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

Title Authors Journal PubMedID Publication Date
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Sanborn, Adrian L; Rao, Suhas S P; Huang, Su-Chen; Durand, Neva C; Huntley, Miriam H; Jewett, Andrew I; Bochkov, Ivan D; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher P; Gnirke, Andreas; Melnikov, Alexandre; McKenna, Doug; Stamenova, Elena K; Lander, Eric S; Aiden, Erez Lieberman Proceedings of the National Academy of Sciences of the United States of America 26499245 2015 Nov 24
Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nagano, Takashi; Lubling, Yaniv; Yaffe, Eitan; Wingett, Steven W; Dean, Wendy; Tanay, Amos; Fraser, Peter Nature protocols. 26540590 2015 Dec;
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun Bioinformatics (Oxford, England). 26543175 2016 03 01;
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun Cell. 26686651 2015 Dec 17
TopDom: an efficient and deterministic method for identifying topological domains in genomes. Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine Nucleic acids research 26704975 2016 Apr 20
The redundancy of the mammalian heterochromatic compartment. Politz, Joan C Ritland; Scalzo, David; Groudine, Mark Curr Opin Genet Dev 26706451 2015 Dec 16
Imaging Transcription: Past, Present, and Future. Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée Cold Spring Harbor symposia on quantitative biology. 26763984 2016 Jan 13
Chemically activatable viral capsid functionalized for cancer targeting. Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland Nanomedicine 26786134 2016 Feb
Understanding Spatial Genome Organization: Methods and Insights. Ramani, Vijay; Shendure, Jay; Duan, Zhijun Genomics Proteomics Bioinformatics 26876719 2016 Feb
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting G3 (Bethesda) 26888867 2016
Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor Nucleus 26900797 2016 Mar
Activation of proto-oncogenes by disruption of chromosome neighborhoods. Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S; Valton, Anne-Laure; Bak, Rasmus O; Li, Charles H; Goldmann, Johanna; Lajoie, Bryan R; Fan, Zi Peng; Sigova, Alla A; Reddy, Jessica; Borges-Rivera, Diego; Lee, Tong Ihn; Jaenisch, Rudolf; Porteus, Matthew H; Dekker, Job; Young, Richard A Science 26940867 2016 Mar 25
Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun Genes & development. 26944681 2016 Mar 1;
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank Proceedings of the National Academy of Sciences of the United States of America 26951677 2016 Mar 22
The 3D Genome as Moderator of Chromosomal Communication. Dekker, Job; Mirny, Leonid Cell 26967279 2016 Mar 10
HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming BMC research notes 26969411 2016 Mar 11
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A J Bioinform Comput Biol 27021249 2016 Apr
A Guide to Packing Your DNA. Dekker, Job; Guttman, Mitchell; Lomvardas, Stavros Cell 27058655 2016 Apr 07
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. Molecular Cell 27067601 2016 April 5
Evolution of Epigenetic Regulation in Vertebrate Genomes. Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting Trends Genet 27080453 2016 May
Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. Nature Biotechnology 27088723 2016 April 18
Jointly characterizing epigenetic dynamics across multiple human cell types. Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C Nucleic acids research. 27095202 2016 08 19;
TAD disruption as oncogenic driver. Valton, Anne-Laure; Dekker, Job Curr Opin Genet Dev 27111891 2016 Feb
Dosage compensation of the sex chromosomes and autosomes. Disteche, Christine M Semin Cell Dev Biol 27112542 2016 Apr 22
Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 27145786 2016 Sep;
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E Cell Stem Cell 27152443 2016 May 5
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming Bioinformatics (Oxford, England). 27153668 2016 09 01;
Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M Disaster medicine and public health preparedness. 27174171 2016 06;
Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Proserpio, Valentina; Piccolo, Andrea; Haim-Vilmovsky, Liora; Kar, Gozde; Lönnberg, Tapio; Svensson, Valentine; Pramanik, Jhuma; Natarajan, Kedar Nath; Zhai, Weichao; Zhang, Xiuwei; Donati, Giacomo; Kayikci, Melis; Kotar, Jurij; McKenzie, Andrew N J; Montandon, Ruddy; Billker, Oliver; Woodhouse, Steven; Cicuta, Pietro; Nicodemi, Mario; Teichmann, Sarah A Genome biology 27176874 2016 May 12
Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. Banigan, Edward J; Marko, John F Physical review. E. 27182590 2016 Apr;
Compaction and segregation of sister chromatids via active loop extrusion. Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid eLife. 27192037 2016 May 18;
Formation of Chromosomal Domains by Loop Extrusion. Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A Cell Rep 27210764 2016 May 19
CRISPR/Cas9 for Human Genome Engineering and Disease Research. Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S Annual review of genomics and human genetics. 27216776 2016 Aug 31;
Chromosome Compaction by Active Loop Extrusion. Goloborodko, Anton; Marko, John F; Mirny, Leonid A Biophysical journal. 27224481 2016 May 24;
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol A Cell. 27238023 2016 Jun 2;
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong Nature communications 27240697 2016 May 31
Use of genome-editing tools to treat sickle cell disease. Tasan, Ipek; Jain, Surbhi; Zhao, Huimin Human genetics. 27250347 2016 Jun 1;
Chromatin Domains: The Unit of Chromosome Organization. Dixon, Jesse R; Gorkin, David U; Ren, Bing Molecular cell. 27259200 2016 Jun 2;
