4D Nucleome (865)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging.Pecori, Federico; Torres-Padilla, Maria-ElenaDevelopmental cell2023 Mar 27435-44936977375
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, WenboNature microbiology2023 Apr679-69436959507
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, DavidNature biotechnology2023 Mar 1336914886
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 AProceedings of the National Academy of Sciences of the United States of America2023 Mar 14e221048012036897969
Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.Kamat, Kartik; Lao, Zhuohan; Qi, Yifeng; Wang, Yuchuan; Ma, Jian; Zhang, BinBiophysical journal2023 Apr 041376-138936871158
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, SuiMolecular biology of the cell2023 Apr 01br536753381
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes.Choudhary, Mayank N K; Quaid, Kara; Xing, Xiaoyun; Schmidt, Heather; Wang, TingNature communications2023 Feb 0663436746940
Capturing Chromosome Conformation Across Length Scales.Yang, Liyan; Akgol Oksuz, Betul; Dekker, Job; Gibcus, Johan HarmenJournal of visualized experiments : JoVE2023 Jan 2036744801
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 CbioRxiv : the preprint server for biology2023 Jan 1036711919
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, RajanGenome biology2023 Jan 231636691074
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, RichardJournal of molecular biology2023 Mar 0116797136690068
Gos: a declarative library for interactive genomics visualization in Python.Manz, Trevor; L'Yi, Sehi; Gehlenborg, NilsBioinformatics (Oxford, England)2023 Jan 0136688709
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, YijunNature communications2023 Jan 1321336639381
SPICEMIX enables integrative single-cell spatial modeling of cell identity.Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, JianNature genetics2023 Jan36624346
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 WeLife2023 Jan 0436598134
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, KaroliniScience2023 Jan 2010577936594010
Eukaryotic gene regulation at equilibrium, or non?Zoller, Benjamin; Gregor, Thomas; Tkačik, GašperCurrent opinion in systems biology2022 Sep36590072
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, JobNature structural & molecular biology2023 Jan38-5136550219
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 LCell systems2022 Dec 21950-97336549273
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, YujiePhysics in medicine and biology2022 Dec 1936533598
Maximum-likelihood model fitting for quantitative analysis of SMLM data.Wu, Yu-Le; Hoess, Philipp; Tschanz, Aline; Matti, Ulf; Mund, Markus; Ries, JonasNature methods2023 Jan139-14836522500
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 TMolecular cell2023 Jan 0536521490
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 EStem cell reports2023 Jan 10159-17436493778
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, ArjunCell systems2022 Dec 2136450286
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, MitchellCell reports2022 Nov 2936450242
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 FPLoS genetics2022 Nov36449519
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, RezaCell2022 Nov 2336423582
A conundrum in 3-D genome organization and expression?Pederson, ThoruMolecular biology of the cell2022 Dec 0136399617
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 ANature structural & molecular biology2022 Nov36369346
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 LScience (New York, N.Y.)2022 Nov 1136356142
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, WenboCell reports2022 Nov 0136323253
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 TNature immunology2022 Nov36289450
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, FengNature2022 Nov36289338
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, ArjunNature methods2022 Nov36280724
Advances in CRISPR therapeutics.Chavez, Michael; Chen, Xinyi; Finn, Paul B; Qi, Lei SNature reviews. Nephrology2023 Jan9-2236280707
Spatially resolved epigenomic profiling of single cells in complex tissues.Lu, Tian; Ang, Cheen Euong; Zhuang, XiaoweiCell2022 Nov 1036272405
Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells.Drayton, Jamie A; Hansen, Anders SMolecular cell2022 Oct 2036270244
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 JMolecular cell2022 Nov 0336265488
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.Zhang, Ruochi; Zhou, Tianming; Ma, JianCell systems2022 Oct 1936265466
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, JayNature protocols2022 Oct 1936261634
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, BasEMBO reports2022 Oct 1736245428
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 MNature communications2022 Oct 1236224177
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, BingCell research2022 Nov1008-102136207411
CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.Liu, Yu; Dekker, JobNature cell biology2022 Oct1516-152736202971
GenoREC: A Recommendation System for Interactive Genomics Data Visualization.Pandey, Aditeya; L'Yi, Sehi; Wang, Qianwen; Borkin, Michelle A; Gehlenborg, NilsIEEE transactions on visualization and computer graphics2022 Oct 0336191105
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 JasmineNature communications2022 Sep 2936175411
Multi-View Design Patterns and Responsive Visualization for Genomics Data.LYi, Sehi; Gehlenborg, NilsIEEE transactions on visualization and computer graphics2023 Jan559-56936166553
A Versatile Micromanipulation Apparatus for Biophysical Assays of the Cell Nucleus.Currey, Marilena L; Kandula, Viswajit; Biggs, Ronald; Marko, John F; Stephens, Andrew DCellular and molecular bioengineering2022 Aug303-31236119136
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, DariuszCells2022 Aug 2536078056
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, TaekjipNature cell biology2022 Sep36064968
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, BasGenome biology2022 Sep 0136050765
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, JorgeNature immunology2023 Jan42-5436050414
Mammalian genome innovation through transposon domestication.Modzelewski, Andrew J; Gan Chong, Johnny; Wang, Ting; He, LinNature cell biology2022 0936008480
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, MagdalenaNature2022 1036007540
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, MelikeNature biomedical engineering2023 Feb177-19135996026
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, LarryJournal of proteome research2022 Sep 0235972904
High throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases.Jones, Ian R; Ren, Xingjie; Shen, YinHuman molecular genetics2022 Aug 1635972825
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 GBioinformatics advances202235967929
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, WenHepatology (Baltimore, Md.)2022 Aug 0635932276
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 KNature immunology2022 0835882933
3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome.Haws, Spencer A; Simandi, Zoltan; Barnett, R Jordan; Phillips-Cremins, Jennifer ECell2022 07 2135868274
Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq.Zhang, Liguo; Chen, Yu; Belmont, Andrew SMethods in molecular biology (Clifton, N.J.)202235867249
Assessing Specific Networks of Chromatin Interactions with HiChIP.Di Giammartino, Dafne Campigli; Polyzos, Alexander; Apostolou, EffieMethods in molecular biology (Clifton, N.J.)202235867248
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, JianNature methods2022 0835864167
Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser.Li, Daofeng; Harrison, Jessica K; Purushotham, Deepak; Wang, TingNature methods2022 0835864166
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 JMolecular pharmaceutics2022 08 0135857429
Characterizing cis-regulatory elements using single-cell epigenomics.Preissl, Sebastian; Gaulton, Kyle J; Ren, BingNature reviews. Genetics2022 Jul 1535840754
Reeling it in: how DNA topology drives loop extrusion by condensin.Narducci, Domenic N; Hansen, Anders SNature structural & molecular biology2022 0735835869
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 JDevelopmental cell2022 Aug 0835835116
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, MarioNature communications2022 07 1335831310
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, FrankNature methods2022 0835817938
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, JayNature2022 0835794474
Nuclear speckles - a driving force in gene expression.Faber, Gabriel P; Nadav-Eliyahu, Shani; Shav-Tal, YaronJournal of cell science2022 Jul 0135788677
Guilt by association: EcDNA as a mobile transactivator in cancer.Zhu, Yanfen; Gong, Liang; Wei, Chia-LinTrends in cancer2022 Jun 2335753910
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, YunBriefings in bioinformatics2022 07 1835753702
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 TCancer cell2022 07 1135750052
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, YaronCells2022 06 1635741072
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, PaulProceedings of the National Academy of Sciences of the United States of America2022 06 2835737842
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, GolnazNature immunology2022 0735726060
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, TingCancer research2022 Aug 0335706127
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, ArjunCell systems2022 Jul 2035705097
Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication.Popay, Tessa M; Dixon, Jesse RThe Journal of biological chemistry2022 0835691341
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, JonasNature communications2022 06 1135690614
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 JNuclear medicine and biology202235680503
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 ENature2022 0635676475
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, JonasNature communications2022 06 0635668089
Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization.Yang, Muyu; Ma, JianJournal of molecular biology2022 08 1535659533
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, TingGenome research2022 0735649578
Scalable biological signal recording in mammalian cells using Cas12a base editors.Kempton, Hannah R; Love, Kasey S; Guo, Lucie Y; Qi, Lei SNature chemical biology2022 Jul35637351
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, TakeshiImmunity2022 07 1235637103
Epigenetic regulation of T cell exhaustion.Belk, Julia A; Daniel, Bence; Satpathy, Ansuman TNature immunology2022 0635624210
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 FCancer cell2022 06 1335623342
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, YijunScientific reports2022 05 2035595799
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, KikuëNature2022 0635585235
Fast and efficient DNA replication with purified human proteins.Baris, Yasemin; Taylor, Martin R G; Aria, Valentina; Yeeles, Joseph T PNature2022 0635585232
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 GCell2022 05 2635525247
Mechanics and functional consequences of nuclear deformations.Kalukula, Yohalie; Stephens, Andrew D; Lammerding, Jan; Gabriele, SylvainNature reviews. Molecular cell biology2022 0935513718
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 SNature2022 0535508662
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, ShengCell metabolism2022 05 0335508105
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, YunAmerican journal of human genetics2022 Jun 0235504290
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, JoergNature methods2022 May35501386
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 JNature methods2022 0535501385
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 JNature communications2022 05 0235501320
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, YunBriefings in bioinformatics2022 05 1335488276
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 CNature cell biology2022 May35484250
Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems.McNamara, Harold M; Ramm, Beatrice; Toettcher, Jared ESeminars in cell & developmental biology2023 May 3033-4235484026
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 LCell2022 05 1235483375
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, RobertMolecular cell2022 06 0235483357
DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations.Nomidis, Stefanos K; Carlon, Enrico; Gruber, Stephan; Marko, John FNucleic acids research2022 05 2035474142
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; PhileLife2022 Apr 2635471149
Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization.Liu, Weifang; Zhong, Wujuan; Chen, Jiawen; Huang, Bo; Hu, Ming; Li, YunGenes2022 Mar 2535456393
Modular and mechanistic changes across stages of colorectal cancer.Rahiminejad, Sara; Maurya, Mano R; Mukund, Kavitha; Subramaniam, ShankarBMC cancer2022 Apr 2135448980
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 SScience (New York, N.Y.)2022 04 2935420890
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 SNature cell biology2022 Apr35414015
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, TingNucleic acids research2022 Jul 05W774-W78135412637
Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes.Nudelman, Ilona; Fernandez-Martinez, Javier; Rout, Michael PMethods in molecular biology (Clifton, N.J.)202235412228
Mapping chromatin loops in single cells.Yu, Miao; Li, Yun; Hu, MingTrends in genetics : TIG2022 Jul35400543
Chromatin interaction-aware gene regulatory modeling with graph attention networks.Karbalayghareh, Alireza; Sahin, Merve; Leslie, Christina SGenome research2022 May35396274
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, ArjunGenome biology2022 Apr 0535382863
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 ABiophysical journal2022 May 0335364106
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, MarioCell reports2022 03 2935354035
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 EMolecular biology of the cell2022 05 1535352962
Stripenn detects architectural stripes from chromatin conformation data using computer vision.Yoon, Sora; Chandra, Aditi; Vahedi, GolnazNature communications2022 Mar 2435332165
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, DiBriefings in bioinformatics2022 05 1335325048
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 ECell reports2022 Mar 2235320726
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, GabriMolecular cell2022 Mar 1735303483
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, MitchellNature structural & molecular biology2022 Mar35301492
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, JayNature genetics2022 Mar35288709
CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control.Dominguez, Antonia A; Chavez, Michael G; Urke, Amanda; Gao, Yuchen; Wang, Lizhong; Qi, Lei SThe CRISPR journal2022 0435271371
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, YunPLoS genetics2022 0335259165
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, ThoruProceedings of the National Academy of Sciences of the United States of America2022 03 1535254895
High-resolution 3D fluorescent imaging of intact tissues.El-Nachef, Danny; Martinson, Amy M; Yang, Xiulan; Murry, Charles E; MacLellan, W RobbInternational journal of cardiology and cardiovascular diseases202135243481
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 PJournal of neurodevelopmental disorders2022 03 0335240980
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, WenlNature metabolism2022 Feb35228745
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, PeterNature biotechnology2022 Jul35210612
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, YaruiMolecular cell2022 Mar 1735196517
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; RouCell2022 03 1735180380
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, IrinaNature cell biology2022 0335177821
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, HuaiyingFrontiers in molecular biosciences202135174207
The use of new CRISPR tools in cardiovascular research and medicine.Nishiga, Masataka; Liu, Chun; Qi, Lei S; Wu, Joseph CNature reviews. Cardiology2022 0835145236
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 SCell reports methods2022 Feb 0135128513
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; SmithNature genetics2022 0235115686
A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis.Jha, Asmita; Hansen, Anders SMethods in molecular biology (Clifton, N.J.)202235103967
Compartmentalization of telomeres through DNA-scaffolded phase separation.Developmental cell2022 01 2435077681
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, NiCell2022 02 1735065713
Technological advances in super-resolution microscopy to study cellular processes.Bond, Charles; Santiago-Ruiz, Adriana N; Tang, Qing; Lakadamyali, MelikeMolecular cell2022 01 2035063099
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, RitambharaJournal of computational biology : a journal of computational molecular cell biology2022 0135050714
Single nucleosome tracking to study chromatin plasticity.Lakadamyali, MelikeCurrent opinion in cell biology2022 Jan 1335033775
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, MitchellNature protocols2022 Jan35013617
Mapping Replication Timing in Single Mammalian Cells.Bartlett, Daniel A; Dileep, Vishnu; Baslan, Timour; Gilbert, David MCurrent protocols2022 Jan34986273
Single-Cell Multiomics Integration by SCOT.Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, RitambharaJournal of computational biology : a journal of computational molecular cell biology2022 0134985990
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 JBioinformatics (Oxford, England)2022 Mar 041729-173134978573
Stress as a Chromatin Landscape Architect.Vertii, AnastassiiaFrontiers in cell and developmental biology202134970548
Integrative approaches in genome structure analysis.Structure (London, England : 1993)2022 01 0634963059
