4D Nucleome (4DN)
4D Nucleome (4DN)
Program Publications
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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; |
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| 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 | 34099725 | 2021 06 07 |
| 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 | 34103507 | 2021 06 08 |
| 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 | 34106828 | 2021 06 09 |
| 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 | 34108665 | 2021 Jun 09 |
| Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. | Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, Jian | Quantitative biology (Beijing, China) | 34113473 | 2019 Jun |
| 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 | 34115980 | 2021 Jul 08 |
| Imaging Organization of RNA Processing within the Nucleus. | Biswas, Jeetayu; Li, Weihan; Singer, Robert H; Coleman, Robert A | Cold Spring Harbor perspectives in biology | 34127450 | 2021 12 01 |
| 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 | 34127974 | 2021 Jun 09 |
| 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 | 34191541 | 2021 08 15 |
| 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.) | 34210887 | 2021 07 02 |
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| 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 | 34230036 | 2021 Jul 06 |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair N | eLife | 34240703 | 2021 07 09 |
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| 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 | 34273560 | 2021 Jul 14 |
| 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 | 34279217 | 2021 07 19 |
| 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 | 34282837 | 2021 08 27 |
| Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. | Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan H | Current protocols | 34286910 | 2021 Jul |
| CRISPRi/a Screening with Human iPSCs. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Methods in molecular biology (Clifton, N.J.) | 34302664 | 2021 |
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| 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 | 34312624 | 2021 Jul 21 |
| 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 | 34334852 | 2020 Jun |
| 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 | 34352221 | 2021 Sep 22 |
| 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 | 34370624 | 2022 01 |
| 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 | 34375583 | 2021 08 19 |
| Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). | Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, Bing | Methods in molecular biology (Clifton, N.J.) | 34382190 | 2021 |
| X-factors in human disease: impact of gene content and dosage regulation. | Fang, He; Deng, Xinxian; Disteche, Christine M | Human molecular genetics | 34387327 | 2021 Oct 01 |
| Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. | Yildirim, Asli; Boninsegna, Lorenzo; Zhan, Yuxiang; Alber, Frank | Cold Spring Harbor perspectives in biology | 34400556 | 2021 Aug 16 |
| Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. | Belmont, Andrew S | Cold Spring Harbor perspectives in biology | 34400557 | 2022 Jul 01 |
| 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.) | 34415534 | 2022 |
| 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 | 34426703 | 2021 Aug 23 |
| 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 | 34428454 | 2021 Aug 13 |
| 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 | 34446921 | 2021 09 |
| CTCF and transcription influence chromatin structure re-configuration after mitosis. | Zhang, Haoyue; Lam, Jessica; Zhang, Di; Lan, Yemin; Vermunt, Marit W; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A | Nature communications | 34453048 | 2021 Aug 27 |
| The 3D Genome Structure of Single Cells. | Zhou, Tianming; Zhang, Ruochi; Ma, Jian | Annual review of biomedical data science | 34465168 | 2021 07 20 |
| 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 | 34480151 | 2021 09 |
| 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 | 34480155 | 2021 09 |
| 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 | 34485947 | 2021 Jul 08 |
| Enhanced Cas12a multi-gene regulation using a CRISPR array separator. | Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei S | eLife | 34499031 | 2021 09 09 |
| Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. | Mirny, Leonid; Dekker, Job | Cold Spring Harbor perspectives in biology | 34518339 | 2022 07 01 |
| 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 | 34520723 | 2021 11 04 |
| 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 | 34524848 | 2021 Sep 17 |
| 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 | 34547287 | 2021 Sep 20 |
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| 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 | 34563051 | 2021 Sep 17 |
| 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 | 34579774 | 2021 09 27 |
| 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.) | 34591592 | 2021 10 29 |
| 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 | 34596551 | 2022 01 |
| 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 | 34611363 | 2021 Oct |
| 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 | 34620850 | 2021 10 07 |
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| 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 | 34635658 | 2021 10 11 |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang, Ruochi; Zhou, Tianming; Ma, Jian | Nature biotechnology | 34635838 | 2021 Oct 11 |
| 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 | 34635849 | 2021 12 |
| 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 | 34644528 | 2021 10 28 |
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| 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 | 34732726 | 2021 11 03 |
