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 (100)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 |
| 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 | |
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