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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.
4D Nucleome (304)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. | Bertero, Alessandro; Fields, Paul A; Ramani, Vijay; Bonora, Giancarlo; Yardimci, Galip G; Reinecke, Hans; Pabon, Lil; Noble, William S; Shendure, Jay; Murry, Charles E | Nature communications. | 2019 04 04; | 30948719 | |
| Transposable elements drive widespread expression of oncogenes in human cancers. | Jang, Hyo Sik; Shah, Nakul M; Du, Alan Y; Dailey, Zea Z; Pehrsson, Erica C; Godoy, Paula M; Zhang, David; Li, Daofeng; Xing, Xiaoyun; Kim, Sungsu; O'Donnell, David; Gordon, Jeffrey I; Wang, Ting | Nature genetics. | 2019 04; | 30926969 | |
| Measuring the reproducibility and quality of Hi-C data. | Yard?mc?, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E G; Ursu, Oana; Yan, Koon-Kiu; Yang, Tao; Chakraborty, Abhijit; Kaul, Arya; Lajoie, Bryan R; Song, Fan; Zhan, Ye; Ay, Ferhat; Gerstein, Mark; Kundaje, Anshul; Li, Qunhua; Taylor, James; Yue, Feng; Dekker, Job; Noble, William S | Genome biology. | 2019 03 19; | 30890172 | |
| Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. | Ma, Hanhui; Tu, Li-Chun; Chung, Yu-Chieh; Naseri, Ardalan; Grunwald, David; Zhang, Shaojie; Pederson, Thoru | The Journal of cell biology. | 2019 Mar 07; | 30846483 | |
| Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. | Finn, Elizabeth H; Pegoraro, Gianluca; Brandão, Hugo B; Valton, Anne-Laure; Oomen, Marlies E; Dekker, Job; Mirny, Leonid; Misteli, Tom | Cell. | 2019 Mar 07; | 30799036 | |
| Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. | Yan, Zhangming; Huang, Norman; Wu, Weixin; Chen, Weizhong; Jiang, Yiqun; Chen, Jingyao; Huang, Xuerui; Wen, Xingzhao; Xu, Jie; Jin, Qiushi; Zhang, Kang; Chen, Zhen; Chien, Shu; Zhong, Sheng | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Feb 19; | 30718424 | |
| Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. | Chapski, Douglas J; Rosa-Garrido, Manuel; Hua, Nan; Alber, Frank; Vondriska, Thomas M | Frontiers in cardiovascular medicine. | 2018; | 30697540 | |
| An automated Bayesian pipeline for rapid analysis of single-molecule binding data. | Smith, Carlas S; Jouravleva, Karina; Huisman, Maximiliaan; Jolly, Samson M; Zamore, Phillip D; Grunwald, David | Nature communications. | 2019 01 17; | 30655518 | |
| CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. | Oomen, Marlies E; Hansen, Anders S; Liu, Yu; Darzacq, Xavier; Dekker, Job | Genome research. | 2019 02; | 30655336 | |
| Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic ? Cell Identity and Function. | Lawlor, Nathan; Márquez, Eladio J; Orchard, Peter; Narisu, Narisu; Shamim, Muhammad Saad; Thibodeau, Asa; Varshney, Arushi; Kursawe, Romy; Erdos, Michael R; Kanke, Matt; Gu, Huiya; Pak, Evgenia; Dutra, Amalia; Russell, Sheikh; Li, Xingwang; Piecuch, Emaly; Luo, Oscar; Chines, Peter S; Fuchbserger, Christian; NIH Intramural Sequencing Center; Sethupathy, Praveen; Aiden, Aviva Presser; Ruan, Yijun; Aiden, Erez Lieberman; Collins, Francis S; Ucar, Duygu; Parker, Stephen C J; Stitzel, Michael L | Cell reports. | 2019 Jan 15; | 30650367 | |
| Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers. | Limi, Saima; Zhao, Yilin; Guo, Peng; Lopez-Jones, Melissa; Zheng, Deyou; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales | Investigative ophthalmology & visual science. | 2019 Jan 02; | 30646012 | |
| LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. | Monahan, Kevin; Horta, Adan; Lomvardas, Stavros | Nature. | 2019 01; | 30626972 | |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, Arjun | PLoS genetics. | 2019 01; | 30625149 | |