| 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 | 34734806 | 2021 Nov 04 |
| 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 | 34739832 | 2021 11 11 |
| 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 | 34767455 | 2021 11 12 |
| 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 | 34772813 | 2021 11 16 |
| Light activation and deactivation of Cas9 for DNA repair studies. | Zou, Roger S; Ha, Taekjip | Methods in enzymology | 34776214 | 2021 |
| 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 | 34789735 | 2021 11 17 |
| 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 | 34789882 | 2021 11 |
| 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 | 34862501 | 2021 12 |
| 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 | 34862503 | 2021 12 |
| Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. | Pourmorady, Ariel; Lomvardas, Stavros | Current opinion in genetics & development | 34896807 | 2022 02 |
| 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 | 34921112 | 2021 12 21 |
| Epigenome rewiring in human pluripotent stem cells. | Yan, Jielin; Huangfu, Danwei | Trends in cell biology | 34955367 | 2021 Dec 23 |
| Integrative approaches in genome structure analysis. | Structure (London, England : 1993) | 34963059 | 2022 01 06 | |
| Stress as a Chromatin Landscape Architect. | Vertii, Anastassiia | Frontiers in cell and developmental biology | 34970548 | 2021 |
| Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. | Lee, Soohyun; Bakker, Clara R; Vitzthum, Carl; Alver, Burak H; Park, Peter J | Bioinformatics (Oxford, England) | 34978573 | 2022 Mar 04 |
| 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 | 34985990 | 2022 01 |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett, Daniel A; Dileep, Vishnu; Baslan, Timour; Gilbert, David M | Current protocols | 34986273 | 2022 Jan |
| 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 | 35013617 | 2022 Jan |
| Single nucleosome tracking to study chromatin plasticity. | Lakadamyali, Melike | Current opinion in cell biology | 35033775 | 2022 Jan 13 |
| 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 | 35050714 | 2022 01 |
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| Compartmentalization of telomeres through DNA-scaffolded phase separation. | Developmental cell | 35077681 | 2022 01 24 | |
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| 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 | 35115686 | 2022 02 |
| 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 | 35128513 | 2022 Feb 01 |
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| 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 | 35501385 | 2022 05 |
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| 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 | 35706127 | 2022 Aug 03 |
| 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 | 35726060 | 2022 07 |
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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 |
| 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 | 35750052 | 2022 07 11 |
| 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 | 35753702 | 2022 07 18 |
| Guilt by association: EcDNA as a mobile transactivator in cancer. | Zhu, Yanfen; Gong, Liang; Wei, Chia-Lin | Trends in cancer | 35753910 | 2022 Jun 23 |
| Nuclear speckles - a driving force in gene expression. | Faber, Gabriel P; Nadav-Eliyahu, Shani; Shav-Tal, Yaron | Journal of cell science | 35788677 | 2022 Jul 01 |
| 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 | 35794474 | 2022 08 |
| 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 | 35817938 | 2022 08 |
| 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 | 35831310 | 2022 07 13 |
| 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 | 35835116 | 2022 Aug 08 |
| Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. | Tang, Xiaona; Li, Taibo; Liu, Sheng; Wisniewski, Jan; Zheng, Qinsi; Rong, Yikang; Lavis, Luke D; Wu, Carl | Nature structural & molecular biology | 35835866 | 2022 Jul |
| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci, Domenic N; Hansen, Anders S | Nature structural & molecular biology | 35835869 | 2022 07 |
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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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| 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 |
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| Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer. | Rodrigues, Aaron; MacQuarrie, Kyle L; Freeman, Emma; Lin, Alicia; Willis, Alexander B; Xu, Zhaofa; Alvarez, Angel A; Ma, Yongchao; White, Bethany E Perez; Foltz, Daniel R; Huang, Sui | Molecular biology of the cell | 36753381 | 2023 Apr 01 |
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| Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function. | Zhan, Yuxiang; Yildirim, Asli; Boninsegna, Lorenzo; Alber, Frank | bioRxiv : the preprint server for biology | 36824908 | 2023 Feb 19 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hart | bioRxiv : the preprint server for biology | 36865282 | 2023 May 07 |
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| Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. | Patterson, Benjamin; Yang, Bing; Tanaka, Yoshiaki; Kim, Kun-Yong; Cakir, Bilal; Xiang, Yangfei; Kim, Jonghun; Wang, Siyuan; Park, In-Hyun | Science advances | 37540754 | 2023 Aug 04 |
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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 |
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| 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 |
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| 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 |
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| 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 |