What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. Symmons, Orsolya; Raj, Arjun Molecular cell. 27259209 2016 Jun 2;
CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop. Beagan, Jonathan A; Phillips-Cremins, Jennifer E Wiley interdisciplinary reviews. Systems biology and medicine. 27265842 2016 Jul;
RTFBSDB: an integrated framework for transcription factor binding site analysis. Wang, Zhong; Martins, André L; Danko, Charles G Bioinformatics (Oxford, England). 27288497 2016 Oct 01;
Enhancer Control of Transcriptional Bursting. Fukaya, Takashi; Lim, Bomyi; Levine, Michael Cell. 27293191 2016 Jul 14;
A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A Genes & development. 27340175 2016 Jun 15;
Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. McGeachie, Michael J; Yates, Katherine P; Zhou, Xiaobo; Guo, Feng; Sternberg, Alice L; Van Natta, Mark L; Wise, Robert A; Szefler, Stanley J; Sharma, Sunita; Kho, Alvin T; Cho, Michael H; Croteau-Chonka, Damien C; Castaldi, Peter J; Jain, Gaurav; Sanyal, American journal of respiratory and critical care medicine. 27367781 2016 Dec 15;
Nanoscale imaging of RNA with expansion microscopy. Chen, Fei; Wassie, Asmamaw T; Cote, Allison J; Sinha, Anubhav; Alon, Shahar; Asano, Shoh; Daugharthy, Evan R; Chang, Jae-Byum; Marblestone, Adam; Church, George M; Raj, Arjun; Boyden, Edward S Nature methods. 27376770 2016 Aug;
Identifying gene regulatory network rewiring using latent differential graphical models. Tian, Dechao; Gu, Quanquan; Ma, Jian Nucleic acids research. 27378774 2016 Sep 30;
Polymer physics of chromosome large-scale 3D organisation. Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario Scientific reports. 27405443 2016 Jul 13;
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman Proceedings of the National Academy of Sciences of the United States of America. 27432957 2016 Aug 02;
Structural organization of the inactive X chromosome in the mouse. Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job Nature. 27437574 2016 Jul 28;
Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. Beagrie, Robert A; Pombo, Ana BioEssays : news and reviews in molecular, cellular and developmental biology. 27452946 2016 09;
Allele-Specific Quantification of Structural Variations in Cancer Genomes. Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian Cell systems. 27453446 2016 Jul;
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez Lieberman Cell systems. 27467249 2016 Jul;
Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, Hiroko Scientific reports. 27516062 2016 Aug 12;
Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions. Shenoy, Shailesh M Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 27516727 2016 Jul;
A new correlation clustering method for cancer mutation analysis. Hou, Jack P; Emad, Amin; Puleo, Gregory J; Ma, Jian; Milenkovic, Olgica Bioinformatics (Oxford, England). 27540270 2016 Aug 18;
CRISPR-Cas9 nuclear dynamics and target recognition in living cells. Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Huisman, Maximiliaan; Zhang, Shaojie; Grunwald, David; Pederson, Thoru The Journal of cell biology. 27551060 2016 Aug 29;
Genome-wide mapping and analysis of chromosome architecture. Schmitt, Anthony D; Hu, Ming; Ren, Bing Nature reviews. Molecular cell biology. 27580841 2016 12;
Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. Stark, Marie; Cheng, R Holland Pharmaceutical patent analyst. 27610752 2016 Sep;
Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng PloS one. 27618313 2016;
Mapping 3D genome architecture through in situ DNase Hi-C. Ramani, Vijay; Cusanovich, Darren A; Hause, Ronald J; Ma, Wenxiu; Qiu, Ruolan; Deng, Xinxian; Blau, C Anthony; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun Nature protocols. 27685100 2016 Nov;
Transferable model for chromosome architecture. Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José N Proceedings of the National Academy of Sciences of the United States of America. 27688758 2016 Oct 25;
ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y Nature methods. 27749837 ;
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S Nature methods. 27776111 2016 Dec;
High-throughput assessment of context-dependent effects of chromatin proteins. Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas Epigenetics & chromatin. 27777628 2016;
An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Micha?; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz Genome research. 27789526 2016 Dec;
The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. Matheson, Timothy D; Kaufman, Paul D Molecular biology of the cell. 27807046 2017 Jan 01;
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, Bing Cell reports. 27851967 2016 Nov 15;
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn A Cell reports. 27851973 2016 Nov 15;
A dynamic mode of mitotic bookmarking by transcription factors. Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert eLife. 27855781 2016 Nov 19;
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Fang, Rongxin; Yu, Miao; Li, Guoqiang; Chee, Sora; Liu, Tristin; Schmitt, Anthony D; Ren, Bing Cell research. 27886167 2016 Dec;
Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. Shin, Yongdae; Berry, Joel; Pannucci, Nicole; Haataja, Mikko P; Toettcher, Jared E; Brangwynne, Clifford P Cell. 28041848 2017 Jan 12;
Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan Genome research. 28049628 2017 Mar;
Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F Molecular biology of the cell. 28057760 2017 Jan 05;
Predicting chromatin architecture from models of polymer physics. Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 28070687 2017 03