Epigenome rewiring in human pluripotent stem cells.Yan, Jielin; Huangfu, DanweiTrends in cell biology2021 Dec 2334955367
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, CaroProceedings of the National Academy of Sciences of the United States of America2021 12 2134921112
Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system.Pourmorady, Ariel; Lomvardas, StavrosCurrent opinion in genetics & development2022 0234896807
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, KevinNature methods2021 1234862503
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 methods2021 1234862501
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,Nature2021 1134789882
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; SandNature communications2021 11 1734789735
Light activation and deactivation of Cas9 for DNA repair studies.Zou, Roger S; Ha, TaekjipMethods in enzymology202134776214
Trading bits in the readout from a genetic network.Bauer, Marianne; Petkova, Mariela D; Gregor, Thomas; Wieschaus, Eric F; Bialek, WilliamProceedings of the National Academy of Sciences of the United States of America2021 11 1634772813
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, JameScience immunology2021 11 1234767455
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, MitchellCell2021 11 1134739832
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, ToshioeLife2021 Nov 0434734806
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, NathanNature communications2021 11 0334732726
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 MNature methods2021 1234654919
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, LinCell2021 10 2834644528
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, StefanieNature methods2021 1234635849
Multiscale and integrative single-cell Hi-C analysis with Higashi.Zhang, Ruochi; Zhou, Tianming; Ma, JianNature biotechnology2021 Oct 1134635838
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, BerndNature communications2021 10 1134635658
Jointly Embedding Multiple Single-Cell Omics Measurements.Liu, Jie; Huang, Yuanhao; Singh, Ritambhara; Vert, Jean-Philippe; Noble, William StaffordAlgorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)2019 Sep 0334632462
Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction.Eeftens, Jorine M; Kapoor, Manya; Michieletto, Davide; Brangwynne, Clifford PNature communications2021 10 0734620850
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, QiaNature genetics2021 Oct34611363
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.L'Yi, Sehi; Wang, Qianwen; Lekschas, Fritz; Gehlenborg, NilsIEEE transactions on visualization and computer graphics2022 0134596551
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, LongScience (New York, N.Y.)2021 10 2934591592
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 MGenome biology2021 09 2734579774
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, YunCurrent issues in molecular biology2021 Sep 1734563051
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 CNature methods2021 Sep 2134548656
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 XJournal of lipid research2021 Sep 2034547287
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 advances2021 Sep 1734524848
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 DMolecular cell2021 11 0434520723
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.Mirny, Leonid; Dekker, JobCold Spring Harbor perspectives in biology2022 07 0134518339
Enhanced Cas12a multi-gene regulation using a CRISPR array separator.Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei SeLife2021 09 0934499031
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, MingHGG advances2021 Jul 0834485947
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 CNature methods2021 0934480155
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 methods2021 0934480151
The 3D Genome Structure of Single Cells.Zhou, Tianming; Zhang, Ruochi; Ma, JianAnnual review of biomedical data science2021 07 2034465168
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, MingNature methods2021 0934446921
Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9.Gao, Yuchen; Han, Mengting; Shang, Stephen; Wang, Haifeng; Qi, Lei SMolecular cell2021 Aug 1334428454
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, MitchellNature biotechnology2021 Aug 2334426703
Analysis of Hi-C Data for Discovery of Structural Variations in Cancer.Song, Fan; Xu, Jie; Dixon, Jesse; Yue, FengMethods in molecular biology (Clifton, N.J.)202234415534
Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture.Belmont, Andrew SCold Spring Harbor perspectives in biology2022 Jul 0134400557
Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Yildirim, Asli; Boninsegna, Lorenzo; Zhan, Yuxiang; Alber, FrankCold Spring Harbor perspectives in biology2021 Aug 1634400556
X-factors in human disease: impact of gene content and dosage regulation.Fang, He; Deng, Xinxian; Disteche, Christine MHuman molecular genetics2021 Oct 0134387327
Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, BingMethods in molecular biology (Clifton, N.J.)202134382190
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 cell2021 08 1934375583
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, HarryAmerican journal of respiratory cell and molecular biology2022 0134370624
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, ArjunCell systems2021 Sep 2234352221
Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning.Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, HanspeterComputer graphics forum : journal of the European Association for Computer Graphics2020 Jun34334852
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, WenbobioRxiv : the preprint server for biology2021 Jul 2134312624
DNA-loop-extruding SMC complexes can traverse one another in vivo.Brandão, Hugo B; Ren, Zhongqing; Karaboja, Xheni; Mirny, Leonid A; Wang, XindanNature structural & molecular biology2021 0834312537
CRISPRi/a Screening with Human iPSCs.Nishiga, Masataka; Qi, Lei S; Wu, Joseph CMethods in molecular biology (Clifton, N.J.)202134302664
Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan HCurrent protocols2021 Jul34286910
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 MBiochemical Society transactions2021 08 2734282837
High-resolution, genome-wide mapping of positive supercoiling in chromosomes.Guo, Monica S; Kawamura, Ryo; Littlehale, Megan L; Marko, John F; Laub, Michael TeLife2021 07 1934279217
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, BoGenomics, proteomics & bioinformatics2021 Jul 1434273560
Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin.Zhang, Yaojun; Lee, Daniel S W; Meir, Yigal; Brangwynne, Clifford P; Wingreen, Ned SPhysical review letters2021 Jun 2534241518
How subtle changes in 3D structure can create large changes in transcription.Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair NeLife2021 07 0934240703
The Impact of Space and Time on the Functional Output of the Genome.Nollmann, Marcelo; Bennabi, Isma; Götz, Markus; Gregor, ThomasCold Spring Harbor perspectives in biology2021 Jul 0634230036
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, RolandJournal of microscopy2021 1034214188
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, ColeScience (New York, N.Y.)2021 07 0234210887
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, JanMolecular biology of the cell2021 08 1534191541
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 SbioRxiv : the preprint server for biology2021 Jun 0934127974
Imaging Organization of RNA Processing within the Nucleus.Biswas, Jeetayu; Li, Weihan; Singer, Robert H; Coleman, Robert ACold Spring Harbor perspectives in biology2021 12 0134127450
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 MCell2021 Jul 0834115980
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, JianQuantitative biology (Beijing, China)2019 Jun34113473
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, WenboCell research2021 Jun 0934108665
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; StepeLife2021 06 0934106828
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 NNature communications2021 06 0834103507
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 SNature communications2021 06 0734099725
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 neuroscience2021 0834059832
Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies.Scourzic, Laurianne; Salataj, Eralda; Apostolou, EffieFrontiers in immunology202134054841
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 HScience (New York, N.Y.)2021 05 2834045355
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, MiNature2021 May 2634040254
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; StrNature methods2021 May 2134021280
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, HelNature methods2021 1234021279
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, BoCommunications biology2021 May 2134021236
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, HuiminACS synthetic biology2021 06 1834006094
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; CoImmunity2021 May 1134004142
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, BingNature genetics2021 May 1734002095
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, DavidNature methods2021 Jun34002092
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; BerMed (New York, N.Y.)2021 May 1433969332
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, MarioNature methods2021 0533963348
Determination of complete chromosomal haplotypes by bulk DNA sequencing.Tourdot, Richard W; Brunette, Gregory J; Pinto, Ricardo A; Zhang, Cheng-ZhongGenome biology2021 May 0633957932
From integrative structural biology to cell biology.Sali, AndrejThe Journal of biological chemistry2021 Jan-Jun33957123
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 StaffordACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine2020 Sep33954299
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; HinsCell reports2021 May 0433951429
The Need for a Human Pangenome Reference Sequence.Miga, Karen H; Wang, TingAnnual review of genomics and human genetics2021 08 3133929893
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, KirankumarInternational journal of molecular sciences2021 Apr 2133919286
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator.Sanborn, Adrian L; Yeh, Benjamin T; Feigerle, Jordan T; Hao, Cynthia V; Townshend, Raphael Jl; Lieberman Aiden, Erez; Dror, Ron O; Kornberg, Roger DeLife2021 Apr 2733904398
Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue.Liu, Miao; Yang, Bing; Hu, Mengwei; Radda, Jonathan S D; Chen, Yanbo; Jin, Shengyan; Cheng, Yubao; Wang, SiyuanNature protocols2021 May33903756
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan JDevelopmental cell2021 May 0333891899
Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo.El-Nachef, Danny; Bugg, Darrian; Beussman, Kevin M; Steczina, Sonette; Martinson, Amy M; Murry, Charles E; Sniadecki, Nathan J; Davis, JenniferCirculation2021 04 2033872080
Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer.Iyyanki, Tejaswi; Zhang, Baozhen; Wang, Qixuan; Hou, Ye; Jin, Qiushi; Xu, Jie; Yang, Hongbo; Liu, Tingting; Wang, Xiaotao; Song, Fan; Luan, Yu; Yamashita, Hironobu; Chien, Ruby; Lyu, Huijue; Zhang, Lijun; Wang, Lu; Warrick, Joshua; Raman, Jay D; Meeks, Joshua J; DeGraff, David J; Yue, FengGenome biology2021 Apr 1533858483
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance.Schep, Ruben; Brinkman, Eva K; Leemans, Christ; Vergara, Xabier; van der Weide, Robin H; Morris, Ben; van Schaik, Tom; Manzo, Stefano G; Peric-Hupkes, Daniel; van den Berg, Jeroen; Beijersbergen, Roderick L; Medema, René H; van Steensel, BasMolecular cell2021 05 2033848455
Single-molecule micromanipulation studies of methylated DNA.Zaichuk, Tetiana; Marko, John FBiophysical journal2021 06 0133838135
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Zhu, Yanfen; Gujar, Amit D; Wong, Chee-Hong; Tjong, Harianto; Ngan, Chew Yee; Gong, Liang; Chen, Yi-An; Kim, Hoon; Liu, Jihe; Li, Meihong; Mil-Homens, Adam; Maurya, Rahul; Kuhlberg, Chris; Sun, Fanyue; Yi, Eunhee; deCarvalho, Ana C; Ruan, Yijun; Verhaak, Roel G W; Wei, Chia-LinCancer cell2021 May 1033836152
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.Markowski, Julia; Kempfer, Rieke; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Loof, Gesa; Kehr, Birte; Pombo, Ana; Rahmann, Sven; Schwarz, Roland FBioinformatics (Oxford, England)2021 Apr 0833830196
Genome-wide enhancer maps link risk variants to disease genes.Nasser, Joseph; Bergman, Drew T; Fulco, Charles P; Guckelberger, Philine; Doughty, Benjamin R; Patwardhan, Tejal A; Jones, Thouis R; Nguyen, Tung H; Ulirsch, Jacob C; Lekschas, Fritz; Mualim, Kristy; Natri, Heini M; Weeks, Elle M; Munson, Glen; Kane, MichNature2021 0533828297
p53 mediates target gene association with nuclear speckles for amplified RNA expression.Alexander, Katherine A; Coté, Allison; Nguyen, Son C; Zhang, Liguo; Gholamalamdari, Omid; Agudelo-Garcia, Paula; Lin-Shiao, Enrique; Tanim, K M A; Lim, Joan; Biddle, Nicolas; Dunagin, Margaret C; Good, Charly R; Mendoza, Mariel R; Little, Shawn C; Belmont, Andrew; Joyce, Eric F; Raj, Arjun; Berger, Shelley LMolecular cell2021 04 1533823140
Interrogating immune cells and cancer with CRISPR-Cas9.Buquicchio, Frank A; Satpathy, Ansuman TTrends in immunology2021 0533812776
Phase separation in genome organization across evolution.Feric, Marina; Misteli, TomTrends in cell biology2021 0833771451
Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention.Hogan, Ann K; Foltz, Daniel RMolecular and cellular biology2021 05 2133753462
See(quence) and ye shall find: higher-order genome folding in intact single cells.Pham, Kenneth; Nikish, Alexandria; Phillips-Cremins, Jennifer EMolecular cell2021 03 1833740473
Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation.Makhija, Suraj; Brown, David; Rudlaff, Rachel M; Doh, Julia K; Bourke, Struan; Wang, Yina; Zhou, Shuqin; Cheloor-Kovilakam, Rasmi; Huang, BoACS chemical biology2021 04 1633734687
RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Bertero, AlessandroFrontiers in genetics202133732290
Toward a Three-Dimensional Chromosome Shape Alphabet.Soto, Carlos; Bryner, Darshan; Neretti, Nicola; Srivastava, AnujJournal of computational biology : a journal of computational molecular cell biology2021 0633720766
Properties of repression condensates in living Ciona embryos.Treen, Nicholas; Shimobayashi, Shunsuke F; Eeftens, Jorine; Brangwynne, Clifford P; Levine, MichaelNature communications2021 03 1033692345
Cas9 deactivation with photocleavable guide RNAs.Zou, Roger S; Liu, Yang; Wu, Bin; Ha, TaekjipMolecular cell2021 04 0133662274
Genome oligopaint via local denaturation fluorescence in situ hybridization.Wang, Yanbo; Cottle, Wayne Taylor; Wang, Haobo; Feng, Xinyu Ashlee; Mallon, John; Gavrilov, Momcilo; Bailey, Scott; Ha, TaekjipMolecular cell2021 04 0133657402
Heterogeneity of fetal hemoglobin production in adult red blood cells.Khandros, Eugene; Blobel, Gerd ACurrent opinion in hematology2021 05 0133631783
Variability within rare cell states enables multiple paths toward drug resistance.Emert, Benjamin L; Cote, Christopher J; Torre, Eduardo A; Dardani, Ian P; Jiang, Connie L; Jain, Naveen; Shaffer, Sydney M; Raj, ArjunNature biotechnology2021 Feb 2233619394
Direct supercritical angle localization microscopy for nanometer 3D superresolution.Dasgupta, Anindita; Deschamps, Joran; Matti, Ulf; Hübner, Uwe; Becker, Jan; Strauss, Sebastian; Jungmann, Ralf; Heintzmann, Rainer; Ries, JonasNature communications2021 02 1933608524
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies.Bokota, Grzegorz; Sroka, Jacek; Basu, Subhadip; Das, Nirmal; Trzaskoma, Pawel; Yushkevich, Yana; Grabowska, Agnieszka; Magalska, Adriana; Plewczynski, DariuszBMC bioinformatics2021 Feb 1733596823
Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration.Zhang, Meng; Yang, Che; Tasan, Ipek; Zhao, HuiminACS synthetic biology2021 03 1933596056
Disruption of nuclear architecture as a cause of COVID-19 induced anosmia.Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Fullard, John F; Shayya, Hani; Omer, Arina; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Roussos, Panos; tenOever, Benjamin R; Overdevest, Jonathan B; Lomvardas, StavrosbioRxiv : the preprint server for biology2021 Feb 0933594368
Physical mechanisms of chromatin spatial organization.Chiariello, Andrea M; Bianco, Simona; Esposito, Andrea; Fiorillo, Luca; Conte, Mattia; Irani, Ehsan; Musella, Francesco; Abraham, Alex; Prisco, Antonella; Nicodemi, MarioThe FEBS journal2022 0333583147
HiCRep.py : Fast comparison of Hi-C contact matrices in Python.Lin, Dejun; Sanders, Justin; Noble, William StaffordBioinformatics (Oxford, England)2021 02 1133576390
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.Belaghzal, Houda; Borrman, Tyler; Stephens, Andrew D; Lafontaine, Denis L; Venev, Sergey V; Weng, Zhiping; Marko, John F; Dekker, JobNature genetics2021 0333574602
Engineering 3D genome organization.Wang, Haifeng; Han, Mengting; Qi, Lei SNature reviews. Genetics2021 0633558716
HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test.Lagler, Taylor M; Abnousi, Armen; Hu, Ming; Yang, Yuchen; Li, YunAmerican journal of human genetics2021 02 0433545029
SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface.Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; BermedRxiv : the preprint server for health sciences2021 Jan 2633532791
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.Miko, Henriette; Qiu, Yunjiang; Gaertner, Bjoern; Sander, Maike; Ohler, UweBMC genomics2021 Jan 2833509077
Integrated spatial genomics reveals global architecture of single nuclei.Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, LongNature2021 0233505024
TALEN outperforms Cas9 in editing heterochromatin target sites.Jain, Surbhi; Shukla, Saurabh; Yang, Che; Zhang, Meng; Fatma, Zia; Lingamaneni, Manasi; Abesteh, Shireen; Lane, Stephan Thomas; Xiong, Xiong; Wang, Yuchuan; Schroeder, Charles M; Selvin, Paul R; Zhao, HuiminNature communications2021 01 2733504770
