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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
4D Nucleome (651)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| BRD4 orchestrates genome folding to promote neural crest differentiation. | Linares-Saldana, Ricardo; Kim, Wonho; Bolar, Nikhita A; Zhang, Haoyue; Koch-Bojalad, Bailey A; Yoon, Sora; Shah, Parisha P; Karnay, Ashley; Park, Daniel S; Luppino, Jennifer M; Nguyen, Son C; Padmanabhan, Arun; Smith, Cheryl L; Poleshko, Andrey; Wang, Qia | Nature genetics | 2021 Oct | 34611363 | |
| Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C | Nature methods | 2021 Sep 21 | 34548656 | |
| Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. | Ren, Xingjie; Wang, Mengchi; Li, Bingkun; Jamieson, Kirsty; Zheng, Lina; Jones, Ian R; Li, Bin; Takagi, Maya Asami; Lee, Jerry; Maliskova, Lenka; Tam, Tsz Wai; Yu, Miao; Hu, Rong; Lee, Lindsay; Abnousi, Armen; Li, Gang; Li, Yun; Hu, Ming; Ren, Bing; Wang, | Science advances | 2021 Sep 17 | 34524848 | |
| Enhanced Cas12a multi-gene regulation using a CRISPR array separator. | Magnusson, Jens P; Rios, Antonio Ray; Wu, Lingling; Qi, Lei S | eLife | 2021 09 09 | 34499031 | |
| MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples. | Liu, Weifang; Yang, Yuchen; Abnousi, Armen; Zhang, Qian; Kubo, Naoki; Beem, Joshua S Martin; Li, Yun; Hu, Ming | HGG advances | 2021 Jul 08 | 34485947 | |
| Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser, Artur; Müller, Lucas-Raphael; Hoess, Philipp; Matti, Ulf; Obara, Christopher J; Legant, Wesley R; Kreshuk, Anna; Macke, Jakob H; Ries, Jonas; Turaga, Srinivas C | Nature methods | 2021 09 | 34480155 | |
| Systematic evaluation of chromosome conformation capture assays. | Akgol Oksuz, Betul; Yang, Liyan; Abraham, Sameer; Venev, Sergey V; Krietenstein, Nils; Parsi, Krishna Mohan; Ozadam, Hakan; Oomen, Marlies E; Nand, Ankita; Mao, Hui; Genga, Ryan M J; Maehr, Rene; Rando, Oliver J; Mirny, Leonid A; Gibcus, Johan H; Dekker, | Nature methods | 2021 09 | 34480151 | |
| The 3D Genome Structure of Single Cells. | Zhou, Tianming; Zhang, Ruochi; Ma, Jian | Annual review of biomedical data science | 2021 07 20 | 34465168 | |
| SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. | Yu, Miao; Abnousi, Armen; Zhang, Yanxiao; Li, Guoqiang; Lee, Lindsay; Chen, Ziyin; Fang, Rongxin; Lagler, Taylor M; Yang, Yuchen; Wen, Jia; Sun, Quan; Li, Yun; Ren, Bing; Hu, Ming | Nature methods | 2021 09 | 34446921 | |
| Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9. | Gao, Yuchen; Han, Mengting; Shang, Stephen; Wang, Haifeng; Qi, Lei S | Molecular cell | 2021 Aug 13 | 34428454 | |
| Single-cell measurement of higher-order 3D genome organization with scSPRITE. | Arrastia, Mary V; Jachowicz, Joanna W; Ollikainen, Noah; Curtis, Matthew S; Lai, Charlotte; Quinodoz, Sofia A; Selck, David A; Ismagilov, Rustem F; Guttman, Mitchell | Nature biotechnology | 2021 Aug 23 | 34426703 | |
| Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. | Song, Fan; Xu, Jie; Dixon, Jesse; Yue, Feng | Methods in molecular biology (Clifton, N.J.) | 2022 | 34415534 | |
| X-factors in human disease: impact of gene content and dosage regulation. | Fang, He; Deng, Xinxian; Disteche, Christine M | Human molecular genetics | 2021 Oct 01 | 34387327 | |
| Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). | Yu, Miao; Juric, Ivan; Abnousi, Armen; Hu, Ming; Ren, Bing | Methods in molecular biology (Clifton, N.J.) | 2021 | 34382190 | |
| Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. | Lee, Joo-Hyung; Wang, Ruoyu; Xiong, Feng; Krakowiak, Joanna; Liao, Zian; Nguyen, Phuoc T; Moroz-Omori, Elena V; Shao, Jiaofang; Zhu, Xiaoyu; Bolt, Michael J; Wu, Haoyi; Singh, Pankaj K; Bi, Mingjun; Shi, Caleb J; Jamal, Naadir; Li, Guojie; Mistry, Ragini; | Molecular cell | 2021 08 19 | 34375583 | |
| Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. | Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter | Computer graphics forum : journal of the European Association for Computer Graphics | 2020 Jun | 34334852 | |
| SARS-CoV-2 Restructures the Host Chromatin Architecture. | Wang, Ruoyu; Lee, Joo-Hyung; Xiong, Feng; Kim, Jieun; Hasani, Lana Al; Yuan, Xiaoyi; Shivshankar, Pooja; Krakowiak, Joanna; Qi, Chuangye; Wang, Yanyu; Eltzschig, Holger K; Li, Wenbo | bioRxiv : the preprint server for biology | 2021 Jul 21 | 34312624 | |
| DNA-loop-extruding SMC complexes can traverse one another in vivo. | Brandão, Hugo B; Ren, Zhongqing; Karaboja, Xheni; Mirny, Leonid A; Wang, Xindan | Nature structural & molecular biology | 2021 08 | 34312537 | |
| CRISPRi/a Screening with Human iPSCs. | Nishiga, Masataka; Qi, Lei S; Wu, Joseph C | Methods in molecular biology (Clifton, N.J.) | 2021 | 34302664 | |
| Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. | Lafontaine, Denis L; Yang, Liyan; Dekker, Job; Gibcus, Johan H | Current protocols | 2021 Jul | 34286910 | |
| High-resolution, genome-wide mapping of positive supercoiling in chromosomes. | Guo, Monica S; Kawamura, Ryo; Littlehale, Megan L; Marko, John F; Laub, Michael T | eLife | 2021 07 19 | 34279217 | |
| AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. | Liu, Shaopeng; Li, Daofeng; Lyu, Cheng; Gontarz, Paul M; Miao, Benpeng; Madden, Pamela A F; Wang, Ting; Zhang, Bo | Genomics, proteomics & bioinformatics | 2021 Jul 14 | 34273560 | |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao, Jordan Yupeng; Hafner, Antonina; Boettiger, Alistair N | eLife | 2021 07 09 | 34240703 | |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan, Sanjay R; Regier, Mary C; Barkan, Eliza; Franks, Jennifer M; Packer, Jonathan S; Grosjean, Parker; Duran, Madeleine; Saxton, Sarah; Ladd, Jon J; Spielmann, Malte; Lois, Carlos; Lampe, Paul D; Shendure, Jay; Stevens, Kelly R; Trapnell, Cole | Science (New York, N.Y.) | 2021 07 02 | 34210887 | |
| Three-dimensional superresolution fluorescence microscopy maps the variable molecular architecture of the nuclear pore complex. | Sabinina, Vilma Jimenez; Hossain, M Julius; Hériché, Jean-Karim; Hoess, Philipp; Nijmeijer, Bianca; Mosalaganti, Shyamal; Kueblbeck, Moritz; Callegari, Andrea; Szymborska, Anna; Beck, Martin; Ries, Jonas; Ellenberg, Jan | Molecular biology of the cell | 2021 08 15 | 34191541 | |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. | Wang, Jiarui; Han, Mengting; Wang, Haifeng; Möckl, Leonhard; Zeng, Leiping; Moerner, W E; Qi, Lei S | bioRxiv : the preprint server for biology | 2021 Jun 09 | 34127974 | |
