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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 (427)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Switchable resolution in soft x-ray tomography of single cells. | Weinhardt, Venera; Chen, Jian-Hua; Ekman, Axel A; Guo, Jessica; Remesh, Soumya G; Hammel, Michal; McDermott, Gerry; Chao, Weilun; Oh, Sharon; Le Gros, Mark A; Larabell, Carolyn A | PloS one. | 2020; | 31978064 | |
| Co-opted transposons help perpetuate conserved higher-order chromosomal structures. | Choudhary, Mayank Nk; Friedman, Ryan Z; Wang, Julia T; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, Ting | Genome biology. | 2020 01 24; | 31973766 | |
| MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. | Tian, Dechao; Zhang, Ruochi; Zhang, Yang; Zhu, Xiaopeng; Ma, Jian | Genome research. | 2020 Jan 06; | 31907193 | |
| Physics and Biology (of Chromosomes). | Marko, John F | Journal of molecular biology. | 2020 Jan 17; | 31866291 | |
| OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. | An, Lin; Yang, Tao; Yang, Jiahao; Nuebler, Johannes; Xiang, Guanjue; Hardison, Ross C; Li, Qunhua; Zhang, Yu | Genome biology. | 2019 12 18; | 31847870 | |
| The epigenomic landscape of transposable elements across normal human development and anatomy. | Pehrsson, Erica C; Choudhary, Mayank N K; Sundaram, Vasavi; Wang, Ting | Nature communications. | 2019 Dec 10; | 31822674 | |
| Localization microscopy at doubled precision with patterned illumination. | Cnossen, Jelmer; Hinsdale, Taylor; Thorsen, Rasmus Ø; Siemons, Marijn; Schueder, Florian; Jungmann, Ralf; Smith, Carlas S; Rieger, Bernd; Stallinga, Sjoerd | Nature methods. | 2020 Jan; | 31819263 | |
| Guided nuclear exploration increases CTCF target search efficiency. | Hansen, Anders S; Amitai, Assaf; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | Nature chemical biology. | 2019 Dec 02; | 31792445 | |
| Probing and engineering liquid-phase organelles. | Bracha, Dan; Walls, Mackenzie T; Brangwynne, Clifford P | Nature biotechnology. | 2019 12; | 31792412 | |
| Chromatin structure dynamics during the mitosis-to-G1 phase transition. | Zhang, Haoyue; Emerson, Daniel J; Gilgenast, Thomas G; Titus, Katelyn R; Lan, Yemin; Huang, Peng; Zhang, Di; Wang, Hongxin; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Phillips-Cremins, Jennifer E; Blobel, Gerd A | Nature. | 2019 12; | 31776509 | |
| Tasks, Techniques, and Tools for Genomic Data Visualization. | Nusrat, S; Harbig, T; Gehlenborg, N | Computer graphics forum : journal of the European Association for Computer Graphics. | 2019 Jun; | 31768085 | |
| Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. | Xiong, Kyle; Ma, Jian | Nature communications. | 2019 11 07; | 31699985 | |
| A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. | Abramo, Kristin; Valton, Anne-Laure; Venev, Sergey V; Ozadam, Hakan; Fox, A Nicole; Dekker, Job | Nature cell biology. | 2019 Nov; | 31685986 | |
| X Inactivation and Escape: Epigenetic and Structural Features. | Fang, He; Disteche, Christine M; Berletch, Joel B | Frontiers in cell and developmental biology. | 2019; | 31632970 | |
| Mapping RNA-chromatin interactions by sequencing with iMARGI. | Wu, Weixin; Yan, Zhangming; Nguyen, Tri C; Bouman Chen, Zhen; Chien, Shu; Zhong, Sheng | Nature protocols. | 2019 Nov; | 31619811 | |
| Photoactivation of silicon rhodamines via a light-induced protonation. | Frei, Michelle S; Hoess, Philipp; Lampe, Marko; Nijmeijer, Bianca; Kueblbeck, Moritz; Ellenberg, Jan; Wadepohl, Hubert; Ries, Jonas; Pitsch, Stefan; Reymond, Luc; Johnsson, Kai | Nature communications. | 2019 Oct 08; | 31594948 | |
| Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. | McSwiggen, David T; Mir, Mustafa; Darzacq, Xavier; Tjian, Robert | Genes & development. | 2019 12 01; | 31594803 | |