| An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. | Zhang, Zhizhuo; Chng, Kern Rei; Lingadahalli, Shreyas; Chen, Zikai; Liu, Mei Hui; Do, Huy Hoang; Cai, Shaojiang; Rinaldi, Nicola; Poh, Huay Mei; Li, Guoliang; Sung, Ying Ying; Heng, Charlie L; Core, Leighton J; Tan, Si Kee; Ruan, Xiaoan; Lis, John T; Kellis, Manolis; Ruan, Yijun; Sung, Wing-Kin; Cheung, Edwin | Genome research. | 2019 02; | 30606742 | |
| Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. | Mir, Mustafa; Stadler, Michael R; Ortiz, Stephan A; Hannon, Colleen E; Harrison, Melissa M; Darzacq, Xavier; Eisen, Michael B | eLife. | 2018 12 27; | 30589412 | |
| Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. | Nir, Guy; Farabella, Irene; Pérez Estrada, Cynthia; Ebeling, Carl G; Beliveau, Brian J; Sasaki, Hiroshi M; Lee, S Dean; Nguyen, Son C; McCole, Ruth B; Chattoraj, Shyamtanu; Erceg, Jelena; AlHaj Abed, Jumana; Martins, Nuno M C; Nguyen, Huy Q; Hannan, Mohammed A; Russell, Sheikh; Durand, Neva C; Rao, Suhas S P; Kishi, Jocelyn Y; Soler-Vila, Paula; Di Pierro, Michele; Onuchic, José N; Callahan, Steven P; Schreiner, John M; Stuckey, Jeff A; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A; Wu, C-Ting | PLoS genetics. | 2018 12; | 30586358 | |
| Models of polymer physics for the architecture of the cell nucleus. | Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Chiariello, Andrea M; Fiorillo, Luca; Nicodemi, Mario | Wiley interdisciplinary reviews. Systems biology and medicine. | 2018 Dec 19; | 30566285 | |
| Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. | Bartman, Caroline R; Hamagami, Nicole; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A; Raj, Arjun | Molecular cell. | 2018 Dec 06; | 30554946 | |
| RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. | Brahma, Sandipan; Henikoff, Steven | Molecular cell. | 2019 Jan 17; | 30554944 | |
| GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. | Calandrelli, Riccardo; Wu, Qiuyang; Guan, Jihong; Zhong, Sheng | Genomics, proteomics & bioinformatics. | 2018 Dec 13; | 30553884 | |
| A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. | Keleher, Madeline Rose; Zaidi, Rabab; Hicks, Lauren; Shah, Shyam; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Cheverud, James M | BMC genomics. | 2018 Dec 07; | 30526554 | |
| Deconstructing transport-distribution reconstruction in the nuclear-pore complex. | Tu, Li-Chun; Huisman, Maximiliaan; Chung, Yu-Chieh; Smith, Carlas Sierd; Grunwald, David | Nature structural & molecular biology. | 2018 Dec; | 30518848 | |
| Impact of optical aberrations on axial position determination by photometry. | Thorsen, Rasmus Ø; Hulleman, Christiaan N; Hammer, Mathias; Grünwald, David; Stallinga, Sjoerd; Rieger, Bernd | Nature methods. | 2018 Dec; | 30504865 | |
| CHRAC/ACF contribute to the repressive ground state of chromatin. | Scacchetti, Alessandro; Brueckner, Laura; Jain, Dhawal; Schauer, Tamas; Zhang, Xu; Schnorrer, Frank; van Steensel, Bas; Straub, Tobias; Becker, Peter B | Life science alliance. | 2018 Jan; | 30456345 | |
| Improved reference genome of Aedes aegypti informs arbovirus vector control. | Matthews, Benjamin J; Dudchenko, Olga; Kingan, Sarah B; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E; Glassford, William J; Herre, Margaret; Redmond, Seth N; Rose, Noah H; Weedall, Gareth D; Wu, Yang; Batra, Sanjit S; Brito-Sierra, Carlos A; Bucki | Nature. | 2018 11; | 30429615 | |
| ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, Arjun | Nature biotechnology. | 2018 Nov 12; | 30418432 | |
| Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. | P?kowska, Aleksandra; Klaus, Bernd; Xiang, Wanqing; Severino, Jacqueline; Daigle, Nathalie; Klein, Felix A; Ole?, Ma?gorzata; Casellas, Rafael; Ellenberg, Jan; Steinmetz, Lars M; Bertone, Paul; Huber, Wolfgang | Cell systems. | 2018 Nov 28; | 30414923 | |
| Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. | Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho; Yuede, Carla; Li, Daofeng; Rensing, Nicholas; Huang, Ju; Baldridge, Dustin; Maloney, Susan E; Dougherty, Joseph D; Constantino, John; Jahani-Asl, Arezu; Wong, Michael; Wozniak, David F; Wang, Ting; Klyachko, Vitaly A; Bonni, Azad | Cell reports. | 2018 Nov 06; | 30403997 | |
| A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. | Dai, Xiaoyu; Lin, Nan; Li, Daofeng; Wang, Ting | Biometrics. | 2018 Nov 02; | 30387496 | |
| CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. | Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Chung, Yu-Chieh; Grunwald, David; Zhang, Shaojie; Pederson, Thoru | Nature methods. | 2018 Nov; | 30377374 | |
| Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. | Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas | Cell systems. | 2018 Oct 24; | 30342881 | |
| Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. | Zoller, Benjamin; Little, Shawn C; Gregor, Thomas | Cell. | 2018 Oct 18; | 30340044 | |
| Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling. | Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura; Wang, Ruipeng; McQuiston, Travis J; Challberg, Sharon S; Pollok, Brian A; Wang, Ting | Cell reports. | 2018 Oct 16; | 30332641 | |
| CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. | Liu, Yanxia; Yu, Chen; Daley, Timothy Patrick; Wang, Fangyuan; Cao, William S; Bhate, Salil; Lin, Xueqiu; Still 2nd, Chris; Liu, Honglei; Zhao, Dehua; Wang, Haifeng; Xie, Xinmin S; Ding, Sheng; Wong, Wing Hung; Wernig, Marius; Qi, Lei S | Cell stem cell. | 2018 Nov 01; | 30318302 | |
| CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. | Wang, Haifeng; Xu, Xiaoshu; Nguyen, Cindy M; Liu, Yanxia; Gao, Yuchen; Lin, Xueqiu; Daley, Timothy; Kipniss, Nathan H; La Russa, Marie; Qi, Lei S | Cell. | 2018 Nov 15; | 30318144 | |
| The adult human testis transcriptional cell atlas. | Guo, Jingtao; Grow, Edward J; Mlcochova, Hana; Maher, Geoffrey J; Lindskog, Cecilia; Nie, Xichen; Guo, Yixuan; Takei, Yodai; Yun, Jina; Cai, Long; Kim, Robin; Carrell, Douglas T; Goriely, Anne; Hotaling, James M; Cairns, Bradley R | Cell research. | 2018 Dec; | 30315278 | |
| Understanding molecular mechanisms of disease through spatial proteomics. | Pankow, Sandra; Martínez-Bartolomé, Salvador; Bamberger, Casimir; Yates, John R | Current opinion in chemical biology. | 2019 Feb; | 30308467 | |
| CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. | Daley, Timothy P; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei S | Genome biology. | 2018 10 08; | 30296940 | |
| The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. | Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N K; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, Feng | Genome biology. | 2018 10 04; | 30286773 | |
| RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. | Chen, Weizhong; Yan, Zhangming; Li, Simin; Huang, Norman; Huang, Xuerui; Zhang, Jin; Zhong, Sheng | iScience. | 2018 Jun 29; | 30240742 | |
| Blank spots on the map: some current questions on nuclear organization and genome architecture. | Adriaens, Carmen; Serebryannyy, Leonid A; Feric, Marina; Schibler, Andria; Meaburn, Karen J; Kubben, Nard; Trzaskoma, Pawel; Shachar, Sigal; Vidak, Sandra; Finn, Elizabeth H; Sood, Varun; Pegoraro, Gianluca; Misteli, Tom | Histochemistry and cell biology. | 2018 Dec; | 30238154 | |
| X-Chromosome Inactivation and Escape from X Inactivation in Mouse. | Ma, Wenxiu; Bonora, Giancarlo; Berletch, Joel B; Deng, Xinxian; Noble, William S; Disteche, Christine M | Methods in molecular biology (Clifton, N.J.). | 2018; | 30218369 | |
| Experimental and computational framework for a dynamic protein atlas of human cell division. | Cai, Yin; Hossain, M Julius; Hériché, Jean-Karim; Politi, Antonio Z; Walther, Nike; Koch, Birgit; Wachsmuth, Malte; Nijmeijer, Bianca; Kueblbeck, Moritz; Martinic-Kavur, Marina; Ladurner, Rene; Alexander, Stephanie; Peters, Jan-Michael; Ellenberg, Jan | Nature. | 2018 09; | 30202089 | |
