Publications Search by Program
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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 (539)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. | Bizhanova, Aizhan; Kaufman, Paul D | Biochimica et biophysica acta. Gene regulatory mechanisms. | 2020 Dec 08; | 33307247 | |
| A map of cis-regulatory elements and 3D genome structures in zebrafish. | Yang, Hongbo; Luan, Yu; Liu, Tingting; Lee, Hyung Joo; Fang, Li; Wang, Yanli; Wang, Xiaotao; Zhang, Bo; Jin, Qiushi; Ang, Khai Chung; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Sriranga, Iyyanki; Khunsriraksakul, Chachrit; Salameh, Tarik; Li, Daofeng; | Nature. | 2020 Dec; | 33239788 | |
| Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. | Wu, Jun; Krchma, Karen; Lee, Hyung Joo; Prabhakar, Sairam; Wang, Xiaoli; Zhao, Haiyong; Xing, Xiaoyun; Seong, Rho H; Fremont, Daved H; Artyomov, Maxim N; Wang, Ting; Choi, Kyunghee | Cell reports. | 2020 Nov 17; | 33207205 | |
| SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. | Banerjee, Abhik K; Blanco, Mario R; Bruce, Emily A; Honson, Drew D; Chen, Linlin M; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A; Loney, Colin; Thai, Jasmine; Miller, Zachary D; Lin, Aaron E; Schmidt, Madaline M; Stewart, Douglas G; Gold | Cell. | 2020 11 25; | 33080218 | |
| Stress-induced RNA-chromatin interactions promote endothelial dysfunction. | Calandrelli, Riccardo; Xu, Lixia; Luo, Yingjun; Wu, Weixin; Fan, Xiaochen; Nguyen, Tri; Chen, Chien-Ju; Sriram, Kiran; Tang, Xiaofang; Burns, Andrew B; Natarajan, Rama; Chen, Zhen Bouman; Zhong, Sheng | Nature communications. | 2020 10 15; | 33060583 | |
| EMU: reconfigurable graphical user interfaces for Micro-Manager. | Deschamps, Joran; Ries, Jonas | BMC bioinformatics. | 2020 Oct 15; | 33059591 | |
| Cell-type-specific 3D epigenomes in the developing human cortex. | Song, Michael; Pebworth, Mark-Phillip; Yang, Xiaoyu; Abnousi, Armen; Fan, Changxu; Wen, Jia; Rosen, Jonathan D; Choudhary, Mayank N K; Cui, Xiekui; Jones, Ian R; Bergenholtz, Seth; Eze, Ugomma C; Juric, Ivan; Li, Bingkun; Maliskova, Lenka; Lee, Jerry; Liu | Nature. | 2020 Oct 14; | 33057195 | |
| Exploring chromosomal structural heterogeneity across multiple cell lines. | Cheng, Ryan R; Contessoto, Vinicius G; Lieberman Aiden, Erez; Wolynes, Peter G; Di Pierro, Michele; Onuchic, Jose N | eLife. | 2020 Oct 13; | 33047670 | |
| Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. | Desai, Parth Rakesh; Brahmachari, Sumitabha; Marko, John F; Das, Siddhartha; Neuman, Keir C | Nucleic acids research. | 2020 11 04; | 33045724 | |
| Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. | Biggs, Ronald J; Liu, Ning; Peng, Yiheng; Marko, John F; Qiao, Huanyu | Communications biology. | 2020 Sep 30; | 32999386 | |
| High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. | Vangala, Pranitha; Murphy, Rachel; Quinodoz, Sofia A; Gellatly, Kyle; McDonel, Patrick; Guttman, Mitchell; Garber, Manuel | Molecular cell. | 2020 10 15; | 32991830 | |
| TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data. | Van Buren, Eric; Hu, Ming; Weng, Chen; Jin, Fulai; Li, Yan; Wu, Di; Li, Yun | Genetic epidemiology. | 2020 Sep 29; | 32989764 | |
| Tissue-specific usage of transposable element-derived promoters in mouse development. | Miao, Benpeng; Fu, Shuhua; Lyu, Cheng; Gontarz, Paul; Wang, Ting; Zhang, Bo | Genome biology. | 2020 Sep 28; | 32988383 | |
| Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. | Lewis, James J; Van Belleghem, Steven M; Papa, Riccardo; Danko, Charles G; Reed, Robert D | Science advances. | 2020 Sep; | 32978147 | |
| Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. | Kim, Hyeon-Jin; Yard?mc?, Galip Gürkan; Bonora, Giancarlo; Ramani, Vijay; Liu, Jie; Qiu, Ruolan; Lee, Choli; Hesson, Jennifer; Ware, Carol B; Shendure, Jay; Duan, Zhijun; Noble, William Stafford | PLoS computational biology. | 2020 09; | 32946435 | |
| The qBED track: a novel genome browser visualization for point processes. | Moudgil, Arnav; Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Wang, Ting; Mitra, Robi D | Bioinformatics (Oxford, England). | 2020 Sep 17; | 32941613 | |
| DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods. | He, Yu; Jang, Hyo Sik; Xing, Xiaoyun; Li, Daofeng; Vasek, Michael J; Dougherty, Joseph D; Wang, Ting | Science advances. | 2020 Jul; | 32937429 | |
| Multi-contact 3C reveals that the human genome during interphase is largely not entangled. | Tavares-Cadete, Filipe; Norouzi, Davood; Dekker, Bastiaan; Liu, Yu; Dekker, Job | Nature structural & molecular biology. | 2020 Sep 14; | 32929283 | |