Determining of canine position by multiple facial landmarks to achieve natural esthetics in complete denture treatment.Srimaneekarn, Natchalee; Arayapisit, Tawepong; Pooktuantong, Ornnicha; Cheng, Holland R; Soonsawad, PanThe Journal of prosthetic dentistry2021 Jan 1633468316
Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors.Vahedi, GolnazImmunological reviews2021 Mar33452686
Resources and challenges for integrative analysis of nuclear architecture data.Jung, Youngsook L; Kirli, Koray; Alver, Burak H; Park, Peter JCurrent opinion in genetics & development2021 Apr33450522
SPIN reveals genome-wide landscape of nuclear compartmentalization.Wang, Yuchuan; Zhang, Yang; Zhang, Ruochi; van Schaik, Tom; Zhang, Liguo; Sasaki, Takayo; Peric-Hupkes, Daniel; Chen, Yu; Gilbert, David M; van Steensel, Bas; Belmont, Andrew S; Ma, JianGenome biology2021 Jan 1433446254
The dynamics of chromatin architecture in brain development and function.Harabula, Izabela; Pombo, AnaCurrent opinion in genetics & development2021 0433421764
CRISPR technologies for precise epigenome editing.Nakamura, Muneaki; Gao, Yuchen; Dominguez, Antonia A; Qi, Lei SNature cell biology2021 Jan33420494
Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression.Rosa-Mercado, Nicolle A; Zimmer, Joshua T; Apostolidi, Maria; Rinehart, Jesse; Simon, Matthew D; Steitz, Joan AMolecular cell2021 02 0433400923
Genetic screening for single-cell variability modulators driving therapy resistance.Torre, Eduardo A; Arai, Eri; Bayatpour, Sareh; Jiang, Connie L; Beck, Lauren E; Emert, Benjamin L; Shaffer, Sydney M; Mellis, Ian A; Fane, Mitchell E; Alicea, Gretchen M; Budinich, Krista A; Weeraratna, Ashani T; Shi, Junwei; Raj, ArjunNature genetics2021 0133398196
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.Kubo, Naoki; Ishii, Haruhiko; Xiong, Xiong; Bianco, Simona; Meitinger, Franz; Hu, Rong; Hocker, James D; Conte, Mattia; Gorkin, David; Yu, Miao; Li, Bin; Dixon, Jesse R; Hu, Ming; Nicodemi, Mario; Zhao, Huimin; Ren, BingNature structural & molecular biology2021 Feb33398174
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.Zhang, Liguo; Zhang, Yang; Chen, Yu; Gholamalamdari, Omid; Wang, Yuchuan; Ma, Jian; Belmont, Andrew SGenome research2020 Dec 1833355299
Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.Shao, Wanqing; Wang, TingGenome research2021 Jan33355230
Implementation of a 4Pi-SMS super-resolution microscope.Wang, Jingyu; Allgeyer, Edward S; Sirinakis, George; Zhang, Yongdeng; Hu, Kevin; Lessard, Mark D; Li, Yiming; Diekmann, Robin; Phillips, Michael A; Dobbie, Ian M; Ries, Jonas; Booth, Martin J; Bewersdorf, JoergNature protocols2021 0233328610
ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization.Hu, Mengwei; Yang, Bing; Cheng, Yubao; Radda, Jonathan S D; Chen, Yanbo; Liu, Miao; Wang, SiyuanScientific reports2020 12 1633328483
Generalized multi-SNP mediation intersection-union test.Zhong, Wujuan; Darville, Toni; Zheng, Xiaojing; Fine, Jason; Li, YunBiometrics2022 Mar33316078
Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries.Bizhanova, Aizhan; Kaufman, Paul DBiochimica et biophysica acta. Gene regulatory mechanisms.2020 Dec 08;33307247
Epigenomic differences in the human and chimpanzee genomes are associated with structural variation.Zhuo, Xiaoyu; Du, Alan Y; Pehrsson, Erica C; Li, Daofeng; Wang, TingGenome research2020 Dec 1033303495
The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine.Serrano, Diego; Cordero, Gustavo; Kawamura, Ryo; Sverzhinsky, Aleksandr; Sarker, Muzaddid; Roy, Shamayita; Malo, Catherine; Pascal, John M; Marko, John F; D'Amours, DamienMolecular cell2020 12 1733301731
The interplay between asymmetric and symmetric DNA loop extrusion.Banigan, Edward J; Mirny, Leonid AeLife2020 12 0933295869
Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription.Feng, Ying; Wang, Yao; Wang, Xiangnan; He, Xiaohui; Yang, Chen; Naseri, Ardalan; Pederson, Thoru; Zheng, Jing; Zhang, Shaojie; Xiao, Xiao; Xie, Wei; Ma, HanhuiGenome biology2020 12 0833292531
Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals.Sanford, Eric M; Emert, Benjamin L; Coté, Allison; Raj, ArjuneLife2020 12 0733284110
Genome architecture and expression 2019-2020: the transition phase.Pederson, ThoruCurrent opinion in genetics & development2021 0433279815
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome.Fang, He; Bonora, Giancarlo; Lewandowski, Jordan P; Thakur, Jitendra; Filippova, Galina N; Henikoff, Steven; Shendure, Jay; Duan, Zhijun; Rinn, John L; Deng, Xinxian; Noble, William S; Disteche, Christine MNature communications2020 11 2733247132
Three-dimensional chromatin organization in cardiac development and disease.Bertero, Alessandro; Rosa-Garrido, ManuelJournal of molecular and cellular cardiology2021 0233242466
A map of cis-regulatory elements and 3D genome structures in zebrafish.Yang, Hongbo; Luan, Yu; Liu, Tingting; Lee, Hyung Joo; Fang, Li; Wang, Yanli; Wang, Xiaotao; Zhang, Bo; Jin, Qiushi; Ang, Khai Chung; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Sriranga, Iyyanki; Khunsriraksakul, Chachrit; Salameh, Tarik; Li, Daofeng;Nature.2020 Dec;33239788
Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors.Wu, Jun; Krchma, Karen; Lee, Hyung Joo; Prabhakar, Sairam; Wang, Xiaoli; Zhao, Haiyong; Xing, Xiaoyun; Seong, Rho H; Fremont, Daved H; Artyomov, Maxim N; Wang, Ting; Choi, KyungheeCell reports.2020 Nov 17;33207205
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus.Ma, Jingwei; Do, Myan; Le Gros, Mark A; Peskin, Charles S; Larabell, Carolyn A; Mori, Yoichiro; Isaacson, Samuel APLoS computational biology2020 1133196636
X-chromosome regulation and sex differences in brain anatomy.Raznahan, Armin; Disteche, Christine MNeuroscience and biobehavioral reviews2021 0133171144
Molecular basis of CTCF binding polarity in genome folding.Nora, Elphège P; Caccianini, Laura; Fudenberg, Geoffrey; So, Kevin; Kameswaran, Vasumathi; Nagle, Abigail; Uebersohn, Alec; Hajj, Bassam; Saux, Agnès Le; Coulon, Antoine; Mirny, Leonid A; Pollard, Katherine S; Dahan, Maxime; Bruneau, Benoit GNature communications2020 11 0533154377
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data.Jain, Dhawal; Chu, Chong; Alver, Burak Han; Lee, Soohyun; Lee, Eunjung Alice; Park, Peter JBioinformatics (Oxford, England)2021 05 2333136153
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses.Banerjee, Abhik K; Blanco, Mario R; Bruce, Emily A; Honson, Drew D; Chen, Linlin M; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A; Loney, Colin; Thai, Jasmine; Miller, Zachary D; Lin, Aaron E; Schmidt, Madaline M; Stewart, Douglas G; GoldCell.2020 11 25;33080218
Stress-induced RNA-chromatin interactions promote endothelial dysfunction.Calandrelli, Riccardo; Xu, Lixia; Luo, Yingjun; Wu, Weixin; Fan, Xiaochen; Nguyen, Tri; Chen, Chien-Ju; Sriram, Kiran; Tang, Xiaofang; Burns, Andrew B; Natarajan, Rama; Chen, Zhen Bouman; Zhong, ShengNature communications.2020 10 15;33060583
EMU: reconfigurable graphical user interfaces for Micro-Manager.Deschamps, Joran; Ries, JonasBMC bioinformatics.2020 Oct 15;33059591
Cell-type-specific 3D epigenomes in the developing human cortex.Song, Michael; Pebworth, Mark-Phillip; Yang, Xiaoyu; Abnousi, Armen; Fan, Changxu; Wen, Jia; Rosen, Jonathan D; Choudhary, Mayank N K; Cui, Xiekui; Jones, Ian R; Bergenholtz, Seth; Eze, Ugomma C; Juric, Ivan; Li, Bingkun; Maliskova, Lenka; Lee, Jerry; LiuNature.2020 Oct 14;33057195
Exploring chromosomal structural heterogeneity across multiple cell lines.Cheng, Ryan R; Contessoto, Vinicius G; Lieberman Aiden, Erez; Wolynes, Peter G; Di Pierro, Michele; Onuchic, Jose NeLife.2020 Oct 13;33047670
Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.Desai, Parth Rakesh; Brahmachari, Sumitabha; Marko, John F; Das, Siddhartha; Neuman, Keir CNucleic acids research.2020 11 04;33045724
A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling.Lekschas, Fritz; Zhou, Xinyi; Chen, Wei; Gehlenborg, Nils; Bach, Benjamin; Pfister, HanspeterIEEE transactions on visualization and computer graphics2021 0233026994
Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization.Biggs, Ronald J; Liu, Ning; Peng, Yiheng; Marko, John F; Qiao, HuanyuCommunications biology.2020 Sep 30;32999386
High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.Vangala, Pranitha; Murphy, Rachel; Quinodoz, Sofia A; Gellatly, Kyle; McDonel, Patrick; Guttman, Mitchell; Garber, ManuelMolecular cell.2020 10 15;32991830
TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data.Van Buren, Eric; Hu, Ming; Weng, Chen; Jin, Fulai; Li, Yan; Wu, Di; Li, YunGenetic epidemiology.2020 Sep 29;32989764
Tissue-specific usage of transposable element-derived promoters in mouse development.Miao, Benpeng; Fu, Shuhua; Lyu, Cheng; Gontarz, Paul; Wang, Ting; Zhang, BoGenome biology.2020 Sep 28;32988383
Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone.Lewis, James J; Van Belleghem, Steven M; Papa, Riccardo; Danko, Charles G; Reed, Robert DScience advances.2020 Sep;32978147
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.Kim, Hyeon-Jin; Yard?mc?, Galip Gürkan; Bonora, Giancarlo; Ramani, Vijay; Liu, Jie; Qiu, Ruolan; Lee, Choli; Hesson, Jennifer; Ware, Carol B; Shendure, Jay; Duan, Zhijun; Noble, William StaffordPLoS computational biology.2020 09;32946435
The qBED track: a novel genome browser visualization for point processes.Moudgil, Arnav; Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Wang, Ting; Mitra, Robi DBioinformatics (Oxford, England).2020 Sep 17;32941613
DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods.He, Yu; Jang, Hyo Sik; Xing, Xiaoyun; Li, Daofeng; Vasek, Michael J; Dougherty, Joseph D; Wang, TingScience advances.2020 Jul;32937429
Multi-contact 3C reveals that the human genome during interphase is largely not entangled.Tavares-Cadete, Filipe; Norouzi, Davood; Dekker, Bastiaan; Liu, Yu; Dekker, JobNature structural & molecular biology.2020 Sep 14;32929283
Nucleated transcriptional condensates amplify gene expression.Wei, Ming-Tzo; Chang, Yi-Che; Shimobayashi, Shunsuke F; Shin, Yongdae; Strom, Amy R; Brangwynne, Clifford PNature cell biology.2020 Oct;32929202
NuSeT: A deep learning tool for reliably separating and analyzing crowded cells.Yang, Linfeng; Ghosh, Rajarshi P; Franklin, J Matthew; Chen, Simon; You, Chenyu; Narayan, Raja R; Melcher, Marc L; Liphardt, Jan TPLoS computational biology.2020 09;32925919
Concerted localization-resets precede YAP-dependent transcription.Franklin, J Matthew; Ghosh, Rajarshi P; Shi, Quanming; Reddick, Michael P; Liphardt, Jan TNature communications.2020 09 11;32917893
Exploring the coronavirus pandemic with the WashU Virus Genome Browser.Flynn, Jennifer A; Purushotham, Deepak; Choudhary, Mayank N K; Zhuo, Xiaoyu; Fan, Changxu; Matt, Gavriel; Li, Daofeng; Wang, TingNature genetics.2020 10;32908257
Cell cycle dynamics of lamina-associated DNA.van Schaik, Tom; Vos, Mabel; Peric-Hupkes, Daan; Hn Celie, Patrick; van Steensel, BasEMBO reports.2020 Nov 05;32893442
The nucleolus as a multiphase liquid condensate.Lafontaine, Denis L J; Riback, Joshua A; Bascetin, Rümeyza; Brangwynne, Clifford PNature reviews. Molecular cell biology2021 0332873929
Alteration of genome folding via contact domain boundary insertion.Zhang, Di; Huang, Peng; Sharma, Malini; Keller, Cheryl A; Giardine, Belinda; Zhang, Haoyue; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E; Hardison, Ross C; Blobel, Gerd ANature genetics.2020 Aug 31;32868908
3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.Fernandez, Lindsey R; Gilgenast, Thomas G; Phillips-Cremins, Jennifer EGenome biology.2020 Aug 28;32859248
Cellular diversity of the regenerating caudal fin.Hou, Yiran; Lee, Hyung Joo; Chen, Yujie; Ge, Jiaxin; Osman, Fujr Osman Ibrahim; McAdow, Anthony R; Mokalled, Mayssa H; Johnson, Stephen L; Zhao, Guoyan; Wang, TingScience advances.2020 Aug;32851162
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.Lee, Byoungkoo; Wang, Jiahui; Cai, Liuyang; Kim, Minji; Namburi, Sandeep; Tjong, Harianto; Feng, Yuliang; Wang, Ping; Tang, Zhonghui; Abbas, Ahmed; Wei, Chia-Lin; Ruan, Yijun; Li, ShengScience advances2020 0732832596
Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells.Tasan, Ipek; Su, Christina Jean; Enghiad, Behnam; Zhang, Meng; Mishra, Shekhar; Zhao, HuiminACS synthetic biology.2020 09 18;32822529
Targeted DNase Hi-C.Duan, ZhijunMethods in molecular biology (Clifton, N.J.).2021;32820399
Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments.Chen, Zhijie; Shaw, Alan; Wilson, Hugh; Woringer, Maxime; Darzacq, Xavier; Marqusee, Susan; Wang, Quan; Bustamante, CarlosProceedings of the National Academy of Sciences of the United States of America.2020 Sep 01;32817484
Optimizing imaging speed and excitation intensity for single-molecule localization microscopy.Diekmann, Robin; Kahnwald, Maurice; Schoenit, Andreas; Deschamps, Joran; Matti, Ulf; Ries, JonasNature methods.2020 Sep;32807954
Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors.Shaffer, Sydney M; Emert, Benjamin L; Reyes Hueros, Raúl A; Cote, Christopher; Harmange, Guillaume; Schaff, Dylan L; Sizemore, Ann E; Gupte, Rohit; Torre, Eduardo; Singh, Abhyudai; Bassett, Danielle S; Raj, ArjunCell.2020 Aug 20;32735851
An integrative ENCODE resource for cancer genomics.Zhang, Jing; Lee, Donghoon; Dhiman, Vineet; Jiang, Peng; Xu, Jie; McGillivray, Patrick; Yang, Hongbo; Liu, Jason; Meyerson, William; Clarke, Declan; Gu, Mengting; Li, Shantao; Lou, Shaoke; Xu, Jinrui; Lochovsky, Lucas; Ung, Matthew; Ma, Lijia; Yu, Shan; CNature communications.2020 07 29;32728046
Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos.Chen, Hongtao; Gregor, ThomasMethods in molecular biology (Clifton, N.J.)202032710421
Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.Lei, Xiao; Zhao, Jun; Sagendorf, Jared M; Rajashekar, Niroop; Xu, Jiang; Dantas Machado, Ana Carolina; Sen, Chandani; Rohs, Remo; Feng, Pinghui; Chen, LinJournal of molecular biology2020 09 0432681840
MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing.Biswas, Jeetayu; Rahman, Reazur; Gupta, Varun; Rosbash, Michael; Singer, Robert HiScience.2020 Jul 24;32674054
A supervised learning framework for chromatin loop detection in genome-wide contact maps.Salameh, Tarik J; Wang, Xiaotao; Song, Fan; Zhang, Bo; Wright, Sage M; Khunsriraksakul, Chachrit; Ruan, Yijun; Yue, FengNature communications.2020 Jul 09;32647330
Free energy-based model of CTCF-mediated chromatin looping in the human genome.Dawson, Wayne K; Lazniewski, Michal; Plewczynski, DariuszMethods (San Diego, Calif.).2020 10 01;32645447
Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation.Conte, Mattia; Fiorillo, Luca; Bianco, Simona; Chiariello, Andrea M; Esposito, Andrea; Nicodemi, MarioNature communications.2020 07 03;32620890
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human.Liu, Shuli; Yu, Ying; Zhang, Shengli; Cole, John B; Tenesa, Albert; Wang, Ting; McDaneld, Tara G; Ma, Li; Liu, George E; Fang, LingzhaoBMC biology.2020 Jul 03;32620158
A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives.El-Nachef, Danny; Shi, Kevin; Beussman, Kevin M; Martinez, Refugio; Regier, Mary C; Everett, Guy W; Murry, Charles E; Stevens, Kelly R; Young, Jessica E; Sniadecki, Nathan J; Davis, JenniferStem cell reports.2020 07 14;32619493
The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells.Wang, Alan S; Chen, Leo C; Wu, R Alex; Hao, Yvonne; McSwiggen, David T; Heckert, Alec B; Richardson, Christopher D; Gowen, Benjamin G; Kazane, Katelynn R; Vu, Jonathan T; Wyman, Stacia K; Shin, Jiyung J; Darzacq, Xavier; Walter, Johannes C; Corn, Jacob EMolecular cell.2020 07 16;32603710
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data.Chen, Xiaoying; Zhang, Bo; Wang, Ting; Bonni, Azad; Zhao, GuoyanBMC bioinformatics.2020 Jun 29;32600248
Single-molecule imaging of transcription dynamics in somatic stem cells.Wheat, Justin C; Sella, Yehonatan; Willcockson, Michael; Skoultchi, Arthur I; Bergman, Aviv; Singer, Robert H; Steidl, UlrichNature.2020 07;32581360
Comparison of differential accessibility analysis strategies for ATAC-seq data.Gontarz, Paul; Fu, Shuhua; Xing, Xiaoyun; Liu, Shaopeng; Miao, Benpeng; Bazylianska, Viktoriia; Sharma, Akhil; Madden, Pamela; Cates, Kitra; Yoo, Andrew; Moszczynska, Anna; Wang, Ting; Zhang, BoScientific reports.2020 Jun 23;32576878
Long Noncoding RNAs: Molecular Modalities to Organismal Functions.Rinn, John L; Chang, Howard YAnnual review of biochemistry.2020 06 20;32569523
MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.Zhang, Ruochi; Ma, JianCell systems.2020 May 20;32550271
Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation.Strehle, Mackenzie; Guttman, MitchellCurrent opinion in cell biology.2020 06;32535328
Loop extrusion: theory meets single-molecule experiments.Banigan, Edward J; Mirny, Leonid ACurrent opinion in cell biology.2020 06;32534241
Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy.Liu, Chia-Feng; Abnousi, Armen; Bazeley, Peter; Ni, Ying; Morley, Michael; Moravec, Christine S; Hu, Ming; Tang, W H WilsonJournal of molecular and cellular cardiology2020 0832533974
Biosystems Design by Machine Learning.Volk, Michael Jeffrey; Lourentzou, Ismini; Mishra, Shekhar; Vo, Lam Tung; Zhai, Chengxiang; Zhao, HuiminACS synthetic biology.2020 07 17;32485108
Evolving methodologies and concepts in 4D nucleome research.Sparks, Thomas M; Harabula, Izabela; Pombo, AnaCurrent opinion in cell biology.2020 May 27;32473574
Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression.Beagan, Jonathan A; Pastuzyn, Elissa D; Fernandez, Lindsey R; Guo, Michael H; Feng, Kelly; Titus, Katelyn R; Chandrashekar, Harshini; Shepherd, Jason D; Phillips-Cremins, Jennifer ENature neuroscience.2020 06;32451484
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.Wlasnowolski, Michal; Sadowski, Michal; Czarnota, Tymon; Jodkowska, Karolina; Szalaj, Przemyslaw; Tang, Zhonghui; Ruan, Yijun; Plewczynski, DariuszNucleic acids research.2020 07 02;32442297
Delta-1 Functionalized Hydrogel Promotes hESC-Cardiomyocyte Graft Proliferation and Maintains Heart Function Post-Injury.Gerbin, Kaytlyn A; Mitzelfelt, Katie A; Guan, Xuan; Martinson, Amy M; Murry, Charles EMolecular therapy. Methods & clinical development.2020 Jun 12;32426414
