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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 (355)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures. | Hulleman, Christiaan N; Huisman, Maximiliaan; Moerland, Robert J; Grünwald, David; Stallinga, Sjoerd; Rieger, Bernd | Small methods. | 2018 Sep 11; | 31240238 | |
| LADL: light-activated dynamic looping for endogenous gene expression control. | Kim, Ji Hun; Rege, Mayuri; Valeri, Jacqueline; Dunagin, Margaret C; Metzger, Aryeh; Titus, Katelyn R; Gilgenast, Thomas G; Gong, Wanfeng; Beagan, Jonathan A; Raj, Arjun; Phillips-Cremins, Jennifer E | Nature methods. | 2019 07; | 31235883 | |
| Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. | Khanna, Nimish; Zhang, Yaojun; Lucas, Joseph S; Dudko, Olga K; Murre, Cornelis | Nature communications. | 2019 06 24; | 31235807 | |
| Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. | Yang, Yang; Zhang, Yang; Ren, Bing; Dixon, Jesse R; Ma, Jian | Cell systems. | 2019 Jun 26; | 31229558 | |
| Determining cellular CTCF and cohesin abundances to constrain 3D genome models. | Cattoglio, Claudia; Pustova, Iryna; Walther, Nike; Ho, Jaclyn J; Hantsche-Grininger, Merle; Inouye, Carla J; Hossain, M Julius; Dailey, Gina M; Ellenberg, Jan; Darzacq, Xavier; Tjian, Robert; Hansen, Anders S | eLife. | 2019 Jun 17; | 31205001 | |
| Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. | Vertii, Anastassiia; Ou, Jianhong; Yu, Jun; Yan, Aimin; Pagès, Hervé; Liu, Haibo; Zhu, Lihua Julie; Kaufman, Paul D | Genome research. | 2019 Jun 14; | 31201210 | |
| Preformed chromatin topology assists transcriptional robustness of Shh during limb development. | Paliou, Christina; Guckelberger, Philine; Schöpflin, Robert; Heinrich, Verena; Esposito, Andrea; Chiariello, Andrea M; Bianco, Simona; Annunziatella, Carlo; Helmuth, Johannes; Haas, Stefan; Jerkovi?, Ivana; Brieske, Norbert; Wittler, Lars; Timmermann, Ber | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Jun 18; | 31147463 | |
| Time varying causal network reconstruction of a mouse cell cycle. | Masnadi-Shirazi, Maryam; Maurya, Mano R; Pao, Gerald; Ke, Eugene; Verma, Inder M; Subramaniam, Shankar | BMC bioinformatics. | 2019 May 29; | 31142274 | |
| Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. | Cheng, Li-Chun; Baboo, Sabyasachi; Lindsay, Cory; Brusman, Liza; Martinez-Bartolomé, Salvador; Tapia, Olga; Zhang, Xi; Yates 3rd, John R; Gerace, Larry | Nucleus (Austin, Tex.). | 2019 Dec; | 31142202 | |
| The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. | Salvarani, Nicolò; Crasto, Silvia; Miragoli, Michele; Bertero, Alessandro; Paulis, Marianna; Kunderfranco, Paolo; Serio, Simone; Forni, Alberto; Lucarelli, Carla; Dal Ferro, Matteo; Larcher, Veronica; Sinagra, Gianfranco; Vezzoni, Paolo; Murry, Charles E; Faggian, Giuseppe; Condorelli, Gianluigi; Di Pasquale, Elisa | Nature communications. | 2019 05 22; | 31118417 | |
| Tibanna: software for scalable execution of portable pipelines on the cloud. | Lee, Soohyun; Johnson, Jeremy; Vitzthum, Carl; K?rl?, Koray; Alver, Burak H; Park, Peter J | Bioinformatics (Oxford, England). | 2019 May 11; | 31077294 | |
| Sensory experience remodels genome architecture in neural circuit to drive motor learning. | Yamada, Tomoko; Yang, Yue; Valnegri, Pamela; Juric, Ivan; Abnousi, Armen; Markwalter, Kelly H; Guthrie, Arden N; Godec, Abigail; Oldenborg, Anna; Hu, Ming; Holy, Timothy E; Bonni, Azad | Nature. | 2019 May; | 31068695 | |
| Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. | Yu, Jingting; Hu, Ming; Li, Chun | BMC genetics. | 2019 Apr 30; | 31039743 | |
