Publications Search by Program
Search Result
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 (465)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| A supervised learning framework for chromatin loop detection in genome-wide contact maps. | Salameh, Tarik J; Wang, Xiaotao; Song, Fan; Zhang, Bo; Wright, Sage M; Khunsriraksakul, Chachrit; Ruan, Yijun; Yue, Feng | Nature communications. | 2020 Jul 09; | 32647330 | |
| Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. | Liu, Shuli; Yu, Ying; Zhang, Shengli; Cole, John B; Tenesa, Albert; Wang, Ting; McDaneld, Tara G; Ma, Li; Liu, George E; Fang, Lingzhao | BMC biology. | 2020 Jul 03; | 32620158 | |
| Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. | Chen, Xiaoying; Zhang, Bo; Wang, Ting; Bonni, Azad; Zhao, Guoyan | BMC bioinformatics. | 2020 Jun 29; | 32600248 | |
| Comparison of differential accessibility analysis strategies for ATAC-seq data. | Gontarz, Paul; Fu, Shuhua; Xing, Xiaoyun; Liu, Shaopeng; Miao, Benpeng; Bazylianska, Viktoriia; Sharma, Akhil; Madden, Pamela; Cates, Kitra; Yoo, Andrew; Moszczynska, Anna; Wang, Ting; Zhang, Bo | Scientific reports. | 2020 Jun 23; | 32576878 | |
| MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. | Zhang, Ruochi; Ma, Jian | Cell systems. | 2020 May 20; | 32550271 | |
| Evolving methodologies and concepts in 4D nucleome research. | Sparks, Thomas M; Harabula, Izabela; Pombo, Ana | Current opinion in cell biology. | 2020 May 27; | 32473574 | |
| Delta-1 Functionalized Hydrogel Promotes hESC-Cardiomyocyte Graft Proliferation and Maintains Heart Function Post-Injury. | Gerbin, Kaytlyn A; Mitzelfelt, Katie A; Guan, Xuan; Martinson, Amy M; Murry, Charles E | Molecular therapy. Methods & clinical development. | 2020 Jun 12; | 32426414 | |
| Composition-dependent thermodynamics of intracellular phase separation. | Riback, Joshua A; Zhu, Lian; Ferrolino, Mylene C; Tolbert, Michele; Mitrea, Diana M; Sanders, David W; Wei, Ming-Tzo; Kriwacki, Richard W; Brangwynne, Clifford P | Nature. | 2020 05; | 32405004 | |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh, Lea; Saint-Antoine, Michael; Sanford, Eric M; Emert, Benjamin L; Singh, Abhyudai; Marr, Carsten; Raj, Arjun; Goyal, Yogesh | Cell systems. | 2020 Apr 22; | 32325034 | |
| Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. | Schreiber, Jacob; Durham, Timothy; Bilmes, Jeffrey; Noble, William Stafford | Genome biology. | 2020 03 30; | 32228704 | |
| Distinct features of nucleolus-associated domains in mouse embryonic stem cells. | Bizhanova, Aizhan; Yan, Aimin; Yu, Jun; Zhu, Lihua Julie; Kaufman, Paul D | Chromosoma. | 2020 Mar 26; | 32219510 | |
| Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. | Zhao, Binhui; Chaturvedi, Pankaj; Zimmerman, David L; Belmont, Andrew S | ACS synthetic biology. | 2020 05 15; | 32216371 | |
| Ultrastructural Details of Mammalian Chromosome Architecture. | Krietenstein, Nils; Abraham, Sameer; Venev, Sergey V; Abdennur, Nezar; Gibcus, Johan; Hsieh, Tsung-Han S; Parsi, Krishna Mohan; Yang, Liyan; Maehr, René; Mirny, Leonid A; Dekker, Job; Rando, Oliver J | Molecular cell. | 2020 Mar 14; | 32213324 | |
| High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. | Zhao, Peiyao A; Sasaki, Takayo; Gilbert, David M | Genome biology. | 2020 03 24; | 32209126 | |
| Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems. | Masnadi-Shirazi, Maryam; Subramaniam, Shankar | Scientific reports. | 2020 Mar 02; | 32123218 | |
| Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. | Lee, Hyung Joo; Hou, Yiran; Chen, Yujie; Dailey, Zea Z; Riddihough, Aiyana; Jang, Hyo Sik; Wang, Ting; Johnson, Stephen L | Genome biology. | 2020 02 27; | 32106888 | |
| Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. | Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Wang, Wenbo; Goldfeder, Rachel L; Choi, Cindy; He, Hao; Gong, Liang; Lin, Junyan; Urban, Barbara; Chow, Julianna; Li, Meihong; Lim, Joanne; Philip, Vivek; Murray, Stephen A; Wang, Haoyi; Wei, Chia-Lin | Nature genetics. | 2020 03; | 32094912 | |
| Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation. | Biswas, Jeetayu; Nunez, Leti; Das, Sulagna; Yoon, Young J; Eliscovich, Carolina; Singer, Robert H | Cold Spring Harbor symposia on quantitative biology. | 2020 Feb 21; | 32086331 | |
| Local rewiring of genome-nuclear lamina interactions by transcription. | Brueckner, Laura; Zhao, Peiyao A; van Schaik, Tom; Leemans, Christ; Sima, Jiao; Peric-Hupkes, Daniel; Gilbert, David M; van Steensel, Bas | The EMBO journal. | 2020 Mar 16; | 32080885 | |
| An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. | Kim, Arthur S; Zimmerman, Ofer; Fox, Julie M; Nelson, Christopher A; Basore, Katherine; Zhang, Rong; Durnell, Lorellin; Desai, Chandni; Bullock, Christopher; Deem, Sharon L; Oppenheimer, Jonas; Shapiro, Beth; Wang, Ting; Cherry, Sara; Coyne, Carolyn B; Ha | Cell host & microbe. | 2020 03 11; | 32075743 | |
| Chemogenetic Control of Nanobodies. | Farrants, Helen; Tarnawski, Miroslaw; Müller, Thorsten G; Otsuka, Shotaro; Hiblot, Julien; Koch, Birgit; Kueblbeck, Moritz; Kräusslich, Hans-Georg; Ellenberg, Jan; Johnsson, Kai | Nature methods. | 2020 03; | 32066961 | |
| ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL. | Wutz, Gordana; Ladurner, Rene; St Hilaire, Brian Glenn; Stocsits, Roman R; Nagasaka, Kota; Pignard, Benoit; Sanborn, Adrian; Tang, Wen; Várnai, Csilla; Ivanov, Miroslav P; Schoenfelder, Stefan; van der Lelij, Petra; Huang, Xingfan; Dürnberger, Gerhard; Roitinger, Elisabeth; Mechtler, Karl; Davidson, Iain Finley; Fraser, Peter; Lieberman-Aiden, Erez; Peters, Jan-Michael | eLife. | 2020 Feb 17; | 32065581 | |
| Derivation of trophoblast stem cells from naïve human pluripotent stem cells. | Dong, Chen; Beltcheva, Mariana; Gontarz, Paul; Zhang, Bo; Popli, Pooja; Fischer, Laura A; Khan, Shafqat A; Park, Kyoung-Mi; Yoon, Eun-Ja; Xing, Xiaoyun; Kommagani, Ramakrishna; Wang, Ting; Solnica-Krezel, Lilianna; Theunissen, Thorold W | eLife. | 2020 Feb 12; | 32048992 | |
| Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine. | Karbassi, Elaheh; Fenix, Aidan; Marchiano, Silvia; Muraoka, Naoto; Nakamura, Kenta; Yang, Xiulan; Murry, Charles E | Nature reviews. Cardiology. | 2020 Feb 03; | 32015528 | |
| Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. | Feodorova, Yana; Falk, Martin; Mirny, Leonid A; Solovei, Irina | Trends in cell biology. | 2020 Apr; | 31980345 | |
| 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 | |
| Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts. | Weyers, Jill J; Gunaje, Jagadambika J; Van Biber, Benjamin; Martinson, Amy; Reinecke, Hans; Mahoney, William M; Schwartz, Stephen M; Cox, Timothy C; Murry, Charles E | PloS one. | 2020; | 31945113 | |
| 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 | |
| An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms. | Yu, Yi; Guo, Yijun; Tian, Qiqi; Lan, Yuanqing; Yeh, Hugh; Zhang, Meng; Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Nature chemical biology. | 2020 04; | 31873222 | |
| Physics and Biology (of Chromosomes). | Marko, John F | Journal of molecular biology. | 2020 Jan 17; | 31866291 | |
| Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells. | Chen, Changya; Yu, Wenbao; Tober, Joanna; Gao, Peng; He, Bing; Lee, Kiwon; Trieu, Tuan; Blobel, Gerd A; Speck, Nancy A; Tan, Kai | Cell reports. | 2019 12 17; | 31851943 | |
| 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 | |
| Chromatin Is Frequently Unknotted at the Megabase Scale. | Goundaroulis, Dimos; Lieberman Aiden, Erez; Stasiak, Andrzej | Biophysical journal. | 2020 May 05; | 31818464 | |
| 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 | |
| Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. | Fulco, Charles P; Nasser, Joseph; Jones, Thouis R; Munson, Glen; Bergman, Drew T; Subramanian, Vidya; Grossman, Sharon R; Anyoha, Rockwell; Doughty, Benjamin R; Patwardhan, Tejal A; Nguyen, Tung H; Kane, Michael; Perez, Elizabeth M; Durand, Neva C; Lareau | Nature genetics. | 2019 12; | 31784727 | |
| 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 | |
| Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. | Brahmachari, Sumitabha; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2019 12 10; | 31757850 | |
| Gene expression amplification by nuclear speckle association. | Kim, Jiah; Venkata, Neha Chivukula; Hernandez Gonzalez, Gabriela Andrea; Khanna, Nimish; Belmont, Andrew S | The Journal of cell biology. | 2020 Jan 06; | 31757787 | |
| Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. | Xiong, Kyle; Ma, Jian | Nature communications. | 2019 11 07; | 31699985 | |
| A Proteomic Perspective on Cardiomyocyte Maturation. | Muraoka, Naoto; Sun, Bingyun; Murry, Charles E | Circulation research. | 2019 11 08; | 31697629 | |
| 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 | |
| Methods for comparative ChIA-PET and Hi-C data analysis. | Capurso, Dan; Tang, Zhonghui; Ruan, Yijun | Methods (San Diego, Calif.). | 2020 01 01; | 31629084 | |
| 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 | |
| Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. | Lari, Azra; Farzam, Farzin; Bensidoun, Pierre; Oeffinger, Marlene; Zenklusen, Daniel; Grunwald, David; Montpetit, Ben | Methods in molecular biology (Clifton, N.J.). | 2019; | 31407282 | |
| 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 | |
| Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells. | Bianco, Simona; Annunziatella, Carlo; Andrey, Guillaume; Chiariello, Andrea M; Esposito, Andrea; Fiorillo, Luca; Prisco, Antonella; Conte, Mattia; Campanile, Raffaele; Nicodemi, Mario | Cell reports. | 2019 08 06; | 31390570 | |
| 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 | |
| Chromatin's physical properties shape the nucleus and its functions. | Stephens, Andrew D; Banigan, Edward J; Marko, John F | Current opinion in cell biology. | 2019 06; | 30889417 | |
| 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 | |
| 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 | |
| Multiplex chromatin interactions with single-molecule precision. | Zheng, Meizhen; Tian, Simon Zhongyuan; Capurso, Daniel; Kim, Minji; Maurya, Rahul; Lee, Byoungkoo; Piecuch, Emaly; Gong, Liang; Zhu, Jacqueline Jufen; Li, Zhihui; Wong, Chee Hong; Ngan, Chew Yee; Wang, Ping; Ruan, Xiaoan; Wei, Chia-Lin; Ruan, Yijun | Nature. | 2019 02; | 30778195 | |
| 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 | |
| Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. | Shin, Yongdae; Chang, Yi-Che; Lee, Daniel S W; Berry, Joel; Sanders, David W; Ronceray, Pierre; Wingreen, Ned S; Haataja, Mikko; Brangwynne, Clifford P | Cell. | 2018 Nov 29; | 30500535 | |
| 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 | |
| The interdependence of gene-regulatory elements and the 3D genome. | Vermunt, Marit W; Zhang, Di; Blobel, Gerd A | The Journal of cell biology. | 2019 01 07; | 30442643 | |
| 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 | |
| PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. | Kordon, Magdalena M; Szczurek, Aleksander; Berniak, Krzysztof; Szelest, Oskar; Solarczyk, Kamil; Tworzyd?o, Magdalena; Wachsmann-Hogiu, Sebastian; Vaahtokari, Anne; Cremer, Christoph; Pederson, Thoru; Dobrucki, Jurek W | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2019 02; | 30260704 | |
| 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 | |
| Integrative detection and analysis of structural variation in cancer genomes. | Dixon, Jesse R; Xu, Jie; Dileep, Vishnu; Zhan, Ye; Song, Fan; Le, Victoria T; Yard?mc?, Galip Gürkan; Chakraborty, Abhijit; Bann, Darrin V; Wang, Yanli; Clark, Royden; Zhang, Lijun; Yang, Hongbo; Liu, Tingting; Iyyanki, Sriranga; An, Lin; Pool, Christophe | Nature genetics. | 2018 Sep 10; | 30202056 | |
| Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. | Skoruppa, Enrico; Nomidis, Stefanos K; Marko, John F; Carlon, Enrico | Physical review letters. | 2018 Aug 24; | 30192578 | |
| Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. | Zhu, Liangliang; Yan, Feihu; Wang, Zhen; Dong, Haiyan; Bian, Chengling; Wang, Ting; Yu, Enda; Li, Jing | International journal of cancer. | 2018 Nov 15; | 30183087 | |
| Interchromosomal interactions: A genomic love story of kissing chromosomes. | Maass, Philipp G; Barutcu, A Rasim; Rinn, John L | The Journal of cell biology. | 2019 Jan 07; | 30181316 | |
| RNA, Action through Interactions. | Nguyen, Tri C; Zaleta-Rivera, Kathia; Huang, Xuerui; Dai, Xiaofeng; Zhong, Sheng | Trends in genetics : TIG. | 2018 Aug 31; | 30177410 | |
| Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. | Sun, James H; Zhou, Linda; Emerson, Daniel J; Phyo, Sai A; Titus, Katelyn R; Gong, Wanfeng; Gilgenast, Thomas G; Beagan, Jonathan A; Davidson, Beverly L; Tassone, Flora; Phillips-Cremins, Jennifer E | Cell. | 2018 Aug 27; | 30173918 | |
| Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. | van Steensel, Bas | EMBO reports. | 2018 Oct; | 30158143 | |
| Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. | Chen, Yu; Zhang, Yang; Wang, Yuchuan; Zhang, Liguo; Brinkman, Eva K; Adam, Stephen A; Goldman, Robert; van Steensel, Bas; Ma, Jian; Belmont, Andrew S | The Journal of cell biology. | 2018 Aug 28; | 30154186 | |
| The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. | Munschauer, Mathias; Nguyen, Celina T; Sirokman, Klara; Hartigan, Christina R; Hogstrom, Larson; Engreitz, Jesse M; Ulirsch, Jacob C; Fulco, Charles P; Subramanian, Vidya; Chen, Jenny; Schenone, Monica; Guttman, Mitchell; Carr, Steven A; Lander, Eric S | Nature. | 2018 09; | 30150775 | |
| Emerging Roles of Non-Coding RNA Transcription. | Kaikkonen, Minna U; Adelman, Karen | Trends in biochemical sciences. | 2018 09; | 30145998 | |
| Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. | Sun, Mingxuan; Biggs, Ronald; Hornick, Jessica; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2018 Dec; | 30143891 | |
| HiGlass: web-based visual exploration and analysis of genome interaction maps. | Kerpedjiev, Peter; Abdennur, Nezar; Lekschas, Fritz; McCallum, Chuck; Dinkla, Kasper; Strobelt, Hendrik; Luber, Jacob M; Ouellette, Scott B; Azhir, Alaleh; Kumar, Nikhil; Hwang, Jeewon; Lee, Soohyun; Alver, Burak H; Pfister, Hanspeter; Mirny, Leonid A; Pa | Genome biology. | 2018 08 24; | 30143029 | |
| DXR: A Toolkit for Building Immersive Data Visualizations. | Sicat, Ronell; Li, Jiabao; Choi, Junyoung; Cordeil, Maxime; Jeong, Won-Ki; Bach, Benjamin; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2019 01; | 30136991 | |
| Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan | The Journal of cell biology. | 2018 Sep 03; | 30135095 | |
| Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. | Wray-Dutra, Michelle N; Chawla, Raghav; Thomas, Kerri R; Seymour, Brenda J; Arkatkar, Tanvi; Sommer, Karen M; Khim, Socheath; Trapnell, Cole; James, Richard G; Rawlings, David J | The Journal of experimental medicine. | 2018 Sep 03; | 30127060 | |
| Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model. | Zhang, Rongrong; Hu, Ming; Zhu, Yu; Qin, Zhaohui; Deng, Ke; Liu, Jun S | IEEE/ACM transactions on computational biology and bioinformatics. | 2020 Mar-Apr; | 30113897 | |
| One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. | Lazniewski, Michal; Dawson, Wayne K; Rusek, Anna Maria; Plewczynski, Dariusz | Seminars in cell & developmental biology. | 2018 Oct 11; | 30096365 | |
| Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. | Pliner, Hannah A; Packer, Jonathan S; McFaline-Figueroa, José L; Cusanovich, Darren A; Daza, Riza M; Aghamirzaie, Delasa; Srivatsan, Sanjay; Qiu, Xiaojie; Jackson, Dana; Minkina, Anna; Adey, Andrew C; Steemers, Frank J; Shendure, Jay; Trapnell, Cole | Molecular cell. | 2018 09 06; | 30078726 | |
| A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. | Cusanovich, Darren A; Hill, Andrew J; Aghamirzaie, Delasa; Daza, Riza M; Pliner, Hannah A; Berletch, Joel B; Filippova, Galina N; Huang, Xingfan; Christiansen, Lena; DeWitt, William S; Lee, Choli; Regalado, Samuel G; Read, David F; Steemers, Frank J; Dist | Cell. | 2018 Aug 23; | 30078704 | |
| Protein motion in the nucleus: from anomalous diffusion to weak interactions. | Woringer, Maxime; Darzacq, Xavier | Biochemical Society transactions. | 2018 Aug 20; | 30065106 | |
| Temporal dynamics of pair-rule stripes in living Drosophila embryos. | Lim, Bomyi; Fukaya, Takashi; Heist, Tyler; Levine, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2018 08 14; | 30061421 | |
| Dynamic interplay between enhancer-promoter topology and gene activity. | Chen, Hongtao; Levo, Michal; Barinov, Lev; Fujioka, Miki; Jaynes, James B; Gregor, Thomas | Nature genetics. | 2018 Sep; | 30038397 | |
| Comparison of OCT Angiography Review Strategies to Identify Vascular Abnormalities in the AVATAR Study. | Babiuch, Amy S; Khan, Mehnaz; Hu, Ming; Kaiser, Peter K; Srivastava, Sunil K; Singh, Rishi P; Watts, Allison; Reese, Jamie L; Ehlers, Justis P | Ophthalmology. Retina. | 2018 Jun; | 30035246 | |
| The three-dimensional organization of the genome in cellular senescence and age-associated diseases. | Evans, Shane A; Horrell, Jeremy; Neretti, Nicola | Seminars in cell & developmental biology. | 2019 Jun; | 30031215 | |
| Computational methods for analyzing and modeling genome structure and organization. | Lin, Dejun; Bonora, Giancarlo; Yard?mc?, Galip Gürkan; Noble, William S | Wiley interdisciplinary reviews. Systems biology and medicine. | 2018 Jul 18; | 30022617 | |
| The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. | Menghi, Francesca; Barthel, Floris P; Yadav, Vinod; Tang, Ming; Ji, Bo; Tang, Zhonghui; Carter, Gregory W; Ruan, Yijun; Scully, Ralph; Verhaak, Roel G W; Jonkers, Jos; Liu, Edison T | Cancer cell. | 2018 08 13; | 30017478 | |
| GIVE: portable genome browsers for personal websites. | Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng | Genome biology. | 2018 07 18; | 30016975 | |
| Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. | Packer, Jonathan; Trapnell, Cole | Trends in genetics : TIG. | ; | 30007833 | |
| Understanding the 3D genome: Emerging impacts on human disease. | Krumm, Anton; Duan, Zhijun | Seminars in cell & developmental biology. | 2019 Jun; | 29990539 | |
| 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. | 2018 Jul 05; | 29979966 | |
| Chromatin organization by an interplay of loop extrusion and compartmental segregation. | Nuebler, Johannes; Fudenberg, Geoffrey; Imakaev, Maxim; Abdennur, Nezar; Mirny, Leonid A | Proceedings of the National Academy of Sciences of the United States of America. | 2018 07 17; | 29967174 | |
| Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. | Limi, Saima; Senecal, Adrien; Coleman, Robert; Lopez-Jones, Melissa; Guo, Peng; Polumbo, Christina; Singer, Robert H; Skoultchi, Arthur I; Cvekl, Ales | The Journal of biological chemistry. | 2018 Aug 24; | 29959226 | |
| Quantitative live and super-resolution microscopy of mitotic chromosomes. | Walther, Nike; Ellenberg, Jan | Methods in cell biology. | 2018; | 29957216 | |
| Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. | Mir, Mustafa; Reimer, Armando; Stadler, Michael; Tangara, Astou; Hansen, Anders S; Hockemeyer, Dirk; Eisen, Michael B; Garcia, Hernan; Darzacq, Xavier | Methods in molecular biology (Clifton, N.J.). | 2018; | 29956254 | |
| Unsupervised embedding of single-cell Hi-C data. | Liu, Jie; Lin, Dejun; Yardimci, Galip Gürkan; Noble, William Stafford | Bioinformatics (Oxford, England). | 2018 07 01; | 29950005 | |
| Predicting CTCF-mediated chromatin loops using CTCF-MP. | Zhang, Ruochi; Wang, Yuchuan; Yang, Yang; Zhang, Yang; Ma, Jian | Bioinformatics (Oxford, England). | 2018 Jul 01; | 29949986 | |
| Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. | Sabath, Niv; Vilborg, Anna; Steitz, Joan A; Shalgi, Reut | Human genomics. | 2018 06 27; | 29945683 | |
| Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction. | Lei, Xiao; Shi, Haoran; Kou, Yi; Rajashekar, Niroop; Wu, Fang; Sen, Chandani; Xu, Jiang; Chen, Lin | Biochemistry. | 2018 07 17; | 29944822 | |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I; Raj, Arjun; Li, Mingyao; Zhang, Nancy R | Nature methods. | 2018 Jul; | 29941873 | |
| A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. | Teves, Sheila S; An, Luye; Bhargava-Shah, Aarohi; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert | eLife. | 2018 06 25; | 29939130 | |
| Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. | Yang, Yang; Gu, Quanquan; Zhang, Yang; Sasaki, Takayo; Crivello, Julianna; O'Neill, Rachel J; Gilbert, David M; Ma, Jian | Cell systems. | 2018 Jun 18; | 29936186 | |
| Imaging dynamic and selective low-complexity domain interactions that control gene transcription. | Chong, Shasha; Dugast-Darzacq, Claire; Liu, Zhe; Dong, Peng; Dailey, Gina M; Cattoglio, Claudia; Heckert, Alec; Banala, Sambashiva; Lavis, Luke; Darzacq, Xavier; Tjian, Robert | Science (New York, N.Y.). | 2018 07 27; | 29930090 | |
| CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. | Tasan, Ipek; Sustackova, Gabriela; Zhang, Liguo; Kim, Jiah; Sivaguru, Mayandi; HamediRad, Mohammad; Wang, Yuchuan; Genova, Justin; Ma, Jian; Belmont, Andrew S; Zhao, Huimin | Nucleic acids research. | 2018 Jun 15; | 29912475 | |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah, Sheel; Takei, Yodai; Zhou, Wen; Lubeck, Eric; Yun, Jina; Eng, Chee-Huat Linus; Koulena, Noushin; Cronin, Christopher; Karp, Christoph; Liaw, Eric J; Amin, Mina; Cai, Long | Cell. | 2018 May 31; | 29887381 | |
| Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. | Quinodoz, Sofia A; Ollikainen, Noah; Tabak, Barbara; Palla, Ali; Schmidt, Jan Marten; Detmar, Elizabeth; Lai, Mason M; Shishkin, Alexander A; Bhat, Prashant; Takei, Yodai; Trinh, Vickie; Aznauryan, Erik; Russell, Pamela; Cheng, Christine; Jovanovic, Marko; Chow, Amy; Cai, Long; McDonel, Patrick; Garber, Manuel; Guttman, Mitchell | Cell. | 2018 Jun 04; | 29887377 | |
| Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers. | Bardales, Jorge A; Wieser, Evin; Kawaji, Hideya; Murakawa, Yasuhiro; Darzacq, Xavier | Genes. | 2018 May 23; | 29882899 | |
| Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. | Dine, Elliot; Gil, Agnieszka A; Uribe, Giselle; Brangwynne, Clifford P; Toettcher, Jared E | Cell systems. | 2018 Jun 27; | 29859829 | |
| Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. | Lu, Huasong; Yu, Dan; Hansen, Anders S; Ganguly, Sourav; Liu, Rongdiao; Heckert, Alec; Darzacq, Xavier; Zhou, Qiang | Nature. | 2018 06; | 29849146 | |
| Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging. | Politi, Antonio Z; Cai, Yin; Walther, Nike; Hossain, M Julius; Koch, Birgit; Wachsmuth, Malte; Ellenberg, Jan | Nature protocols. | 2018 06; | 29844523 | |
| Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. | Koch, Birgit; Nijmeijer, Bianca; Kueblbeck, Moritz; Cai, Yin; Walther, Nike; Ellenberg, Jan | Nature protocols. | 2018 06; | 29844520 | |
| Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods. | Chen, Chun Chieh; Stark, Marie; Baikoghli, Mo; Cheng, R Holland | Journal of visualized experiments : JoVE. | 2018 05 11; | 29806824 | |
| Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. | Gustavsson, Anna-Karin; Petrov, Petar N; Moerner, W E | Optics express. | 2018 May 14; | 29801343 | |
| Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. | Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Jarvis, James N | Journal of reproductive immunology. | 2018 Aug; | 29800761 | |
| 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. | Kim, Ji Hun; Titus, Katelyn R; Gong, Wanfeng; Beagan, Jonathan A; Cao, Zhendong; Phillips-Cremins, Jennifer E | Methods (San Diego, Calif.). | ; | 29772275 | |
| Quantitative imaging of chromatin decompaction in living cells. | Dultz, Elisa; Mancini, Roberta; Polles, Guido; Vallotton, Pascal; Alber, Frank; Weis, Karsten | Molecular biology of the cell. | ; | 29771637 | |
| Gene regulation in the 3D genome. | Li, Yun; Hu, Ming; Shen, Yin | Human molecular genetics. | 2018 08 01; | 29767704 | |
| qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. | Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I | Scientific reports. | ; | 29743503 | |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. | Gao, Xin D; Tu, Li-Chun; Mir, Aamir; Rodriguez, Tomás; Ding, Yuehe; Leszyk, John; Dekker, Job; Shaffer, Scott A; Zhu, Lihua Julie; Wolfe, Scot A; Sontheimer, Erik J | Nature methods. | 2018 May 07; | 29735996 | |
| Allele-specific control of replication timing and genome organization during development. | Rivera-Mulia, Juan Carlos; Dimond, Andrew; Vera, Daniel; Trevilla-Garcia, Claudia; Sasaki, Takayo; Zimmerman, Jared; Dupont, Catherine; Gribnau, Joost; Fraser, Peter; Gilbert, David M | Genome research. | 2018 06; | 29735606 | |
| Emerging Evidence of Chromosome Folding by Loop Extrusion. | Fudenberg, Geoffrey; Abdennur, Nezar; Imakaev, Maxim; Goloborodko, Anton; Mirny, Leonid A | Cold Spring Harbor symposia on quantitative biology. | 2017; | 29728444 | |
| The Energetics and Physiological Impact of Cohesin Extrusion. | Vian, Laura; P?kowska, Aleksandra; Rao, Suhas S P; Kieffer-Kwon, Kyong-Rim; Jung, Seolkyoung; Baranello, Laura; Huang, Su-Chen; El Khattabi, Laila; Dose, Marei; Pruett, Nathanael; Sanborn, Adrian L; Canela, Andres; Maman, Yaakov; Oksanen, Anna; Resch, Wolfgang; Li, Xingwang; Lee, Byoungkoo; Kovalchuk, Alexander L; Tang, Zhonghui; Nelson, Steevenson; Di Pierro, Michele; Cheng, Ryan R; Machol, Ido; St Hilaire, Brian Glenn; Durand, Neva C; Shamim, Muhammad S; Stamenova, Elena K; Onuchic, José N; Ruan, Yijun; Nussenzweig, Andre; Levens, David; Aiden, Erez Lieberman; Casellas, Rafael | Cell. | 2018 May 17; | 29706548 | |
| Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. | Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E | Proceedings of SPIE--the International Society for Optical Engineering. | 2018 Feb; | 29681676 | |
| Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes. | Tsai, Albert; Singer, Robert H; Crocker, Justin | Molecular cell. | 2018 Apr 19; | 29677489 | |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. | Bonora, G; Deng, X; Fang, H; Ramani, V; Qiu, R; Berletch, J B; Filippova, G N; Duan, Z; Shendure, J; Noble, W S; Disteche, C M | Nature communications. | 2018 Apr 13; | 29654302 | |
| Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia. | Carvajal, Luis A; Neriah, Daniela Ben; Senecal, Adrien; Benard, Lumie; Thiruthuvanathan, Victor; Yatsenko, Tatyana; Narayanagari, Swathi-Rao; Wheat, Justin C; Todorova, Tihomira I; Mitchell, Kelly; Kenworthy, Charles; Guerlavais, Vincent; Annis, D Allen; Bartholdy, Boris; Will, Britta; Anampa, Jesus D; Mantzaris, Ioannis; Aivado, Manuel; Singer, Robert H; Coleman, Robert A; Verma, Amit; Steidl, Ulrich | Science translational medicine. | 2018 Apr 11; | 29643228 | |
| A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. | Walther, Nike; Hossain, M Julius; Politi, Antonio Z; Koch, Birgit; Kueblbeck, Moritz; Ødegård-Fougner, Øyvind; Lampe, Marko; Ellenberg, Jan | The Journal of cell biology. | 2018 Apr 09; | 29632028 | |
| Real-time 3D single-molecule localization using experimental point spread functions. | Li, Yiming; Mund, Markus; Hoess, Philipp; Deschamps, Joran; Matti, Ulf; Nijmeijer, Bianca; Sabinina, Vilma Jimenez; Ellenberg, Jan; Schoen, Ingmar; Ries, Jonas | Nature methods. | 2018 May; | 29630062 | |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L | Molecular cell. | 2018 Apr 05; | 29625035 | |
| Producing genome structure populations with the dynamic and automated PGS software. | Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank | Nature protocols. | 2018 May; | 29622804 | |
| Visualization of Transvection in Living Drosophila Embryos. | Lim, Bomyi; Heist, Tyler; Levine, Michael; Fukaya, Takashi | Molecular cell. | 2018 Apr 19; | 29606591 | |
| Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. | Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M | Nature protocols. | 2018 May; | 29599440 | |
| Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. | Scientific reports. | 2018 Mar 26; | 29581440 | ||
| Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan | The Journal of cell biology. | 2018 Jun 04; | 29572382 | |
| Three-dimensional organization and dynamics of the genome. | Szalaj, Przemyslaw; Plewczynski, Dariusz | Cell biology and toxicology. | 2018 Oct; | 29568981 | |
| Effects of electrostatic interactions on ligand dissociation kinetics. | Erba?, Aykut; de la Cruz, Monica Olvera; Marko, John F | Physical review. E. | 2018 Feb; | 29548245 | |
| Defect-facilitated buckling in supercoiled double-helix DNA. | Brahmachari, Sumitabha; Dittmore, Andrew; Takagi, Yasuharu; Neuman, Keir C; Marko, John F | Physical review. E. | 2018 Feb; | 29548184 | |
| Integrative structure and functional anatomy of a nuclear pore complex. | Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P | Nature. | 2018 Mar 22; | 29539637 | |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass, Philipp G; Barutcu, A Rasim; Weiner, Catherine L; Rinn, John L | Molecular cell. | 2018 Mar 15; | 29526697 | |
| Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. | Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto; Hopp, Hannah; Das, Devika; Alber, Frank; Chiolo, Irene | Methods in enzymology. | ; | 29523239 | |
| Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin. | Annunziatella, Carlo; Chiariello, Andrea M; Esposito, Andrea; Bianco, Simona; Fiorillo, Luca; Nicodemi, Mario | Methods (San Diego, Calif.). | 2018 06 01; | 29522804 | |
| ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. | Barton, Carl; Morganella, Sandro; Ødegård-Fougner, Øyvind; Alexander, Stephanie; Ries, Jonas; Fitzgerald, Tomas; Ellenberg, Jan; Birney, Ewan | PLoS computational biology. | 2018 Mar; | 29522506 | |
| dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. | Tsui, Chiahao; Inouye, Carla; Levy, Michaella; Lu, Andrew; Florens, Laurence; Washburn, Michael P; Tjian, Robert | Proceedings of the National Academy of Sciences of the United States of America. | 2018 03 20; | 29507191 | |
| Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations. | Stevens, Kelly R; Murry, Charles E | Cell stem cell. | 2018 Mar 01; | 29499147 | |
| Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. | Patriarchi, Tommaso; Shen, Ao; He, Wei; Baikoghli, Mo; Cheng, R Holland; Xiang, Yang K; Coleman, Matthew A; Tian, Lin | Scientific reports. | 2018 Feb 23; | 29476125 | |
| Quantitative 3-D morphometric analysis of individual dendritic spines. | Basu, Subhadip; Saha, Punam Kumar; Roszkowska, Matylda; Magnowska, Marta; Baczynska, Ewa; Das, Nirmal; Plewczynski, Dariusz; Wlodarczyk, Jakub | Scientific reports. | 2018 Feb 23; | 29476060 | |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun | Cell systems. | 2018 Feb 28; | 29454938 | |
| Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. | Robinson, James T; Turner, Douglass; Durand, Neva C; Thorvaldsdóttir, Helga; Mesirov, Jill P; Aiden, Erez Lieberman | Cell systems. | 2018 Feb 28; | 29428417 | |
| Single-cell replication profiling to measure stochastic variation in mammalian replication timing. | Dileep, Vishnu; Gilbert, David M | Nature communications. | 2018 Jan 30; | 29382831 | |
| Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. | Ma, Wenxiu; Ay, Ferhat; Lee, Choli; Gulsoy, Gunhan; Deng, Xinxian; Cook, Savannah; Hesson, Jennifer; Cavanaugh, Christopher; Ware, Carol B; Krumm, Anton; Shendure, Jay; Blau, C Anthony; Disteche, Christine M; Noble, William S; Duan, ZhiJun | Methods (San Diego, Calif.). | 2018 Jan 31; | 29382556 | |
| Dynamic evolution of regulatory element ensembles in primate CD4+T cells. | Danko, Charles G; Choate, Lauren A; Marks, Brooke A; Rice, Edward J; Wang, Zhong; Chu, Tinyi; Martins, Andre L; Dukler, Noah; Coonrod, Scott A; Tait Wojno, Elia D; Lis, John T; Kraus, W Lee; Siepel, Adam | Nature ecology & evolution. | 2018 Mar; | 29379187 | |
| A pathway for mitotic chromosome formation. | Gibcus, Johan H; Samejima, Kumiko; Goloborodko, Anton; Samejima, Itaru; Naumova, Natalia; Nuebler, Johannes; Kanemaki, Masato T; Xie, Linfeng; Paulson, James R; Earnshaw, William C; Mirny, Leonid A; Dekker, Job | Science (New York, N.Y.). | 2018 02 09; | 29348367 | |
| Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). | Maass, Philipp G; Barutcu, A Rasim; Shechner, David M; Weiner, Catherine L; Melé, Marta; Rinn, John L | Nature structural & molecular biology. | 2018 Feb; | 29343869 | |
| High-throughput identification of RNA nuclear enrichment sequences. | Shukla, Chinmay J; McCorkindale, Alexandra L; Gerhardinger, Chiara; Korthauer, Keegan D; Cabili, Moran N; Shechner, David M; Irizarry, Rafael A; Maass, Philipp G; Rinn, John L | The EMBO journal. | 2018 Mar 15; | 29335281 | |
| Detecting hierarchical genome folding with network modularity. | Norton, Heidi K; Emerson, Daniel J; Huang, Harvey; Kim, Jesi; Titus, Katelyn R; Gu, Shi; Bassett, Danielle S; Phillips-Cremins, Jennifer E | Nature methods. | 2018 Feb; | 29334377 | |
| Ki-67: more than a proliferation marker. | Sun, Xiaoming; Kaufman, Paul D | Chromosoma. | 2018 Jan 10; | 29322240 | |
| 3D single-molecule super-resolution microscopy with a tilted light sheet. | Gustavsson, Anna-Karin; Petrov, Petar N; Lee, Maurice Y; Shechtman, Yoav; Moerner, W E | Nature communications. | 2018 Jan 09; | 29317629 | |
| Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. | Yan, Jian; Chen, Shi-An A; Local, Andrea; Liu, Tristin; Qiu, Yunjiang; Dorighi, Kristel M; Preissl, Sebastian; Rivera, Chloe M; Wang, Chaochen; Ye, Zhen; Ge, Kai; Hu, Ming; Wysocka, Joanna; Ren, Bing | Cell research. | 2018 Feb; | 29313530 | |
| Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. | Gerace, Larry; Tapia, Olga | Current opinion in cell biology. | 2018 Jun; | 29306725 | |
| Robust model-based analysis of single-particle tracking experiments with Spot-On. | Hansen, Anders S; Woringer, Maxime; Grimm, Jonathan B; Lavis, Luke D; Tjian, Robert; Darzacq, Xavier | eLife. | 2018 Jan 04; | 29300163 | |
| Extrusion without a motor: a new take on the loop extrusion model of genome organization. | Brackley, C A; Johnson, J; Michieletto, D; Morozov, A N; Nicodemi, M; Cook, P R; Marenduzzo, D | Nucleus (Austin, Tex.). | 2018 01 01; | 29300120 | |
| Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions. | Shechtman, Yoav; Gustavsson, Anna-Karin; Petrov, Petar N; Dultz, Elisa; Lee, Maurice Y; Weis, Karsten; Moerner, W E | Biomedical optics express. | 2017 Dec 01; | 29296501 | |
| A mixed-scale dense convolutional neural network for image analysis. | Pelt, Daniël M; Sethian, James A | Proceedings of the National Academy of Sciences of the United States of America. | 2018 Jan 09; | 29279403 | |
| Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. | Baddeley, David; Bewersdorf, Joerg | Annual review of biochemistry. | 2018 06 20; | 29272143 | |
| The structural variability of the influenza A hemagglutinin receptor-binding site. | Lazniewski, Michal; Dawson, Wayne K; Szczepinska, Teresa; Plewczynski, Dariusz | Briefings in functional genomics. | 2018 11 26; | 29253080 | |
| Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. | Mukund, Kavitha; Subramaniam, Shankar | Frontiers in physiology. | 2017; | 29249983 | |
| Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. | Kaewsapsak, Pornchai; Shechner, David Michael; Mallard, William; Rinn, John L; Ting, Alice Y | eLife. | 2017 Dec 14; | 29239719 | |
| Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, Ting | Methods in molecular biology (Clifton, N.J.). | 2018; | 29224147 | |
| Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. | Brahmachari, Sumitabha; Gunn, Kathryn H; Giuntoli, Rebecca D; Mondragón, Alfonso; Marko, John F | Physical review letters. | 2017 Nov 03; | 29219598 | |
| Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. | Wutz, Gordana; Várnai, Csilla; Nagasaka, Kota; Cisneros, David A; Stocsits, Roman R; Tang, Wen; Schoenfelder, Stefan; Jessberger, Gregor; Muhar, Matthias; Hossain, M Julius; Walther, Nike; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Zuber, Johannes; | The EMBO journal. | 2017 12 15; | 29217591 | |
| A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. | Gassler, Johanna; Brandão, Hugo B; Imakaev, Maxim; Flyamer, Ilya M; Ladstätter, Sabrina; Bickmore, Wendy A; Peters, Jan-Michael; Mirny, Leonid A; Tachibana, Kikuë | The EMBO journal. | 2017 12 15; | 29217590 | |
| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. | Sundaram, Vasavi; Wang, Ting | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2018 Jan; | 29206283 | |
| Corrigendum: The 4D nucleome project. | Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network | Nature. | 2017 12 14; | 29168505 | |
| Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. | Stephens, Andrew D; Liu, Patrick Z; Banigan, Edward J; Almassalha, Luay M; Backman, Vadim; Adam, Stephen A; Goldman, Robert D; Marko, John F | Molecular biology of the cell. | 2018 Jan 15; | 29142071 | |
| Live Imaging of mRNA Synthesis in Drosophila. | Garcia, Hernan G; Gregor, Thomas | Methods in molecular biology (Clifton, N.J.). | 2018; | 29130209 | |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E C | Molecular psychiatry. | 2017 Nov 07; | 29112194 | |
| Nuclear microenvironments modulate transcription from low-affinity enhancers. | Tsai, Albert; Muthusamy, Anand K; Alves, Mariana Rp; Lavis, Luke D; Singer, Robert H; Stern, David L; Crocker, Justin | eLife. | 2017 Nov 02; | 29095143 | |
| Two independent modes of chromatin organization revealed by cohesin removal. | Schwarzer, Wibke; Abdennur, Nezar; Goloborodko, Anton; Pekowska, Aleksandra; Fudenberg, Geoffrey; Loe-Mie, Yann; Fonseca, Nuno A; Huber, Wolfgang; H Haering, Christian; Mirny, Leonid; Spitz, Francois | Nature. | 2017 Nov 02; | 29094699 | |
| Simultaneous measurement of emission color and 3D position of single molecules. | Smith, Carlas; Huisman, Max; Siemons, Marijn; Grünwald, David; Stallinga, Sjoerd | Optics express. | 2016 Mar 07; | 29092328 | |
| De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. | Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez; Wolynes, Peter G; Onuchic, José N | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Nov 14; | 29087948 | |
| Oligomerization and ATP stimulate condensin-mediated DNA compaction. | Keenholtz, Ross A; Dhanaraman, Thillaivillalan; Palou, Roger; Yu, Jia; D'Amours, Damien; Marko, John F | Scientific reports. | 2017 Oct 27; | 29079757 | |
| STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus. | Li, Peng; Mitra, Suman; Spolski, Rosanne; Oh, Jangsuk; Liao, Wei; Tang, Zhonghui; Mo, Fei; Li, Xingwang; West, Erin E; Gromer, Daniel; Lin, Jian-Xin; Liu, Chengyu; Ruan, Yijun; Leonard, Warren J | Proceedings of the National Academy of Sciences of the United States of America. | 2017 11 14; | 29078395 | |
| Recent evidence that TADs and chromatin loops are dynamic structures. | Hansen, Anders S; Cattoglio, Claudia; Darzacq, Xavier; Tjian, Robert | Nucleus (Austin, Tex.). | 2018 01 01; | 29077530 | |
| A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. | Gallagher, Michael D; Posavi, Marijan; Huang, Peng; Unger, Travis L; Berlyand, Yosef; Gruenewald, Analise L; Chesi, Alessandra; Manduchi, Elisabetta; Wells, Andrew D; Grant, Struan F A; Blobel, Gerd A; Brown, Christopher D; Chen-Plotkin, Alice S | American journal of human genetics. | 2017 Nov 02; | 29056226 | |
| Supercoiling DNA Locates Mismatches. | Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F; Neuman, Keir C | Physical review letters. | 2017 Oct 06; | 29053317 | |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan, Edward J; Stephens, Andrew D; Marko, John F | Biophysical journal. | 2017 Oct 17; | 29045860 | |
| RNA structure interactions and ribonucleoprotein processes of the influenza A virus. | Dawson, Wayne K; Lazniewski, Michal; Plewczynski, Dariusz | Briefings in functional genomics. | 2018 11 26; | 29040388 | |
| DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. | Sun, Zhe; Wang, Ting; Deng, Ke; Wang, Xiao-Feng; Lafyatis, Robert; Ding, Ying; Hu, Ming; Chen, Wei | Bioinformatics (Oxford, England). | 2018 01 01; | 29036318 | |
| Cohesin Loss Eliminates All Loop Domains. | Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian; Engreitz, Jesse M; Perez, Elizabeth M; Kieffer-Kwon, Kyong-Rim; Sanborn, Adrian L; Johnstone, Sarah E; Bascom, Gavin D; Bochkov, Ivan D; Huang, Xingfan; Shamim, Muhammad S; Shin, Jaeweon; Turner, Douglass; Ye, Ziyi; Omer, Arina D; Robinson, James T; Schlick, Tamar; Bernstein, Bradley E; Casellas, Rafael; Lander, Eric S; Aiden, Erez Lieberman | Cell. | 2017 Oct 05; | 28985562 | |
| Dense Bicoid hubs accentuate binding along the morphogen gradient. | Mir, Mustafa; Reimer, Armando; Haines, Jenna E; Li, Xiao-Yong; Stadler, Michael; Garcia, Hernan; Eisen, Michael B; Darzacq, Xavier | Genes & development. | 2017 Sep 01; | 28982761 | |
| Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. | Germier, Thomas; Kocanova, Silvia; Walther, Nike; Bancaud, Aurélien; Shaban, Haitham Ahmed; Sellou, Hafida; Politi, Antonio Zaccaria; Ellenberg, Jan; Gallardo, Franck; Bystricky, Kerstin | Biophysical journal. | 2017 Oct 03; | 28978433 | |
| From structure to function, how bioinformatics help to reveal functions of our genomes. | Zheng, Xiaoqi; Zhong, Sheng | Genome biology. | 2017 Sep 26; | 28950915 | |
| Structural aspects of the inactive X chromosome. | Bonora, Giancarlo; Disteche, Christine M | Philosophical transactions of the Royal Society of London. Series B, Biological sciences. | 2017 Nov 05; | 28947656 | |
| Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. | Isoda, Takeshi; Moore, Amanda J; He, Zhaoren; Chandra, Vivek; Aida, Masatoshi; Denholtz, Matthew; Piet van Hamburg, Jan; Fisch, Kathleen M; Chang, Aaron N; Fahl, Shawn P; Wiest, David L; Murre, Cornelis | Cell. | 2017 Sep 21; | 28938112 | |
| Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. | Rege, Mayuri; Phillips-Cremins, Jennifer E | Molecular cell. | 2017 Sep 21; | 28938095 | |
| Liquid phase condensation in cell physiology and disease. | Shin, Yongdae; Brangwynne, Clifford P | Science (New York, N.Y.). | 2017 09 22; | 28935776 | |
| 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 | |
| The 4D nucleome project. | Dekker, Job; Belmont, Andrew S; Guttman, Mitchell; Leshyk, Victor O; Lis, John T; Lomvardas, Stavros; Mirny, Leonid A; O'Shea, Clodagh C; Park, Peter J; Ren, Bing; Politz, Joan C Ritland; Shendure, Jay; Zhong, Sheng; 4D Nucleome Network | Nature. | 2017 Sep 13; | 28905911 | |
| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting | BMC genomics. | 2017 Sep 12; | 28899353 | |
| Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. | Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek; Hess, Gaelen T; Shamim, Muhammad Saad; Machol, Ido; Love, Michael I; Aiden, Erez Lieberman; Bassik, Michael C; Snyder, Michael P | Molecular cell. | 2017 Sep 21; | 28890333 | |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| 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 | |
| HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. | Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics. | 2018 Jan; | 28866592 | |
| 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 | |
| Engineering biological systems using automated biofoundries. | Chao, Ran; Mishra, Shekhar; Si, Tong; Zhao, Huimin | Metabolic engineering. | 2017 Jul; | 28602523 | |
| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, Ting | BMC genomics. | 2017 Jun 05; | 28583088 | |
| HUGIn: Hi-C Unifying Genomic Interrogator. | Martin, Joshua S; Xu, Zheng; Reiner, Alex P; Mohlke, Karen L; Sullivan, Patrick; Ren, Bing; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2017 Dec 01; | 28582503 | |
| The dynamic three-dimensional organization of the diploid yeast genome. | Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G; Cook, Kate; Noble, William S; Brickner, Jason H; Shendure, Jay; Dunham, Maitreya J | eLife. | 2017 May 24; | 28537556 | |
| 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 | |
| Combinatorial chemistry in drug discovery. | Liu, Ruiwu; Li, Xiaocen; Lam, Kit S | Current opinion in chemical biology. | 2017 Jun; | 28494316 | |
| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan J | Nature methods. | 2017 Jun; | 28481362 | |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen, Anders S; Pustova, Iryna; Cattoglio, Claudia; Tjian, Robert; Darzacq, Xavier | eLife. | 2017 May 03; | 28467304 | |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Current biology : CB. | 2017 May 08; | 28457866 | |
| Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. | Belaghzal, Houda; Dekker, Job; Gibcus, Johan H | Methods (San Diego, Calif.). | 2017 Apr 18; | 28435001 | |
| 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 | |
| Causes and consequences of nuclear gene positioning. | Shachar, Sigal; Misteli, Tom | Journal of cell science. | 2017 May 01; | 28404786 | |
| The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. | Hsu, Sarah C; Gilgenast, Thomas G; Bartman, Caroline R; Edwards, Christopher R; Stonestrom, Aaron J; Huang, Peng; Emerson, Daniel J; Evans, Perry; Werner, Michael T; Keller, Cheryl A; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Phillips-Cremins, Jenn | Molecular cell. | 2017 Apr 06; | 28388437 | |
| Facilitated dissociation of transcription factors from single DNA binding sites. | Kamar, Ramsey I; Banigan, Edward J; Erbas, Aykut; Giuntoli, Rebecca D; Olvera de la Cruz, Monica; Johnson, Reid C; Marko, John F | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 18; | 28364020 | |
| Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. | Li, Xingwang; Luo, Oscar Junhong; Wang, Ping; Zheng, Meizhen; Wang, Danjuan; Piecuch, Emaly; Zhu, Jacqueline Jufen; Tian, Simon Zhongyuan; Tang, Zhonghui; Li, Guoliang; Ruan, Yijun | Nature protocols. | 2017 May; | 28358394 | |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté, Allison J; Raj, Arjun | Biophysical journal. | 2017 Mar 28; | 28355532 | |
| Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. | Flyamer, Ilya M; Gassler, Johanna; Imakaev, Maxim; Brandão, Hugo B; Ulianov, Sergey V; Abdennur, Nezar; Razin, Sergey V; Mirny, Leonid A; Tachibana-Konwalski, Kikuë | Nature. | 2017 04 06; | 28355183 | |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, Ting | Nature communications. | 2017 Mar 28; | 28348391 | |