A New Era of Genome Integration-Simply Cut and Paste! Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, Huimin ACS synthetic biology. 28073246 2017 04 21;
Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, Ting Neoplasia (New York, N.Y.). 28088687 2017 Feb;
Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. Chao, Ran; Liang, Jing; Tasan, Ipek; Si, Tong; Ju, Linyang; Zhao, Huimin ACS synthetic biology. 28103009 2017 Apr 21;
Single-cell mRNA quantification and differential analysis with Census. Qiu, Xiaojie; Hill, Andrew; Packer, Jonathan; Lin, Dejun; Ma, Yi-An; Trapnell, Cole Nature methods. 28114287 2017 Mar;
ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis. Li, Zhaomin; Zhang, Peng; Yan, Aimin; Guo, Zhengyu; Ban, Yuguang; Li, Jin; Chen, Shi; Yang, Hui; He, Yongzheng; Li, Jianping; Guo, Ying; Zhang, Wen; Hajiramezanali, Ehsan; An, Huangda; Fajardo, Darlene; Harbour, J William; Ruan, Yijun; Nimer, Stephen D; Yu, Peng; Chen, Xi; Xu, Mingjiang; Yang, Feng-Chun Science advances. 28116354 2017 Jan;
High-throughput automated microfluidic sample preparation for accurate microbial genomics. Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C Nature communications. 28128213 2017 Jan 27;
Massively multiplex single-cell Hi-C. Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Gunderson, Kevin L; Steemers, Frank J; Disteche, Christine M; Noble, William S; Duan, Zhijun; Shendure, Jay Nature methods. 28135255 2017 Mar;
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E Molecular cell. 28157505 2017 Feb 02;
Software tools for visualizing Hi-C data. Yard?mc?, Galip Gürkan; Noble, William Stafford Genome biology. 28159004 2017 Feb 03;
Comprehensive characterization of neutrophil genome topology. Zhu, Yina; Gong, Ke; Denholtz, Matthew; Chandra, Vivek; Kamps, Mark P; Alber, Frank; Murre, Cornelis Genes & development. 28167501 2017 Jan 15;
Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. Finn, Elizabeth H; Pegoraro, Gianluca; Shachar, Sigal; Misteli, Tom Methods (San Diego, Calif.). 28179124 2017 Jul 01;
A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, Huimin ACS synthetic biology. 28215080 2017 Mar 07;
Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Oomen, Marlies E; Dekker, Job Critical reviews in biochemistry and molecular biology. 28228067 2017 Apr;
Multivalent Small-Molecule Pan-RAS Inhibitors. Welsch, Matthew E; Kaplan, Anna; Chambers, Jennifer M; Stokes, Michael E; Bos, Pieter H; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A; Huang, Christine S; Tran, Timothy H; Akkiraju, Hemanth; Brown, Lewis M; Nandakumar, Renu; Cremers, Serge; Yang, Wan Seok; Tong, Liang; Olive, Kenneth P; Ferrando, Adolfo; Stockwell, Brent R Cell. 28235199 ;
Unearthing worm replication origins. Sasaki, Takayo; Gilbert, David M Nature structural & molecular biology. 28257138 2017 03 03;
Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem; Bandaria, Jigar; Mir, Mustafa; Szlachta, Karol; Singh, Ritambhara; Darzacq, Xavier; Yildiz, Ahmet; Adli, Mazhar Nature communications. 28290446 2017 Mar 14;
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. Lowdon, Rebecca F; Wang, Ting PloS one. 28333948 2017;
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman Science (New York, N.Y.). 28336562 2017 Apr 07;
Form and function of topologically associating genomic domains in budding yeast. Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M Proceedings of the National Academy of Sciences of the United States of America. 28348222 2017 Apr 11;
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting Nature communications. 28348391 2017 Mar 28;
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë Nature. 28355183 2017 04 06;
FISHing Out the Details of CRISPR Genome Tracks. Coté, Allison J; Raj, Arjun Biophysical journal. 28355532 2017 Mar 28;
Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun Nature protocols. 28358394 2017 May;
Facilitated dissociation of transcription factors from single DNA binding sites. Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F Proceedings of the National Academy of Sciences of the United States of America. 28364020 2017 Apr 18;
The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu, Sarah C; Gilgenast, Thomas G; Bartman, Caroline R; Edwards, Christopher R; Stonestrom, Aaron J; Huang, Peng; Emerson, Daniel J; Evans, Perry; Werner, Michael T; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Phillips-Cremins, Jenn Molecular cell. 28388437 2017 Apr 06;
Causes and consequences of nuclear gene positioning. Shachar, Sigal; Misteli, Tom Journal of cell science. 28404786 2017 May 01;
An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso Nature structural & molecular biology. 28414321 2017 May;
p53 dynamically directs TFIID assembly on target gene promoters. Coleman, R A; Qiao, Z; Singh, S K; Peng, C S; Cianfrocco, M; Zhang, Z; Piasecka, A; Aldeborgh, H; Basishvili, G; Liu, W L Molecular and cellular biology. 28416636 2017 Apr 17;
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long Biophysical journal. 28427715 2017 May 09;
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Belaghzal, Houda; Dekker, Job; Gibcus, Johan H Methods (San Diego, Calif.). 28435001 2017 Apr 18;
Rapid Rates of Pol II Elongation in the Drosophila Embryo. Fukaya, Takashi; Lim, Bomyi; Levine, Michael Current biology : CB. 28457866 2017 May 08;
ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee The Journal of experimental medicine. 28461595 2017 May 01;
CTCF and cohesin regulate chromatin loop stability with distinct dynamics. Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier eLife. 28467304 2017 May 03;
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Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx. Möckl, Leonhard; Pedram, Kayvon; Roy, Anish R; Krishnan, Venkatesh; Gustavsson, Anna-Karin; Dorigo, Oliver; Bertozzi, Carolyn R; Moerner, W E Developmental cell. 31105009 2019 Jul 01;
