4D Nucleome (4DN)
4D Nucleome (4DN)
Program Publications
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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.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| HybriSeq: Probe-based Device-free Single-cell RNA Profiling. | Foyt, Daniel; Brown, David; Zhou, Shuqin; Huang, Bo | bioRxiv : the preprint server for biology | 37808850 | 2024 Sep 18 |
| Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types. | Kumar, Pradeep; Gholamalamdari, Omid; Zhang, Yang; Zhang, Liguo; Vertii, Anastassiia; van Schaik, Tom; Peric-Hupkes, Daan; Sasaki, Takayo; Gilbert, David M; van Steensel, Bas; Ma, Jian; Kaufman, Paul D; Belmont, Andrew S | Communications biology | 39271748 | 2024 Sep 13 |
| YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. | Lam, Jessica C; Aboreden, Nicholas G; Midla, Susannah C; Wang, Siqing; Huang, Anran; Keller, Cheryl A; Giardine, Belinda; Henderson, Kate A; Hardison, Ross C; Zhang, Haoyue; Blobel, Gerd A | Nature genetics | 39210046 | 2024 Sep |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. | Andronov, Leonid; Han, Mengting; Zhu, Yanyu; Balaji, Ashwin; Roy, Anish R; Barentine, Andrew E S; Patel, Puja; Garhyan, Jaishree; Qi, Lei S; Moerner, W E | Nature communications | 38821943 | 2024 May 31 |
| Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis. | Brunner, Andreas; Morero, Natalia RosalÍa; Zhang, Wanlu; Hossain, M Julius; Lampe, Marko; Pflaumer, Hannah; Halavatyi, Aliaksandr; Peters, Jan-Michael; Beckwith, Kai S; Ellenberg, Jan | bioRxiv : the preprint server for biology | 38854067 | 2024 May 30 |
| MYC phase separation selectively modulates the transcriptome. | Yang, Junjiao; Chung, Chan-I; Koach, Jessica; Liu, Hongjiang; Navalkar, Ambuja; He, Hao; Ma, Zhimin; Zhao, Qian; Yang, Xiaoyu; He, Liang; Mittag, Tanja; Shen, Yin; Weiss, William A; Shu, Xiaokun | Nature structural & molecular biology | 38811792 | 2024 May 29 |
| DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture. | Eskndir, Nebiyat; Hossain, Manseeb; Currey, Marilena L; Pho, Mai; Berrada, Yasmin; Stephens, Andrew D | bioRxiv : the preprint server for biology | 38853925 | 2024 May 29 |
| Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. | Martinez-Sarmiento, Jose A; Cosma, Maria Pia; Lakadamyali, Melike | Cell reports | 38700983 | 2024 May 28 |
| Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix. | Tang, Chenwei; Sun, Quan; Zeng, Xinyue; Yang, Xiaoyu; Liu, Fei; Zhao, Jinying; Shen, Yin; Liu, Bixiang; Wen, Jia; Li, Yun | bioRxiv : the preprint server for biology | 38826297 | 2024 May 24 |
| A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex. | Liang, Xiaoyi G; Hoang, Kendy; Meyerink, Brandon L; Kc, Pratiksha; Paraiso, Kitt; Wang, Li; Jones, Ian R; Zhang, Yue; Katzman, Sol; Finn, Thomas S; Tsyporin, Jeremiah; Qu, Fangyuan; Chen, Zhaoxu; Visel, Axel; Kriegstein, Arnold; Shen, Yin; Pilaz, Louis-Jan; Chen, Bin | Proceedings of the National Academy of Sciences of the United States of America | 38713624 | 2024 May 14 |
| Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. | Chiariello, Andrea M; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Fontana, Andrea; Vercellone, Francesca; Conte, Mattia; Nicodemi, Mario | Nature communications | 38740770 | 2024 May 13 |
