4D Nucleome (123)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Simultaneous measurement of emission color and 3D position of single molecules.Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, SjoerdOptics express.2016 Mar 07;29092328
Oligomerization and ATP stimulate condensin-mediated DNA compaction.Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John FScientific reports.2017 Oct 27;29079757
Supercoiling DNA Locates Mismatches.Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir CPhysical review letters.2017 Oct 06;29053317
Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei.Banigan, Edward J; Stephens, Andrew D; Marko, John FBiophysical journal.2017 Oct 17;29045860
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, KerstinBiophysical journal.2017 Oct 03;28978433
From structure to function, how bioinformatics help to reveal functions of our genomes.Zheng, Xiaoqi; Zhong, ShengGenome biology.2017 Sep 26;28950915
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, CornelisCell.2017 Sep 21;28938112
Liquid phase condensation in cell physiology and disease.Shin, Yongdae; Brangwynne, Clifford PScience (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 AGenes & development.2017 Aug 15;28916711
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 NetworkNature.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, TingBMC 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 PMolecular 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 SCell stem cell.2017 Sep 07;28886366
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, JonathanNature 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, DavidLab on a chip.2017 Sep 12;28809985
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, FrankGenome 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 CScience (New York, N.Y.).2017 07 28;28751582
Integrative modelling of cellular assemblies.Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, MayaCurrent 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, AmosNature.2017 07 05;28682332
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 DMolecular and cellular biology.2017 Jun 19;28630280
Torque and buckling in stretched intertwined double-helix DNAs.Brahmachari, Sumitabha; Marko, John FPhysical 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 JJCI 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, TingBioinformatics (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 HNature methods.2017 Jun 12;28604724
FISH-ing for captured contacts: towards reconciling FISH and 3C.Fudenberg, Geoffrey; Imakaev, MaximNature methods.2017 Jul;28604723
Engineering biological systems using automated biofoundries.Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, HuiminMetabolic 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, TingBMC 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 JeLife.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 GCell.2017 May 18;28525758
Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression.van Steensel, Bas; Belmont, Andrew SCell.2017 May 18;28525751
Combinatorial chemistry in drug discovery.Liu, Ruiwu; Li, Xiaocen; Lam, Kit SCurrent 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 JNature methods.2017 Jun;28481362
CTCF and cohesin regulate chromatin loop stability with distinct dynamics.Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, XaviereLife.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, KyungheeThe Journal of experimental medicine.2017 May 01;28461595
Rapid Rates of Pol II Elongation in the Drosophila Embryo.Fukaya, Takashi; Lim, Bomyi; Levine, MichaelCurrent 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 HMethods (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 LMolecular 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, AlfonsoNature structural & molecular biology.2017 May;28414321
Causes and consequences of nuclear gene positioning.Shachar, Sigal; Misteli, TomJournal 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, JennMolecular 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 FProceedings 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, YijunNature protocols.2017 May;28358394
FISHing Out the Details of CRISPR Genome Tracks.Coté, Allison J; Raj, ArjunBiophysical 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, KikuëNature.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, TingNature 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 MProceedings 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 LiebermanScience (New York, N.Y.).2017 Apr 07;28336562
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer.Lowdon, Rebecca F; Wang, TingPloS 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, MazharNature communications.2017 Mar 14;28290446
Epigenetic characteristics of the mitotic chromosome in 1D and 3D.Oomen, Marlies E; Dekker, JobCritical 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, HuiminACS 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, TomMethods (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, CornelisGenes & development.2017 Jan 15;28167501
Software tools for visualizing Hi-C data.Yard?mc?, Galip Gürkan; Noble, William StaffordGenome 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 EMolecular 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, JayNature 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, ColeNature 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, HuiminACS 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, TingNeoplasia (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 FMolecular 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, DanGenome 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 PCell.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, RoberteLife.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 ACell 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, BingCell 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 DMolecular 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, DariuszGenome 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, BasEpigenetics & 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 SNature 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 YNature methods.;27749837
Transferable model for chromosome architecture.Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José NProceedings 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, ZhijunNature 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, YonghengPloS one.2016;27618313
Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery.Stark, Marie; Cheng, R HollandPharmaceutical 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, ThoruThe 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, OlgicaBioinformatics (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 MMicroscopy 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, HirokoScientific 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 LiebermanCell systems.2016 Jul;27467249
Allele-Specific Quantification of Structural Variations in Cancer Genomes.Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, JianCell 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, JobNature.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 LiebermanProceedings 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, MarioScientific reports.2016 Jul 13;27405443
Identifying gene regulatory network rewiring using latent differential graphical models.Tian, Dechao; Gu, Quanquan; Ma, JianNucleic 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 SNature 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 AGenes & development.2016 Jun 15;27340175
Enhancer Control of Transcriptional Bursting.Fukaya, Takashi; Lim, Bomyi; Levine, MichaelCell.2016 Jul 14;27293191
RTFBSDB: an integrated framework for transcription factor binding site analysis.Wang, Zhong; Martins, André L; Danko, Charles GBioinformatics (Oxford, England).2016 Oct 01;27288497
What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism.Symmons, Orsolya; Raj, ArjunMolecular cell.2016 Jun 2;27259209
Chromatin Domains: The Unit of Chromosome Organization.Dixon, Jesse R; Gorkin, David U; Ren, BingMolecular cell.2016 Jun 2;27259200
Use of genome-editing tools to treat sickle cell disease.Tasan, Ipek; Jain, Surbhi; Zhao, HuiminHuman 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, XianghongNature 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 ACell.2016 Jun 2;27238023
Chromosome Compaction by Active Loop Extrusion.Goloborodko, Anton; Marko, John F; Mirny, Leonid ABiophysical journal.2016 May 24;27224481
Formation of Chromosomal Domains by Loop Extrusion.Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid ACell Rep2016 May 1927210764
Compaction and segregation of sister chromatids via active loop extrusion.Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, LeonideLife.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 FPhysical 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 AGenome 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 ECell Stem Cell2016 May 5P:611-2427152443
Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines.Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John FChromosome 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 MSemin Cell Dev Biol2016 Apr 2227112542
TAD disruption as oncogenic driver.Valton, Anne-Laure; Dekker, JobCurr Opin Genet Dev2016 FebP:34-4027111891
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 Biotechnology2016 April 18Epub ahead of print27088723
Evolution of Epigenetic Regulation in Vertebrate Genomes.Lowdon, Rebecca F; Jang, Hyo Sik; Wang, TingTrends Genet2016 MayP:269-8327080453
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping.Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA.Molecular Cell2016 April 5V:62 P:1-1127067601
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid AJ Bioinform Comput Biol2016 AprP:164100227021249
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, MingBMC research notes.2016;26969411
The 3D Genome as Moderator of Chromosomal Communication.Dekker, Job; Mirny, LeonidCell2016 Mar 10V:164 P:1110-2126967279
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, FrankProceedings 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, ArjunGenes & 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 AScience2016 Mar 25V:351 P:1454-826940867
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, HéctorNucleus2016 MarP:84-10226900797
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, TingG3 (Bethesda)2016P:973-8626888867
Understanding Spatial Genome Organization: Methods and Insights.Ramani, Vijay; Shendure, Jay; Duan, ZhijunGenomics Proteomics Bioinformatics2016 FebP:7-2026876719
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 HollandNanomedicine2016 Feb P:377-9026786134
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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 JasmineNucleic acids research.2016 Apr 20;26704975
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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 LiebermanProceedings of the National Academy of Sciences of the United States of America.2015 Nov 24;26499245