| Nucleated transcriptional condensates amplify gene expression. | Wei, Ming-Tzo; Chang, Yi-Che; Shimobayashi, Shunsuke F; Shin, Yongdae; Strom, Amy R; Brangwynne, Clifford P | Nature cell biology. | 2020 Oct; | 32929202 | |
| NuSeT: A deep learning tool for reliably separating and analyzing crowded cells. | Yang, Linfeng; Ghosh, Rajarshi P; Franklin, J Matthew; Chen, Simon; You, Chenyu; Narayan, Raja R; Melcher, Marc L; Liphardt, Jan T | PLoS computational biology. | 2020 09; | 32925919 | |
| Concerted localization-resets precede YAP-dependent transcription. | Franklin, J Matthew; Ghosh, Rajarshi P; Shi, Quanming; Reddick, Michael P; Liphardt, Jan T | Nature communications. | 2020 09 11; | 32917893 | |
| Exploring the coronavirus pandemic with the WashU Virus Genome Browser. | Flynn, Jennifer A; Purushotham, Deepak; Choudhary, Mayank N K; Zhuo, Xiaoyu; Fan, Changxu; Matt, Gavriel; Li, Daofeng; Wang, Ting | Nature genetics. | 2020 10; | 32908257 | |
| Cell cycle dynamics of lamina-associated DNA. | van Schaik, Tom; Vos, Mabel; Peric-Hupkes, Daan; Hn Celie, Patrick; van Steensel, Bas | EMBO reports. | 2020 Nov 05; | 32893442 | |
| Alteration of genome folding via contact domain boundary insertion. | Zhang, Di; Huang, Peng; Sharma, Malini; Keller, Cheryl A; Giardine, Belinda; Zhang, Haoyue; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E; Hardison, Ross C; Blobel, Gerd A | Nature genetics. | 2020 Aug 31; | 32868908 | |
| 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. | Fernandez, Lindsey R; Gilgenast, Thomas G; Phillips-Cremins, Jennifer E | Genome biology. | 2020 Aug 28; | 32859248 | |
| Cellular diversity of the regenerating caudal fin. | Hou, Yiran; Lee, Hyung Joo; Chen, Yujie; Ge, Jiaxin; Osman, Fujr Osman Ibrahim; McAdow, Anthony R; Mokalled, Mayssa H; Johnson, Stephen L; Zhao, Guoyan; Wang, Ting | Science advances. | 2020 Aug; | 32851162 | |
| Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. | Tasan, Ipek; Su, Christina Jean; Enghiad, Behnam; Zhang, Meng; Mishra, Shekhar; Zhao, Huimin | ACS synthetic biology. | 2020 09 18; | 32822529 | |
| Targeted DNase Hi-C. | Duan, Zhijun | Methods in molecular biology (Clifton, N.J.). | 2021; | 32820399 | |
| Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments. | Chen, Zhijie; Shaw, Alan; Wilson, Hugh; Woringer, Maxime; Darzacq, Xavier; Marqusee, Susan; Wang, Quan; Bustamante, Carlos | Proceedings of the National Academy of Sciences of the United States of America. | 2020 Sep 01; | 32817484 | |
| Optimizing imaging speed and excitation intensity for single-molecule localization microscopy. | Diekmann, Robin; Kahnwald, Maurice; Schoenit, Andreas; Deschamps, Joran; Matti, Ulf; Ries, Jonas | Nature methods. | 2020 Sep; | 32807954 | |
| Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. | Shaffer, Sydney M; Emert, Benjamin L; Reyes Hueros, Raúl A; Cote, Christopher; Harmange, Guillaume; Schaff, Dylan L; Sizemore, Ann E; Gupte, Rohit; Torre, Eduardo; Singh, Abhyudai; Bassett, Danielle S; Raj, Arjun | Cell. | 2020 Aug 20; | 32735851 | |
| An integrative ENCODE resource for cancer genomics. | Zhang, Jing; Lee, Donghoon; Dhiman, Vineet; Jiang, Peng; Xu, Jie; McGillivray, Patrick; Yang, Hongbo; Liu, Jason; Meyerson, William; Clarke, Declan; Gu, Mengting; Li, Shantao; Lou, Shaoke; Xu, Jinrui; Lochovsky, Lucas; Ung, Matthew; Ma, Lijia; Yu, Shan; C | Nature communications. | 2020 07 29; | 32728046 | |
| MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing. | Biswas, Jeetayu; Rahman, Reazur; Gupta, Varun; Rosbash, Michael; Singer, Robert H | iScience. | 2020 Jul 24; | 32674054 | |
| A supervised learning framework for chromatin loop detection in genome-wide contact maps. | Salameh, Tarik J; Wang, Xiaotao; Song, Fan; Zhang, Bo; Wright, Sage M; Khunsriraksakul, Chachrit; Ruan, Yijun; Yue, Feng | Nature communications. | 2020 Jul 09; | 32647330 | |
| Free energy-based model of CTCF-mediated chromatin looping in the human genome. | Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz | Methods (San Diego, Calif.). | 2020 10 01; | 32645447 | |
| Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation. | Conte, Mattia; Fiorillo, Luca; Bianco, Simona; Chiariello, Andrea M; Esposito, Andrea; Nicodemi, Mario | Nature communications. | 2020 07 03; | 32620890 | |
| Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. | Liu, Shuli; Yu, Ying; Zhang, Shengli; Cole, John B; Tenesa, Albert; Wang, Ting; McDaneld, Tara G; Ma, Li; Liu, George E; Fang, Lingzhao | BMC biology. | 2020 Jul 03; | 32620158 | |