| Form and function of topologically associating genomic domains in budding yeast. | Eser, Umut; Chandler-Brown, Devon; Ay, Ferhat; Straight, Aaron F; Duan, Zhijun; Noble, William Stafford; Skotheim, Jan M | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Apr 11; | 28348222 | |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman | Science (New York, N.Y.). | 2017 Apr 07; | 28336562 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS one. | 2017; | 28333948 | |
| Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. | Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem; Bandaria, Jigar; Mir, Mustafa; Szlachta, Karol; Singh, Ritambhara; Darzacq, Xavier; Yildiz, Ahmet; Adli, Mazhar | Nature communications. | 2017 Mar 14; | 28290446 | |
| Unearthing worm replication origins. | Sasaki, Takayo; Gilbert, David M | Nature structural & molecular biology. | 2017 03 03; | 28257138 | |
| 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 | |
| Single-cell mRNA quantification and differential analysis with Census. | Qiu, Xiaojie; Hill, Andrew; Packer, Jonathan; Lin, Dejun; Ma, Yi-An; Trapnell, Cole | Nature methods. | 2017 Mar; | 28114287 | |
| Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. | Chao, Ran; Liang, Jing; Tasan, Ipek; Si, Tong; Ju, Linyang; Zhao, Huimin | ACS synthetic biology. | 2017 Apr 21; | 28103009 | |
| Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. | Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, Ting | Neoplasia (New York, N.Y.). | 2017 Feb; | 28088687 | |
| A New Era of Genome Integration-Simply Cut and Paste! | Liu, Zihe; Liang, Youyun; Ang, Ee Lui; Zhao, Huimin | ACS synthetic biology. | 2017 04 21; | 28073246 | |
| Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. | Stephens, Andrew D; Banigan, Edward J; Adam, Stephen A; Goldman, Robert D; Marko, John F | Molecular biology of the cell. | 2017 Jan 05; | 28057760 | |
| Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. | Blumberg, Amit; Rice, Edward J; Kundaje, Anshul; Danko, Charles G; Mishmar, Dan | Genome research. | 2017 Mar; | 28049628 | |
| Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. | Shin, Yongdae; Berry, Joel; Pannucci, Nicole; Haataja, Mikko P; Toettcher, Jared E; Brangwynne, Clifford P | Cell. | 2017 Jan 12; | 28041848 | |
| Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. | Fang, Rongxin; Yu, Miao; Li, Guoqiang; Chee, Sora; Liu, Tristin; Schmitt, Anthony D; Ren, Bing | Cell research. | 2016 Dec; | 27886167 | |
| A dynamic mode of mitotic bookmarking by transcription factors. | Teves, Sheila S; An, Luye; Hansen, Anders S; Xie, Liangqi; Darzacq, Xavier; Tjian, Robert | eLife. | 2016 Nov 19; | 27855781 | |
| Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. | Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn A | Cell reports. | 2016 Nov 15; | 27851973 | |
| A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. | Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, Bing | Cell reports. | 2016 Nov 15; | 27851967 | |
| The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. | Matheson, Timothy D; Kaufman, Paul D | Molecular biology of the cell. | 2017 Jan 01; | 27807046 | |
| An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. | Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Micha?; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz | Genome research. | 2016 Dec; | 27789526 | |
| High-throughput assessment of context-dependent effects of chromatin proteins. | Brueckner, Laura; van Arensbergen, Joris; Akhtar, Waseem; Pagie, Ludo; van Steensel, Bas | Epigenetics & chromatin. | 2016; | 27777628 | |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S | Nature methods. | 2016 Dec; | 27776111 | |
| ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. | Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y | Nature methods. | ; | 27749837 | |
| Transferable model for chromosome architecture. | Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman; Wolynes, Peter G; Onuchic, José N | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Oct 25; | 27688758 | |
| Mapping 3D genome architecture through in situ DNase Hi-C. | Ramani, Vijay; Cusanovich, Darren A; Hause, Ronald J; Ma, Wenxiu; Qiu, Ruolan; Deng, Xinxian; Blau, C Anthony; Disteche, Christine M; Noble, William S; Shendure, Jay; Duan, Zhijun | Nature protocols. | 2016 Nov; | 27685100 | |
| Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. | Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng | PloS one. | 2016; | 27618313 | |
| Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. | Stark, Marie; Cheng, R Holland | Pharmaceutical patent analyst. | 2016 Sep; | 27610752 | |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt, Anthony D; Hu, Ming; Ren, Bing | Nature reviews. Molecular cell biology. | 2016 12; | 27580841 | |
| CRISPR-Cas9 nuclear dynamics and target recognition in living cells. | Ma, Hanhui; Tu, Li-Chun; Naseri, Ardalan; Huisman, Maximiliaan; Zhang, Shaojie; Grunwald, David; Pederson, Thoru | The Journal of cell biology. | 2016 Aug 29; | 27551060 | |
| A new correlation clustering method for cancer mutation analysis. | Hou, Jack P; Emad, Amin; Puleo, Gregory J; Ma, Jian; Milenkovic, Olgica | Bioinformatics (Oxford, England). | 2016 Aug 18; | 27540270 | |
| Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions. | Shenoy, Shailesh M | Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. | 2016 Jul; | 27516727 | |
| Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. | Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, Hiroko | Scientific reports. | 2016 Aug 12; | 27516062 | |
| Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. | Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Rao, Suhas S P; Huntley, Miriam H; Lander, Eric S; Aiden, Erez Lieberman | Cell systems. | 2016 Jul; | 27467249 | |
| Allele-Specific Quantification of Structural Variations in Cancer Genomes. | Li, Yang; Zhou, Shiguo; Schwartz, David C; Ma, Jian | Cell systems. | 2016 Jul; | 27453446 | |
| Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. | Beagrie, Robert A; Pombo, Ana | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2016 09; | 27452946 | |
| Structural organization of the inactive X chromosome in the mouse. | Giorgetti, Luca; Lajoie, Bryan R; Carter, Ava C; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y; Heard, Edith; Dekker, Job | Nature. | 2016 Jul 28; | 27437574 | |
| Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. | Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Aug 02; | 27432957 | |
| Polymer physics of chromosome large-scale 3D organisation. | Chiariello, Andrea M; Annunziatella, Carlo; Bianco, Simona; Esposito, Andrea; Nicodemi, Mario | Scientific reports. | 2016 Jul 13; | 27405443 | |
| Identifying gene regulatory network rewiring using latent differential graphical models. | Tian, Dechao; Gu, Quanquan; Ma, Jian | Nucleic acids research. | 2016 Sep 30; | 27378774 | |
| Nanoscale imaging of RNA with expansion microscopy. | Chen, Fei; Wassie, Asmamaw T; Cote, Allison J; Sinha, Anubhav; Alon, Shahar; Asano, Shoh; Daugharthy, Evan R; Chang, Jae-Byum; Marblestone, Adam; Church, George M; Raj, Arjun; Boyden, Edward S | Nature methods. | 2016 Aug; | 27376770 | |
| Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. | McGeachie, Michael J; Yates, Katherine P; Zhou, Xiaobo; Guo, Feng; Sternberg, Alice L; Van Natta, Mark L; Wise, Robert A; Szefler, Stanley J; Sharma, Sunita; Kho, Alvin T; Cho, Michael H; Croteau-Chonka, Damien C; Castaldi, Peter J; Jain, Gaurav; Sanyal, | American journal of respiratory and critical care medicine. | 2016 Dec 15; | 27367781 | |
| A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. | Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A | Genes & development. | 2016 Jun 15; | 27340175 | |
