, Da; Stasiak, Lena A; Reshmi, Shalini C; Gastier-Foster, Julie; Smith Nature genetics 35115686 2022 02
Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. Wang, Jiarui; Han, Mengting; Roy, Anish R; Wang, Haifeng; Möckl, Leonhard; Zeng, Leiping; Moerner, W E; Qi, Lei S Cell reports methods 35128513 2022 Feb 01
The use of new CRISPR tools in cardiovascular research and medicine. Nishiga, Masataka; Liu, Chun; Qi, Lei S; Wu, Joseph C Nature reviews. Cardiology 35145236 2022 08
CRISPR Cas13-Based Tools to Track and Manipulate Endogenous Telomeric Repeat-Containing RNAs in Live Cells. Xu, Meng; Chigumira, Tafadzwa; Chen, Ziheng; Tones, Jason; Zhao, Rongwei; Dahl, Kris Noel; Chenoweth, David M; Zhang, Huaiying Frontiers in molecular biosciences 35174207 2021
Spatial organization of transcribed eukaryotic genes. Leidescher, Susanne; Ribisel, Johannes; Ullrich, Simon; Feodorova, Yana; Hildebrand, Erica; Galitsyna, Alexandra; Bultmann, Sebastian; Link, Stephanie; Thanisch, Katharina; Mulholland, Christopher; Dekker, Job; Leonhardt, Heinrich; Mirny, Leonid; Solovei, Irina Nature cell biology 35177821 2022 03
Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Frere, Justin; Fullard, John F; Shayya, Hani; McArthur, Natalie G; Moeller, Rasmus; Uhl, Skyler; Omer, Arina D; Gottesman, Max E; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Rou Cell 35180380 2022 03 17
HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Wei, Xiaolin; Xiang, Yu; Peters, Derek T; Marius, Choiselle; Sun, Tongyu; Shan, Ruocheng; Ou, Jianhong; Lin, Xin; Yue, Feng; Li, Wei; Southerland, Kevin W; Diao, Yarui Molecular cell 35196517 2022 Mar 17
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Miller, Tyler E; Lareau, Caleb A; Verga, Julia A; DePasquale, Erica A K; Liu, Vincent; Ssozi, Daniel; Sandor, Katalin; Yin, Yajie; Ludwig, Leif S; El Farran, Chadi A; Morgan, Duncan M; Satpathy, Ansuman T; Griffin, Gabriel K; Lane, Andrew A; Love, J Christopher; Bernstein, Bradley E; Sankaran, Vijay G; van Galen, Peter Nature biotechnology 35210612 2022 Jul
Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. Fasolino, Maria; Schwartz, Gregory W; Patil, Abhijeet R; Mongia, Aanchal; Golson, Maria L; Wang, Yue J; Morgan, Ashleigh; Liu, Chengyang; Schug, Jonathan; Liu, Jinping; Wu, Minghui; Traum, Daniel; Kondo, Ayano; May, Catherine L; Goldman, Naomi; Wang, Wenl Nature metabolism 35228745 2022 Feb
Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. Liu, Weifang; Sun, Quan; Huang, Le; Bhattacharya, Arjun; Wang, Geoffery W; Tan, Xianming; Kuban, Karl C K; Joseph, Robert M; O'Shea, T Michael; Fry, Rebecca C; Li, Yun; Santos Jr, Hudson P Journal of neurodevelopmental disorders 35240980 2022 03 03
High-resolution 3D fluorescent imaging of intact tissues. El-Nachef, Danny; Martinson, Amy M; Yang, Xiulan; Murry, Charles E; MacLellan, W Robb International journal of cardiology and cardiovascular diseases 35243481 2021
The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling. Kordon, Magdalena M; Arron, Sarah; Cleaver, James E; Bezrookove, Vladimir; Karentz, Deneb; Lu, Brian; Perr, Eli; Chang, Darwin; Pederson, Thoru Proceedings of the National Academy of Sciences of the United States of America 35254895 2022 03 15
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. Rowland, Bryce; Huh, Ruth; Hou, Zoey; Crowley, Cheynna; Wen, Jia; Shen, Yin; Hu, Ming; Giusti-Rodríguez, Paola; Sullivan, Patrick F; Li, Yun PLoS genetics 35259165 2022 03
CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control. Dominguez, Antonia A; Chavez, Michael G; Urke, Amanda; Gao, Yuchen; Wang, Lizhong; Qi, Lei S The CRISPR journal 35271371 2022 04
Systematic reconstruction of cellular trajectories across mouse embryogenesis. Qiu, Chengxiang; Cao, Junyue; Martin, Beth K; Li, Tony; Welsh, Ian C; Srivatsan, Sanjay; Huang, Xingfan; Calderon, Diego; Noble, William Stafford; Disteche, Christine M; Murray, Stephen A; Spielmann, Malte; Moens, Cecilia B; Trapnell, Cole; Shendure, Jay Nature genetics 35288709 2022 Mar
Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Jachowicz, Joanna W; Strehle, Mackenzie; Banerjee, Abhik K; Blanco, Mario R; Thai, Jasmine; Guttman, Mitchell Nature structural & molecular biology 35301492 2022 Mar
Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Biancon, Giulia; Joshi, Poorval; Zimmer, Joshua T; Hunck, Torben; Gao, Yimeng; Lessard, Mark D; Courchaine, Edward; Barentine, Andrew E S; Machyna, Martin; Botti, Valentina; Qin, Ashley; Gbyli, Rana; Patel, Amisha; Song, Yuanbin; Kiefer, Lea; Viero, Gabri Molecular cell 35303483 2022 Mar 17
Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. Singh, Anand P; Wu, Ping; Ryabichko, Sergey; Raimundo, João; Swan, Michael; Wieschaus, Eric; Gregor, Thomas; Toettcher, Jared E Cell reports 35320726 2022 Mar 22
TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation. Van Buren, Eric; Hu, Ming; Cheng, Liang; Wrobel, John; Wilhelmsen, Kirk; Su, Lishan; Li, Yun; Wu, Di Briefings in bioinformatics 35325048 2022 05 13
Stripenn detects architectural stripes from chromatin conformation data using computer vision. Yoon, Sora; Chandra, Aditi; Vahedi, Golnaz Nature communications 35332165 2022 Mar 24
Fast and parallel nanoscale three-dimensional tracking of heterogeneous mammalian chromatin dynamics. Gustavsson, Anna-Karin; Ghosh, Rajarshi P; Petrov, Petar N; Liphardt, Jan T; Moerner, W E Molecular biology of the cell 35352962 2022 05 15
Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states. Esposito, Andrea; Bianco, Simona; Chiariello, Andrea M; Abraham, Alex; Fiorillo, Luca; Conte, Mattia; Campanile, Raffaele; Nicodemi, Mario Cell reports 35354035 2022 03 29
Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. Kenworthy, Charles A; Haque, Nayem; Liou, Shu-Hao; Chandris, Panagiotis; Wong, Vincent; Dziuba, Patrycja; Lavis, Luke D; Liu, Wei-Li; Singer, Robert H; Coleman, Robert A Biophysical journal 35364106 2022 May 03
Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. Jiang, Connie L; Goyal, Yogesh; Jain, Naveen; Wang, Qiaohong; Truitt, Rachel E; Coté, Allison J; Emert, Benjamin; Mellis, Ian A; Kiani, Karun; Yang, Wenli; Jain, Rajan; Raj, Arjun Genome biology 35382863 2022 Apr 05
Chromatin interaction-aware gene regulatory modeling with graph attention networks. Karbalayghareh, Alireza; Sahin, Merve; Leslie, Christina S Genome research 35396274 2022 May
Mapping chromatin loops in single cells. Yu, Miao; Li, Yun; Hu, Ming Trends in genetics : TIG 35400543 2022 Jul
Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes. Nudelman, Ilona; Fernandez-Martinez, Javier; Rout, Michael P Methods in molecular biology (Clifton, N.J.) 35412228 2022
WashU Epigenome Browser update 2022. Li, Daofeng; Purushotham, Deepak; Harrison, Jessica K; Hsu, Silas; Zhuo, Xiaoyu; Fan, Changxu; Liu, Shane; Xu, Vincent; Chen, Samuel; Xu, Jason; Ouyang, Shinyi; Wu, Angela S; Wang, Ting Nucleic acids research 35412637 2022 Jul 05
Multiplexed genome regulation in vivo with hyper-efficient Cas12a. Guo, Lucie Y; Bian, Jing; Davis, Alexander E; Liu, Pingting; Kempton, Hannah R; Zhang, Xiaowei; Chemparathy, Augustine; Gu, Baokun; Lin, Xueqiu; Rane, Draven A; Xu, Xiaoshu; Jamiolkowski, Ryan M; Hu, Yang; Wang, Sui; Qi, Lei S Nature cell biology 35414015 2022 Apr
Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Gabriele, Michele; Brandão, Hugo B; Grosse-Holz, Simon; Jha, Asmita; Dailey, Gina M; Cattoglio, Claudia; Hsieh, Tsung-Han S; Mirny, Leonid; Zechner, Christoph; Hansen, Anders S Science (New York, N.Y.) 35420890 2022 04 29
Modular and mechanistic changes across stages of colorectal cancer. Rahiminejad, Sara; Maurya, Mano R; Mukund, Kavitha; Subramaniam, Shankar BMC cancer 35448980 2022 Apr 21
Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. Liu, Weifang; Zhong, Wujuan; Chen, Jiawen; Huang, Bo; Hu, Ming; Li, Yun Genes 35456393 2022 Mar 25
Cohesin-dependence of neuronal gene expression relates to chromatin loop length. Calderon, Lesly; Weiss, Felix D; Beagan, Jonathan A; Oliveira, Marta S; Georgieva, Radina; Wang, Yi-Fang; Carroll, Thomas S; Dharmalingam, Gopuraja; Gong, Wanfeng; Tossell, Kyoko; de Paola, Vincenzo; Whilding, Chad; Ungless, Mark A; Fisher, Amanda G; Phil eLife 35471149 2022 Apr 26
DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. Nomidis, Stefanos K; Carlon, Enrico; Gruber, Stephan; Marko, John F Nucleic acids research 35474142 2022 05 20
Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. Chong, Shasha; Graham, Thomas G W; Dugast-Darzacq, Claire; Dailey, Gina M; Darzacq, Xavier; Tjian, Robert Molecular cell 35483357 2022 06 02
Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. Labanieh, Louai; Majzner, Robbie G; Klysz, Dorota; Sotillo, Elena; Fisher, Chris J; Vilches-Moure, José G; Pacheco, Kaithlen Zen B; Malipatlolla, Meena; Xu, Peng; Hui, Jessica H; Murty, Tara; Theruvath, Johanna; Mehta, Nishant; Yamada-Hunter, Sean A; Weber, Evan W; Heitzeneder, Sabine; Parker, Kevin R; Satpathy, Ansuman T; Chang, Howard Y; Lin, Michael Z; Cochran, Jennifer R; Mackall, Crystal L Cell 35483375 2022 05 12
Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. McNamara, Harold M; Ramm, Beatrice; Toettcher, Jared E Seminars in cell & developmental biology 35484026 2023 May 30
NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. Choi, Kyoung-Jae; Quan, My Diem; Qi, Chuangye; Lee, Joo-Hyung; Tsoi, Phoebe S; Zahabiyon, Mahla; Bajic, Aleksandar; Hu, Liya; Prasad, B V Venkataram; Liao, Shih-Chu Jeff; Li, Wenbo; Ferreon, Allan Chris M; Ferreon, Josephine C Nature cell biology 35484250 2022 May
A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Huang, Le; Yang, Yuchen; Li, Gang; Jiang, Minzhi; Wen, Jia; Abnousi, Armen; Rosen, Jonathan D; Hu, Ming; Li, Yun Briefings in bioinformatics 35488276 2022 05 13
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Reiff, Sarah B; Schroeder, Andrew J; Kırlı, Koray; Cosolo, Andrea; Bakker, Clara; Lee, Soohyun; Veit, Alexander D; Balashov, Alexander K; Vitzthum, Carl; Ronchetti, William; Pitman, Kent M; Johnson, Jeremy; Ehmsen, Shannon R; Kerpedjiev, Peter; Abdennur, Nezar; Imakaev, Maxim; Öztürk, Serkan Utku; Çamoğlu, Uğur; Mirny, Leonid A; Gehlenborg, Nils; Alver, Burak H; Park, Peter J Nature communications 35501320 2022 05 02
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J Nature methods 35501385 2022 05
Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. Chung, Kenny K H; Zhang, Zhao; Kidd, Phylicia; Zhang, Yongdeng; Williams, Nathan D; Rollins, Bennett; Yang, Yang; Lin, Chenxiang; Baddeley, David; Bewersdorf, Joerg Nature methods 35501386 2022 May
TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. Huang, Le; Rosen, Jonathan D; Sun, Quan; Chen, Jiawen; Wheeler, Marsha M; Zhou, Ying; Min, Yuan-I; Kooperberg, Charles; Conomos, Matthew P; Stilp, Adrienne M; Rich, Stephen S; Rotter, Jerome I; Manichaikul, Ani; Loos, Ruth J F; Kenny, Eimear E; Blackwell, Thomas W; Smith, Albert V; Jun, Goo; Sedlazeck, Fritz J; Metcalf, Ginger; Boerwinkle, Eric; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Raffield, Laura M; Reiner, Alex P; Auer, Paul L; Li, Yun American journal of human genetics 35504290 2022 Jun 02
PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng Cell metabolism 35508105 2022 05 03
Transcriptional coupling of distant regulatory genes in living embryos. Levo, Michal; Raimundo, João; Bing, Xin Yang; Sisco, Zachary; Batut, Philippe J; Ryabichko, Sergey; Gregor, Thomas; Levine, Michael S Nature 35508662 2022 05
Mechanics and functional consequences of nuclear deformations. Kalukula, Yohalie; Stephens, Andrew D; Lammerding, Jan; Gabriele, Sylvain Nature reviews. Molecular cell biology 35513718 2022 09
An improved 4'-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA. Wielenberg, Kevin; Wang, Miao; Yang, Min; Ozer, Abdullah; Lis, John T; Lin, Hening RSC advances 35515418 2020 Oct 27
Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. Reticker-Flynn, Nathan E; Zhang, Weiruo; Belk, Julia A; Basto, Pamela A; Escalante, Nichole K; Pilarowski, Genay O W; Bejnood, Alborz; Martins, Maria M; Kenkel, Justin A; Linde, Ian L; Bagchi, Sreya; Yuan, Robert; Chang, Serena; Spitzer, Matthew H; Carmi, Yaron; Cheng, Jiahan; Tolentino, Lorna L; Choi, Okmi; Wu, Nancy; Kong, Christina S; Gentles, Andrew J; Sunwoo, John B; Satpathy, Ansuman T; Plevritis, Sylvia K; Engleman, Edgar G Cell 35525247 2022 05 26
Fast and efficient DNA replication with purified human proteins. Baris, Yasemin; Taylor, Martin R G; Aria, Valentina; Yeeles, Joseph T P Nature 35585232 2022 06
MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Dequeker, Bart J H; Scherr, Matthias J; Brandão, Hugo B; Gassler, Johanna; Powell, Sean; Gaspar, Imre; Flyamer, Ilya M; Lalic, Aleksandar; Tang, Wen; Stocsits, Roman; Davidson, Iain F; Peters, Jan-Michael; Duderstadt, Karl E; Mirny, Leonid A; Tachibana, Kikuë Nature 35585235 2022 06
Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. Parteka-Tojek, Zofia; Zhu, Jacqueline Jufen; Lee, Byoungkoo; Jodkowska, Karolina; Wang, Ping; Aaron, Jesse; Chew, Teng-Leong; Banecki, Krzysztof; Plewczynski, Dariusz; Ruan, Yijun Scientific reports 35595799 2022 05 20
Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer. Kersten, Kelly; Hu, Kenneth H; Combes, Alexis J; Samad, Bushra; Harwin, Tory; Ray, Arja; Rao, Arjun Arkal; Cai, En; Marchuk, Kyle; Artichoker, Jordan; Courau, Tristan; Shi, Quanming; Belk, Julia; Satpathy, Ansuman T; Krummel, Matthew F Cancer cell 35623342 2022 06 13
Epigenetic regulation of T cell exhaustion. Belk, Julia A; Daniel, Bence; Satpathy, Ansuman T Nature immunology 35624210 2022 06
BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4+ T cell responses to persistent antigen. Xia, Yu; Sandor, Katalin; Pai, Joy A; Daniel, Bence; Raju, Saravanan; Wu, Renee; Hsiung, Sunnie; Qi, Yanyan; Yangdon, Tenzin; Okamoto, Mariko; Chou, Chun; Hiam-Galvez, Kamir J; Schreiber, Robert D; Murphy, Kenneth M; Satpathy, Ansuman T; Egawa, Takeshi Immunity 35637103 2022 07 12
Scalable biological signal recording in mammalian cells using Cas12a base editors. Kempton, Hannah R; Love, Kasey S; Guo, Lucie Y; Qi, Lei S Nature chemical biology 35637351 2022 Jul
Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Lee, Hyung Joo; Hou, Yiran; Maeng, Ju Heon; Shah, Nakul M; Chen, Yujie; Lawson, Heather A; Yang, Hongbo; Yue, Feng; Wang, Ting Genome research 35649578 2022 07
Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization. Yang, Muyu; Ma, Jian Journal of molecular biology 35659533 2022 08 15
Global fitting for high-accuracy multi-channel single-molecule localization. Li, Yiming; Shi, Wei; Liu, Sheng; Cavka, Ivana; Wu, Yu-Le; Matti, Ulf; Wu, Decheng; Koehler, Simone; Ries, Jonas Nature communications 35668089 2022 06 06
Cohesin-mediated loop anchors confine the locations of human replication origins. Emerson, Daniel J; Zhao, Peiyao A; Cook, Ashley L; Barnett, R Jordan; Klein, Kyle N; Saulebekova, Dalila; Ge, Chunmin; Zhou, Linda; Simandi, Zoltan; Minsk, Miriam K; Titus, Katelyn R; Wang, Weitao; Gong, Wanfeng; Zhang, Di; Yang, Liyan; Venev, Sergey V; Gibcus, Johan H; Yang, Hongbo; Sasaki, Takayo; Kanemaki, Masato T; Yue, Feng; Dekker, Job; Chen, Chun-Long; Gilbert, David M; Phillips-Cremins, Jennifer E Nature 35676475 2022 06
Synthesis and ex vivo biodistribution of two 68Ga-labeled tetrazine tracers: Comparison of pharmacokinetics. Lambidis, Elisavet; Lumén, Dave; Koskipahta, Elina; Imlimthan, Surachet; Lopez, Brianda B; Sánchez, Ana Isabel Fraguas; Sarparanta, Mirkka; Cheng, R Holland; Airaksinen, Anu J Nuclear medicine and biology 35680503 2022
Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy. Diekmann, Robin; Deschamps, Joran; Li, Yiming; Deguchi, Takahiro; Tschanz, Aline; Kahnwald, Maurice; Matti, Ulf; Ries, Jonas Nature communications 35690614 2022 06 11
Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication. Popay, Tessa M; Dixon, Jesse R The Journal of biological chemistry 35691341 2022 08
Systematically quantifying morphological features reveals constraints on organoid phenotypes. Beck, Lauren E; Lee, Jasmine; Coté, Christopher; Dunagin, Margaret C; Lukonin, Ilya; Salla, Nikkita; Chang, Marcello K; Hughes, Alex J; Mornin, Joseph D; Gartner, Zev J; Liberali, Prisca; Raj, Arjun Cell systems 35705097 2022 Jul 20
Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. Karlow, Jennifer A; Devarakonda, Siddhartha; Xing, Xiaoyun; Jang, Hyo Sik; Govindan, Ramaswamy; Watson, Mark; Wang, Ting Cancer research 35706127 2022 Aug 03
TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. Wang, Wenliang; Chandra, Aditi; Goldman, Naomi; Yoon, Sora; Ferrari, Emily K; Nguyen, Son C; Joyce, Eric F; Vahedi, Golnaz Nature immunology 35726060 2022 07
Latent space of a small genetic network: Geometry of dynamics and information. Seyboldt, Rabea; Lavoie, Juliette; Henry, Adrien; Vanaret, Jules; Petkova, Mariela D; Gregor, Thomas; François, Paul Proceedings of the National Academy of Sciences of the United States of America 35737842 2022 06 28
The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells. Hasenson, Sarah E; Alkalay, Ella; Atrash, Mohammad K; Boocholez, Alon; Gershbaum, Julianna; Hochberg-Laufer, Hodaya; Shav-Tal, Yaron Cells 35741072 2022 06 16
Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Belk, Julia A; Yao, Winnie; Ly, Nghi; Freitas, Katherine A; Chen, Yan-Ting; Shi, Quanming; Valencia, Alfredo M; Shifrut, Eric; Kale, Nupura; Yost, Kathryn E; Duffy, Connor V; Daniel, Bence; Hwee, Madeline A; Miao, Zhuang; Ashworth, Alan; Mackall, Crystal L; Marson, Alexander; Carnevale, Julia; Vardhana, Santosh A; Satpathy, Ansuman T Cancer cell 35750052 2022 07 11