| Cronos Titin Is Expressed in Human Cardiomyocytes and Necessary for Normal Sarcomere Function. | Zaunbrecher, Rebecca J; Abel, Ashley N; Beussman, Kevin; Leonard, Andrea; von Frieling-Salewsky, Marion; Fields, Paul A; Pabon, Lil; Reinecke, Hans; Yang, Xiulan; Macadangdang, Jesse; Kim, Deok-Ho; Linke, Wolfgang A; Sniadecki, Nathan J; Regnier, Michael; Murry, Charles E | Circulation. | 2019 Nov 12; | 31587567 | |
| How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. | Erba?, Aykut; Marko, John F | Current opinion in chemical biology. | 2019 Oct 02; | 31586479 | |
| Highly structured homolog pairing reflects functional organization of the Drosophila genome. | AlHaj Abed, Jumana; Erceg, Jelena; Goloborodko, Anton; Nguyen, Son C; McCole, Ruth B; Saylor, Wren; Fudenberg, Geoffrey; Lajoie, Bryan R; Dekker, Job; Mirny, Leonid A; Wu, C-Ting | Nature communications. | 2019 Oct 03; | 31582763 | |
| The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. | Erceg, Jelena; AlHaj Abed, Jumana; Goloborodko, Anton; Lajoie, Bryan R; Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; McCole, Ruth B; Nguyen, Son C; Saylor, Wren; Joyce, Eric F; Senaratne, T Niroshini; Hannan, Mohammed A; Nir, Guy; Dekker, Job; Mirny, Leonid A; Wu, C-Ting | Nature communications. | 2019 Oct 03; | 31582744 | |
| Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells. | Yang, Xiulan; Rodriguez, Marita L; Leonard, Andrea; Sun, Lihua; Fischer, Karin A; Wang, Yuliang; Ritterhoff, Julia; Zhao, Limei; Kolwicz Jr, Stephen C; Pabon, Lil; Reinecke, Hans; Sniadecki, Nathan J; Tian, Rong; Ruohola-Baker, Hannele; Xu, Haodong; Murry | Stem cell reports. | 2019 10 08; | 31564645 | |
| Nuclear pores as versatile reference standards for quantitative superresolution microscopy. | Thevathasan, Jervis Vermal; Kahnwald, Maurice; Cie?li?ski, Konstanty; Hoess, Philipp; Peneti, Sudheer Kumar; Reitberger, Manuel; Heid, Daniel; Kasuba, Krishna Chaitanya; Hoerner, Sarah Janice; Li, Yiming; Wu, Yu-Le; Mund, Markus; Matti, Ulf; Pereira, Pedro Matos; Henriques, Ricardo; Nijmeijer, Bianca; Kueblbeck, Moritz; Sabinina, Vilma Jimenez; Ellenberg, Jan; Ries, Jonas | Nature methods. | 2019 Oct; | 31562488 | |
| Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. | Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Lee, Choli; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun | Methods (San Diego, Calif.). | 2019 Sep 16; | 31536770 | |
| Jonathan R. Warner (1936-2019)-pioneer of ribosome biosynthesis. | Pederson, Thoru | RNA (New York, N.Y.). | 2019 Dec; | 31534010 | |
| Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. | Hansen, Anders S; Hsieh, Tsung-Han S; Cattoglio, Claudia; Pustova, Iryna; Saldaña-Meyer, Ricardo; Reinberg, Danny; Darzacq, Xavier; Tjian, Robert | Molecular cell. | 2019 11 07; | 31522987 | |
| The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. | Zhang, Yu; Zhang, Xuefei; Ba, Zhaoqing; Liang, Zhuoyi; Dring, Edward W; Hu, Hongli; Lou, Jiangman; Kyritsis, Nia; Zurita, Jeffrey; Shamim, Muhammad S; Presser Aiden, Aviva; Lieberman Aiden, Erez; Alt, Frederick W | Nature. | 2019 Sep; | 31511698 | |
| Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. | Ray, Judhajeet; Munn, Paul R; Vihervaara, Anniina; Lewis, James J; Ozer, Abdullah; Danko, Charles G; Lis, John T | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Sep 24; | 31506350 | |
| Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods. | 2019 Oct; | 31501545 | |
| High-Throughput Single-Cell Sequencing with Linear Amplification. | Yin, Yi; Jiang, Yue; Lam, Kwan-Wood Gabriel; Berletch, Joel B; Disteche, Christine M; Noble, William S; Steemers, Frank J; Camerini-Otero, R Daniel; Adey, Andrew C; Shendure, Jay | Molecular cell. | 2019 Aug 28; | 31495564 | |
| Olfactory receptor genes make the case for inter-chromosomal interactions. | Bashkirova, Elizaveta; Lomvardas, Stavros | Current opinion in genetics & development. | 2019 Apr; | 31491591 | |
| CRISPR-mediated live imaging of genome editing and transcription. | Wang, Haifeng; Nakamura, Muneaki; Abbott, Timothy R; Zhao, Dehua; Luo, Kaiwen; Yu, Cordelia; Nguyen, Cindy M; Lo, Albert; Daley, Timothy P; La Russa, Marie; Liu, Yanxia; Qi, Lei S | Science (New York, N.Y.). | 2019 09 20; | 31488703 | |