| Integrative detection and analysis of structural variation in cancer genomes. | Dixon, Jesse R; Xu, Jie; Dileep, Vishnu; Zhan, Ye; Song, Fan; Le, Victoria T; Yard?mc?, Galip Gürkan; Chakraborty, Abhijit; Bann, Darrin V; Wang, Yanli; Clark, Royden; Zhang, Lijun; Yang, Hongbo; Liu, Tingting; Iyyanki, Sriranga; An, Lin; Pool, Christophe | Nature genetics. | 2018 Sep 10; | 30202056 | |
| Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. | Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F; Carlon, Enrico | Physical review letters. | 2018 Aug 24; | 30192578 | |
| Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. | Zhu, Liangliang; Yan, Feihu; Wang, Zhen; Dong, Haiyan; Bian, Chengling; Wang, Ting; Yu, Enda; Li, Jing | International journal of cancer. | 2018 Nov 15; | 30183087 | |
| Interchromosomal interactions: A genomic love story of kissing chromosomes. | Maass, Philipp G; Barutcu, A Rasim; Rinn, John L | The Journal of cell biology. | 2019 Jan 07; | 30181316 | |
| Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. | Sun, James H; Zhou, Linda; Emerson, Daniel J; Phyo, Sai A; Titus, Katelyn R; Gong, Wanfeng; Gilgenast, Thomas G; Beagan, Jonathan A; Davidson, Beverly L; Tassone, Flora; Phillips-Cremins, Jennifer E | Cell. | 2018 Aug 27; | 30173918 | |
| Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. | van Steensel, Bas | EMBO reports. | 2018 Oct; | 30158143 | |
| Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. | Chen, Yu; Zhang, Yang; Wang, Yuchuan; Zhang, Liguo; Brinkman, Eva K; Adam, Stephen A; Goldman, Robert; van Steensel, Bas; Ma, Jian; Belmont, Andrew S | The Journal of cell biology. | 2018 Aug 28; | 30154186 | |
| The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. | Munschauer, Mathias; Nguyen, Celina T; Sirokman, Klara; Hartigan, Christina R; Hogstrom, Larson; Engreitz, Jesse M; Ulirsch, Jacob C; Fulco, Charles P; Subramanian, Vidya; Chen, Jenny; Schenone, Monica; Guttman, Mitchell; Carr, Steven A; Lander, Eric S | Nature. | 2018 09; | 30150775 | |
| Emerging Roles of Non-Coding RNA Transcription. | Kaikkonen, Minna U; Adelman, Karen | Trends in biochemical sciences. | 2018 09; | 30145998 | |
| Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. | Sun, Mingxuan; Biggs, Ronald; Hornick, Jessica; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2018 Dec; | 30143891 | |
| HiGlass: web-based visual exploration and analysis of genome interaction maps. | Kerpedjiev, Peter; Abdennur, Nezar; Lekschas, Fritz; McCallum, Chuck; Dinkla, Kasper; Strobelt, Hendrik; Luber, Jacob M; Ouellette, Scott B; Azhir, Alaleh; Kumar, Nikhil; Hwang, Jeewon; Lee, Soohyun; Alver, Burak H; Pfister, Hanspeter; Mirny, Leonid A; Pa | Genome biology. | 2018 08 24; | 30143029 | |
| Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan | The Journal of cell biology. | 2018 Sep 03; | 30135095 | |
| Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. | Wray-Dutra, Michelle N; Chawla, Raghav; Thomas, Kerri R; Seymour, Brenda J; Arkatkar, Tanvi; Sommer, Karen M; Khim, Socheath; Trapnell, Cole; James, Richard G; Rawlings, David J | The Journal of experimental medicine. | 2018 Sep 03; | 30127060 | |
| One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. | Lazniewski, Michal; Dawson, Wayne K; Rusek, Anna Maria; Plewczynski, Dariusz | Seminars in cell & developmental biology. | 2018 Oct 11; | 30096365 | |
| Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. | Pliner, Hannah A; Packer, Jonathan S; McFaline-Figueroa, José L; Cusanovich, Darren A; Daza, Riza M; Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana; Minkina, Anna; Adey, Andrew C; Steemers, Frank J; Shendure, Jay; Trapnell, Cole | Molecular cell. | 2018 09 06; | 30078726 | |
| Protein motion in the nucleus: from anomalous diffusion to weak interactions. | Woringer, Maxime; Darzacq, Xavier | Biochemical Society transactions. | 2018 Aug 20; | 30065106 | |
