Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
4D Nucleome (820)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. | Fang, Weixiang; Bell, Claire M; Sapirstein, Abel; Asami, Soichiro; Leeper, Kathleen; Zack, Donald J; Ji, Hongkai; Kalhor, Reza | Cell | 2022 Nov 23 | 36423582 | |
| Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. | Zhu, Xiaoyu; Qi, Chuangye; Wang, Ruoyu; Lee, Joo-Hyung; Shao, Jiaofang; Bei, Lanxin; Xiong, Feng; Nguyen, Phuoc T; Li, Guojie; Krakowiak, Joanna; Koh, Su-Pin; Simon, Lukas M; Han, Leng; Moore, Travis I; Li, Wenbo | Cell reports | 2022 Nov 01 | 36323253 | |
| Divergent clonal differentiation trajectories of T cell exhaustion. | Daniel, Bence; Yost, Kathryn E; Hsiung, Sunnie; Sandor, Katalin; Xia, Yu; Qi, Yanyan; Hiam-Galvez, Kamir J; Black, Mollie; J Raposo, Colin; Shi, Quanming; Meier, Stefanie L; Belk, Julia A; Giles, Josephine R; Wherry, E John; Chang, Howard Y; Egawa, Takeshi; Satpathy, Ansuman T | Nature immunology | 2022 Nov | 36289450 | |
| Subtype-specific 3D genome alteration in acute myeloid leukaemia. | Xu, Jie; Song, Fan; Lyu, Huijue; Kobayashi, Mikoto; Zhang, Baozhen; Zhao, Ziyu; Hou, Ye; Wang, Xiaotao; Luan, Yu; Jia, Bei; Stasiak, Lena; Wong, Josiah Hiu-Yuen; Wang, Qixuan; Jin, Qi; Jin, Qiushi; Fu, Yihao; Yang, Hongbo; Hardison, Ross C; Dovat, Sinisa; Platanias, Leonidas C; Diao, Yarui; Yang, Yue; Yamada, Tomoko; Viny, Aaron D; Levine, Ross L; Claxton, David; Broach, James R; Zheng, Hong; Yue, Feng | Nature | 2022 Nov | 36289338 | |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu, Tian; Ang, Cheen Euong; Zhuang, Xiaowei | Cell | 2022 Nov 10 | 36272405 | |
| RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. | Kaminski, Nicole; Wondisford, Anne R; Kwon, Youngho; Lynskey, Michelle Lee; Bhargava, Ragini; Barroso-González, Jonathan; García-Expósito, Laura; He, Boxue; Xu, Meng; Mellacheruvu, Dattatreya; Watkins, Simon C; Modesti, Mauro; Miller, Kyle M; Nesvizhskii, Alexey I; Zhang, Huaiying; Sung, Patrick; O'Sullivan, Roderick J | Molecular cell | 2022 Nov 03 | 36265488 | |
| Optimized single-nucleus transcriptional profiling by combinatorial indexing. | Martin, Beth K; Qiu, Chengxiang; Nichols, Eva; Phung, Melissa; Green-Gladden, Rula; Srivatsan, Sanjay; Blecher-Gonen, Ronnie; Beliveau, Brian J; Trapnell, Cole; Cao, Junyue; Shendure, Jay | Nature protocols | 2022 Oct 19 | 36261634 | |
| Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67. | van Schaik, Tom; Manzo, Stefano G; Vouzas, Athanasios E; Liu, Ning Qing; Teunissen, Hans; de Wit, Elzo; Gilbert, David M; van Steensel, Bas | EMBO reports | 2022 Oct 17 | 36245428 | |
| GenoREC: A Recommendation System for Interactive Genomics Data Visualization. | Pandey, Aditeya; L'Yi, Sehi; Wang, Qianwen; Borkin, Michelle A; Gehlenborg, Nils | IEEE transactions on visualization and computer graphics | 2022 Oct 03 | 36191105 | |
| Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. | Stackpole, Mary L; Zeng, Weihua; Li, Shuo; Liu, Chun-Chi; Zhou, Yonggang; He, Shanshan; Yeh, Angela; Wang, Ziye; Sun, Fengzhu; Li, Qingjiao; Yuan, Zuyang; Yildirim, Asli; Chen, Pin-Jung; Winograd, Paul; Tran, Benjamin; Lee, Yi-Te; Li, Paul Shize; Noor, Zorawar; Yokomizo, Megumi; Ahuja, Preeti; Zhu, Yazhen; Tseng, Hsian-Rong; Tomlinson, James S; Garon, Edward; French, Samuel; Magyar, Clara E; Dry, Sarah; Lajonchere, Clara; Geschwind, Daniel; Choi, Gina; Saab, Sammy; Alber, Frank; Wong, Wing Hung; Dubinett, Steven M; Aberle, Denise R; Agopian, Vatche; Han, Steven-Huy B; Ni, Xiaohui; Li, Wenyuan; Zhou, Xianghong Jasmine | Nature communications | 2022 Sep 29 | 36175411 | |
| Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN. | Banik, Anik; Podder, Souvik; Saha, Sovan; Chatterjee, Piyali; Halder, Anup Kumar; Nasipuri, Mita; Basu, Subhadip; Plewczynski, Dariusz | Cells | 2022 Aug 25 | 36078056 | |
| Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites. | Zou, Roger S; Marin-Gonzalez, Alberto; Liu, Yang; Liu, Hans B; Shen, Leo; Dveirin, Rachel K; Luo, Jay X J; Kalhor, Reza; Ha, Taekjip | Nature cell biology | 2022 Sep | 36064968 | |
| CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. | van Schaik, Tom; Liu, Ning Qing; Manzo, Stefano G; Peric-Hupkes, Daan; de Wit, Elzo; van Steensel, Bas | Genome biology | 2022 Sep 01 | 36050765 | |
| Mammalian genome innovation through transposon domestication. | Modzelewski, Andrew J; Gan Chong, Johnny; Wang, Ting; He, Lin | Nature cell biology | 2022 09 | 36008480 | |
| Embryo model completes gastrulation to neurulation and organogenesis. | Amadei, Gianluca; Handford, Charlotte E; Qiu, Chengxiang; De Jonghe, Joachim; Greenfeld, Hannah; Tran, Martin; Martin, Beth K; Chen, Dong-Yuan; Aguilera-Castrejon, Alejandro; Hanna, Jacob H; Elowitz, Michael B; Hollfelder, Florian; Shendure, Jay; Glover, David M; Zernicka-Goetz, Magdalena | Nature | 2022 10 | 36007540 | |
| Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. | Cheng, Li-Chun; Zhang, Xi; Abhinav, Kanishk; Nguyen, Julie A; Baboo, Sabyasachi; Martinez-Bartolomé, Salvador; Branon, Tess C; Ting, Alice Y; Loose, Esther; Yates 3rd, John R; Gerace, Larry | Journal of proteome research | 2022 Sep 02 | 35972904 | |
| High throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. | Jones, Ian R; Ren, Xingjie; Shen, Yin | Human molecular genetics | 2022 Aug 16 | 35972825 | |
| Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis. | Blair, Andrew P; Hu, Robert K; Farah, Elie N; Chi, Neil C; Pollard, Katherine S; Przytycki, Pawel F; Kathiriya, Irfan S; Bruneau, Benoit G | Bioinformatics advances | 2022 | 35967929 | |
| Multiomics characterization of mouse hepatoblastoma identifies yes-associated protein 1 target genes. | Rodríguez, Tomás C; Kwan, Suet-Yan; Smith, Jordan L; Dadafarin, Sina; Wu, Chern-Horng; Sontheimer, Erik J; Xue, Wen | Hepatology (Baltimore, Md.) | 2022 Aug 06 | 35932276 | |
| Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells. | Fonseca, Raíssa; Burn, Thomas N; Gandolfo, Luke C; Devi, Sapna; Park, Simone L; Obers, Andreas; Evrard, Maximilien; Christo, Susan N; Buquicchio, Frank A; Lareau, Caleb A; McDonald, Keely M; Sandford, Sarah K; Zamudio, Natasha M; Zanluqui, Nagela G; Zaid, Ali; Speed, Terence P; Satpathy, Ansuman T; Mueller, Scott N; Carbone, Francis R; Mackay, Laura K | Nature immunology | 2022 08 | 35882933 | |
| 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. | Haws, Spencer A; Simandi, Zoltan; Barnett, R Jordan; Phillips-Cremins, Jennifer E | Cell | 2022 07 21 | 35868274 | |
| Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq. | Zhang, Liguo; Chen, Yu; Belmont, Andrew S | Methods in molecular biology (Clifton, N.J.) | 2022 | 35867249 | |
| Assessing Specific Networks of Chromatin Interactions with HiChIP. | Di Giammartino, Dafne Campigli; Polyzos, Alexander; Apostolou, Effie | Methods in molecular biology (Clifton, N.J.) | 2022 | 35867248 | |
| Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. | Zhu, Xiaopeng; Zhang, Yang; Wang, Yuchuan; Tian, Dechao; Belmont, Andrew S; Swedlow, Jason R; Ma, Jian | Nature methods | 2022 08 | 35864167 | |
| Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser. | Li, Daofeng; Harrison, Jessica K; Purushotham, Deepak; Wang, Ting | Nature methods | 2022 08 | 35864166 | |
| Development of 68Ga-Labeled Hepatitis E Virus Nanoparticles for Targeted Drug Delivery and Diagnostics with PET. | Lambidis, Elisavet; Chen, Chun-Chieh; Baikoghli, Mo; Imlimthan, Surachet; Khng, You Cheng; Sarparanta, Mirkka; Cheng, R Holland; Airaksinen, Anu J | Molecular pharmaceutics | 2022 08 01 | 35857429 | |
| Characterizing cis-regulatory elements using single-cell epigenomics. | Preissl, Sebastian; Gaulton, Kyle J; Ren, Bing | Nature reviews. Genetics | 2022 Jul 15 | 35840754 | |
| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci, Domenic N; Hansen, Anders S | Nature structural & molecular biology | 2022 07 | 35835869 | |
| Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. | Voortman, Lukas; Anderson, Caitlin; Urban, Elizabeth; Yuan, Luorongxin; Tran, Sang; Neuhaus-Follini, Alexandra; Derrick, Josh; Gregor, Thomas; Johnston Jr, Robert J | Developmental cell | 2022 Aug 08 | 35835116 | |
| Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. | Conte, Mattia; Irani, Ehsan; Chiariello, Andrea M; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario | Nature communications | 2022 07 13 | 35831310 | |
| Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. | Boninsegna, Lorenzo; Yildirim, Asli; Polles, Guido; Zhan, Yuxiang; Quinodoz, Sofia A; Finn, Elizabeth H; Guttman, Mitchell; Zhou, Xianghong Jasmine; Alber, Frank | Nature methods | 2022 08 | 35817938 | |
| A time-resolved, multi-symbol molecular recorder via sequential genome editing. | Choi, Junhong; Chen, Wei; Minkina, Anna; Chardon, Florence M; Suiter, Chase C; Regalado, Samuel G; Domcke, Silvia; Hamazaki, Nobuhiko; Lee, Choli; Martin, Beth; Daza, Riza M; Shendure, Jay | Nature | 2022 08 | 35794474 | |
| Nuclear speckles - a driving force in gene expression. | Faber, Gabriel P; Nadav-Eliyahu, Shani; Shav-Tal, Yaron | Journal of cell science | 2022 Jul 01 | 35788677 | |
| Guilt by association: EcDNA as a mobile transactivator in cancer. | Zhu, Yanfen; Gong, Liang; Wei, Chia-Lin | Trends in cancer | 2022 Jun 23 | 35753910 | |
| A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. | Chen, Jiawen; Liu, Weifang; Luo, Tianyou; Yu, Zhentao; Jiang, Minzhi; Wen, Jia; Gupta, Gaorav P; Giusti, Paola; Zhu, Hongtu; Yang, Yuchen; Li, Yun | Briefings in bioinformatics | 2022 07 18 | 35753702 | |
| Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. | Belk, Julia A; Yao, Winnie; Ly, Nghi; Freitas, Katherine A; Chen, Yan-Ting; Shi, Quanming; Valencia, Alfredo M; Shifrut, Eric; Kale, Nupura; Yost, Kathryn E; Duffy, Connor V; Daniel, Bence; Hwee, Madeline A; Miao, Zhuang; Ashworth, Alan; Mackall, Crystal L; Marson, Alexander; Carnevale, Julia; Vardhana, Santosh A; Satpathy, Ansuman T | Cancer cell | 2022 07 11 | 35750052 | |
| The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells. | Hasenson, Sarah E; Alkalay, Ella; Atrash, Mohammad K; Boocholez, Alon; Gershbaum, Julianna; Hochberg-Laufer, Hodaya; Shav-Tal, Yaron | Cells | 2022 06 16 | 35741072 | |
| Latent space of a small genetic network: Geometry of dynamics and information. | Seyboldt, Rabea; Lavoie, Juliette; Henry, Adrien; Vanaret, Jules; Petkova, Mariela D; Gregor, Thomas; François, Paul | Proceedings of the National Academy of Sciences of the United States of America | 2022 06 28 | 35737842 | |
| TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. | Wang, Wenliang; Chandra, Aditi; Goldman, Naomi; Yoon, Sora; Ferrari, Emily K; Nguyen, Son C; Joyce, Eric F; Vahedi, Golnaz | Nature immunology | 2022 07 | 35726060 | |
| Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. | Karlow, Jennifer A; Devarakonda, Siddhartha; Xing, Xiaoyun; Jang, Hyo Sik; Govindan, Ramaswamy; Watson, Mark; Wang, Ting | Cancer research | 2022 Aug 03 | 35706127 | |
| Systematically quantifying morphological features reveals constraints on organoid phenotypes. | Beck, Lauren E; Lee, Jasmine; Coté, Christopher; Dunagin, Margaret C; Lukonin, Ilya; Salla, Nikkita; Chang, Marcello K; Hughes, Alex J; Mornin, Joseph D; Gartner, Zev J; Liberali, Prisca; Raj, Arjun | Cell systems | 2022 Jul 20 | 35705097 | |
| Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication. | Popay, Tessa M; Dixon, Jesse R | The Journal of biological chemistry | 2022 08 | 35691341 | |
| Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy. | Diekmann, Robin; Deschamps, Joran; Li, Yiming; Deguchi, Takahiro; Tschanz, Aline; Kahnwald, Maurice; Matti, Ulf; Ries, Jonas | Nature communications | 2022 06 11 | 35690614 | |
| Cohesin-mediated loop anchors confine the locations of human replication origins. | Emerson, Daniel J; Zhao, Peiyao A; Cook, Ashley L; Barnett, R Jordan; Klein, Kyle N; Saulebekova, Dalila; Ge, Chunmin; Zhou, Linda; Simandi, Zoltan; Minsk, Miriam K; Titus, Katelyn R; Wang, Weitao; Gong, Wanfeng; Zhang, Di; Yang, Liyan; Venev, Sergey V; Gibcus, Johan H; Yang, Hongbo; Sasaki, Takayo; Kanemaki, Masato T; Yue, Feng; Dekker, Job; Chen, Chun-Long; Gilbert, David M; Phillips-Cremins, Jennifer E | Nature | 2022 06 | 35676475 | |
| Global fitting for high-accuracy multi-channel single-molecule localization. | Li, Yiming; Shi, Wei; Liu, Sheng; Cavka, Ivana; Wu, Yu-Le; Matti, Ulf; Wu, Decheng; Koehler, Simone; Ries, Jonas | Nature communications | 2022 06 06 | 35668089 | |
| Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization. | Yang, Muyu; Ma, Jian | Journal of molecular biology | 2022 08 15 | 35659533 | |
| Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. | Lee, Hyung Joo; Hou, Yiran; Maeng, Ju Heon; Shah, Nakul M; Chen, Yujie; Lawson, Heather A; Yang, Hongbo; Yue, Feng; Wang, Ting | Genome research | 2022 07 | 35649578 | |
| Scalable biological signal recording in mammalian cells using Cas12a base editors. | Kempton, Hannah R; Love, Kasey S; Guo, Lucie Y; Qi, Lei S | Nature chemical biology | 2022 Jul | 35637351 | |
| BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4+ T cell responses to persistent antigen. | Xia, Yu; Sandor, Katalin; Pai, Joy A; Daniel, Bence; Raju, Saravanan; Wu, Renee; Hsiung, Sunnie; Qi, Yanyan; Yangdon, Tenzin; Okamoto, Mariko; Chou, Chun; Hiam-Galvez, Kamir J; Schreiber, Robert D; Murphy, Kenneth M; Satpathy, Ansuman T; Egawa, Takeshi | Immunity | 2022 07 12 | 35637103 | |
| Epigenetic regulation of T cell exhaustion. | Belk, Julia A; Daniel, Bence; Satpathy, Ansuman T | Nature immunology | 2022 06 | 35624210 | |
| Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer. | Kersten, Kelly; Hu, Kenneth H; Combes, Alexis J; Samad, Bushra; Harwin, Tory; Ray, Arja; Rao, Arjun Arkal; Cai, En; Marchuk, Kyle; Artichoker, Jordan; Courau, Tristan; Shi, Quanming; Belk, Julia; Satpathy, Ansuman T; Krummel, Matthew F | Cancer cell | 2022 06 13 | 35623342 | |
| Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. | Parteka-Tojek, Zofia; Zhu, Jacqueline Jufen; Lee, Byoungkoo; Jodkowska, Karolina; Wang, Ping; Aaron, Jesse; Chew, Teng-Leong; Banecki, Krzysztof; Plewczynski, Dariusz; Ruan, Yijun | Scientific reports | 2022 05 20 | 35595799 | |
| MCM complexes are barriers that restrict cohesin-mediated loop extrusion. | Dequeker, Bart J H; Scherr, Matthias J; Brandão, Hugo B; Gassler, Johanna; Powell, Sean; Gaspar, Imre; Flyamer, Ilya M; Lalic, Aleksandar; Tang, Wen; Stocsits, Roman; Davidson, Iain F; Peters, Jan-Michael; Duderstadt, Karl E; Mirny, Leonid A; Tachibana, Kikuë | Nature | 2022 06 | 35585235 | |
| Fast and efficient DNA replication with purified human proteins. | Baris, Yasemin; Taylor, Martin R G; Aria, Valentina; Yeeles, Joseph T P | Nature | 2022 06 | 35585232 | |
| Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. | Reticker-Flynn, Nathan E; Zhang, Weiruo; Belk, Julia A; Basto, Pamela A; Escalante, Nichole K; Pilarowski, Genay O W; Bejnood, Alborz; Martins, Maria M; Kenkel, Justin A; Linde, Ian L; Bagchi, Sreya; Yuan, Robert; Chang, Serena; Spitzer, Matthew H; Carmi, Yaron; Cheng, Jiahan; Tolentino, Lorna L; Choi, Okmi; Wu, Nancy; Kong, Christina S; Gentles, Andrew J; Sunwoo, John B; Satpathy, Ansuman T; Plevritis, Sylvia K; Engleman, Edgar G | Cell | 2022 05 26 | 35525247 | |
| Mechanics and functional consequences of nuclear deformations. | Kalukula, Yohalie; Stephens, Andrew D; Lammerding, Jan; Gabriele, Sylvain | Nature reviews. Molecular cell biology | 2022 09 | 35513718 | |
| Transcriptional coupling of distant regulatory genes in living embryos. | Levo, Michal; Raimundo, João; Bing, Xin Yang; Sisco, Zachary; Batut, Philippe J; Ryabichko, Sergey; Gregor, Thomas; Levine, Michael S | Nature | 2022 05 | 35508662 | |
| PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng | Cell metabolism | 2022 05 03 | 35508105 | |
| TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. | Huang, Le; Rosen, Jonathan D; Sun, Quan; Chen, Jiawen; Wheeler, Marsha M; Zhou, Ying; Min, Yuan-I; Kooperberg, Charles; Conomos, Matthew P; Stilp, Adrienne M; Rich, Stephen S; Rotter, Jerome I; Manichaikul, Ani; Loos, Ruth J F; Kenny, Eimear E; Blackwell, Thomas W; Smith, Albert V; Jun, Goo; Sedlazeck, Fritz J; Metcalf, Ginger; Boerwinkle, Eric; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; Raffield, Laura M; Reiner, Alex P; Auer, Paul L; Li, Yun | American journal of human genetics | 2022 Jun 02 | 35504290 | |
| Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. | Chung, Kenny K H; Zhang, Zhao; Kidd, Phylicia; Zhang, Yongdeng; Williams, Nathan D; Rollins, Bennett; Yang, Yang; Lin, Chenxiang; Baddeley, David; Bewersdorf, Joerg | Nature methods | 2022 May | 35501386 | |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J | Nature methods | 2022 05 | 35501385 | |
| The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. | Reiff, Sarah B; Schroeder, Andrew J; Kırlı, Koray; Cosolo, Andrea; Bakker, Clara; Lee, Soohyun; Veit, Alexander D; Balashov, Alexander K; Vitzthum, Carl; Ronchetti, William; Pitman, Kent M; Johnson, Jeremy; Ehmsen, Shannon R; Kerpedjiev, Peter; Abdennur, Nezar; Imakaev, Maxim; Öztürk, Serkan Utku; Çamoğlu, Uğur; Mirny, Leonid A; Gehlenborg, Nils; Alver, Burak H; Park, Peter J | Nature communications | 2022 05 02 | 35501320 | |
| A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. | Huang, Le; Yang, Yuchen; Li, Gang; Jiang, Minzhi; Wen, Jia; Abnousi, Armen; Rosen, Jonathan D; Hu, Ming; Li, Yun | Briefings in bioinformatics | 2022 05 13 | 35488276 | |
| NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. | Choi, Kyoung-Jae; Quan, My Diem; Qi, Chuangye; Lee, Joo-Hyung; Tsoi, Phoebe S; Zahabiyon, Mahla; Bajic, Aleksandar; Hu, Liya; Prasad, B V Venkataram; Liao, Shih-Chu Jeff; Li, Wenbo; Ferreon, Allan Chris M; Ferreon, Josephine C | Nature cell biology | 2022 May | 35484250 | |
| Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. | Labanieh, Louai; Majzner, Robbie G; Klysz, Dorota; Sotillo, Elena; Fisher, Chris J; Vilches-Moure, José G; Pacheco, Kaithlen Zen B; Malipatlolla, Meena; Xu, Peng; Hui, Jessica H; Murty, Tara; Theruvath, Johanna; Mehta, Nishant; Yamada-Hunter, Sean A; Weber, Evan W; Heitzeneder, Sabine; Parker, Kevin R; Satpathy, Ansuman T; Chang, Howard Y; Lin, Michael Z; Cochran, Jennifer R; Mackall, Crystal L | Cell | 2022 05 12 | 35483375 | |
| Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. | Chong, Shasha; Graham, Thomas G W; Dugast-Darzacq, Claire; Dailey, Gina M; Darzacq, Xavier; Tjian, Robert | Molecular cell | 2022 06 02 | 35483357 | |
| DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. | Nomidis, Stefanos K; Carlon, Enrico; Gruber, Stephan; Marko, John F | Nucleic acids research | 2022 05 20 | 35474142 | |
| Cohesin-dependence of neuronal gene expression relates to chromatin loop length. | Calderon, Lesly; Weiss, Felix D; Beagan, Jonathan A; Oliveira, Marta S; Georgieva, Radina; Wang, Yi-Fang; Carroll, Thomas S; Dharmalingam, Gopuraja; Gong, Wanfeng; Tossell, Kyoko; de Paola, Vincenzo; Whilding, Chad; Ungless, Mark A; Fisher, Amanda G; Phil | eLife | 2022 Apr 26 | 35471149 | |
| Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. | Liu, Weifang; Zhong, Wujuan; Chen, Jiawen; Huang, Bo; Hu, Ming; Li, Yun | Genes | 2022 Mar 25 | 35456393 | |
| Modular and mechanistic changes across stages of colorectal cancer. | Rahiminejad, Sara; Maurya, Mano R; Mukund, Kavitha; Subramaniam, Shankar | BMC cancer | 2022 Apr 21 | 35448980 | |
| Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. | Gabriele, Michele; Brandão, Hugo B; Grosse-Holz, Simon; Jha, Asmita; Dailey, Gina M; Cattoglio, Claudia; Hsieh, Tsung-Han S; Mirny, Leonid; Zechner, Christoph; Hansen, Anders S | Science (New York, N.Y.) | 2022 04 29 | 35420890 | |
| Multiplexed genome regulation in vivo with hyper-efficient Cas12a. | Guo, Lucie Y; Bian, Jing; Davis, Alexander E; Liu, Pingting; Kempton, Hannah R; Zhang, Xiaowei; Chemparathy, Augustine; Gu, Baokun; Lin, Xueqiu; Rane, Draven A; Xu, Xiaoshu; Jamiolkowski, Ryan M; Hu, Yang; Wang, Sui; Qi, Lei S | Nature cell biology | 2022 Apr | 35414015 | |
| Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes. | Nudelman, Ilona; Fernandez-Martinez, Javier; Rout, Michael P | Methods in molecular biology (Clifton, N.J.) | 2022 | 35412228 | |
| Mapping chromatin loops in single cells. | Yu, Miao; Li, Yun; Hu, Ming | Trends in genetics : TIG | 2022 Jul | 35400543 | |
| Chromatin interaction-aware gene regulatory modeling with graph attention networks. | Karbalayghareh, Alireza; Sahin, Merve; Leslie, Christina S | Genome research | 2022 May | 35396274 | |
| Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. | Jiang, Connie L; Goyal, Yogesh; Jain, Naveen; Wang, Qiaohong; Truitt, Rachel E; Coté, Allison J; Emert, Benjamin; Mellis, Ian A; Kiani, Karun; Yang, Wenli; Jain, Rajan; Raj, Arjun | Genome biology | 2022 Apr 05 | 35382863 | |
| Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. | Kenworthy, Charles A; Haque, Nayem; Liou, Shu-Hao; Chandris, Panagiotis; Wong, Vincent; Dziuba, Patrycja; Lavis, Luke D; Liu, Wei-Li; Singer, Robert H; Coleman, Robert A | Biophysical journal | 2022 May 03 | 35364106 | |
| Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states. | Esposito, Andrea; Bianco, Simona; Chiariello, Andrea M; Abraham, Alex; Fiorillo, Luca; Conte, Mattia; Campanile, Raffaele; Nicodemi, Mario | Cell reports | 2022 03 29 | 35354035 | |
| Fast and parallel nanoscale three-dimensional tracking of heterogeneous mammalian chromatin dynamics. | Gustavsson, Anna-Karin; Ghosh, Rajarshi P; Petrov, Petar N; Liphardt, Jan T; Moerner, W E | Molecular biology of the cell | 2022 05 15 | 35352962 | |
| Stripenn detects architectural stripes from chromatin conformation data using computer vision. | Yoon, Sora; Chandra, Aditi; Vahedi, Golnaz | Nature communications | 2022 Mar 24 | 35332165 | |
| TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation. | Van Buren, Eric; Hu, Ming; Cheng, Liang; Wrobel, John; Wilhelmsen, Kirk; Su, Lishan; Li, Yun; Wu, Di | Briefings in bioinformatics | 2022 05 13 | 35325048 | |
| Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. | Singh, Anand P; Wu, Ping; Ryabichko, Sergey; Raimundo, João; Swan, Michael; Wieschaus, Eric; Gregor, Thomas; Toettcher, Jared E | Cell reports | 2022 Mar 22 | 35320726 | |
| Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. | Biancon, Giulia; Joshi, Poorval; Zimmer, Joshua T; Hunck, Torben; Gao, Yimeng; Lessard, Mark D; Courchaine, Edward; Barentine, Andrew E S; Machyna, Martin; Botti, Valentina; Qin, Ashley; Gbyli, Rana; Patel, Amisha; Song, Yuanbin; Kiefer, Lea; Viero, Gabri | Molecular cell | 2022 Mar 17 | 35303483 | |
| Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. | Jachowicz, Joanna W; Strehle, Mackenzie; Banerjee, Abhik K; Blanco, Mario R; Thai, Jasmine; Guttman, Mitchell | Nature structural & molecular biology | 2022 Mar | 35301492 | |
| Systematic reconstruction of cellular trajectories across mouse embryogenesis. | Qiu, Chengxiang; Cao, Junyue; Martin, Beth K; Li, Tony; Welsh, Ian C; Srivatsan, Sanjay; Huang, Xingfan; Calderon, Diego; Noble, William Stafford; Disteche, Christine M; Murray, Stephen A; Spielmann, Malte; Moens, Cecilia B; Trapnell, Cole; Shendure, Jay | Nature genetics | 2022 Mar | 35288709 | |
| CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control. | Dominguez, Antonia A; Chavez, Michael G; Urke, Amanda; Gao, Yuchen; Wang, Lizhong; Qi, Lei S | The CRISPR journal | 2022 04 | 35271371 | |
| THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. | Rowland, Bryce; Huh, Ruth; Hou, Zoey; Crowley, Cheynna; Wen, Jia; Shen, Yin; Hu, Ming; Giusti-Rodríguez, Paola; Sullivan, Patrick F; Li, Yun | PLoS genetics | 2022 03 | 35259165 | |
| The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling. | Kordon, Magdalena M; Arron, Sarah; Cleaver, James E; Bezrookove, Vladimir; Karentz, Deneb; Lu, Brian; Perr, Eli; Chang, Darwin; Pederson, Thoru | Proceedings of the National Academy of Sciences of the United States of America | 2022 03 15 | 35254895 | |
| High-resolution 3D fluorescent imaging of intact tissues. | El-Nachef, Danny; Martinson, Amy M; Yang, Xiulan; Murry, Charles E; MacLellan, W Robb | International journal of cardiology and cardiovascular diseases | 2021 | 35243481 | |
| Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. | Liu, Weifang; Sun, Quan; Huang, Le; Bhattacharya, Arjun; Wang, Geoffery W; Tan, Xianming; Kuban, Karl C K; Joseph, Robert M; O'Shea, T Michael; Fry, Rebecca C; Li, Yun; Santos Jr, Hudson P | Journal of neurodevelopmental disorders | 2022 03 03 | 35240980 | |
| Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. | Fasolino, Maria; Schwartz, Gregory W; Patil, Abhijeet R; Mongia, Aanchal; Golson, Maria L; Wang, Yue J; Morgan, Ashleigh; Liu, Chengyang; Schug, Jonathan; Liu, Jinping; Wu, Minghui; Traum, Daniel; Kondo, Ayano; May, Catherine L; Goldman, Naomi; Wang, Wenl | Nature metabolism | 2022 Feb | 35228745 | |
| Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. | Miller, Tyler E; Lareau, Caleb A; Verga, Julia A; DePasquale, Erica A K; Liu, Vincent; Ssozi, Daniel; Sandor, Katalin; Yin, Yajie; Ludwig, Leif S; El Farran, Chadi A; Morgan, Duncan M; Satpathy, Ansuman T; Griffin, Gabriel K; Lane, Andrew A; Love, J Christopher; Bernstein, Bradley E; Sankaran, Vijay G; van Galen, Peter | Nature biotechnology | 2022 Jul | 35210612 | |
| HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. | Wei, Xiaolin; Xiang, Yu; Peters, Derek T; Marius, Choiselle; Sun, Tongyu; Shan, Ruocheng; Ou, Jianhong; Lin, Xin; Yue, Feng; Li, Wei; Southerland, Kevin W; Diao, Yarui | Molecular cell | 2022 Mar 17 | 35196517 | |
| Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. | Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Frere, Justin; Fullard, John F; Shayya, Hani; McArthur, Natalie G; Moeller, Rasmus; Uhl, Skyler; Omer, Arina D; Gottesman, Max E; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Rou | Cell | 2022 03 17 | 35180380 | |
| Spatial organization of transcribed eukaryotic genes. | Leidescher, Susanne; Ribisel, Johannes; Ullrich, Simon; Feodorova, Yana; Hildebrand, Erica; Galitsyna, Alexandra; Bultmann, Sebastian; Link, Stephanie; Thanisch, Katharina; Mulholland, Christopher; Dekker, Job; Leonhardt, Heinrich; Mirny, Leonid; Solovei, Irina | Nature cell biology | 2022 03 | 35177821 | |
| CRISPR Cas13-Based Tools to Track and Manipulate Endogenous Telomeric Repeat-Containing RNAs in Live Cells. | Xu, Meng; Chigumira, Tafadzwa; Chen, Ziheng; Tones, Jason; Zhao, Rongwei; Dahl, Kris Noel; Chenoweth, David M; Zhang, Huaiying | Frontiers in molecular biosciences | 2021 | 35174207 | |
| The use of new CRISPR tools in cardiovascular research and medicine. | Nishiga, Masataka; Liu, Chun; Qi, Lei S; Wu, Joseph C | Nature reviews. Cardiology | 2022 08 | 35145236 | |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. | Wang, Jiarui; Han, Mengting; Roy, Anish R; Wang, Haifeng; Möckl, Leonhard; Zeng, Leiping; Moerner, W E; Qi, Lei S | Cell reports methods | 2022 Feb 01 | 35128513 | |
| Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. | Yang, Hongbo; Zhang, Hui; Luan, Yu; Liu, Tingting; Yang, Wentao; Roberts, Kathryn G; Qian, Mao-Xiang; Zhang, Bo; Yang, Wenjian; Perez-Andreu, Virginia; Xu, Jie; Iyyanki, Sriranga; Kuang, Da; Stasiak, Lena A; Reshmi, Shalini C; Gastier-Foster, Julie; Smith | Nature genetics | 2022 02 | 35115686 | |
| A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis. | Jha, Asmita; Hansen, Anders S | Methods in molecular biology (Clifton, N.J.) | 2022 | 35103967 | |
| Compartmentalization of telomeres through DNA-scaffolded phase separation. | Developmental cell | 2022 01 24 | 35077681 | ||
| A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. | Knoedler, Joseph R; Inoue, Sayaka; Bayless, Daniel W; Yang, Taehong; Tantry, Adarsh; Davis, Chung-Ha; Leung, Nicole Y; Parthasarathy, Srinivas; Wang, Grace; Alvarado, Maricruz; Rizvi, Abbas H; Fenno, Lief E; Ramakrishnan, Charu; Deisseroth, Karl; Shah, Ni | Cell | 2022 02 17 | 35065713 | |
| Technological advances in super-resolution microscopy to study cellular processes. | Bond, Charles; Santiago-Ruiz, Adriana N; Tang, Qing; Lakadamyali, Melike | Molecular cell | 2022 01 20 | 35063099 | |
| SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. | Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, Ritambhara | Journal of computational biology : a journal of computational molecular cell biology | 2022 01 | 35050714 | |
| Single nucleosome tracking to study chromatin plasticity. | Lakadamyali, Melike | Current opinion in cell biology | 2022 Jan 13 | 35033775 | |
| SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. | Quinodoz, Sofia A; Bhat, Prashant; Chovanec, Peter; Jachowicz, Joanna W; Ollikainen, Noah; Detmar, Elizabeth; Soehalim, Elizabeth; Guttman, Mitchell | Nature protocols | 2022 Jan | 35013617 | |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett, Daniel A; Dileep, Vishnu; Baslan, Timour; Gilbert, David M | Current protocols | 2022 Jan | 34986273 | |
| Single-Cell Multiomics Integration by SCOT. | Demetci, Pinar; Santorella, Rebecca; Sandstede, Björn; Noble, William Stafford; Singh, Ritambhara | Journal of computational biology : a journal of computational molecular cell biology | 2022 01 | 34985990 | |
| Stress as a Chromatin Landscape Architect. | Vertii, Anastassiia | Frontiers in cell and developmental biology | 2021 | 34970548 | |
| Integrative approaches in genome structure analysis. | Structure (London, England : 1993) | 2022 01 06 | 34963059 | ||
| Epigenome rewiring in human pluripotent stem cells. | Yan, Jielin; Huangfu, Danwei | Trends in cell biology | 2021 Dec 23 | 34955367 | |
| Transcriptional network orchestrating regional patterning of cortical progenitors. | Ypsilanti, Athéna R; Pattabiraman, Kartik; Catta-Preta, Rinaldo; Golonzhka, Olga; Lindtner, Susan; Tang, Ke; Jones, Ian R; Abnousi, Armen; Juric, Ivan; Hu, Ming; Shen, Yin; Dickel, Diane E; Visel, Axel; Pennachio, Len A; Hawrylycz, Michael; Thompson, Caro | Proceedings of the National Academy of Sciences of the United States of America | 2021 12 21 | 34921112 | |
| Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. | Pourmorady, Ariel; Lomvardas, Stavros | Current opinion in genetics & development | 2022 02 | 34896807 | |
| Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. | Rigano, Alessandro; Ehmsen, Shannon; Öztürk, Serkan Utku; Ryan, Joel; Balashov, Alexander; Hammer, Mathias; Kirli, Koray; Boehm, Ulrike; Brown, Claire M; Bellve, Karl; Chambers, James J; Cosolo, Andrea; Coleman, Robert A; Faklaris, Orestis; Fogarty, Kevin | Nature methods | 2021 12 | 34862503 | |
| Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. | Hammer, Mathias; Huisman, Maximiliaan; Rigano, Alessandro; Boehm, Ulrike; Chambers, James J; Gaudreault, Nathalie; North, Alison J; Pimentel, Jaime A; Sudar, Damir; Bajcsy, Peter; Brown, Claire M; Corbett, Alexander D; Faklaris, Orestis; Lacoste, Judith; | Nature methods | 2021 12 | 34862501 | |
| Cell-type specialization is encoded by specific chromatin topologies. | Winick-Ng, Warren; Kukalev, Alexander; Harabula, Izabela; Zea-Redondo, Luna; Szabó, Dominik; Meijer, Mandy; Serebreni, Leonid; Zhang, Yingnan; Bianco, Simona; Chiariello, Andrea M; Irastorza-Azcarate, Ibai; Thieme, Christoph J; Sparks, Thomas M; Carvalho, | Nature | 2021 11 | 34789882 | |
| Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. | Geusz, Ryan J; Wang, Allen; Lam, Dieter K; Vinckier, Nicholas K; Alysandratos, Konstantinos-Dionysios; Roberts, David A; Wang, Jinzhao; Kefalopoulou, Samy; Ramirez, Araceli; Qiu, Yunjiang; Chiou, Joshua; Gaulton, Kyle J; Ren, Bing; Kotton, Darrell N; Sand | Nature communications | 2021 11 17 | 34789735 | |
| Light activation and deactivation of Cas9 for DNA repair studies. | Zou, Roger S; Ha, Taekjip | Methods in enzymology | 2021 | 34776214 | |