A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. Chen, Jiawen; Liu, Weifang; Luo, Tianyou; Yu, Zhentao; Jiang, Minzhi; Wen, Jia; Gupta, Gaorav P; Giusti, Paola; Zhu, Hongtu; Yang, Yuchen; Li, Yun Briefings in bioinformatics 35753702 2022 07 18
Guilt by association: EcDNA as a mobile transactivator in cancer. Zhu, Yanfen; Gong, Liang; Wei, Chia-Lin Trends in cancer 35753910 2022 Jun 23
Nuclear speckles - a driving force in gene expression. Faber, Gabriel P; Nadav-Eliyahu, Shani; Shav-Tal, Yaron Journal of cell science 35788677 2022 Jul 01
A time-resolved, multi-symbol molecular recorder via sequential genome editing. Choi, Junhong; Chen, Wei; Minkina, Anna; Chardon, Florence M; Suiter, Chase C; Regalado, Samuel G; Domcke, Silvia; Hamazaki, Nobuhiko; Lee, Choli; Martin, Beth; Daza, Riza M; Shendure, Jay Nature 35794474 2022 08
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Boninsegna, Lorenzo; Yildirim, Asli; Polles, Guido; Zhan, Yuxiang; Quinodoz, Sofia A; Finn, Elizabeth H; Guttman, Mitchell; Zhou, Xianghong Jasmine; Alber, Frank Nature methods 35817938 2022 08
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. Conte, Mattia; Irani, Ehsan; Chiariello, Andrea M; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario Nature communications 35831310 2022 07 13
Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Voortman, Lukas; Anderson, Caitlin; Urban, Elizabeth; Yuan, Luorongxin; Tran, Sang; Neuhaus-Follini, Alexandra; Derrick, Josh; Gregor, Thomas; Johnston Jr, Robert J Developmental cell 35835116 2022 Aug 08
Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. Tang, Xiaona; Li, Taibo; Liu, Sheng; Wisniewski, Jan; Zheng, Qinsi; Rong, Yikang; Lavis, Luke D; Wu, Carl Nature structural & molecular biology 35835866 2022 Jul
Reeling it in: how DNA topology drives loop extrusion by condensin. Narducci, Domenic N; Hansen, Anders S Nature structural & molecular biology 35835869 2022 07
Characterizing cis-regulatory elements using single-cell epigenomics. Preissl, Sebastian; Gaulton, Kyle J; Ren, Bing Nature reviews. Genetics 35840754 2022 Jul 15
Development of 68Ga-Labeled Hepatitis E Virus Nanoparticles for Targeted Drug Delivery and Diagnostics with PET. Lambidis, Elisavet; Chen, Chun-Chieh; Baikoghli, Mo; Imlimthan, Surachet; Khng, You Cheng; Sarparanta, Mirkka; Cheng, R Holland; Airaksinen, Anu J Molecular pharmaceutics 35857429 2022 08 01
Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser. Li, Daofeng; Harrison, Jessica K; Purushotham, Deepak; Wang, Ting Nature methods 35864166 2022 08
Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. Zhu, Xiaopeng; Zhang, Yang; Wang, Yuchuan; Tian, Dechao; Belmont, Andrew S; Swedlow, Jason R; Ma, Jian Nature methods 35864167 2022 08
Assessing Specific Networks of Chromatin Interactions with HiChIP. Di Giammartino, Dafne Campigli; Polyzos, Alexander; Apostolou, Effie Methods in molecular biology (Clifton, N.J.) 35867248 2022
Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq. Zhang, Liguo; Chen, Yu; Belmont, Andrew S Methods in molecular biology (Clifton, N.J.) 35867249 2022
3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. Haws, Spencer A; Simandi, Zoltan; Barnett, R Jordan; Phillips-Cremins, Jennifer E Cell 35868274 2022 07 21
Sex-biased and parental allele-specific gene regulation by KDM6A. Ma, Wenxiu; Fang, He; Pease, Nicolas; Filippova, Galina N; Disteche, Christine M; Berletch, Joel B Biology of sex differences 35871105 2022 Jul 23
Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells. Fonseca, Raíssa; Burn, Thomas N; Gandolfo, Luke C; Devi, Sapna; Park, Simone L; Obers, Andreas; Evrard, Maximilien; Christo, Susan N; Buquicchio, Frank A; Lareau, Caleb A; McDonald, Keely M; Sandford, Sarah K; Zamudio, Natasha M; Zanluqui, Nagela G; Zaid, Ali; Speed, Terence P; Satpathy, Ansuman T; Mueller, Scott N; Carbone, Francis R; Mackay, Laura K Nature immunology 35882933 2022 08
Multiomics characterization of mouse hepatoblastoma identifies yes-associated protein 1 target genes. Rodríguez, Tomás C; Kwan, Suet-Yan; Smith, Jordan L; Dadafarin, Sina; Wu, Chern-Horng; Sontheimer, Erik J; Xue, Wen Hepatology (Baltimore, Md.) 35932276 2022 Aug 06
Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis. Blair, Andrew P; Hu, Robert K; Farah, Elie N; Chi, Neil C; Pollard, Katherine S; Przytycki, Pawel F; Kathiriya, Irfan S; Bruneau, Benoit G Bioinformatics advances 35967929 2022
High throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Jones, Ian R; Ren, Xingjie; Shen, Yin Human molecular genetics 35972825 2022 Aug 16
Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. Cheng, Li-Chun; Zhang, Xi; Abhinav, Kanishk; Nguyen, Julie A; Baboo, Sabyasachi; Martinez-Bartolomé, Salvador; Branon, Tess C; Ting, Alice Y; Loose, Esther; Yates 3rd, John R; Gerace, Larry Journal of proteome research 35972904 2022 Sep 02
Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. Heo, Su-Jin; Thakur, Shreyasi; Chen, Xingyu; Loebel, Claudia; Xia, Boao; McBeath, Rowena; Burdick, Jason A; Shenoy, Vivek B; Mauck, Robert L; Lakadamyali, Melike Nature biomedical engineering 35996026 2023 Feb
Embryo model completes gastrulation to neurulation and organogenesis. Amadei, Gianluca; Handford, Charlotte E; Qiu, Chengxiang; De Jonghe, Joachim; Greenfeld, Hannah; Tran, Martin; Martin, Beth K; Chen, Dong-Yuan; Aguilera-Castrejon, Alejandro; Hanna, Jacob H; Elowitz, Michael B; Hollfelder, Florian; Shendure, Jay; Glover, David M; Zernicka-Goetz, Magdalena Nature 36007540 2022 10
Mammalian genome innovation through transposon domestication. Modzelewski, Andrew J; Gan Chong, Johnny; Wang, Ting; He, Lin Nature cell biology 36008480 2022 09
Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. Michieletto, Michaël F; Tello-Cajiao, John J; Mowel, Walter K; Chandra, Aditi; Yoon, Sora; Joannas, Leonel; Clark, Megan L; Jimenez, Monica T; Wright, Jasmine M; Lundgren, Patrick; Williams, Adam; Thaiss, Christoph A; Vahedi, Golnaz; Henao-Mejia, Jorge Nature immunology 36050414 2023 Jan
CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. van Schaik, Tom; Liu, Ning Qing; Manzo, Stefano G; Peric-Hupkes, Daan; de Wit, Elzo; van Steensel, Bas Genome biology 36050765 2022 Sep 01
Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites. Zou, Roger S; Marin-Gonzalez, Alberto; Liu, Yang; Liu, Hans B; Shen, Leo; Dveirin, Rachel K; Luo, Jay X J; Kalhor, Reza; Ha, Taekjip Nature cell biology 36064968 2022 Sep
Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN. Banik, Anik; Podder, Souvik; Saha, Sovan; Chatterjee, Piyali; Halder, Anup Kumar; Nasipuri, Mita; Basu, Subhadip; Plewczynski, Dariusz Cells 36078056 2022 Aug 25
A Versatile Micromanipulation Apparatus for Biophysical Assays of the Cell Nucleus. Currey, Marilena L; Kandula, Viswajit; Biggs, Ronald; Marko, John F; Stephens, Andrew D Cellular and molecular bioengineering 36119136 2022 Aug
Polyphony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis. Cheng, Furui; Keller, Mark S; Qu, Huamin; Gehlenborg, Nils; Wang, Qianwen IEEE transactions on visualization and computer graphics 36155452 2022 Sep 26
Multi-View Design Patterns and Responsive Visualization for Genomics Data. LYi, Sehi; Gehlenborg, Nils IEEE transactions on visualization and computer graphics 36166553 2023 Jan
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Stackpole, Mary L; Zeng, Weihua; Li, Shuo; Liu, Chun-Chi; Zhou, Yonggang; He, Shanshan; Yeh, Angela; Wang, Ziye; Sun, Fengzhu; Li, Qingjiao; Yuan, Zuyang; Yildirim, Asli; Chen, Pin-Jung; Winograd, Paul; Tran, Benjamin; Lee, Yi-Te; Li, Paul Shize; Noor, Zorawar; Yokomizo, Megumi; Ahuja, Preeti; Zhu, Yazhen; Tseng, Hsian-Rong; Tomlinson, James S; Garon, Edward; French, Samuel; Magyar, Clara E; Dry, Sarah; Lajonchere, Clara; Geschwind, Daniel; Choi, Gina; Saab, Sammy; Alber, Frank; Wong, Wing Hung; Dubinett, Steven M; Aberle, Denise R; Agopian, Vatche; Han, Steven-Huy B; Ni, Xiaohui; Li, Wenyuan; Zhou, Xianghong Jasmine Nature communications 36175411 2022 Sep 29
GenoREC: A Recommendation System for Interactive Genomics Data Visualization. Pandey, Aditeya; L'Yi, Sehi; Wang, Qianwen; Borkin, Michelle A; Gehlenborg, Nils IEEE transactions on visualization and computer graphics 36191105 2022 Oct 03
CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Liu, Yu; Dekker, Job Nature cell biology 36202971 2022 Oct
Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Zhang, Yanxiao; Amaral, Maria Luisa; Zhu, Chenxu; Grieco, Steven Francis; Hou, Xiaomeng; Lin, Lin; Buchanan, Justin; Tong, Liqi; Preissl, Sebastian; Xu, Xiangmin; Ren, Bing Cell research 36207411 2022 Nov