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Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber Med (New York, N.Y.) 33969332 2021 May 14
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Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. Scourzic, Laurianne; Salataj, Eralda; Apostolou, Effie Frontiers in immunology 34054841 2021
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Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization. Yang, Muyu; Ma, Jian Journal of molecular biology 35659533 2022 08 15
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The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells. Hasenson, Sarah E; Alkalay, Ella; Atrash, Mohammad K; Boocholez, Alon; Gershbaum, Julianna; Hochberg-Laufer, Hodaya; Shav-Tal, Yaron Cells 35741072 2022 06 16
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Development of 68Ga-Labeled Hepatitis E Virus Nanoparticles for Targeted Drug Delivery and Diagnostics with PET. Lambidis, Elisavet; Chen, Chun-Chieh; Baikoghli, Mo; Imlimthan, Surachet; Khng, You Cheng; Sarparanta, Mirkka; Cheng, R Holland; Airaksinen, Anu J Molecular pharmaceutics 35857429 2022 08 01
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Assessing Specific Networks of Chromatin Interactions with HiChIP. Di Giammartino, Dafne Campigli; Polyzos, Alexander; Apostolou, Effie Methods in molecular biology (Clifton, N.J.) 35867248 2022
Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq. Zhang, Liguo; Chen, Yu; Belmont, Andrew S Methods in molecular biology (Clifton, N.J.) 35867249 2022
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Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells. Fonseca, Raíssa; Burn, Thomas N; Gandolfo, Luke C; Devi, Sapna; Park, Simone L; Obers, Andreas; Evrard, Maximilien; Christo, Susan N; Buquicchio, Frank A; Lareau, Caleb A; McDonald, Keely M; Sandford, Sarah K; Zamudio, Natasha M; Zanluqui, Nagela G; Zaid, Ali; Speed, Terence P; Satpathy, Ansuman T; Mueller, Scott N; Carbone, Francis R; Mackay, Laura K Nature immunology 35882933 2022 08
Multiomics characterization of mouse hepatoblastoma identifies yes-associated protein 1 target genes. Rodríguez, Tomás C; Kwan, Suet-Yan; Smith, Jordan L; Dadafarin, Sina; Wu, Chern-Horng; Sontheimer, Erik J; Xue, Wen Hepatology (Baltimore, Md.) 35932276 2022 Aug 06
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Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. Cheng, Li-Chun; Zhang, Xi; Abhinav, Kanishk; Nguyen, Julie A; Baboo, Sabyasachi; Martinez-Bartolomé, Salvador; Branon, Tess C; Ting, Alice Y; Loose, Esther; Yates 3rd, John R; Gerace, Larry Journal of proteome research 35972904 2022 Sep 02
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Mammalian genome innovation through transposon domestication. Modzelewski, Andrew J; Gan Chong, Johnny; Wang, Ting; He, Lin Nature cell biology 36008480 2022 09
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The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies. Courchaine, Edward; Gelles-Watnick, Sara; Machyna, Martin; Straube, Korinna; Sauyet, Sarah; Enright, Jade; Neugebauer, Karla M Nature communications 36224177 2022 Oct 12
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Advances in CRISPR therapeutics. Chavez, Michael; Chen, Xinyi; Finn, Paul B; Qi, Lei S Nature reviews. Nephrology 36280707 2023 Jan
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Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Fang, Weixiang; Bell, Claire M; Sapirstein, Abel; Asami, Soichiro; Leeper, Kathleen; Zack, Donald J; Ji, Hongkai; Kalhor, Reza Cell 36423582 2022 Nov 23
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Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. Boe, Ryan H; Ayyappan, Vinay; Schuh, Lea; Raj, Arjun Cell systems 36450286 2022 Dec 21
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Aberrant chromatin organization at the nexus of laminopathy disease pathways. Santini, Garrett T; Shah, Parisha P; Karnay, Ashley; Jain, Rajan Nucleus (Austin, Tex.) 36503349 2022 Dec
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Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. Shi, Tuo; Beaulieu, Marielle O; Saunders, Lauren M; Fabian, Peter; Trapnell, Cole; Segil, Neil; Crump, J Gage; Raible, David W eLife 36598134 2023 Jan 04
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Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E bioRxiv : the preprint server for biology 36945584 2023 Mar 10
Probing neural circuit mechanisms in Alzheimer's disease using novel technologies. Grieco, Steven F; Holmes, Todd C; Xu, Xiangmin Molecular psychiatry 36959497 2023 Oct
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Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. Zou, Roger S; Liu, Yang; Gaido, Oscar E Reyes; Konig, Maximilian F; Mog, Brian J; Shen, Leo L; Aviles-Vazquez, Franklin; Marin-Gonzalez, Alberto; Ha, Taekjip Nature methods 37024653 2023 May
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Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser. Zhuo, Xiaoyu; Hsu, Silas; Purushotham, Deepak; Kuntala, Prashant Kumar; Harrison, Jessica K; Du, Alan Y; Chen, Samuel; Li, Daofeng; Wang, Ting Genome research 37156621 2023 May
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Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Luo, Renhe; Yan, Jielin; Oh, Jin Woo; Xi, Wang; Shigaki, Dustin; Wong, Wilfred; Cho, Hyein S; Murphy, Dylan; Cutler, Ronald; Rosen, Bess P; Pulecio, Julian; Yang, Dapeng; Glenn, Rachel A; Chen, Tingxu; Li, Qing V; Vierbuchen, Thomas; Sidoli, Simone; Apostolou, Effie; Huangfu, Danwei; Beer, Michael A Nature genetics 37488417 2023 Aug