| Trading bits in the readout from a genetic network. | Bauer, Marianne; Petkova, Mariela D; Gregor, Thomas; Wieschaus, Eric F; Bialek, William | Proceedings of the National Academy of Sciences of the United States of America | 2021 11 16 | 34772813 | |
| Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. | Wang, Jiaxi; Lareau, Caleb A; Bautista, Jhoanne L; Gupta, Alexander R; Sandor, Katalin; Germino, Joe; Yin, Yajie; Arvedson, Matthew P; Reeder, Gabriella C; Cramer, Nathan T; Xie, Fang; Ntranos, Vasilis; Satpathy, Ansuman T; Anderson, Mark S; Gardner, Jame | Science immunology | 2021 11 12 | 34767455 | |
| RNA promotes the formation of spatial compartments in the nucleus. | Quinodoz, Sofia A; Jachowicz, Joanna W; Bhat, Prashant; Ollikainen, Noah; Banerjee, Abhik K; Goronzy, Isabel N; Blanco, Mario R; Chovanec, Peter; Chow, Amy; Markaki, Yolanda; Thai, Jasmine; Plath, Kathrin; Guttman, Mitchell | Cell | 2021 11 11 | 34739832 | |
| Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. | Swygert, Sarah G; Lin, Dejun; Portillo-Ledesma, Stephanie; Lin, Po-Yen; Hunt, Dakota R; Kao, Cheng-Fu; Schlick, Tamar; Noble, William S; Tsukiyama, Toshio | eLife | 2021 Nov 04 | 34734806 | |
| Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. | Fenix, Aidan M; Miyaoka, Yuichiro; Bertero, Alessandro; Blue, Steven M; Spindler, Matthew J; Tan, Kenneth K B; Perez-Bermejo, Juan A; Chan, Amanda H; Mayerl, Steven J; Nguyen, Trieu D; Russell, Caitlin R; Lizarraga, Paweena P; Truong, Annie; So, Po-Lin; Kulkarni, Aishwarya; Chetal, Kashish; Sathe, Shashank; Sniadecki, Nathan J; Yeo, Gene W; Murry, Charles E; Conklin, Bruce R; Salomonis, Nathan | Nature communications | 2021 11 03 | 34732726 | |
| MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. | Ryan, Joel; Pengo, Thomas; Rigano, Alex; Llopis, Paula Montero; Itano, Michelle S; Cameron, Lisa A; Marqués, Guillermo; Strambio-De-Castillia, Caterina; Sanders, Mark A; Brown, Claire M | Nature methods | 2021 12 | 34654919 | |
| A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. | Modzelewski, Andrew J; Shao, Wanqing; Chen, Jingqi; Lee, Angus; Qi, Xin; Noon, Mackenzie; Tjokro, Kristy; Sales, Gabriele; Biton, Anne; Anand, Aparna; Speed, Terence P; Xuan, Zhenyu; Wang, Ting; Risso, Davide; He, Lin | Cell | 2021 10 28 | 34644528 | |
| MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community. | Kunis, Susanne; Hänsch, Sebastian; Schmidt, Christian; Wong, Frances; Strambio-De-Castillia, Caterina; Weidtkamp-Peters, Stefanie | Nature methods | 2021 12 | 34635849 | |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang, Ruochi; Zhou, Tianming; Ma, Jian | Nature biotechnology | 2021 Oct 11 | 34635838 | |
| Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. | Hulleman, Christiaan N; Thorsen, Rasmus Ø; Kim, Eugene; Dekker, Cees; Stallinga, Sjoerd; Rieger, Bernd | Nature communications | 2021 10 11 | 34635658 | |
| Jointly Embedding Multiple Single-Cell Omics Measurements. | Liu, Jie; Huang, Yuanhao; Singh, Ritambhara; Vert, Jean-Philippe; Noble, William Stafford | Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) | 2019 Sep 03 | 34632462 | |
| Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction. | Eeftens, Jorine M; Kapoor, Manya; Michieletto, Davide; Brangwynne, Clifford P | Nature communications | 2021 10 07 | 34620850 | |
| BRD4 orchestrates genome folding to promote neural crest differentiation. | Linares-Saldana, Ricardo; Kim, Wonho; Bolar, Nikhita A; Zhang, Haoyue; Koch-Bojalad, Bailey A; Yoon, Sora; Shah, Parisha P; Karnay, Ashley; Park, Daniel S; Luppino, Jennifer M; Nguyen, Son C; Padmanabhan, Arun; Smith, Cheryl L; Poleshko, Andrey; Wang, Qia | Nature genetics | 2021 Oct | 34611363 | |
| Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. | L'Yi, Sehi; Wang, Qianwen; Lekschas, Fritz; Gehlenborg, Nils | IEEE transactions on visualization and computer graphics | 2022 01 | 34596551 | |
| Single-cell nuclear architecture across cell types in the mouse brain. | Takei, Yodai; Zheng, Shiwei; Yun, Jina; Shah, Sheel; Pierson, Nico; White, Jonathan; Schindler, Simone; Tischbirek, Carsten H; Yuan, Guo-Cheng; Cai, Long | Science (New York, N.Y.) | 2021 10 29 | 34591592 | |
| Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. | Bonora, Giancarlo; Ramani, Vijay; Singh, Ritambhara; Fang, He; Jackson, Dana L; Srivatsan, Sanjay; Qiu, Ruolan; Lee, Choli; Trapnell, Cole; Shendure, Jay; Duan, Zhijun; Deng, Xinxian; Noble, William S; Disteche, Christine M | Genome biology | 2021 09 27 | 34579774 | |
| HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets. | Rosen, Jonathan D; Yang, Yuchen; Abnousi, Armen; Chen, Jiawen; Song, Michael; Jones, Ian R; Shen, Yin; Hu, Ming; Li, Yun | Current issues in molecular biology | 2021 Sep 17 | 34563051 | |
| Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C | Nature methods | 2021 Sep 21 | 34548656 | |
| The maternal blood lipidome is indicative of the pathogenesis of severe preeclampsia. | He, Bing; Liu, Yu; Maurya, Mano R; Benny, Paula; Lassiter, Cameron; Li, Hui; Subramaniam, Shankar; Garmire, Lana X | Journal of lipid research | 2021 Sep 20 | 34547287 | |
| Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. | Ren, Xingjie; Wang, Mengchi; Li, Bingkun; Jamieson, Kirsty; Zheng, Lina; Jones, Ian R; Li, Bin; Takagi, Maya Asami; Lee, Jerry; Maliskova, Lenka; Tam, Tsz Wai; Yu, Miao; Hu, Rong; Lee, Lindsay; Abnousi, Armen; Li, Gang; Li, Yun; Hu, Ming; Ren, Bing; Wang, | Science advances | 2021 Sep 17 | 34524848 | |
| STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. | Zimmer, Joshua T; Rosa-Mercado, Nicolle A; Canzio, Daniele; Steitz, Joan A; Simon, Matthew D | Molecular cell | 2021 11 04 | 34520723 | |
| Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. | Mirny, Leonid; Dekker, Job | Cold Spring Harbor perspectives in biology | 2022 07 01 | 34518339 | |
| Enhanced Cas12a multi-gene regulation using a CRISPR array separator. | Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei S | eLife | 2021 09 09 | 34499031 | |
| MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples. | Liu, Weifang; Yang, Yuchen; Abnousi, Armen; Zhang, Qian; Kubo, Naoki; Beem, Joshua S Martin; Li, Yun; Hu, Ming | HGG advances | 2021 Jul 08 | 34485947 | |
| Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C | Nature methods | 2021 09 | 34480155 | |
| Systematic evaluation of chromosome conformation capture assays. | Akgol Oksuz, Betul; Yang, Liyan; Abraham, Sameer; Venev, Sergey V; Krietenstein, Nils; Parsi, Krishna Mohan; Ozadam, Hakan; Oomen, Marlies E; Nand, Ankita; Mao, Hui; Genga, Ryan M J; Maehr, Rene; Rando, Oliver J; Mirny, Leonid A; Gibcus, Johan H; Dekker, | Nature methods | 2021 09 | 34480151 | |
| The 3D Genome Structure of Single Cells. | Zhou, Tianming; Zhang, Ruochi; Ma, Jian | Annual review of biomedical data science | 2021 07 20 | 34465168 | |
| SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. | Yu, Miao; Abnousi, Armen; Zhang, Yanxiao; Li, Guoqiang; Lee, Lindsay; Chen, Ziyin; Fang, Rongxin; Lagler, Taylor M; Yang, Yuchen; Wen, Jia; Sun, Quan; Li, Yun; Ren, Bing; Hu, Ming | Nature methods | 2021 09 | 34446921 | |
| Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9. | Gao, Yuchen; Han, Mengting; Shang, Stephen; Wang, Haifeng; Qi, Lei S | Molecular cell | 2021 Aug 13 | 34428454 | |
| Single-cell measurement of higher-order 3D genome organization with scSPRITE. | Arrastia, Mary V; Jachowicz, Joanna W; Ollikainen, Noah; Curtis, Matthew S; Lai, Charlotte; Quinodoz, Sofia A; Selck, David A; Ismagilov, Rustem F; Guttman, Mitchell | Nature biotechnology | 2021 Aug 23 | 34426703 | |
| Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. | Song, Fan; Xu, Jie; Dixon, Jesse; Yue, Feng | Methods in molecular biology (Clifton, N.J.) | 2022 | 34415534 | |
| Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. | Yildirim, Asli; Boninsegna, Lorenzo; Zhan, Yuxiang; Alber, Frank | Cold Spring Harbor perspectives in biology | 2021 Aug 16 | 34400556 | |
| X-factors in human disease: impact of gene content and dosage regulation. | Fang, He; Deng, Xinxian; Disteche, Christine M | Human molecular genetics | 2021 Oct 01 | 34387327 | |
| Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). | Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, Bing | Methods in molecular biology (Clifton, N.J.) | 2021 | 34382190 | |
| Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. | Lee, Joo-Hyung; Wang, Ruoyu; Xiong, Feng; Krakowiak, Joanna; Liao, Zian; Nguyen, Phuoc T; Moroz-Omori, Elena V; Shao, Jiaofang; Zhu, Xiaoyu; Bolt, Michael J; Wu, Haoyi; Singh, Pankaj K; Bi, Mingjun; Shi, Caleb J; Jamal, Naadir; Li, Guojie; Mistry, Ragini; | Molecular cell | 2021 08 19 | 34375583 | |
| Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. | Hanmandlu, Ankit; Zhu, Lisha; Mertens, Tinne C J; Collum, Scott; Bi, Weizhen; Xiong, Feng; Wang, Ruoyu; Amirthalingam, Rajarajan T; Ren, Dewei; Han, Leng; Jyothula, Soma S S K; Li, Wenbo; Zheng, W Jim; Karmouty-Quintana, Harry | American journal of respiratory cell and molecular biology | 2022 01 | 34370624 | |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. | Mellis, Ian A; Edelstein, Hailey I; Truitt, Rachel; Goyal, Yogesh; Beck, Lauren E; Symmons, Orsolya; Dunagin, Margaret C; Linares Saldana, Ricardo A; Shah, Parisha P; Pérez-Bermejo, Juan A; Padmanabhan, Arun; Yang, Wenli; Jain, Rajan; Raj, Arjun | Cell systems | 2021 Sep 22 | 34352221 | |
| Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. | Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter | Computer graphics forum : journal of the European Association for Computer Graphics | 2020 Jun | 34334852 | |
| SARS-CoV-2 Restructures the Host Chromatin Architecture. | Wang, Ruoyu; Lee, Joo-Hyung; Xiong, Feng; Kim, Jieun; Hasani, Lana Al; Yuan, Xiaoyi; Shivshankar, Pooja; Krakowiak, Joanna; Qi, Chuangye; Wang, Yanyu; Eltzschig, Holger K; Li, Wenbo | bioRxiv : the preprint server for biology | 2021 Jul 21 | 34312624 | |
| DNA-loop-extruding SMC complexes can traverse one another in vivo. | Brandão, Hugo B; Ren, Zhongqing; Karaboja, Xheni; Mirny, Leonid A; Wang, Xindan | Nature structural & molecular biology | 2021 08 | 34312537 | |
| CRISPRi/a Screening with Human iPSCs. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Methods in molecular biology (Clifton, N.J.) | 2021 | 34302664 | |
| Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. | Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan H | Current protocols | 2021 Jul | 34286910 | |
| Polymer models are a versatile tool to study chromatin 3D organization. | Esposito, Andrea; Bianco, Simona; Fiorillo, Luca; Conte, Mattia; Abraham, Alex; Musella, Francesco; Nicodemi, Mario; Prisco, Antonella; Chiariello, Andrea M | Biochemical Society transactions | 2021 08 27 | 34282837 | |
| High-resolution, genome-wide mapping of positive supercoiling in chromosomes. | Guo, Monica S; Kawamura, Ryo; Littlehale, Megan L; Marko, John F; Laub, Michael T | eLife | 2021 07 19 | 34279217 | |
| AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. | Liu, Shaopeng; Li, Daofeng; Lyu, Cheng; Gontarz, Paul M; Miao, Benpeng; Madden, Pamela A F; Wang, Ting; Zhang, Bo | Genomics, proteomics & bioinformatics | 2021 Jul 14 | 34273560 | |
| Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin. | Zhang, Yaojun; Lee, Daniel S W; Meir, Yigal; Brangwynne, Clifford P; Wingreen, Ned S | Physical review letters | 2021 Jun 25 | 34241518 | |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair N | eLife | 2021 07 09 | 34240703 | |
| The Impact of Space and Time on the Functional Output of the Genome. | Nollmann, Marcelo; Bennabi, Isma; Götz, Markus; Gregor, Thomas | Cold Spring Harbor perspectives in biology | 2021 Jul 06 | 34230036 | |
| QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. | Nelson, Glyn; Boehm, Ulrike; Bagley, Steve; Bajcsy, Peter; Bischof, Johanna; Brown, Claire M; Dauphin, Aurélien; Dobbie, Ian M; Eriksson, John E; Faklaris, Orestis; Fernandez-Rodriguez, Julia; Ferrand, Alexia; Gelman, Laurent; Gheisari, Ali; Hartmann, Hella; Kukat, Christian; Laude, Alex; Mitkovski, Miso; Munck, Sebastian; North, Alison J; Rasse, Tobias M; Resch-Genger, Ute; Schuetz, Lucas C; Seitz, Arne; Strambio-De-Castillia, Caterina; Swedlow, Jason R; Alexopoulos, Ioannis; Aumayr, Karin; Avilov, Sergiy; Bakker, Gert-Jan; Bammann, Rodrigo R; Bassi, Andrea; Beckert, Hannes; Beer, Sebastian; Belyaev, Yury; Bierwagen, Jakob; Birngruber, Konstantin A; Bosch, Manel; Breitlow, Juergen; Cameron, Lisa A; Chalfoun, Joe; Chambers, James J; Chen, Chieh-Li; Conde-Sousa, Eduardo; Corbett, Alexander D; Cordelieres, Fabrice P; Nery, Elaine Del; Dietzel, Ralf; Eismann, Frank; Fazeli, Elnaz; Felscher, Andreas; Fried, Hans; Gaudreault, Nathalie; Goh, Wah Ing; Guilbert, Thomas; Hadleigh, Roland; Hemmerich, Peter; Holst, Gerhard A; Itano, Michelle S; Jaffe, Claudia B; Jambor, Helena K; Jarvis, Stuart C; Keppler, Antje; Kirchenbuechler, David; Kirchner, Marcel; Kobayashi, Norio; Krens, Gabriel; Kunis, Susanne; Lacoste, Judith; Marcello, Marco; Martins, Gabriel G; Metcalf, Daniel J; Mitchell, Claire A; Moore, Joshua; Mueller, Tobias; Nelson, Michael S; Ogg, Stephen; Onami, Shuichi; Palmer, Alexandra L; Paul-Gilloteaux, Perrine; Pimentel, Jaime A; Plantard, Laure; Podder, Santosh; Rexhepaj, Elton; Royon, Arnaud; Saari, Markku A; Schapman, Damien; Schoonderwoert, Vincent; Schroth-Diez, Britta; Schwartz, Stanley; Shaw, Michael; Spitaler, Martin; Stoeckl, Martin T; Sudar, Damir; Teillon, Jeremie; Terjung, Stefan; Thuenauer, Roland; Wilms, Christian D; Wright, Graham D; Nitschke, Roland | Journal of microscopy | 2021 10 | 34214188 | |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan, Sanjay R; Regier, Mary C; Barkan, Eliza; Franks, Jennifer M; Packer, Jonathan S; Grosjean, Parker; Duran, Madeleine; Saxton, Sarah; Ladd, Jon J; Spielmann, Malte; Lois, Carlos; Lampe, Paul D; Shendure, Jay; Stevens, Kelly R; Trapnell, Cole | Science (New York, N.Y.) | 2021 07 02 | 34210887 | |
| Three-dimensional superresolution fluorescence microscopy maps the variable molecular architecture of the nuclear pore complex. | Sabinina, Vilma Jimenez; Hossain, M Julius; Hériché, Jean-Karim; Hoess, Philipp; Nijmeijer, Bianca; Mosalaganti, Shyamal; Kueblbeck, Moritz; Callegari, Andrea; Szymborska, Anna; Beck, Martin; Ries, Jonas; Ellenberg, Jan | Molecular biology of the cell | 2021 08 15 | 34191541 | |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. | Wang, Jiarui; Han, Mengting; Wang, Haifeng; Möckl, Leonhard; Zeng, Leiping; Moerner, W E; Qi, Lei S | bioRxiv : the preprint server for biology | 2021 Jun 09 | 34127974 | |
| Imaging Organization of RNA Processing within the Nucleus. | Biswas, Jeetayu; Li, Weihan; Singer, Robert H; Coleman, Robert A | Cold Spring Harbor perspectives in biology | 2021 12 01 | 34127450 | |
| DMA-tudor interaction modules control the specificity of in vivo condensates. | Courchaine, Edward M; Barentine, Andrew E S; Straube, Korinna; Lee, Dong-Ryoung; Bewersdorf, Joerg; Neugebauer, Karla M | Cell | 2021 Jul 08 | 34115980 | |
| Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. | Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, Jian | Quantitative biology (Beijing, China) | 2019 Jun | 34113473 | |
| RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. | Xiong, Feng; Wang, Ruoyu; Lee, Joo-Hyung; Li, Shenglan; Chen, Shin-Fu; Liao, Zian; Hasani, Lana Al; Nguyen, Phuoc T; Zhu, Xiaoyu; Krakowiak, Joanna; Lee, Dung-Fang; Han, Leng; Tsai, Kuang-Lei; Liu, Ying; Li, Wenbo | Cell research | 2021 Jun 09 | 34108665 | |
| HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. | Strom, Amy R; Biggs, Ronald J; Banigan, Edward J; Wang, Xiaotao; Chiu, Katherine; Herman, Cameron; Collado, Jimena; Yue, Feng; Ritland Politz, Joan C; Tait, Leah J; Scalzo, David; Telling, Agnes; Groudine, Mark; Brangwynne, Clifford P; Marko, John F; Step | eLife | 2021 06 09 | 34106828 | |
| Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. | Rajpurkar, Aparna R; Mateo, Leslie J; Murphy, Sedona E; Boettiger, Alistair N | Nature communications | 2021 06 08 | 34103507 | |
| HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | Sahin, Merve; Wong, Wilfred; Zhan, Yingqian; Van Deynze, Kinsey; Koche, Richard; Leslie, Christina S | Nature communications | 2021 06 07 | 34099725 | |
| Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. | Lin, Yen-Chen; Kumar, Meenakshi Sundaram; Ramesh, Nandini; Anderson, Eric N; Nguyen, Aivi T; Kim, Boram; Cheung, Simon; McDonough, Justin A; Skarnes, William C; Lopez-Gonzalez, Rodrigo; Landers, John E; Fawzi, Nicolas L; Mackenzie, Ian R A; Lee, Edward B; | Nature neuroscience | 2021 08 | 34059832 | |
| Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. | Scourzic, Laurianne; Salataj, Eralda; Apostolou, Effie | Frontiers in immunology | 2021 | 34054841 | |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. | Hoencamp, Claire; Dudchenko, Olga; Elbatsh, Ahmed M O; Brahmachari, Sumitabha; Raaijmakers, Jonne A; van Schaik, Tom; Sedeño Cacciatore, Ángela; Contessoto, Vinícius G; van Heesbeen, Roy G H P; van den Broek, Bram; Mhaskar, Aditya N; Teunissen, Hans; St H | Science (New York, N.Y.) | 2021 05 28 | 34045355 | |
| Enhancer release and retargeting activates disease-susceptibility genes. | Oh, Soohwan; Shao, Jiaofang; Mitra, Joydeep; Xiong, Feng; D'Antonio, Matteo; Wang, Ruoyu; Garcia-Bassets, Ivan; Ma, Qi; Zhu, Xiaoyu; Lee, Joo-Hyung; Nair, Sreejith J; Yang, Feng; Ohgi, Kenneth; Frazer, Kelly A; Zhang, Zhengdong D; Li, Wenbo; Rosenfeld, Mi | Nature | 2021 May 26 | 34040254 | |
| REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. | Sarkans, Ugis; Chiu, Wah; Collinson, Lucy; Darrow, Michele C; Ellenberg, Jan; Grunwald, David; Hériché, Jean-Karim; Iudin, Andrii; Martins, Gabriel G; Meehan, Terry; Narayan, Kedar; Patwardhan, Ardan; Russell, Matthew Robert Geoffrey; Saibil, Helen R; Str | Nature methods | 2021 May 21 | 34021280 | |
| QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. | Boehm, Ulrike; Nelson, Glyn; Brown, Claire M; Bagley, Steve; Bajcsy, Peter; Bischof, Johanna; Dauphin, Aurelien; Dobbie, Ian M; Eriksson, John E; Faklaris, Orestis; Fernandez-Rodriguez, Julia; Ferrand, Alexia; Gelman, Laurent; Gheisari, Ali; Hartmann, Hel | Nature methods | 2021 12 | 34021279 | |
| Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow, Jennifer A; Miao, Benpeng; Xing, Xiaoyun; Wang, Ting; Zhang, Bo | Communications biology | 2021 May 21 | 34021236 | |
| Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers. | Jain, Surbhi; Xun, Guanhua; Abesteh, Shireen; Ho, Sherri; Lingamaneni, Manasi; Martin, Teresa A; Tasan, Ipek; Yang, Che; Zhao, Huimin | ACS synthetic biology | 2021 06 18 | 34006094 | |
| Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. | Huang, Xiao; Ferris, Stephen T; Kim, Sunkyung; Choudhary, Mayank N K; Belk, Julia A; Fan, Changxu; Qi, Yanyan; Sudan, Raki; Xia, Yu; Desai, Pritesh; Chen, Jing; Ly, Nghi; Shi, Quanming; Bagadia, Prachi; Liu, Tiantian; Guilliams, Martin; Egawa, Takeshi; Co | Immunity | 2021 May 11 | 34004142 | |
| CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains. | Huang, Hui; Zhu, Quan; Jussila, Adam; Han, Yuanyuan; Bintu, Bogdan; Kern, Colin; Conte, Mattia; Zhang, Yanxiao; Bianco, Simona; Chiariello, Andrea M; Yu, Miao; Hu, Rong; Tastemel, Melodi; Juric, Ivan; Hu, Ming; Nicodemi, Mario; Zhuang, Xiaowei; Ren, Bing | Nature genetics | 2021 May 17 | 34002095 | |
| PYMEVisualize: an open-source tool for exploring 3D super-resolution data. | Marin, Zach; Graff, Michael; Barentine, Andrew E S; Soeller, Christian; Chung, Kenny Kwok Hin; Fuentes, Lukas A; Baddeley, David | Nature methods | 2021 Jun | 34002092 | |
| Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. | Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber | Med (New York, N.Y.) | 2021 May 14 | 33969332 | |
| Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin. | Fiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario | Nature methods | 2021 05 | 33963348 | |
| Determination of complete chromosomal haplotypes by bulk DNA sequencing. | Tourdot, Richard W; Brunette, Gregory J; Pinto, Ricardo A; Zhang, Cheng-Zhong | Genome biology | 2021 May 06 | 33957932 | |
| From integrative structural biology to cell biology. | Sali, Andrej | The Journal of biological chemistry | 2021 Jan-Jun | 33957123 | |
| Unsupervised manifold alignment for single-cell multi-omics data. | Singh, Ritambhara; Demetci, Pinar; Bonora, Giancarlo; Ramani, Vijay; Lee, Choli; Fang, He; Duan, Zhijun; Deng, Xinxian; Shendure, Jay; Disteche, Christine; Noble, William Stafford | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 2020 Sep | 33954299 | |
| Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. | Pettinato, Anthony M; Yoo, Dasom; VanOudenhove, Jennifer; Chen, Yu-Sheng; Cohn, Rachel; Ladha, Feria A; Yang, Xiulan; Thakar, Ketan; Romano, Robert; Legere, Nicolas; Meredith, Emily; Robson, Paul; Regnier, Michael; Cotney, Justin L; Murry, Charles E; Hins | Cell reports | 2021 May 04 | 33951429 | |
| The Need for a Human Pangenome Reference Sequence. | Miga, Karen H; Wang, Ting | Annual review of genomics and human genetics | 2021 08 31 | 33929893 | |
| Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. | Kaur, Parwinder; Lui, Christopher; Dudchenko, Olga; Nandety, Raja Sekhar; Hurgobin, Bhavna; Pham, Melanie; Lieberman Aiden, Erez; Wen, Jiangqi; Mysore, Kirankumar | International journal of molecular sciences | 2021 Apr 21 | 33919286 | |
| Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. | Sanborn, Adrian L; Yeh, Benjamin T; Feigerle, Jordan T; Hao, Cynthia V; Townshend, Raphael Jl; Lieberman Aiden, Erez; Dror, Ron O; Kornberg, Roger D | eLife | 2021 Apr 27 | 33904398 | |
| Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. | Liu, Miao; Yang, Bing; Hu, Mengwei; Radda, Jonathan S D; Chen, Yanbo; Jin, Shengyan; Cheng, Yubao; Wang, Siyuan | Nature protocols | 2021 May | 33903756 | |
| Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan J | Developmental cell | 2021 May 03 | 33891899 | |
| Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo. | El-Nachef, Danny; Bugg, Darrian; Beussman, Kevin M; Steczina, Sonette; Martinson, Amy M; Murry, Charles E; Sniadecki, Nathan J; Davis, Jennifer | Circulation | 2021 04 20 | 33872080 | |
| Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. | Iyyanki, Tejaswi; Zhang, Baozhen; Wang, Qixuan; Hou, Ye; Jin, Qiushi; Xu, Jie; Yang, Hongbo; Liu, Tingting; Wang, Xiaotao; Song, Fan; Luan, Yu; Yamashita, Hironobu; Chien, Ruby; Lyu, Huijue; Zhang, Lijun; Wang, Lu; Warrick, Joshua; Raman, Jay D; Meeks, Joshua J; DeGraff, David J; Yue, Feng | Genome biology | 2021 Apr 15 | 33858483 | |
| Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. | Schep, Ruben; Brinkman, Eva K; Leemans, Christ; Vergara, Xabier; van der Weide, Robin H; Morris, Ben; van Schaik, Tom; Manzo, Stefano G; Peric-Hupkes, Daniel; van den Berg, Jeroen; Beijersbergen, Roderick L; Medema, René H; van Steensel, Bas | Molecular cell | 2021 05 20 | 33848455 | |
| Single-molecule micromanipulation studies of methylated DNA. | Zaichuk, Tetiana; Marko, John F | Biophysical journal | 2021 06 01 | 33838135 | |
| Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. | Zhu, Yanfen; Gujar, Amit D; Wong, Chee-Hong; Tjong, Harianto; Ngan, Chew Yee; Gong, Liang; Chen, Yi-An; Kim, Hoon; Liu, Jihe; Li, Meihong; Mil-Homens, Adam; Maurya, Rahul; Kuhlberg, Chris; Sun, Fanyue; Yi, Eunhee; deCarvalho, Ana C; Ruan, Yijun; Verhaak, Roel G W; Wei, Chia-Lin | Cancer cell | 2021 May 10 | 33836152 | |
| GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. | Markowski, Julia; Kempfer, Rieke; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Loof, Gesa; Kehr, Birte; Pombo, Ana; Rahmann, Sven; Schwarz, Roland F | Bioinformatics (Oxford, England) | 2021 Apr 08 | 33830196 | |
| Genome-wide enhancer maps link risk variants to disease genes. | Nasser, Joseph; Bergman, Drew T; Fulco, Charles P; Guckelberger, Philine; Doughty, Benjamin R; Patwardhan, Tejal A; Jones, Thouis R; Nguyen, Tung H; Ulirsch, Jacob C; Lekschas, Fritz; Mualim, Kristy; Natri, Heini M; Weeks, Elle M; Munson, Glen; Kane, Mich | Nature | 2021 05 | 33828297 | |
| p53 mediates target gene association with nuclear speckles for amplified RNA expression. | Alexander, Katherine A; Coté, Allison; Nguyen, Son C; Zhang, Liguo; Gholamalamdari, Omid; Agudelo-Garcia, Paula; Lin-Shiao, Enrique; Tanim, K M A; Lim, Joan; Biddle, Nicolas; Dunagin, Margaret C; Good, Charly R; Mendoza, Mariel R; Little, Shawn C; Belmont, Andrew; Joyce, Eric F; Raj, Arjun; Berger, Shelley L | Molecular cell | 2021 04 15 | 33823140 | |
| Interrogating immune cells and cancer with CRISPR-Cas9. | Buquicchio, Frank A; Satpathy, Ansuman T | Trends in immunology | 2021 05 | 33812776 | |
| Phase separation in genome organization across evolution. | Feric, Marina; Misteli, Tom | Trends in cell biology | 2021 08 | 33771451 | |
| Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention. | Hogan, Ann K; Foltz, Daniel R | Molecular and cellular biology | 2021 05 21 | 33753462 | |
| See(quence) and ye shall find: higher-order genome folding in intact single cells. | Pham, Kenneth; Nikish, Alexandria; Phillips-Cremins, Jennifer E | Molecular cell | 2021 03 18 | 33740473 | |
| Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation. | Makhija, Suraj; Brown, David; Rudlaff, Rachel M; Doh, Julia K; Bourke, Struan; Wang, Yina; Zhou, Shuqin; Cheloor-Kovilakam, Rasmi; Huang, Bo | ACS chemical biology | 2021 04 16 | 33734687 | |
| RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. | Bertero, Alessandro | Frontiers in genetics | 2021 | 33732290 | |
| Toward a Three-Dimensional Chromosome Shape Alphabet. | Soto, Carlos; Bryner, Darshan; Neretti, Nicola; Srivastava, Anuj | Journal of computational biology : a journal of computational molecular cell biology | 2021 06 | 33720766 | |
| Properties of repression condensates in living Ciona embryos. | Treen, Nicholas; Shimobayashi, Shunsuke F; Eeftens, Jorine; Brangwynne, Clifford P; Levine, Michael | Nature communications | 2021 03 10 | 33692345 | |
| Cas9 deactivation with photocleavable guide RNAs. | Zou, Roger S; Liu, Yang; Wu, Bin; Ha, Taekjip | Molecular cell | 2021 04 01 | 33662274 | |
| Genome oligopaint via local denaturation fluorescence in situ hybridization. | Wang, Yanbo; Cottle, Wayne Taylor; Wang, Haobo; Feng, Xinyu Ashlee; Mallon, John; Gavrilov, Momcilo; Bailey, Scott; Ha, Taekjip | Molecular cell | 2021 04 01 | 33657402 | |
| Heterogeneity of fetal hemoglobin production in adult red blood cells. | Khandros, Eugene; Blobel, Gerd A | Current opinion in hematology | 2021 05 01 | 33631783 | |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert, Benjamin L; Cote, Christopher J; Torre, Eduardo A; Dardani, Ian P; Jiang, Connie L; Jain, Naveen; Shaffer, Sydney M; Raj, Arjun | Nature biotechnology | 2021 Feb 22 | 33619394 | |
| Direct supercritical angle localization microscopy for nanometer 3D superresolution. | Dasgupta, Anindita; Deschamps, Joran; Matti, Ulf; Hübner, Uwe; Becker, Jan; Strauss, Sebastian; Jungmann, Ralf; Heintzmann, Rainer; Ries, Jonas | Nature communications | 2021 02 19 | 33608524 | |
| PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. | Bokota, Grzegorz; Sroka, Jacek; Basu, Subhadip; Das, Nirmal; Trzaskoma, Pawel; Yushkevich, Yana; Grabowska, Agnieszka; Magalska, Adriana; Plewczynski, Dariusz | BMC bioinformatics | 2021 Feb 17 | 33596823 | |
| Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. | Zhang, Meng; Yang, Che; Tasan, Ipek; Zhao, Huimin | ACS synthetic biology | 2021 03 19 | 33596056 | |
| Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. | Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Fullard, John F; Shayya, Hani; Omer, Arina; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Roussos, Panos; tenOever, Benjamin R; Overdevest, Jonathan B; Lomvardas, Stavros | bioRxiv : the preprint server for biology | 2021 Feb 09 | 33594368 | |
| Physical mechanisms of chromatin spatial organization. | Chiariello, Andrea M; Bianco, Simona; Esposito, Andrea; Fiorillo, Luca; Conte, Mattia; Irani, Ehsan; Musella, Francesco; Abraham, Alex; Prisco, Antonella; Nicodemi, Mario | The FEBS journal | 2022 03 | 33583147 | |
| HiCRep.py : Fast comparison of Hi-C contact matrices in Python. | Lin, Dejun; Sanders, Justin; Noble, William Stafford | Bioinformatics (Oxford, England) | 2021 02 11 | 33576390 | |
| Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. | Belaghzal, Houda; Borrman, Tyler; Stephens, Andrew D; Lafontaine, Denis L; Venev, Sergey V; Weng, Zhiping; Marko, John F; Dekker, Job | Nature genetics | 2021 03 | 33574602 | |
| Engineering 3D genome organization. | Wang, Haifeng; Han, Mengting; Qi, Lei S | Nature reviews. Genetics | 2021 06 | 33558716 | |
| HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test. | Lagler, Taylor M; Abnousi, Armen; Hu, Ming; Yang, Yuchen; Li, Yun | American journal of human genetics | 2021 02 04 | 33545029 | |
| SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. | Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber | medRxiv : the preprint server for health sciences | 2021 Jan 26 | 33532791 | |
| Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. | Miko, Henriette; Qiu, Yunjiang; Gaertner, Bjoern; Sander, Maike; Ohler, Uwe | BMC genomics | 2021 Jan 28 | 33509077 | |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 2021 02 | 33505024 | |
| TALEN outperforms Cas9 in editing heterochromatin target sites. | Jain, Surbhi; Shukla, Saurabh; Yang, Che; Zhang, Meng; Fatma, Zia; Lingamaneni, Manasi; Abesteh, Shireen; Lane, Stephan Thomas; Xiong, Xiong; Wang, Yuchuan; Schroeder, Charles M; Selvin, Paul R; Zhao, Huimin | Nature communications | 2021 01 27 | 33504770 | |
| Determining of canine position by multiple facial landmarks to achieve natural esthetics in complete denture treatment. | Srimaneekarn, Natchalee; Arayapisit, Tawepong; Pooktuantong, Ornnicha; Cheng, Holland R; Soonsawad, Pan | The Journal of prosthetic dentistry | 2021 Jan 16 | 33468316 | |
| Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. | Vahedi, Golnaz | Immunological reviews | 2021 Mar | 33452686 | |
| Resources and challenges for integrative analysis of nuclear architecture data. | Jung, Youngsook L; Kirli, Koray; Alver, Burak H; Park, Peter J | Current opinion in genetics & development | 2021 Apr | 33450522 | |
| SPIN reveals genome-wide landscape of nuclear compartmentalization. | Wang, Yuchuan; Zhang, Yang; Zhang, Ruochi; van Schaik, Tom; Zhang, Liguo; Sasaki, Takayo; Peric-Hupkes, Daniel; Chen, Yu; Gilbert, David M; van Steensel, Bas; Belmont, Andrew S; Ma, Jian | Genome biology | 2021 Jan 14 | 33446254 | |
| The dynamics of chromatin architecture in brain development and function. | Harabula, Izabela; Pombo, Ana | Current opinion in genetics & development | 2021 04 | 33421764 | |
| CRISPR technologies for precise epigenome editing. | Nakamura, Muneaki; Gao, Yuchen; Dominguez, Antonia A; Qi, Lei S | Nature cell biology | 2021 Jan | 33420494 | |
| Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. | Rosa-Mercado, Nicolle A; Zimmer, Joshua T; Apostolidi, Maria; Rinehart, Jesse; Simon, Matthew D; Steitz, Joan A | Molecular cell | 2021 02 04 | 33400923 | |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre, Eduardo A; Arai, Eri; Bayatpour, Sareh; Jiang, Connie L; Beck, Lauren E; Emert, Benjamin L; Shaffer, Sydney M; Mellis, Ian A; Fane, Mitchell E; Alicea, Gretchen M; Budinich, Krista A; Weeraratna, Ashani T; Shi, Junwei; Raj, Arjun | Nature genetics | 2021 01 | 33398196 | |
| Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. | Kubo, Naoki; Ishii, Haruhiko; Xiong, Xiong; Bianco, Simona; Meitinger, Franz; Hu, Rong; Hocker, James D; Conte, Mattia; Gorkin, David; Yu, Miao; Li, Bin; Dixon, Jesse R; Hu, Ming; Nicodemi, Mario; Zhao, Huimin; Ren, Bing | Nature structural & molecular biology | 2021 Feb | 33398174 | |
| TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. | Zhang, Liguo; Zhang, Yang; Chen, Yu; Gholamalamdari, Omid; Wang, Yuchuan; Ma, Jian; Belmont, Andrew S | Genome research | 2020 Dec 18 | 33355299 | |
| Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. | Shao, Wanqing; Wang, Ting | Genome research | 2021 Jan | 33355230 | |
| Implementation of a 4Pi-SMS super-resolution microscope. | Wang, Jingyu; Allgeyer, Edward S; Sirinakis, George; Zhang, Yongdeng; Hu, Kevin; Lessard, Mark D; Li, Yiming; Diekmann, Robin; Phillips, Michael A; Dobbie, Ian M; Ries, Jonas; Booth, Martin J; Bewersdorf, Joerg | Nature protocols | 2021 02 | 33328610 | |
| ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. | Hu, Mengwei; Yang, Bing; Cheng, Yubao; Radda, Jonathan S D; Chen, Yanbo; Liu, Miao; Wang, Siyuan | Scientific reports | 2020 12 16 | 33328483 | |
| Generalized multi-SNP mediation intersection-union test. | Zhong, Wujuan; Darville, Toni; Zheng, Xiaojing; Fine, Jason; Li, Yun | Biometrics | 2022 Mar | 33316078 | |
| Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. | Bizhanova, Aizhan; Kaufman, Paul D | Biochimica 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, Ting | Genome research | 2020 Dec 10 | 33303495 | |
| The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. | Serrano, Diego; Cordero, Gustavo; Kawamura, Ryo; Sverzhinsky, Aleksandr; Sarker, Muzaddid; Roy, Shamayita; Malo, Catherine; Pascal, John M; Marko, John F; D'Amours, Damien | Molecular cell | 2020 12 17 | 33301731 | |
| The interplay between asymmetric and symmetric DNA loop extrusion. | Banigan, Edward J; Mirny, Leonid A | eLife | 2020 12 09 | 33295869 | |
| Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. | Feng, Ying; Wang, Yao; Wang, Xiangnan; He, Xiaohui; Yang, Chen; Naseri, Ardalan; Pederson, Thoru; Zheng, Jing; Zhang, Shaojie; Xiao, Xiao; Xie, Wei; Ma, Hanhui | Genome biology | 2020 12 08 | 33292531 | |
| Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. | Sanford, Eric M; Emert, Benjamin L; Coté, Allison; Raj, Arjun | eLife | 2020 12 07 | 33284110 | |
| Genome architecture and expression 2019-2020: the transition phase. | Pederson, Thoru | Current opinion in genetics & development | 2021 04 | 33279815 | |
| Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. | Fang, He; Bonora, Giancarlo; Lewandowski, Jordan P; Thakur, Jitendra; Filippova, Galina N; Henikoff, Steven; Shendure, Jay; Duan, Zhijun; Rinn, John L; Deng, Xinxian; Noble, William S; Disteche, Christine M | Nature communications | 2020 11 27 | 33247132 | |
| Three-dimensional chromatin organization in cardiac development and disease. | Bertero, Alessandro; Rosa-Garrido, Manuel | Journal of molecular and cellular cardiology | 2021 02 | 33242466 | |
| 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, Kyunghee | Cell 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 A | PLoS computational biology | 2020 11 | 33196636 | |
| X-chromosome regulation and sex differences in brain anatomy. | Raznahan, Armin; Disteche, Christine M | Neuroscience and biobehavioral reviews | 2021 01 | 33171144 | |
| Molecular basis of CTCF binding polarity in genome folding. | Nora, Elphège P; Caccianini, Laura; Fudenberg, Geoffrey; So, Kevin; Kameswaran, Vasumathi; Nagle, Abigail; Uebersohn, Alec; Hajj, Bassam; Saux, Agnès Le; Coulon, Antoine; Mirny, Leonid A; Pollard, Katherine S; Dahan, Maxime; Bruneau, Benoit G | Nature communications | 2020 11 05 | 33154377 | |
| HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. | Jain, Dhawal; Chu, Chong; Alver, Burak Han; Lee, Soohyun; Lee, Eunjung Alice; Park, Peter J | Bioinformatics (Oxford, England) | 2021 05 23 | 33136153 | |
| SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. | Banerjee, Abhik K; Blanco, Mario R; Bruce, Emily A; Honson, Drew D; Chen, Linlin M; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A; Loney, Colin; Thai, Jasmine; Miller, Zachary D; Lin, Aaron E; Schmidt, Madaline M; Stewart, Douglas G; Gold | Cell. | 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, Sheng | Nature communications. | 2020 10 15; | 33060583 | |
| EMU: reconfigurable graphical user interfaces for Micro-Manager. | Deschamps, Joran; Ries, Jonas | BMC 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; Liu | Nature. | 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 N | eLife. | 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 C | Nucleic 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, Hanspeter | IEEE transactions on visualization and computer graphics | 2021 02 | 33026994 | |
| Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. | Biggs, Ronald J; Liu, Ning; Peng, Yiheng; Marko, John F; Qiao, Huanyu | Communications biology. | 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, Manuel | Molecular 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, Yun | Genetic 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, Bo | Genome 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 D | Science 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 Stafford | PLoS 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 D | Bioinformatics (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, Ting | Science 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, Job | Nature 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 P | Nature 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 T | PLoS 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 T | Nature 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, Ting | Nature genetics. | 2020 10; | 32908257 | |
| Cell cycle dynamics of lamina-associated DNA. | van Schaik, Tom; Vos, Mabel; Peric-Hupkes, Daan; Hn Celie, Patrick; van Steensel, Bas | EMBO reports. | 2020 Nov 05; | 32893442 | |
| The nucleolus as a multiphase liquid condensate. | Lafontaine, Denis L J; Riback, Joshua A; Bascetin, Rümeyza; Brangwynne, Clifford P | Nature reviews. Molecular cell biology | 2021 03 | 32873929 | |
| Alteration of genome folding via contact domain boundary insertion. | Zhang, Di; Huang, Peng; Sharma, Malini; Keller, Cheryl A; Giardine, Belinda; Zhang, Haoyue; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E; Hardison, Ross C; Blobel, Gerd A | Nature genetics. | 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 E | Genome 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, Ting | Science 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, Sheng | Science advances | 2020 07 | 32832596 | |
| Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. | Tasan, Ipek; Su, Christina Jean; Enghiad, Behnam; Zhang, Meng; Mishra, Shekhar; Zhao, Huimin | ACS synthetic biology. | 2020 09 18; | 32822529 | |
| Targeted DNase Hi-C. | Duan, Zhijun | Methods 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, Carlos | Proceedings 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, Jonas | Nature 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, Arjun | Cell. | 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; C | Nature communications. | 2020 07 29; | 32728046 | |
| Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. | Chen, Hongtao; Gregor, Thomas | Methods in molecular biology (Clifton, N.J.) | 2020 | 32710421 | |
| Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. | Lei, Xiao; Zhao, Jun; Sagendorf, Jared M; Rajashekar, Niroop; Xu, Jiang; Dantas Machado, Ana Carolina; Sen, Chandani; Rohs, Remo; Feng, Pinghui; Chen, Lin | Journal of molecular biology | 2020 09 04 | 32681840 | |
| MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing. | Biswas, Jeetayu; Rahman, Reazur; Gupta, Varun; Rosbash, Michael; Singer, Robert H | iScience. | 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, Feng | Nature communications. | 2020 Jul 09; | 32647330 | |
| Free energy-based model of CTCF-mediated chromatin looping in the human genome. | Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz | Methods (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, Mario | Nature 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, Lingzhao | BMC 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, Jennifer | Stem 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 E | Molecular 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, Guoyan | BMC 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, Ulrich | Nature. | 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, Bo | Scientific reports. | 2020 Jun 23; | 32576878 | |
| Long Noncoding RNAs: Molecular Modalities to Organismal Functions. | Rinn, John L; Chang, Howard Y | Annual review of biochemistry. | 2020 06 20; | 32569523 | |
| MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. | Zhang, Ruochi; Ma, Jian | Cell systems. | 2020 May 20; | 32550271 | |
| Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. | Strehle, Mackenzie; Guttman, Mitchell | Current opinion in cell biology. | 2020 06; | 32535328 | |
| Loop extrusion: theory meets single-molecule experiments. | Banigan, Edward J; Mirny, Leonid A | Current 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 Wilson | Journal of molecular and cellular cardiology | 2020 08 | 32533974 | |
| Biosystems Design by Machine Learning. | Volk, Michael Jeffrey; Lourentzou, Ismini; Mishra, Shekhar; Vo, Lam Tung; Zhai, Chengxiang; Zhao, Huimin | ACS synthetic biology. | 2020 07 17; | 32485108 | |
| Evolving methodologies and concepts in 4D nucleome research. | Sparks, Thomas M; Harabula, Izabela; Pombo, Ana | Current 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 E | Nature 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, Dariusz | Nucleic 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 E | Molecular therapy. Methods & clinical development. | 2020 Jun 12; | 32426414 | |
| Histone Signatures Predict Therapeutic Efficacy in Breast Cancer. | Mollah, Shamim A; Subramaniam, Shankar | IEEE open journal of engineering in medicine and biology | 2020 | 32412527 | |
| Composition-dependent thermodynamics of intracellular phase separation. | Riback, Joshua A; Zhu, Lian; Ferrolino, Mylene C; Tolbert, Michele; Mitrea, Diana M; Sanders, David W; Wei, Ming-Tzo; Kriwacki, Richard W; Brangwynne, Clifford P | Nature. | 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, Yijun | Genome biology | 2020 05 11 | 32393309 | |
| Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. | Zhang, Xiaotian; Jeong, Mira; Huang, Xingfan; Wang, Xue Qing; Wang, Xinyu; Zhou, Wanding; Shamim, Muhammad S; Gore, Haley; Himadewi, Pamela; Liu, Yushuai; Bochkov, Ivan D; Reyes, Jaime; Doty, Madison; Huang, Yung-Hsin; Jung, Haiyoung; Heikamp, Emily; Aide | Molecular cell. | 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; Parteka | Nature 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, D | GigaScience | 2020 05 01 | 32352532 | |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh, Lea; Saint-Antoine, Michael; Sanford, Eric M; Emert, Benjamin L; Singh, Abhyudai; Marr, Carsten; Raj, Arjun; Goyal, Yogesh | Cell systems. | 2020 Apr 22; | 32325034 | |
| Chromatin Viscoelasticity Measured by Local Dynamic Analysis. | Vivante, Anat; Bronshtein, Irena; Garini, Yuval | Biophysical 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, P | Cell. | 2020 04 16; | 32302570 | |
| Sci-fate characterizes the dynamics of gene expression in single cells. | Cao, Junyue; Zhou, Wei; Steemers, Frank; Trapnell, Cole; Shendure, Jay | Nature 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 A | eLife | 2020 04 06 | 32250245 | |
| Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. | Field, Matt A; Rosen, Benjamin D; Dudchenko, Olga; Chan, Eva K F; Minoche, Andre E; Edwards, Richard J; Barton, Kirston; Lyons, Ruth J; Tuipulotu, Daniel Enosi; Hayes, Vanessa M; D Omer, Arina; Colaric, Zane; Keilwagen, Jens; Skvortsova, Ksenia; Bogdanovi | GigaScience. | 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 Stafford | Genome 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 D | Chromosoma. | 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 S | ACS 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 J | Molecular 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, Xavier | Molecular 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 M | Genome biology. | 2020 03 24; | 32209126 | |
| Cost-efficient open source laser engine for microscopy. | Schröder, Daniel; Deschamps, Joran; Dasgupta, Anindita; Matti, Ulf; Ries, Jonas | Biomedical optics express. | 2020 Feb 01; | 32206389 | |
| Evaluating Enhancer Function and Transcription. | Field, Andrew; Adelman, Karen | Annual 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, Maria | Annual 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, Dariusz | Journal of computational biology : a journal of computational molecular cell biology | 2020 09 | 32175768 | |
| Advanced 3D Analysis and Optimization of Single-Molecule FISH in Drosophila Muscle. | Noma, Akiko; Smith, Carlas S; Huisman, Maximiliaan; Martin, Robert M; Moore, Melissa J; Grunwald, David | Small methods. | 2018 Sep 11; | 32158910 | |
| Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems. | Masnadi-Shirazi, Maryam; Subramaniam, Shankar | Scientific 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 L | Genome 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-Lin | Nature genetics. | 2020 03; | 32094912 | |
| Therapeutic genome editing in cardiovascular diseases. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Advanced 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 H | Cold 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, Bas | The 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, V | Cell 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; Ha | Cell 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, Kai | Nature 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-Michael | eLife. | 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 W | eLife. | 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, Mario | Current 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, Yijun | Bioinformatics (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 L | Cell 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 E | Nature 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 J | Bioinformatics (Oxford, England). | 2020 05 01; | 32003786 | |
| Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. | Feodorova, Yana; Falk, Martin; Mirny, Leonid A; Solovei, Irina | Trends 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 A | PloS 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, Ting | Genome 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 E | PloS one. | 2020; | 31945113 | |
| On the existence and functionality of topologically associating domains. | Beagan, Jonathan A; Phillips-Cremins, Jennifer E | Nature genetics. | 2020 01; | 31925403 | |
| MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. | Tian, Dechao; Zhang, Ruochi; Zhang, Yang; Zhu, Xiaopeng; Ma, Jian | Genome 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, Huimin | Nature chemical biology. | 2020 04; | 31873222 | |
| Physics and Biology (of Chromosomes). | Marko, John F | Journal 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, Kai | Cell 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, Yu | Genome 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, Ting | Nature 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, Sjoerd | Nature methods. | 2020 Jan; | 31819263 | |
| Chromatin Is Frequently Unknotted at the Megabase Scale. | Goundaroulis, Dimos; Lieberman Aiden, Erez; Stasiak, Andrzej | Biophysical journal. | 2020 May 05; | 31818464 | |
| Guided nuclear exploration increases CTCF target search efficiency. | Hansen, Anders S; Amitai, Assaf; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | Nature chemical biology. | 2019 Dec 02; | 31792445 | |
| Probing and engineering liquid-phase organelles. | Bracha, Dan; Walls, Mackenzie T; Brangwynne, Clifford P | Nature biotechnology. | 2019 12; | 31792412 | |
| Spring Model - Chromatin Modeling Tool Based on OpenMM. | Kadlof, Michal; Rozycka, Julia; Plewczynski, Dariusz | Methods (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; Lareau | Nature 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, Bing | Genome biology | 2019 11 28 | 31779666 | |