Histone Signatures Predict Therapeutic Efficacy in Breast Cancer.Mollah, Shamim A; Subramaniam, ShankarIEEE open journal of engineering in medicine and biology202032412527
Composition-dependent thermodynamics of intracellular phase separation.Riback, Joshua A; Zhu, Lian; Ferrolino, Mylene C; Tolbert, Michele; Mitrea, Diana M; Sanders, David W; Wei, Ming-Tzo; Kriwacki, Richard W; Brangwynne, Clifford PNature.2020 05;32405004
Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia.Wang, Ping; Tang, Zhonghui; Lee, Byoungkoo; Zhu, Jacqueline Jufen; Cai, Liuyang; Szalaj, Przemyslaw; Tian, Simon Zhongyuan; Zheng, Meizhen; Plewczynski, Dariusz; Ruan, Xiaoan; Liu, Edison T; Wei, Chia-Lin; Ruan, YijunGenome biology2020 05 1132393309
Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.Zhang, Xiaotian; Jeong, Mira; Huang, Xingfan; Wang, Xue Qing; Wang, Xinyu; Zhou, Wanding; Shamim, Muhammad S; Gore, Haley; Himadewi, Pamela; Liu, Yushuai; Bochkov, Ivan D; Reyes, Jaime; Doty, Madison; Huang, Yung-Hsin; Jung, Haiyoung; Heikamp, Emily; AideMolecular cell.2020 05 07;32386543
Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.Trzaskoma, Pawe?; Ruszczycki, B?a?ej; Lee, Byoungkoo; Pels, Katarzyna K; Krawczyk, Katarzyna; Bokota, Grzegorz; Szczepankiewicz, Andrzej A; Aaron, Jesse; Walczak, Agnieszka; ?liwi?ska, Ma?gorzata A; Magalska, Adriana; Kadlof, Michal; Wolny, Artur; PartekaNature communications.2020 05 01;32358536
The gene-rich genome of the scallop Pecten maximus.Kenny, Nathan J; McCarthy, Shane A; Dudchenko, Olga; James, Katherine; Betteridge, Emma; Corton, Craig; Dolucan, Jale; Mead, Dan; Oliver, Karen; Omer, Arina D; Pelan, Sarah; Ryan, Yan; Sims, Ying; Skelton, Jason; Smith, Michelle; Torrance, James; Weisz, DGigaScience2020 05 0132352532
Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer.Schuh, Lea; Saint-Antoine, Michael; Sanford, Eric M; Emert, Benjamin L; Singh, Abhyudai; Marr, Carsten; Raj, Arjun; Goyal, YogeshCell systems.2020 Apr 22;32325034
Chromatin Viscoelasticity Measured by Local Dynamic Analysis.Vivante, Anat; Bronshtein, Irena; Garini, YuvalBiophysical journal.2020 05 05;32320676
Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization.Sanders, David W; Kedersha, Nancy; Lee, Daniel S W; Strom, Amy R; Drake, Victoria; Riback, Joshua A; Bracha, Dan; Eeftens, Jorine M; Iwanicki, Allana; Wang, Alicia; Wei, Ming-Tzo; Whitney, Gena; Lyons, Shawn M; Anderson, Paul; Jacobs, William M; Ivanov, PCell.2020 04 16;32302570
Sci-fate characterizes the dynamics of gene expression in single cells.Cao, Junyue; Zhou, Wei; Steemers, Frank; Trapnell, Cole; Shendure, JayNature biotechnology.2020 Aug;32284584
Chromosome organization by one-sided and two-sided loop extrusion.Banigan, Edward J; van den Berg, Aafke A; Brandão, Hugo B; Marko, John F; Mirny, Leonid AeLife2020 04 0632250245
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C.Field, Matt A; Rosen, Benjamin D; Dudchenko, Olga; Chan, Eva K F; Minoche, Andre E; Edwards, Richard J; Barton, Kirston; Lyons, Ruth J; Tuipulotu, Daniel Enosi; Hayes, Vanessa M; D Omer, Arina; Colaric, Zane; Keilwagen, Jens; Skvortsova, Ksenia; BogdanoviGigaScience.2020 04 01;32236524
Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome.Schreiber, Jacob; Durham, Timothy; Bilmes, Jeffrey; Noble, William StaffordGenome biology.2020 03 30;32228704
Distinct features of nucleolus-associated domains in mouse embryonic stem cells.Bizhanova, Aizhan; Yan, Aimin; Yu, Jun; Zhu, Lihua Julie; Kaufman, Paul DChromosoma.2020 Mar 26;32219510
Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit.Zhao, Binhui; Chaturvedi, Pankaj; Zimmerman, David L; Belmont, Andrew SACS synthetic biology.2020 05 15;32216371
Ultrastructural Details of Mammalian Chromosome Architecture.Krietenstein, Nils; Abraham, Sameer; Venev, Sergey V; Abdennur, Nezar; Gibcus, Johan; Hsieh, Tsung-Han S; Parsi, Krishna Mohan; Yang, Liyan; Maehr, René; Mirny, Leonid A; Dekker, Job; Rando, Oliver JMolecular cell.2020 Mar 14;32213324
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.Hsieh, Tsung-Han S; Cattoglio, Claudia; Slobodyanyuk, Elena; Hansen, Anders S; Rando, Oliver J; Tjian, Robert; Darzacq, XavierMolecular cell.2020 05 07;32213323
High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.Zhao, Peiyao A; Sasaki, Takayo; Gilbert, David MGenome biology.2020 03 24;32209126
Cost-efficient open source laser engine for microscopy.Schröder, Daniel; Deschamps, Joran; Dasgupta, Anindita; Matti, Ulf; Ries, JonasBiomedical optics express.2020 Feb 01;32206389
Evaluating Enhancer Function and Transcription.Field, Andrew; Adelman, KarenAnnual review of biochemistry.2020 06 20;32197056
Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.Sato, Hanae; Das, Sulagna; Singer, Robert H; Vera, MariaAnnual review of biochemistry.2020 06 20;32176523
The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process.Urban, Paulina; Rezaei Tabar, Vahid; Denkiewicz, Michał; Bokota, Grzegorz; Das, Nirmal; Basu, Subhadip; Plewczynski, DariuszJournal of computational biology : a journal of computational molecular cell biology2020 0932175768
Advanced 3D Analysis and Optimization of Single-Molecule FISH in Drosophila Muscle.Noma, Akiko; Smith, Carlas S; Huisman, Maximiliaan; Martin, Robert M; Moore, Melissa J; Grunwald, DavidSmall methods.2018 Sep 11;32158910
Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems.Masnadi-Shirazi, Maryam; Subramaniam, ShankarScientific reports.2020 Mar 02;32123218
Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility.Lee, Hyung Joo; Hou, Yiran; Chen, Yujie; Dailey, Zea Z; Riddihough, Aiyana; Jang, Hyo Sik; Wang, Ting; Johnson, Stephen LGenome biology.2020 02 27;32106888
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Wang, Wenbo; Goldfeder, Rachel L; Choi, Cindy; He, Hao; Gong, Liang; Lin, Junyan; Urban, Barbara; Chow, Julianna; Li, Meihong; Lim, Joanne; Philip, Vivek; Murray, Stephen A; Wang, Haoyi; Wei, Chia-LinNature genetics.2020 03;32094912
Therapeutic genome editing in cardiovascular diseases.Nishiga, Masataka; Qi, Lei S; Wu, Joseph CAdvanced drug delivery reviews.2020 Feb 21;32092381
Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation.Biswas, Jeetayu; Nunez, Leti; Das, Sulagna; Yoon, Young J; Eliscovich, Carolina; Singer, Robert HCold Spring Harbor symposia on quantitative biology.2020 Feb 21;32086331
Local rewiring of genome-nuclear lamina interactions by transcription.Brueckner, Laura; Zhao, Peiyao A; van Schaik, Tom; Leemans, Christ; Sima, Jiao; Peric-Hupkes, Daniel; Gilbert, David M; van Steensel, BasThe EMBO journal.2020 Mar 16;32080885
A Dynamic Folded Hairpin Conformation Is Associated with ?-Globin Activation in Erythroid Cells.Chiariello, Andrea M; Bianco, Simona; Oudelaar, A Marieke; Esposito, Andrea; Annunziatella, Carlo; Fiorillo, Luca; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Larke, Martin S C; Telenius, Jelena M; Sciarretta, Renato; Musella, Francesco; Buckle, VCell reports.2020 02 18;32075757
An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis.Kim, Arthur S; Zimmerman, Ofer; Fox, Julie M; Nelson, Christopher A; Basore, Katherine; Zhang, Rong; Durnell, Lorellin; Desai, Chandni; Bullock, Christopher; Deem, Sharon L; Oppenheimer, Jonas; Shapiro, Beth; Wang, Ting; Cherry, Sara; Coyne, Carolyn B; HaCell host & microbe.2020 03 11;32075743
Chemogenetic Control of Nanobodies.Farrants, Helen; Tarnawski, Miroslaw; Müller, Thorsten G; Otsuka, Shotaro; Hiblot, Julien; Koch, Birgit; Kueblbeck, Moritz; Kräusslich, Hans-Georg; Ellenberg, Jan; Johnsson, KaiNature methods.2020 03;32066961
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL.Wutz, Gordana; Ladurner, Rene; St Hilaire, Brian Glenn; Stocsits, Roman R; Nagasaka, Kota; Pignard, Benoit; Sanborn, Adrian; Tang, Wen; Várnai, Csilla; Ivanov, Miroslav P; Schoenfelder, Stefan; van der Lelij, Petra; Huang, Xingfan; Dürnberger, Gerhard; Roitinger, Elisabeth; Mechtler, Karl; Davidson, Iain Finley; Fraser, Peter; Lieberman-Aiden, Erez; Peters, Jan-MichaeleLife.2020 Feb 17;32065581
Derivation of trophoblast stem cells from naïve human pluripotent stem cells.Dong, Chen; Beltcheva, Mariana; Gontarz, Paul; Zhang, Bo; Popli, Pooja; Fischer, Laura A; Khan, Shafqat A; Park, Kyoung-Mi; Yoon, Eun-Ja; Xing, Xiaoyun; Kommagani, Ramakrishna; Wang, Ting; Solnica-Krezel, Lilianna; Theunissen, Thorold WeLife.2020 Feb 12;32048992
Computational approaches from polymer physics to investigate chromatin folding.Bianco, Simona; Chiariello, Andrea M; Conte, Mattia; Esposito, Andrea; Fiorillo, Luca; Musella, Francesco; Nicodemi, MarioCurrent opinion in cell biology.2020 06;32045823
pyBedGraph: a python package for fast operations on 1D genomic signal tracks.Zhang, Henry B; Kim, Minji; Chuang, Jeffrey H; Ruan, YijunBioinformatics (Oxford, England).2020 05 01;32044918
Dynamic Assembly and Disassembly of the Human DNA Polymerase ? Holoenzyme on the Genome In Vivo.Drosopoulos, William C; Vierra, David A; Kenworthy, Charles A; Coleman, Robert A; Schildkraut, Carl LCell reports.2020 02 04;32023453
Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine.Karbassi, Elaheh; Fenix, Aidan; Marchiano, Silvia; Muraoka, Naoto; Nakamura, Kenta; Yang, Xiulan; Murry, Charles ENature reviews. Cardiology.2020 Feb 03;32015528
GiniQC: a measure for quantifying noise in single-cell Hi-C data.Horton, Connor A; Alver, Burak H; Park, Peter JBioinformatics (Oxford, England).2020 05 01;32003786
Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals.Feodorova, Yana; Falk, Martin; Mirny, Leonid A; Solovei, IrinaTrends in cell biology.2020 Apr;31980345
Switchable resolution in soft x-ray tomography of single cells.Weinhardt, Venera; Chen, Jian-Hua; Ekman, Axel A; Guo, Jessica; Remesh, Soumya G; Hammel, Michal; McDermott, Gerry; Chao, Weilun; Oh, Sharon; Le Gros, Mark A; Larabell, Carolyn APloS one.2020;31978064
Co-opted transposons help perpetuate conserved higher-order chromosomal structures.Choudhary, Mayank Nk; Friedman, Ryan Z; Wang, Julia T; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, TingGenome biology.2020 01 24;31973766
Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts.Weyers, Jill J; Gunaje, Jagadambika J; Van Biber, Benjamin; Martinson, Amy; Reinecke, Hans; Mahoney, William M; Schwartz, Stephen M; Cox, Timothy C; Murry, Charles EPloS one.2020;31945113
On the existence and functionality of topologically associating domains.Beagan, Jonathan A; Phillips-Cremins, Jennifer ENature genetics.2020 01;31925403
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.Tian, Dechao; Zhang, Ruochi; Zhang, Yang; Zhu, Xiaopeng; Ma, JianGenome research.2020 Jan 06;31907193
An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms.Yu, Yi; Guo, Yijun; Tian, Qiqi; Lan, Yuanqing; Yeh, Hugh; Zhang, Meng; Tasan, Ipek; Jain, Surbhi; Zhao, HuiminNature chemical biology.2020 04;31873222
Physics and Biology (of Chromosomes).Marko, John FJournal of molecular biology.2020 Jan 17;31866291
Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells.Chen, Changya; Yu, Wenbao; Tober, Joanna; Gao, Peng; He, Bing; Lee, Kiwon; Trieu, Tuan; Blobel, Gerd A; Speck, Nancy A; Tan, KaiCell reports.2019 12 17;31851943
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries.An, Lin; Yang, Tao; Yang, Jiahao; Nuebler, Johannes; Xiang, Guanjue; Hardison, Ross C; Li, Qunhua; Zhang, YuGenome biology.2019 12 18;31847870
The epigenomic landscape of transposable elements across normal human development and anatomy.Pehrsson, Erica C; Choudhary, Mayank N K; Sundaram, Vasavi; Wang, TingNature communications.2019 Dec 10;31822674
Localization microscopy at doubled precision with patterned illumination.Cnossen, Jelmer; Hinsdale, Taylor; Thorsen, Rasmus Ø; Siemons, Marijn; Schueder, Florian; Jungmann, Ralf; Smith, Carlas S; Rieger, Bernd; Stallinga, SjoerdNature methods.2020 Jan;31819263
Chromatin Is Frequently Unknotted at the Megabase Scale.Goundaroulis, Dimos; Lieberman Aiden, Erez; Stasiak, AndrzejBiophysical journal.2020 May 05;31818464
Guided nuclear exploration increases CTCF target search efficiency.Hansen, Anders S; Amitai, Assaf; Cattoglio, Claudia; Tjian, Robert; Darzacq, XavierNature chemical biology.2019 Dec 02;31792445
Probing and engineering liquid-phase organelles.Bracha, Dan; Walls, Mackenzie T; Brangwynne, Clifford PNature biotechnology.2019 12;31792412
Spring Model - Chromatin Modeling Tool Based on OpenMM.Kadlof, Michal; Rozycka, Julia; Plewczynski, DariuszMethods (San Diego, Calif.).2020 10 01;31790732
Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.Fulco, Charles P; Nasser, Joseph; Jones, Thouis R; Munson, Glen; Bergman, Drew T; Subramanian, Vidya; Grossman, Sharon R; Anyoha, Rockwell; Doughty, Benjamin R; Patwardhan, Tejal A; Nguyen, Tung H; Kane, Michael; Perez, Elizabeth M; Durand, Neva C; LareauNature genetics.2019 12;31784727
Common DNA sequence variation influences 3-dimensional conformation of the human genome.Gorkin, David U; Qiu, Yunjiang; Hu, Ming; Fletez-Brant, Kipper; Liu, Tristin; Schmitt, Anthony D; Noor, Amina; Chiou, Joshua; Gaulton, Kyle J; Sebat, Jonathan; Li, Yun; Hansen, Kasper D; Ren, BingGenome biology2019 11 2831779666
Chromatin structure dynamics during the mitosis-to-G1 phase transition.Zhang, Haoyue; Emerson, Daniel J; Gilgenast, Thomas G; Titus, Katelyn R; Lan, Yemin; Huang, Peng; Zhang, Di; Wang, Hongxin; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Phillips-Cremins, Jennifer E; Blobel, Gerd ANature.2019 12;31776509
Tasks, Techniques, and Tools for Genomic Data Visualization.Nusrat, S; Harbig, T; Gehlenborg, NComputer graphics forum : journal of the European Association for Computer Graphics.2019 Jun;31768085
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms.Kim, Minji; Zheng, Meizhen; Tian, Simon Zhongyuan; Lee, Byoungkoo; Chuang, Jeffrey H; Ruan, YijunGenome biology2019 11 2531767038
Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures.Brahmachari, Sumitabha; Marko, John FProceedings of the National Academy of Sciences of the United States of America.2019 12 10;31757850
Gene expression amplification by nuclear speckle association.Kim, Jiah; Venkata, Neha Chivukula; Hernandez Gonzalez, Gabriela Andrea; Khanna, Nimish; Belmont, Andrew SThe Journal of cell biology.2020 Jan 06;31757787
The liquid nucleome - phase transitions in the nucleus at a glance.Strom, Amy R; Brangwynne, Clifford PJournal of cell science.2019 11 21;31754043
Aggregated network centrality shows non-random structure of genomic and proteomic networks.Halder, Anup Kumar; Denkiewicz, Micha?; Sengupta, Kaustav; Basu, Subhadip; Plewczynski, DariuszMethods (San Diego, Calif.).2020 10 01;31740366
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.Xiong, Kyle; Ma, JianNature communications.2019 11 07;31699985
A Proteomic Perspective on Cardiomyocyte Maturation.Muraoka, Naoto; Sun, Bingyun; Murry, Charles ECirculation research.2019 11 08;31697629
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.Abramo, Kristin; Valton, Anne-Laure; Venev, Sergey V; Ozadam, Hakan; Fox, A Nicole; Dekker, JobNature cell biology.2019 Nov;31685986
X Inactivation and Escape: Epigenetic and Structural Features.Fang, He; Disteche, Christine M; Berletch, Joel BFrontiers in cell and developmental biology.2019;31632970
Methods for comparative ChIA-PET and Hi-C data analysis.Capurso, Dan; Tang, Zhonghui; Ruan, YijunMethods (San Diego, Calif.).2020 01 01;31629084
Mapping RNA-chromatin interactions by sequencing with iMARGI.Wu, Weixin; Yan, Zhangming; Nguyen, Tri C; Bouman Chen, Zhen; Chien, Shu; Zhong, ShengNature protocols.2019 Nov;31619811
Inference of chromosome 3D structures from GAM data by a physics computational approach.Fiorillo, Luca; Bianco, Simona; Chiariello, Andrea M; Barbieri, Mariano; Esposito, Andrea; Annunziatella, Carlo; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Pombo, Ana; Nicodemi, MarioMethods (San Diego, Calif.).2020 10 01;31604121
Photoactivation of silicon rhodamines via a light-induced protonation.Frei, Michelle S; Hoess, Philipp; Lampe, Marko; Nijmeijer, Bianca; Kueblbeck, Moritz; Ellenberg, Jan; Wadepohl, Hubert; Ries, Jonas; Pitsch, Stefan; Reymond, Luc; Johnsson, KaiNature communications.2019 Oct 08;31594948
Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences.McSwiggen, David T; Mir, Mustafa; Darzacq, Xavier; Tjian, RobertGenes & development.2019 12 01;31594803
Cronos Titin Is Expressed in Human Cardiomyocytes and Necessary for Normal Sarcomere Function.Zaunbrecher, Rebecca J; Abel, Ashley N; Beussman, Kevin; Leonard, Andrea; von Frieling-Salewsky, Marion; Fields, Paul A; Pabon, Lil; Reinecke, Hans; Yang, Xiulan; Macadangdang, Jesse; Kim, Deok-Ho; Linke, Wolfgang A; Sniadecki, Nathan J; Regnier, Michael; Murry, Charles ECirculation.2019 Nov 12;31587567
How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation.Erba?, Aykut; Marko, John FCurrent opinion in chemical biology.2019 Oct 02;31586479
Highly structured homolog pairing reflects functional organization of the Drosophila genome.AlHaj Abed, Jumana; Erceg, Jelena; Goloborodko, Anton; Nguyen, Son C; McCole, Ruth B; Saylor, Wren; Fudenberg, Geoffrey; Lajoie, Bryan R; Dekker, Job; Mirny, Leonid A; Wu, C-TingNature communications.2019 Oct 03;31582763
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.Erceg, Jelena; AlHaj Abed, Jumana; Goloborodko, Anton; Lajoie, Bryan R; Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; McCole, Ruth B; Nguyen, Son C; Saylor, Wren; Joyce, Eric F; Senaratne, T Niroshini; Hannan, Mohammed A; Nir, Guy; Dekker, Job; Mirny, Leonid A; Wu, C-TingNature communications.2019 Oct 03;31582744
Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging.Zheng, Qinsi; Ayala, Anthony X; Chung, Inhee; Weigel, Aubrey V; Ranjan, Anand; Falco, Natalie; Grimm, Jonathan B; Tkachuk, Ariana N; Wu, Carl; Lippincott-Schwartz, Jennifer; Singer, Robert H; Lavis, Luke DACS central science.2019 Sep 25;31572787
Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells.Yang, Xiulan; Rodriguez, Marita L; Leonard, Andrea; Sun, Lihua; Fischer, Karin A; Wang, Yuliang; Ritterhoff, Julia; Zhao, Limei; Kolwicz Jr, Stephen C; Pabon, Lil; Reinecke, Hans; Sniadecki, Nathan J; Tian, Rong; Ruohola-Baker, Hannele; Xu, Haodong; MurryStem cell reports.2019 10 08;31564645
