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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 (170)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Effects of electrostatic interactions on ligand dissociation kinetics. | Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F | Physical review. E. | 2018 Feb; | 29548245 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| Live Imaging of mRNA Synthesis in Drosophila. | Garcia, Hernan G; Gregor, Thomas | Methods in molecular biology (Clifton, N.J.). | 2018; | 29130209 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
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