High throughput PRIME editing screens identify functional DNA variants in the human genome. Ren, Xingjie; Yang, Han; Nierenberg, Jovia L; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin bioRxiv : the preprint server for biology 37502948 2023 Jul 12
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Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. Chung, Chan-I; Yang, Junjiao; Shu, Xiaokun ACS central science 37521779 2023 Jul 26
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To Cut or not to Cut: Next-generation Genome Editors for Precision Genome Engineering. Zhang, Meng; Zhu, Zhixin; Xun, Guanhua; Zhao, Huimin Current opinion in biomedical engineering 37593347 2023 Dec
Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E Development (Cambridge, England) 37602510 2023 Sep 01
Nucleolar structure connects with global nuclear organization. Wang, Chen; Ma, Hanhui; Baserga, Susan J; Pederson, Thoru; Huang, Sui Molecular biology of the cell 37610836 2023 Nov 01
A molecular proximity sensor based on an engineered, dual-component guide RNA. Choi, Junhong; Chen, Wei; Liao, Hanna; Li, Xiaoyi; Shendure, Jay bioRxiv : the preprint server for biology 37645782 2023 Aug 14
SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. Lee, Lindsay; Yu, Miao; Li, Xiaoqi; Zhu, Chenxu; Zhang, Yanxiao; Yu, Hongyu; Chen, Ziyin; Mishra, Shreya; Ren, Bing; Li, Yun; Hu, Ming Briefings in bioinformatics 37649383 2023 Sep 20
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Hormonal Imbalances in Prader-Willi and Schaaf-Yang Syndromes Imply the Evolution of Specific Regulation of Hypothalamic Neuroendocrine Function in Mammals. Hoyos Sanchez, Maria Camila; Bayat, Tara; Gee, Rebecca R Florke; Fon Tacer, Klementina International journal of molecular sciences 37685915 2023 Aug 23
Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M eLife 37695017 2023 Sep 11
Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Abdulhay, Nour J; Hsieh, Laura J; McNally, Colin P; Ostrowski, Megan S; Moore, Camille M; Ketavarapu, Mythili; Kasinathan, Sivakanthan; Nanda, Arjun S; Wu, Ke; Chio, Un Seng; Zhou, Ziling; Goodarzi, Hani; Narlikar, Geeta J; Ramani, Vijay Nature structural & molecular biology 37696956 2023 Oct
Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. Chang, Li-Hsin; Ghosh, Sourav; Papale, Andrea; Luppino, Jennifer M; Miranda, Mélanie; Piras, Vincent; Degrouard, Jéril; Edouard, Joanne; Poncelet, Mallory; Lecouvreur, Nathan; Bloyer, Sébastien; Leforestier, Amélie; Joyce, Eric F; Holcman, David; Noordermeer, Daan Nature communications 37699887 2023 Sep 12
SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. Zhang, Meng; Ehmann, Mary Elisabeth; Matukumalli, Srija; Boob, Aashutosh Girish; Gilbert, David M; Zhao, Huimin Nature communications 37699958 2023 Sep 12
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Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Deshpande, Rajashree A; Marin-Gonzalez, Alberto; Barnes, Hannah K; Woolley, Phillip R; Ha, Taekjip; Paull, Tanya T Nature communications 37717054 2023 Sep 16
CTCF is essential for proper mitotic spindle structure and anaphase segregation. Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D Chromosoma 37728741 2023 Sep 20
Perturbations in 3D genome organization can promote acquired drug resistance. Manjón, Anna G; Manzo, Stefano Giustino; Prekovic, Stefan; Potgeter, Leon; van Schaik, Tom; Liu, Ning Qing; Flach, Koen; Peric-Hupkes, Daniel; Joosten, Stacey; Teunissen, Hans; Friskes, Anoek; Ilic, Mila; Hintzen, Dorine; Franceschini-Santos, Vinícius H; Zwart, Wilbert; de Wit, Elzo; van Steensel, Bas; Medema, René H Cell reports 37733591 2023 Oct 31
Alu transposable elements rewire enhancer-promoter network through RNA pairing. Wen, Xingzhao; Zhong, Sheng Molecular cell 37738962 2023 Sep 21
Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. Karlow, Jennifer A; Pehrsson, Erica C; Xing, Xiaoyun; Watson, Mark; Devarakonda, Siddhartha; Govindan, Ramaswamy; Wang, Ting Genomics, proteomics & bioinformatics 37742993 2023 Oct
Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. Berg, Isabel K; Currey, Marilena L; Gupta, Sarthak; Berrada, Yasmin; Nguyen, Bao V; Pho, Mai; Patteson, Alison E; Schwarz, J M; Banigan, Edward J; Stephens, Andrew D Journal of cell science 37756607 2023 Oct 15
HybriSeq: Probe-based Device-free Single-cell RNA Profiling. Foyt, Daniel; Brown, David; Zhou, Shuqin; Huang, Bo bioRxiv : the preprint server for biology 37808850 2023 Sep 29
HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials. Wei, Xiaolin; Tran, Duc; Diao, Yarui Current protocols 37818863 2023 Oct
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Calandrelli, Riccardo; Wen, Xingzhao; Charles Richard, John Lalith; Luo, Zhifei; Nguyen, Tri C; Chen, Chien-Ju; Qi, Zhijie; Xue, Shuanghong; Chen, Weizhong; Yan, Zhangming; Wu, Weixin; Zaleta-Rivera, Kathia; Hu, Rong; Yu, Miao; Wang, Yuchuan; Li, Wenbo; Ma, Jian; Ren, Bing; Zhong, Sheng Nature communications 37845234 2023 Oct 16
In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. Gunsalus, Laura M; Keiser, Michael J; Pollard, Katherine S Cell genomics 37868032 2023 Oct 11
PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. Deng, Yihe; Zhang, Ruochi; Xu, Pan; Ma, Jian; Gu, Quanquan bioRxiv : the preprint server for biology 37873233 2023 Oct 02
Single-cell chromatin state transitions during epigenetic memory formation. Fujimori, Taihei; Rios-Martinez, Carolina; Thurm, Abby R; Hinks, Michaela M; Doughty, Benjamin R; Sinha, Joydeb; Le, Derek; Hafner, Antonina; Greenleaf, William J; Boettiger, Alistair N; Bintu, Lacramioara bioRxiv : the preprint server for biology 37873344 2023 Oct 05