Nuclear pores as versatile reference standards for quantitative superresolution microscopy.Thevathasan, Jervis Vermal; Kahnwald, Maurice; Cie?li?ski, Konstanty; Hoess, Philipp; Peneti, Sudheer Kumar; Reitberger, Manuel; Heid, Daniel; Kasuba, Krishna Chaitanya; Hoerner, Sarah Janice; Li, Yiming; Wu, Yu-Le; Mund, Markus; Matti, Ulf; Pereira, Pedro Matos; Henriques, Ricardo; Nijmeijer, Bianca; Kueblbeck, Moritz; Sabinina, Vilma Jimenez; Ellenberg, Jan; Ries, JonasNature methods.2019 Oct;31562488
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Lee, Choli; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, ZhijunMethods (San Diego, Calif.).2019 Sep 16;31536770
Jonathan R. Warner (1936-2019)-pioneer of ribosome biosynthesis.Pederson, ThoruRNA (New York, N.Y.).2019 Dec;31534010
Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF.Hansen, Anders S; Hsieh, Tsung-Han S; Cattoglio, Claudia; Pustova, Iryna; Saldaña-Meyer, Ricardo; Reinberg, Danny; Darzacq, Xavier; Tjian, RobertMolecular cell.2019 11 07;31522987
The fundamental role of chromatin loop extrusion in physiological V(D)J recombination.Zhang, Yu; Zhang, Xuefei; Ba, Zhaoqing; Liang, Zhuoyi; Dring, Edward W; Hu, Hongli; Lou, Jiangman; Kyritsis, Nia; Zurita, Jeffrey; Shamim, Muhammad S; Presser Aiden, Aviva; Lieberman Aiden, Erez; Alt, Frederick WNature.2019 Sep;31511698
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.Ray, Judhajeet; Munn, Paul R; Vihervaara, Anniina; Lewis, James J; Ozer, Abdullah; Danko, Charles G; Lis, John TProceedings of the National Academy of Sciences of the United States of America.2019 Sep 24;31506350
Supervised classification enables rapid annotation of cell atlases.Pliner, Hannah A; Shendure, Jay; Trapnell, ColeNature methods.2019 Oct;31501545
High-Throughput Single-Cell Sequencing with Linear Amplification.Yin, Yi; Jiang, Yue; Lam, Kwan-Wood Gabriel; Berletch, Joel B; Disteche, Christine M; Noble, William S; Steemers, Frank J; Camerini-Otero, R Daniel; Adey, Andrew C; Shendure, JayMolecular cell.2019 Aug 28;31495564
Olfactory receptor genes make the case for inter-chromosomal interactions.Bashkirova, Elizaveta; Lomvardas, StavrosCurrent opinion in genetics & development.2019 Apr;31491591
CRISPR-mediated live imaging of genome editing and transcription.Wang, Haifeng; Nakamura, Muneaki; Abbott, Timothy R; Zhao, Dehua; Luo, Kaiwen; Yu, Cordelia; Nguyen, Cindy M; Lo, Albert; Daley, Timothy P; La Russa, Marie; Liu, Yanxia; Qi, Lei SScience (New York, N.Y.).2019 09 20;31488703
Molecular basis and biological function of variability in spatial genome organization.Finn, Elizabeth H; Misteli, TomScience (New York, N.Y.).2019 09 06;31488662
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition.McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, ColeNature genetics.2019 Sep;31477929
Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets.Lekschas, Fritz; Behrisch, Michael; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, HanspeterIEEE transactions on visualization and computer graphics.2020 Jan;31442989
Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases.Wei, Chia-Lin; Nicolis, Silvia K; Zhu, Yanfen; Pagin, MiriamJournal of experimental neuroscience.2019;31431802
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, BingNature genetics.2019 Sep;31427791
Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds.Dahlke, Katelyn; Zhao, Jing; Sing, Charles E; Banigan, Edward JBiophysical journal.2019 Sep 17;31427067
Skeletal muscle: A review of molecular structure and function, in health and disease.Mukund, Kavitha; Subramaniam, ShankarWiley interdisciplinary reviews. Systems biology and medicine2020 0131407867
Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast.Lari, Azra; Farzam, Farzin; Bensidoun, Pierre; Oeffinger, Marlene; Zenklusen, Daniel; Grunwald, David; Montpetit, BenMethods in molecular biology (Clifton, N.J.).2019;31407282
Controlling the material properties and rRNA processing function of the nucleolus using light.Zhu, Lian; Richardson, Tiffany M; Wacheul, Ludivine; Wei, Ming-Tzo; Feric, Marina; Whitney, Gena; Lafontaine, Denis L J; Brangwynne, Clifford PProceedings of the National Academy of Sciences of the United States of America.2019 Aug 09;31399547
Visual Pattern-Driven Exploration of Big Data.Behrisch, Michael; Schreck, Tobias; Krüger, Robert; Gehlenborg, Nils; Lekschas, Fritz; Pfister, Hanspeter2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany).2018 Oct;31396383
Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy.Bertero, Alessandro; Fields, Paul A; Smith, Alec S T; Leonard, Andrea; Beussman, Kevin; Sniadecki, Nathan J; Kim, Deok-Ho; Tse, Hung-Fat; Pabon, Lil; Shendure, Jay; Noble, William S; Murry, Charles EThe Journal of cell biology.2019 Sep 02;31395619
Genome organization around nuclear speckles.Chen, Yu; Belmont, Andrew SCurrent opinion in genetics & development.2019 Apr;31394307
Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells.Bianco, Simona; Annunziatella, Carlo; Andrey, Guillaume; Chiariello, Andrea M; Esposito, Andrea; Fiorillo, Luca; Prisco, Antonella; Conte, Mattia; Campanile, Raffaele; Nicodemi, MarioCell reports.2019 08 06;31390570
Learn from Your Elders: Developmental Biology Lessons to Guide Maturation of Stem Cell-Derived Cardiomyocytes.Marchianò, Silvia; Bertero, Alessandro; Murry, Charles EPediatric cardiology.2019 Oct;31388700
Joint profiling of DNA methylation and chromatin architecture in single cells.Li, Guoqiang; Liu, Yaping; Zhang, Yanxiao; Kubo, Naoki; Yu, Miao; Fang, Rongxin; Kellis, Manolis; Ren, BingNature methods.2019 Oct;31384045
Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation.Stephens, Andrew D; Liu, Patrick Z; Kandula, Viswajit; Chen, Haimei; Almassalha, Luay M; Herman, Cameron; Backman, Vadim; O'Halloran, Thomas; Adam, Stephen A; Goldman, Robert D; Banigan, Edward J; Marko, John FMolecular biology of the cell.2019 Aug 01;31365328
Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.Sadowski, Michal; Kraft, Agnieszka; Szalaj, Przemyslaw; Wlasnowolski, Michal; Tang, Zhonghui; Ruan, Yijun; Plewczynski, DariuszGenome biology2019 07 3031362752
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, RalfAngewandte Chemie (International ed. in English).2019 09 09;31314157
Cooler: scalable storage for Hi-C data and other genomically-labeled arrays.Abdennur, Nezar; Mirny, LeonidBioinformatics (Oxford, England).2019 Jul 10;31290943
Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene.Lalonde, Simon; Codina-Fauteux, Valérie-Anne; de Bellefon, Sébastian Méric; Leblanc, Francis; Beaudoin, Mélissa; Simon, Marie-Michelle; Dali, Rola; Kwan, Tony; Lo, Ken Sin; Pastinen, Tomi; Lettre, GuillaumeGenome biology2019 07 0831287004
Large distances separate coregulated genes in living Drosophila embryos.Heist, Tyler; Fukaya, Takashi; Levine, MichaelProceedings of the National Academy of Sciences of the United States of America.2019 07 23;31285341
Archiving and disseminating integrative structure models.Vallat, Brinda; Webb, Benjamin; Westbrook, John; Sali, Andrej; Berman, Helen MJournal of biomolecular NMR.2019 Jul;31278630
A subset of topologically associating domains fold into mesoscale core-periphery networks.Huang, Harvey; Chen, Sunnia T; Titus, Katelyn R; Emerson, Daniel J; Bassett, Danielle S; Phillips-Cremins, Jennifer EScientific reports.2019 Jul 02;31266973
Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures.Hulleman, Christiaan N; Huisman, Maximiliaan; Moerland, Robert J; Grünwald, David; Stallinga, Sjoerd; Rieger, BerndSmall methods.2018 Sep 11;31240238
LADL: light-activated dynamic looping for endogenous gene expression control.Kim, Ji Hun; Rege, Mayuri; Valeri, Jacqueline; Dunagin, Margaret C; Metzger, Aryeh; Titus, Katelyn R; Gilgenast, Thomas G; Gong, Wanfeng; Beagan, Jonathan A; Raj, Arjun; Phillips-Cremins, Jennifer ENature methods.2019 07;31235883
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, CornelisNature communications.2019 06 24;31235807
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.Yang, Yang; Zhang, Yang; Ren, Bing; Dixon, Jesse R; Ma, JianCell systems.2019 Jun 26;31229558
Two major mechanisms of chromosome organization.Mirny, Leonid A; Imakaev, Maxim; Abdennur, NezarCurrent opinion in cell biology.2019 Jun;31228682
Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data.Rosenthal, Michael; Bryner, Darshan; Huffer, Fred; Evans, Shane; Srivastava, Anuj; Neretti, NicolaJournal of computational biology : a journal of computational molecular cell biology.2019 Nov;31211598
Determining cellular CTCF and cohesin abundances to constrain 3D genome models.Cattoglio, Claudia; Pustova, Iryna; Walther, Nike; Ho, Jaclyn J; Hantsche-Grininger, Merle; Inouye, Carla J; Hossain, M Julius; Dailey, Gina M; Ellenberg, Jan; Darzacq, Xavier; Tjian, Robert; Hansen, Anders SeLife.2019 Jun 17;31205001
Absolute quantification of cohesin, CTCF and their regulators in human cells.Holzmann, Johann; Politi, Antonio Z; Nagasaka, Kota; Hantsche-Grininger, Merle; Walther, Nike; Koch, Birgit; Fuchs, Johannes; Dürnberger, Gerhard; Tang, Wen; Ladurner, Rene; Stocsits, Roman R; Busslinger, Georg A; Novák, Béla; Mechtler, Karl; Davidson, IaeLife.2019 06 17;31204999
Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin.Vertii, Anastassiia; Ou, Jianhong; Yu, Jun; Yan, Aimin; Pagès, Hervé; Liu, Haibo; Zhu, Lihua Julie; Kaufman, Paul DGenome research.2019 Jun 14;31201210
FunPred 3.0: improved protein function prediction using protein interaction network.Saha, Sovan; Chatterjee, Piyali; Basu, Subhadip; Nasipuri, Mita; Plewczynski, DariuszPeerJ.2019;31198622
Heterochromatin drives compartmentalization of inverted and conventional nuclei.Falk, Martin; Feodorova, Yana; Naumova, Natalia; Imakaev, Maxim; Lajoie, Bryan R; Leonhardt, Heinrich; Joffe, Boris; Dekker, Job; Fudenberg, Geoffrey; Solovei, Irina; Mirny, Leonid ANature.2019 Jun;31168090
WashU Epigenome Browser update 2019.Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Sears, Renee L; Wang, TingNucleic acids research.2019 Jul 02;31165883
Principles for Integrative Structural Biology Studies.Rout, Michael P; Sali, AndrejCell.2019 May 30;31150619
Preformed chromatin topology assists transcriptional robustness of Shh during limb development.Paliou, Christina; Guckelberger, Philine; Schöpflin, Robert; Heinrich, Verena; Esposito, Andrea; Chiariello, Andrea M; Bianco, Simona; Annunziatella, Carlo; Helmuth, Johannes; Haas, Stefan; Jerkovi?, Ivana; Brieske, Norbert; Wittler, Lars; Timmermann, BerProceedings of the National Academy of Sciences of the United States of America.2019 Jun 18;31147463
Time varying causal network reconstruction of a mouse cell cycle.Masnadi-Shirazi, Maryam; Maurya, Mano R; Pao, Gerald; Ke, Eugene; Verma, Inder M; Subramaniam, ShankarBMC bioinformatics.2019 May 29;31142274
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, LarryNucleus (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, ElisaNature communications.2019 05 22;31118417
EpiAlignment: alignment with both DNA sequence and epigenomic data.Lu, Jia; Cao, Xiaoyi; Zhong, ShengNucleic acids research.2019 Jul 02;31114924
Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms.Li, Peipei; Marshall, Lee; Oh, Gabriel; Jakubowski, Jennifer L; Groot, Daniel; He, Yu; Wang, Ting; Petronis, Arturas; Labrie, VivianeNature communications.2019 05 21;31113950
Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains.Sato, Hanae; Wu, Bin; Delahaye, Fabien; Singer, Robert H; Greally, John MThe Journal of cell biology.2019 Jun 03;31110057
Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx.Möckl, Leonhard; Pedram, Kayvon; Roy, Anish R; Krishnan, Venkatesh; Gustavsson, Anna-Karin; Dorigo, Oliver; Bertozzi, Carolyn R; Moerner, W EDevelopmental cell.2019 Jul 01;31105009
Long-range enhancer-promoter contacts in gene expression control.Schoenfelder, Stefan; Fraser, PeterNature reviews. Genetics.2019 08;31086298
A combination of transcription factors mediates inducible interchromosomal contacts.Kim, Seungsoo; Dunham, Maitreya J; Shendure, JayeLife2019 05 1331081754
Tibanna: software for scalable execution of portable pipelines on the cloud.Lee, Soohyun; Johnson, Jeremy; Vitzthum, Carl; K?rl?, Koray; Alver, Burak H; Park, Peter JBioinformatics (Oxford, England).2019 May 11;31077294
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, AzadNature.2019 May;31068695
Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes.Yu, Jingting; Hu, Ming; Li, ChunBMC genetics.2019 Apr 30;31039743
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation.McSwiggen, David Trombley; Hansen, Anders S; Teves, Sheila S; Marie-Nelly, Hervé; Hao, Yvonne; Heckert, Alec Basil; Umemoto, Kayla K; Dugast-Darzacq, Claire; Tjian, Robert; Darzacq, XaviereLife2019 05 0731038454
Receptor-Ligand Rebinding Kinetics in Confinement.Erba?, Aykut; Olvera de la Cruz, Monica; Marko, John FBiophysical journal.2019 May 07;31029377
Topological and functional comparison of community detection algorithms in biological networks.Rahiminejad, Sara; Maurya, Mano R; Subramaniam, ShankarBMC bioinformatics.2019 Apr 27;31029085
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, ToddThe 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, BoFrontiers 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 FPhysical 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, MingPLoS 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, BasCell.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 ENature 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 CGenome 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, TingNature 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 DProceedings 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 TThe Plant cell.2019 05;30923229
Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications.He, Ming; Huang, Tse-Shun; Li, Shuai; Hong, Hsiao-Chin; Chen, Zhen; Martin, Marcy; Zhou, Xin; Huang, Hsi-Yuan; Su, Shu-Han; Zhang, Jiao; Wang, Wei-Ting; Kang, Jian; Huang, Hsien-Da; Zhang, Jin; Chien, Shu; Shyy, John Y-JArteriosclerosis, thrombosis, and vascular biology.2019 May;30917677
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, LongNature.2019 Apr;30911168
Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.Gilgenast, Thomas G; Phillips-Cremins, Jennifer ECell systems.2019 Mar 27;30904376
Measuring the reproducibility and quality of Hi-C data.Yard?mc?, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E G; Ursu, Oana; Yan, Koon-Kiu; Yang, Tao; Chakraborty, Abhijit; Kaul, Arya; Lajoie, Bryan R; Song, Fan; Zhan, Ye; Ay, Ferhat; Gerstein, Mark; Kundaje, Anshul; Li, Qunhua; Taylor, James; Yue, Feng; Dekker, Job; Noble, William SGenome biology.2019 03 19;30890172
Chromatin's physical properties shape the nucleus and its functions.Stephens, Andrew D; Banigan, Edward J; Marko, John FCurrent opinion in cell biology.2019 06;30889417
Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.Al Bkhetan, Ziad; Kadlof, Michal; Kraft, Agnieszka; Plewczynski, DariuszMethods (San Diego, Calif.).2019 Aug 15;30853548
Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance.Bertolini, Jessica A; Favaro, Rebecca; Zhu, Yanfen; Pagin, Miriam; Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Vermunt, Marit W; Martynoga, Ben; Barone, Cristiana; Mariani, Jessica; Cardozo, Marcos Julián; Tabanera, Noemi; Zambelli, Federico; Mercurio, Sara; Ottolenghi, Sergio; Robson, Paul; Creyghton, Menno P; Bovolenta, Paola; Pavesi, Giulio; Guillemot, Francois; Nicolis, Silvia K; Wei, Chia-LinCell stem cell.2019 Mar 07;30849367
Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region.Ma, Hanhui; Tu, Li-Chun; Chung, Yu-Chieh; Naseri, Ardalan; Grunwald, David; Zhang, Shaojie; Pederson, ThoruThe Journal of cell biology.2019 Mar 07;30846483
Intermingling of chromosome territories.Szczepińska, Teresa; Rusek, Anna Maria; Plewczynski, DariuszGenes, chromosomes & cancer2019 0730828902
Dendritic Spines Taxonomy: The Functional and Structural Classification ? Time-Dependent Probabilistic Model of Neuronal Activation.Urban, Paulina; Rezaei, Vahid; Bokota, Grzegorz; Denkiewicz, Micha?; Basu, Subhadip; Plewczy?ski, DariuszJournal of computational biology : a journal of computational molecular cell biology.2019 Apr;30810368
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.Finn, Elizabeth H; Pegoraro, Gianluca; Brandão, Hugo B; Valton, Anne-Laure; Oomen, Marlies E; Dekker, Job; Mirny, Leonid; Misteli, TomCell.2019 Mar 07;30799036
The single-cell transcriptional landscape of mammalian organogenesis.Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, JayNature.2019 02;30787437
Multiplex chromatin interactions with single-molecule precision.Zheng, Meizhen; Tian, Simon Zhongyuan; Capurso, Daniel; Kim, Minji; Maurya, Rahul; Lee, Byoungkoo; Piecuch, Emaly; Gong, Liang; Zhu, Jacqueline Jufen; Li, Zhihui; Wong, Chee Hong; Ngan, Chew Yee; Wang, Ping; Ruan, Xiaoan; Wei, Chia-Lin; Ruan, YijunNature.2019 02;30778195
Replication Timing Becomes Intertwined with 3D Genome Organization.Ma, Jian; Duan, ZhijunCell.2019 Feb 07;30735630
Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells.Hollerer, Ina; Barker, Juliet C; Jorgensen, Victoria; Tresenrider, Amy; Dugast-Darzacq, Claire; Chan, Leon Y; Darzacq, Xavier; Tjian, Robert; Ünal, Elçin; Brar, Gloria AG3 (Bethesda, Md.).2019 04 09;30723103
Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs.Yan, Zhangming; Huang, Norman; Wu, Weixin; Chen, Weizhong; Jiang, Yiqun; Chen, Jingyao; Huang, Xuerui; Wen, Xingzhao; Xu, Jie; Jin, Qiushi; Zhang, Kang; Chen, Zhen; Chien, Shu; Zhong, ShengProceedings of the National Academy of Sciences of the United States of America.2019 Feb 19;30718424
Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation.Chapski, Douglas J; Rosa-Garrido, Manuel; Hua, Nan; Alber, Frank; Vondriska, Thomas MFrontiers in cardiovascular medicine.2018;30697540
Adapting dCas9-APEX2 for subnuclear proteomic profiling.Gao, Xin D; Rodríguez, Tomás C; Sontheimer, Erik JMethods in enzymology.2019;30691651