| A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. | El-Nachef, Danny; Shi, Kevin; Beussman, Kevin M; Martinez, Refugio; Regier, Mary C; Everett, Guy W; Murry, Charles E; Stevens, Kelly R; Young, Jessica E; Sniadecki, Nathan J; Davis, Jennifer | Stem cell reports. | 2020 07 14; | 32619493 | |
| The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. | Wang, Alan S; Chen, Leo C; Wu, R Alex; Hao, Yvonne; McSwiggen, David T; Heckert, Alec B; Richardson, Christopher D; Gowen, Benjamin G; Kazane, Katelynn R; Vu, Jonathan T; Wyman, Stacia K; Shin, Jiyung J; Darzacq, Xavier; Walter, Johannes C; Corn, Jacob E | Molecular cell. | 2020 07 16; | 32603710 | |
| Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. | Chen, Xiaoying; Zhang, Bo; Wang, Ting; Bonni, Azad; Zhao, Guoyan | BMC bioinformatics. | 2020 Jun 29; | 32600248 | |
| Single-molecule imaging of transcription dynamics in somatic stem cells. | Wheat, Justin C; Sella, Yehonatan; Willcockson, Michael; Skoultchi, Arthur I; Bergman, Aviv; Singer, Robert H; Steidl, Ulrich | Nature. | 2020 07; | 32581360 | |
| Comparison of differential accessibility analysis strategies for ATAC-seq data. | Gontarz, Paul; Fu, Shuhua; Xing, Xiaoyun; Liu, Shaopeng; Miao, Benpeng; Bazylianska, Viktoriia; Sharma, Akhil; Madden, Pamela; Cates, Kitra; Yoo, Andrew; Moszczynska, Anna; Wang, Ting; Zhang, Bo | Scientific reports. | 2020 Jun 23; | 32576878 | |
| Long Noncoding RNAs: Molecular Modalities to Organismal Functions. | Rinn, John L; Chang, Howard Y | Annual review of biochemistry. | 2020 06 20; | 32569523 | |
| MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. | Zhang, Ruochi; Ma, Jian | Cell systems. | 2020 May 20; | 32550271 | |
| Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. | Strehle, Mackenzie; Guttman, Mitchell | Current opinion in cell biology. | 2020 06; | 32535328 | |
| Loop extrusion: theory meets single-molecule experiments. | Banigan, Edward J; Mirny, Leonid A | Current opinion in cell biology. | 2020 06; | 32534241 | |
| Biosystems Design by Machine Learning. | Volk, Michael Jeffrey; Lourentzou, Ismini; Mishra, Shekhar; Vo, Lam Tung; Zhai, Chengxiang; Zhao, Huimin | ACS synthetic biology. | 2020 07 17; | 32485108 | |
| Evolving methodologies and concepts in 4D nucleome research. | Sparks, Thomas M; Harabula, Izabela; Pombo, Ana | Current opinion in cell biology. | 2020 May 27; | 32473574 | |
| Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. | Beagan, Jonathan A; Pastuzyn, Elissa D; Fernandez, Lindsey R; Guo, Michael H; Feng, Kelly; Titus, Katelyn R; Chandrashekar, Harshini; Shepherd, Jason D; Phillips-Cremins, Jennifer E | Nature neuroscience. | 2020 06; | 32451484 | |
| 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. | Wlasnowolski, Michal; Sadowski, Michal; Czarnota, Tymon; Jodkowska, Karolina; Szalaj, Przemyslaw; Tang, Zhonghui; Ruan, Yijun; Plewczynski, Dariusz | Nucleic acids research. | 2020 07 02; | 32442297 | |
| Delta-1 Functionalized Hydrogel Promotes hESC-Cardiomyocyte Graft Proliferation and Maintains Heart Function Post-Injury. | Gerbin, Kaytlyn A; Mitzelfelt, Katie A; Guan, Xuan; Martinson, Amy M; Murry, Charles E | Molecular therapy. Methods & clinical development. | 2020 Jun 12; | 32426414 | |
| Composition-dependent thermodynamics of intracellular phase separation. | Riback, Joshua A; Zhu, Lian; Ferrolino, Mylene C; Tolbert, Michele; Mitrea, Diana M; Sanders, David W; Wei, Ming-Tzo; Kriwacki, Richard W; Brangwynne, Clifford P | Nature. | 2020 05; | 32405004 | |
| Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. | Zhang, Xiaotian; Jeong, Mira; Huang, Xingfan; Wang, Xue Qing; Wang, Xinyu; Zhou, Wanding; Shamim, Muhammad S; Gore, Haley; Himadewi, Pamela; Liu, Yushuai; Bochkov, Ivan D; Reyes, Jaime; Doty, Madison; Huang, Yung-Hsin; Jung, Haiyoung; Heikamp, Emily; Aide | Molecular cell. | 2020 05 07; | 32386543 | |
| Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. | Trzaskoma, Pawe?; Ruszczycki, B?a?ej; Lee, Byoungkoo; Pels, Katarzyna K; Krawczyk, Katarzyna; Bokota, Grzegorz; Szczepankiewicz, Andrzej A; Aaron, Jesse; Walczak, Agnieszka; ?liwi?ska, Ma?gorzata A; Magalska, Adriana; Kadlof, Michal; Wolny, Artur; Parteka | Nature communications. | 2020 05 01; | 32358536 | |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh, Lea; Saint-Antoine, Michael; Sanford, Eric M; Emert, Benjamin L; Singh, Abhyudai; Marr, Carsten; Raj, Arjun; Goyal, Yogesh | Cell systems. | 2020 Apr 22; | 32325034 | |
| Chromatin Viscoelasticity Measured by Local Dynamic Analysis. | Vivante, Anat; Bronshtein, Irena; Garini, Yuval | Biophysical journal. | 2020 05 05; | 32320676 | |
| Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. | Sanders, David W; Kedersha, Nancy; Lee, Daniel S W; Strom, Amy R; Drake, Victoria; Riback, Joshua A; Bracha, Dan; Eeftens, Jorine M; Iwanicki, Allana; Wang, Alicia; Wei, Ming-Tzo; Whitney, Gena; Lyons, Shawn M; Anderson, Paul; Jacobs, William M; Ivanov, P | Cell. | 2020 04 16; | 32302570 | |
| Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. | Field, Matt A; Rosen, Benjamin D; Dudchenko, Olga; Chan, Eva K F; Minoche, Andre E; Edwards, Richard J; Barton, Kirston; Lyons, Ruth J; Tuipulotu, Daniel Enosi; Hayes, Vanessa M; D Omer, Arina; Colaric, Zane; Keilwagen, Jens; Skvortsova, Ksenia; Bogdanovi | GigaScience. | 2020 04 01; | 32236524 | |
| Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. | Schreiber, Jacob; Durham, Timothy; Bilmes, Jeffrey; Noble, William Stafford | Genome biology. | 2020 03 30; | 32228704 | |
| Distinct features of nucleolus-associated domains in mouse embryonic stem cells. | Bizhanova, Aizhan; Yan, Aimin; Yu, Jun; Zhu, Lihua Julie; Kaufman, Paul D | Chromosoma. | 2020 Mar 26; | 32219510 | |
| Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. | Zhao, Binhui; Chaturvedi, Pankaj; Zimmerman, David L; Belmont, Andrew S | ACS synthetic biology. | 2020 05 15; | 32216371 | |
| Ultrastructural Details of Mammalian Chromosome Architecture. | Krietenstein, Nils; Abraham, Sameer; Venev, Sergey V; Abdennur, Nezar; Gibcus, Johan; Hsieh, Tsung-Han S; Parsi, Krishna Mohan; Yang, Liyan; Maehr, René; Mirny, Leonid A; Dekker, Job; Rando, Oliver J | Molecular cell. | 2020 Mar 14; | 32213324 | |
| Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. | Hsieh, Tsung-Han S; Cattoglio, Claudia; Slobodyanyuk, Elena; Hansen, Anders S; Rando, Oliver J; Tjian, Robert; Darzacq, Xavier | Molecular cell. | 2020 05 07; | 32213323 | |
| High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. | Zhao, Peiyao A; Sasaki, Takayo; Gilbert, David M | Genome biology. | 2020 03 24; | 32209126 | |
| Cost-efficient open source laser engine for microscopy. | Schröder, Daniel; Deschamps, Joran; Dasgupta, Anindita; Matti, Ulf; Ries, Jonas | Biomedical optics express. | 2020 Feb 01; | 32206389 | |
| Evaluating Enhancer Function and Transcription. | Field, Andrew; Adelman, Karen | Annual review of biochemistry. | 2020 06 20; | 32197056 | |
| Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. | Sato, Hanae; Das, Sulagna; Singer, Robert H; Vera, Maria | Annual review of biochemistry. | 2020 06 20; | 32176523 | |
| Advanced 3D Analysis and Optimization of Single-Molecule FISH in Drosophila Muscle. | Noma, Akiko; Smith, Carlas S; Huisman, Maximiliaan; Martin, Robert M; Moore, Melissa J; Grunwald, David | Small methods. | 2018 Sep 11; | 32158910 | |
| Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems. | Masnadi-Shirazi, Maryam; Subramaniam, Shankar | Scientific reports. | 2020 Mar 02; | 32123218 | |
| Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. | Lee, Hyung Joo; Hou, Yiran; Chen, Yujie; Dailey, Zea Z; Riddihough, Aiyana; Jang, Hyo Sik; Wang, Ting; Johnson, Stephen L | Genome biology. | 2020 02 27; | 32106888 | |
| Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. | Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Wang, Wenbo; Goldfeder, Rachel L; Choi, Cindy; He, Hao; Gong, Liang; Lin, Junyan; Urban, Barbara; Chow, Julianna; Li, Meihong; Lim, Joanne; Philip, Vivek; Murray, Stephen A; Wang, Haoyi; Wei, Chia-Lin | Nature genetics. | 2020 03; | 32094912 | |
| Therapeutic genome editing in cardiovascular diseases. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Advanced drug delivery reviews. | 2020 Feb 21; | 32092381 | |
| Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation. | Biswas, Jeetayu; Nunez, Leti; Das, Sulagna; Yoon, Young J; Eliscovich, Carolina; Singer, Robert H | Cold Spring Harbor symposia on quantitative biology. | 2020 Feb 21; | 32086331 | |
| Local rewiring of genome-nuclear lamina interactions by transcription. | Brueckner, Laura; Zhao, Peiyao A; van Schaik, Tom; Leemans, Christ; Sima, Jiao; Peric-Hupkes, Daniel; Gilbert, David M; van Steensel, Bas | The EMBO journal. | 2020 Mar 16; | 32080885 | |
| A Dynamic Folded Hairpin Conformation Is Associated with ?-Globin Activation in Erythroid Cells. | Chiariello, Andrea M; Bianco, Simona; Oudelaar, A Marieke; Esposito, Andrea; Annunziatella, Carlo; Fiorillo, Luca; Conte, Mattia; Corrado, Alfonso; Prisco, Antonella; Larke, Martin S C; Telenius, Jelena M; Sciarretta, Renato; Musella, Francesco; Buckle, V | Cell reports. | 2020 02 18; | 32075757 | |
| An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. | Kim, Arthur S; Zimmerman, Ofer; Fox, Julie M; Nelson, Christopher A; Basore, Katherine; Zhang, Rong; Durnell, Lorellin; Desai, Chandni; Bullock, Christopher; Deem, Sharon L; Oppenheimer, Jonas; Shapiro, Beth; Wang, Ting; Cherry, Sara; Coyne, Carolyn B; Ha | Cell host & microbe. | 2020 03 11; | 32075743 | |
