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The search results on this publication page are automated on a monthly schedule based on acknowledgment 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.
4D Nucleome (865)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. | Pecori, Federico; Torres-Padilla, Maria-Elena | Developmental cell | 2023 Mar 27 | 435-449 | 36977375 |
| 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 | 2023 Apr | 679-694 | 36959507 |
| 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 | 2023 Mar 13 | 36914886 | |
| 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 | 2023 Mar 14 | e2210480120 | 36897969 |
| Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. | Kamat, Kartik; Lao, Zhuohan; Qi, Yifeng; Wang, Yuchuan; Ma, Jian; Zhang, Bin | Biophysical journal | 2023 Apr 04 | 1376-1389 | 36871158 |
| 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 | 2023 Apr 01 | br5 | 36753381 |
| 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 | 2023 Feb 06 | 634 | 36746940 |
| Capturing Chromosome Conformation Across Length Scales. | Yang, Liyan; Akgol Oksuz, Betul; Dekker, Job; Gibcus, Johan Harmen | Journal of visualized experiments : JoVE | 2023 Jan 20 | 36744801 | |
| 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 | 2023 Jan 10 | 36711919 | |
| 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 | 2023 Jan 23 | 16 | 36691074 |
| 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 | 2023 Mar 01 | 167971 | 36690068 |
| Gos: a declarative library for interactive genomics visualization in Python. | Manz, Trevor; L'Yi, Sehi; Gehlenborg, Nils | Bioinformatics (Oxford, England) | 2023 Jan 01 | 36688709 | |
| 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 | 2023 Jan 13 | 213 | 36639381 |
| SPICEMIX enables integrative single-cell spatial modeling of cell identity. | Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian | Nature genetics | 2023 Jan | 36624346 | |
| 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 | 2023 Jan 04 | 36598134 | |
| 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 | 2023 Jan 20 | 105779 | 36594010 |
| Eukaryotic gene regulation at equilibrium, or non? | Zoller, Benjamin; Gregor, Thomas; Tkačik, Gašper | Current opinion in systems biology | 2022 Sep | 36590072 | |
| 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 | 2023 Jan | 38-51 | 36550219 |
| 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 | 2022 Dec 21 | 950-973 | 36549273 |
| 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 | 2022 Dec 19 | 36533598 | |
| 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 | 2023 Jan | 139-148 | 36522500 |
| 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 | 2023 Jan 05 | 36521490 | |
| 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 | 2023 Jan 10 | 159-174 | 36493778 |
| 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 | 2022 Dec 21 | 36450286 | |
| 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 | 2022 Nov 29 | 36450242 | |
| 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 | 2022 Nov | 36449519 | |
| 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 | 2022 Nov 23 | 36423582 | |
| A conundrum in 3-D genome organization and expression? | Pederson, Thoru | Molecular biology of the cell | 2022 Dec 01 | 36399617 | |
| 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 | 2022 Nov | 36369346 | |
| 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.) | 2022 Nov 11 | 36356142 | |
| 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 | 2022 Nov 01 | 36323253 | |
| 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 | 2022 Nov | 36289450 | |
| 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 | 2022 Nov | 36289338 | |
| 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 | 2022 Nov | 36280724 | |
| Advances in CRISPR therapeutics. | Chavez, Michael; Chen, Xinyi; Finn, Paul B; Qi, Lei S | Nature reviews. Nephrology | 2023 Jan | 9-22 | 36280707 |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu, Tian; Ang, Cheen Euong; Zhuang, Xiaowei | Cell | 2022 Nov 10 | 36272405 | |
| Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells. | Drayton, Jamie A; Hansen, Anders S | Molecular cell | 2022 Oct 20 | 36270244 | |
| 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 | 2022 Nov 03 | 36265488 | |
| Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi. | Zhang, Ruochi; Zhou, Tianming; Ma, Jian | Cell systems | 2022 Oct 19 | 36265466 | |
| 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 | 2022 Oct 19 | 36261634 | |
| 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 | 2022 Oct 17 | 36245428 | |
| 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 | 2022 Oct 12 | 36224177 | |
| 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 | 2022 Nov | 1008-1021 | 36207411 |
| CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. | Liu, Yu; Dekker, Job | Nature cell biology | 2022 Oct | 1516-1527 | 36202971 |
| 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 | 2022 Oct 03 | 36191105 | |
| 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 | 2022 Sep 29 | 36175411 | |