| A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. | Szabó, Dominik; Franke, Vedran; Bianco, Simona; Batiuk, Mykhailo Y; Paul, Eleanor J; Kukalev, Alexander; Pfisterer, Ulrich G; Irastorza-Azcarate, Ibai; Chiariello, Andrea M; Demharter, Samuel; Zea-Redondo, Luna; Lopez-Atalaya, Jose P; Nicodemi, Mario; Akalin, Altuna; Khodosevich, Konstantin; Ungless, Mark A; Winick-Ng, Warren; Pombo, Ana | bioRxiv : the preprint server for biology | 38766140 | 2024 May 12 |
| Super-enhancer interactomes from single cells link clustering and transcription. | Le, Derek J; Hafner, Antonina; Gaddam, Sadhana; Wang, Kevin C; Boettiger, Alistair N | bioRxiv : the preprint server for biology | 38766104 | 2024 May 10 |
| MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing. | Su, Chuanbin; Chandradoss, Keerthivasan Raanin; Malachowski, Thomas; Boya, Ravi; Ryu, Han-Seul; Brennand, Kristen J; Phillips-Cremins, Jennifer E | bioRxiv : the preprint server for biology | 38746155 | 2024 May 02 |
| H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. | Kubo, Naoki; Chen, Poshen B; Hu, Rong; Ye, Zhen; Sasaki, Hiroyuki; Ren, Bing | Molecular cell | 38513661 | 2024 May 02 |
| Cooltools: Enabling high-resolution Hi-C analysis in Python. | Open2C; Abdennur, Nezar; Abraham, Sameer; Fudenberg, Geoffrey; Flyamer, Ilya M; Galitsyna, Aleksandra A; Goloborodko, Anton; Imakaev, Maxim; Oksuz, Betul A; Venev, Sergey V; Xiao, Yao | PLoS computational biology | 38709825 | 2024 May |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong, Kyle; Zhang, Ruochi; Ma, Jian | Nature methods | 38589516 | 2024 May |
| FOXO1 is a master regulator of memory programming in CAR T cells. | Doan, Alexander E; Mueller, Katherine P; Chen, Andy Y; Rouin, Geoffrey T; Chen, Yingshi; Daniel, Bence; Lattin, John; Markovska, Martina; Mozarsky, Brett; Arias-Umana, Jose; Hapke, Robert; Jung, In-Young; Wang, Alice; Xu, Peng; Klysz, Dorota; Zuern, Gabrielle; Bashti, Malek; Quinn, Patrick J; Miao, Zhuang; Sandor, Katalin; Zhang, Wenxi; Chen, Gregory M; Ryu, Faith; Logun, Meghan; Hall, Junior; Tan, Kai; Grupp, Stephan A; McClory, Susan E; Lareau, Caleb A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W | Nature | 38600391 | 2024 May |
| Genome organization around nuclear speckles drives mRNA splicing efficiency. | Bhat, Prashant; Chow, Amy; Emert, Benjamin; Ettlin, Olivia; Quinodoz, Sofia A; Strehle, Mackenzie; Takei, Yodai; Burr, Alex; Goronzy, Isabel N; Chen, Allen W; Huang, Wesley; Ferrer, Jose Lorenzo M; Soehalim, Elizabeth; Goh, Say-Tar; Chari, Tara; Sullivan, Delaney K; Blanco, Mario R; Guttman, Mitchell | Nature | 38720076 | 2024 May |
| Pairtools: From sequencing data to chromosome contacts. | Open2C; Abdennur, Nezar; Fudenberg, Geoffrey; Flyamer, Ilya M; Galitsyna, Aleksandra A; Goloborodko, Anton; Imakaev, Maxim; Venev, Sergey V | PLoS computational biology | 38809952 | 2024 May |
| Multifaceted roles of cohesin in regulating transcriptional loops. | Kim, Minji; Wang, Ping; Clow, Patricia A; Chien, I Eli; Wang, Xiaotao; Peng, Jianhao; Chai, Haoxi; Liu, Xiyuan; Lee, Byoungkoo; Ngan, Chew Yee; Yue, Feng; Milenkovic, Olgica; Chuang, Jeffrey H; Wei, Chia-Lin; Casellas, Rafael; Cheng, Albert W; Ruan, Yijun | bioRxiv : the preprint server for biology | 38585764 | 2024 Mar 27 |
| Removing unwanted variation between samples in Hi-C experiments. | Fletez-Brant, Kipper; Qiu, Yunjiang; Gorkin, David U; Hu, Ming; Hansen, Kasper D | Briefings in bioinformatics | 38711367 | 2024 Mar 27 |