| Temporal dynamics of pair-rule stripes in living Drosophila embryos. | Lim, Bomyi; Fukaya, Takashi; Heist, Tyler; Levine, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2018 08 14; | 30061421 | |
| Dynamic interplay between enhancer-promoter topology and gene activity. | Chen, Hongtao; Levo, Michal; Barinov, Lev; Fujioka, Miki; Jaynes, James B; Gregor, Thomas | Nature genetics. | 2018 Sep; | 30038397 | |
| Comparison of OCT Angiography Review Strategies to Identify Vascular Abnormalities in the AVATAR Study. | Babiuch, Amy S; Khan, Mehnaz; Hu, Ming; Kaiser, Peter K; Srivastava, Sunil K; Singh, Rishi P; Watts, Allison; Reese, Jamie L; Ehlers, Justis P | Ophthalmology. Retina. | 2018 Jun; | 30035246 | |
| Computational methods for analyzing and modeling genome structure and organization. | Lin, Dejun; Bonora, Giancarlo; Yard?mc?, Galip Gürkan; Noble, William S | Wiley interdisciplinary reviews. Systems biology and medicine. | 2018 Jul 18; | 30022617 | |
| GIVE: portable genome browsers for personal websites. | Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng | Genome biology. | 2018 07 18; | 30016975 | |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E | Molecular cell. | 2018 Jul 05; | 29979966 | |
| Chromatin organization by an interplay of loop extrusion and compartmental segregation. | Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Abdennur, Nezar; Mirny, Leonid A | Proceedings of the National Academy of Sciences of the United States of America. | 2018 07 17; | 29967174 | |
| Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. | Limi, Saima; Senecal, Adrien; Coleman, Robert; Lopez-Jones, Melissa; Guo, Peng; Polumbo, Christina; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales | The Journal of biological chemistry. | 2018 Aug 24; | 29959226 | |
| Quantitative live and super-resolution microscopy of mitotic chromosomes. | Walther, Nike; Ellenberg, Jan | Methods in cell biology. | 2018; | 29957216 | |
| Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. | Mir, Mustafa; Reimer, Armando; Stadler, Michael; Tangara, Astou; Hansen, Anders S; Hockemeyer, Dirk; Eisen, Michael B; Garcia, Hernan; Darzacq, Xavier | Methods in molecular biology (Clifton, N.J.). | 2018; | 29956254 | |
| Unsupervised embedding of single-cell Hi-C data. | Liu, Jie; Lin, Dejun; Yardimci, Galip Gürkan; Noble, William Stafford | Bioinformatics (Oxford, England). | 2018 07 01; | 29950005 | |
| Predicting CTCF-mediated chromatin loops using CTCF-MP. | Zhang, Ruochi; Wang, Yuchuan; Yang, Yang; Zhang, Yang; Ma, Jian | Bioinformatics (Oxford, England). | 2018 Jul 01; | 29949986 | |
| Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. | Sabath, Niv; Vilborg, Anna; Steitz, Joan A; Shalgi, Reut | Human genomics. | 2018 06 27; | 29945683 | |
| Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction. | Lei, Xiao; Shi, Haoran; Kou, Yi; Rajashekar, Niroop; Wu, Fang; Sen, Chandani; Xu, Jiang; Chen, Lin | Biochemistry. | 2018 07 17; | 29944822 | |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I; Raj, Arjun; Li, Mingyao; Zhang, Nancy R | Nature methods. | 2018 Jul; | 29941873 | |
| Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. | Yang, Yang; Gu, Quanquan; Zhang, Yang; Sasaki, Takayo; Crivello, Julianna; O'Neill, Rachel J; Gilbert, David M; Ma, Jian | Cell systems. | 2018 Jun 18; | 29936186 | |
| Imaging dynamic and selective low-complexity domain interactions that control gene transcription. | Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe; Dong, Peng; Dailey, Gina M; Cattoglio, Claudia; Heckert, Alec; Banala, Sambashiva; Lavis, Luke; Darzacq, Xavier; Tjian, Robert | Science (New York, N.Y.). | 2018 07 27; | 29930090 | |
| CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. | Tasan, Ipek; Sustackova, Gabriela; Zhang, Liguo; Kim, Jiah; Sivaguru, Mayandi; HamediRad, Mohammad; Wang, Yuchuan; Genova, Justin; Ma, Jian; Belmont, Andrew S; Zhao, Huimin | Nucleic acids research. | 2018 Jun 15; | 29912475 | |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah, Sheel; Takei, Yodai; Zhou, Wen; Lubeck, Eric; Yun, Jina; Eng, Chee-Huat Linus; Koulena, Noushin; Cronin, Christopher; Karp, Christoph; Liaw, Eric J; Amin, Mina; Cai, Long | Cell. | 2018 May 31; | 29887381 | |
| Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. | Quinodoz, Sofia A; Ollikainen, Noah; Tabak, Barbara; Palla, Ali; Schmidt, Jan Marten; Detmar, Elizabeth; Lai, Mason M; Shishkin, Alexander A; Bhat, Prashant; Takei, Yodai; Trinh, Vickie; Aznauryan, Erik; Russell, Pamela; Cheng, Christine; Jovanovic, Marko; Chow, Amy; Cai, Long; McDonel, Patrick; Garber, Manuel; Guttman, Mitchell | Cell. | 2018 Jun 04; | 29887377 | |
| Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. | Dine, Elliot; Gil, Agnieszka A; Uribe, Giselle; Brangwynne, Clifford P; Toettcher, Jared E | Cell systems. | 2018 Jun 27; | 29859829 | |
| Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. | Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Jarvis, James N | Journal of reproductive immunology. | 2018 Aug; | 29800761 | |
| 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. | Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E | Methods (San Diego, Calif.). | ; | 29772275 | |
| Quantitative imaging of chromatin decompaction in living cells. | Dultz, Elisa; Mancini, Roberta; Polles, Guido; Vallotton, Pascal; Alber, Frank; Weis, Karsten | Molecular biology of the cell. | ; | 29771637 | |
| Gene regulation in the 3D genome. | Li, Yun; Hu, Ming; Shen, Yin | Human molecular genetics. | 2018 08 01; | 29767704 | |
| qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. | Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I | Scientific reports. | ; | 29743503 | |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. | Gao, Xin D; Tu, Li-Chun; Mir, Aamir; Rodriguez, Tomás; Ding, Yuehe; Leszyk, John; Dekker, Job; Shaffer, Scott A; Zhu, Lihua Julie; Wolfe, Scot A; Sontheimer, Erik J | Nature methods. | 2018 May 07; | 29735996 | |
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| Formation of Chromosomal Domains by Loop Extrusion. | Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A | Cell Rep | 2016 May 19 | 27210764 | |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid | eLife. | 2016 May 18; | 27192037 | |
| Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. | Banigan, Edward J; Marko, John F | Physical review. E. | 2016 Apr; | 27182590 | |
| Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. | Proserpio, Valentina; Piccolo, Andrea; Haim-Vilmovsky, Liora; Kar, Gozde; Lönnberg, Tapio; Svensson, Valentine; Pramanik, Jhuma; Natarajan, Kedar Nath; Zhai, Weichao; Zhang, Xiuwei; Donati, Giacomo; Kayikci, Melis; Kotar, Jurij; McKenzie, Andrew N J; Montandon, Ruddy; Billker, Oliver; Woodhouse, Steven; Cicuta, Pietro; Nicodemi, Mario; Teichmann, Sarah A | Genome biology. | 2016; | 27176874 | |
| Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. | Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M | Disaster medicine and public health preparedness. | 2016 06; | 27174171 | |
| FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. | Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming | Bioinformatics (Oxford, England). | 2016 09 01; | 27153668 | |
| Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. | Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E | Cell Stem Cell | 2016 May 5 | P:611-24 | 27152443 |
| Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. | Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2016 Sep; | 27145786 | |
| Dosage compensation of the sex chromosomes and autosomes. | Disteche, Christine M | Semin Cell Dev Biol | 2016 Apr 22 | 27112542 | |