| Molecular basis and biological function of variability in spatial genome organization. | Finn, Elizabeth H; Misteli, Tom | Science (New York, N.Y.). | 2019 09 06; | 31488662 | |
| A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole | Nature genetics. | 2019 Sep; | 31477929 | |
| Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets. | Lekschas, Fritz; Behrisch, Michael; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2020 Jan; | 31442989 | |
| Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. | Wei, Chia-Lin; Nicolis, Silvia K; Zhu, Yanfen; Pagin, Miriam | Journal of experimental neuroscience. | 2019; | 31431802 | |
| Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. | Zhang, Yanxiao; Li, Ting; Preissl, Sebastian; Amaral, Maria Luisa; Grinstein, Jonathan D; Farah, Elie N; Destici, Eugin; Qiu, Yunjiang; Hu, Rong; Lee, Ah Young; Chee, Sora; Ma, Kaiyue; Ye, Zhen; Zhu, Quan; Huang, Hui; Fang, Rongxin; Yu, Leqian; Izpisua Belmonte, Juan Carlos; Wu, Jun; Evans, Sylvia M; Chi, Neil C; Ren, Bing | Nature genetics. | 2019 Sep; | 31427791 | |
| Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. | Dahlke, Katelyn; Zhao, Jing; Sing, Charles E; Banigan, Edward J | Biophysical journal. | 2019 Sep 17; | 31427067 | |
| Controlling the material properties and rRNA processing function of the nucleolus using light. | Zhu, Lian; Richardson, Tiffany M; Wacheul, Ludivine; Wei, Ming-Tzo; Feric, Marina; Whitney, Gena; Lafontaine, Denis L J; Brangwynne, Clifford P | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Aug 09; | 31399547 | |
| Visual Pattern-Driven Exploration of Big Data. | Behrisch, Michael; Schreck, Tobias; Krüger, Robert; Gehlenborg, Nils; Lekschas, Fritz; Pfister, Hanspeter | 2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany). | 2018 Oct; | 31396383 | |
| Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. | Bertero, Alessandro; Fields, Paul A; Smith, Alec S T; Leonard, Andrea; Beussman, Kevin; Sniadecki, Nathan J; Kim, Deok-Ho; Tse, Hung-Fat; Pabon, Lil; Shendure, Jay; Noble, William S; Murry, Charles E | The Journal of cell biology. | 2019 Sep 02; | 31395619 | |
| Genome organization around nuclear speckles. | Chen, Yu; Belmont, Andrew S | Current opinion in genetics & development. | 2019 Apr; | 31394307 | |
| Learn from Your Elders: Developmental Biology Lessons to Guide Maturation of Stem Cell-Derived Cardiomyocytes. | Marchianò, Silvia; Bertero, Alessandro; Murry, Charles E | Pediatric cardiology. | 2019 Oct; | 31388700 | |
| Joint profiling of DNA methylation and chromatin architecture in single cells. | Li, Guoqiang; Liu, Yaping; Zhang, Yanxiao; Kubo, Naoki; Yu, Miao; Fang, Rongxin; Kellis, Manolis; Ren, Bing | Nature methods. | 2019 Oct; | 31384045 | |
| Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. | Stephens, Andrew D; Liu, Patrick Z; Kandula, Viswajit; Chen, Haimei; Almassalha, Luay M; Herman, Cameron; Backman, Vadim; O'Halloran, Thomas; Adam, Stephen A; Goldman, Robert D; Banigan, Edward J; Marko, John F | Molecular biology of the cell. | 2019 Aug 01; | 31365328 | |
| Cooler: scalable storage for Hi-C data and other genomically-labeled arrays. | Abdennur, Nezar; Mirny, Leonid | Bioinformatics (Oxford, England). | 2019 Jul 10; | 31290943 | |
| Archiving and disseminating integrative structure models. | Vallat, Brinda; Webb, Benjamin; Westbrook, John; Sali, Andrej; Berman, Helen M | Journal of biomolecular NMR. | 2019 Jul; | 31278630 | |
| A subset of topologically associating domains fold into mesoscale core-periphery networks. | Huang, Harvey; Chen, Sunnia T; Titus, Katelyn R; Emerson, Daniel J; Bassett, Danielle S; Phillips-Cremins, Jennifer E | Scientific reports. | 2019 Jul 02; | 31266973 | |
| 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 | |
| Two major mechanisms of chromosome organization. | Mirny, Leonid A; Imakaev, Maxim; Abdennur, Nezar | Current opinion in cell biology. | 2019 Jun; | 31228682 | |
| Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data. | Rosenthal, Michael; Bryner, Darshan; Huffer, Fred; Evans, Shane; Srivastava, Anuj; Neretti, Nicola | Journal of computational biology : a journal of computational molecular cell biology. | 2019 Nov; | 31211598 | |
| 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 | |
| Heterochromatin drives compartmentalization of inverted and conventional nuclei. | Falk, Martin; Feodorova, Yana; Naumova, Natalia; Imakaev, Maxim; Lajoie, Bryan R; Leonhardt, Heinrich; Joffe, Boris; Dekker, Job; Fudenberg, Geoffrey; Solovei, Irina; Mirny, Leonid A | Nature. | 2019 Jun; | 31168090 | |
| WashU Epigenome Browser update 2019. | Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Sears, Renee L; Wang, Ting | Nucleic acids research. | 2019 Jul 02; | 31165883 | |
| Principles for Integrative Structural Biology Studies. | Rout, Michael P; Sali, Andrej | Cell. | 2019 May 30; | 31150619 | |
| 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 | |
| EpiAlignment: alignment with both DNA sequence and epigenomic data. | Lu, Jia; Cao, Xiaoyi; Zhong, Sheng | Nucleic acids research. | 2019 Jul 02; | 31114924 | |
| Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. | Li, Peipei; Marshall, Lee; Oh, Gabriel; Jakubowski, Jennifer L; Groot, Daniel; He, Yu; Wang, Ting; Petronis, Arturas; Labrie, Viviane | Nature communications. | 2019 05 21; | 31113950 | |
| Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx. | Möckl, Leonhard; Pedram, Kayvon; Roy, Anish R; Krishnan, Venkatesh; Gustavsson, Anna-Karin; Dorigo, Oliver; Bertozzi, Carolyn R; Moerner, W E | Developmental cell. | 2019 Jul 01; | 31105009 | |
| Long-range enhancer-promoter contacts in gene expression control. | Schoenfelder, Stefan; Fraser, Peter | Nature reviews. Genetics. | 2019 08; | 31086298 | |
| 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 | |
| Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. | Jean-Baptiste, Ken; McFaline-Figueroa, José L; Alexandre, Cristina M; Dorrity, Michael W; Saunders, Lauren; Bubb, Kerry L; Trapnell, Cole; Fields, Stanley; Queitsch, Christine; Cuperus, Josh T | The Plant cell. | 2019 05; | 30923229 | |
| 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 | |
| Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. | Gilgenast, Thomas G; Phillips-Cremins, Jennifer E | Cell systems. | 2019 Mar 27; | 30904376 | |
| 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 | |
| Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells. | Al Bkhetan, Ziad; Kadlof, Michal; Kraft, Agnieszka; Plewczynski, Dariusz | Methods (San Diego, Calif.). | 2019 Aug 15; | 30853548 | |
| 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 | |
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| 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 | |
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| 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 | |
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| 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 | |
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| Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, Stavros | eLife. | 2017 Sep 21; | 28933695 | |
| Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. | Huang, Peng; Keller, Cheryl A; Giardine, Belinda; Grevet, Jeremy D; Davies, James O J; Hughes, Jim R; Kurita, Ryo; Nakamura, Yukio; Hardison, Ross C; Blobel, Gerd A | Genes & development. | 2017 Aug 15; | 28916711 | |
| Targeting Specificity of the CRISPR/Cas9 System. | Tasan, Ipek; Zhao, Huimin | ACS synthetic biology. | 2017 09 15; | 28911233 | |
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| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting | BMC genomics. | 2017 Sep 12; | 28899353 | |
| Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. | Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P | Molecular cell. | 2017 Sep 21; | 28890333 | |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang, Yang; Zhang, Ruochi; Singh, Shashank; Ma, Jian | Bioinformatics (Oxford, England). | 2017 Jul 15; | 28881991 | |