| The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. | Longhurst, Adam D; Wang, Kyle; Suresh, Harsha Garadi; Ketavarapu, Mythili; Ward, Henry N; Jones, Ian R; Narayan, Vivek; Hundley, Frances V; Hassan, Arshia Zernab; Boone, Charles; Myers, Chad L; Shen, Yin; Ramani, Vijay; Andrews, Brenda J; Toczyski, David P | bioRxiv : the preprint server for biology | 38562687 | 2024 Mar 19 |
| Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness. | Liu, Ning; Qiang, Wenan; Jordan, Philip; Marko, John; Qiao, Huanyu | bioRxiv : the preprint server for biology | 38559262 | 2024 Mar 11 |
| TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells. | Xu, Meng; Senanayaka, Dulmi; Zhao, Rongwei; Chigumira, Tafadzwa; Tripathi, Astha; Tones, Jason; Lackner, Rachel M; Wondisford, Anne R; Moneysmith, Laurel N; Hirschi, Alexander; Craig, Sara; Alishiri, Sahar; O'Sullivan, Roderick J; Chenoweth, David M; Reiter, Nicholas J; Zhang, Huaiying | Nature communications | 38461301 | 2024 Mar 09 |
| Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. | Daniel, Bence; Chen, Andy Y; Sandor, Katalin; Zhang, Wenxi; Miao, Zhuang; Lareau, Caleb A; Yost, Kathryn E; Chang, Howard Y; Satpathy, Ansuman T | bioRxiv : the preprint server for biology | 38496446 | 2024 Mar 04 |
| Single-cell multiplex chromatin and RNA interactions in aging human brain. | Wen, Xingzhao; Luo, Zhifei; Zhao, Wenxin; Calandrelli, Riccardo; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng | bioRxiv : the preprint server for biology | 37425846 | 2024 Mar 04 |
| Nuclear morphology is shaped by loop-extrusion programs. | Patta, Indumathi; Zand, Maryam; Lee, Lindsay; Mishra, Shreya; Bortnick, Alexandra; Lu, Hanbin; Prusty, Arpita; McArdle, Sara; Mikulski, Zbigniew; Wang, Huan-You; Cheng, Christine S; Fisch, Kathleen M; Hu, Ming; Murre, Cornelis | Nature | 38355805 | 2024 Mar |
| Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. | Murphy, Sedona Eve; Boettiger, Alistair Nicol | Nature genetics | 38361032 | 2024 Mar |
| Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories. | Dixon, Julie C; Frick, Christopher L; Leveille, Chantelle L; Garrison, Philip; Lee, Peyton A; Mogre, Saurabh S; Morris, Benjamin; Nivedita, Nivedita; Vasan, Ritvik; Chen, Jianxu; Fraser, Cameron L; Gamlin, Clare R; Harris, Leigh K; Hendershott, Melissa C; Johnson, Graham T; Klein, Kyle N; Oluoch, Sandra A; Thirstrup, Derek J; Sluzewski, M Filip; Wilhelm, Lyndsay; Yang, Ruian; Toloudis, Daniel M; Viana, Matheus P; Theriot, Julie A; Rafelski, Susanne M | bioRxiv : the preprint server for biology | 38979140 | 2024 Jun 30 |
| Gene activity fully predicts transcriptional bursting dynamics. | Chen, Po-Ta; Levo, Michal; Zoller, Benjamin; Gregor, Thomas | ArXiv | 37131882 | 2024 Jun 28 |
| Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins. | Wakim, Joseph G; Spakowitz, Andrew J | Proceedings of the National Academy of Sciences of the United States of America | 38900792 | 2024 Jun 25 |
| A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. | Chavan, Ankita; Isenhart, Randi; Nguyen, Son C; Kotb, Noor M; Harke, Jailynn; Sintsova, Anna; Ulukaya, Gulay; Uliana, Federico; Ashiono, Caroline; Kutay, Ulrike; Pegoraro, Gianluca; Rangan, Prashanth; Joyce, Eric F; Jagannathan, Madhav | Genes & development | 38866555 | 2024 Jun 25 |
| Widespread chromatin context-dependencies of DNA double-strand break repair proteins. | Vergara, Xabier; Manjón, Anna G; de Haas, Marcel; Morris, Ben; Schep, Ruben; Leemans, Christ; Friskes, Anoek; Beijersbergen, Roderick L; Sanders, Mathijs A; Medema, René H; van Steensel, Bas | Nature communications | 38909016 | 2024 Jun 22 |