| Chromatin structure dynamics during the mitosis-to-G1 phase transition. | Zhang, Haoyue; Emerson, Daniel J; Gilgenast, Thomas G; Titus, Katelyn R; Lan, Yemin; Huang, Peng; Zhang, Di; Wang, Hongxin; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Phillips-Cremins, Jennifer E; Blobel, Gerd A | Nature. | 2019 12; | 31776509 | |
| Tasks, Techniques, and Tools for Genomic Data Visualization. | Nusrat, S; Harbig, T; Gehlenborg, N | Computer graphics forum : journal of the European Association for Computer Graphics. | 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, Yijun | Genome biology | 2019 11 25 | 31767038 | |
| Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. | Brahmachari, Sumitabha; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2019 12 10; | 31757850 | |
| Gene expression amplification by nuclear speckle association. | Kim, Jiah; Venkata, Neha Chivukula; Hernandez Gonzalez, Gabriela Andrea; Khanna, Nimish; Belmont, Andrew S | The Journal of cell biology. | 2020 Jan 06; | 31757787 | |
| The liquid nucleome - phase transitions in the nucleus at a glance. | Strom, Amy R; Brangwynne, Clifford P | Journal 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, Dariusz | Methods (San Diego, Calif.). | 2020 10 01; | 31740366 | |
| Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. | Xiong, Kyle; Ma, Jian | Nature communications. | 2019 11 07; | 31699985 | |
| A Proteomic Perspective on Cardiomyocyte Maturation. | Muraoka, Naoto; Sun, Bingyun; Murry, Charles E | Circulation 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, Job | Nature cell biology. | 2019 Nov; | 31685986 | |
| X Inactivation and Escape: Epigenetic and Structural Features. | Fang, He; Disteche, Christine M; Berletch, Joel B | Frontiers in cell and developmental biology. | 2019; | 31632970 | |
| Methods for comparative ChIA-PET and Hi-C data analysis. | Capurso, Dan; Tang, Zhonghui; Ruan, Yijun | Methods (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, Sheng | Nature 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, Mario | Methods (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, Kai | Nature communications. | 2019 Oct 08; | 31594948 | |
| Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. | McSwiggen, David T; Mir, Mustafa; Darzacq, Xavier; Tjian, Robert | Genes & 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 E | Circulation. | 2019 Nov 12; | 31587567 | |
| How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. | Erba?, Aykut; Marko, John F | Current 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-Ting | Nature 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-Ting | Nature 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 D | ACS 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; Murry | Stem 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, Jonas | Nature 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, Zhijun | Methods (San Diego, Calif.). | 2019 Sep 16; | 31536770 | |
| Jonathan R. Warner (1936-2019)-pioneer of ribosome biosynthesis. | Pederson, Thoru | RNA (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, Robert | Molecular 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 W | Nature. | 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 T | Proceedings 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, Cole | Nature 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, Jay | Molecular cell. | 2019 Aug 28; | 31495564 | |
| Olfactory receptor genes make the case for inter-chromosomal interactions. | Bashkirova, Elizaveta; Lomvardas, Stavros | Current 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 S | Science (New York, N.Y.). | 2019 09 20; | 31488703 | |
| Molecular basis and biological function of variability in spatial genome organization. | Finn, Elizabeth H; Misteli, Tom | Science (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, Cole | Nature 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, Hanspeter | IEEE 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, Miriam | Journal 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, Bing | Nature genetics. | 2019 Sep; | 31427791 | |
| Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. | Dahlke, Katelyn; Zhao, Jing; Sing, Charles E; Banigan, Edward J | Biophysical journal. | 2019 Sep 17; | 31427067 | |
| Skeletal muscle: A review of molecular structure and function, in health and disease. | Mukund, Kavitha; Subramaniam, Shankar | Wiley interdisciplinary reviews. Systems biology and medicine | 2020 01 | 31407867 | |
| Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. | Lari, Azra; Farzam, Farzin; Bensidoun, Pierre; Oeffinger, Marlene; Zenklusen, Daniel; Grunwald, David; Montpetit, Ben | Methods in molecular biology (Clifton, N.J.). | 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 P | Proceedings 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, Hanspeter | 2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany). | 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 E | The Journal of cell biology. | 2019 Sep 02; | 31395619 | |
| Genome organization around nuclear speckles. | Chen, Yu; Belmont, Andrew S | Current 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, Mario | Cell 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 E | Pediatric 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, Bing | Nature 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 F | Molecular 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, Dariusz | Genome biology | 2019 07 30 | 31362752 | |
| Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT. | Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Auer, Alexander; Nijmeijer, Bianca; Kueblbeck, Moritz; Jimenez Sabinina, Vilma; Thevathasan, Jervis V; Ries, Jonas; Ellenberg, Jan; Jungmann, Ralf | Angewandte Chemie (International ed. in English). | 2019 09 09; | 31314157 | |
| Cooler: scalable storage for Hi-C data and other genomically-labeled arrays. | Abdennur, Nezar; Mirny, Leonid | Bioinformatics (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, Guillaume | Genome biology | 2019 07 08 | 31287004 | |
| Large distances separate coregulated genes in living Drosophila embryos. | Heist, Tyler; Fukaya, Takashi; Levine, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2019 07 23; | 31285341 | |
| Archiving and disseminating integrative structure models. | Vallat, Brinda; Webb, Benjamin; Westbrook, John; Sali, Andrej; Berman, Helen M | Journal 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 E | Scientific 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, Bernd | Small 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 E | Nature 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, Cornelis | Nature 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, Jian | Cell systems. | 2019 Jun 26; | 31229558 | |
| Two major mechanisms of chromosome organization. | Mirny, Leonid A; Imakaev, Maxim; Abdennur, Nezar | Current 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, Nicola | Journal 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 S | eLife. | 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, Ia | eLife. | 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 D | Genome 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, Dariusz | PeerJ. | 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 A | Nature. | 2019 Jun; | 31168090 | |
| WashU Epigenome Browser update 2019. | Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Sears, Renee L; Wang, Ting | Nucleic acids research. | 2019 Jul 02; | 31165883 | |
| Principles for Integrative Structural Biology Studies. | Rout, Michael P; Sali, Andrej | Cell. | 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, Ber | Proceedings 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, Shankar | BMC 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, Larry | Nucleus (Austin, Tex.). | 2019 Dec; | 31142202 | |
| The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. | Salvarani, Nicolò; Crasto, Silvia; Miragoli, Michele; Bertero, Alessandro; Paulis, Marianna; Kunderfranco, Paolo; Serio, Simone; Forni, Alberto; Lucarelli, Carla; Dal Ferro, Matteo; Larcher, Veronica; Sinagra, Gianfranco; Vezzoni, Paolo; Murry, Charles E; Faggian, Giuseppe; Condorelli, Gianluigi; Di Pasquale, Elisa | Nature communications. | 2019 05 22; | 31118417 | |
| EpiAlignment: alignment with both DNA sequence and epigenomic data. | Lu, Jia; Cao, Xiaoyi; Zhong, Sheng | Nucleic 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, Viviane | Nature 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 M | The 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 E | Developmental cell. | 2019 Jul 01; | 31105009 | |
| Long-range enhancer-promoter contacts in gene expression control. | Schoenfelder, Stefan; Fraser, Peter | Nature reviews. Genetics. | 2019 08; | 31086298 | |
| A combination of transcription factors mediates inducible interchromosomal contacts. | Kim, Seungsoo; Dunham, Maitreya J; Shendure, Jay | eLife | 2019 05 13 | 31081754 | |
| Tibanna: software for scalable execution of portable pipelines on the cloud. | Lee, Soohyun; Johnson, Jeremy; Vitzthum, Carl; K?rl?, Koray; Alver, Burak H; Park, Peter J | Bioinformatics (Oxford, England). | 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, Azad | Nature. | 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, Chun | BMC 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, Xavier | eLife | 2019 05 07 | 31038454 | |
| Receptor-Ligand Rebinding Kinetics in Confinement. | Erba?, Aykut; Olvera de la Cruz, Monica; Marko, John F | Biophysical journal. | 2019 May 07; | 31029377 | |
| Topological and functional comparison of community detection algorithms in biological networks. | Rahiminejad, Sara; Maurya, Mano R; Subramaniam, Shankar | BMC 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, Todd | The Journal of biological chemistry. | 2019 May 31; | 31010829 | |
| FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. | Ma, Chun-Yu; Madden, Pamela; Gontarz, Paul; Wang, Ting; Zhang, Bo | Frontiers in genetics. | 2019; | 31001319 | |
| Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. | Nomidis, Stefanos K; Skoruppa, Enrico; Carlon, Enrico; Marko, John F | Physical review. E. | 2019 Mar; | 30999490 | |
| MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. | Juric, Ivan; Yu, Miao; Abnousi, Armen; Raviram, Ramya; Fang, Rongxin; Zhao, Yuan; Zhang, Yanxiao; Qiu, Yunjiang; Yang, Yuchen; Li, Yun; Ren, Bing; Hu, Ming | PLoS computational biology. | 2019 04; | 30986246 | |
| Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. | Leemans, Christ; van der Zwalm, Marloes C H; Brueckner, Laura; Comoglio, Federico; van Schaik, Tom; Pagie, Ludo; van Arensbergen, Joris; van Steensel, Bas | Cell. | 2019 May 02; | 30982597 | |
| Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. | Bertero, Alessandro; Fields, Paul A; Ramani, Vijay; Bonora, Giancarlo; Yardimci, Galip G; Reinecke, Hans; Pabon, Lil; Noble, William S; Shendure, Jay; Murry, Charles E | Nature communications. | 2019 04 04; | 30948719 | |
| The accessible chromatin landscape of the murine hippocampus at single-cell resolution. | Sinnamon, John R; Torkenczy, Kristof A; Linhoff, Michael W; Vitak, Sarah A; Mulqueen, Ryan M; Pliner, Hannah A; Trapnell, Cole; Steemers, Frank J; Mandel, Gail; Adey, Andrew C | Genome research. | 2019 05; | 30936163 | |
| Transposable elements drive widespread expression of oncogenes in human cancers. | Jang, Hyo Sik; Shah, Nakul M; Du, Alan Y; Dailey, Zea Z; Pehrsson, Erica C; Godoy, Paula M; Zhang, David; Li, Daofeng; Xing, Xiaoyun; Kim, Sungsu; O'Donnell, David; Gordon, Jeffrey I; Wang, Ting | Nature genetics. | 2019 04; | 30926969 | |
| Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. | Boeynaems, Steven; Holehouse, Alex S; Weinhardt, Venera; Kovacs, Denes; Van Lindt, Joris; Larabell, Carolyn; Van Den Bosch, Ludo; Das, Rhiju; Tompa, Peter S; Pappu, Rohit V; Gitler, Aaron D | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Apr 16; | 30926670 | |
| Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. | Jean-Baptiste, Ken; McFaline-Figueroa, José L; Alexandre, Cristina M; Dorrity, Michael W; Saunders, Lauren; Bubb, Kerry L; Trapnell, Cole; Fields, Stanley; Queitsch, Christine; Cuperus, Josh T | The Plant cell. | 2019 05; | 30923229 | |
| Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications. | He, Ming; Huang, Tse-Shun; Li, Shuai; Hong, Hsiao-Chin; Chen, Zhen; Martin, Marcy; Zhou, Xin; Huang, Hsi-Yuan; Su, Shu-Han; Zhang, Jiao; Wang, Wei-Ting; Kang, Jian; Huang, Hsien-Da; Zhang, Jin; Chien, Shu; Shyy, John Y-J | Arteriosclerosis, thrombosis, and vascular biology. | 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, Long | Nature. | 2019 Apr; | 30911168 | |
| Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. | Gilgenast, Thomas G; Phillips-Cremins, Jennifer E | Cell 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 S | Genome biology. | 2019 03 19; | 30890172 | |
| Chromatin's physical properties shape the nucleus and its functions. | Stephens, Andrew D; Banigan, Edward J; Marko, John F | Current 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, Dariusz | Methods (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-Lin | Cell 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, Thoru | The Journal of cell biology. | 2019 Mar 07; | 30846483 | |
| Intermingling of chromosome territories. | Szczepińska, Teresa; Rusek, Anna Maria; Plewczynski, Dariusz | Genes, chromosomes & cancer | 2019 07 | 30828902 | |
| Dendritic Spines Taxonomy: The Functional and Structural Classification ? Time-Dependent Probabilistic Model of Neuronal Activation. | Urban, Paulina; Rezaei, Vahid; Bokota, Grzegorz; Denkiewicz, Micha?; Basu, Subhadip; Plewczy?ski, Dariusz | Journal of computational biology : a journal of computational molecular cell biology. | 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, Tom | Cell. | 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, Jay | Nature. | 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, Yijun | Nature. | 2019 02; | 30778195 | |
| Replication Timing Becomes Intertwined with 3D Genome Organization. | Ma, Jian; Duan, Zhijun | Cell. | 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 A | G3 (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, Sheng | Proceedings 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 M | Frontiers in cardiovascular medicine. | 2018; | 30697540 | |
| Adapting dCas9-APEX2 for subnuclear proteomic profiling. | Gao, Xin D; Rodríguez, Tomás C; Sontheimer, Erik J | Methods 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, Doug | Cell. | 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, David | Nature 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, Job | Genome 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 L | Cell 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, Ales | Investigative ophthalmology & visual science. | 2019 Jan 02; | 30646012 | |
| LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. | Monahan, Kevin; Horta, Adan; Lomvardas, Stavros | Nature. | 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, Arjun | PLoS 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 F | Molecular 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, Edwin | Genome 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 B | eLife. | 2018 12 27; | 30589412 | |
| A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. | Lu, Jia; Cao, Xiaoyi; Zhong, Sheng | PLoS 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-Ting | PLoS 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, Mario | Wiley 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, Arjun | Molecular cell. | 2018 Dec 06; | 30554946 | |
| RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. | Brahma, Sandipan; Henikoff, Steven | Molecular 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, Sheng | Genomics, 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 M | BMC 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, David | Nature 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, Bernd | Nature 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 P | Cell. | 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 P | Cell. | 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, Yingxiao | Proceedings 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 B | Life science alliance. | 2018 Jan; | 30456345 | |
| The interdependence of gene-regulatory elements and the 3D genome. | Vermunt, Marit W; Zhang, Di; Blobel, Gerd A | The 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; Bucki | Nature. | 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, Arjun | Nature 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 J | Molecular 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, Wolfgang | Cell 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, Azad | Cell 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, Ting | Biometrics. | 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, Thoru | Nature methods. | 2018 Nov; | 30377374 | |
| Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. | Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas | Cell systems. | 2018 Oct 24; | 30342881 | |
| Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. | Zoller, Benjamin; Little, Shawn C; Gregor, Thomas | Cell. | 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, Ting | Cell 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 S | Cell 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 S | Cell. | 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 R | Cell research. | 2018 Dec; | 30315278 | |
| Understanding molecular mechanisms of disease through spatial proteomics. | Pankow, Sandra; Martínez-Bartolomé, Salvador; Bamberger, Casimir; Yates, John R | Current 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 S | Genome 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, Feng | Genome biology. | 2018 10 04; | 30286773 | |
| Developmental enhancers and chromosome topology. | Furlong, Eileen E M; Levine, Michael | Science (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 W | FASEB 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, Sheng | iScience. | 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, Tom | Histochemistry 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 M | Methods 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, Jan | Nature. | 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, Christophe | Nature genetics. | 2018 Sep 10; | 30202056 | |
| Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. | Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F; Carlon, Enrico | Physical 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, Jing | International journal of cancer. | 2018 Nov 15; | 30183087 | |
| Interchromosomal interactions: A genomic love story of kissing chromosomes. | Maass, Philipp G; Barutcu, A Rasim; Rinn, John L | The Journal of cell biology. | 2019 Jan 07; | 30181316 | |
| RNA, Action through Interactions. | Nguyen, Tri C; Zaleta-Rivera, Kathia; Huang, Xuerui; Dai, Xiaofeng; Zhong, Sheng | Trends 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 E | Cell. | 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, Bas | EMBO 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 S | The 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 S | Nature. | 2018 09; | 30150775 | |
| Emerging Roles of Non-Coding RNA Transcription. | Kaikkonen, Minna U; Adelman, Karen | Trends 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 F | Chromosome 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; Pa | Genome 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, Hanspeter | IEEE 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, Jan | The 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 J | The 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 S | IEEE/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, Dariusz | Seminars 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, Cole | Molecular 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; Dist | Cell. | 2018 Aug 23; | 30078704 | |
| Protein motion in the nucleus: from anomalous diffusion to weak interactions. | Woringer, Maxime; Darzacq, Xavier | Biochemical Society transactions. | 2018 Aug 20; | 30065106 | |
| Temporal dynamics of pair-rule stripes in living Drosophila embryos. | Lim, Bomyi; Fukaya, Takashi; Heist, Tyler; Levine, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 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, Thomas | Nature 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 P | Ophthalmology. Retina. | 2018 Jun; | 30035246 | |
| The three-dimensional organization of the genome in cellular senescence and age-associated diseases. | Evans, Shane A; Horrell, Jeremy; Neretti, Nicola | Seminars in cell & developmental biology. | 2019 Jun; | 30031215 | |
| Computational methods for analyzing and modeling genome structure and organization. | Lin, Dejun; Bonora, Giancarlo; Yard?mc?, Galip Gürkan; Noble, William S | Wiley interdisciplinary reviews. Systems biology and medicine. | 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 T | Cancer cell. | 2018 08 13; | 30017478 | |
| GIVE: portable genome browsers for personal websites. | Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng | Genome biology. | 2018 07 18; | 30016975 | |
| Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. | Packer, Jonathan; Trapnell, Cole | Trends in genetics : TIG. | ; | 30007833 | |
| Understanding the 3D genome: Emerging impacts on human disease. | Krumm, Anton; Duan, Zhijun | Seminars 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, Wouter | Nature genetics | 2018 08 | 29988121 | |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E | Molecular cell. | 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 A | Proceedings 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, Ales | The Journal of biological chemistry. | 2018 Aug 24; | 29959226 | |
| Quantitative live and super-resolution microscopy of mitotic chromosomes. | Walther, Nike; Ellenberg, Jan | Methods 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, Xavier | Methods 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 Stafford | Bioinformatics (Oxford, England). | 2018 07 01; | 29950005 | |
| Predicting CTCF-mediated chromatin loops using CTCF-MP. | Zhang, Ruochi; Wang, Yuchuan; Yang, Yang; Zhang, Yang; Ma, Jian | Bioinformatics (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, Reut | Human 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, Lin | Biochemistry. | 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 R | Nature 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, Robert | eLife. | 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, Jian | Cell 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, Robert | Science (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, Huimin | Nucleic 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, Long | Cell. | 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, Mitchell | Cell. | 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, Xavier | Genes. | 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 E | Cell 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, Qiang | Nature. | 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, Jan | Nature 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, Jan | Nature protocols. | 2018 06; | 29844520 | |
| Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods. | Chen, Chun Chieh; Stark, Marie; Baikoghli, Mo; Cheng, R Holland | Journal of visualized experiments : JoVE. | 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 E | Optics 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 N | Journal 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 E | Methods (San Diego, Calif.). | ; | 29772275 | |
| Quantitative imaging of chromatin decompaction in living cells. | Dultz, Elisa; Mancini, Roberta; Polles, Guido; Vallotton, Pascal; Alber, Frank; Weis, Karsten | Molecular biology of the cell. | ; | 29771637 | |
| Gene regulation in the 3D genome. | Li, Yun; Hu, Ming; Shen, Yin | Human 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 I | Scientific 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 J | Nature 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 M | Genome research. | 2018 06; | 29735606 | |
| Emerging Evidence of Chromosome Folding by Loop Extrusion. | Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; Goloborodko, Anton; Mirny, Leonid A | Cold Spring Harbor symposia on quantitative biology. | 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, Rafael | Cell. | 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 E | Proceedings 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, Justin | Molecular 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 L | Nature communications | 2018 04 13 | 29654311 | |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. | Bonora, G; Deng, X; Fang, H; Ramani, V; Qiu, R; Berletch, J B; Filippova, G N; Duan, Z; Shendure, J; Noble, W S; Disteche, C M | Nature communications. | 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, Ulrich | Science 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, Jan | The 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, Jonas | Nature 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 L | Molecular 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, Frank | Nature protocols. | 2018 May; | 29622804 | |
| Visualization of Transvection in Living Drosophila Embryos. | Lim, Bomyi; Heist, Tyler; Levine, Michael; Fukaya, Takashi | Molecular 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 M | Nature 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, Jan | The Journal of cell biology. | 2018 Jun 04; | 29572382 | |
| Three-dimensional organization and dynamics of the genome. | Szalaj, Przemyslaw; Plewczynski, Dariusz | Cell biology and toxicology. | 2018 Oct; | 29568981 | |
| Effects of electrostatic interactions on ligand dissociation kinetics. | Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F | Physical review. E. | 2018 Feb; | 29548245 | |
| Defect-facilitated buckling in supercoiled double-helix DNA. | Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu; Neuman, Keir C; Marko, John F | Physical 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 P | Nature. | 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 L | Molecular 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, Irene | Methods 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, Mario | Methods (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, Ewan | PLoS 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, Robert | Proceedings 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 E | Cell 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, Lin | Scientific 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, Jakub | Scientific 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, Arjun | Cell 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 Lieberman | Cell systems. | 2018 Feb 28; | 29428417 | |
| Single-cell replication profiling to measure stochastic variation in mammalian replication timing. | Dileep, Vishnu; Gilbert, David M | Nature 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, ZhiJun | Methods (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, Adam | Nature 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, Job | Science (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 L | Nature 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 L | The 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 E | Nature methods. | 2018 Feb; | 29334377 | |
| Ki-67: more than a proliferation marker. | Sun, Xiaoming; Kaufman, Paul D | Chromosoma. | 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 E | Nature 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, Bing | Cell research. | 2018 Feb; | 29313530 | |
| Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. | Gerace, Larry; Tapia, Olga | Current 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, Xavier | eLife. | 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, D | Nucleus (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 E | Biomedical optics express. | 2017 Dec 01; | 29296501 | |
| A mixed-scale dense convolutional neural network for image analysis. | Pelt, Daniël M; Sethian, James A | Proceedings of the National Academy of Sciences of the United States of America. | 2018 Jan 09; | 29279403 | |
| Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. | Baddeley, David; Bewersdorf, Joerg | Annual 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, Dariusz | Briefings in functional genomics. | 2018 11 26; | 29253080 | |
| Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. | Mukund, Kavitha; Subramaniam, Shankar | Frontiers 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 Y | eLife. | 2017 Dec 14; | 29239719 | |
| Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, Ting | Methods in molecular biology (Clifton, N.J.). | 2018; | 29224147 | |
| Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. | Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D; Mondragón, Alfonso; Marko, John F | Physical review letters. | 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, Kikuë | The 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, Ting | BioEssays : 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 Network | Nature. | 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 F | Molecular biology of the cell. | 2018 Jan 15; | 29142071 | |
| Live Imaging of mRNA Synthesis in Drosophila. | Garcia, Hernan G; Gregor, Thomas | Methods in molecular biology (Clifton, N.J.). | 2018; | 29130209 | |
| Single mRNA Molecule Detection in Drosophila. | Little, Shawn C; Gregor, Thomas | Methods 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 C | Molecular 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, Justin | eLife. | 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, Francois | Nature. | 2017 Nov 02; | 29094699 | |
| Simultaneous measurement of emission color and 3D position of single molecules. | Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, Sjoerd | Optics 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 N | Proceedings 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 F | Scientific 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 J | Proceedings 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, Robert | Nucleus (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 S | American journal of human genetics. | 2017 Nov 02; | 29056226 | |
| Supercoiling DNA Locates Mismatches. | Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir C | Physical review letters. | 2017 Oct 06; | 29053317 | |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan, Edward J; Stephens, Andrew D; Marko, John F | Biophysical journal. | 2017 Oct 17; | 29045860 | |
| RNA structure interactions and ribonucleoprotein processes of the influenza A virus. | Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz | Briefings 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, Wei | Bioinformatics (Oxford, England). | 2018 01 01; | 29036318 | |
| Transvection. | Fukaya, Takashi; Levine, Michael | Current 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 Lieberman | Cell. | 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, Xavier | Genes & 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, Kerstin | Biophysical journal. | 2017 Oct 03; | 28978433 | |
| From structure to function, how bioinformatics help to reveal functions of our genomes. | Zheng, Xiaoqi; Zhong, Sheng | Genome biology. | 2017 Sep 26; | 28950915 | |