| DMA-tudor interaction modules control the specificity of in vivo condensates. | Courchaine, Edward M; Barentine, Andrew E S; Straube, Korinna; Lee, Dong-Ryoung; Bewersdorf, Joerg; Neugebauer, Karla M | Cell | 2021 Jul 08 | 34115980 | |
| Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. | Singh, Shashank; Yang, Yang; Póczos, Barnabás; Ma, Jian | Quantitative biology (Beijing, China) | 2019 Jun | 34113473 | |
| RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. | Xiong, Feng; Wang, Ruoyu; Lee, Joo-Hyung; Li, Shenglan; Chen, Shin-Fu; Liao, Zian; Hasani, Lana Al; Nguyen, Phuoc T; Zhu, Xiaoyu; Krakowiak, Joanna; Lee, Dung-Fang; Han, Leng; Tsai, Kuang-Lei; Liu, Ying; Li, Wenbo | Cell research | 2021 Jun 09 | 34108665 | |
| HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. | Strom, Amy R; Biggs, Ronald J; Banigan, Edward J; Wang, Xiaotao; Chiu, Katherine; Herman, Cameron; Collado, Jimena; Yue, Feng; Ritland Politz, Joan C; Tait, Leah J; Scalzo, David; Telling, Agnes; Groudine, Mark; Brangwynne, Clifford P; Marko, John F; Step | eLife | 2021 06 09 | 34106828 | |
| Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. | Rajpurkar, Aparna R; Mateo, Leslie J; Murphy, Sedona E; Boettiger, Alistair N | Nature communications | 2021 06 08 | 34103507 | |
| HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | Sahin, Merve; Wong, Wilfred; Zhan, Yingqian; Van Deynze, Kinsey; Koche, Richard; Leslie, Christina S | Nature communications | 2021 06 07 | 34099725 | |
| Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. | Lin, Yen-Chen; Kumar, Meenakshi Sundaram; Ramesh, Nandini; Anderson, Eric N; Nguyen, Aivi T; Kim, Boram; Cheung, Simon; McDonough, Justin A; Skarnes, William C; Lopez-Gonzalez, Rodrigo; Landers, John E; Fawzi, Nicolas L; Mackenzie, Ian R A; Lee, Edward B; | Nature neuroscience | 2021 08 | 34059832 | |
| Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. | Scourzic, Laurianne; Salataj, Eralda; Apostolou, Effie | Frontiers in immunology | 2021 | 34054841 | |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. | Hoencamp, Claire; Dudchenko, Olga; Elbatsh, Ahmed M O; Brahmachari, Sumitabha; Raaijmakers, Jonne A; van Schaik, Tom; Sedeño Cacciatore, Ángela; Contessoto, Vinícius G; van Heesbeen, Roy G H P; van den Broek, Bram; Mhaskar, Aditya N; Teunissen, Hans; St H | Science (New York, N.Y.) | 2021 05 28 | 34045355 | |
| Enhancer release and retargeting activates disease-susceptibility genes. | Oh, Soohwan; Shao, Jiaofang; Mitra, Joydeep; Xiong, Feng; D'Antonio, Matteo; Wang, Ruoyu; Garcia-Bassets, Ivan; Ma, Qi; Zhu, Xiaoyu; Lee, Joo-Hyung; Nair, Sreejith J; Yang, Feng; Ohgi, Kenneth; Frazer, Kelly A; Zhang, Zhengdong D; Li, Wenbo; Rosenfeld, Mi | Nature | 2021 May 26 | 34040254 | |
| REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. | Sarkans, Ugis; Chiu, Wah; Collinson, Lucy; Darrow, Michele C; Ellenberg, Jan; Grunwald, David; Hériché, Jean-Karim; Iudin, Andrii; Martins, Gabriel G; Meehan, Terry; Narayan, Kedar; Patwardhan, Ardan; Russell, Matthew Robert Geoffrey; Saibil, Helen R; Str | Nature methods | 2021 May 21 | 34021280 | |
| Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow, Jennifer A; Miao, Benpeng; Xing, Xiaoyun; Wang, Ting; Zhang, Bo | Communications biology | 2021 May 21 | 34021236 | |
| Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers. | Jain, Surbhi; Xun, Guanhua; Abesteh, Shireen; Ho, Sherri; Lingamaneni, Manasi; Martin, Teresa A; Tasan, Ipek; Yang, Che; Zhao, Huimin | ACS synthetic biology | 2021 06 18 | 34006094 | |
| Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. | Huang, Xiao; Ferris, Stephen T; Kim, Sunkyung; Choudhary, Mayank N K; Belk, Julia A; Fan, Changxu; Qi, Yanyan; Sudan, Raki; Xia, Yu; Desai, Pritesh; Chen, Jing; Ly, Nghi; Shi, Quanming; Bagadia, Prachi; Liu, Tiantian; Guilliams, Martin; Egawa, Takeshi; Co | Immunity | 2021 May 11 | 34004142 | |
| CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains. | Huang, Hui; Zhu, Quan; Jussila, Adam; Han, Yuanyuan; Bintu, Bogdan; Kern, Colin; Conte, Mattia; Zhang, Yanxiao; Bianco, Simona; Chiariello, Andrea M; Yu, Miao; Hu, Rong; Tastemel, Melodi; Juric, Ivan; Hu, Ming; Nicodemi, Mario; Zhuang, Xiaowei; Ren, Bing | Nature genetics | 2021 May 17 | 34002095 | |
| PYMEVisualize: an open-source tool for exploring 3D super-resolution data. | Marin, Zach; Graff, Michael; Barentine, Andrew E S; Soeller, Christian; Chung, Kenny Kwok Hin; Fuentes, Lukas A; Baddeley, David | Nature methods | 2021 Jun | 34002092 | |
| Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. | Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber | Med (New York, N.Y.) | 2021 May 14 | 33969332 | |
| Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin. | Fiorillo, Luca; Musella, Francesco; Conte, Mattia; Kempfer, Rieke; Chiariello, Andrea M; Bianco, Simona; Kukalev, Alexander; Irastorza-Azcarate, Ibai; Esposito, Andrea; Abraham, Alex; Prisco, Antonella; Pombo, Ana; Nicodemi, Mario | Nature methods | 2021 05 | 33963348 | |
| Determination of complete chromosomal haplotypes by bulk DNA sequencing. | Tourdot, Richard W; Brunette, Gregory J; Pinto, Ricardo A; Zhang, Cheng-Zhong | Genome biology | 2021 May 06 | 33957932 | |
| From integrative structural biology to cell biology. | Sali, Andrej | The Journal of biological chemistry | 2021 Jan-Jun | 33957123 | |
| Unsupervised manifold alignment for single-cell multi-omics data. | Singh, Ritambhara; Demetci, Pinar; Bonora, Giancarlo; Ramani, Vijay; Lee, Choli; Fang, He; Duan, Zhijun; Deng, Xinxian; Shendure, Jay; Disteche, Christine; Noble, William Stafford | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 2020 Sep | 33954299 | |
| Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. | Pettinato, Anthony M; Yoo, Dasom; VanOudenhove, Jennifer; Chen, Yu-Sheng; Cohn, Rachel; Ladha, Feria A; Yang, Xiulan; Thakar, Ketan; Romano, Robert; Legere, Nicolas; Meredith, Emily; Robson, Paul; Regnier, Michael; Cotney, Justin L; Murry, Charles E; Hins | Cell reports | 2021 May 04 | 33951429 | |
| The Need for a Human Pangenome Reference Sequence. | Miga, Karen H; Wang, Ting | Annual review of genomics and human genetics | 2021 08 31 | 33929893 | |
| Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. | Sanborn, Adrian L; Yeh, Benjamin T; Feigerle, Jordan T; Hao, Cynthia V; Townshend, Raphael Jl; Lieberman Aiden, Erez; Dror, Ron O; Kornberg, Roger D | eLife | 2021 Apr 27 | 33904398 | |
| Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. | Liu, Miao; Yang, Bing; Hu, Mengwei; Radda, Jonathan S D; Chen, Yanbo; Jin, Shengyan; Cheng, Yubao; Wang, Siyuan | Nature protocols | 2021 May | 33903756 | |
| Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan J | Developmental cell | 2021 May 03 | 33891899 | |
| Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. | Iyyanki, Tejaswi; Zhang, Baozhen; Wang, Qixuan; Hou, Ye; Jin, Qiushi; Xu, Jie; Yang, Hongbo; Liu, Tingting; Wang, Xiaotao; Song, Fan; Luan, Yu; Yamashita, Hironobu; Chien, Ruby; Lyu, Huijue; Zhang, Lijun; Wang, Lu; Warrick, Joshua; Raman, Jay D; Meeks, Joshua J; DeGraff, David J; Yue, Feng | Genome biology | 2021 Apr 15 | 33858483 | |
| Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. | Schep, Ruben; Brinkman, Eva K; Leemans, Christ; Vergara, Xabier; van der Weide, Robin H; Morris, Ben; van Schaik, Tom; Manzo, Stefano G; Peric-Hupkes, Daniel; van den Berg, Jeroen; Beijersbergen, Roderick L; Medema, René H; van Steensel, Bas | Molecular cell | 2021 05 20 | 33848455 | |
| Single-molecule micromanipulation studies of methylated DNA. | Zaichuk, Tetiana; Marko, John F | Biophysical journal | 2021 06 01 | 33838135 | |
| Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. | Zhu, Yanfen; Gujar, Amit D; Wong, Chee-Hong; Tjong, Harianto; Ngan, Chew Yee; Gong, Liang; Chen, Yi-An; Kim, Hoon; Liu, Jihe; Li, Meihong; Mil-Homens, Adam; Maurya, Rahul; Kuhlberg, Chris; Sun, Fanyue; Yi, Eunhee; deCarvalho, Ana C; Ruan, Yijun; Verhaak, Roel G W; Wei, Chia-Lin | Cancer cell | 2021 May 10 | 33836152 | |
| Genome-wide enhancer maps link risk variants to disease genes. | Nasser, Joseph; Bergman, Drew T; Fulco, Charles P; Guckelberger, Philine; Doughty, Benjamin R; Patwardhan, Tejal A; Jones, Thouis R; Nguyen, Tung H; Ulirsch, Jacob C; Lekschas, Fritz; Mualim, Kristy; Natri, Heini M; Weeks, Elle M; Munson, Glen; Kane, Mich | Nature | 2021 05 | 33828297 | |
| p53 mediates target gene association with nuclear speckles for amplified RNA expression. | Alexander, Katherine A; Coté, Allison; Nguyen, Son C; Zhang, Liguo; Gholamalamdari, Omid; Agudelo-Garcia, Paula; Lin-Shiao, Enrique; Tanim, K M A; Lim, Joan; Biddle, Nicolas; Dunagin, Margaret C; Good, Charly R; Mendoza, Mariel R; Little, Shawn C; Belmont, Andrew; Joyce, Eric F; Raj, Arjun; Berger, Shelley L | Molecular cell | 2021 04 15 | 33823140 | |
| Interrogating immune cells and cancer with CRISPR-Cas9. | Buquicchio, Frank A; Satpathy, Ansuman T | Trends in immunology | 2021 05 | 33812776 | |
| Phase separation in genome organization across evolution. | Feric, Marina; Misteli, Tom | Trends in cell biology | 2021 08 | 33771451 | |
| Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention. | Hogan, Ann K; Foltz, Daniel R | Molecular and cellular biology | 2021 05 21 | 33753462 | |
| See(quence) and ye shall find: higher-order genome folding in intact single cells. | Pham, Kenneth; Nikish, Alexandria; Phillips-Cremins, Jennifer E | Molecular cell | 2021 03 18 | 33740473 | |
| Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation. | Makhija, Suraj; Brown, David; Rudlaff, Rachel M; Doh, Julia K; Bourke, Struan; Wang, Yina; Zhou, Shuqin; Cheloor-Kovilakam, Rasmi; Huang, Bo | ACS chemical biology | 2021 04 16 | 33734687 | |
| RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. | Bertero, Alessandro | Frontiers in genetics | 2021 | 33732290 | |
| Toward a Three-Dimensional Chromosome Shape Alphabet. | Soto, Carlos; Bryner, Darshan; Neretti, Nicola; Srivastava, Anuj | Journal of computational biology : a journal of computational molecular cell biology | 2021 06 | 33720766 | |
| Properties of repression condensates in living Ciona embryos. | Treen, Nicholas; Shimobayashi, Shunsuke F; Eeftens, Jorine; Brangwynne, Clifford P; Levine, Michael | Nature communications | 2021 03 10 | 33692345 | |
| Cas9 deactivation with photocleavable guide RNAs. | Zou, Roger S; Liu, Yang; Wu, Bin; Ha, Taekjip | Molecular cell | 2021 04 01 | 33662274 | |
| Genome oligopaint via local denaturation fluorescence in situ hybridization. | Wang, Yanbo; Cottle, Wayne Taylor; Wang, Haobo; Feng, Xinyu Ashlee; Mallon, John; Gavrilov, Momcilo; Bailey, Scott; Ha, Taekjip | Molecular cell | 2021 04 01 | 33657402 | |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert, Benjamin L; Cote, Christopher J; Torre, Eduardo A; Dardani, Ian P; Jiang, Connie L; Jain, Naveen; Shaffer, Sydney M; Raj, Arjun | Nature biotechnology | 2021 Feb 22 | 33619394 | |
| Direct supercritical angle localization microscopy for nanometer 3D superresolution. | Dasgupta, Anindita; Deschamps, Joran; Matti, Ulf; Hübner, Uwe; Becker, Jan; Strauss, Sebastian; Jungmann, Ralf; Heintzmann, Rainer; Ries, Jonas | Nature communications | 2021 02 19 | 33608524 | |
| Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. | Zhang, Meng; Yang, Che; Tasan, Ipek; Zhao, Huimin | ACS synthetic biology | 2021 03 19 | 33596056 | |
| Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. | Zazhytska, Marianna; Kodra, Albana; Hoagland, Daisy A; Fullard, John F; Shayya, Hani; Omer, Arina; Firestein, Stuart; Gong, Qizhi; Canoll, Peter D; Goldman, James E; Roussos, Panos; tenOever, Benjamin R; Overdevest, Jonathan B; Lomvardas, Stavros | bioRxiv : the preprint server for biology | 2021 Feb 09 | 33594368 | |
| HiCRep.py : Fast comparison of Hi-C contact matrices in Python. | Lin, Dejun; Sanders, Justin; Noble, William Stafford | Bioinformatics (Oxford, England) | 2021 02 11 | 33576390 | |
| Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. | Belaghzal, Houda; Borrman, Tyler; Stephens, Andrew D; Lafontaine, Denis L; Venev, Sergey V; Weng, Zhiping; Marko, John F; Dekker, Job | Nature genetics | 2021 03 | 33574602 | |
| Engineering 3D genome organization. | Wang, Haifeng; Han, Mengting; Qi, Lei S | Nature reviews. Genetics | 2021 06 | 33558716 | |
| HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test. | Lagler, Taylor M; Abnousi, Armen; Hu, Ming; Yang, Yuchen; Li, Yun | American journal of human genetics | 2021 02 04 | 33545029 | |
| SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. | Lu-Culligan, Alice; Chavan, Arun R; Vijayakumar, Pavithra; Irshaid, Lina; Courchaine, Edward M; Milano, Kristin M; Tang, Zhonghua; Pope, Scott D; Song, Eric; Vogels, Chantal B F; Lu-Culligan, William J; Campbell, Katherine H; Casanovas-Massana, Arnau; Ber | medRxiv : the preprint server for health sciences | 2021 Jan 26 | 33532791 | |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 2021 02 | 33505024 | |