A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets.Sharon, Nadav; Chawla, Raghav; Mueller, Jonas; Vanderhooft, Jordan; Whitehorn, Luke James; Rosenthal, Benjamin; Gürtler, Mads; Estanboulieh, Ralph R; Shvartsman, Dmitry; Gifford, David K; Trapnell, Cole; Melton, DougCell.2019 Feb 07;30661759
An automated Bayesian pipeline for rapid analysis of single-molecule binding data.Smith, Carlas S; Jouravleva, Karina; Huisman, Maximiliaan; Jolly, Samson M; Zamore, Phillip D; Grunwald, DavidNature communications.2019 01 17;30655518
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.Oomen, Marlies E; Hansen, Anders S; Liu, Yu; Darzacq, Xavier; Dekker, JobGenome research.2019 02;30655336
Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic ? Cell Identity and Function.Lawlor, Nathan; Márquez, Eladio J; Orchard, Peter; Narisu, Narisu; Shamim, Muhammad Saad; Thibodeau, Asa; Varshney, Arushi; Kursawe, Romy; Erdos, Michael R; Kanke, Matt; Gu, Huiya; Pak, Evgenia; Dutra, Amalia; Russell, Sheikh; Li, Xingwang; Piecuch, Emaly; Luo, Oscar; Chines, Peter S; Fuchbserger, Christian; NIH Intramural Sequencing Center; Sethupathy, Praveen; Aiden, Aviva Presser; Ruan, Yijun; Aiden, Erez Lieberman; Collins, Francis S; Ucar, Duygu; Parker, Stephen C J; Stitzel, Michael LCell reports.2019 Jan 15;30650367
Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers.Limi, Saima; Zhao, Yilin; Guo, Peng; Lopez-Jones, Melissa; Zheng, Deyou; Singer, Robert H; Skoultchi, Arthur I; Cvekl, AlesInvestigative ophthalmology & visual science.2019 Jan 02;30646012
LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice.Monahan, Kevin; Horta, Adan; Lomvardas, StavrosNature.2019 01;30626972
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting.Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, ArjunPLoS genetics.2019 01;30625149
Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics.Biggs, Ronald; Liu, Patrick Z; Stephens, Andrew D; Marko, John FMolecular biology of the cell.2019 03 21;30625026
An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.Zhang, Zhizhuo; Chng, Kern Rei; Lingadahalli, Shreyas; Chen, Zikai; Liu, Mei Hui; Do, Huy Hoang; Cai, Shaojiang; Rinaldi, Nicola; Poh, Huay Mei; Li, Guoliang; Sung, Ying Ying; Heng, Charlie L; Core, Leighton J; Tan, Si Kee; Ruan, Xiaoan; Lis, John T; Kellis, Manolis; Ruan, Yijun; Sung, Wing-Kin; Cheung, EdwinGenome research.2019 02;30606742
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.Sima, Jiao; Chakraborty, Abhijit; Dileep, Vishnu; Michalski, Marco; Klein, Kyle N; Holcomb, Nicolas P; Turner, Jesse L; Paulsen, Michelle T; Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Bartlett, Daniel A; Zhao, Peiyao A; Washburn, Brian K; Nora, Cell.2019 Feb 07;30595451
Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.Mir, Mustafa; Stadler, Michael R; Ortiz, Stephan A; Hannon, Colleen E; Harrison, Melissa M; Darzacq, Xavier; Eisen, Michael BeLife.2018 12 27;30589412
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.Lu, Jia; Cao, Xiaoyi; Zhong, ShengPLoS computational biology.2018 Dec;30586383
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.Nir, Guy; Farabella, Irene; Pérez Estrada, Cynthia; Ebeling, Carl G; Beliveau, Brian J; Sasaki, Hiroshi M; Lee, S Dean; Nguyen, Son C; McCole, Ruth B; Chattoraj, Shyamtanu; Erceg, Jelena; AlHaj Abed, Jumana; Martins, Nuno M C; Nguyen, Huy Q; Hannan, Mohammed A; Russell, Sheikh; Durand, Neva C; Rao, Suhas S P; Kishi, Jocelyn Y; Soler-Vila, Paula; Di Pierro, Michele; Onuchic, José N; Callahan, Steven P; Schreiner, John M; Stuckey, Jeff A; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A; Wu, C-TingPLoS genetics.2018 12;30586358
Models of polymer physics for the architecture of the cell nucleus.Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Chiariello, Andrea M; Fiorillo, Luca; Nicodemi, MarioWiley interdisciplinary reviews. Systems biology and medicine.2018 Dec 19;30566285
Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.Bartman, Caroline R; Hamagami, Nicole; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A; Raj, ArjunMolecular cell.2018 Dec 06;30554946
RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast.Brahma, Sandipan; Henikoff, StevenMolecular cell.2019 Jan 17;30554944
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data.Calandrelli, Riccardo; Wu, Qiuyang; Guan, Jihong; Zhong, ShengGenomics, proteomics & bioinformatics.2018 Dec 13;30553884
A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice.Keleher, Madeline Rose; Zaidi, Rabab; Hicks, Lauren; Shah, Shyam; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Cheverud, James MBMC genomics.2018 Dec 07;30526554
Deconstructing transport-distribution reconstruction in the nuclear-pore complex.Tu, Li-Chun; Huisman, Maximiliaan; Chung, Yu-Chieh; Smith, Carlas Sierd; Grunwald, DavidNature structural & molecular biology.2018 Dec;30518848
Impact of optical aberrations on axial position determination by photometry.Thorsen, Rasmus Ø; Hulleman, Christiaan N; Hammer, Mathias; Grünwald, David; Stallinga, Sjoerd; Rieger, BerndNature methods.2018 Dec;30504865
Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome.Shin, Yongdae; Chang, Yi-Che; Lee, Daniel S W; Berry, Joel; Sanders, David W; Ronceray, Pierre; Wingreen, Ned S; Haataja, Mikko; Brangwynne, Clifford PCell.2018 Nov 29;30500535
Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds.Bracha, Dan; Walls, Mackenzie T; Wei, Ming-Tzo; Zhu, Lian; Kurian, Martin; Avalos, José L; Toettcher, Jared E; Brangwynne, Clifford PCell.2018 Nov 29;30500534
Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors.Peng, Qin; Lu, Shaoying; Shi, Yuxin; Pan, Yijia; Limsakul, Praopim; Chernov, Andrei V; Qiu, Juhui; Chai, Xiaoqi; Shi, Yiwen; Wang, Pengzhi; Ji, Yanmin; Li, Yi-Shuan J; Strongin, Alex Y; Verkhusha, Vladislav V; Izpisua Belmonte, Juan Carlos; Ren, Bing; Wang, Yuanliang; Chien, Shu; Wang, YingxiaoProceedings of the National Academy of Sciences of the United States of America.2018 12 11;30478057
CHRAC/ACF contribute to the repressive ground state of chromatin.Scacchetti, Alessandro; Brueckner, Laura; Jain, Dhawal; Schauer, Tamas; Zhang, Xu; Schnorrer, Frank; van Steensel, Bas; Straub, Tobias; Becker, Peter BLife science alliance.2018 Jan;30456345
The interdependence of gene-regulatory elements and the 3D genome.Vermunt, Marit W; Zhang, Di; Blobel, Gerd AThe Journal of cell biology.2019 01 07;30442643
Improved reference genome of Aedes aegypti informs arbovirus vector control.Matthews, Benjamin J; Dudchenko, Olga; Kingan, Sarah B; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E; Glassford, William J; Herre, Margaret; Redmond, Seth N; Rose, Noah H; Weedall, Gareth D; Wu, Yang; Batra, Sanjit S; Brito-Sierra, Carlos A; BuckiNature.2018 11;30429615
ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification.Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, ArjunNature biotechnology.2018 Nov 12;30418432
Higher-Order Organization Principles of Pre-translational mRNPs.Metkar, Mihir; Ozadam, Hakan; Lajoie, Bryan R; Imakaev, Maxim; Mirny, Leonid A; Dekker, Job; Moore, Melissa JMolecular cell.2018 11 15;30415953
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.P?kowska, Aleksandra; Klaus, Bernd; Xiang, Wanqing; Severino, Jacqueline; Daigle, Nathalie; Klein, Felix A; Ole?, Ma?gorzata; Casellas, Rafael; Ellenberg, Jan; Steinmetz, Lars M; Bertone, Paul; Huber, WolfgangCell systems.2018 Nov 28;30414923
Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome.Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho; Yuede, Carla; Li, Daofeng; Rensing, Nicholas; Huang, Ju; Baldridge, Dustin; Maloney, Susan E; Dougherty, Joseph D; Constantino, John; Jahani-Asl, Arezu; Wong, Michael; Wozniak, David F; Wang, Ting; Klyachko, Vitaly A; Bonni, AzadCell reports.2018 Nov 06;30403997
A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests.Dai, Xiaoyu; Lin, Nan; Li, Daofeng; Wang, TingBiometrics.2018 Nov 02;30387496
CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Chung, Yu-Chieh; Grunwald, David; Zhang, Shaojie; Pederson, ThoruNature methods.2018 Nov;30377374
Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells.Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, LucasCell systems.2018 Oct 24;30342881
Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.Zoller, Benjamin; Little, Shawn C; Gregor, ThomasCell.2018 Oct 18;30340044
Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling.Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura; Wang, Ruipeng; McQuiston, Travis J; Challberg, Sharon S; Pollok, Brian A; Wang, TingCell reports.2018 Oct 16;30332641
CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming.Liu, Yanxia; Yu, Chen; Daley, Timothy Patrick; Wang, Fangyuan; Cao, William S; Bhate, Salil; Lin, Xueqiu; Still 2nd, Chris; Liu, Honglei; Zhao, Dehua; Wang, Haifeng; Xie, Xinmin S; Ding, Sheng; Wong, Wing Hung; Wernig, Marius; Qi, Lei SCell stem cell.2018 Nov 01;30318302
CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization.Wang, Haifeng; Xu, Xiaoshu; Nguyen, Cindy M; Liu, Yanxia; Gao, Yuchen; Lin, Xueqiu; Daley, Timothy; Kipniss, Nathan H; La Russa, Marie; Qi, Lei SCell.2018 Nov 15;30318144
The adult human testis transcriptional cell atlas.Guo, Jingtao; Grow, Edward J; Mlcochova, Hana; Maher, Geoffrey J; Lindskog, Cecilia; Nie, Xichen; Guo, Yixuan; Takei, Yodai; Yun, Jina; Cai, Long; Kim, Robin; Carrell, Douglas T; Goriely, Anne; Hotaling, James M; Cairns, Bradley RCell research.2018 Dec;30315278
Understanding molecular mechanisms of disease through spatial proteomics.Pankow, Sandra; Martínez-Bartolomé, Salvador; Bamberger, Casimir; Yates, John RCurrent opinion in chemical biology.2019 Feb;30308467
CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.Daley, Timothy P; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei SGenome biology.2018 10 08;30296940
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N K; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, FengGenome biology.2018 10 04;30286773
Developmental enhancers and chromosome topology.Furlong, Eileen E M; Levine, MichaelScience (New York, N.Y.).2018 09 28;30262496
PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks.Kordon, Magdalena M; Szczurek, Aleksander; Berniak, Krzysztof; Szelest, Oskar; Solarczyk, Kamil; Tworzyd?o, Magdalena; Wachsmann-Hogiu, Sebastian; Vaahtokari, Anne; Cremer, Christoph; Pederson, Thoru; Dobrucki, Jurek WFASEB journal : official publication of the Federation of American Societies for Experimental Biology.2019 02;30260704
RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome.Chen, Weizhong; Yan, Zhangming; Li, Simin; Huang, Norman; Huang, Xuerui; Zhang, Jin; Zhong, ShengiScience.2018 Jun 29;30240742
Blank spots on the map: some current questions on nuclear organization and genome architecture.Adriaens, Carmen; Serebryannyy, Leonid A; Feric, Marina; Schibler, Andria; Meaburn, Karen J; Kubben, Nard; Trzaskoma, Pawel; Shachar, Sigal; Vidak, Sandra; Finn, Elizabeth H; Sood, Varun; Pegoraro, Gianluca; Misteli, TomHistochemistry and cell biology.2018 Dec;30238154
X-Chromosome Inactivation and Escape from X Inactivation in Mouse.Ma, Wenxiu; Bonora, Giancarlo; Berletch, Joel B; Deng, Xinxian; Noble, William S; Disteche, Christine MMethods in molecular biology (Clifton, N.J.).2018;30218369
Experimental and computational framework for a dynamic protein atlas of human cell division.Cai, Yin; Hossain, M Julius; Hériché, Jean-Karim; Politi, Antonio Z; Walther, Nike; Koch, Birgit; Wachsmuth, Malte; Nijmeijer, Bianca; Kueblbeck, Moritz; Martinic-Kavur, Marina; Ladurner, Rene; Alexander, Stephanie; Peters, Jan-Michael; Ellenberg, JanNature.2018 09;30202089
Integrative detection and analysis of structural variation in cancer genomes.Dixon, Jesse R; Xu, Jie; Dileep, Vishnu; Zhan, Ye; Song, Fan; Le, Victoria T; Yard?mc?, Galip Gürkan; Chakraborty, Abhijit; Bann, Darrin V; Wang, Yanli; Clark, Royden; Zhang, Lijun; Yang, Hongbo; Liu, Tingting; Iyyanki, Sriranga; An, Lin; Pool, ChristopheNature genetics.2018 Sep 10;30202056
Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F; Carlon, EnricoPhysical review letters.2018 Aug 24;30192578
Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways.Zhu, Liangliang; Yan, Feihu; Wang, Zhen; Dong, Haiyan; Bian, Chengling; Wang, Ting; Yu, Enda; Li, JingInternational journal of cancer.2018 Nov 15;30183087
Interchromosomal interactions: A genomic love story of kissing chromosomes.Maass, Philipp G; Barutcu, A Rasim; Rinn, John LThe Journal of cell biology.2019 Jan 07;30181316
RNA, Action through Interactions.Nguyen, Tri C; Zaleta-Rivera, Kathia; Huang, Xuerui; Dai, Xiaofeng; Zhong, ShengTrends in genetics : TIG.2018 Aug 31;30177410
Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries.Sun, James H; Zhou, Linda; Emerson, Daniel J; Phyo, Sai A; Titus, Katelyn R; Gong, Wanfeng; Gilgenast, Thomas G; Beagan, Jonathan A; Davidson, Beverly L; Tassone, Flora; Phillips-Cremins, Jennifer ECell.2018 Aug 27;30173918
Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results.van Steensel, BasEMBO reports.2018 Oct;30158143
Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.Chen, Yu; Zhang, Yang; Wang, Yuchuan; Zhang, Liguo; Brinkman, Eva K; Adam, Stephen A; Goldman, Robert; van Steensel, Bas; Ma, Jian; Belmont, Andrew SThe Journal of cell biology.2018 Aug 28;30154186
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability.Munschauer, Mathias; Nguyen, Celina T; Sirokman, Klara; Hartigan, Christina R; Hogstrom, Larson; Engreitz, Jesse M; Ulirsch, Jacob C; Fulco, Charles P; Subramanian, Vidya; Chen, Jenny; Schenone, Monica; Guttman, Mitchell; Carr, Steven A; Lander, Eric SNature.2018 09;30150775
Emerging Roles of Non-Coding RNA Transcription.Kaikkonen, Minna U; Adelman, KarenTrends in biochemical sciences.2018 09;30145998
Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold.Sun, Mingxuan; Biggs, Ronald; Hornick, Jessica; Marko, John FChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology.2018 Dec;30143891
HiGlass: web-based visual exploration and analysis of genome interaction maps.Kerpedjiev, Peter; Abdennur, Nezar; Lekschas, Fritz; McCallum, Chuck; Dinkla, Kasper; Strobelt, Hendrik; Luber, Jacob M; Ouellette, Scott B; Azhir, Alaleh; Kumar, Nikhil; Hwang, Jeewon; Lee, Soohyun; Alver, Burak H; Pfister, Hanspeter; Mirny, Leonid A; PaGenome biology.2018 08 24;30143029
DXR: A Toolkit for Building Immersive Data Visualizations.Sicat, Ronell; Li, Jiabao; Choi, Junyoung; Cordeil, Maxime; Jeong, Won-Ki; Bach, Benjamin; Pfister, HanspeterIEEE transactions on visualization and computer graphics.2019 01;30136991
Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, JanThe Journal of cell biology.2018 Sep 03;30135095
Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation.Wray-Dutra, Michelle N; Chawla, Raghav; Thomas, Kerri R; Seymour, Brenda J; Arkatkar, Tanvi; Sommer, Karen M; Khim, Socheath; Trapnell, Cole; James, Richard G; Rawlings, David JThe Journal of experimental medicine.2018 Sep 03;30127060
Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model.Zhang, Rongrong; Hu, Ming; Zhu, Yu; Qin, Zhaohui; Deng, Ke; Liu, Jun SIEEE/ACM transactions on computational biology and bioinformatics.2020 Mar-Apr;30113897
One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease.Lazniewski, Michal; Dawson, Wayne K; Rusek, Anna Maria; Plewczynski, DariuszSeminars in cell & developmental biology.2018 Oct 11;30096365
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.Pliner, Hannah A; Packer, Jonathan S; McFaline-Figueroa, José L; Cusanovich, Darren A; Daza, Riza M; Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana; Minkina, Anna; Adey, Andrew C; Steemers, Frank J; Shendure, Jay; Trapnell, ColeMolecular cell.2018 09 06;30078726
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.Cusanovich, Darren A; Hill, Andrew J; Aghamirzaie, Delasa; Daza, Riza M; Pliner, Hannah A; Berletch, Joel B; Filippova, Galina N; Huang, Xingfan; Christiansen, Lena; DeWitt, William S; Lee, Choli; Regalado, Samuel G; Read, David F; Steemers, Frank J; DistCell.2018 Aug 23;30078704
Protein motion in the nucleus: from anomalous diffusion to weak interactions.Woringer, Maxime; Darzacq, XavierBiochemical Society transactions.2018 Aug 20;30065106
Temporal dynamics of pair-rule stripes in living Drosophila embryos.Lim, Bomyi; Fukaya, Takashi; Heist, Tyler; Levine, MichaelProceedings of the National Academy of Sciences of the United States of America.2018 08 14;30061421
Dynamic interplay between enhancer-promoter topology and gene activity.Chen, Hongtao; Levo, Michal; Barinov, Lev; Fujioka, Miki; Jaynes, James B; Gregor, ThomasNature genetics.2018 Sep;30038397
Comparison of OCT Angiography Review Strategies to Identify Vascular Abnormalities in the AVATAR Study.Babiuch, Amy S; Khan, Mehnaz; Hu, Ming; Kaiser, Peter K; Srivastava, Sunil K; Singh, Rishi P; Watts, Allison; Reese, Jamie L; Ehlers, Justis POphthalmology. Retina.2018 Jun;30035246
The three-dimensional organization of the genome in cellular senescence and age-associated diseases.Evans, Shane A; Horrell, Jeremy; Neretti, NicolaSeminars in cell & developmental biology.2019 Jun;30031215
Computational methods for analyzing and modeling genome structure and organization.Lin, Dejun; Bonora, Giancarlo; Yard?mc?, Galip Gürkan; Noble, William SWiley interdisciplinary reviews. Systems biology and medicine.2018 Jul 18;30022617
The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.Menghi, Francesca; Barthel, Floris P; Yadav, Vinod; Tang, Ming; Ji, Bo; Tang, Zhonghui; Carter, Gregory W; Ruan, Yijun; Scully, Ralph; Verhaak, Roel G W; Jonkers, Jos; Liu, Edison TCancer cell.2018 08 13;30017478
GIVE: portable genome browsers for personal websites.Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, ShengGenome biology.2018 07 18;30016975
Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation.Packer, Jonathan; Trapnell, ColeTrends in genetics : TIG.;30007833
Understanding the 3D genome: Emerging impacts on human disease.Krumm, Anton; Duan, ZhijunSeminars in cell & developmental biology.2019 Jun;29990539