| Multi-View Design Patterns and Responsive Visualization for Genomics Data. | LYi, Sehi; Gehlenborg, Nils | IEEE transactions on visualization and computer graphics | 2023 Jan | 559-569 | 36166553 |
| 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 | 2022 Aug | 303-312 | 36119136 |
| 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 | 2022 Aug 25 | 36078056 | |
| 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 | 2022 Sep | 36064968 | |
| 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 | 2022 Sep 01 | 36050765 | |
| 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 | 2023 Jan | 42-54 | 36050414 |
| Mammalian genome innovation through transposon domestication. | Modzelewski, Andrew J; Gan Chong, Johnny; Wang, Ting; He, Lin | Nature cell biology | 2022 09 | 36008480 | |
| 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 | 2022 10 | 36007540 | |
| 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 | 2023 Feb | 177-191 | 35996026 |
| 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 | 2022 Sep 02 | 35972904 | |
| High throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. | Jones, Ian R; Ren, Xingjie; Shen, Yin | Human molecular genetics | 2022 Aug 16 | 35972825 | |
| 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 | 2022 | 35967929 | |
| 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.) | 2022 Aug 06 | 35932276 | |
| 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 | 2022 08 | 35882933 | |
| 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 | 2022 07 21 | 35868274 | |
| 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.) | 2022 | 35867249 | |
| Assessing Specific Networks of Chromatin Interactions with HiChIP. | Di Giammartino, Dafne Campigli; Polyzos, Alexander; Apostolou, Effie | Methods in molecular biology (Clifton, N.J.) | 2022 | 35867248 | |
| 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 | 2022 08 | 35864167 | |
| Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser. | Li, Daofeng; Harrison, Jessica K; Purushotham, Deepak; Wang, Ting | Nature methods | 2022 08 | 35864166 | |
| 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 | 2022 08 01 | 35857429 | |
| Characterizing cis-regulatory elements using single-cell epigenomics. | Preissl, Sebastian; Gaulton, Kyle J; Ren, Bing | Nature reviews. Genetics | 2022 Jul 15 | 35840754 | |
| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci, Domenic N; Hansen, Anders S | Nature structural & molecular biology | 2022 07 | 35835869 | |
| 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 | 2022 Aug 08 | 35835116 | |
| 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 | 2022 07 13 | 35831310 | |
| 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 | 2022 08 | 35817938 | |
| 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 | 2022 08 | 35794474 | |
| Nuclear speckles - a driving force in gene expression. | Faber, Gabriel P; Nadav-Eliyahu, Shani; Shav-Tal, Yaron | Journal of cell science | 2022 Jul 01 | 35788677 | |
| Guilt by association: EcDNA as a mobile transactivator in cancer. | Zhu, Yanfen; Gong, Liang; Wei, Chia-Lin | Trends in cancer | 2022 Jun 23 | 35753910 | |
| 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 | 2022 07 18 | 35753702 | |
| 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 | 2022 07 11 | 35750052 | |
| 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 | 2022 06 16 | 35741072 | |
| 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 | 2022 06 28 | 35737842 | |
| 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 | 2022 07 | 35726060 | |
| 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 | 2022 Aug 03 | 35706127 | |
| 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 | 2022 Jul 20 | 35705097 | |
| 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 | 2022 08 | 35691341 | |
| 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 | 2022 06 11 | 35690614 | |
| 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 | 2022 | 35680503 | |
| 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 | 2022 06 | 35676475 | |
| 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 | 2022 06 06 | 35668089 | |
| Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization. | Yang, Muyu; Ma, Jian | Journal of molecular biology | 2022 08 15 | 35659533 | |
| 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 | 2022 07 | 35649578 | |
| 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 | 2022 Jul | 35637351 | |
| 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 | 2022 07 12 | 35637103 | |
| Epigenetic regulation of T cell exhaustion. | Belk, Julia A; Daniel, Bence; Satpathy, Ansuman T | Nature immunology | 2022 06 | 35624210 | |
| 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 | 2022 06 13 | 35623342 | |
| 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 | 2022 05 20 | 35595799 | |
| 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 | 2022 06 | 35585235 | |
| Fast and efficient DNA replication with purified human proteins. | Baris, Yasemin; Taylor, Martin R G; Aria, Valentina; Yeeles, Joseph T P | Nature | 2022 06 | 35585232 | |