| Chemogenetic Control of Nanobodies. | Farrants, Helen; Tarnawski, Miroslaw; Müller, Thorsten G; Otsuka, Shotaro; Hiblot, Julien; Koch, Birgit; Kueblbeck, Moritz; Kräusslich, Hans-Georg; Ellenberg, Jan; Johnsson, Kai | Nature methods. | 2020 03; | 32066961 | |
| ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL. | Wutz, Gordana; Ladurner, Rene; St Hilaire, Brian Glenn; Stocsits, Roman R; Nagasaka, Kota; Pignard, Benoit; Sanborn, Adrian; Tang, Wen; Várnai, Csilla; Ivanov, Miroslav P; Schoenfelder, Stefan; van der Lelij, Petra; Huang, Xingfan; Dürnberger, Gerhard; Roitinger, Elisabeth; Mechtler, Karl; Davidson, Iain Finley; Fraser, Peter; Lieberman-Aiden, Erez; Peters, Jan-Michael | eLife. | 2020 Feb 17; | 32065581 | |
| Derivation of trophoblast stem cells from naïve human pluripotent stem cells. | Dong, Chen; Beltcheva, Mariana; Gontarz, Paul; Zhang, Bo; Popli, Pooja; Fischer, Laura A; Khan, Shafqat A; Park, Kyoung-Mi; Yoon, Eun-Ja; Xing, Xiaoyun; Kommagani, Ramakrishna; Wang, Ting; Solnica-Krezel, Lilianna; Theunissen, Thorold W | eLife. | 2020 Feb 12; | 32048992 | |
| Computational approaches from polymer physics to investigate chromatin folding. | Bianco, Simona; Chiariello, Andrea M; Conte, Mattia; Esposito, Andrea; Fiorillo, Luca; Musella, Francesco; Nicodemi, Mario | Current opinion in cell biology. | 2020 06; | 32045823 | |
| pyBedGraph: a python package for fast operations on 1D genomic signal tracks. | Zhang, Henry B; Kim, Minji; Chuang, Jeffrey H; Ruan, Yijun | Bioinformatics (Oxford, England). | 2020 05 01; | 32044918 | |
| Dynamic Assembly and Disassembly of the Human DNA Polymerase ? Holoenzyme on the Genome In Vivo. | Drosopoulos, William C; Vierra, David A; Kenworthy, Charles A; Coleman, Robert A; Schildkraut, Carl L | Cell reports. | 2020 02 04; | 32023453 | |
| Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine. | Karbassi, Elaheh; Fenix, Aidan; Marchiano, Silvia; Muraoka, Naoto; Nakamura, Kenta; Yang, Xiulan; Murry, Charles E | Nature reviews. Cardiology. | 2020 Feb 03; | 32015528 | |
| GiniQC: a measure for quantifying noise in single-cell Hi-C data. | Horton, Connor A; Alver, Burak H; Park, Peter J | Bioinformatics (Oxford, England). | 2020 05 01; | 32003786 | |
| Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. | Feodorova, Yana; Falk, Martin; Mirny, Leonid A; Solovei, Irina | Trends in cell biology. | 2020 Apr; | 31980345 | |
| Switchable resolution in soft x-ray tomography of single cells. | Weinhardt, Venera; Chen, Jian-Hua; Ekman, Axel A; Guo, Jessica; Remesh, Soumya G; Hammel, Michal; McDermott, Gerry; Chao, Weilun; Oh, Sharon; Le Gros, Mark A; Larabell, Carolyn A | PloS one. | 2020; | 31978064 | |
| Co-opted transposons help perpetuate conserved higher-order chromosomal structures. | Choudhary, Mayank Nk; Friedman, Ryan Z; Wang, Julia T; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, Ting | Genome biology. | 2020 01 24; | 31973766 | |
| Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts. | Weyers, Jill J; Gunaje, Jagadambika J; Van Biber, Benjamin; Martinson, Amy; Reinecke, Hans; Mahoney, William M; Schwartz, Stephen M; Cox, Timothy C; Murry, Charles E | PloS one. | 2020; | 31945113 | |
| On the existence and functionality of topologically associating domains. | Beagan, Jonathan A; Phillips-Cremins, Jennifer E | Nature genetics. | 2020 01; | 31925403 | |
| MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. | Tian, Dechao; Zhang, Ruochi; Zhang, Yang; Zhu, Xiaopeng; Ma, Jian | Genome research. | 2020 Jan 06; | 31907193 | |
| An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms. | Yu, Yi; Guo, Yijun; Tian, Qiqi; Lan, Yuanqing; Yeh, Hugh; Zhang, Meng; Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Nature chemical biology. | 2020 04; | 31873222 | |
| Physics and Biology (of Chromosomes). | Marko, John F | Journal of molecular biology. | 2020 Jan 17; | 31866291 | |
| Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells. | Chen, Changya; Yu, Wenbao; Tober, Joanna; Gao, Peng; He, Bing; Lee, Kiwon; Trieu, Tuan; Blobel, Gerd A; Speck, Nancy A; Tan, Kai | Cell reports. | 2019 12 17; | 31851943 | |
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| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. | Sundaram, Vasavi; Wang, Ting | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2018 Jan; | 29206283 | |
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| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E C | Molecular psychiatry. | 2017 Nov 07; | 29112194 | |