The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies. Courchaine, Edward; Gelles-Watnick, Sara; Machyna, Martin; Straube, Korinna; Sauyet, Sarah; Enright, Jade; Neugebauer, Karla M Nature communications 36224177 2022 Oct 12
The dynseq browser track shows context-specific features at nucleotide resolution. Nair, Surag; Barrett, Arjun; Li, Daofeng; Raney, Brian J; Lee, Brian T; Kerpedjiev, Peter; Ramalingam, Vivekanandan; Pampari, Anusri; Lekschas, Fritz; Wang, Ting; Haeussler, Maximilian; Kundaje, Anshul Nature genetics 36241719 2022 Nov
Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67. van Schaik, Tom; Manzo, Stefano G; Vouzas, Athanasios E; Liu, Ning Qing; Teunissen, Hans; de Wit, Elzo; Gilbert, David M; van Steensel, Bas EMBO reports 36245428 2022 Oct 17
Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. Zhang, Ran; Meng-Papaxanthos, Laetitia; Vert, Jean-Philippe; Noble, William Stafford Journal of computational biology : a journal of computational molecular cell biology 36251758 2022 Nov
Optimized single-nucleus transcriptional profiling by combinatorial indexing. Martin, Beth K; Qiu, Chengxiang; Nichols, Eva; Phung, Melissa; Green-Gladden, Rula; Srivatsan, Sanjay; Blecher-Gonen, Ronnie; Beliveau, Brian J; Trapnell, Cole; Cao, Junyue; Shendure, Jay Nature protocols 36261634 2022 Oct 19
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi. Zhang, Ruochi; Zhou, Tianming; Ma, Jian Cell systems 36265466 2022 Oct 19
RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Kaminski, Nicole; Wondisford, Anne R; Kwon, Youngho; Lynskey, Michelle Lee; Bhargava, Ragini; Barroso-González, Jonathan; García-Expósito, Laura; He, Boxue; Xu, Meng; Mellacheruvu, Dattatreya; Watkins, Simon C; Modesti, Mauro; Miller, Kyle M; Nesvizhskii, Alexey I; Zhang, Huaiying; Sung, Patrick; O'Sullivan, Roderick J Molecular cell 36265488 2022 Nov 03
Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells. Drayton, Jamie A; Hansen, Anders S Molecular cell 36270244 2022 Oct 20
Spatially resolved epigenomic profiling of single cells in complex tissues. Lu, Tian; Ang, Cheen Euong; Zhuang, Xiaowei Cell 36272405 2022 Nov 10
Advances in CRISPR therapeutics. Chavez, Michael; Chen, Xinyi; Finn, Paul B; Qi, Lei S Nature reviews. Nephrology 36280707 2023 Jan
ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. Dardani, Ian; Emert, Benjamin L; Goyal, Yogesh; Jiang, Connie L; Kaur, Amanpreet; Lee, Jasmine; Rouhanifard, Sara H; Alicea, Gretchen M; Fane, Mitchell E; Xiao, Min; Herlyn, Meenhard; Weeraratna, Ashani T; Raj, Arjun Nature methods 36280724 2022 Nov
Subtype-specific 3D genome alteration in acute myeloid leukaemia. Xu, Jie; Song, Fan; Lyu, Huijue; Kobayashi, Mikoto; Zhang, Baozhen; Zhao, Ziyu; Hou, Ye; Wang, Xiaotao; Luan, Yu; Jia, Bei; Stasiak, Lena; Wong, Josiah Hiu-Yuen; Wang, Qixuan; Jin, Qi; Jin, Qiushi; Fu, Yihao; Yang, Hongbo; Hardison, Ross C; Dovat, Sinisa; Platanias, Leonidas C; Diao, Yarui; Yang, Yue; Yamada, Tomoko; Viny, Aaron D; Levine, Ross L; Claxton, David; Broach, James R; Zheng, Hong; Yue, Feng Nature 36289338 2022 Nov
Divergent clonal differentiation trajectories of T cell exhaustion. Daniel, Bence; Yost, Kathryn E; Hsiung, Sunnie; Sandor, Katalin; Xia, Yu; Qi, Yanyan; Hiam-Galvez, Kamir J; Black, Mollie; J Raposo, Colin; Shi, Quanming; Meier, Stefanie L; Belk, Julia A; Giles, Josephine R; Wherry, E John; Chang, Howard Y; Egawa, Takeshi; Satpathy, Ansuman T Nature immunology 36289450 2022 Nov
Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. Zhu, Xiaoyu; Qi, Chuangye; Wang, Ruoyu; Lee, Joo-Hyung; Shao, Jiaofang; Bei, Lanxin; Xiong, Feng; Nguyen, Phuoc T; Li, Guojie; Krakowiak, Joanna; Koh, Su-Pin; Simon, Lukas M; Han, Leng; Moore, Travis I; Li, Wenbo Cell reports 36323253 2022 Nov 01
Enhanced T cell effector activity by targeting the Mediator kinase module. Freitas, Katherine A; Belk, Julia A; Sotillo, Elena; Quinn, Patrick J; Ramello, Maria C; Malipatlolla, Meena; Daniel, Bence; Sandor, Katalin; Klysz, Dorota; Bjelajac, Jeremy; Xu, Peng; Burdsall, Kylie A; Tieu, Victor; Duong, Vandon T; Donovan, Micah G; Weber, Evan W; Chang, Howard Y; Majzner, Robbie G; Espinosa, Joaquin M; Satpathy, Ansuman T; Mackall, Crystal L Science (New York, N.Y.) 36356142 2022 Nov 11
CTCF blocks antisense transcription initiation at divergent promoters. Luan, Jing; Vermunt, Marit W; Syrett, Camille M; Coté, Allison; Tome, Jacob M; Zhang, Haoyue; Huang, Anran; Luppino, Jennifer M; Keller, Cheryl A; Giardine, Belinda M; Zhang, Shiping; Dunagin, Margaret C; Zhang, Zhe; Joyce, Eric F; Lis, John T; Raj, Arjun; Hardison, Ross C; Blobel, Gerd A Nature structural & molecular biology 36369346 2022 Nov
A conundrum in 3-D genome organization and expression? Pederson, Thoru Molecular biology of the cell 36399617 2022 Dec 01
Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Fang, Weixiang; Bell, Claire M; Sapirstein, Abel; Asami, Soichiro; Leeper, Kathleen; Zack, Donald J; Ji, Hongkai; Kalhor, Reza Cell 36423582 2022 Nov 23
Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. Luppino, Jennifer M; Field, Andrew; Nguyen, Son C; Park, Daniel S; Shah, Parisha P; Abdill, Richard J; Lan, Yemin; Yunker, Rebecca; Jain, Rajan; Adelman, Karen; Joyce, Eric F PLoS genetics 36449519 2022 Nov
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Goronzy, Isabel N; Quinodoz, Sofia A; Jachowicz, Joanna W; Ollikainen, Noah; Bhat, Prashant; Guttman, Mitchell Cell reports 36450242 2022 Nov 29
Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. Boe, Ryan H; Ayyappan, Vinay; Schuh, Lea; Raj, Arjun Cell systems 36450286 2022 Dec 21
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation. Alavattam, Kris G; Mitzelfelt, Katie A; Bonora, Giancarlo; Fields, Paul A; Yang, Xiulan; Chiu, Han Sheng; Pabon, Lil; Bertero, Alessandro; Palpant, Nathan J; Noble, William S; Murry, Charles E Stem cell reports 36493778 2023 Jan 10
Aberrant chromatin organization at the nexus of laminopathy disease pathways. Santini, Garrett T; Shah, Parisha P; Karnay, Ashley; Jain, Rajan Nucleus (Austin, Tex.) 36503349 2022 Dec
Maf family transcription factors are required for nutrient uptake in the mouse neonatal gut. Bara, Anne M; Chen, Lei; Ma, Celina; Underwood, Julie; Moreci, Rebecca S; Sumigray, Kaelyn; Sun, Tongyu; Diao, Yarui; Verzi, Michael; Lechler, Terry Development (Cambridge, England) 36504079 2022 Dec 01
Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. Daniel, Bence; Belk, Julia A; Meier, Stefanie L; Chen, Andy Y; Sandor, Katalin; Czimmerer, Zsolt; Varga, Zsofia; Bene, Krisztian; Buquicchio, Frank A; Qi, Yanyan; Kitano, Hugo; Wheeler, Joshua R; Foster, Deshka S; Januszyk, Michael; Longaker, Michael T; Chang, Howard Y; Satpathy, Ansuman T Molecular cell 36521490 2023 Jan 05
Maximum-likelihood model fitting for quantitative analysis of SMLM data. Wu, Yu-Le; Hoess, Philipp; Tschanz, Aline; Matti, Ulf; Mund, Markus; Ries, Jonas Nature methods 36522500 2023 Jan
Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation. Sitmukhambetov, Satzhan; Dinh, Bryan; Lai, Youfang; Banigan, Edward J; Pan, Zui; Jia, Xun; Chi, Yujie Physics in medicine and biology 36533598 2022 Dec 19
The sound of silence: Transgene silencing in mammalian cell engineering. Cabrera, Alan; Edelstein, Hailey I; Glykofrydis, Fokion; Love, Kasey S; Palacios, Sebastian; Tycko, Josh; Zhang, Meng; Lensch, Sarah; Shields, Cara E; Livingston, Mark; Weiss, Ron; Zhao, Huimin; Haynes, Karmella A; Morsut, Leonardo; Chen, Yvonne Y; Khalil, Ahmad S; Wong, Wilson W; Collins, James J; Rosser, Susan J; Polizzi, Karen; Elowitz, Michael B; Fussenegger, Martin; Hilton, Isaac B; Leonard, Joshua N; Bintu, Lacramioara; Galloway, Kate E; Deans, Tara L Cell systems 36549273 2022 Dec 21
Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Spracklin, George; Abdennur, Nezar; Imakaev, Maxim; Chowdhury, Neil; Pradhan, Sriharsa; Mirny, Leonid A; Dekker, Job Nature structural & molecular biology 36550219 2023 Jan
Eukaryotic gene regulation at equilibrium, or non? Zoller, Benjamin; Gregor, Thomas; Tkačik, Gašper Current opinion in systems biology 36590072 2022 Sep
A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. Jia, Bojing Blair; Jussila, Adam; Kern, Colin; Zhu, Quan; Ren, Bing Nature biotechnology 36593410 2023 Jan 02
Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. Mahadevan, Jyothi; Jha, Asmita; Rudolph, Johannes; Bowerman, Samuel; Narducci, Domenic; Hansen, Anders S; Luger, Karolin iScience 36594010 2023 Jan 20
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Varoquaux, Nelle; Noble, William S; Vert, Jean-Philippe Bioinformatics (Oxford, England) 36594573 2023 Jan 01
Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. Shi, Tuo; Beaulieu, Marielle O; Saunders, Lauren M; Fabian, Peter; Trapnell, Cole; Segil, Neil; Crump, J Gage; Raible, David W eLife 36598134 2023 Jan 04
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian Nature genetics 36624346 2023 Jan
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. Chai, Haoxi; Tjong, Harianto; Li, Peng; Liao, Wei; Wang, Ping; Wong, Chee Hong; Ngan, Chew Yee; Leonard, Warren J; Wei, Chia-Lin; Ruan, Yijun Nature communications 36639381 2023 Jan 13
Gos: a declarative library for interactive genomics visualization in Python. Manz, Trevor; L'Yi, Sehi; Gehlenborg, Nils Bioinformatics (Oxford, England) 36688709 2023 Jan 01
Phase Separation in Biology and Disease; Current Perspectives and Open Questions. Boeynaems, Steven; Chong, Shasha; Gsponer, Jörg; Holt, Liam; Milovanovic, Dragomir; Mitrea, Diana M; Mueller-Cajar, Oliver; Portz, Bede; Reilly, John F; Reinkemeier, Christopher D; Sabari, Benjamin R; Sanulli, Serena; Shorter, James; Sontag, Emily; Strader, Lucia; Stachowiak, Jeanne; Weber, Stephanie C; White, Michael; Zhang, Huaiying; Zweckstetter, Markus; Elbaum-Garfinkle, Shana; Kriwacki, Richard Journal of molecular biology 36690068 2023 Mar 01
An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Shah, Parisha P; Keough, Kathleen C; Gjoni, Ketrin; Santini, Garrett T; Abdill, Richard J; Wickramasinghe, Nadeera M; Dundes, Carolyn E; Karnay, Ashley; Chen, Angela; Salomon, Rachel E A; Walsh, Patrick J; Nguyen, Son C; Whalen, Sean; Joyce, Eric F; Loh, Kyle M; Dubois, Nicole; Pollard, Katherine S; Jain, Rajan Genome biology 36691074 2023 Jan 23
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Brückner, David B; Chen, Hongtao; Barinov, Lev; Zoller, Benjamin; Gregor, Thomas bioRxiv : the preprint server for biology 36711618 2023 Feb 13
Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis. He, Shuonan; Shao, Wanqing; Chen, Shiyuan Cynthia; Wang, Ting; Gibson, Matthew C bioRxiv : the preprint server for biology 36711919 2023 Jan 10
CTCF is essential for proper mitotic spindle structure and anaphase segregation. Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D bioRxiv : the preprint server for biology 36712070 2023 Jan 10
Capturing Chromosome Conformation Across Length Scales. Yang, Liyan; Akgol Oksuz, Betul; Dekker, Job; Gibcus, Johan Harmen Journal of visualized experiments : JoVE 36744801 2023 Jan 20
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. Choudhary, Mayank N K; Quaid, Kara; Xing, Xiaoyun; Schmidt, Heather; Wang, Ting Nature communications 36746940 2023 Feb 06
Deep learning enables fast, gentle STED microscopy. Ebrahimi, Vahid; Stephan, Till; Kim, Jiah; Carravilla, Pablo; Eggeling, Christian; Jakobs, Stefan; Han, Kyu Young bioRxiv : the preprint server for biology 36747618 2023 Jan 27
Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer. Rodrigues, Aaron; MacQuarrie, Kyle L; Freeman, Emma; Lin, Alicia; Willis, Alexander B; Xu, Zhaofa; Alvarez, Angel A; Ma, Yongchao; White, Bethany E Perez; Foltz, Daniel R; Huang, Sui Molecular biology of the cell 36753381 2023 Apr 01
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Lareau, Caleb A; Liu, Vincent; Muus, Christoph; Praktiknjo, Samantha D; Nitsch, Lena; Kautz, Pauline; Sandor, Katalin; Yin, Yajie; Gutierrez, Jacob C; Pelka, Karin; Satpathy, Ansuman T; Regev, Aviv; Sankaran, Vijay G; Ludwig, Leif S Nature protocols 36792778 2023 May
Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. Jain, Naveen; Goyal, Yogesh; Dunagin, Margaret C; Cote, Christopher J; Mellis, Ian A; Emert, Benjamin; Jiang, Connie L; Dardani, Ian P; Reffsin, Sam; Raj, Arjun bioRxiv : the preprint server for biology 36798299 2023 Feb 10
Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq. Spracklin, George; Yang, Liyan; Pradhan, Sriharsa; Dekker, Job Methods in molecular biology (Clifton, N.J.) 36807063 2023
Community-developed checklists for publishing images and image analyses. Schmied, Christopher; Nelson, Michael S; Avilov, Sergiy; Bakker, Gert-Jan; Bertocchi, Cristina; Bischof, Johanna; Boehm, Ulrike; Brocher, Jan; Carvalho, Mariana; Chiritescu, Catalin; Christopher, Jana; Cimini, Beth A; Conde-Sousa, Eduardo; Ebner, Michael; Ecker, Rupert; Eliceiri, Kevin; Fernandez-Rodriguez, Julia; Gaudreault, Nathalie; Gelman, Laurent; Grunwald, David; Gu, Tingting; Halidi, Nadia; Hammer, Mathias; Hartley, Matthew; Held, Marie; Jug, Florian; Kapoor, Varun; Koksoy, Ayse Aslihan; Lacoste, Judith; Dévédec, Sylvia Le; Guyader, Sylvie Le; Liu, Penghuan; Martins, Gabriel G; Mathur, Aastha; Miura, Kota; Montero Llopis, Paula; Nitschke, Roland; North, Alison; Parslow, Adam C; Payne-Dwyer, Alex; Plantard, Laure; Ali, Rizwan; Schroth-Diez, Britta; Schütz, Lucas; Scott, Ryan T; Seitz, Arne; Selchow, Olaf; Sharma, Ved P; Spitaler, Martin; Srinivasan, Sathya; Strambio-De-Castillia, Caterina; Taatjes, Douglas; Tischer, Christian; Jambor, Helena Klara ArXiv 36824427 2023 Sep 14
Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function. Zhan, Yuxiang; Yildirim, Asli; Boninsegna, Lorenzo; Alber, Frank bioRxiv : the preprint server for biology 36824908 2023 Feb 19
OME-Zarr: a cloud-optimized bioimaging file format with international community support. Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hart bioRxiv : the preprint server for biology 36865282 2023 May 07
Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. Liu, Zhi; Lee, Dong-Sung; Liang, Yuqiong; Zheng, Ye; Dixon, Jesse bioRxiv : the preprint server for biology 36865315 2023 Mar 21
Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. Kamat, Kartik; Lao, Zhuohan; Qi, Yifeng; Wang, Yuchuan; Ma, Jian; Zhang, Bin Biophysical journal 36871158 2023 Apr 04
Transcription shapes 3D chromatin organization by interacting with loop extrusion. Banigan, Edward J; Tang, Wen; van den Berg, Aafke A; Stocsits, Roman R; Wutz, Gordana; Brandão, Hugo B; Busslinger, Georg A; Peters, Jan-Michael; Mirny, Leonid A Proceedings of the National Academy of Sciences of the United States of America 36897969 2023 Mar 14
An integrated platform for high-throughput nanoscopy. Barentine, Andrew E S; Lin, Yu; Courvan, Edward M; Kidd, Phylicia; Liu, Miao; Balduf, Leonhard; Phan, Timy; Rivera-Molina, Felix; Grace, Michael R; Marin, Zach; Lessard, Mark; Rios Chen, Juliana; Wang, Siyuan; Neugebauer, Karla M; Bewersdorf, Joerg; Baddeley, David Nature biotechnology 36914886 2023 Mar 13
High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling. Booth, Gregory T; Daza, Riza M; Srivatsan, Sanjay R; McFaline-Figueroa, Jos L; Gladden, Rula Green; Furlan, Scott N; Shendure, Jay; Trapnell, Cole bioRxiv : the preprint server for biology 36945538 2023 Mar 06
Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E bioRxiv : the preprint server for biology 36945584 2023 Mar 10
Probing neural circuit mechanisms in Alzheimer's disease using novel technologies. Grieco, Steven F; Holmes, Todd C; Xu, Xiangmin Molecular psychiatry 36959497 2023 Oct
SARS-CoV-2 restructures host chromatin architecture. Wang, Ruoyu; Lee, Joo-Hyung; Kim, Jieun; Xiong, Feng; Hasani, Lana Al; Shi, Yuqiang; Simpson, Erin N; Zhu, Xiaoyu; Chen, Yi-Ting; Shivshankar, Pooja; Krakowiak, Joanna; Wang, Yanyu; Gilbert, David M; Yuan, Xiaoyi; Eltzschig, Holger K; Li, Wenbo Nature microbiology 36959507 2023 Apr
Mapping cellular responses to DNA double-strand breaks using CRISPR technologies. Liu, Yang; Cottle, W Taylor; Ha, Taekjip Trends in genetics : TIG 36967246 2023 Jul
Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. Pecori, Federico; Torres-Padilla, Maria-Elena Developmental cell 36977375 2023 Mar 27
Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. Bashkirova, Elizaveta V; Klimpert, Nell; Monahan, Kevin; Campbell, Christine E; Osinski, Jason M; Tan, Longzhi; Schieren, Ira; Pourmorady, Ariel; Stecky, Beka; Barnea, Gilad; Xie, X Sunnie; Abdus-Saboor, Ishmail; Shykind, Benjamin; Jones-Marlin, Bianca; Gronostajski, Richard M; Fleischmann, Alexander; Lomvardas, Stavros bioRxiv : the preprint server for biology 36993168 2023 Sep 19
Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. Chen, Liang-Fu; Long, Hannah Katherine; Park, Minhee; Swigut, Tomek; Boettiger, Alistair Nicol; Wysocka, Joanna Molecular cell 36996812 2023 May 04
Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. Pai, Joy A; Hellmann, Matthew D; Sauter, Jennifer L; Mattar, Marissa; Rizvi, Hira; Woo, Hyung Jun; Shah, Nisargbhai; Nguyen, Evelyn M; Uddin, Fathema Z; Quintanal-Villalonga, Alvaro; Chan, Joseph M; Manoj, Parvathy; Allaj, Viola; Baine, Marina K; Bhanot, Cancer cell 37001526 2023 Apr 10
