Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
4D Nucleome (235)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. | Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I | Scientific reports. | ; | 29743503 | |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. | Gao, Xin D; Tu, Li-Chun; Mir, Aamir; Rodriguez, Tomás; Ding, Yuehe; Leszyk, John; Dekker, Job; Shaffer, Scott A; Zhu, Lihua Julie; Wolfe, Scot A; Sontheimer, Erik J | Nature methods. | 2018 May 07; | 29735996 | |
| Allele-specific control of replication timing and genome organization during development. | Rivera-Mulia, Juan Carlos; Dimond, Andrew; Vera, Daniel; Trevilla-Garcia, Claudia; Sasaki, Takayo; Zimmerman, Jared; Dupont, Catherine; Gribnau, Joost; Fraser, Peter; Gilbert, David M | Genome research. | 2018 06; | 29735606 | |
| The Energetics and Physiological Impact of Cohesin Extrusion. | Vian, Laura; P?kowska, Aleksandra; Rao, Suhas S P; Kieffer-Kwon, Kyong-Rim; Jung, Seolkyoung; Baranello, Laura; Huang, Su-Chen; El Khattabi, Laila; Dose, Marei; Pruett, Nathanael; Sanborn, Adrian L; Canela, Andres; Maman, Yaakov; Oksanen, Anna; Resch, Wolfgang; Li, Xingwang; Lee, Byoungkoo; Kovalchuk, Alexander L; Tang, Zhonghui; Nelson, Steevenson; Di Pierro, Michele; Cheng, Ryan R; Machol, Ido; St Hilaire, Brian Glenn; Durand, Neva C; Shamim, Muhammad S; Stamenova, Elena K; Onuchic, José N; Ruan, Yijun; Nussenzweig, Andre; Levens, David; Aiden, Erez Lieberman; Casellas, Rafael | Cell. | 2018 May 17; | 29706548 | |
| Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. | Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E | Proceedings of SPIE--the International Society for Optical Engineering. | 2018 Feb; | 29681676 | |
| Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes. | Tsai, Albert; Singer, Robert H; Crocker, Justin | Molecular cell. | 2018 Apr 19; | 29677489 | |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. | Bonora, G; Deng, X; Fang, H; Ramani, V; Qiu, R; Berletch, J B; Filippova, G N; Duan, Z; Shendure, J; Noble, W S; Disteche, C M | Nature communications. | 2018 Apr 13; | 29654302 | |
| Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia. | Carvajal, Luis A; Neriah, Daniela Ben; Senecal, Adrien; Benard, Lumie; Thiruthuvanathan, Victor; Yatsenko, Tatyana; Narayanagari, Swathi-Rao; Wheat, Justin C; Todorova, Tihomira I; Mitchell, Kelly; Kenworthy, Charles; Guerlavais, Vincent; Annis, D Allen; Bartholdy, Boris; Will, Britta; Anampa, Jesus D; Mantzaris, Ioannis; Aivado, Manuel; Singer, Robert H; Coleman, Robert A; Verma, Amit; Steidl, Ulrich | Science translational medicine. | 2018 Apr 11; | 29643228 | |
| A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. | Walther, Nike; Hossain, M Julius; Politi, Antonio Z; Koch, Birgit; Kueblbeck, Moritz; Ødegård-Fougner, Øyvind; Lampe, Marko; Ellenberg, Jan | The Journal of cell biology. | 2018 Apr 09; | 29632028 | |
| Real-time 3D single-molecule localization using experimental point spread functions. | Li, Yiming; Mund, Markus; Hoess, Philipp; Deschamps, Joran; Matti, Ulf; Nijmeijer, Bianca; Sabinina, Vilma Jimenez; Ellenberg, Jan; Schoen, Ingmar; Ries, Jonas | Nature methods. | 2018 May; | 29630062 | |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L | Molecular cell. | 2018 Apr 05; | 29625035 | |
| Producing genome structure populations with the dynamic and automated PGS software. | Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank | Nature protocols. | 2018 May; | 29622804 | |
| Visualization of Transvection in Living Drosophila Embryos. | Lim, Bomyi; Heist, Tyler; Levine, Michael; Fukaya, Takashi | Molecular cell. | 2018 Apr 19; | 29606591 | |
| Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. | Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M | Nature protocols. | 2018 May; | 29599440 | |
| Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. | Scientific reports. | 2018 Mar 26; | 29581440 | ||
| Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan | The Journal of cell biology. | 2018 Jun 04; | 29572382 | |
| Effects of electrostatic interactions on ligand dissociation kinetics. | Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F | Physical review. E. | 2018 Feb; | 29548245 | |
| Defect-facilitated buckling in supercoiled double-helix DNA. | Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu; Neuman, Keir C; Marko, John F | Physical review. E. | 2018 Feb; | 29548184 | |
| Integrative structure and functional anatomy of a nuclear pore complex. | Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P | Nature. | 2018 Mar 22; | 29539637 | |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L | Molecular cell. | 2018 Mar 15; | 29526697 | |
| Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. | Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto; Hopp, Hannah; Das, Devika; Alber, Frank; Chiolo, Irene | Methods in enzymology. | ; | 29523239 | |
| ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. | Barton, Carl; Morganella, Sandro; Ødegård-Fougner, Øyvind; Alexander, Stephanie; Ries, Jonas; Fitzgerald, Tomas; Ellenberg, Jan; Birney, Ewan | PLoS computational biology. | 2018 Mar; | 29522506 | |
| Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. | Patriarchi, Tommaso; Shen, Ao; He, Wei; Baikoghli, Mo; Cheng, R Holland; Xiang, Yang K; Coleman, Matthew A; Tian, Lin | Scientific reports. | 2018 Feb 23; | 29476125 | |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun | Cell systems. | 2018 Feb 28; | 29454938 | |
| Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. | Robinson, James T; Turner, Douglass; Durand, Neva C; Thorvaldsdóttir, Helga; Mesirov, Jill P; Aiden, Erez Lieberman | Cell systems. | 2018 Feb 28; | 29428417 | |
| Single-cell replication profiling to measure stochastic variation in mammalian replication timing. | Dileep, Vishnu; Gilbert, David M | Nature communications. | 2018 Jan 30; | 29382831 | |
| Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. | Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun | Methods (San Diego, Calif.). | 2018 Jan 31; | 29382556 | |
| Dynamic evolution of regulatory element ensembles in primate CD4+T cells. | Danko, Charles G; Choate, Lauren A; Marks, Brooke A; Rice, Edward J; Wang, Zhong; Chu, Tinyi; Martins, Andre L; Dukler, Noah; Coonrod, Scott A; Tait Wojno, Elia D; Lis, John T; Kraus, W Lee; Siepel, Adam | Nature ecology & evolution. | 2018 Mar; | 29379187 | |
| A pathway for mitotic chromosome formation. | Gibcus, Johan H; Samejima, Kumiko; Goloborodko, Anton; Samejima, Itaru; Naumova, Natalia; Nuebler, Johannes; Kanemaki, Masato T; Xie, Linfeng; Paulson, James R; Earnshaw, William C; Mirny, Leonid A; Dekker, Job | Science (New York, N.Y.). | 2018 02 09; | 29348367 | |
| Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). | Maass, Philipp G; Barutcu, A Rasim; Shechner, David M; Weiner, Catherine L; Melé, Marta; Rinn, John L | Nature structural & molecular biology. | 2018 Feb; | 29343869 | |
| High-throughput identification of RNA nuclear enrichment sequences. | Shukla, Chinmay J; McCorkindale, Alexandra L; Gerhardinger, Chiara; Korthauer, Keegan D; Cabili, Moran N; Shechner, David M; Irizarry, Rafael A; Maass, Philipp G; Rinn, John L | The EMBO journal. | 2018 Mar 15; | 29335281 | |
| Detecting hierarchical genome folding with network modularity. | Norton, Heidi K; Emerson, Daniel J; Huang, Harvey; Kim, Jesi; Titus, Katelyn R; Gu, Shi; Bassett, Danielle S; Phillips-Cremins, Jennifer E | Nature methods. | 2018 Feb; | 29334377 | |
| Ki-67: more than a proliferation marker. | Sun, Xiaoming; Kaufman, Paul D | Chromosoma. | 2018 Jan 10; | 29322240 | |
| 3D single-molecule super-resolution microscopy with a tilted light sheet. | Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E | Nature communications. | 2018 Jan 09; | 29317629 | |
| Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. | Yan, Jian; Chen, Shi-An A; Local, Andrea; Liu, Tristin; Qiu, Yunjiang; Dorighi, Kristel M; Preissl, Sebastian; Rivera, Chloe M; Wang, Chaochen; Ye, Zhen; Ge, Kai; Hu, Ming; Wysocka, Joanna; Ren, Bing | Cell research. | 2018 Feb; | 29313530 | |
| Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. | Gerace, Larry; Tapia, Olga | Current opinion in cell biology. | 2018 Jun; | 29306725 | |
| Robust model-based analysis of single-particle tracking experiments with Spot-On. | Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier | eLife. | 2018 Jan 04; | 29300163 | |
| Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions. | Shechtman, Yoav; Gustavsson, Anna-Karin; Petrov, Petar N; Dultz, Elisa; Lee, Maurice Y; Weis, Karsten; Moerner, W E | Biomedical optics express. | 2017 Dec 01; | 29296501 | |
| A mixed-scale dense convolutional neural network for image analysis. | Pelt, Daniël M; Sethian, James A | Proceedings of the National Academy of Sciences of the United States of America. | 2018 Jan 09; | 29279403 | |
| Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. | Mukund, Kavitha; Subramaniam, Shankar | Frontiers in physiology. | 2017; | 29249983 | |
| Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. | Kaewsapsak, Pornchai; Shechner, David Michael; Mallard, William; Rinn, John L; Ting, Alice Y | eLife. | 2017 Dec 14; | 29239719 | |
| Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, Ting | Methods in molecular biology (Clifton, N.J.). | 2018; | 29224147 | |
| Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. | Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D; Mondragón, Alfonso; Marko, John F | Physical review letters. | 2017 Nov 03; | 29219598 | |
| Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. | Wutz, Gordana; Várnai, Csilla; Nagasaka, Kota; Cisneros, David A; Stocsits, Roman R; Tang, Wen; Schoenfelder, Stefan; Jessberger, Gregor; Muhar, Matthias; Hossain, M Julius; Walther, Nike; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Zuber, Johannes; | The EMBO journal. | 2017 12 15; | 29217591 | |
| A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. | Gassler, Johanna; Brandão, Hugo B; Imakaev, Maxim; Flyamer, Ilya M; Ladstätter, Sabrina; Bickmore, Wendy A; Peters, Jan-Michael; Mirny, Leonid A; Tachibana, Kikuë | The EMBO journal. | 2017 12 15; | 29217590 | |
| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. | Sundaram, Vasavi; Wang, Ting | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2018 Jan; | 29206283 | |
| Corrigendum: The 4D nucleome project. | Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network | Nature. | 2017 12 14; | 29168505 | |
| Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. | Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J; Almassalha, Luay M; Backman, Vadim; Adam, Stephen A; Goldman, Robert D; Marko, John F | Molecular biology of the cell. | 2018 Jan 15; | 29142071 | |
| Live Imaging of mRNA Synthesis in Drosophila. | Garcia, Hernan G; Gregor, Thomas | Methods in molecular biology (Clifton, N.J.). | 2018; | 29130209 | |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E C | Molecular psychiatry. | 2017 Nov 07; | 29112194 | |
| Nuclear microenvironments modulate transcription from low-affinity enhancers. | Tsai, Albert; Muthusamy, Anand K; Alves, Mariana Rp; Lavis, Luke D; Singer, Robert H; Stern, David L; Crocker, Justin | eLife. | 2017 Nov 02; | 29095143 | |
| Two independent modes of chromatin organization revealed by cohesin removal. | Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois | Nature. | 2017 Nov 02; | 29094699 | |
| Simultaneous measurement of emission color and 3D position of single molecules. | Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, Sjoerd | Optics express. | 2016 Mar 07; | 29092328 | |
| De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. | Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez; Wolynes, Peter G; Onuchic, José N | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Nov 14; | 29087948 | |
| Oligomerization and ATP stimulate condensin-mediated DNA compaction. | Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John F | Scientific reports. | 2017 Oct 27; | 29079757 | |
| 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 | |
| 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 | |
| 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 | |
| Liquid phase condensation in cell physiology and disease. | Shin, Yongdae; Brangwynne, Clifford P | Science (New York, N.Y.). | 2017 09 22; | 28935776 | |
| Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, Stavros | eLife. | 2017 Sep 21; | 28933695 | |
| Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. | Huang, Peng; Keller, Cheryl A; Giardine, Belinda; Grevet, Jeremy D; Davies, James O J; Hughes, Jim R; Kurita, Ryo; Nakamura, Yukio; Hardison, Ross C; Blobel, Gerd A | Genes & development. | 2017 Aug 15; | 28916711 | |
| Targeting Specificity of the CRISPR/Cas9 System. | Tasan, Ipek; Zhao, Huimin | ACS synthetic biology. | 2017 09 15; | 28911233 | |
| The 4D nucleome project. | Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network | Nature. | 2017 Sep 13; | 28905911 | |
| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting | BMC genomics. | 2017 Sep 12; | 28899353 | |
| Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. | Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P | Molecular cell. | 2017 Sep 21; | 28890333 | |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, Jian | Bioinformatics (Oxford, England). | 2017 Jul 15; | 28881991 | |
| LAIT: a local ancestry inference toolkit. | Hui, Daniel; Fang, Zhou; Lin, Jerome; Duan, Qing; Li, Yun; Hu, Ming; Chen, Wei | BMC genetics. | 2017 09 06; | 28877673 | |
| HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. | Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2018 Jan; | 28866592 | |
| 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 | |
| Reversed graph embedding resolves complex single-cell trajectories. | Qiu, Xiaojie; Mao, Qi; Tang, Ying; Wang, Li; Chawla, Raghav; Pliner, Hannah A; Trapnell, Cole | Nature methods. | 2017 Oct; | 28825705 | |