| Enhancer Control of Transcriptional Bursting. | Fukaya, Takashi; Lim, Bomyi; Levine, Michael | Cell. | 2016 Jul 14; | 27293191 | |
| RTFBSDB: an integrated framework for transcription factor binding site analysis. | Wang, Zhong; Martins, André L; Danko, Charles G | Bioinformatics (Oxford, England). | 2016 Oct 01; | 27288497 | |
| CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop. | Beagan, Jonathan A; Phillips-Cremins, Jennifer E | Wiley interdisciplinary reviews. Systems biology and medicine. | 2016 Jul; | 27265842 | |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons, Orsolya; Raj, Arjun | Molecular cell. | 2016 Jun 2; | 27259209 | |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular cell. | 2016 Jun 2; | 27259200 | |
| Use of genome-editing tools to treat sickle cell disease. | Tasan, Ipek; Jain, Surbhi; Zhao, Huimin | Human genetics. | 2016 Jun 1; | 27250347 | |
| Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. | Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong | Nature communications. | 2016; | 27240697 | |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol A | Cell. | 2016 Jun 2; | 27238023 | |
| Chromosome Compaction by Active Loop Extrusion. | Goloborodko, Anton; Marko, John F; Mirny, Leonid A | Biophysical journal. | 2016 May 24; | 27224481 | |
| CRISPR/Cas9 for Human Genome Engineering and Disease Research. | Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S | Annual review of genomics and human genetics. | 2016 Aug 31; | 27216776 | |
| Formation of Chromosomal Domains by Loop Extrusion. | Fudenberg, Geoffrey; Imakaev, Maxim; Lu, Carolyn; Goloborodko, Anton; Abdennur, Nezar; Mirny, Leonid A | Cell Rep | 2016 May 19 | 27210764 | |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid | eLife. | 2016 May 18; | 27192037 | |
| Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. | Banigan, Edward J; Marko, John F | Physical review. E. | 2016 Apr; | 27182590 | |
| Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. | Proserpio, Valentina; Piccolo, Andrea; Haim-Vilmovsky, Liora; Kar, Gozde; Lönnberg, Tapio; Svensson, Valentine; Pramanik, Jhuma; Natarajan, Kedar Nath; Zhai, Weichao; Zhang, Xiuwei; Donati, Giacomo; Kayikci, Melis; Kotar, Jurij; McKenzie, Andrew N J; Montandon, Ruddy; Billker, Oliver; Woodhouse, Steven; Cicuta, Pietro; Nicodemi, Mario; Teichmann, Sarah A | Genome biology. | 2016; | 27176874 | |
| Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. | Smith, Silas W; Jamin, Catherine T; Malik, Sidrah; Abrukin, Liliya; Tupchong, Keegan M; Portelli, Ian; Asaeda, Glenn; Prezant, David J; Wang, Binhuan; Hu, Ming; Goldfrank, Lewis R; Meyers, Chad M | Disaster medicine and public health preparedness. | 2016 06; | 27174171 | |
| FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. | Xu, Zheng; Zhang, Guosheng; Wu, Cong; Li, Yun; Hu, Ming | Bioinformatics (Oxford, England). | 2016 09 01; | 27153668 | |
| Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. | Beagan, Jonathan A; Gilgenast, Thomas G; Kim, Jesi; Plona, Zachary; Norton, Heidi K; Hu, Gui; Hsu, Sarah C; Shields, Emily J; Lyu, Xiaowen; Apostolou, Effie; Hochedlinger, Konrad; Corces, Victor G; Dekker, Job; Phillips-Cremins, Jennifer E | Cell Stem Cell | 2016 May 5 | P:611-24 | 27152443 |
| Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. | Eastland, Adrienne; Hornick, Jessica; Kawamura, Ryo; Nanavati, Dhaval; Marko, John F | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. | 2016 Sep; | 27145786 | |
| Dosage compensation of the sex chromosomes and autosomes. | Disteche, Christine M | Semin Cell Dev Biol | 2016 Apr 22 | 27112542 | |
| TAD disruption as oncogenic driver. | Valton, Anne-Laure; Dekker, Job | Curr Opin Genet Dev | 2016 Feb | P:34-40 | 27111891 |
| Jointly characterizing epigenetic dynamics across multiple human cell types. | Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C | Nucleic acids research. | 2016 08 19; | 27095202 | |
| Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. | Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. | Nature Biotechnology | 2016 April 18 | Epub ahead of print | 27088723 |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting | Trends Genet | 2016 May | P:269-83 | 27080453 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. | Molecular Cell | 2016 April 5 | V:62 P:1-11 | 27067601 |
| History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. | Khrameeva, Ekaterina E; Fudenberg, Geoffrey; Gelfand, Mikhail S; Mirny, Leonid A | J Bioinform Comput Biol | 2016 Apr | P:1641002 | 27021249 |
| HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. | Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming | BMC research notes. | 2016; | 26969411 | |
| The 3D Genome as Moderator of Chromosomal Communication. | Dekker, Job; Mirny, Leonid | Cell | 2016 Mar 10 | V:164 P:1110-21 | 26967279 |
| Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. | Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank | Proceedings of the National Academy of Sciences of the United States of America. | 2016 Mar 22; | 26951677 | |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun | Genes & development. | 2016 Mar 1; | 26944681 | |
| Activation of proto-oncogenes by disruption of chromosome neighborhoods. | Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S; Valton, Anne-Laure; Bak, Rasmus O; Li, Charles H; Goldmann, Johanna; Lajoie, Bryan R; Fan, Zi Peng; Sigova, Alla A; Reddy, Jessica; Borges-Rivera, Diego; Lee, Tong Ihn; Jaenisch, Rudolf; Porteus, Matthew H; Dekker, Job; Young, Richard A | Science | 2016 Mar 25 | V:351 P:1454-8 | 26940867 |
| Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. | Casasola, Andrea; Scalzo, David; Nandakumar, Vivek; Halow, Jessica; Recillas-Targa, Félix; Groudine, Mark; Rincón-Arano, Héctor | Nucleus | 2016 Mar | P:84-102 | 26900797 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, Ting | G3 (Bethesda) | 2016 | P:973-86 | 26888867 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani, Vijay; Shendure, Jay; Duan, Zhijun | Genomics Proteomics Bioinformatics | 2016 Feb | P:7-20 | 26876719 |
| Chemically activatable viral capsid functionalized for cancer targeting. | Chen, Chun-Chieh; Xing, Li; Stark, Marie; Ou, Tingwei; Holla, Prasida; Xiao, Kai; Kamita, Shizuo G; Hammock, Bruce D; Lam, Kit; Cheng, R Holland | Nanomedicine | 2016 Feb | P:377-90 | 26786134 |
| Imaging Transcription: Past, Present, and Future. | Coleman, Robert A; Liu, Zhe; Darzacq, Xavier; Tjian, Robert; Singer, Robert H; Lionnet, Timothée | Cold Spring Harbor symposia on quantitative biology. | 2016 Jan 13 | 26763984 | |
| The redundancy of the mammalian heterochromatic compartment. | Politz, Joan C Ritland; Scalzo, David; Groudine, Mark | Curr Opin Genet Dev | 2015 Dec 16 | P:1-8 | 26706451 |
| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine | Nucleic acids research. | 2016 Apr 20; | 26704975 | |
| CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. | Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun | Cell. | 2015 Dec 17 | V:163 P:1611-27 | 26686651 |
| A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. | Xu, Zheng; Zhang, Guosheng; Jin, Fulai; Chen, Mengjie; Furey, Terrence S; Sullivan, Patrick F; Qin, Zhaohui; Hu, Ming; Li, Yun | Bioinformatics (Oxford, England). | 2016 03 01; | 26543175 | |
| Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. | Nagano, Takashi; Lubling, Yaniv; Yaffe, Eitan; Wingett, Steven W; Dean, Wendy; Tanay, Amos; Fraser, Peter | Nature protocols. | 2015 Dec; | 26540590 | |
| 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 Lieberman | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Nov 24; | 26499245 |