| TALEN outperforms Cas9 in editing heterochromatin target sites. | Jain, Surbhi; Shukla, Saurabh; Yang, Che; Zhang, Meng; Fatma, Zia; Lingamaneni, Manasi; Abesteh, Shireen; Lane, Stephan Thomas; Xiong, Xiong; Wang, Yuchuan; Schroeder, Charles M; Selvin, Paul R; Zhao, Huimin | Nature communications | 2021 01 27 | 33504770 | |
| Determining of canine position by multiple facial landmarks to achieve natural esthetics in complete denture treatment. | Srimaneekarn, Natchalee; Arayapisit, Tawepong; Pooktuantong, Ornnicha; Cheng, Holland R; Soonsawad, Pan | The Journal of prosthetic dentistry | 2021 Jan 16 | 33468316 | |
| Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. | Vahedi, Golnaz | Immunological reviews | 2021 Mar | 33452686 | |
| Resources and challenges for integrative analysis of nuclear architecture data. | Jung, Youngsook L; Kirli, Koray; Alver, Burak H; Park, Peter J | Current opinion in genetics & development | 2021 Apr | 33450522 | |
| SPIN reveals genome-wide landscape of nuclear compartmentalization. | Wang, Yuchuan; Zhang, Yang; Zhang, Ruochi; van Schaik, Tom; Zhang, Liguo; Sasaki, Takayo; Peric-Hupkes, Daniel; Chen, Yu; Gilbert, David M; van Steensel, Bas; Belmont, Andrew S; Ma, Jian | Genome biology | 2021 Jan 14 | 33446254 | |
| The dynamics of chromatin architecture in brain development and function. | Harabula, Izabela; Pombo, Ana | Current opinion in genetics & development | 2021 04 | 33421764 | |
| CRISPR technologies for precise epigenome editing. | Nakamura, Muneaki; Gao, Yuchen; Dominguez, Antonia A; Qi, Lei S | Nature cell biology | 2021 Jan | 33420494 | |
| Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. | Rosa-Mercado, Nicolle A; Zimmer, Joshua T; Apostolidi, Maria; Rinehart, Jesse; Simon, Matthew D; Steitz, Joan A | Molecular cell | 2021 02 04 | 33400923 | |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre, Eduardo A; Arai, Eri; Bayatpour, Sareh; Jiang, Connie L; Beck, Lauren E; Emert, Benjamin L; Shaffer, Sydney M; Mellis, Ian A; Fane, Mitchell E; Alicea, Gretchen M; Budinich, Krista A; Weeraratna, Ashani T; Shi, Junwei; Raj, Arjun | Nature genetics | 2021 01 | 33398196 | |
| Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. | Kubo, Naoki; Ishii, Haruhiko; Xiong, Xiong; Bianco, Simona; Meitinger, Franz; Hu, Rong; Hocker, James D; Conte, Mattia; Gorkin, David; Yu, Miao; Li, Bin; Dixon, Jesse R; Hu, Ming; Nicodemi, Mario; Zhao, Huimin; Ren, Bing | Nature structural & molecular biology | 2021 Feb | 33398174 | |
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| Large distances separate coregulated genes in living Drosophila embryos. | Heist, Tyler; Fukaya, Takashi; Levine, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2019 07 23; | 31285341 | |
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| 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 | |
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| 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 | |
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| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong 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 |