| SMC complexes differentially compact mitotic chromosomes according to genomic context. | Schalbetter, Stephanie Andrea; Goloborodko, Anton; Fudenberg, Geoffrey; Belton, Jon-Matthew; Miles, Catrina; Yu, Miao; Dekker, Job; Mirny, Leonid; Baxter, Jonathan | Nature cell biology. | 2017 Sep; | 28825700 | |
| Comprehensive single-cell transcriptional profiling of a multicellular organism. | Cao, Junyue; Packer, Jonathan S; Ramani, Vijay; Cusanovich, Darren A; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N; Steemers, Frank J; Adey, Andrew; Waterston, Robert H; Trapnell, Cole; Shendure, Jay | Science (New York, N.Y.). | 2017 08 18; | 28818938 | |
| A magnetic micropore chip for rapid ( | Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, David | Lab on a chip. | 2017 Sep 12; | 28809985 | |
| Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. | Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P; Xu, Jianliang; Jung, Seolkyoung; Pekowska, Aleksandra; Dose, Marei; Stevens, Evan; Mathe, Ewy; Dong, Peng; Huang, Su-Chen; Ricci, Maria Aurelia; Baranello, Laura; Zheng, Ying; Tomassoni Ardori, Francesco; Resch, Wolfgang; Stavreva, Diana; Nelson, Steevenson; McAndrew, Michael; Casellas, Adriel; Finn, Elizabeth; Gregory, Charles; St Hilaire, Brian Glenn; Johnson, Steven M; Dubois, Wendy; Cosma, Maria Pia; Batchelor, Eric; Levens, David; Phair, Robert D; Misteli, Tom; Tessarollo, Lino; Hager, Gordon; Lakadamyali, Melike; Liu, Zhe; Floer, Monique; Shroff, Hari; Aiden, Erez Lieberman; Casellas, Rafael | Molecular cell. | ; | 28803781 | |
| A new era of studying p53-mediated transcription activation. | Liu, Wei-Li; Coleman, Robert A; Singh, Sameer K | Transcription. | 2018; | 28795863 | |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual review of cell and developmental biology. | 2017 Oct 06; | 28783961 | |
| Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. | Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger D | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Aug 15; | 28765367 | |
| The three-dimensional genome organization of Drosophila melanogaster through data integration. | Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank | Genome biology. | 2017 Jul 31; | 28760140 | |
| ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. | Ou, Horng D; Phan, Sébastien; Deerinck, Thomas J; Thor, Andrea; Ellisman, Mark H; O'Shea, Clodagh C | Science (New York, N.Y.). | 2017 07 28; | 28751582 | |
| Genome Organization Drives Chromosome Fragility. | Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André | Cell. | 2017 Jul 27; | 28735753 | |
| Integrative modelling of cellular assemblies. | Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, Maya | Current opinion in structural biology. | 2017 Jul 20; | 28735107 | |
| Cell-cycle dynamics of chromosomal organization at single-cell resolution. | Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, Amos | Nature. | 2017 07 05; | 28682332 | |
| Phase separation drives heterochromatin domain formation. | Strom, Amy R; Emelyanov, Alexander V; Mir, Mustafa; Fyodorov, Dmitry V; Darzacq, Xavier; Karpen, Gary H | Nature. | 2017 07 13; | 28636597 | |
| Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. | Sun, Xiaoming; Bizhanova, Aizhan; Matheson, Timothy D; Yu, Jun; Zhu, Julie L; Kaufman, Paul D | Molecular and cellular biology. | 2017 Jun 19; | 28630280 | |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari, Sumitabha; Marko, John F | Physical review. E. | 2017 May; | 28618488 | |
| DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. | Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis J | JCI insight. | 2017 Jun 15; | 28614801 | |
| EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He, Yu; Wang, Ting | Bioinformatics (Oxford, England). | 2017 Jun 09; | 28605501 | |
| DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. | Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; | Nature genetics. | 2017 Jul; | 28604729 | |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H | Nature methods. | 2017 Jun 12; | 28604724 | |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg, Geoffrey; Imakaev, Maxim | Nature methods. | 2017 Jul; | 28604723 | |
| Engineering biological systems using automated biofoundries. | Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin | Metabolic engineering. | 2017 Jul; | 28602523 | |
| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, Ting | BMC genomics. | 2017 Jun 05; | 28583088 | |
| HUGIn: Hi-C Unifying Genomic Interrogator. | Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2017 Dec 01; | 28582503 | |
| The dynamic three-dimensional organization of the diploid yeast genome. | Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya J | eLife. | 2017 May 24; | 28537556 | |
| YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. | Beagan, Jonathan A; Duong, Michael T; Titus, Katelyn R; Zhou, Linda; Cao, Zhendong; Ma, Jingjing; Lachanski, Caroline V; Gillis, Daniel R; Phillips-Cremins, Jennifer E | Genome research. | 2017 07; | 28536180 | |
| Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. | Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G | Cell. | 2017 May 18; | 28525758 | |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel, Bas; Belmont, Andrew S | Cell. | 2017 May 18; | 28525751 | |
| Combinatorial chemistry in drug discovery. | Liu, Ruiwu; Li, Xiaocen; Lam, Kit S | Current opinion in chemical biology. | 2017 Jun; | 28494316 | |
| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan J | Nature methods. | 2017 Jun; | 28481362 | |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | eLife. | 2017 May 03; | 28467304 | |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Current biology : CB. | 2017 May 08; | 28457866 | |
| Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. | Belaghzal, Houda; Dekker, Job; Gibcus, Johan H | Methods (San Diego, Calif.). | 2017 Apr 18; | 28435001 | |
| Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long | Biophysical journal. | 2017 May 09; | 28427715 | |
| p53 dynamically directs TFIID assembly on target gene promoters. | Coleman, R A; Qiao, Z; Singh, S K; Peng, C S; Cianfrocco, M; Zhang, Z; Piasecka, A; Aldeborgh, H; Basishvili, G; Liu, W L | Molecular and cellular biology. | 2017 Apr 17; | 28416636 | |
| An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. | Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso | Nature structural & molecular biology. | 2017 May; | 28414321 | |
| Causes and consequences of nuclear gene positioning. | Shachar, Sigal; Misteli, Tom | Journal of cell science. | 2017 May 01; | 28404786 | |
| The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. | Hsu, Sarah C; Gilgenast, Thomas G; Bartman, Caroline R; Edwards, Christopher R; Stonestrom, Aaron J; Huang, Peng; Emerson, Daniel J; Evans, Perry; Werner, Michael T; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Phillips-Cremins, Jenn | Molecular cell. | 2017 Apr 06; | 28388437 | |
| Facilitated dissociation of transcription factors from single DNA binding sites. | Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 18; | 28364020 | |
| Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. | Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun | Nature protocols. | 2017 May; | 28358394 | |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté, Allison J; Raj, Arjun | Biophysical journal. | 2017 Mar 28; | 28355532 | |
| Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. | Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë | Nature. | 2017 04 06; | 28355183 | |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting | Nature communications. | 2017 Mar 28; | 28348391 | |
| Form and function of topologically associating genomic domains in budding yeast. | Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 11; | 28348222 | |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman | Science (New York, N.Y.). | 2017 Apr 07; | 28336562 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS one. | 2017; | 28333948 | |
| Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. | Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem; Bandaria, Jigar; Mir, Mustafa; Szlachta, Karol; Singh, Ritambhara; Darzacq, Xavier; Yildiz, Ahmet; Adli, Mazhar | Nature communications. | 2017 Mar 14; | 28290446 | |
| Unearthing worm replication origins. | Sasaki, Takayo; Gilbert, David M | Nature structural & molecular biology. | 2017 03 03; | 28257138 | |
| Multivalent Small-Molecule Pan-RAS Inhibitors. | Welsch, Matthew E; Kaplan, Anna; Chambers, Jennifer M; Stokes, Michael E; Bos, Pieter H; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A; Huang, Christine S; Tran, Timothy H; Akkiraju, Hemanth; Brown, Lewis M; Nandakumar, Renu; Cremers, Serge; Yang, Wan Seok; Tong, Liang; Olive, Kenneth P; Ferrando, Adolfo; Stockwell, Brent R | Cell. | ; | 28235199 | |
| Epigenetic characteristics of the mitotic chromosome in 1D and 3D. | Oomen, Marlies E; Dekker, Job | Critical reviews in biochemistry and molecular biology. | 2017 Apr; | 28228067 | |
| A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. | Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, Huimin | ACS synthetic biology. | 2017 Mar 07; | 28215080 | |
| Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. | Finn, Elizabeth H; Pegoraro, Gianluca; Shachar, Sigal; Misteli, Tom | Methods (San Diego, Calif.). | 2017 Jul 01; | 28179124 | |
| Comprehensive characterization of neutrophil genome topology. | Zhu, Yina; Gong, Ke; Denholtz, Matthew; Chandra, Vivek; Kamps, Mark P; Alber, Frank; Murre, Cornelis | Genes & development. | 2017 Jan 15; | 28167501 | |