| LAIT: a local ancestry inference toolkit. | Hui, Daniel; Fang, Zhou; Lin, Jerome; Duan, Qing; Li, Yun; Hu, Ming; Chen, Wei | BMC genetics. | 2017 09 06; | 28877673 | |
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| The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality? | Bach, Benjamin; Sicat, Ronell; Beyer, Johanna; Cordeil, Maxime; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2018 01; | 28866590 | |
| HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. | Yang, Tao; Zhang, Feipeng; Yard?mc?, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua | Genome research. | 2017 Nov; | 28855260 | |
| Crossed wires: 3D genome misfolding in human disease. | Norton, Heidi K; Phillips-Cremins, Jennifer E | The Journal of cell biology. | 2017 11 06; | 28855250 | |
| Evolutionarily Conserved Principles Predict 3D Chromatin Organization. | Rowley, M Jordan; Nichols, Michael H; Lyu, Xiaowen; Ando-Kuri, Masami; Rivera, I Sarahi M; Hermetz, Karen; Wang, Ping; Ruan, Yijun; Corces, Victor G | Molecular cell. | 2017 Sep 07; | 28826674 | |
| Reversed graph embedding resolves complex single-cell trajectories. | Qiu, Xiaojie; Mao, Qi; Tang, Ying; Wang, Li; Chawla, Raghav; Pliner, Hannah A; Trapnell, Cole | Nature methods. | 2017 Oct; | 28825705 | |
| SMC complexes differentially compact mitotic chromosomes according to genomic context. | Schalbetter, Stephanie Andrea; Goloborodko, Anton; Fudenberg, Geoffrey; Belton, Jon-Matthew; Miles, Catrina; Yu, Miao; Dekker, Job; Mirny, Leonid; Baxter, Jonathan | Nature cell biology. | 2017 Sep; | 28825700 | |
| Comprehensive single-cell transcriptional profiling of a multicellular organism. | Cao, Junyue; Packer, Jonathan S; Ramani, Vijay; Cusanovich, Darren A; Huynh, Chau; Daza, Riza; Qiu, Xiaojie; Lee, Choli; Furlan, Scott N; Steemers, Frank J; Adey, Andrew; Waterston, Robert H; Trapnell, Cole; Shendure, Jay | Science (New York, N.Y.). | 2017 08 18; | 28818938 | |
| A magnetic micropore chip for rapid ( | Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, David | Lab on a chip. | 2017 Sep 12; | 28809985 | |
| Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. | Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P; Xu, Jianliang; Jung, Seolkyoung; Pekowska, Aleksandra; Dose, Marei; Stevens, Evan; Mathe, Ewy; Dong, Peng; Huang, Su-Chen; Ricci, Maria Aurelia; Baranello, Laura; Zheng, Ying; Tomassoni Ardori, Francesco; Resch, Wolfgang; Stavreva, Diana; Nelson, Steevenson; McAndrew, Michael; Casellas, Adriel; Finn, Elizabeth; Gregory, Charles; St Hilaire, Brian Glenn; Johnson, Steven M; Dubois, Wendy; Cosma, Maria Pia; Batchelor, Eric; Levens, David; Phair, Robert D; Misteli, Tom; Tessarollo, Lino; Hager, Gordon; Lakadamyali, Melike; Liu, Zhe; Floer, Monique; Shroff, Hari; Aiden, Erez Lieberman; Casellas, Rafael | Molecular cell. | ; | 28803781 | |
| A new era of studying p53-mediated transcription activation. | Liu, Wei-Li; Coleman, Robert A; Singh, Sameer K | Transcription. | 2018; | 28795863 | |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual review of cell and developmental biology. | 2017 Oct 06; | 28783961 | |
| Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. | Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger D | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Aug 15; | 28765367 | |
| The three-dimensional genome organization of Drosophila melanogaster through data integration. | Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank | Genome biology. | 2017 Jul 31; | 28760140 | |
| ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. | Ou, Horng D; Phan, Sébastien; Deerinck, Thomas J; Thor, Andrea; Ellisman, Mark H; O'Shea, Clodagh C | Science (New York, N.Y.). | 2017 07 28; | 28751582 | |
| Genome Organization Drives Chromosome Fragility. | Canela, Andres; Maman, Yaakov; Jung, Seolkyoung; Wong, Nancy; Callen, Elsa; Day, Amanda; Kieffer-Kwon, Kyong-Rim; Pekowska, Aleksandra; Zhang, Hongliang; Rao, Suhas S P; Huang, Su-Chen; Mckinnon, Peter J; Aplan, Peter D; Pommier, Yves; Aiden, Erez Lieberman; Casellas, Rafael; Nussenzweig, André | Cell. | 2017 Jul 27; | 28735753 | |