| 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 | 2022 05 26 | 35525247 | |
| Mechanics and functional consequences of nuclear deformations. | Kalukula, Yohalie; Stephens, Andrew D; Lammerding, Jan; Gabriele, Sylvain | Nature reviews. Molecular cell biology | 2022 09 | 35513718 | |
| 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 | 2022 05 | 35508662 | |
| 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 | 2022 05 03 | 35508105 | |
| 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 | 2022 Jun 02 | 35504290 | |
| 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 | 2022 May | 35501386 | |
| 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 | 2022 05 | 35501385 | |
| 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 | 2022 05 02 | 35501320 | |
| 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 | 2022 05 13 | 35488276 | |
| 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 | 2022 May | 35484250 | |
| Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. | McNamara, Harold M; Ramm, Beatrice; Toettcher, Jared E | Seminars in cell & developmental biology | 2023 May 30 | 33-42 | 35484026 |
| 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 | 2022 05 12 | 35483375 | |
| 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 | 2022 06 02 | 35483357 | |
| 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 | 2022 05 20 | 35474142 | |
| 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 | 2022 Apr 26 | 35471149 | |
| 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 | 2022 Mar 25 | 35456393 | |
| Modular and mechanistic changes across stages of colorectal cancer. | Rahiminejad, Sara; Maurya, Mano R; Mukund, Kavitha; Subramaniam, Shankar | BMC cancer | 2022 Apr 21 | 35448980 | |
| 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.) | 2022 04 29 | 35420890 | |
| 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 | 2022 Apr | 35414015 | |
| 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 | 2022 Jul 05 | W774-W781 | 35412637 |
| Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes. | Nudelman, Ilona; Fernandez-Martinez, Javier; Rout, Michael P | Methods in molecular biology (Clifton, N.J.) | 2022 | 35412228 | |
| Mapping chromatin loops in single cells. | Yu, Miao; Li, Yun; Hu, Ming | Trends in genetics : TIG | 2022 Jul | 35400543 | |
| Chromatin interaction-aware gene regulatory modeling with graph attention networks. | Karbalayghareh, Alireza; Sahin, Merve; Leslie, Christina S | Genome research | 2022 May | 35396274 | |
| 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 | 2022 Apr 05 | 35382863 | |
| 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 | 2022 May 03 | 35364106 | |
| 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 | 2022 03 29 | 35354035 | |
| 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 | 2022 05 15 | 35352962 | |
| Stripenn detects architectural stripes from chromatin conformation data using computer vision. | Yoon, Sora; Chandra, Aditi; Vahedi, Golnaz | Nature communications | 2022 Mar 24 | 35332165 | |
| 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 | 2022 05 13 | 35325048 | |
| 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 | 2022 Mar 22 | 35320726 | |
| 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 | 2022 Mar 17 | 35303483 | |
| 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 | 2022 Mar | 35301492 | |
| 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 | 2022 Mar | 35288709 | |
| 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 | 2022 04 | 35271371 | |
| 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 | 2022 03 | 35259165 | |
| 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 | 2022 03 15 | 35254895 | |
| 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 | 2021 | 35243481 | |
| 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 | 2022 03 03 | 35240980 | |
| 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 | 2022 Feb | 35228745 | |
| 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 | 2022 Jul | 35210612 | |
| 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 | 2022 Mar 17 | 35196517 | |
| 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 | 2022 03 17 | 35180380 | |
| 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 | 2022 03 | 35177821 | |
| 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 | 2021 | 35174207 | |
| The use of new CRISPR tools in cardiovascular research and medicine. | Nishiga, Masataka; Liu, Chun; Qi, Lei S; Wu, Joseph C | Nature reviews. Cardiology | 2022 08 | 35145236 | |
| 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 | 2022 Feb 01 | 35128513 | |
| 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 | 2022 02 | 35115686 | |
| 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.) | 2022 | 35103967 | |
| Compartmentalization of telomeres through DNA-scaffolded phase separation. | Developmental cell | 2022 01 24 | 35077681 | ||
| 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 | 2022 02 17 | 35065713 | |
| Technological advances in super-resolution microscopy to study cellular processes. | Bond, Charles; Santiago-Ruiz, Adriana N; Tang, Qing; Lakadamyali, Melike | Molecular cell | 2022 01 20 | 35063099 | |