Enhancer hubs and loop collisions identified from single-allele topologies.Allahyar, Amin; Vermeulen, Carlo; Bouwman, Britta A M; Krijger, Peter H L; Verstegen, Marjon J A M; Geeven, Geert; van Kranenburg, Melissa; Pieterse, Mark; Straver, Roy; Haarhuis, Judith H I; Jalink, Kees; Teunissen, Hans; Renkens, Ivo J; Kloosterman, Wigard P; Rowland, Benjamin D; de Wit, Elzo; de Ridder, Jeroen; de Laat, WouterNature genetics2018 0829988121
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.2018 Jul 05;29979966
Chromatin organization by an interplay of loop extrusion and compartmental segregation.Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Abdennur, Nezar; Mirny, Leonid AProceedings of the National Academy of Sciences of the United States of America.2018 07 17;29967174
Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process.Limi, Saima; Senecal, Adrien; Coleman, Robert; Lopez-Jones, Melissa; Guo, Peng; Polumbo, Christina; Singer, Robert H; Skoultchi, Arthur I; Cvekl, AlesThe Journal of biological chemistry.2018 Aug 24;29959226
Quantitative live and super-resolution microscopy of mitotic chromosomes.Walther, Nike; Ellenberg, JanMethods in cell biology.2018;29957216
Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy.Mir, Mustafa; Reimer, Armando; Stadler, Michael; Tangara, Astou; Hansen, Anders S; Hockemeyer, Dirk; Eisen, Michael B; Garcia, Hernan; Darzacq, XavierMethods in molecular biology (Clifton, N.J.).2018;29956254
Unsupervised embedding of single-cell Hi-C data.Liu, Jie; Lin, Dejun; Yardimci, Galip Gürkan; Noble, William StaffordBioinformatics (Oxford, England).2018 07 01;29950005
Predicting CTCF-mediated chromatin loops using CTCF-MP.Zhang, Ruochi; Wang, Yuchuan; Yang, Yang; Zhang, Yang; Ma, JianBioinformatics (Oxford, England).2018 Jul 01;29949986
Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal.Sabath, Niv; Vilborg, Anna; Steitz, Joan A; Shalgi, ReutHuman genomics.2018 06 27;29945683
Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction.Lei, Xiao; Shi, Haoran; Kou, Yi; Rajashekar, Niroop; Wu, Fang; Sen, Chandani; Xu, Jiang; Chen, LinBiochemistry.2018 07 17;29944822
SAVER: gene expression recovery for single-cell RNA sequencing.Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I; Raj, Arjun; Li, Mingyao; Zhang, Nancy RNature methods.2018 Jul;29941873
A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes.Teves, Sheila S; An, Luye; Bhargava-Shah, Aarohi; Xie, Liangqi; Darzacq, Xavier; Tjian, RoberteLife.2018 06 25;29939130
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.Yang, Yang; Gu, Quanquan; Zhang, Yang; Sasaki, Takayo; Crivello, Julianna; O'Neill, Rachel J; Gilbert, David M; Ma, JianCell systems.2018 Jun 18;29936186
Imaging dynamic and selective low-complexity domain interactions that control gene transcription.Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe; Dong, Peng; Dailey, Gina M; Cattoglio, Claudia; Heckert, Alec; Banala, Sambashiva; Lavis, Luke; Darzacq, Xavier; Tjian, RobertScience (New York, N.Y.).2018 07 27;29930090
CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.Tasan, Ipek; Sustackova, Gabriela; Zhang, Liguo; Kim, Jiah; Sivaguru, Mayandi; HamediRad, Mohammad; Wang, Yuchuan; Genova, Justin; Ma, Jian; Belmont, Andrew S; Zhao, HuiminNucleic acids research.2018 Jun 15;29912475
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.Shah, Sheel; Takei, Yodai; Zhou, Wen; Lubeck, Eric; Yun, Jina; Eng, Chee-Huat Linus; Koulena, Noushin; Cronin, Christopher; Karp, Christoph; Liaw, Eric J; Amin, Mina; Cai, LongCell.2018 May 31;29887381
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.Quinodoz, Sofia A; Ollikainen, Noah; Tabak, Barbara; Palla, Ali; Schmidt, Jan Marten; Detmar, Elizabeth; Lai, Mason M; Shishkin, Alexander A; Bhat, Prashant; Takei, Yodai; Trinh, Vickie; Aznauryan, Erik; Russell, Pamela; Cheng, Christine; Jovanovic, Marko; Chow, Amy; Cai, Long; McDonel, Patrick; Garber, Manuel; Guttman, MitchellCell.2018 Jun 04;29887377
Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers.Bardales, Jorge A; Wieser, Evin; Kawaji, Hideya; Murakawa, Yasuhiro; Darzacq, XavierGenes.2018 May 23;29882899
Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli.Dine, Elliot; Gil, Agnieszka A; Uribe, Giselle; Brangwynne, Clifford P; Toettcher, Jared ECell systems.2018 Jun 27;29859829
Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II.Lu, Huasong; Yu, Dan; Hansen, Anders S; Ganguly, Sourav; Liu, Rongdiao; Heckert, Alec; Darzacq, Xavier; Zhou, QiangNature.2018 06;29849146
Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging.Politi, Antonio Z; Cai, Yin; Walther, Nike; Hossain, M Julius; Koch, Birgit; Wachsmuth, Malte; Ellenberg, JanNature protocols.2018 06;29844523
Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing.Koch, Birgit; Nijmeijer, Bianca; Kueblbeck, Moritz; Cai, Yin; Walther, Nike; Ellenberg, JanNature protocols.2018 06;29844520
Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods.Chen, Chun Chieh; Stark, Marie; Baikoghli, Mo; Cheng, R HollandJournal of visualized experiments : JoVE.2018 05 11;29806824
Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited].Gustavsson, Anna-Karin; Petrov, Petar N; Moerner, W EOptics express.2018 May 14;29801343
Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts.Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Jarvis, James NJournal of reproductive immunology.2018 Aug;29800761
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer EMethods (San Diego, Calif.).;29772275
Quantitative imaging of chromatin decompaction in living cells.Dultz, Elisa; Mancini, Roberta; Polles, Guido; Vallotton, Pascal; Alber, Frank; Weis, KarstenMolecular biology of the cell.;29771637
Gene regulation in the 3D genome.Li, Yun; Hu, Ming; Shen, YinHuman molecular genetics.2018 08 01;29767704
qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I IScientific reports.;29743503
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.Gao, Xin D; Tu, Li-Chun; Mir, Aamir; Rodriguez, Tomás; Ding, Yuehe; Leszyk, John; Dekker, Job; Shaffer, Scott A; Zhu, Lihua Julie; Wolfe, Scot A; Sontheimer, Erik JNature methods.2018 May 07;29735996
Allele-specific control of replication timing and genome organization during development.Rivera-Mulia, Juan Carlos; Dimond, Andrew; Vera, Daniel; Trevilla-Garcia, Claudia; Sasaki, Takayo; Zimmerman, Jared; Dupont, Catherine; Gribnau, Joost; Fraser, Peter; Gilbert, David MGenome research.2018 06;29735606
Emerging Evidence of Chromosome Folding by Loop Extrusion.Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; Goloborodko, Anton; Mirny, Leonid ACold Spring Harbor symposia on quantitative biology.2017;29728444
The Energetics and Physiological Impact of Cohesin Extrusion.Vian, Laura; P?kowska, Aleksandra; Rao, Suhas S P; Kieffer-Kwon, Kyong-Rim; Jung, Seolkyoung; Baranello, Laura; Huang, Su-Chen; El Khattabi, Laila; Dose, Marei; Pruett, Nathanael; Sanborn, Adrian L; Canela, Andres; Maman, Yaakov; Oksanen, Anna; Resch, Wolfgang; Li, Xingwang; Lee, Byoungkoo; Kovalchuk, Alexander L; Tang, Zhonghui; Nelson, Steevenson; Di Pierro, Michele; Cheng, Ryan R; Machol, Ido; St Hilaire, Brian Glenn; Durand, Neva C; Shamim, Muhammad S; Stamenova, Elena K; Onuchic, José N; Ruan, Yijun; Nussenzweig, Andre; Levens, David; Aiden, Erez Lieberman; Casellas, RafaelCell.2018 May 17;29706548
Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells.Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W EProceedings of SPIE--the International Society for Optical Engineering.2018 Feb;29681676
Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes.Tsai, Albert; Singer, Robert H; Crocker, JustinMolecular cell.2018 Apr 19;29677489
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.Barutcu, A Rasim; Maass, Philipp G; Lewandowski, Jordan P; Weiner, Catherine L; Rinn, John LNature communications2018 04 1329654311
Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.Bonora, G; Deng, X; Fang, H; Ramani, V; Qiu, R; Berletch, J B; Filippova, G N; Duan, Z; Shendure, J; Noble, W S; Disteche, C MNature communications.2018 Apr 13;29654302
Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia.Carvajal, Luis A; Neriah, Daniela Ben; Senecal, Adrien; Benard, Lumie; Thiruthuvanathan, Victor; Yatsenko, Tatyana; Narayanagari, Swathi-Rao; Wheat, Justin C; Todorova, Tihomira I; Mitchell, Kelly; Kenworthy, Charles; Guerlavais, Vincent; Annis, D Allen; Bartholdy, Boris; Will, Britta; Anampa, Jesus D; Mantzaris, Ioannis; Aivado, Manuel; Singer, Robert H; Coleman, Robert A; Verma, Amit; Steidl, UlrichScience translational medicine.2018 Apr 11;29643228
A quantitative map of human Condensins provides new insights into mitotic chromosome architecture.Walther, Nike; Hossain, M Julius; Politi, Antonio Z; Koch, Birgit; Kueblbeck, Moritz; Ødegård-Fougner, Øyvind; Lampe, Marko; Ellenberg, JanThe Journal of cell biology.2018 Apr 09;29632028
Real-time 3D single-molecule localization using experimental point spread functions.Li, Yiming; Mund, Markus; Hoess, Philipp; Deschamps, Joran; Matti, Ulf; Nijmeijer, Bianca; Sabinina, Vilma Jimenez; Ellenberg, Jan; Schoen, Ingmar; Ries, JonasNature methods.2018 May;29630062
Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John LMolecular cell.2018 Apr 05;29625035
Producing genome structure populations with the dynamic and automated PGS software.Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, FrankNature protocols.2018 May;29622804
Visualization of Transvection in Living Drosophila Embryos.Lim, Bomyi; Heist, Tyler; Levine, Michael; Fukaya, TakashiMolecular cell.2018 Apr 19;29606591
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David MNature protocols.2018 May;29599440
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction.Scientific reports.2018 Mar 26;29581440
Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, JanThe Journal of cell biology.2018 Jun 04;29572382
Three-dimensional organization and dynamics of the genome.Szalaj, Przemyslaw; Plewczynski, DariuszCell biology and toxicology.2018 Oct;29568981
Effects of electrostatic interactions on ligand dissociation kinetics.Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John FPhysical review. E.2018 Feb;29548245
Defect-facilitated buckling in supercoiled double-helix DNA.Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu; Neuman, Keir C; Marko, John FPhysical review. E.2018 Feb;29548184
Integrative structure and functional anatomy of a nuclear pore complex.Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael PNature.2018 Mar 22;29539637
Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John LMolecular cell.2018 Mar 15;29526697
Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto; Hopp, Hannah; Das, Devika; Alber, Frank; Chiolo, IreneMethods in enzymology.;29523239
Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin.Annunziatella, Carlo; Chiariello, Andrea M; Esposito, Andrea; Bianco, Simona; Fiorillo, Luca; Nicodemi, MarioMethods (San Diego, Calif.).2018 06 01;29522804
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.Barton, Carl; Morganella, Sandro; Ødegård-Fougner, Øyvind; Alexander, Stephanie; Ries, Jonas; Fitzgerald, Tomas; Ellenberg, Jan; Birney, EwanPLoS computational biology.2018 Mar;29522506
dCas9-targeted locus-specific protein isolation method identifies histone gene regulators.Tsui, Chiahao; Inouye, Carla; Levy, Michaella; Lu, Andrew; Florens, Laurence; Washburn, Michael P; Tjian, RobertProceedings of the National Academy of Sciences of the United States of America.2018 03 20;29507191
Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations.Stevens, Kelly R; Murry, Charles ECell stem cell.2018 Mar 01;29499147
Nanodelivery of a functional membrane receptor to manipulate cellular phenotype.Patriarchi, Tommaso; Shen, Ao; He, Wei; Baikoghli, Mo; Cheng, R Holland; Xiang, Yang K; Coleman, Matthew A; Tian, LinScientific reports.2018 Feb 23;29476125
Quantitative 3-D morphometric analysis of individual dendritic spines.Basu, Subhadip; Saha, Punam Kumar; Roszkowska, Matylda; Magnowska, Marta; Baczynska, Ewa; Das, Nirmal; Plewczynski, Dariusz; Wlodarczyk, JakubScientific reports.2018 Feb 23;29476060
Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, ArjunCell systems.2018 Feb 28;29454938
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.Robinson, James T; Turner, Douglass; Durand, Neva C; Thorvaldsdóttir, Helga; Mesirov, Jill P; Aiden, Erez LiebermanCell systems.2018 Feb 28;29428417
Single-cell replication profiling to measure stochastic variation in mammalian replication timing.Dileep, Vishnu; Gilbert, David MNature communications.2018 Jan 30;29382831
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJunMethods (San Diego, Calif.).2018 Jan 31;29382556
Dynamic evolution of regulatory element ensembles in primate CD4+T cells.Danko, Charles G; Choate, Lauren A; Marks, Brooke A; Rice, Edward J; Wang, Zhong; Chu, Tinyi; Martins, Andre L; Dukler, Noah; Coonrod, Scott A; Tait Wojno, Elia D; Lis, John T; Kraus, W Lee; Siepel, AdamNature ecology & evolution.2018 Mar;29379187
A pathway for mitotic chromosome formation.Gibcus, Johan H; Samejima, Kumiko; Goloborodko, Anton; Samejima, Itaru; Naumova, Natalia; Nuebler, Johannes; Kanemaki, Masato T; Xie, Linfeng; Paulson, James R; Earnshaw, William C; Mirny, Leonid A; Dekker, JobScience (New York, N.Y.).2018 02 09;29348367
Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING).Maass, Philipp G; Barutcu, A Rasim; Shechner, David M; Weiner, Catherine L; Melé, Marta; Rinn, John LNature structural & molecular biology.2018 Feb;29343869
High-throughput identification of RNA nuclear enrichment sequences.Shukla, Chinmay J; McCorkindale, Alexandra L; Gerhardinger, Chiara; Korthauer, Keegan D; Cabili, Moran N; Shechner, David M; Irizarry, Rafael A; Maass, Philipp G; Rinn, John LThe EMBO journal.2018 Mar 15;29335281
Detecting hierarchical genome folding with network modularity.Norton, Heidi K; Emerson, Daniel J; Huang, Harvey; Kim, Jesi; Titus, Katelyn R; Gu, Shi; Bassett, Danielle S; Phillips-Cremins, Jennifer ENature methods.2018 Feb;29334377
Ki-67: more than a proliferation marker.Sun, Xiaoming; Kaufman, Paul DChromosoma.2018 Jan 10;29322240
3D single-molecule super-resolution microscopy with a tilted light sheet.Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W ENature communications.2018 Jan 09;29317629
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers.Yan, Jian; Chen, Shi-An A; Local, Andrea; Liu, Tristin; Qiu, Yunjiang; Dorighi, Kristel M; Preissl, Sebastian; Rivera, Chloe M; Wang, Chaochen; Ye, Zhen; Ge, Kai; Hu, Ming; Wysocka, Joanna; Ren, BingCell research.2018 Feb;29313530
Messages from the voices within: regulation of signaling by proteins of the nuclear lamina.Gerace, Larry; Tapia, OlgaCurrent opinion in cell biology.2018 Jun;29306725
Robust model-based analysis of single-particle tracking experiments with Spot-On.Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, XaviereLife.2018 Jan 04;29300163
Extrusion without a motor: a new take on the loop extrusion model of genome organization.Brackley, C A; Johnson, J; Michieletto, D; Morozov, A N; Nicodemi, M; Cook, P R; Marenduzzo, DNucleus (Austin, Tex.).2018 01 01;29300120
Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions.Shechtman, Yoav; Gustavsson, Anna-Karin; Petrov, Petar N; Dultz, Elisa; Lee, Maurice Y; Weis, Karsten; Moerner, W EBiomedical optics express.2017 Dec 01;29296501
A mixed-scale dense convolutional neural network for image analysis.Pelt, Daniël M; Sethian, James AProceedings of the National Academy of Sciences of the United States of America.2018 Jan 09;29279403
Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images.Baddeley, David; Bewersdorf, JoergAnnual review of biochemistry.2018 06 20;29272143
The structural variability of the influenza A hemagglutinin receptor-binding site.Lazniewski, Michal; Dawson, Wayne K; Szczepinska, Teresa; Plewczynski, DariuszBriefings in functional genomics.2018 11 26;29253080
Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle.Mukund, Kavitha; Subramaniam, ShankarFrontiers in physiology.2017;29249983
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking.Kaewsapsak, Pornchai; Shechner, David Michael; Mallard, William; Rinn, John L; Ting, Alice YeLife.2017 Dec 14;29239719
Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq.Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, TingMethods in molecular biology (Clifton, N.J.).2018;29224147
Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices.Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D; Mondragón, Alfonso; Marko, John FPhysical review letters.2017 Nov 03;29219598
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.Wutz, Gordana; Várnai, Csilla; Nagasaka, Kota; Cisneros, David A; Stocsits, Roman R; Tang, Wen; Schoenfelder, Stefan; Jessberger, Gregor; Muhar, Matthias; Hossain, M Julius; Walther, Nike; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Zuber, Johannes; The EMBO journal.2017 12 15;29217591
A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture.Gassler, Johanna; Brandão, Hugo B; Imakaev, Maxim; Flyamer, Ilya M; Ladstätter, Sabrina; Bickmore, Wendy A; Peters, Jan-Michael; Mirny, Leonid A; Tachibana, KikuëThe EMBO journal.2017 12 15;29217590
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model.Sundaram, Vasavi; Wang, TingBioEssays : news and reviews in molecular, cellular and developmental biology.2018 Jan;29206283
Corrigendum: The 4D nucleome project.Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome NetworkNature.2017 12 14;29168505
Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins.Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J; Almassalha, Luay M; Backman, Vadim; Adam, Stephen A; Goldman, Robert D; Marko, John FMolecular biology of the cell.2018 Jan 15;29142071
Live Imaging of mRNA Synthesis in Drosophila.Garcia, Hernan G; Gregor, ThomasMethods in molecular biology (Clifton, N.J.).2018;29130209
Single mRNA Molecule Detection in Drosophila.Little, Shawn C; Gregor, ThomasMethods in molecular biology (Clifton, N.J.).2018;29130194
Genome-wide association study identifies a novel locus for cannabis dependence.Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E CMolecular psychiatry.2017 Nov 07;29112194
Nuclear microenvironments modulate transcription from low-affinity enhancers.Tsai, Albert; Muthusamy, Anand K; Alves, Mariana Rp; Lavis, Luke D; Singer, Robert H; Stern, David L; Crocker, JustineLife.2017 Nov 02;29095143
