4D Nucleome (77)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
CTCF and cohesin regulate chromatin loop stability with distinct dynamics.Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, XaviereLife.2017 May 03;28467304
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, KyungheeThe Journal of experimental medicine.2017 May 01;28461595
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.Belaghzal, Houda; Dekker, Job; Gibcus, Johan HMethods (San Diego, Calif.).2017 Apr 18;28435001
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 LMolecular and cellular biology.2017 Apr 17;28416636
An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases.Gunn, Kathryn H; Marko, John F; Mondragón, AlfonsoNature structural & molecular biology.2017 May;28414321
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, JennMolecular cell.2017 Apr 06;28388437
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 FProceedings of the National Academy of Sciences of the United States of America.2017 Apr 18;28364020
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, TingNature communications.2017 Mar 28;28348391
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer.Lowdon, Rebecca F; Wang, TingPloS one.2017;28333948
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, MazharNature communications.2017 Mar 14;28290446
Epigenetic characteristics of the mitotic chromosome in 1D and 3D.Oomen, Marlies E; Dekker, JobCritical reviews in biochemistry and molecular biology.2017 Apr;28228067
Comprehensive characterization of neutrophil genome topology.Zhu, Yina; Gong, Ke; Denholtz, Matthew; Chandra, Vivek; Kamps, Mark P; Alber, Frank; Murre, CornelisGenes & development.2017 Jan 15;28167501
Software tools for visualizing Hi-C data.Yard?mc?, Galip Gürkan; Noble, William StaffordGenome biology.2017 Feb 03;28159004
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 EMolecular cell.2017 Feb 02;28157505
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, JayNature methods.2017 Mar;28135255
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, TingNeoplasia (New York, N.Y.).2017 Feb;28088687
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 FMolecular biology of the cell.2017 Jan 05;28057760
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, DanGenome research.2017 Mar;28049628
A dynamic mode of mitotic bookmarking by transcription factors.Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, RoberteLife.2016 Nov 19;27855781
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 ACell reports.2016 Nov 15;27851973
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, BingCell reports.2016 Nov 15;27851967
The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer.Matheson, Timothy D; Kaufman, Paul DMolecular biology of the cell.2017 Jan 01;27807046
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, DariuszGenome research.2016 Dec;27789526
High-throughput assessment of context-dependent effects of chromatin proteins.Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, BasEpigenetics & chromatin.2016;27777628
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei SNature methods.2016 Dec;27776111
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 YNature methods.;27749837
Transferable model for chromosome architecture.Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José NProceedings of the National Academy of Sciences of the United States of America.2016 Oct 25;27688758
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, ZhijunNature protocols.2016 Nov;27685100
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, YonghengPloS one.2016;27618313
Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery.Stark, Marie; Cheng, R HollandPharmaceutical patent analyst.2016 Sep;27610752
CRISPR-Cas9 nuclear dynamics and target recognition in living cells.Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Huisman, Maximiliaan; Zhang, Shaojie; Grunwald, David; Pederson, ThoruThe Journal of cell biology.2016 Aug 29;27551060
A new correlation clustering method for cancer mutation analysis.Hou, Jack P; Emad, Amin; Puleo, Gregory J; Ma, Jian; Milenkovic, OlgicaBioinformatics (Oxford, England).2016 Aug 18;27540270
Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.Shenoy, Shailesh MMicroscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada.2016 Jul;27516727
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, HirokoScientific reports.2016 Aug 12;27516062
Allele-Specific Quantification of Structural Variations in Cancer Genomes.Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, JianCell systems.2016 Jul;27453446
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, JobNature.2016 Jul 28;27437574
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 LiebermanProceedings of the National Academy of Sciences of the United States of America.2016 Aug 02;27432957