| Software tools for visualizing Hi-C data. | Yard?mc?, Galip Gürkan; Noble, William Stafford | Genome biology. | 2017 Feb 03; | 28159004 | |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E | Molecular cell. | 2017 Feb 02; | 28157505 | |
| Massively multiplex single-cell Hi-C. | Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Gunderson, Kevin L; Steemers, Frank J; Disteche, Christine M; Noble, William S; Duan, Zhijun; Shendure, Jay | Nature methods. | 2017 Mar; | 28135255 | |
| High-throughput automated microfluidic sample preparation for accurate microbial genomics. | Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C | Nature communications. | 2017 Jan 27; | 28128213 | |
| Single-cell mRNA quantification and differential analysis with Census. | Qiu, Xiaojie; Hill, Andrew; Packer, Jonathan; Lin, Dejun; Ma, Yi-An; Trapnell, Cole | Nature methods. | 2017 Mar; | 28114287 | |
| Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. | Chao, Ran; Liang, Jing; Tasan, Ipek; Si, Tong; Ju, Linyang; Zhao, Huimin | ACS synthetic biology. | 2017 Apr 21; | 28103009 | |
| Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. | Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, Ting | Neoplasia (New York, N.Y.). | 2017 Feb; | 28088687 | |
| A New Era of Genome Integration-Simply Cut and Paste! | Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, Huimin | ACS synthetic biology. | 2017 04 21; | 28073246 | |
| Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. | Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F | Molecular biology of the cell. | 2017 Jan 05; | 28057760 | |
| Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. | Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan | Genome research. | 2017 Mar; | 28049628 | |
| Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. | Shin, Yongdae; Berry, Joel; Pannucci, Nicole; Haataja, Mikko P; Toettcher, Jared E; Brangwynne, Clifford P | Cell. | 2017 Jan 12; | 28041848 | |
| Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. | Fang, Rongxin; Yu, Miao; Li, Guoqiang; Chee, Sora; Liu, Tristin; Schmitt, Anthony D; Ren, Bing | Cell research. | 2016 Dec; | 27886167 | |
| A dynamic mode of mitotic bookmarking by transcription factors. | Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert | eLife. | 2016 Nov 19; | 27855781 | |
| Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. | Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn A | Cell reports. | 2016 Nov 15; | 27851973 | |
| A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. | Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, Bing | Cell reports. | 2016 Nov 15; | 27851967 | |
| The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. | Matheson, Timothy D; Kaufman, Paul D | Molecular biology of the cell. | 2017 Jan 01; | 27807046 | |
| An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. | Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Micha?; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz | Genome research. | 2016 Dec; | 27789526 | |
| High-throughput assessment of context-dependent effects of chromatin proteins. | Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas | Epigenetics & chromatin. | 2016; | 27777628 | |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S | Nature methods. | 2016 Dec; | 27776111 | |
| ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. | Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y | Nature methods. | ; | 27749837 | |
| Transferable model for chromosome architecture. | Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José N | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Oct 25; | 27688758 | |
| Mapping 3D genome architecture through in situ DNase Hi-C. | Ramani, Vijay; Cusanovich, Darren A; Hause, Ronald J; Ma, Wenxiu; Qiu, Ruolan; Deng, Xinxian; Blau, C Anthony; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun | Nature protocols. | 2016 Nov; | 27685100 | |
| Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. | Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng | PloS one. | 2016; | 27618313 | |
| Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. | Stark, Marie; Cheng, R Holland | Pharmaceutical patent analyst. | 2016 Sep; | 27610752 | |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt, Anthony D; Hu, Ming; Ren, Bing | Nature reviews. Molecular cell biology. | 2016 12; | 27580841 | |
| CRISPR-Cas9 nuclear dynamics and target recognition in living cells. | Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Huisman, Maximiliaan; Zhang, Shaojie; Grunwald, David; Pederson, Thoru | The Journal of cell biology. | 2016 Aug 29; | 27551060 | |