| Receptor-Ligand Rebinding Kinetics in Confinement. | Erba?, Aykut; Olvera de la Cruz, Monica; Marko, John F | Biophysical journal. | 2019 May 07; | 31029377 | |
| Topological and functional comparison of community detection algorithms in biological networks. | Rahiminejad, Sara; Maurya, Mano R; Subramaniam, Shankar | BMC bioinformatics. | 2019 Apr 27; | 31029085 | |
| Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. | Kim, Jung-Sik; He, Xiaoyuan; Liu, Jie; Duan, Zhijun; Kim, Taeyeon; Gerard, Julia; Kim, Brian; Pillai, Manoj M; Lane, William S; Noble, William S; Budnik, Bogdan; Waldman, Todd | The Journal of biological chemistry. | 2019 May 31; | 31010829 | |
| FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. | Ma, Chun-Yu; Madden, Pamela; Gontarz, Paul; Wang, Ting; Zhang, Bo | Frontiers in genetics. | 2019; | 31001319 | |
| Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. | Nomidis, Stefanos K; Skoruppa, Enrico; Carlon, Enrico; Marko, John F | Physical review. E. | 2019 Mar; | 30999490 | |
| MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. | Juric, Ivan; Yu, Miao; Abnousi, Armen; Raviram, Ramya; Fang, Rongxin; Zhao, Yuan; Zhang, Yanxiao; Qiu, Yunjiang; Yang, Yuchen; Li, Yun; Ren, Bing; Hu, Ming | PLoS computational biology. | 2019 04; | 30986246 | |
| Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. | Leemans, Christ; van der Zwalm, Marloes C H; Brueckner, Laura; Comoglio, Federico; van Schaik, Tom; Pagie, Ludo; van Arensbergen, Joris; van Steensel, Bas | Cell. | 2019 May 02; | 30982597 | |
| Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. | Bertero, Alessandro; Fields, Paul A; Ramani, Vijay; Bonora, Giancarlo; Yardimci, Galip G; Reinecke, Hans; Pabon, Lil; Noble, William S; Shendure, Jay; Murry, Charles E | Nature communications. | 2019 04 04; | 30948719 | |
| The accessible chromatin landscape of the murine hippocampus at single-cell resolution. | Sinnamon, John R; Torkenczy, Kristof A; Linhoff, Michael W; Vitak, Sarah A; Mulqueen, Ryan M; Pliner, Hannah A; Trapnell, Cole; Steemers, Frank J; Mandel, Gail; Adey, Andrew C | Genome research. | 2019 05; | 30936163 | |
| Transposable elements drive widespread expression of oncogenes in human cancers. | Jang, Hyo Sik; Shah, Nakul M; Du, Alan Y; Dailey, Zea Z; Pehrsson, Erica C; Godoy, Paula M; Zhang, David; Li, Daofeng; Xing, Xiaoyun; Kim, Sungsu; O'Donnell, David; Gordon, Jeffrey I; Wang, Ting | Nature genetics. | 2019 04; | 30926969 | |
| Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. | Boeynaems, Steven; Holehouse, Alex S; Weinhardt, Venera; Kovacs, Denes; Van Lindt, Joris; Larabell, Carolyn; Van Den Bosch, Ludo; Das, Rhiju; Tompa, Peter S; Pappu, Rohit V; Gitler, Aaron D | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Apr 16; | 30926670 | |
| Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications. | He, Ming; Huang, Tse-Shun; Li, Shuai; Hong, Hsiao-Chin; Chen, Zhen; Martin, Marcy; Zhou, Xin; Huang, Hsi-Yuan; Su, Shu-Han; Zhang, Jiao; Wang, Wei-Ting; Kang, Jian; Huang, Hsien-Da; Zhang, Jin; Chien, Shu; Shyy, John Y-J | Arteriosclerosis, thrombosis, and vascular biology. | 2019 May; | 30917677 | |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long | Nature. | 2019 Apr; | 30911168 | |
| Measuring the reproducibility and quality of Hi-C data. | Yard?mc?, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E G; Ursu, Oana; Yan, Koon-Kiu; Yang, Tao; Chakraborty, Abhijit; Kaul, Arya; Lajoie, Bryan R; Song, Fan; Zhan, Ye; Ay, Ferhat; Gerstein, Mark; Kundaje, Anshul; Li, Qunhua; Taylor, James; Yue, Feng; Dekker, Job; Noble, William S | Genome biology. | 2019 03 19; | 30890172 | |
| Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance. | Bertolini, Jessica A; Favaro, Rebecca; Zhu, Yanfen; Pagin, Miriam; Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Vermunt, Marit W; Martynoga, Ben; Barone, Cristiana; Mariani, Jessica; Cardozo, Marcos Julián; Tabanera, Noemi; Zambelli, Federico; Mercurio, Sara; Ottolenghi, Sergio; Robson, Paul; Creyghton, Menno P; Bovolenta, Paola; Pavesi, Giulio; Guillemot, Francois; Nicolis, Silvia K; Wei, Chia-Lin | Cell stem cell. | 2019 Mar 07; | 30849367 | |
| Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. | Ma, Hanhui; Tu, Li-Chun; Chung, Yu-Chieh; Naseri, Ardalan; Grunwald, David; Zhang, Shaojie; Pederson, Thoru | The Journal of cell biology. | 2019 Mar 07; | 30846483 | |
| Dendritic Spines Taxonomy: The Functional and Structural Classification ? Time-Dependent Probabilistic Model of Neuronal Activation. | Urban, Paulina; Rezaei, Vahid; Bokota, Grzegorz; Denkiewicz, Micha?; Basu, Subhadip; Plewczy?ski, Dariusz | Journal of computational biology : a journal of computational molecular cell biology. | 2019 Apr; | 30810368 | |
| Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. | Finn, Elizabeth H; Pegoraro, Gianluca; Brandão, Hugo B; Valton, Anne-Laure; Oomen, Marlies E; Dekker, Job; Mirny, Leonid; Misteli, Tom | Cell. | 2019 Mar 07; | 30799036 | |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay | Nature. | 2019 02; | 30787437 | |
| Replication Timing Becomes Intertwined with 3D Genome Organization. | Ma, Jian; Duan, Zhijun | Cell. | 2019 Feb 07; | 30735630 | |
| Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. | Hollerer, Ina; Barker, Juliet C; Jorgensen, Victoria; Tresenrider, Amy; Dugast-Darzacq, Claire; Chan, Leon Y; Darzacq, Xavier; Tjian, Robert; Ünal, Elçin; Brar, Gloria A | G3 (Bethesda, Md.). | 2019 04 09; | 30723103 | |
| Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. | Yan, Zhangming; Huang, Norman; Wu, Weixin; Chen, Weizhong; Jiang, Yiqun; Chen, Jingyao; Huang, Xuerui; Wen, Xingzhao; Xu, Jie; Jin, Qiushi; Zhang, Kang; Chen, Zhen; Chien, Shu; Zhong, Sheng | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Feb 19; | 30718424 | |
| Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. | Chapski, Douglas J; Rosa-Garrido, Manuel; Hua, Nan; Alber, Frank; Vondriska, Thomas M | Frontiers in cardiovascular medicine. | 2018; | 30697540 | |
| Adapting dCas9-APEX2 for subnuclear proteomic profiling. | Gao, Xin D; Rodríguez, Tomás C; Sontheimer, Erik J | Methods in enzymology. | 2019; | 30691651 | |
| A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. | Sharon, Nadav; Chawla, Raghav; Mueller, Jonas; Vanderhooft, Jordan; Whitehorn, Luke James; Rosenthal, Benjamin; Gürtler, Mads; Estanboulieh, Ralph R; Shvartsman, Dmitry; Gifford, David K; Trapnell, Cole; Melton, Doug | Cell. | 2019 Feb 07; | 30661759 | |
| An automated Bayesian pipeline for rapid analysis of single-molecule binding data. | Smith, Carlas S; Jouravleva, Karina; Huisman, Maximiliaan; Jolly, Samson M; Zamore, Phillip D; Grunwald, David | Nature communications. | 2019 01 17; | 30655518 | |
| CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. | Oomen, Marlies E; Hansen, Anders S; Liu, Yu; Darzacq, Xavier; Dekker, Job | Genome research. | 2019 02; | 30655336 | |
| Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic ? Cell Identity and Function. | Lawlor, Nathan; Márquez, Eladio J; Orchard, Peter; Narisu, Narisu; Shamim, Muhammad Saad; Thibodeau, Asa; Varshney, Arushi; Kursawe, Romy; Erdos, Michael R; Kanke, Matt; Gu, Huiya; Pak, Evgenia; Dutra, Amalia; Russell, Sheikh; Li, Xingwang; Piecuch, Emaly; Luo, Oscar; Chines, Peter S; Fuchbserger, Christian; NIH Intramural Sequencing Center; Sethupathy, Praveen; Aiden, Aviva Presser; Ruan, Yijun; Aiden, Erez Lieberman; Collins, Francis S; Ucar, Duygu; Parker, Stephen C J; Stitzel, Michael L | Cell reports. | 2019 Jan 15; | 30650367 | |
| Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers. | Limi, Saima; Zhao, Yilin; Guo, Peng; Lopez-Jones, Melissa; Zheng, Deyou; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales | Investigative ophthalmology & visual science. | 2019 Jan 02; | 30646012 | |
| LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. | Monahan, Kevin; Horta, Adan; Lomvardas, Stavros | Nature. | 2019 01; | 30626972 | |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, Arjun | PLoS genetics. | 2019 01; | 30625149 | |
| Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics. | Biggs, Ronald; Liu, Patrick Z; Stephens, Andrew D; Marko, John F | Molecular biology of the cell. | 2019 03 21; | 30625026 | |
| An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. | Zhang, Zhizhuo; Chng, Kern Rei; Lingadahalli, Shreyas; Chen, Zikai; Liu, Mei Hui; Do, Huy Hoang; Cai, Shaojiang; Rinaldi, Nicola; Poh, Huay Mei; Li, Guoliang; Sung, Ying Ying; Heng, Charlie L; Core, Leighton J; Tan, Si Kee; Ruan, Xiaoan; Lis, John T; Kellis, Manolis; Ruan, Yijun; Sung, Wing-Kin; Cheung, Edwin | Genome research. | 2019 02; | 30606742 | |
| Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. | Sima, Jiao; Chakraborty, Abhijit; Dileep, Vishnu; Michalski, Marco; Klein, Kyle N; Holcomb, Nicolas P; Turner, Jesse L; Paulsen, Michelle T; Rivera-Mulia, Juan Carlos; Trevilla-Garcia, Claudia; Bartlett, Daniel A; Zhao, Peiyao A; Washburn, Brian K; Nora, | Cell. | 2019 Feb 07; | 30595451 | |
| Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. | Mir, Mustafa; Stadler, Michael R; Ortiz, Stephan A; Hannon, Colleen E; Harrison, Melissa M; Darzacq, Xavier; Eisen, Michael B | eLife. | 2018 12 27; | 30589412 | |
| A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. | Lu, Jia; Cao, Xiaoyi; Zhong, Sheng | PLoS computational biology. | 2018 Dec; | 30586383 | |
| Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. | Nir, Guy; Farabella, Irene; Pérez Estrada, Cynthia; Ebeling, Carl G; Beliveau, Brian J; Sasaki, Hiroshi M; Lee, S Dean; Nguyen, Son C; McCole, Ruth B; Chattoraj, Shyamtanu; Erceg, Jelena; AlHaj Abed, Jumana; Martins, Nuno M C; Nguyen, Huy Q; Hannan, Mohammed A; Russell, Sheikh; Durand, Neva C; Rao, Suhas S P; Kishi, Jocelyn Y; Soler-Vila, Paula; Di Pierro, Michele; Onuchic, José N; Callahan, Steven P; Schreiner, John M; Stuckey, Jeff A; Yin, Peng; Aiden, Erez Lieberman; Marti-Renom, Marc A; Wu, C-Ting | PLoS genetics. | 2018 12; | 30586358 | |
| Models of polymer physics for the architecture of the cell nucleus. | Esposito, Andrea; Annunziatella, Carlo; Bianco, Simona; Chiariello, Andrea M; Fiorillo, Luca; Nicodemi, Mario | Wiley interdisciplinary reviews. Systems biology and medicine. | 2018 Dec 19; | 30566285 | |
| Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. | Bartman, Caroline R; Hamagami, Nicole; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Blobel, Gerd A; Raj, Arjun | Molecular cell. | 2018 Dec 06; | 30554946 | |
| RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. | Brahma, Sandipan; Henikoff, Steven | Molecular cell. | 2019 Jan 17; | 30554944 | |
| GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. | Calandrelli, Riccardo; Wu, Qiuyang; Guan, Jihong; Zhong, Sheng | Genomics, proteomics & bioinformatics. | 2018 Dec 13; | 30553884 | |
| A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. | Keleher, Madeline Rose; Zaidi, Rabab; Hicks, Lauren; Shah, Shyam; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Cheverud, James M | BMC genomics. | 2018 Dec 07; | 30526554 | |
| Deconstructing transport-distribution reconstruction in the nuclear-pore complex. | Tu, Li-Chun; Huisman, Maximiliaan; Chung, Yu-Chieh; Smith, Carlas Sierd; Grunwald, David | Nature structural & molecular biology. | 2018 Dec; | 30518848 | |
| Impact of optical aberrations on axial position determination by photometry. | Thorsen, Rasmus Ø; Hulleman, Christiaan N; Hammer, Mathias; Grünwald, David; Stallinga, Sjoerd; Rieger, Bernd | Nature methods. | 2018 Dec; | 30504865 | |
| Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. | Bracha, Dan; Walls, Mackenzie T; Wei, Ming-Tzo; Zhu, Lian; Kurian, Martin; Avalos, José L; Toettcher, Jared E; Brangwynne, Clifford P | Cell. | 2018 Nov 29; | 30500534 | |
| Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. | Peng, Qin; Lu, Shaoying; Shi, Yuxin; Pan, Yijia; Limsakul, Praopim; Chernov, Andrei V; Qiu, Juhui; Chai, Xiaoqi; Shi, Yiwen; Wang, Pengzhi; Ji, Yanmin; Li, Yi-Shuan J; Strongin, Alex Y; Verkhusha, Vladislav V; Izpisua Belmonte, Juan Carlos; Ren, Bing; Wang, Yuanliang; Chien, Shu; Wang, Yingxiao | Proceedings of the National Academy of Sciences of the United States of America. | 2018 12 11; | 30478057 | |
| CHRAC/ACF contribute to the repressive ground state of chromatin. | Scacchetti, Alessandro; Brueckner, Laura; Jain, Dhawal; Schauer, Tamas; Zhang, Xu; Schnorrer, Frank; van Steensel, Bas; Straub, Tobias; Becker, Peter B | Life science alliance. | 2018 Jan; | 30456345 | |
| Improved reference genome of Aedes aegypti informs arbovirus vector control. | Matthews, Benjamin J; Dudchenko, Olga; Kingan, Sarah B; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E; Glassford, William J; Herre, Margaret; Redmond, Seth N; Rose, Noah H; Weedall, Gareth D; Wu, Yang; Batra, Sanjit S; Brito-Sierra, Carlos A; Bucki | Nature. | 2018 11; | 30429615 | |
| ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, Arjun | Nature biotechnology. | 2018 Nov 12; | 30418432 | |
| Higher-Order Organization Principles of Pre-translational mRNPs. | Metkar, Mihir; Ozadam, Hakan; Lajoie, Bryan R; Imakaev, Maxim; Mirny, Leonid A; Dekker, Job; Moore, Melissa J | Molecular cell. | 2018 11 15; | 30415953 | |
| Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. | P?kowska, Aleksandra; Klaus, Bernd; Xiang, Wanqing; Severino, Jacqueline; Daigle, Nathalie; Klein, Felix A; Ole?, Ma?gorzata; Casellas, Rafael; Ellenberg, Jan; Steinmetz, Lars M; Bertone, Paul; Huber, Wolfgang | Cell systems. | 2018 Nov 28; | 30414923 | |
| Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. | Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho; Yuede, Carla; Li, Daofeng; Rensing, Nicholas; Huang, Ju; Baldridge, Dustin; Maloney, Susan E; Dougherty, Joseph D; Constantino, John; Jahani-Asl, Arezu; Wong, Michael; Wozniak, David F; Wang, Ting; Klyachko, Vitaly A; Bonni, Azad | Cell reports. | 2018 Nov 06; | 30403997 | |
| A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. | Dai, Xiaoyu; Lin, Nan; Li, Daofeng; Wang, Ting | Biometrics. | 2018 Nov 02; | 30387496 | |
| CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. | Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Chung, Yu-Chieh; Grunwald, David; Zhang, Shaojie; Pederson, Thoru | Nature methods. | 2018 Nov; | 30377374 | |
| Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. | Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas | Cell systems. | 2018 Oct 24; | 30342881 | |
| Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. | Zoller, Benjamin; Little, Shawn C; Gregor, Thomas | Cell. | 2018 Oct 18; | 30340044 | |
| Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling. | Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura; Wang, Ruipeng; McQuiston, Travis J; Challberg, Sharon S; Pollok, Brian A; Wang, Ting | Cell reports. | 2018 Oct 16; | 30332641 | |
| CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. | Liu, Yanxia; Yu, Chen; Daley, Timothy Patrick; Wang, Fangyuan; Cao, William S; Bhate, Salil; Lin, Xueqiu; Still 2nd, Chris; Liu, Honglei; Zhao, Dehua; Wang, Haifeng; Xie, Xinmin S; Ding, Sheng; Wong, Wing Hung; Wernig, Marius; Qi, Lei S | Cell stem cell. | 2018 Nov 01; | 30318302 | |
| CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. | Wang, Haifeng; Xu, Xiaoshu; Nguyen, Cindy M; Liu, Yanxia; Gao, Yuchen; Lin, Xueqiu; Daley, Timothy; Kipniss, Nathan H; La Russa, Marie; Qi, Lei S | Cell. | 2018 Nov 15; | 30318144 | |
| The adult human testis transcriptional cell atlas. | Guo, Jingtao; Grow, Edward J; Mlcochova, Hana; Maher, Geoffrey J; Lindskog, Cecilia; Nie, Xichen; Guo, Yixuan; Takei, Yodai; Yun, Jina; Cai, Long; Kim, Robin; Carrell, Douglas T; Goriely, Anne; Hotaling, James M; Cairns, Bradley R | Cell research. | 2018 Dec; | 30315278 | |
| Understanding molecular mechanisms of disease through spatial proteomics. | Pankow, Sandra; Martínez-Bartolomé, Salvador; Bamberger, Casimir; Yates, John R | Current opinion in chemical biology. | 2019 Feb; | 30308467 | |
| CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. | Daley, Timothy P; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei S | Genome biology. | 2018 10 08; | 30296940 | |
| The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. | Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N K; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, Feng | Genome biology. | 2018 10 04; | 30286773 | |
| RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. | Chen, Weizhong; Yan, Zhangming; Li, Simin; Huang, Norman; Huang, Xuerui; Zhang, Jin; Zhong, Sheng | iScience. | 2018 Jun 29; | 30240742 | |
| Blank spots on the map: some current questions on nuclear organization and genome architecture. | Adriaens, Carmen; Serebryannyy, Leonid A; Feric, Marina; Schibler, Andria; Meaburn, Karen J; Kubben, Nard; Trzaskoma, Pawel; Shachar, Sigal; Vidak, Sandra; Finn, Elizabeth H; Sood, Varun; Pegoraro, Gianluca; Misteli, Tom | Histochemistry and cell biology. | 2018 Dec; | 30238154 | |
| X-Chromosome Inactivation and Escape from X Inactivation in Mouse. | Ma, Wenxiu; Bonora, Giancarlo; Berletch, Joel B; Deng, Xinxian; Noble, William S; Disteche, Christine M | Methods in molecular biology (Clifton, N.J.). | 2018; | 30218369 | |
| Experimental and computational framework for a dynamic protein atlas of human cell division. | Cai, Yin; Hossain, M Julius; Hériché, Jean-Karim; Politi, Antonio Z; Walther, Nike; Koch, Birgit; Wachsmuth, Malte; Nijmeijer, Bianca; Kueblbeck, Moritz; Martinic-Kavur, Marina; Ladurner, Rene; Alexander, Stephanie; Peters, Jan-Michael; Ellenberg, Jan | Nature. | 2018 09; | 30202089 | |
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| 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 | |
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