| Integrative modelling of cellular assemblies. | Joseph, Agnel Praveen; Polles, Guido; Alber, Frank; Topf, Maya | Current opinion in structural biology. | 2017 Jul 20; | 28735107 | |
| Cell-cycle dynamics of chromosomal organization at single-cell resolution. | Nagano, Takashi; Lubling, Yaniv; Várnai, Csilla; Dudley, Carmel; Leung, Wing; Baran, Yael; Mendelson Cohen, Netta; Wingett, Steven; Fraser, Peter; Tanay, Amos | Nature. | 2017 07 05; | 28682332 | |
| Phase separation drives heterochromatin domain formation. | Strom, Amy R; Emelyanov, Alexander V; Mir, Mustafa; Fyodorov, Dmitry V; Darzacq, Xavier; Karpen, Gary H | Nature. | 2017 07 13; | 28636597 | |
| Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. | Sun, Xiaoming; Bizhanova, Aizhan; Matheson, Timothy D; Yu, Jun; Zhu, Julie L; Kaufman, Paul D | Molecular and cellular biology. | 2017 Jun 19; | 28630280 | |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari, Sumitabha; Marko, John F | Physical review. E. | 2017 May; | 28618488 | |
| DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. | Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis J | JCI insight. | 2017 Jun 15; | 28614801 | |
| EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He, Yu; Wang, Ting | Bioinformatics (Oxford, England). | 2017 Jun 09; | 28605501 | |
| DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. | Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; | Nature genetics. | 2017 Jul; | 28604729 | |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H | Nature methods. | 2017 Jun 12; | 28604724 | |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg, Geoffrey; Imakaev, Maxim | Nature methods. | 2017 Jul; | 28604723 | |
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| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, Ting | BMC genomics. | 2017 Jun 05; | 28583088 | |
| HUGIn: Hi-C Unifying Genomic Interrogator. | Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2017 Dec 01; | 28582503 | |
| The dynamic three-dimensional organization of the diploid yeast genome. | Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya J | eLife. | 2017 May 24; | 28537556 | |
| YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. | Beagan, Jonathan A; Duong, Michael T; Titus, Katelyn R; Zhou, Linda; Cao, Zhendong; Ma, Jingjing; Lachanski, Caroline V; Gillis, Daniel R; Phillips-Cremins, Jennifer E | Genome research. | 2017 07; | 28536180 | |
| Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. | Nora, Elphège P; Goloborodko, Anton; Valton, Anne-Laure; Gibcus, Johan H; Uebersohn, Alec; Abdennur, Nezar; Dekker, Job; Mirny, Leonid A; Bruneau, Benoit G | Cell. | 2017 May 18; | 28525758 | |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel, Bas; Belmont, Andrew S | Cell. | 2017 May 18; | 28525751 | |
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| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan J | Nature methods. | 2017 Jun; | 28481362 | |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | eLife. | 2017 May 03; | 28467304 | |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Current biology : CB. | 2017 May 08; | 28457866 | |
| Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. | Belaghzal, Houda; Dekker, Job; Gibcus, Johan H | Methods (San Diego, Calif.). | 2017 Apr 18; | 28435001 | |
| Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long | Biophysical journal. | 2017 May 09; | 28427715 | |
| p53 dynamically directs TFIID assembly on target gene promoters. | Coleman, R A; Qiao, Z; Singh, S K; Peng, C S; Cianfrocco, M; Zhang, Z; Piasecka, A; Aldeborgh, H; Basishvili, G; Liu, W L | Molecular and cellular biology. | 2017 Apr 17; | 28416636 | |
| An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. | Gunn, Kathryn H; Marko, John F; Mondragón, Alfonso | Nature structural & molecular biology. | 2017 May; | 28414321 | |
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| Facilitated dissociation of transcription factors from single DNA binding sites. | Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 18; | 28364020 | |
| Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. | Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun | Nature protocols. | 2017 May; | 28358394 | |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté, Allison J; Raj, Arjun | Biophysical journal. | 2017 Mar 28; | 28355532 | |
| Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. | Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë | Nature. | 2017 04 06; | 28355183 | |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting | Nature communications. | 2017 Mar 28; | 28348391 | |
| Form and function of topologically associating genomic domains in budding yeast. | Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 11; | 28348222 | |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman | Science (New York, N.Y.). | 2017 Apr 07; | 28336562 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS one. | 2017; | 28333948 | |
| Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. | Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem; Bandaria, Jigar; Mir, Mustafa; Szlachta, Karol; Singh, Ritambhara; Darzacq, Xavier; Yildiz, Ahmet; Adli, Mazhar | Nature communications. | 2017 Mar 14; | 28290446 | |
| Unearthing worm replication origins. | Sasaki, Takayo; Gilbert, David M | Nature structural & molecular biology. | 2017 03 03; | 28257138 | |
| Multivalent Small-Molecule Pan-RAS Inhibitors. | Welsch, Matthew E; Kaplan, Anna; Chambers, Jennifer M; Stokes, Michael E; Bos, Pieter H; Zask, Arie; Zhang, Yan; Sanchez-Martin, Marta; Badgley, Michael A; Huang, Christine S; Tran, Timothy H; Akkiraju, Hemanth; Brown, Lewis M; Nandakumar, Renu; Cremers, Serge; Yang, Wan Seok; Tong, Liang; Olive, Kenneth P; Ferrando, Adolfo; Stockwell, Brent R | Cell. | ; | 28235199 | |
| Epigenetic characteristics of the mitotic chromosome in 1D and 3D. | Oomen, Marlies E; Dekker, Job | Critical reviews in biochemistry and molecular biology. | 2017 Apr; | 28228067 | |
| A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. | Xiong, Xiong; Zhang, Yanxiao; Yan, Jian; Jain, Surbhi; Chee, Sora; Ren, Bing; Zhao, Huimin | ACS synthetic biology. | 2017 Mar 07; | 28215080 | |
| Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. | Finn, Elizabeth H; Pegoraro, Gianluca; Shachar, Sigal; Misteli, Tom | Methods (San Diego, Calif.). | 2017 Jul 01; | 28179124 | |
| Comprehensive characterization of neutrophil genome topology. | Zhu, Yina; Gong, Ke; Denholtz, Matthew; Chandra, Vivek; Kamps, Mark P; Alber, Frank; Murre, Cornelis | Genes & development. | 2017 Jan 15; | 28167501 | |
| Software tools for visualizing Hi-C data. | Yard?mc?, Galip Gürkan; Noble, William Stafford | Genome biology. | 2017 Feb 03; | 28159004 | |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu, Sharmistha; Ji, Fei; Sunwoo, Hongjae; Jain, Gaurav; Lee, Jeannie T; Sadreyev, Ruslan I; Dekker, Job; Kingston, Robert E | Molecular cell. | 2017 Feb 02; | 28157505 | |
| Massively multiplex single-cell Hi-C. | Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Gunderson, Kevin L; Steemers, Frank J; Disteche, Christine M; Noble, William S; Duan, Zhijun; Shendure, Jay | Nature methods. | 2017 Mar; | 28135255 | |
| High-throughput automated microfluidic sample preparation for accurate microbial genomics. | Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C | Nature communications. | 2017 Jan 27; | 28128213 | |
| ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis. | Li, Zhaomin; Zhang, Peng; Yan, Aimin; Guo, Zhengyu; Ban, Yuguang; Li, Jin; Chen, Shi; Yang, Hui; He, Yongzheng; Li, Jianping; Guo, Ying; Zhang, Wen; Hajiramezanali, Ehsan; An, Huangda; Fajardo, Darlene; Harbour, J William; Ruan, Yijun; Nimer, Stephen D; Yu, Peng; Chen, Xi; Xu, Mingjiang; Yang, Feng-Chun | Science advances. | 2017 Jan; | 28116354 | |
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| 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 | |
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