The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. Sinha, Joydeb; Nickels, Jan F; Thurm, Abby R; Ludwig, Connor H; Archibald, Bella N; Hinks, Michaela M; Wan, Jun; Fang, Dong; Bintu, Lacramioara bioRxiv : the preprint server for biology 37873347 2023 Oct 14
Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels. Haroush, Netta; Levo, Michal; Wieschaus, Eric F; Gregor, Thomas Developmental cell 37890488 2023 Dec 04
Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity. Pal, Mrinmoy; Altamirano-Pacheco, Luis; Schauer, Tamas; Torres-Padilla, Maria-Elena Genes & development 37914351 2023 Oct 01
Chromoscope: interactive multiscale visualization for structural variation in human genomes. L'Yi, Sehi; Maziec, Dominika; Stevens, Victoria; Manz, Trevor; Veit, Alexander; Berselli, Michele; Park, Peter J; Głodzik, Dominik; Gehlenborg, Nils Nature methods 37914857 2023 Dec
Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. Liu, Zhi; Lee, Dong-Sung; Liang, Yuqiong; Zheng, Ye; Dixon, Jesse R Nature communications 37932264 2023 Nov 06
TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons. Zhao, Shuai; Lu, Jiuwei; Pan, Bo; Fan, Huitao; Byrum, Stephanie D; Xu, Chenxi; Kim, Arum; Guo, Yiran; Kanchi, Krishna L; Gong, Weida; Sun, Tongyu; Storey, Aaron J; Burkholder, Nathaniel T; Mackintosh, Samuel G; Kuhlers, Peyton C; Edmondson, Ricky D; Strahl, Brian D; Diao, Yarui; Tackett, Alan J; Raab, Jesse R; Cai, Ling; Song, Jikui; Wang, Gang Greg Nature 37938770 2023 Nov
SIKs Regulate HDAC7 Stabilization and Cytokine Recall in Late-Stage T Cell Effector Differentiation. Helms, Rachel S; Marin-Gonzalez, Alberto; Patel, Chirag H; Sun, Im-Hong; Wen, Jiayu; Leone, Robert D; Duvall, Bridget; Gao, Run-Duo; Ha, Taekjip; Tsukamoto, Takashi; Slusher, Barbara S; Pomerantz, Joel L; Powell, Jonathan D Journal of immunology (Baltimore, Md. : 1950) 37947442 2023 Dec 15
Proteostasis governs differential temperature sensitivity across embryonic cell types. Dorrity, Michael W; Saunders, Lauren M; Duran, Madeleine; Srivatsan, Sanjay R; Barkan, Eliza; Jackson, Dana L; Sattler, Sydney M; Ewing, Brent; Queitsch, Christine; Shendure, Jay; Raible, David W; Kimelman, David; Trapnell, Cole Cell 37949057 2023 Nov 09
Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. Southerland, Kevin W; Xu, Yueyuan; Peters, Derek T; Lin, Xin; Wei, Xiaolin; Xiang, Yu; Fei, Kaileen; Olivere, Lindsey A; Morowitz, Jeremy M; Otto, James; Dai, Qunsheng; Kontos, Christopher D; Diao, Yarui Genome medicine 37950327 2023 Nov 10
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. Gjoni, Ketrin; Pollard, Katherine S bioRxiv : the preprint server for biology 37961123 2023 Nov 05
Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. Kuang, Shuzhen; Pollard, Katherine S bioRxiv : the preprint server for biology 37961712 2023 Oct 24
FOXO1 is a master regulator of CAR T memory programming. Doan, Alexander; Mueller, Katherine P; Chen, Andy; Rouin, Geoffrey T; Daniel, Bence; Lattin, John; Chen, Yingshi; Mozarsky, Brett; Markovska, Martina; Arias-Umana, Jose; Hapke, Robert; Jung, Inyoung; Xu, Peng; Klysz, Dorota; Bashti, Malek; Quinn, Patrick J; Sandor, Katalin; Zhang, Wenxi; Hall, Junior; Lareau, Caleb; Grupp, Stephan A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W Research square 37986944 2023 Nov 07
Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. Andronov, Leonid; Han, Mengting; Zhu, Yanyu; Roy, Anish R; Barentine, Andrew E S; Garhyan, Jaishree; Qi, Lei S; Moerner, W E bioRxiv : the preprint server for biology 37986994 2023 Nov 29
Genome folding principles revealed in condensin-depleted mitotic chromosomes. Zhao, Han; Lin, Yinzhi; Lin, En; Liu, Fuhai; Shu, Lirong; Jing, Dannan; Wang, Baiyue; Wang, Manzhu; Shan, Fengnian; Zhang, Lin; Lam, Jessica C; Midla, Susannah C; Giardine, Belinda M; Keller, Cheryl A; Hardison, Ross C; Blobel, Gerd A; Zhang, Haoyue bioRxiv : the preprint server for biology 38014261 2023 Nov 13
ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization. Gunsalus, Laura M; Keiser, Michael J; Pollard, Katherine S bioRxiv : the preprint server for biology 38045231 2023 Nov 22
High-capacity sample multiplexing for single cell chromatin accessibility profiling. Booth, Gregory T; Daza, Riza M; Srivatsan, Sanjay R; McFaline-Figueroa, José L; Gladden, Rula Green; Mullen, Andrew C; Furlan, Scott N; Shendure, Jay; Trapnell, Cole BMC genomics 38049719 2023 Dec 04
3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie Nature structural & molecular biology 38053013 2024 Jan
DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. Wang, Qianwen; L'Yi, Sehi; Gehlenborg, Nils Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference 38074525 2023 Apr
Actin contraction controls nuclear blebbing and rupture independent of actin confinement. Pho, Mai; Berrada, Yasmin; Gunda, Aachal; Lavallee, Anya; Chiu, Katherine; Padam, Arimita; Currey, Marilena L; Stephens, Andrew D Molecular biology of the cell 38088876 2024 Feb 01
Conserved and divergent gene regulatory programs of the mammalian neocortex. Zemke, Nathan R; Armand, Ethan J; Wang, Wenliang; Lee, Seoyeon; Zhou, Jingtian; Li, Yang Eric; Liu, Hanqing; Tian, Wei; Nery, Joseph R; Castanon, Rosa G; Bartlett, Anna; Osteen, Julia K; Li, Daofeng; Zhuo, Xiaoyu; Xu, Vincent; Chang, Lei; Dong, Keyi; Indralingam, Hannah S; Rink, Jonathan A; Xie, Yang; Miller, Michael; Krienen, Fenna M; Zhang, Qiangge; Taskin, Naz; Ting, Jonathan; Feng, Guoping; McCarroll, Steven A; Callaway, Edward M; Wang, Ting; Lein, Ed S; Behrens, M Margarita; Ecker, Joseph R; Ren, Bing Nature 38092918 2023 Dec
Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells. Roberts, Thomas C; Kushner, Max; Crowley, Jack C; Ozer, Abdullah; Wang, Juan; Ray, Judhajeet; Lis, John T; Zipfel, Warren R bioRxiv : the preprint server for biology 38105945 2023 Dec 06