| A new correlation clustering method for cancer mutation analysis. | Hou, Jack P; Emad, Amin; Puleo, Gregory J; Ma, Jian; Milenkovic, Olgica | Bioinformatics (Oxford, England). | 2016 Aug 18; | 27540270 | |
| Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions. | Shenoy, Shailesh M | Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. | 2016 Jul; | 27516727 | |
| Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. | Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, Hiroko | Scientific reports. | 2016 Aug 12; | 27516062 | |
| Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. | Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez Lieberman | Cell systems. | 2016 Jul; | 27467249 | |
| Allele-Specific Quantification of Structural Variations in Cancer Genomes. | Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian | Cell systems. | 2016 Jul; | 27453446 | |
| Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. | Beagrie, Robert A; Pombo, Ana | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2016 09; | 27452946 | |
| Structural organization of the inactive X chromosome in the mouse. | Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job | Nature. | 2016 Jul 28; | 27437574 | |
| Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. | Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Aug 02; | 27432957 | |
| Polymer physics of chromosome large-scale 3D organisation. | Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario | Scientific reports. | 2016 Jul 13; | 27405443 | |
| Identifying gene regulatory network rewiring using latent differential graphical models. | Tian, Dechao; Gu, Quanquan; Ma, Jian | Nucleic acids research. | 2016 Sep 30; | 27378774 | |
| Nanoscale imaging of RNA with expansion microscopy. | Chen, Fei; Wassie, Asmamaw T; Cote, Allison J; Sinha, Anubhav; Alon, Shahar; Asano, Shoh; Daugharthy, Evan R; Chang, Jae-Byum; Marblestone, Adam; Church, George M; Raj, Arjun; Boyden, Edward S | Nature methods. | 2016 Aug; | 27376770 | |
| Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. | McGeachie, Michael J; Yates, Katherine P; Zhou, Xiaobo; Guo, Feng; Sternberg, Alice L; Van Natta, Mark L; Wise, Robert A; Szefler, Stanley J; Sharma, Sunita; Kho, Alvin T; Cho, Michael H; Croteau-Chonka, Damien C; Castaldi, Peter J; Jain, Gaurav; Sanyal, | American journal of respiratory and critical care medicine. | 2016 Dec 15; | 27367781 | |
| A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. | Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A | Genes & development. | 2016 Jun 15; | 27340175 | |
| Enhancer Control of Transcriptional Bursting. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Cell. | 2016 Jul 14; | 27293191 | |
| RTFBSDB: an integrated framework for transcription factor binding site analysis. | Wang, Zhong; Martins, André L; Danko, Charles G | Bioinformatics (Oxford, England). | 2016 Oct 01; | 27288497 | |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons, Orsolya; Raj, Arjun | Molecular cell. | 2016 Jun 2; | 27259209 | |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular cell. | 2016 Jun 2; | 27259200 | |
| Use of genome-editing tools to treat sickle cell disease. | Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Human genetics. | 2016 Jun 1; | 27250347 | |
| Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. | Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong | Nature communications. | 2016; | 27240697 | |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol A | Cell. | 2016 Jun 2; | 27238023 | |
| Chromosome Compaction by Active Loop Extrusion. | Goloborodko, Anton; Marko, John F; Mirny, Leonid A | Biophysical journal. | 2016 May 24; | 27224481 | |
| CRISPR/Cas9 for Human Genome Engineering and Disease Research. | Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S | Annual review of genomics and human genetics. | 2016 Aug 31; | 27216776 | |
| Formation of Chromosomal Domains by Loop Extrusion. | Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A | Cell Rep | 2016 May 19 | 27210764 | |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid | eLife. | 2016 May 18; | 27192037 | |
| Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. | Banigan, Edward J; Marko, John F | Physical review. E. | 2016 Apr; | 27182590 | |
| Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. | Proserpio, Valentina; Piccolo, Andrea; Haim-Vilmovsky, Liora; Kar, Gozde; Lönnberg, Tapio; Svensson, Valentine; Pramanik, Jhuma; Natarajan, Kedar Nath; Zhai, Weichao; Zhang, Xiuwei; Donati, Giacomo; Kayikci, Melis; Kotar, Jurij; McKenzie, Andrew N J; Montandon, Ruddy; Billker, Oliver; Woodhouse, Steven; Cicuta, Pietro; Nicodemi, Mario; Teichmann, Sarah A | Genome biology. | 2016; | 27176874 | |
| Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. | Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M | Disaster medicine and public health preparedness. | 2016 06; | 27174171 | |
| FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. | Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming | Bioinformatics (Oxford, England). | 2016 09 01; | 27153668 | |
| Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. | Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E | Cell Stem Cell | 2016 May 5 | P:611-24 | 27152443 |
| Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. | Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2016 Sep; | 27145786 | |
| Dosage compensation of the sex chromosomes and autosomes. | Disteche, Christine M | Semin Cell Dev Biol | 2016 Apr 22 | 27112542 | |
| TAD disruption as oncogenic driver. | Valton, Anne-Laure; Dekker, Job | Curr Opin Genet Dev | 2016 Feb | P:34-40 | 27111891 |
| Jointly characterizing epigenetic dynamics across multiple human cell types. | Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C | Nucleic acids research. | 2016 08 19; | 27095202 | |
| Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. | Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. | Nature Biotechnology | 2016 April 18 | Epub ahead of print | 27088723 |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting | Trends Genet | 2016 May | P:269-83 | 27080453 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. | Molecular Cell | 2016 April 5 | V:62 P:1-11 | 27067601 |
| History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. | Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A | J Bioinform Comput Biol | 2016 Apr | P:1641002 | 27021249 |
| HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. | Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming | BMC research notes. | 2016; | 26969411 | |
| The 3D Genome as Moderator of Chromosomal Communication. | Dekker, Job; Mirny, Leonid | Cell | 2016 Mar 10 | V:164 P:1110-21 | 26967279 |
| Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. | Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Mar 22; | 26951677 | |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun | Genes & development. | 2016 Mar 1; | 26944681 | |
| Activation of proto-oncogenes by disruption of chromosome neighborhoods. | Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S; Valton, Anne-Laure; Bak, Rasmus O; Li, Charles H; Goldmann, Johanna; Lajoie, Bryan R; Fan, Zi Peng; Sigova, Alla A; Reddy, Jessica; Borges-Rivera, Diego; Lee, Tong Ihn; Jaenisch, Rudolf; Porteus, Matthew H; Dekker, Job; Young, Richard A | Science | 2016 Mar 25 | V:351 P:1454-8 | 26940867 |
| Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. | Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor | Nucleus | 2016 Mar | P:84-102 | 26900797 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting | G3 (Bethesda) | 2016 | P:973-86 | 26888867 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani, Vijay; Shendure, Jay; Duan, Zhijun | Genomics Proteomics Bioinformatics | 2016 Feb | P:7-20 | 26876719 |
| Chemically activatable viral capsid functionalized for cancer targeting. | Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland | Nanomedicine | 2016 Feb | P:377-90 | 26786134 |
| Imaging Transcription: Past, Present, and Future. | Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée | Cold Spring Harbor symposia on quantitative biology. | 2016 Jan 13 | 26763984 | |
| The redundancy of the mammalian heterochromatic compartment. | Politz, Joan C Ritland; Scalzo, David; Groudine, Mark | Curr Opin Genet Dev | 2015 Dec 16 | P:1-8 | 26706451 |
| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine | Nucleic acids research. | 2016 Apr 20; | 26704975 | |
| CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. | Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun | Cell. | 2015 Dec 17 | V:163 P:1611-27 | 26686651 |
| A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. | Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2016 03 01; | 26543175 | |
| Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. | Nagano, Takashi; Lubling, Yaniv; Yaffe, Eitan; Wingett, Steven W; Dean, Wendy; Tanay, Amos; Fraser, Peter | Nature protocols. | 2015 Dec; | 26540590 | |
| Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. | Sanborn, Adrian L; Rao, Suhas S P; Huang, Su-Chen; Durand, Neva C; Huntley, Miriam H; Jewett, Andrew I; Bochkov, Ivan D; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher P; Gnirke, Andreas; Melnikov, Alexandre; McKenna, Doug; Stamenova, Elena K; Lander, Eric S; Aiden, Erez Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Nov 24; | 26499245 |