Polymer physics of chromosome large-scale 3D organisation.Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, MarioScientific reports.2016 Jul 13;27405443
Identifying gene regulatory network rewiring using latent differential graphical models.Tian, Dechao; Gu, Quanquan; Ma, JianNucleic acids research.2016 Sep 30;27378774
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 SNature methods.2016 Aug;27376770
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.2016 Dec 15;27367781
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 AGenes & development.2016 Jun 15;27340175
Enhancer Control of Transcriptional Bursting.Fukaya, Takashi; Lim, Bomyi; Levine, MichaelCell.2016 Jul 14;27293191
RTFBSDB: an integrated framework for transcription factor binding site analysis.Wang, Zhong; Martins, André L; Danko, Charles GBioinformatics (Oxford, England).2016 Oct 01;27288497
What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism.Symmons, Orsolya; Raj, ArjunMolecular cell.2016 Jun 2;27259209
Chromatin Domains: The Unit of Chromosome Organization.Dixon, Jesse R; Gorkin, David U; Ren, BingMolecular cell.2016 Jun 2;27259200
Use of genome-editing tools to treat sickle cell disease.Tasan, Ipek; Jain, Surbhi; Zhao, HuiminHuman genetics.2016 Jun 1;27250347
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, XianghongNature communications.2016;27240697
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 ACell.2016 Jun 2;27238023
Chromosome Compaction by Active Loop Extrusion.Goloborodko, Anton; Marko, John F; Mirny, Leonid ABiophysical journal.2016 May 24;27224481
Formation of Chromosomal Domains by Loop Extrusion.Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid ACell Rep2016 May 1927210764
Compaction and segregation of sister chromatids via active loop extrusion.Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, LeonideLife.2016 May 18;27192037
Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)].Banigan, Edward J; Marko, John FPhysical review. E.2016 Apr;27182590
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 AGenome biology.2016;27176874
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 ECell Stem Cell2016 May 5P:611-2427152443
Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines.Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John FChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology.2016 Sep;27145786
Dosage compensation of the sex chromosomes and autosomes.Disteche, Christine MSemin Cell Dev Biol2016 Apr 2227112542
TAD disruption as oncogenic driver.Valton, Anne-Laure; Dekker, JobCurr Opin Genet Dev2016 FebP:34-4027111891
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 Biotechnology2016 April 18Epub ahead of print27088723
Evolution of Epigenetic Regulation in Vertebrate Genomes.Lowdon, Rebecca F; Jang, Hyo Sik; Wang, TingTrends Genet2016 MayP:269-8327080453
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping.Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA.Molecular Cell2016 April 5V:62 P:1-1127067601
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid AJ Bioinform Comput Biol2016 AprP:164100227021249
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, MingBMC research notes.2016;26969411
The 3D Genome as Moderator of Chromosomal Communication.Dekker, Job; Mirny, LeonidCell2016 Mar 10V:164 P:1110-2126967279
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, FrankProceedings of the National Academy of Sciences of the United States of America.2016 Mar 22;26951677
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, ArjunGenes & development.2016 Mar 1;26944681
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 AScience2016 Mar 25V:351 P:1454-826940867
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, HéctorNucleus2016 MarP:84-10226900797
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, TingG3 (Bethesda)2016P:973-8626888867
Understanding Spatial Genome Organization: Methods and Insights.Ramani, Vijay; Shendure, Jay; Duan, ZhijunGenomics Proteomics Bioinformatics2016 FebP:7-2026876719
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 HollandNanomedicine2016 Feb P:377-9026786134
Imaging Transcription: Past, Present, and Future.Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, TimothéeCold Spring Harbor symposia on quantitative biology.2016 Jan 1326763984
The redundancy of the mammalian heterochromatic compartment.Politz, Joan C Ritland; Scalzo, David; Groudine, MarkCurr Opin Genet Dev2015 Dec 16P:1-826706451
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 JasmineNucleic acids research.2016 Apr 20;26704975
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, YijunCell.2015 Dec 17V:163 P:1611-2726686651
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, PeterNature protocols.2015 Dec;26540590
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 LiebermanProceedings of the National Academy of Sciences of the United States of America.2015 Nov 24;26499245