Two independent modes of chromatin organization revealed by cohesin removal.Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, FrancoisNature.2017 Nov 02;29094699
Simultaneous measurement of emission color and 3D position of single molecules.Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, SjoerdOptics express.2016 Mar 07;29092328
De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez; Wolynes, Peter G; Onuchic, José NProceedings of the National Academy of Sciences of the United States of America.2017 Nov 14;29087948
Oligomerization and ATP stimulate condensin-mediated DNA compaction.Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John FScientific reports.2017 Oct 27;29079757
STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus.Li, Peng; Mitra, Suman; Spolski, Rosanne; Oh, Jangsuk; Liao, Wei; Tang, Zhonghui; Mo, Fei; Li, Xingwang; West, Erin E; Gromer, Daniel; Lin, Jian-Xin; Liu, Chengyu; Ruan, Yijun; Leonard, Warren JProceedings of the National Academy of Sciences of the United States of America.2017 11 14;29078395
Recent evidence that TADs and chromatin loops are dynamic structures.Hansen, Anders S; Cattoglio, Claudia; Darzacq, Xavier; Tjian, RobertNucleus (Austin, Tex.).2018 01 01;29077530
A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression.Gallagher, Michael D; Posavi, Marijan; Huang, Peng; Unger, Travis L; Berlyand, Yosef; Gruenewald, Analise L; Chesi, Alessandra; Manduchi, Elisabetta; Wells, Andrew D; Grant, Struan F A; Blobel, Gerd A; Brown, Christopher D; Chen-Plotkin, Alice SAmerican journal of human genetics.2017 Nov 02;29056226
Supercoiling DNA Locates Mismatches.Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir CPhysical review letters.2017 Oct 06;29053317
Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei.Banigan, Edward J; Stephens, Andrew D; Marko, John FBiophysical journal.2017 Oct 17;29045860
RNA structure interactions and ribonucleoprotein processes of the influenza A virus.Dawson, Wayne K; Lazniewski, Michal; Plewczynski, DariuszBriefings in functional genomics.2018 11 26;29040388
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.Sun, Zhe; Wang, Ting; Deng, Ke; Wang, Xiao-Feng; Lafyatis, Robert; Ding, Ying; Hu, Ming; Chen, WeiBioinformatics (Oxford, England).2018 01 01;29036318
Transvection.Fukaya, Takashi; Levine, MichaelCurrent biology : CB.2017 Oct 09;29017034
Cohesin Loss Eliminates All Loop Domains.Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian; Engreitz, Jesse M; Perez, Elizabeth M; Kieffer-Kwon, Kyong-Rim; Sanborn, Adrian L; Johnstone, Sarah E; Bascom, Gavin D; Bochkov, Ivan D; Huang, Xingfan; Shamim, Muhammad S; Shin, Jaeweon; Turner, Douglass; Ye, Ziyi; Omer, Arina D; Robinson, James T; Schlick, Tamar; Bernstein, Bradley E; Casellas, Rafael; Lander, Eric S; Aiden, Erez LiebermanCell.2017 Oct 05;28985562
Dense Bicoid hubs accentuate binding along the morphogen gradient.Mir, Mustafa; Reimer, Armando; Haines, Jenna E; Li, Xiao-Yong; Stadler, Michael; Garcia, Hernan; Eisen, Michael B; Darzacq, XavierGenes & development.2017 Sep 01;28982761
Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement.Germier, Thomas; Kocanova, Silvia; Walther, Nike; Bancaud, Aurélien; Shaban, Haitham Ahmed; Sellou, Hafida; Politi, Antonio Zaccaria; Ellenberg, Jan; Gallardo, Franck; Bystricky, KerstinBiophysical journal.2017 Oct 03;28978433
From structure to function, how bioinformatics help to reveal functions of our genomes.Zheng, Xiaoqi; Zhong, ShengGenome biology.2017 Sep 26;28950915
Structural aspects of the inactive X chromosome.Bonora, Giancarlo; Disteche, Christine MPhilosophical transactions of the Royal Society of London. Series B, Biological sciences.2017 Nov 05;28947656
Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate.Isoda, Takeshi; Moore, Amanda J; He, Zhaoren; Chandra, Vivek; Aida, Masatoshi; Denholtz, Matthew; Piet van Hamburg, Jan; Fisch, Kathleen M; Chang, Aaron N; Fahl, Shawn P; Wiest, David L; Murre, CornelisCell.2017 Sep 21;28938112
Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage.Rege, Mayuri; Phillips-Cremins, Jennifer EMolecular cell.2017 Sep 21;28938095
Liquid phase condensation in cell physiology and disease.Shin, Yongdae; Brangwynne, Clifford PScience (New York, N.Y.).2017 09 22;28935776
Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons.Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, StavroseLife.2017 Sep 21;28933695
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element.Huang, Peng; Keller, Cheryl A; Giardine, Belinda; Grevet, Jeremy D; Davies, James O J; Hughes, Jim R; Kurita, Ryo; Nakamura, Yukio; Hardison, Ross C; Blobel, Gerd AGenes & development.2017 Aug 15;28916711
Targeting Specificity of the CRISPR/Cas9 System.Tasan, Ipek; Zhao, HuiminACS synthetic biology.2017 09 15;28911233
The 4D nucleome project.Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome NetworkNature.2017 Sep 13;28905911
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, TingBMC genomics.2017 Sep 12;28899353
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael PMolecular cell.2017 Sep 21;28890333
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 SCell stem cell.2017 Sep 07;28886366
Exploiting sequence-based features for predicting enhancer-promoter interactions.Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, JianBioinformatics (Oxford, England).2017 Jul 15;28881991
LAIT: a local ancestry inference toolkit.Hui, Daniel; Fang, Zhou; Lin, Jerome; Duan, Qing; Li, Yun; Hu, Ming; Chen, WeiBMC genetics.2017 09 06;28877673
HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, HanspeterIEEE transactions on visualization and computer graphics.2018 Jan;28866592
The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality?Bach, Benjamin; Sicat, Ronell; Beyer, Johanna; Cordeil, Maxime; Pfister, HanspeterIEEE transactions on visualization and computer graphics.2018 01;28866590
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.Yang, Tao; Zhang, Feipeng; Yard?mc?, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, QunhuaGenome research.2017 Nov;28855260
Crossed wires: 3D genome misfolding in human disease.Norton, Heidi K; Phillips-Cremins, Jennifer EThe Journal of cell biology.2017 11 06;28855250
Evolutionarily Conserved Principles Predict 3D Chromatin Organization.Rowley, M Jordan; Nichols, Michael H; Lyu, Xiaowen; Ando-Kuri, Masami; Rivera, I Sarahi M; Hermetz, Karen; Wang, Ping; Ruan, Yijun; Corces, Victor GMolecular cell.2017 Sep 07;28826674
Reversed graph embedding resolves complex single-cell trajectories.Qiu, Xiaojie; Mao, Qi; Tang, Ying; Wang, Li; Chawla, Raghav; Pliner, Hannah A; Trapnell, ColeNature methods.2017 Oct;28825705
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, JonathanNature cell biology.2017 Sep;28825700
Comprehensive single-cell transcriptional profiling of a multicellular organism.Cao, Junyue; Packer, Jonathan S; Ramani, Vijay; Cusanovich, Darren A; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N; Steemers, Frank J; Adey, Andrew; Waterston, Robert H; Trapnell, Cole; Shendure, JayScience (New York, N.Y.).2017 08 18;28818938
A magnetic micropore chip for rapid (Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, DavidLab on a chip.2017 Sep 12;28809985
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P; Xu, Jianliang; Jung, Seolkyoung; Pekowska, Aleksandra; Dose, Marei; Stevens, Evan; Mathe, Ewy; Dong, Peng; Huang, Su-Chen; Ricci, Maria Aurelia; Baranello, Laura; Zheng, Ying; Tomassoni Ardori, Francesco; Resch, Wolfgang; Stavreva, Diana; Nelson, Steevenson; McAndrew, Michael; Casellas, Adriel; Finn, Elizabeth; Gregory, Charles; St Hilaire, Brian Glenn; Johnson, Steven M; Dubois, Wendy; Cosma, Maria Pia; Batchelor, Eric; Levens, David; Phair, Robert D; Misteli, Tom; Tessarollo, Lino; Hager, Gordon; Lakadamyali, Melike; Liu, Zhe; Floer, Monique; Shroff, Hari; Aiden, Erez Lieberman; Casellas, RafaelMolecular cell.;28803781
A new era of studying p53-mediated transcription activation.Liu, Wei-Li; Coleman, Robert A; Singh, Sameer KTranscription.2018;28795863
The Three-Dimensional Organization of Mammalian Genomes.Yu, Miao; Ren, BingAnnual review of cell and developmental biology.2017 Oct 06;28783961
Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map.Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger DProceedings of the National Academy of Sciences of the United States of America.2017 Aug 15;28765367
The three-dimensional genome organization of Drosophila melanogaster through data integration.Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, FrankGenome biology.2017 Jul 31;28760140
ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.Ou, Horng D; Phan, Sébastien; Deerinck, Thomas J; Thor, Andrea; Ellisman, Mark H; O'Shea, Clodagh CScience (New York, N.Y.).2017 07 28;28751582
Genome Organization Drives Chromosome Fragility.Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, AndréCell.2017 Jul 27;28735753
Integrative modelling of cellular assemblies.Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, MayaCurrent opinion in structural biology.2017 Jul 20;28735107
Cell-cycle dynamics of chromosomal organization at single-cell resolution.Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, AmosNature.2017 07 05;28682332
Phase separation drives heterochromatin domain formation.Strom, Amy R; Emelyanov, Alexander V; Mir, Mustafa; Fyodorov, Dmitry V; Darzacq, Xavier; Karpen, Gary HNature.2017 07 13;28636597
Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells.Sun, Xiaoming; Bizhanova, Aizhan; Matheson, Timothy D; Yu, Jun; Zhu, Julie L; Kaufman, Paul DMolecular and cellular biology.2017 Jun 19;28630280
Torque and buckling in stretched intertwined double-helix DNAs.Brahmachari, Sumitabha; Marko, John FPhysical review. E.2017 May;28618488
DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism.Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis JJCI insight.2017 Jun 15;28614801
EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.He, Yu; Wang, TingBioinformatics (Oxford, England).2017 Jun 09;28605501
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Nature genetics.2017 Jul;28604729
Visualizing adenosine-to-inosine RNA editing in single mammalian cells.Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara HNature methods.2017 Jun 12;28604724
FISH-ing for captured contacts: towards reconciling FISH and 3C.Fudenberg, Geoffrey; Imakaev, MaximNature methods.2017 Jul;28604723
Engineering biological systems using automated biofoundries.Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, HuiminMetabolic engineering.2017 Jul;28602523
Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues.Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, TingBMC genomics.2017 Jun 05;28583088
HUGIn: Hi-C Unifying Genomic Interrogator.Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, YunBioinformatics (Oxford, England).2017 Dec 01;28582503
The dynamic three-dimensional organization of the diploid yeast genome.Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya JeLife.2017 May 24;28537556
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment.Beagan, Jonathan A; Duong, Michael T; Titus, Katelyn R; Zhou, Linda; Cao, Zhendong; Ma, Jingjing; Lachanski, Caroline V; Gillis, Daniel R; Phillips-Cremins, Jennifer EGenome research.2017 07;28536180
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit GCell.2017 May 18;28525758
Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression.van Steensel, Bas; Belmont, Andrew SCell.2017 May 18;28525751
Combinatorial chemistry in drug discovery.Liu, Ruiwu; Li, Xiaocen; Lam, Kit SCurrent opinion in chemical biology.2017 Jun;28494316
Genetic interaction mapping in mammalian cells using CRISPR interference.Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan JNature methods.2017 Jun;28481362
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
Rapid Rates of Pol II Elongation in the Drosophila Embryo.Fukaya, Takashi; Lim, Bomyi; Levine, MichaelCurrent biology : CB.2017 May 08;28457866
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
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH.Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, LongBiophysical journal.2017 May 09;28427715
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
Causes and consequences of nuclear gene positioning.Shachar, Sigal; Misteli, TomJournal of cell science.2017 May 01;28404786
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
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions.Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, YijunNature protocols.2017 May;28358394
FISHing Out the Details of CRISPR Genome Tracks.Coté, Allison J; Raj, ArjunBiophysical journal.2017 Mar 28;28355532
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition.Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, KikuëNature.2017 04 06;28355183
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
Form and function of topologically associating genomic domains in budding yeast.Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan MProceedings of the National Academy of Sciences of the United States of America.2017 Apr 11;28348222
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez LiebermanScience (New York, N.Y.).2017 Apr 07;28336562
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
Unearthing worm replication origins.Sasaki, Takayo; Gilbert, David MNature structural & molecular biology.2017 03 03;28257138
Multivalent Small-Molecule Pan-RAS Inhibitors.Welsch, Matthew E; Kaplan, Anna; Chambers, Jennifer M; Stokes, Michael E; Bos, Pieter H; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A; Huang, Christine S; Tran, Timothy H; Akkiraju, Hemanth; Brown, Lewis M; Nandakumar, Renu; Cremers, Serge; Yang, Wan Seok; Tong, Liang; Olive, Kenneth P; Ferrando, Adolfo; Stockwell, Brent RCell.;28235199
Epigenetic characteristics of the mitotic chromosome in 1D and 3D.Oomen, Marlies E; Dekker, JobCritical reviews in biochemistry and molecular biology.2017 Apr;28228067
A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, HuiminACS synthetic biology.2017 Mar 07;28215080
Comparative analysis of 2D and 3D distance measurements to study spatial genome organization.Finn, Elizabeth H; Pegoraro, Gianluca; Shachar, Sigal; Misteli, TomMethods (San Diego, Calif.).2017 Jul 01;28179124
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
High-throughput automated microfluidic sample preparation for accurate microbial genomics.Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul CNature communications.2017 Jan 27;28128213
ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis.Li, Zhaomin; Zhang, Peng; Yan, Aimin; Guo, Zhengyu; Ban, Yuguang; Li, Jin; Chen, Shi; Yang, Hui; He, Yongzheng; Li, Jianping; Guo, Ying; Zhang, Wen; Hajiramezanali, Ehsan; An, Huangda; Fajardo, Darlene; Harbour, J William; Ruan, Yijun; Nimer, Stephen D; Yu, Peng; Chen, Xi; Xu, Mingjiang; Yang, Feng-ChunScience advances.2017 Jan;28116354
Single-cell mRNA quantification and differential analysis with Census.Qiu, Xiaojie; Hill, Andrew; Packer, Jonathan; Lin, Dejun; Ma, Yi-An; Trapnell, ColeNature methods.2017 Mar;28114287
Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry.Chao, Ran; Liang, Jing; Tasan, Ipek; Si, Tong; Ju, Linyang; Zhao, HuiminACS synthetic biology.2017 Apr 21;28103009
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
A New Era of Genome Integration-Simply Cut and Paste!Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, HuiminACS synthetic biology.2017 04 21;28073246
Predicting chromatin architecture from models of polymer physics.Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, MarioChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology2017 0328070687
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
Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets.Shin, Yongdae; Berry, Joel; Pannucci, Nicole; Haataja, Mikko P; Toettcher, Jared E; Brangwynne, Clifford PCell.2017 Jan 12;28041848
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.Fang, Rongxin; Yu, Miao; Li, Guoqiang; Chee, Sora; Liu, Tristin; Schmitt, Anthony D; Ren, BingCell research.2016 Dec;27886167
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
Genome-wide mapping and analysis of chromosome architecture.Schmitt, Anthony D; Hu, Ming; Ren, BingNature reviews. Molecular cell biology.2016 12;27580841
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
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez LiebermanCell systems.2016 Jul;27467249
Allele-Specific Quantification of Structural Variations in Cancer Genomes.Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, JianCell systems.2016 Jul;27453446
Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription.Beagrie, Robert A; Pombo, AnaBioEssays : 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, 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
CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop.Beagan, Jonathan A; Phillips-Cremins, Jennifer EWiley interdisciplinary reviews. Systems biology and medicine.2016 Jul;27265842
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
CRISPR/Cas9 for Human Genome Engineering and Disease Research.Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei SAnnual review of genomics and human genetics.2016 Aug 31;27216776
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
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 MDisaster medicine and public health preparedness.2016 06;27174171
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data.Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, MingBioinformatics (Oxford, England).2016 09 01;27153668
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
Jointly characterizing epigenetic dynamics across multiple human cell types.Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross CNucleic acids research.2016 08 19;27095202
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
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, YunBioinformatics (Oxford, England).2016 03 01;26543175
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