Cell-type-specific 3D-genome organization and transcription regulation in the brain. Liu, Shiwei; Zheng, Pu; Wang, Cosmos Yuqi; Jia, Bojing Blair; Zemke, Nathan R; Ren, Bing; Zhuang, Xiaowei bioRxiv : the preprint server for biology 38105994 2023 Dec 05
Electrostatic encoding of genome organization principles within single native nucleosomes. Park, Sangwoo; Athreya, Advait; Carrizo, Gustavo Ezequiel; Benning, Nils A; Mitchener, Michelle M; Bhanu, Natarajan V; Garcia, Benjamin A; Zhang, Bin; Muir, Tom W; Pearce, Erika L; Ha, Taekjip bioRxiv : the preprint server for biology 38106048 2023 Dec 09
Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. Titus, Katelyn R; Simandi, Zoltan; Chandrashekar, Harshini; Paquet, Dominik; Phillips-Cremins, Jennifer E bioRxiv : the preprint server for biology 38106199 2023 Dec 05
Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. Bashkirova, Elizaveta V; Klimpert, Nell; Monahan, Kevin; Campbell, Christine E; Osinski, Jason; Tan, Longzhi; Schieren, Ira; Pourmorady, Ariel; Stecky, Beka; Barnea, Gilad; Xie, Xiaoliang Sunney; Abdus-Saboor, Ishmail; Shykind, Benjamin M; Marlin, Bianca J; Gronostajski, Richard M; Fleischmann, Alexander; Lomvardas, Stavros eLife 38108811 2023 Dec 18
Modbed track: Visualization of modified bases in single-molecule sequencing. Li, Daofeng; Zhuo, Xiaoyu; Harrison, Jessica K; Liu, Shane; Wang, Ting Cell genomics 38116122 2023 Dec 13
Emergence of replication timing during early mammalian development. Nakatani, Tsunetoshi; Schauer, Tamas; Altamirano-Pacheco, Luis; Klein, Kyle N; Ettinger, Andreas; Pal, Mrinmoy; Gilbert, David M; Torres-Padilla, Maria-Elena Nature 38123678 2024 Jan
RNA-mediated symmetry breaking enables singular olfactory receptor choice. Pourmorady, Ariel D; Bashkirova, Elizaveta V; Chiariello, Andrea M; Belagzhal, Houda; Kodra, Albana; Duffié, Rachel; Kahiapo, Jerome; Monahan, Kevin; Pulupa, Joan; Schieren, Ira; Osterhoudt, Alexa; Dekker, Job; Nicodemi, Mario; Lomvardas, Stavros Nature 38123679 2024 Jan
Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. Malachowski, Thomas; Chandradoss, Keerthivasan Raanin; Boya, Ravi; Zhou, Linda; Cook, Ashley L; Su, Chuanbin; Pham, Kenneth; Haws, Spencer A; Kim, Ji Hun; Ryu, Han-Seul; Ge, Chunmin; Luppino, Jennifer M; Nguyen, Son C; Titus, Katelyn R; Gong, Wanfeng; Wallace, Owen; Joyce, Eric F; Wu, Hao; Rojas, Luis Alejandro; Phillips-Cremins, Jennifer E Cell 38134876 2023 Dec 21
High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Ren, Xingjie; Yang, Han; Nierenberg, Jovia L; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin Molecular cell 38134886 2023 Dec 21
Machine learning reveals the diversity of human 3D chromatin contact patterns. Gilbertson, Erin N; Brand, Colin M; McArthur, Evonne; Rinker, David C; Kuang, Shuzhen; Pollard, Katherine S; Capra, John A bioRxiv : the preprint server for biology 38187606 2023 Dec 23
A fast, scalable and versatile tool for analysis of single-cell omics data. Zhang, Kai; Zemke, Nathan R; Armand, Ethan J; Ren, Bing Nature methods 38191932 2024 Feb
Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation. Khurana, Sakshi; Foltz, Daniel R bioRxiv : the preprint server for biology 38234763 2023 Dec 27
Epigenetic regulatory layers in the 3D nucleus. Willemin, Andréa; Szabó, Dominik; Pombo, Ana Molecular cell 38242127 2024 Feb 01
Toward a common standard for data and specimen provenance in life sciences. Wittner, Rudolf; Holub, Petr; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Plass, Markus; Allocca, Clare; Betsou, Fay; Burdett, Tony; Cancio, Ibon; Chapman, Adriane; Chapman, Martin; Courtot, Mélanie; Curcin, Vasa; Eder, Johann; Elliot, Mark; Exter, Katrina; Goble, Carole; Golebiewski, Martin; Kisler, Bron; Kremer, Andreas; Leo, Simone; Lin-Gibson, Sheng; Marsano, Anna; Mattavelli, Marco; Moore, Josh; Nakae, Hiroki; Perseil, Isabelle; Salman, Ayat; Sluka, James; Soiland-Reyes, Stian; Strambio-De-Castillia, Caterina; Sussman, Michael; Swedlow, Jason R; Zatloukal, Kurt; Geiger, Jörg Learning health systems 38249839 2024 Jan
mRNA initiation and termination are spatially coordinated. Calvo-Roitberg, Ezequiel; Carroll, Christine L; Venev, Sergey V; Kim, GyeungYun; Mick, Steven T; Dekker, Job; Fiszbein, Ana; Pai, Athma A bioRxiv : the preprint server for biology 38260419 2024 Jan 07
The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. Makeyev, Eugene V; Huang, Sui Nucleus (Austin, Tex.) 38281066 2024 Dec
SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. Yu, Hongyu; Wu, Daiqing; Shen, Guning; Hu, Ming; Li, Yun bioRxiv : the preprint server for biology 38293083 2024 Jan 15
Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. Brumbaugh-Reed, Ellen H; Aoki, Kazuhiro; Toettcher, Jared E bioRxiv : the preprint server for biology 38293146 2024 Jan 17
Toward a comprehensive view of gene architecture during transcription. Woodworth, Marcus A; Lakadamyali, Melike Current opinion in genetics & development 38309073 2024 Apr
Phase separation of YAP-MAML2 differentially regulates the transcriptome. Chung, Chan-I; Yang, Junjiao; Yang, Xiaoyu; Liu, Hongjiang; Ma, Zhimin; Szulzewsky, Frank; Holland, Eric C; Shen, Yin; Shu, Xiaokun Proceedings of the National Academy of Sciences of the United States of America 38315854 2024 Feb 13
Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development. Kaplan, Harris S; Logeman, Brandon L; Zhang, Kai; Santiago, Celine; Sohail, Noor; Naumenko, Serhiy; Ho Sui, Shannan J; Ginty, David D; Ren, Bing; Dulac, Catherine bioRxiv : the preprint server for biology 38328205 2024 Jan 23
Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. Jain, Naveen; Goyal, Yogesh; Dunagin, Margaret C; Cote, Christopher J; Mellis, Ian A; Emert, Benjamin; Jiang, Connie L; Dardani, Ian P; Reffsin, Sam; Arnett, Miles; Yang, Wenli; Raj, Arjun Cell systems 38335955 2024 Feb 21