| Structural aspects of the inactive X chromosome. | Bonora, Giancarlo; Disteche, Christine M | Philosophical 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, Cornelis | Cell. | 2017 Sep 21; | 28938112 | |
| Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. | Rege, Mayuri; Phillips-Cremins, Jennifer E | Molecular cell. | 2017 Sep 21; | 28938095 | |
| Liquid phase condensation in cell physiology and disease. | Shin, Yongdae; Brangwynne, Clifford P | Science (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, Stavros | eLife. | 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 A | Genes & development. | 2017 Aug 15; | 28916711 | |
| Targeting Specificity of the CRISPR/Cas9 System. | Tasan, Ipek; Zhao, Huimin | ACS 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 Network | Nature. | 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, Ting | BMC 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 P | Molecular 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 S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, Jian | Bioinformatics (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, Wei | BMC 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, Hanspeter | IEEE 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, Hanspeter | IEEE 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, Qunhua | Genome research. | 2017 Nov; | 28855260 | |
| Crossed wires: 3D genome misfolding in human disease. | Norton, Heidi K; Phillips-Cremins, Jennifer E | The 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 G | Molecular 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, Cole | Nature 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, Jonathan | Nature 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, Jay | Science (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, David | Lab 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, Rafael | Molecular cell. | ; | 28803781 | |
| A new era of studying p53-mediated transcription activation. | Liu, Wei-Li; Coleman, Robert A; Singh, Sameer K | Transcription. | 2018; | 28795863 | |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual 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 D | Proceedings 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, Frank | Genome 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 C | Science (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, André | Cell. | 2017 Jul 27; | 28735753 | |
| Integrative modelling of cellular assemblies. | Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, Maya | Current 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, Amos | Nature. | 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 H | Nature. | 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 D | Molecular and cellular biology. | 2017 Jun 19; | 28630280 | |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari, Sumitabha; Marko, John F | Physical 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 J | JCI 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, Ting | Bioinformatics (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 H | Nature methods. | 2017 Jun 12; | 28604724 | |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg, Geoffrey; Imakaev, Maxim | Nature methods. | 2017 Jul; | 28604723 | |
| Engineering biological systems using automated biofoundries. | Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin | Metabolic 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, Ting | BMC 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, Yun | Bioinformatics (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 J | eLife. | 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 E | Genome 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 G | Cell. | 2017 May 18; | 28525758 | |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel, Bas; Belmont, Andrew S | Cell. | 2017 May 18; | 28525751 | |
| Combinatorial chemistry in drug discovery. | Liu, Ruiwu; Li, Xiaocen; Lam, Kit S | Current 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 J | Nature methods. | 2017 Jun; | 28481362 | |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | eLife. | 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, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Current 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 H | Methods (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, Long | Biophysical 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 L | Molecular 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, Alfonso | Nature structural & molecular biology. | 2017 May; | 28414321 | |
| Causes and consequences of nuclear gene positioning. | Shachar, Sigal; Misteli, Tom | Journal 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, Jenn | Molecular 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 F | Proceedings 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, Yijun | Nature protocols. | 2017 May; | 28358394 | |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté, Allison J; Raj, Arjun | Biophysical 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, Kikuë | Nature. | 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, Ting | Nature 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 M | Proceedings 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 Lieberman | Science (New York, N.Y.). | 2017 Apr 07; | 28336562 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS 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, Mazhar | Nature communications. | 2017 Mar 14; | 28290446 | |
| Unearthing worm replication origins. | Sasaki, Takayo; Gilbert, David M | Nature 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 R | Cell. | ; | 28235199 | |
| Epigenetic characteristics of the mitotic chromosome in 1D and 3D. | Oomen, Marlies E; Dekker, Job | Critical 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, Huimin | ACS 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, Tom | Methods (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, Cornelis | Genes & development. | 2017 Jan 15; | 28167501 | |
| Software tools for visualizing Hi-C data. | Yard?mc?, Galip Gürkan; Noble, William Stafford | Genome 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 E | Molecular 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, Jay | Nature 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 C | Nature 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-Chun | Science 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, Cole | Nature 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, Huimin | ACS 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, Ting | Neoplasia (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, Huimin | ACS synthetic biology. | 2017 04 21; | 28073246 | |
| Predicting chromatin architecture from models of polymer physics. | Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 2017 03 | 28070687 | |
| Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. | Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F | Molecular biology of the cell. | 2017 Jan 05; | 28057760 | |
| Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. | Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan | Genome research. | 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 P | Cell. | 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, Bing | Cell 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, Robert | eLife. | 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 A | Cell reports. | 2016 Nov 15; | 27851973 | |
| A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. | Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, Bing | Cell reports. | 2016 Nov 15; | 27851967 | |
| The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. | Matheson, Timothy D; Kaufman, Paul D | Molecular biology of the cell. | 2017 Jan 01; | 27807046 | |
| An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. | Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Micha?; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz | Genome research. | 2016 Dec; | 27789526 | |
| High-throughput assessment of context-dependent effects of chromatin proteins. | Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas | Epigenetics & chromatin. | 2016; | 27777628 | |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S | Nature methods. | 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 Y | Nature methods. | ; | 27749837 | |
| Transferable model for chromosome architecture. | Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José N | Proceedings of the National Academy of Sciences of the United States of America. | 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, Zhijun | Nature protocols. | 2016 Nov; | 27685100 | |
| Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. | Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng | PloS one. | 2016; | 27618313 | |
| Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. | Stark, Marie; Cheng, R Holland | Pharmaceutical patent analyst. | 2016 Sep; | 27610752 | |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt, Anthony D; Hu, Ming; Ren, Bing | Nature 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, Thoru | The 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, Olgica | Bioinformatics (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 M | Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. | 2016 Jul; | 27516727 | |
| Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. | Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, Hiroko | Scientific reports. | 2016 Aug 12; | 27516062 | |
| Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. | Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez Lieberman | Cell systems. | 2016 Jul; | 27467249 | |
| Allele-Specific Quantification of Structural Variations in Cancer Genomes. | Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian | Cell systems. | 2016 Jul; | 27453446 | |
| Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. | Beagrie, Robert A; Pombo, Ana | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2016 09; | 27452946 | |
| Structural organization of the inactive X chromosome in the mouse. | Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job | Nature. | 2016 Jul 28; | 27437574 | |
| Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. | Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Aug 02; | 27432957 | |
| Polymer physics of chromosome large-scale 3D organisation. | Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario | Scientific reports. | 2016 Jul 13; | 27405443 | |
| Identifying gene regulatory network rewiring using latent differential graphical models. | Tian, Dechao; Gu, Quanquan; Ma, Jian | Nucleic 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 S | Nature 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 A | Genes & development. | 2016 Jun 15; | 27340175 | |
| Enhancer Control of Transcriptional Bursting. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Cell. | 2016 Jul 14; | 27293191 | |
| RTFBSDB: an integrated framework for transcription factor binding site analysis. | Wang, Zhong; Martins, André L; Danko, Charles G | Bioinformatics (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 E | Wiley 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, Arjun | Molecular cell. | 2016 Jun 2; | 27259209 | |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular cell. | 2016 Jun 2; | 27259200 | |
| Use of genome-editing tools to treat sickle cell disease. | Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Human genetics. | 2016 Jun 1; | 27250347 | |
| Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. | Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong | Nature communications. | 2016; | 27240697 | |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol A | Cell. | 2016 Jun 2; | 27238023 | |
| Chromosome Compaction by Active Loop Extrusion. | Goloborodko, Anton; Marko, John F; Mirny, Leonid A | Biophysical 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 S | Annual 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 A | Cell Rep | 2016 May 19 | 27210764 | |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid | eLife. | 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 F | Physical 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 A | Genome biology. | 2016; | 27176874 | |
| Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. | Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M | Disaster medicine and public health preparedness. | 2016 06; | 27174171 | |
| FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. | Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming | Bioinformatics (Oxford, England). | 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 E | Cell Stem Cell | 2016 May 5 | P:611-24 | 27152443 |
| Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. | Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2016 Sep; | 27145786 | |
| Dosage compensation of the sex chromosomes and autosomes. | Disteche, Christine M | Semin Cell Dev Biol | 2016 Apr 22 | 27112542 | |
| TAD disruption as oncogenic driver. | Valton, Anne-Laure; Dekker, Job | Curr Opin Genet Dev | 2016 Feb | P:34-40 | 27111891 |
| Jointly characterizing epigenetic dynamics across multiple human cell types. | Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C | Nucleic 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 Biotechnology | 2016 April 18 | Epub ahead of print | 27088723 |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting | Trends Genet | 2016 May | P:269-83 | 27080453 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. | Molecular Cell | 2016 April 5 | V:62 P:1-11 | 27067601 |
| History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. | Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A | J Bioinform Comput Biol | 2016 Apr | P:1641002 | 27021249 |
| HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. | Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming | BMC research notes. | 2016; | 26969411 | |
| The 3D Genome as Moderator of Chromosomal Communication. | Dekker, Job; Mirny, Leonid | Cell | 2016 Mar 10 | V:164 P:1110-21 | 26967279 |
| Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. | Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank | Proceedings of the National Academy of Sciences of the United States of America. | 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, Arjun | Genes & 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 A | Science | 2016 Mar 25 | V:351 P:1454-8 | 26940867 |
| Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. | Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor | Nucleus | 2016 Mar | P:84-102 | 26900797 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting | G3 (Bethesda) | 2016 | P:973-86 | 26888867 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani, Vijay; Shendure, Jay; Duan, Zhijun | Genomics Proteomics Bioinformatics | 2016 Feb | P:7-20 | 26876719 |
| Chemically activatable viral capsid functionalized for cancer targeting. | Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland | Nanomedicine | 2016 Feb | P:377-90 | 26786134 |
| Imaging Transcription: Past, Present, and Future. | Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée | Cold Spring Harbor symposia on quantitative biology. | 2016 Jan 13 | 26763984 | |
| The redundancy of the mammalian heterochromatic compartment. | Politz, Joan C Ritland; Scalzo, David; Groudine, Mark | Curr Opin Genet Dev | 2015 Dec 16 | P:1-8 | 26706451 |
| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine | Nucleic acids research. | 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, Yijun | Cell. | 2015 Dec 17 | V:163 P:1611-27 | 26686651 |
| A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. | Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 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, Peter | Nature 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 Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Nov 24; | 26499245 |