GAGA-associated factor fosters loop formation in the Drosophila genome. Li, Xiao; Tang, Xiaona; Bing, Xinyang; Catalano, Christopher; Li, Taibo; Dolsten, Gabriel; Wu, Carl; Levine, Michael Molecular cell 37003261 2023 May 04
Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. Zou, Roger S; Liu, Yang; Gaido, Oscar E Reyes; Konig, Maximilian F; Mog, Brian J; Shen, Leo L; Aviles-Vazquez, Franklin; Marin-Gonzalez, Alberto; Ha, Taekjip Nature methods 37024653 2023 May
Nucleolar structure connects with global nuclear organization. Wang, Chen; Ma, Hanhui; Baserga, Susan J; Pederson, Thoru; Huang, Sui bioRxiv : the preprint server for biology 37034708 2023 Mar 31
Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. Xiong, Xiong; Tasan, Ipek; Yang, Che; Zhang, Meng; Hernandez Gonzalez, Gabriela A; Liu, Shuting; Chaturvedi, Pankaj; Belmont, Andrew S; Zhao, Huimin ACS synthetic biology 37058298 2023 May 19
3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles. Uyehara, Christopher M; Apostolou, Effie Cell reports 37059094 2023 Apr 06
Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. Chiliński, Mateusz; Lipiński, Jakub; Agarwal, Abhishek; Ruan, Yijun; Plewczynski, Dariusz bioRxiv : the preprint server for biology 37066361 2023 Apr 06
Genome folding dynamics during the M-to-G1-phase transition. Zhang, Haoyue; Blobel, Gerd A Current opinion in genetics & development 37099832 2023 Jun
The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. Shrestha, Roshan L; Balachandra, Vinutha; Kim, Jee Hun; Rossi, Austin; Vadlamani, Pranathi; Sethi, Subhash Chandra; Ozbun, Laurent; Lin, Shinjen; Cheng, Ken Chin-Chien; Chari, Raj; Karpova, Tatiana S; Pegoraro, Gianluca; Foltz, Daniel R; Caplen, Natasha J Journal of cell science 37129573 2023 May 15
Loop stacking organizes genome folding from TADs to chromosomes. Hafner, Antonina; Park, Minhee; Berger, Scott E; Murphy, Sedona E; Nora, Elphège P; Boettiger, Alistair N Molecular cell 37146570 2023 May 04
Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser. Zhuo, Xiaoyu; Hsu, Silas; Purushotham, Deepak; Kuntala, Prashant Kumar; Harrison, Jessica K; Du, Alan Y; Chen, Samuel; Li, Daofeng; Wang, Ting Genome research 37156621 2023 May
Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. Goel, Viraat Y; Huseyin, Miles K; Hansen, Anders S Nature genetics 37157000 2023 Jun
Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. Faber, Gabriel P; Hauschner, Hagit; Atrash, Mohammad K; Bilinsky, Liat; Shav-Tal, Yaron Cytometry. Part A : the journal of the International Society for Analytical Cytology 37158244 2023 Aug
Interpreting non-coding disease-associated human variants using single-cell epigenomics. Gaulton, Kyle J; Preissl, Sebastian; Ren, Bing Nature reviews. Genetics 37161089 2023 May 09
UNADON: Transformer-based model to predict genome-wide chromosome spatial position. Yang, Muyu; Ma, Jian ArXiv 37163136 2023 Apr 26
Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche. Haensel, Daniel; Daniel, Bence; Gaddam, Sadhana; Pan, Cory; Fabo, Tania; Bjelajac, Jeremy; Jussila, Anna R; Gonzalez, Fernanda; Li, Nancy Yanzhe; Chen, Yun; Hou, JinChao; Patel, Tiffany; Aasi, Sumaira; Satpathy, Ansuman T; Oro, Anthony E Nature communications 37164949 2023 May 10
Spatially resolved epigenomic profiling of single cells in complex tissues. Lu, Tian; Ang, Cheen Euong; Zhuang, Xiaowei Cell 37172568 2023 May 11
Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. Patil, Abhijeet R; Schug, Jonathan; Naji, Ali; Kaestner, Klaus H; Faryabi, Robert B; Vahedi, Golnaz Nature metabolism 37188822 2023 May
High-content CRISPR screening. Bock, Christoph; Datlinger, Paul; Chardon, Florence; Coelho, Matthew A; Dong, Matthew B; Lawson, Keith A; Lu, Tian; Maroc, Laetitia; Norman, Thomas M; Song, Bicna; Stanley, Geoff; Chen, Sidi; Garnett, Mathew; Li, Wei; Moffat, Jason; Qi, Lei S; Shapiro, Re Nature reviews. Methods primers 37214176 2022
Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. Chandra, Aditi; Yoon, Sora; Michieletto, Michaël F; Goldman, Naomi; Ferrari, Emily K; Abedi, Maryam; Johnson, Isabelle; Fasolino, Maria; Pham, Kenneth; Joannas, Leonel; Kee, Barbara L; Henao-Mejia, Jorge; Vahedi, Golnaz Immunity 37263273 2023 Jul 11
Light-switchable transcription factors obtained by direct screening in mammalian cells. Zhu, Liyuan; McNamara, Harold M; Toettcher, Jared E Nature communications 37268649 2023 Jun 02
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals. Yang, Rui; Das, Arnav; Gao, Vianne R; Karbalayghareh, Alireza; Noble, William S; Bilmes, Jeffery A; Leslie, Christina S Genome biology 37280678 2023 Jun 06
Comparing chromatin contact maps at scale: methods and insights. Gunsalus, Laura; McArthur, Evonne; Gjoni, Ketrin; Kuang, Shuzhen; Pittman, Maureen; Capra, John; Pollard, Katherine Research square 37292728 2023 May 23
scGHOST: Identifying single-cell 3D genome subcompartments. Xiong, Kyle; Zhang, Ruochi; Ma, Jian bioRxiv : the preprint server for biology 37292994 2023 May 25
Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis. He, Shuonan; Shao, Wanqing; Chen, Shiyuan Cynthia; Wang, Ting; Gibson, Matthew C Current biology : CB 37315559 2023 Jul 10
Chromosome and protein folding: In search for unified principles. Mirny, Leonid A Current opinion in structural biology 37327690 2023 Aug
SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. Wolin, Erica; Guo, Jimmy K; Blanco, Mario R; Perez, Andrew A; Goronzy, Isabel N; Abdou, Ahmed A; Gorhe, Darvesh; Guttman, Mitchell; Jovanovic, Marko bioRxiv : the preprint server for biology 37333139 2023 Jun 07
Recording morphogen signals reveals origins of gastruloid symmetry breaking. McNamara, Harold M; Solley, Sabrina C; Adamson, Britt; Chan, Michelle M; Toettcher, Jared E bioRxiv : the preprint server for biology 37333235 2023 Jun 05
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. Beagrie, Robert A; Thieme, Christoph J; Annunziatella, Carlo; Baugher, Catherine; Zhang, Yingnan; Schueler, Markus; Kukalev, Alexander; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Li, Yichao; Davis, Trenton; Scialdone, Antonio; Welch, Lonnie R; Nicodemi, Mario; Pombo, Ana Nature methods 37336949 2023 Jul
Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. Van Buren, Eric; Radicioni, Giorgia; Lester, Sarah; O'Neal, Wanda K; Dang, Hong; Kasela, Silva; Garudadri, Suresh; Curtis, Jeffrey L; Han, MeiLan K; Krishnan, Jerry A; Wan, Emily S; Silverman, Edwin K; Hastie, Annette; Ortega, Victor E; Lappalainen, Tuuli; Nawijn, Martijn C; Berge, Maarten van den; Christenson, Stephanie A; Li, Yun; Cho, Michael H; Kesimer, Mehmet; Kelada, Samir N P PLoS genetics 37352370 2023 Jun
PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. McNamar, Rachel; Freeman, Emma; Baylor, Kairo N; Fakhouri, Aula M; Huang, Sui; Knutson, Bruce A; Rothblum, Lawrence I The Journal of biological chemistry 37356716 2023 Aug
Deep learning enables fast, gentle STED microscopy. Ebrahimi, Vahid; Stephan, Till; Kim, Jiah; Carravilla, Pablo; Eggeling, Christian; Jakobs, Stefan; Han, Kyu Young Communications biology 37369761 2023 Jun 27
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Brückner, David B; Chen, Hongtao; Barinov, Lev; Zoller, Benjamin; Gregor, Thomas Science (New York, N.Y.) 37384691 2023 Jun 30
UNADON: transformer-based model to predict genome-wide chromosome spatial position. Yang, Muyu; Ma, Jian Bioinformatics (Oxford, England) 37387176 2023 Jun 30
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Dekker, Job; Alber, Frank; Aufmkolk, Sarah; Beliveau, Brian J; Bruneau, Benoit G; Belmont, Andrew S; Bintu, Lacramioara; Boettiger, Alistair; Calandrelli, Riccardo; Disteche, Christine M; Gilbert, David M; Gregor, Thomas; Hansen, Anders S; Huang, Bo; Huangfu, Danwei; Kalhor, Reza; Leslie, Christina S; Li, Wenbo; Li, Yun; Ma, Jian; Noble, William S; Park, Peter J; Phillips-Cremins, Jennifer E; Pollard, Katherine S; Rafelski, Susanne M; Ren, Bing; Ruan, Yijun; Shav-Tal, Yaron; Shen, Yin; Shendure, Jay; Shu, Xiaokun; Strambio-De-Castillia, Caterina; Vertii, Anastassiia; Zhang, Huaiying; Zhong, Sheng Molecular cell 37419111 2023 Aug 03
Regulation of mammalian totipotency: a molecular perspective from in vivo and in vitro studies. Nakatani, Tsunetoshi; Torres-Padilla, Maria-Elena Current opinion in genetics & development 37421903 2023 Aug
Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. Luo, Zhifei; Wen, Xingzhao; Zhao, Wenxin; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng bioRxiv : the preprint server for biology 37425846 2023 Jun 28
Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. Catta-Preta, Rinaldo; Lindtner, Susan; Ypsilanti, Athena; Price, James; Abnousi, Armen; Su-Feher, Linda; Wang, Yurong; Juric, Ivan; Jones, Ian R; Akiyama, Jennifer A; Hu, Ming; Shen, Yin; Visel, Axel; Pennacchio, Len A; Dickel, Diane; Rubenstein, John L R; Nord, Alex S bioRxiv : the preprint server for biology 37425940 2023 Jun 28
Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. Cheng, Li-Chun; Zhang, Xi; Baboo, Sabyasachi; Nguyen, Julie A; Martinez-Bartolomé, Salvador; Loose, Esther; Diedrich, Jolene; Yates 3rd, John R; Gerace, Larry Life science alliance 37433644 2023 Sep
High-throughput Oligopaint screen identifies druggable 3D genome regulators. Park, Daniel S; Nguyen, Son C; Isenhart, Randi; Shah, Parisha P; Kim, Wonho; Barnett, R Jordan; Chandra, Aditi; Luppino, Jennifer M; Harke, Jailynn; Wai, May; Walsh, Patrick J; Abdill, Richard J; Yang, Rachel; Lan, Yemin; Yoon, Sora; Yunker, Rebecca; Kanemaki, Masato T; Vahedi, Golnaz; Phillips-Cremins, Jennifer E; Jain, Rajan; Joyce, Eric F Nature 37438531 2023 Aug
Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. Chiliński, Mateusz; Lipiński, Jakub; Agarwal, Abhishek; Ruan, Yijun; Plewczynski, Dariusz Scientific reports 37474564 2023 Jul 20
Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Sun, Tongyu; Xu, Yueyuan; Xiang, Yu; Ou, Jianhong; Soderblom, Erik J; Diao, Yarui Nature genetics 37474847 2023 Aug
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Luo, Renhe; Yan, Jielin; Oh, Jin Woo; Xi, Wang; Shigaki, Dustin; Wong, Wilfred; Cho, Hyein S; Murphy, Dylan; Cutler, Ronald; Rosen, Bess P; Pulecio, Julian; Yang, Dapeng; Glenn, Rachel A; Chen, Tingxu; Li, Qing V; Vierbuchen, Thomas; Sidoli, Simone; Apostolou, Effie; Huangfu, Danwei; Beer, Michael A Nature genetics 37488417 2023 Aug
High throughput PRIME editing screens identify functional DNA variants in the human genome. Ren, Xingjie; Yang, Han; Nierenberg, Jovia L; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin bioRxiv : the preprint server for biology 37502948 2023 Jul 12
Phase separation of ecDNA aggregates establishes in-trans contact domains boosting selective MYC regulatory interactions. Conte, Mattia; Matteuzzi, Tommaso; Esposito, Andrea; Chiariello, Andrea M; Bianco, Simona; Vercellone, Francesca; Nicodemi, Mario bioRxiv : the preprint server for biology 37503084 2023 Jul 17
Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. Chung, Chan-I; Yang, Junjiao; Shu, Xiaokun ACS central science 37521779 2023 Jul 26
Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Mohana, Giriram; Dorier, Julien; Li, Xiao; Mouginot, Marion; Smith, Rebecca C; Malek, Héléna; Leleu, Marion; Rodriguez, Daniel; Khadka, Jenisha; Rosa, Patrycja; Cousin, Pascal; Iseli, Christian; Restrepo, Simon; Guex, Nicolas; McCabe, Brian D; Jankowski, Aleksander; Levine, Michael S; Gambetta, Maria Cristina Cell 37536338 2023 Aug 31
CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Zhang, Hongshan; Shi, Zhubing; Banigan, Edward J; Kim, Yoori; Yu, Hongtao; Bai, Xiao-Chen; Finkelstein, Ilya J Molecular cell 37536339 2023 Aug 17
Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. Patterson, Benjamin; Yang, Bing; Tanaka, Yoshiaki; Kim, Kun-Yong; Cakir, Bilal; Xiang, Yangfei; Kim, Jonghun; Wang, Siyuan; Park, In-Hyun Science advances 37540754 2023 Aug 04
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. Zhou, Tianming; Zhang, Ruochi; Jia, Deyong; Doty, Raymond T; Munday, Adam D; Gao, Daniel; Xin, Li; Abkowitz, Janis L; Duan, Zhijun; Ma, Jian bioRxiv : the preprint server for biology 37546900 2023 Jul 25
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. Gao, Vianne R; Yang, Rui; Das, Arnav; Luo, Renhe; Luo, Hanzhi; McNally, Dylan R; Karagiannidis, Ioannis; Rivas, Martin A; Wang, Zhong-Min; Barisic, Darko; Karbalayghareh, Alireza; Wong, Wilfred; Zhan, Yingqian A; Chin, Christopher R; Noble, William; Bilmes, Jeff A; Apostolou, Effie; Kharas, Michael G; Béguelin, Wendy; Viny, Aaron D; Huangfu, Danwei; Rudensky, Alexander Y; Melnick, Ari M; Leslie, Christina S bioRxiv : the preprint server for biology 37546906 2023 Jul 28
Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. Chiariello, Andrea M; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Vercellone, Francesca; Conte, Mattia; Fontana, Andrea; Nicodemi, Mario bioRxiv : the preprint server for biology 37546924 2023 Jul 28
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Lee, Lindsay; Yu, Hongyu; Jia, Bojing Blair; Jussila, Adam; Zhu, Chenxu; Chen, Jiawen; Xie, Liangqi; Hafner, Antonina; Mishra, Shreya; Wang, Duan Dennis; Strambio-De-Castillia, Caterina; Boettiger, Alistair; Ren, Bing; Li, Yun; Hu, Ming Nature communications 37573342 2023 Aug 12
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie bioRxiv : the preprint server for biology 37577543 2023 Jul 19
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling. Yildirim, Asli; Hua, Nan; Boninsegna, Lorenzo; Zhan, Yuxiang; Polles, Guido; Gong, Ke; Hao, Shengli; Li, Wenyuan; Zhou, Xianghong Jasmine; Alber, Frank Nature structural & molecular biology 37580627 2023 Aug
Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Goldman, Naomi; Chandra, Aditi; Johnson, Isabelle; Sullivan, Matthew A; Patil, Abhijeet R; Vanderbeck, Ashley; Jay, Atishay; Zhou, Yeqiao; Ferrari, Emily K; Mayne, Leland; Aguilan, Jennifer; Xue, Hai-Hui; Faryabi, Robert B; John Wherry, E; Sidoli, Simone; Maillard, Ivan; Vahedi, Golnaz Nature immunology 37592014 2023 Oct
To Cut or not to Cut: Next-generation Genome Editors for Precision Genome Engineering. Zhang, Meng; Zhu, Zhixin; Xun, Guanhua; Zhao, Huimin Current opinion in biomedical engineering 37593347 2023 Dec
Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E Development (Cambridge, England) 37602510 2023 Sep 01
A molecular proximity sensor based on an engineered, dual-component guide RNA. Choi, Junhong; Chen, Wei; Liao, Hanna; Li, Xiaoyi; Shendure, Jay bioRxiv : the preprint server for biology 37645782 2023 Aug 14
SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. Lee, Lindsay; Yu, Miao; Li, Xiaoqi; Zhu, Chenxu; Zhang, Yanxiao; Yu, Hongyu; Chen, Ziyin; Mishra, Shreya; Ren, Bing; Li, Yun; Hu, Ming Briefings in bioinformatics 37649383 2023 Sep 20
Computational methods for analysing multiscale 3D genome organization. Zhang, Yang; Boninsegna, Lorenzo; Yang, Muyu; Misteli, Tom; Alber, Frank; Ma, Jian Nature reviews. Genetics 37673975 2023 Sep 06
Hormonal Imbalances in Prader-Willi and Schaaf-Yang Syndromes Imply the Evolution of Specific Regulation of Hypothalamic Neuroendocrine Function in Mammals. Hoyos Sanchez, Maria Camila; Bayat, Tara; Gee, Rebecca R Florke; Fon Tacer, Klementina International journal of molecular sciences 37685915 2023 Aug 23
Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M eLife 37695017 2023 Sep 11
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Abdulhay, Nour J; Hsieh, Laura J; McNally, Colin P; Ostrowski, Megan S; Moore, Camille M; Ketavarapu, Mythili; Kasinathan, Sivakanthan; Nanda, Arjun S; Wu, Ke; Chio, Un Seng; Zhou, Ziling; Goodarzi, Hani; Narlikar, Geeta J; Ramani, Vijay Nature structural & molecular biology 37696956 2023 Oct
Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Chang, Li-Hsin; Ghosh, Sourav; Papale, Andrea; Luppino, Jennifer M; Miranda, Mélanie; Piras, Vincent; Degrouard, Jéril; Edouard, Joanne; Poncelet, Mallory; Lecouvreur, Nathan; Bloyer, Sébastien; Leforestier, Amélie; Joyce, Eric F; Holcman, David; Noordermeer, Daan Nature communications 37699887 2023 Sep 12
SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. Zhang, Meng; Ehmann, Mary Elisabeth; Matukumalli, Srija; Boob, Aashutosh Girish; Gilbert, David M; Zhao, Huimin Nature communications 37699958 2023 Sep 12
Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Deshpande, Rajashree A; Marin-Gonzalez, Alberto; Barnes, Hannah K; Woolley, Phillip R; Ha, Taekjip; Paull, Tanya T Nature communications 37717054 2023 Sep 16
CTCF is essential for proper mitotic spindle structure and anaphase segregation. Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D Chromosoma 37728741 2023 Sep 20
Perturbations in 3D genome organization can promote acquired drug resistance. Manjón, Anna G; Manzo, Stefano Giustino; Prekovic, Stefan; Potgeter, Leon; van Schaik, Tom; Liu, Ning Qing; Flach, Koen; Peric-Hupkes, Daniel; Joosten, Stacey; Teunissen, Hans; Friskes, Anoek; Ilic, Mila; Hintzen, Dorine; Franceschini-Santos, Vinícius H; Zwart, Wilbert; de Wit, Elzo; van Steensel, Bas; Medema, René H Cell reports 37733591 2023 Oct 31
Alu transposable elements rewire enhancer-promoter network through RNA pairing. Wen, Xingzhao; Zhong, Sheng Molecular cell 37738962 2023 Sep 21
Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. Berg, Isabel K; Currey, Marilena L; Gupta, Sarthak; Berrada, Yasmin; Nguyen, Bao V; Pho, Mai; Patteson, Alison E; Schwarz, J M; Banigan, Edward J; Stephens, Andrew D Journal of cell science 37756607 2023 Oct 15
HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials. Wei, Xiaolin; Tran, Duc; Diao, Yarui Current protocols 37818863 2023 Oct
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Calandrelli, Riccardo; Wen, Xingzhao; Charles Richard, John Lalith; Luo, Zhifei; Nguyen, Tri C; Chen, Chien-Ju; Qi, Zhijie; Xue, Shuanghong; Chen, Weizhong; Yan, Zhangming; Wu, Weixin; Zaleta-Rivera, Kathia; Hu, Rong; Yu, Miao; Wang, Yuchuan; Li, Wenbo; Ma, Jian; Ren, Bing; Zhong, Sheng Nature communications 37845234 2023 Oct 16
Single-cell chromatin state transitions during epigenetic memory formation. Fujimori, Taihei; Rios-Martinez, Carolina; Thurm, Abby R; Hinks, Michaela M; Doughty, Benjamin R; Sinha, Joydeb; Le, Derek; Hafner, Antonina; Greenleaf, William J; Boettiger, Alistair N; Bintu, Lacramioara bioRxiv : the preprint server for biology 37873344 2023 Oct 05
The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. Sinha, Joydeb; Nickels, Jan F; Thurm, Abby R; Ludwig, Connor H; Archibald, Bella N; Hinks, Michaela M; Wan, Jun; Fang, Dong; Bintu, Lacramioara bioRxiv : the preprint server for biology 37873347 2023 Oct 14
Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels. Haroush, Netta; Levo, Michal; Wieschaus, Eric F; Gregor, Thomas Developmental cell 37890488 2023 Dec 04
Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity. Pal, Mrinmoy; Altamirano-Pacheco, Luis; Schauer, Tamas; Torres-Padilla, Maria-Elena Genes & development 37914351 2023 Oct 01
Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. Liu, Zhi; Lee, Dong-Sung; Liang, Yuqiong; Zheng, Ye; Dixon, Jesse R Nature communications 37932264 2023 Nov 06
SIKs Regulate HDAC7 Stabilization and Cytokine Recall in Late-Stage T Cell Effector Differentiation. Helms, Rachel S; Marin-Gonzalez, Alberto; Patel, Chirag H; Sun, Im-Hong; Wen, Jiayu; Leone, Robert D; Duvall, Bridget; Gao, Run-Duo; Ha, Taekjip; Tsukamoto, Takashi; Slusher, Barbara S; Pomerantz, Joel L; Powell, Jonathan D Journal of immunology (Baltimore, Md. : 1950) 37947442 2023 Dec 15
Proteostasis governs differential temperature sensitivity across embryonic cell types. Dorrity, Michael W; Saunders, Lauren M; Duran, Madeleine; Srivatsan, Sanjay R; Barkan, Eliza; Jackson, Dana L; Sattler, Sydney M; Ewing, Brent; Queitsch, Christine; Shendure, Jay; Raible, David W; Kimelman, David; Trapnell, Cole Cell 37949057 2023 Nov 09
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. Gjoni, Ketrin; Pollard, Katherine S bioRxiv : the preprint server for biology 37961123 2023 Nov 05
Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. Kuang, Shuzhen; Pollard, Katherine S bioRxiv : the preprint server for biology 37961712 2023 Oct 24
FOXO1 is a master regulator of CAR T memory programming. Doan, Alexander; Mueller, Katherine P; Chen, Andy; Rouin, Geoffrey T; Daniel, Bence; Lattin, John; Chen, Yingshi; Mozarsky, Brett; Markovska, Martina; Arias-Umana, Jose; Hapke, Robert; Jung, Inyoung; Xu, Peng; Klysz, Dorota; Bashti, Malek; Quinn, Patrick J; Sandor, Katalin; Zhang, Wenxi; Hall, Junior; Lareau, Caleb; Grupp, Stephan A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W Research square 37986944 2023 Nov 07
Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Andronov, Leonid; Han, Mengting; Zhu, Yanyu; Roy, Anish R; Barentine, Andrew E S; Garhyan, Jaishree; Qi, Lei S; Moerner, W E bioRxiv : the preprint server for biology 37986994 2023 Nov 29
Genome folding principles revealed in condensin-depleted mitotic chromosomes. Zhao, Han; Lin, Yinzhi; Lin, En; Liu, Fuhai; Shu, Lirong; Jing, Dannan; Wang, Baiyue; Wang, Manzhu; Shan, Fengnian; Zhang, Lin; Lam, Jessica C; Midla, Susannah C; Giardine, Belinda M; Keller, Cheryl A; Hardison, Ross C; Blobel, Gerd A; Zhang, Haoyue bioRxiv : the preprint server for biology 38014261 2023 Nov 13
ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization. Gunsalus, Laura M; Keiser, Michael J; Pollard, Katherine S bioRxiv : the preprint server for biology 38045231 2023 Nov 22
High-capacity sample multiplexing for single cell chromatin accessibility profiling. Booth, Gregory T; Daza, Riza M; Srivatsan, Sanjay R; McFaline-Figueroa, José L; Gladden, Rula Green; Mullen, Andrew C; Furlan, Scott N; Shendure, Jay; Trapnell, Cole BMC genomics 38049719 2023 Dec 04
3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie Nature structural & molecular biology 38053013 2024 Jan
DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. Wang, Qianwen; L'Yi, Sehi; Gehlenborg, Nils Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference 38074525 2023 Apr
Conserved and divergent gene regulatory programs of the mammalian neocortex. Zemke, Nathan R; Armand, Ethan J; Wang, Wenliang; Lee, Seoyeon; Zhou, Jingtian; Li, Yang Eric; Liu, Hanqing; Tian, Wei; Nery, Joseph R; Castanon, Rosa G; Bartlett, Anna; Osteen, Julia K; Li, Daofeng; Zhuo, Xiaoyu; Xu, Vincent; Chang, Lei; Dong, Keyi; Indralingam, Hannah S; Rink, Jonathan A; Xie, Yang; Miller, Michael; Krienen, Fenna M; Zhang, Qiangge; Taskin, Naz; Ting, Jonathan; Feng, Guoping; McCarroll, Steven A; Callaway, Edward M; Wang, Ting; Lein, Ed S; Behrens, M Margarita; Ecker, Joseph R; Ren, Bing Nature 38092918 2023 Dec
Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells. Roberts, Thomas C; Kushner, Max; Crowley, Jack C; Ozer, Abdullah; Wang, Juan; Ray, Judhajeet; Lis, John T; Zipfel, Warren R bioRxiv : the preprint server for biology 38105945 2023 Dec 06
Cell-type-specific 3D-genome organization and transcription regulation in the brain. Liu, Shiwei; Zheng, Pu; Wang, Cosmos Yuqi; Jia, Bojing Blair; Zemke, Nathan R; Ren, Bing; Zhuang, Xiaowei bioRxiv : the preprint server for biology 38105994 2023 Dec 05
Electrostatic encoding of genome organization principles within single native nucleosomes. Park, Sangwoo; Athreya, Advait; Carrizo, Gustavo Ezequiel; Benning, Nils A; Mitchener, Michelle M; Bhanu, Natarajan V; Garcia, Benjamin A; Zhang, Bin; Muir, Tom W; Pearce, Erika L; Ha, Taekjip bioRxiv : the preprint server for biology 38106048 2023 Dec 09
Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. Titus, Katelyn R; Simandi, Zoltan; Chandrashekar, Harshini; Paquet, Dominik; Phillips-Cremins, Jennifer E bioRxiv : the preprint server for biology 38106199 2023 Dec 05
RNA-mediated symmetry breaking enables singular olfactory receptor choice. Pourmorady, Ariel D; Bashkirova, Elizaveta V; Chiariello, Andrea M; Belagzhal, Houda; Kodra, Albana; Duffié, Rachel; Kahiapo, Jerome; Monahan, Kevin; Pulupa, Joan; Schieren, Ira; Osterhoudt, Alexa; Dekker, Job; Nicodemi, Mario; Lomvardas, Stavros Nature 38123679 2024 Jan
Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Malachowski, Thomas; Chandradoss, Keerthivasan Raanin; Boya, Ravi; Zhou, Linda; Cook, Ashley L; Su, Chuanbin; Pham, Kenneth; Haws, Spencer A; Kim, Ji Hun; Ryu, Han-Seul; Ge, Chunmin; Luppino, Jennifer M; Nguyen, Son C; Titus, Katelyn R; Gong, Wanfeng; Wallace, Owen; Joyce, Eric F; Wu, Hao; Rojas, Luis Alejandro; Phillips-Cremins, Jennifer E Cell 38134876 2023 Dec 21
High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Ren, Xingjie; Yang, Han; Nierenberg, Jovia L; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin Molecular cell 38134886 2023 Dec 21
Machine learning reveals the diversity of human 3D chromatin contact patterns. Gilbertson, Erin N; Brand, Colin M; McArthur, Evonne; Rinker, David C; Kuang, Shuzhen; Pollard, Katherine S; Capra, John A bioRxiv : the preprint server for biology 38187606 2023 Dec 23
A fast, scalable and versatile tool for analysis of single-cell omics data. Zhang, Kai; Zemke, Nathan R; Armand, Ethan J; Ren, Bing Nature methods 38191932 2024 Feb
Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation. Khurana, Sakshi; Foltz, Daniel R bioRxiv : the preprint server for biology 38234763 2023 Dec 27
The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. Makeyev, Eugene V; Huang, Sui Nucleus (Austin, Tex.) 38281066 2024 Dec
SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. Yu, Hongyu; Wu, Daiqing; Shen, Guning; Hu, Ming; Li, Yun bioRxiv : the preprint server for biology 38293083 2024 Jan 15
Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. Brumbaugh-Reed, Ellen H; Aoki, Kazuhiro; Toettcher, Jared E bioRxiv : the preprint server for biology 38293146 2024 Jan 17
Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development. Kaplan, Harris S; Logeman, Brandon L; Zhang, Kai; Santiago, Celine; Sohail, Noor; Naumenko, Serhiy; Ho Sui, Shannan J; Ginty, David D; Ren, Bing; Dulac, Catherine bioRxiv : the preprint server for biology 38328205 2024 Jan 23
Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Murphy, Sedona Eve; Boettiger, Alistair Nicol Nature genetics 38361032 2024 Feb 15

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