| TAD disruption as oncogenic driver. | Valton, Anne-Laure; Dekker, Job | Curr Opin Genet Dev | 2016 Feb | P:34-40 | 27111891 |
| Jointly characterizing epigenetic dynamics across multiple human cell types. | Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C | Nucleic acids research. | 2016 08 19; | 27095202 | |
| Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. | Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. | Nature Biotechnology | 2016 April 18 | Epub ahead of print | 27088723 |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting | Trends Genet | 2016 May | P:269-83 | 27080453 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. | Molecular Cell | 2016 April 5 | V:62 P:1-11 | 27067601 |
| History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. | Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A | J Bioinform Comput Biol | 2016 Apr | P:1641002 | 27021249 |
| HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. | Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming | BMC research notes. | 2016; | 26969411 | |
| The 3D Genome as Moderator of Chromosomal Communication. | Dekker, Job; Mirny, Leonid | Cell | 2016 Mar 10 | V:164 P:1110-21 | 26967279 |
| Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. | Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Mar 22; | 26951677 | |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun | Genes & development. | 2016 Mar 1; | 26944681 | |
| Activation of proto-oncogenes by disruption of chromosome neighborhoods. | Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S; Valton, Anne-Laure; Bak, Rasmus O; Li, Charles H; Goldmann, Johanna; Lajoie, Bryan R; Fan, Zi Peng; Sigova, Alla A; Reddy, Jessica; Borges-Rivera, Diego; Lee, Tong Ihn; Jaenisch, Rudolf; Porteus, Matthew H; Dekker, Job; Young, Richard A | Science | 2016 Mar 25 | V:351 P:1454-8 | 26940867 |
| Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. | Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor | Nucleus | 2016 Mar | P:84-102 | 26900797 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting | G3 (Bethesda) | 2016 | P:973-86 | 26888867 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani, Vijay; Shendure, Jay; Duan, Zhijun | Genomics Proteomics Bioinformatics | 2016 Feb | P:7-20 | 26876719 |
| Chemically activatable viral capsid functionalized for cancer targeting. | Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland | Nanomedicine | 2016 Feb | P:377-90 | 26786134 |
| Imaging Transcription: Past, Present, and Future. | Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée | Cold Spring Harbor symposia on quantitative biology. | 2016 Jan 13 | 26763984 | |
| The redundancy of the mammalian heterochromatic compartment. | Politz, Joan C Ritland; Scalzo, David; Groudine, Mark | Curr Opin Genet Dev | 2015 Dec 16 | P:1-8 | 26706451 |
| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine | Nucleic acids research. | 2016 Apr 20; | 26704975 | |
| CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. | Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun | Cell. | 2015 Dec 17 | V:163 P:1611-27 | 26686651 |
| A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. | Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2016 03 01; | 26543175 | |
| Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. | Nagano, Takashi; Lubling, Yaniv; Yaffe, Eitan; Wingett, Steven W; Dean, Wendy; Tanay, Amos; Fraser, Peter | Nature protocols. | 2015 Dec; | 26540590 | |
| Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. | Sanborn, Adrian L; Rao, Suhas S P; Huang, Su-Chen; Durand, Neva C; Huntley, Miriam H; Jewett, Andrew I; Bochkov, Ivan D; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher P; Gnirke, Andreas; Melnikov, Alexandre; McKenna, Doug; Stamenova, Elena K; Lander, Eric S; Aiden, Erez Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Nov 24; | 26499245 |