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Qiu, Chengxiang; Martin, Beth K; Welsh, Ian C; Daza, Riza M; Le, Truc-Mai; Huang, Xingfan; Nichols, Eva K; Taylor, Megan L; Fulton, Olivia; O'Day, Diana R; Gomes, Anne Roshella; Ilcisin, Saskia; Srivatsan, Sanjay; Deng, Xinxian; Disteche, Christine M; Noble, William Stafford; Hamazaki, Nobuhiko; Moens, Cecilia B; Kimelman, David; Cao, Junyue; Schier, Alexander F; Spielmann, Malte; Murray, Stephen A; Trapnell, Cole; Shendure, Jay Nature 38355799 2024 Feb
Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Murphy, Sedona Eve; Boettiger, Alistair Nicol Nature genetics 38361032 2024 Feb 15
Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. Stein, Johannes; Ericsson, Maria; Nofal, Michel; Magni, Lorenzo; Aufmkolk, Sarah; McMillan, Ryan B; Breimann, Laura; Herlihy, Conor P; Lee, S Dean; Willemin, Andréa; Wohlmann, Jens; Arguedas-Jimenez, Laura; Yin, Peng; Pombo, Ana; Church, George M; Wu, Chao-Kng bioRxiv : the preprint server for biology 38370628 2024 Feb 05
Bigtools: a high-performance BigWig and BigBed library in Rust. Huey, Jack D; Abdennur, Nezar bioRxiv : the preprint server for biology 38370777 2024 Feb 08
DNA density is a better indicator of a nuclear bleb than lamin B loss. Bunner, Samantha; Prince, Kelsey; Srikrishna, Karan; Pujadas, Emily Marie; McCarthy, Antonia Amonu; Kuklinski, Anna; Jackson, Olivia; Pellegrino, Pedro; Jagtap, Shrushti; Eweka, Imuetiyan; Lawlor, Colman; Eastin, Emma; Yas, Griffin; Aiello, Julianna; LaPointe, Nathan; von Blucher, Isabelle Schramm; Hardy, Jillian; Chen, Jason; Backman, Vadim; Janssen, Anne; Packard, Mary; Dorfman, Katherine; Almassalha, Luay; Bahiru, Michael Seifu; Stephens, A D bioRxiv : the preprint server for biology 38370828 2024 Feb 07
Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Guo, Jimmy K; Blanco, Mario R; Walkup 4th, Ward G; Bonesteele, Grant; Urbinati, Carl R; Banerjee, Abhik K; Chow, Amy; Ettlin, Olivia; Strehle, Mackenzie; Peyda, Parham; Amaya, Enrique; Trinh, Vickie; Guttman, Mitchell Molecular cell 38387462 2024 Feb 20
Bioframe: operations on genomic intervals in Pandas dataframes. Open2C; Abdennur, Nezar; Fudenberg, Geoffrey; Flyamer, Ilya M; Galitsyna, Aleksandra A; Goloborodko, Anton; Imakaev, Maxim; Venev, Sergey Bioinformatics (Oxford, England) 38402507 2024 Feb 01
Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types. Hamazaki, Nobuhiko; Yang, Wei; Kubo, Connor; Qiu, Chengxiang; Martin, Beth K; Garge, Riddhiman K; Regalado, Samuel G; Nichols, Eva; Lee, Choli; Daza, Riza M; Srivatsan, Sanjay; Shendure, Jay bioRxiv : the preprint server for biology 38405970 2024 Feb 12
Nuclear shape is affected differentially by loss of lamin A, lamin C, or both lamin A and C. Pho, Mai; Berrada, Yasmin; Gunda, Aachal; Stephens, Andrew D microPublication biology 38440331 2024
TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells. Xu, Meng; Senanayaka, Dulmi; Zhao, Rongwei; Chigumira, Tafadzwa; Tripathi, Astha; Tones, Jason; Lackner, Rachel M; Wondisford, Anne R; Moneysmith, Laurel N; Hirschi, Alexander; Craig, Sara; Alishiri, Sahar; O'Sullivan, Roderick J; Chenoweth, David M; Reiter, Nicholas J; Zhang, Huaiying Nature communications 38461301 2024 Mar 09
A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations. Chandrashekar, Harshini; Simandi, Zoltan; Choi, Heesun; Ryu, Han-Seul; Waldman, Abraham J; Nikish, Alexandria; Muppidi, Srikar S; Gong, Wanfeng; Paquet, Dominik; Phillips-Cremins, Jennifer E bioRxiv : the preprint server for biology 38463966 2024 Feb 27
SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML. Zhao, Rongwei; Xu, Meng; Wondisford, Anne R; Lackner, Rachel M; Salsman, Jayme; Dellaire, Graham; Chenoweth, David M; O'Sullivan, Roderick J; Zhao, Xiaolan; Zhang, Huaiying bioRxiv : the preprint server for biology 38463993 2024 Feb 29
Transcription factor clusters as information transfer agents. Munshi, Rahul; Ling, Jia; Ryabichko, Sergey; Wieschaus, Eric; Gregor, Thomas ArXiv 38495568 2024 Mar 05
Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. Daniel, Bence; Chen, Andy Y; Sandor, Katalin; Zhang, Wenxi; Miao, Zhuang; Lareau, Caleb A; Yost, Kathryn E; Chang, Howard Y; Satpathy, Ansuman T bioRxiv : the preprint server for biology 38496446 2024 Mar 04
H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. Kubo, Naoki; Chen, Poshen B; Hu, Rong; Ye, Zhen; Sasaki, Hiroyuki; Ren, Bing Molecular cell 38513661 2024 Mar 15
Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Hildebrand, Erica M; Polovnikov, Kirill; Dekker, Bastiaan; Liu, Yu; Lafontaine, Denis L; Fox, A Nicole; Li, Ying; Venev, Sergey V; Mirny, Leonid A; Dekker, Job Molecular cell 38521067 2024 Mar 13
Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness. Liu, Ning; Qiang, Wenan; Jordan, Philip; Marko, John; Qiao, Huanyu bioRxiv : the preprint server for biology 38559262 2024 Mar 11
The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. Longhurst, Adam D; Wang, Kyle; Suresh, Harsha Garadi; Ketavarapu, Mythili; Ward, Henry N; Jones, Ian R; Narayan, Vivek; Hundley, Frances V; Hassan, Arshia Zernab; Boone, Charles; Myers, Chad L; Shen, Yin; Ramani, Vijay; Andrews, Brenda J; Toczyski, David P bioRxiv : the preprint server for biology 38562687 2024 Mar 19
Post-transcriptional splicing can occur in a slow-moving zone around the gene. Coté, Allison; O'Farrell, Aoife; Dardani, Ian; Dunagin, Margaret; Coté, Chris; Wan, Yihan; Bayatpour, Sareh; Drexler, Heather L; Alexander, Katherine A; Chen, Fei; Wassie, Asmamaw T; Patel, Rohan; Pham, Kenneth; Boyden, Edward S; Berger, Shelly; Phillips-Cremins, Jennifer; Churchman, L Stirling; Raj, Arjun eLife 38577979 2024 Apr 05

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