| 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 | 2022 01 | 35050714 | |
| Single nucleosome tracking to study chromatin plasticity. | Lakadamyali, Melike | Current opinion in cell biology | 2022 Jan 13 | 35033775 | |
| 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 | 2022 Jan | 35013617 | |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett, Daniel A; Dileep, Vishnu; Baslan, Timour; Gilbert, David M | Current protocols | 2022 Jan | 34986273 | |
| 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 | 2022 01 | 34985990 | |
| 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) | 2022 Mar 04 | 1729-1731 | 34978573 |
| Stress as a Chromatin Landscape Architect. | Vertii, Anastassiia | Frontiers in cell and developmental biology | 2021 | 34970548 | |
| Integrative approaches in genome structure analysis. | Structure (London, England : 1993) | 2022 01 06 | 34963059 | ||
| Epigenome rewiring in human pluripotent stem cells. | Yan, Jielin; Huangfu, Danwei | Trends in cell biology | 2021 Dec 23 | 34955367 | |
| 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 | 2021 12 21 | 34921112 | |
| Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. | Pourmorady, Ariel; Lomvardas, Stavros | Current opinion in genetics & development | 2022 02 | 34896807 | |
| 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 | 2021 12 | 34862503 | |
| 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 | 2021 12 | 34862501 | |
| 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 | 2021 11 | 34789882 | |
| 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 | 2021 11 17 | 34789735 | |
| Light activation and deactivation of Cas9 for DNA repair studies. | Zou, Roger S; Ha, Taekjip | Methods in enzymology | 2021 | 34776214 | |
| 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 | 2021 11 16 | 34772813 | |
| 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 | 2021 11 12 | 34767455 | |
| 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 | 2021 11 11 | 34739832 | |
| 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 | 2021 Nov 04 | 34734806 | |
| 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 | 2021 11 03 | 34732726 | |
| 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 | 2021 12 | 34654919 | |
| 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 | 2021 10 28 | 34644528 | |
| 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 | 2021 12 | 34635849 | |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang, Ruochi; Zhou, Tianming; Ma, Jian | Nature biotechnology | 2021 Oct 11 | 34635838 | |
| 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 | 2021 10 11 | 34635658 | |
| 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) | 2019 Sep 03 | 34632462 | |
| 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 | 2021 10 07 | 34620850 | |
| 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 | 2021 Oct | 34611363 | |
| 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 | 2022 01 | 34596551 | |
| 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.) | 2021 10 29 | 34591592 | |
| 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 | 2021 09 27 | 34579774 | |
| 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 | 2021 Sep 17 | 34563051 | |
| 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 | 2021 Sep 21 | 34548656 | |
| 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 | 2021 Sep 20 | 34547287 | |
| 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 | 2021 Sep 17 | 34524848 | |
| 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 | 2021 11 04 | 34520723 | |
| Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. | Mirny, Leonid; Dekker, Job | Cold Spring Harbor perspectives in biology | 2022 07 01 | 34518339 | |
| Enhanced Cas12a multi-gene regulation using a CRISPR array separator. | Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei S | eLife | 2021 09 09 | 34499031 | |
| 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 | 2021 Jul 08 | 34485947 | |
| 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 | 2021 09 | 34480155 | |
| 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 | 2021 09 | 34480151 | |
| The 3D Genome Structure of Single Cells. | Zhou, Tianming; Zhang, Ruochi; Ma, Jian | Annual review of biomedical data science | 2021 07 20 | 34465168 | |
| 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 | 2021 09 | 34446921 | |
| 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 | 2021 Aug 13 | 34428454 | |
| 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 | 2021 Aug 23 | 34426703 | |
| 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.) | 2022 | 34415534 | |
| 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 | 2022 Jul 01 | 34400557 | |
| Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. | Yildirim, Asli; Boninsegna, Lorenzo; Zhan, Yuxiang; Alber, Frank | Cold Spring Harbor perspectives in biology | 2021 Aug 16 | 34400556 | |
| X-factors in human disease: impact of gene content and dosage regulation. | Fang, He; Deng, Xinxian; Disteche, Christine M | Human molecular genetics | 2021 Oct 01 | 34387327 | |
| Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). | Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, Bing | Methods in molecular biology (Clifton, N.J.) | 2021 | 34382190 | |
| 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 | 2021 08 19 | 34375583 | |
| 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 | 2022 01 | 34370624 | |
| 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 | 2021 Sep 22 | 34352221 | |
| 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 | 2020 Jun | 34334852 | |
| 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 | 2021 Jul 21 | 34312624 | |
| 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 | 2021 08 | 34312537 | |
| CRISPRi/a Screening with Human iPSCs. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Methods in molecular biology (Clifton, N.J.) | 2021 | 34302664 | |
| Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. | Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan H | Current protocols | 2021 Jul | 34286910 | |
| 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 | 2021 08 27 | 34282837 | |
| 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 | 2021 07 19 | 34279217 | |
| 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 | 2021 Jul 14 | 34273560 | |
| 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 | 2021 Jun 25 | 34241518 | |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair N | eLife | 2021 07 09 | 34240703 | |
| 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 | 2021 Jul 06 | 34230036 | |
| 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 | 2021 10 | 34214188 | |
| 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.) | 2021 07 02 | 34210887 | |
| 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 | 2021 08 15 | 34191541 | |
| 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 | 2021 Jun 09 | 34127974 | |
| Imaging Organization of RNA Processing within the Nucleus. | Biswas, Jeetayu; Li, Weihan; Singer, Robert H; Coleman, Robert A | Cold Spring Harbor perspectives in biology | 2021 12 01 | 34127450 | |
| 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 | 2021 Jul 08 | 34115980 | |
| Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. | Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, Jian | Quantitative biology (Beijing, China) | 2019 Jun | 34113473 | |
| 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 | 2021 Jun 09 | 34108665 | |
| 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 | 2021 06 09 | 34106828 | |
| 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 | 2021 06 08 | 34103507 | |
| 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 | 2021 06 07 | 34099725 | |
| 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 | 2021 08 | 34059832 | |
| Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. | Scourzic, Laurianne; Salataj, Eralda; Apostolou, Effie | Frontiers in immunology | 2021 | 34054841 | |
| 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.) | 2021 05 28 | 34045355 | |
| 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 | 2021 May 26 | 34040254 | |
| 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 | 2021 May 21 | 34021280 | |
| 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 | 2021 12 | 34021279 | |
| 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 | 2021 May 21 | 34021236 | |
| 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 | 2021 06 18 | 34006094 | |
| 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 | 2021 May 11 | 34004142 | |
| 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 | 2021 May 17 | 34002095 | |
| 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 | 2021 Jun | 34002092 | |
| 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.) | 2021 May 14 | 33969332 | |
| 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 | 2021 05 | 33963348 | |
| Determination of complete chromosomal haplotypes by bulk DNA sequencing. | Tourdot, Richard W; Brunette, Gregory J; Pinto, Ricardo A; Zhang, Cheng-Zhong | Genome biology | 2021 May 06 | 33957932 | |
| From integrative structural biology to cell biology. | Sali, Andrej | The Journal of biological chemistry | 2021 Jan-Jun | 33957123 | |
| 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 | 2020 Sep | 33954299 | |
| 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 | 2021 May 04 | 33951429 | |
| The Need for a Human Pangenome Reference Sequence. | Miga, Karen H; Wang, Ting | Annual review of genomics and human genetics | 2021 08 31 | 33929893 | |
| 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 | 2021 Apr 21 | 33919286 | |
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| 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. | 2019 Sep; | 31427791 | |
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| Learn from Your Elders: Developmental Biology Lessons to Guide Maturation of Stem Cell-Derived Cardiomyocytes. | Marchianò, Silvia; Bertero, Alessandro; Murry, Charles E | Pediatric cardiology. | 2019 Oct; | 31388700 | |