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| Oligomerization and ATP stimulate condensin-mediated DNA compaction. | Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John F | Scientific reports. | 2017 Oct 27; | 29079757 | |
| STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus. | Li, Peng; Mitra, Suman; Spolski, Rosanne; Oh, Jangsuk; Liao, Wei; Tang, Zhonghui; Mo, Fei; Li, Xingwang; West, Erin E; Gromer, Daniel; Lin, Jian-Xin; Liu, Chengyu; Ruan, Yijun; Leonard, Warren J | Proceedings of the National Academy of Sciences of the United States of America. | 2017 11 14; | 29078395 | |
| Recent evidence that TADs and chromatin loops are dynamic structures. | Hansen, Anders S; Cattoglio, Claudia; Darzacq, Xavier; Tjian, Robert | Nucleus (Austin, Tex.). | 2018 01 01; | 29077530 | |
| A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. | Gallagher, Michael D; Posavi, Marijan; Huang, Peng; Unger, Travis L; Berlyand, Yosef; Gruenewald, Analise L; Chesi, Alessandra; Manduchi, Elisabetta; Wells, Andrew D; Grant, Struan F A; Blobel, Gerd A; Brown, Christopher D; Chen-Plotkin, Alice S | American journal of human genetics. | 2017 Nov 02; | 29056226 | |
| Supercoiling DNA Locates Mismatches. | Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir C | Physical review letters. | 2017 Oct 06; | 29053317 | |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan, Edward J; Stephens, Andrew D; Marko, John F | Biophysical journal. | 2017 Oct 17; | 29045860 | |
| RNA structure interactions and ribonucleoprotein processes of the influenza A virus. | Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz | Briefings in functional genomics. | 2018 11 26; | 29040388 | |
| DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. | Sun, Zhe; Wang, Ting; Deng, Ke; Wang, Xiao-Feng; Lafyatis, Robert; Ding, Ying; Hu, Ming; Chen, Wei | Bioinformatics (Oxford, England). | 2018 01 01; | 29036318 | |
| Transvection. | Fukaya, Takashi; Levine, Michael | Current biology : CB. | 2017 Oct 09; | 29017034 | |
| Cohesin Loss Eliminates All Loop Domains. | Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian; Engreitz, Jesse M; Perez, Elizabeth M; Kieffer-Kwon, Kyong-Rim; Sanborn, Adrian L; Johnstone, Sarah E; Bascom, Gavin D; Bochkov, Ivan D; Huang, Xingfan; Shamim, Muhammad S; Shin, Jaeweon; Turner, Douglass; Ye, Ziyi; Omer, Arina D; Robinson, James T; Schlick, Tamar; Bernstein, Bradley E; Casellas, Rafael; Lander, Eric S; Aiden, Erez Lieberman | Cell. | 2017 Oct 05; | 28985562 | |
| Dense Bicoid hubs accentuate binding along the morphogen gradient. | Mir, Mustafa; Reimer, Armando; Haines, Jenna E; Li, Xiao-Yong; Stadler, Michael; Garcia, Hernan; Eisen, Michael B; Darzacq, Xavier | Genes & development. | 2017 Sep 01; | 28982761 | |
| Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. | Germier, Thomas; Kocanova, Silvia; Walther, Nike; Bancaud, Aurélien; Shaban, Haitham Ahmed; Sellou, Hafida; Politi, Antonio Zaccaria; Ellenberg, Jan; Gallardo, Franck; Bystricky, Kerstin | Biophysical journal. | 2017 Oct 03; | 28978433 | |
| From structure to function, how bioinformatics help to reveal functions of our genomes. | Zheng, Xiaoqi; Zhong, Sheng | Genome biology. | 2017 Sep 26; | 28950915 | |
| Structural aspects of the inactive X chromosome. | Bonora, Giancarlo; Disteche, Christine M | Philosophical transactions of the Royal Society of London. Series B, Biological sciences. | 2017 Nov 05; | 28947656 | |
| Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. | Isoda, Takeshi; Moore, Amanda J; He, Zhaoren; Chandra, Vivek; Aida, Masatoshi; Denholtz, Matthew; Piet van Hamburg, Jan; Fisch, Kathleen M; Chang, Aaron N; Fahl, Shawn P; Wiest, David L; Murre, Cornelis | Cell. | 2017 Sep 21; | 28938112 | |
| Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. | Rege, Mayuri; Phillips-Cremins, Jennifer E | Molecular cell. | 2017 Sep 21; | 28938095 | |
| Liquid phase condensation in cell physiology and disease. | Shin, Yongdae; Brangwynne, Clifford P | Science (New York, N.Y.). | 2017 09 22; | 28935776 | |
| Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, Stavros | eLife. | 2017 Sep 21; | 28933695 | |
| Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. | Huang, Peng; Keller, Cheryl A; Giardine, Belinda; Grevet, Jeremy D; Davies, James O J; Hughes, Jim R; Kurita, Ryo; Nakamura, Yukio; Hardison, Ross C; Blobel, Gerd A | Genes & development. | 2017 Aug 15; | 28916711 | |
| Targeting Specificity of the CRISPR/Cas9 System. | Tasan, Ipek; Zhao, Huimin | ACS synthetic biology. | 2017 09 15; | 28911233 | |
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| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting | BMC genomics. | 2017 Sep 12; | 28899353 | |
| Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. | Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P | Molecular cell. | 2017 Sep 21; | 28890333 | |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, Jian | Bioinformatics (Oxford, England). | 2017 Jul 15; | 28881991 | |
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| HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. | Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2018 Jan; | 28866592 | |
| The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality? | Bach, Benjamin; Sicat, Ronell; Beyer, Johanna; Cordeil, Maxime; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2018 01; | 28866590 | |
| HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. | Yang, Tao; Zhang, Feipeng; Yard?mc?, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua | Genome research. | 2017 Nov; | 28855260 | |
| Crossed wires: 3D genome misfolding in human disease. | Norton, Heidi K; Phillips-Cremins, Jennifer E | The Journal of cell biology. | 2017 11 06; | 28855250 | |
| Evolutionarily Conserved Principles Predict 3D Chromatin Organization. | Rowley, M Jordan; Nichols, Michael H; Lyu, Xiaowen; Ando-Kuri, Masami; Rivera, I Sarahi M; Hermetz, Karen; Wang, Ping; Ruan, Yijun; Corces, Victor G | Molecular cell. | 2017 Sep 07; | 28826674 | |
| Reversed graph embedding resolves complex single-cell trajectories. | Qiu, Xiaojie; Mao, Qi; Tang, Ying; Wang, Li; Chawla, Raghav; Pliner, Hannah A; Trapnell, Cole | Nature methods. | 2017 Oct; | 28825705 | |
| SMC complexes differentially compact mitotic chromosomes according to genomic context. | Schalbetter, Stephanie Andrea; Goloborodko, Anton; Fudenberg, Geoffrey; Belton, Jon-Matthew; Miles, Catrina; Yu, Miao; Dekker, Job; Mirny, Leonid; Baxter, Jonathan | Nature cell biology. | 2017 Sep; | 28825700 | |
| Comprehensive single-cell transcriptional profiling of a multicellular organism. | Cao, Junyue; Packer, Jonathan S; Ramani, Vijay; Cusanovich, Darren A; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N; Steemers, Frank J; Adey, Andrew; Waterston, Robert H; Trapnell, Cole; Shendure, Jay | Science (New York, N.Y.). | 2017 08 18; | 28818938 | |
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| Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. | Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P; Xu, Jianliang; Jung, Seolkyoung; Pekowska, Aleksandra; Dose, Marei; Stevens, Evan; Mathe, Ewy; Dong, Peng; Huang, Su-Chen; Ricci, Maria Aurelia; Baranello, Laura; Zheng, Ying; Tomassoni Ardori, Francesco; Resch, Wolfgang; Stavreva, Diana; Nelson, Steevenson; McAndrew, Michael; Casellas, Adriel; Finn, Elizabeth; Gregory, Charles; St Hilaire, Brian Glenn; Johnson, Steven M; Dubois, Wendy; Cosma, Maria Pia; Batchelor, Eric; Levens, David; Phair, Robert D; Misteli, Tom; Tessarollo, Lino; Hager, Gordon; Lakadamyali, Melike; Liu, Zhe; Floer, Monique; Shroff, Hari; Aiden, Erez Lieberman; Casellas, Rafael | Molecular cell. | ; | 28803781 | |
| A new era of studying p53-mediated transcription activation. | Liu, Wei-Li; Coleman, Robert A; Singh, Sameer K | Transcription. | 2018; | 28795863 | |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual review of cell and developmental biology. | 2017 Oct 06; | 28783961 | |
| Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. | Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger D | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Aug 15; | 28765367 | |
| The three-dimensional genome organization of Drosophila melanogaster through data integration. | Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank | Genome biology. | 2017 Jul 31; | 28760140 | |
| ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. | Ou, Horng D; Phan, Sébastien; Deerinck, Thomas J; Thor, Andrea; Ellisman, Mark H; O'Shea, Clodagh C | Science (New York, N.Y.). | 2017 07 28; | 28751582 | |
| Genome Organization Drives Chromosome Fragility. | Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André | Cell. | 2017 Jul 27; | 28735753 | |
| Integrative modelling of cellular assemblies. | Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, Maya | Current opinion in structural biology. | 2017 Jul 20; | 28735107 | |
| Cell-cycle dynamics of chromosomal organization at single-cell resolution. | Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, Amos | Nature. | 2017 07 05; | 28682332 | |
| Phase separation drives heterochromatin domain formation. | Strom, Amy R; Emelyanov, Alexander V; Mir, Mustafa; Fyodorov, Dmitry V; Darzacq, Xavier; Karpen, Gary H | Nature. | 2017 07 13; | 28636597 | |
| Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. | Sun, Xiaoming; Bizhanova, Aizhan; Matheson, Timothy D; Yu, Jun; Zhu, Julie L; Kaufman, Paul D | Molecular and cellular biology. | 2017 Jun 19; | 28630280 | |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari, Sumitabha; Marko, John F | Physical review. E. | 2017 May; | 28618488 | |
| DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. | Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis J | JCI insight. | 2017 Jun 15; | 28614801 | |
| EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He, Yu; Wang, Ting | Bioinformatics (Oxford, England). | 2017 Jun 09; | 28605501 | |
| DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. | Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; | Nature genetics. | 2017 Jul; | 28604729 | |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H | Nature methods. | 2017 Jun 12; | 28604724 | |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg, Geoffrey; Imakaev, Maxim | Nature methods. | 2017 Jul; | 28604723 | |
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| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, Ting | BMC genomics. | 2017 Jun 05; | 28583088 | |
| HUGIn: Hi-C Unifying Genomic Interrogator. | Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2017 Dec 01; | 28582503 | |
| The dynamic three-dimensional organization of the diploid yeast genome. | Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya J | eLife. | 2017 May 24; | 28537556 | |
| YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. | Beagan, Jonathan A; Duong, Michael T; Titus, Katelyn R; Zhou, Linda; Cao, Zhendong; Ma, Jingjing; Lachanski, Caroline V; Gillis, Daniel R; Phillips-Cremins, Jennifer E | Genome research. | 2017 07; | 28536180 | |
| Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. | Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G | Cell. | 2017 May 18; | 28525758 | |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel, Bas; Belmont, Andrew S | Cell. | 2017 May 18; | 28525751 | |
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| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan J | Nature methods. | 2017 Jun; | 28481362 | |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | eLife. | 2017 May 03; | 28467304 | |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Current biology : CB. | 2017 May 08; | 28457866 | |
| Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. | Belaghzal, Houda; Dekker, Job; Gibcus, Johan H | Methods (San Diego, Calif.). | 2017 Apr 18; | 28435001 | |
| Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long | Biophysical journal. | 2017 May 09; | 28427715 | |
| p53 dynamically directs TFIID assembly on target gene promoters. | Coleman, R A; Qiao, Z; Singh, S K; Peng, C S; Cianfrocco, M; Zhang, Z; Piasecka, A; Aldeborgh, H; Basishvili, G; Liu, W L | Molecular and cellular biology. | 2017 Apr 17; | 28416636 | |
| An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. | Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso | Nature structural & molecular biology. | 2017 May; | 28414321 | |
| Causes and consequences of nuclear gene positioning. | Shachar, Sigal; Misteli, Tom | Journal of cell science. | 2017 May 01; | 28404786 | |
| The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. | Hsu, Sarah C; Gilgenast, Thomas G; Bartman, Caroline R; Edwards, Christopher R; Stonestrom, Aaron J; Huang, Peng; Emerson, Daniel J; Evans, Perry; Werner, Michael T; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Phillips-Cremins, Jenn | Molecular cell. | 2017 Apr 06; | 28388437 | |
| Facilitated dissociation of transcription factors from single DNA binding sites. | Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 18; | 28364020 | |
| Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. | Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun | Nature protocols. | 2017 May; | 28358394 | |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté, Allison J; Raj, Arjun | Biophysical journal. | 2017 Mar 28; | 28355532 | |
| Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. | Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë | Nature. | 2017 04 06; | 28355183 | |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting | Nature communications. | 2017 Mar 28; | 28348391 | |
| Form and function of topologically associating genomic domains in budding yeast. | Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 11; | 28348222 | |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman | Science (New York, N.Y.). | 2017 Apr 07; | 28336562 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS one. | 2017; | 28333948 | |
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