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| 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). | 2019 09 09; | 31314157 | |
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| 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. | 2019 06 24; | 31235807 | |
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| 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.). | 2019 Dec; | 31142202 | |
| 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. | 2019 05 22; | 31118417 | |
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| 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. | 2019 May; | 31068695 | |
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| 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. | 2019 May 31; | 31010829 | |
| 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. | 2019; | 31001319 | |
| 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. | 2019 Mar; | 30999490 | |
| 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. | 2019 04; | 30986246 | |
| 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. | 2019 May 02; | 30982597 | |
| 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. | 2019 04 04; | 30948719 | |
| 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. | 2019 05; | 30936163 | |
| 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. | 2019 04; | 30926969 | |
| 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. | 2019 Apr 16; | 30926670 | |
| 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. | 2019 05; | 30923229 | |
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| 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. | 2017 Sep 07; | 28886366 | |
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| 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. | 2017 Sep; | 28825700 | |
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| 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 | 2017 03 | 28070687 | |
| 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. | 2017 Jan 05; | 28057760 | |
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| 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. | 2017 Jan 12; | 28041848 | |
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| 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. | 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, Bing | Cell 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 D | Molecular 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, Dariusz | Genome 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, Bas | Epigenetics & chromatin. | 2016; | 27777628 | |
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| 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 | |
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| 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. | 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, Yongheng | PloS one. | 2016; | 27618313 | |
| Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. | Stark, Marie; Cheng, R Holland | Pharmaceutical patent analyst. | 2016 Sep; | 27610752 | |
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| 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. | 2016 Aug 29; | 27551060 | |
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| 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. | 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, Hiroko | Scientific reports. | 2016 Aug 12; | 27516062 | |
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| Allele-Specific Quantification of Structural Variations in Cancer Genomes. | Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian | Cell systems. | 2016 Jul; | 27453446 | |
| 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. | 2016 09; | 27452946 | |
| 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. | 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 Lieberman | Proceedings 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, Mario | Scientific reports. | 2016 Jul 13; | 27405443 | |
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| 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 A | Genes & development. | 2016 Jun 15; | 27340175 | |
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| 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. | 2016 Jul; | 27265842 | |
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| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular cell. | 2016 Jun 2; | 27259200 | |
| Use of genome-editing tools to treat sickle cell disease. | Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Human 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, Xianghong | Nature 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 A | Cell. | 2016 Jun 2; | 27238023 | |
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| 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. | 2016; | 27176874 | |
| 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. | 2016 06; | 27174171 | |
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| 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 | 2016 May 5 | P:611-24 | 27152443 |
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