| An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. | Waterbury, Amanda L; Kwok, Hui Si; Lee, Ceejay; Narducci, Domenic N; Freedy, Allyson M; Su, Cindy; Raval, Shaunak; Reiter, Andrew H; Hawkins, William; Lee, Kwangwoon; Li, Jiaming; Hoenig, Samuel M; Vinyard, Michael E; Cole, Philip A; Hansen, Anders S; Carr, Steven A; Papanastasiou, Malvina; Liau, Brian B | Molecular cell | 38870936 | 2024 Jun 20 |
| FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data. | Patel, Rohan; Pham, Kenneth; Chandrashekar, Harshini; Phillips-Cremins, Jennifer E | bioRxiv : the preprint server for biology | 38948824 | 2024 Jun 18 |
| The temporal progression of lung immune remodeling during breast cancer metastasis. | McGinnis, Christopher S; Miao, Zhuang; Superville, Daphne; Yao, Winnie; Goga, Andrei; Reticker-Flynn, Nathan E; Winkler, Juliane; Satpathy, Ansuman T | Cancer cell | 38821060 | 2024 Jun 10 |
| ULV: A robust statistical method for clustered data, with applications to multi-subject, single-cell omics data. | Du, Mingyu; Johnston, Kevin; Berrocal, Veronica; Li, Wei; Xu, Xiangmin; Yu, Zhaoxia | ArXiv | 38947924 | 2024 Jun 10 |
| HLH-30/TFEB rewires the chaperone network to promote proteostasis under conditions of Coenzyme A and Iron-Sulfur Cluster Deficiency. | Shalash, Rewayd; Levi-Ferber, Mor; von Chrzanowski, Henrik; Atrash, Mohammad Khaled; Shav-Tal, Yaron; Henis-Korenblit, Sivan | bioRxiv : the preprint server for biology | 38895373 | 2024 Jun 06 |
| Bigtools: a high-performance BigWig and BigBed library in Rust. | Huey, Jack D; Abdennur, Nezar | Bioinformatics (Oxford, England) | 38837370 | 2024 Jun 03 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni, Ketrin; Pollard, Katherine S | Bioinformatics (Oxford, England) | 38796686 | 2024 Jun 03 |
| Building momentum through networks: Bioimaging across the Americas. | De Niz, Mariana; Escobedo García, Rodrigo; Terán Ramirez, Celina; Pakowski, Ysa; Abonza, Yuriney; Bialy, Nikki; Orr, Vanessa L; Olivera, Andres; Abonza, Victor; Alleva, Karina; Allodi, Silvana; Almeida, Michael F; Becerril Cuevas, Alexis Ricardo; Bonnet, Frederic; Burgos Solorio, Armando; Chew, Teng-Leong; Chiabrando, Gustavo; Cimini, Beth; Cleret-Buhot, Aurélie; Contreras Jiménez, Gastón; Daza, Laura; De Sá, Vanessa; De Val, Natalia; Delgado-Álvarez, Diego L; Eliceiri, Kevin; Fiolka, Reto; Grecco, Hernan; Hanein, Dorit; Hernández Herrera, Paúl; Hockberger, Phil; Hernandez, Haydee O; Hernandez Guadarrama, Yael; Itano, Michelle; Jacobs, Caron A; Jiménez-García, Luis F; Jiménez Sabinina, Vilma; Kamaid, Andres; Keppler, Antje; Kumar, Abhishek; Lacoste, Judith; Lovy, Alenka; Luby-Phelps, Kate; Mahadevan-Jansen, Anita; Malacrida, Leonel; Mehta, Shalin B; Miller, Caroline; Miranda, Kildare; Moore, Joshua A; North, Alison; O'Toole, Peter; Olivares Urbano, Mariana; Pietrasanta, Lía I; Portugal, Rodrigo V; Rossi, Andrés H; Sanchez Contreras, Jonathan; Strambio-De-Castilla, Caterina; Soldevila, Gloria; Vale, Bruno; Vazquez, Diana; Wood, Chris; Brown, Claire M; Guerrero, Adan | Journal of microscopy | 38747464 | 2024 Jun |
| Genome folding principles uncovered in condensin-depleted mitotic chromosomes. | Zhao, Han; Lin, Yinzhi; Lin, En; Liu, Fuhai; Shu, Lirong; Jing, Dannan; Wang, Baiyue; Wang, Manzhu; Shan, Fengnian; Zhang, Lin; Lam, Jessica C; Midla, Susannah C; Giardine, Belinda M; Keller, Cheryl A; Hardison, Ross C; Blobel, Gerd A; Zhang, Haoyue | Nature genetics | 38802567 | 2024 Jun |
| Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. | Mowery, Cody T; Freimer, Jacob W; Chen, Zeyu; Casaní-Galdón, Salvador; Umhoefer, Jennifer M; Arce, Maya M; Gjoni, Ketrin; Daniel, Bence; Sandor, Katalin; Gowen, Benjamin G; Nguyen, Vinh; Simeonov, Dimitre R; Garrido, Christian M; Curie, Gemma L; Schmidt, Ralf; Steinhart, Zachary; Satpathy, Ansuman T; Pollard, Katherine S; Corn, Jacob E; Bernstein, Bradley E; Ye, Chun Jimmie; Marson, Alexander | Nature genetics | 38811842 | 2024 Jun |
| Exploring the roles of RNAs in chromatin architecture using deep learning. | Kuang, Shuzhen; Pollard, Katherine S | Nature communications | 39075082 | 2024 Jul 29 |
| Peripherical Blood hsa-miR-335-5p Quantification as a Prognostic, but Not Diagnostic, Marker of Gastric Cancer. | Ramírez-Vidal, Lizbeth; Becerril-Rico, Jared; Monroy-Mora, Alberto; Tinajero-Rodríguez, Jose Manuel; Centeno-Cruz, Federico; Oñate-Ocaña, Luis F; Ortiz-Sánchez, Elizabeth | Diagnostics (Basel, Switzerland) | 39125490 | 2024 Jul 26 |
| AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance. | Li, Jingxin; Ravindran, Pavithran T; O'Farrell, Aoife; Busch, Gianna T; Boe, Ryan H; Niu, Zijian; Woo, Sean; Dunagin, Margaret C; Jain, Naveen; Goyal, Yogesh; Sarma, Kavitha; Herlyn, Meenhard; Raj, Arjun | bioRxiv : the preprint server for biology | 39091739 | 2024 Jul 25 |
| Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. | Do, Catherine; Jiang, Guimei; Cova, Giulia; Katsifis, Christos C; Narducci, Domenic N; Yang, Jie; Sakellaropoulos, Theodore; Vidal, Raphael; Lhoumaud, Priscillia; Tsirigos, Aristotelis; Regis, Faye Fara D; Kakabadze, Nata; Nora, Elphege P; Noyes, Marcus; Cheng, Xiaodong; Hansen, Anders S; Skok, Jane A | Research square | 39070636 | 2024 Jul 19 |
| Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. | Conte, Mattia; Abraham, Alex; Esposito, Andrea; Yang, Liyan; Gibcus, Johan H; Parsi, Krishna M; Vercellone, Francesca; Fontana, Andrea; Pierno, Florinda Di; Dekker, Job; Nicodemi, Mario | bioRxiv : the preprint server for biology | 39071404 | 2024 Jul 16 |
| PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. | Rodríguez, Tomás C; Yurkovetskiy, Leonid; Nagalekshmi, Karthika; Lam, Chin Hung Oscar; Jazbec, Eva; Maitland, Stacy A; Wolfe, Scot A; Sontheimer, Erik J; Luban, Jeremy | bioRxiv : the preprint server for biology | 39026796 | 2024 Jul 13 |
| A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. | Knoedler, Joseph R; Inoue, Sayaka; Bayless, Daniel W; Yang, Taehong; Tantry, Adarsh; Davis, Chung-Ha; Leung, Nicole Y; Parthasarathy, Srinivas; Wang, Grace; Alvarado, Maricruz; Rizvi, Abbas H; Fenno, Lief E; Ramakrishnan, Charu; Deisseroth, Karl; Shah, Nirao M | Cell | 38810647 | 2024 Jul 11 |
| Vcam1+ Fibro-adipogenic Progenitors Mark Fatty Infiltration in Chronic Limb Threatening Ischemia. | Dai, Qunsheng; Wan, Changxin; Xu, Yueyuan; Fei, Kaileen; Olivere, Lindsey A; Garrett, Brianna; Akers, Leo; Peters, Derek; Otto, James; Kontos, Christopher D; Ji, Zhiceng; Diao, Yarui; Southerland, Kevin W | bioRxiv : the preprint server for biology | 39026697 | 2024 Jul 11 |
| Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing. | Nguyen, Long T; Rakestraw, Noah R; Pizzano, Brianna L M; Young, Cullen B; Huang, Yujia; Beerensson, Kate T; Fang, Anne; Antal, Sydney G; Anamisis, Katerina V; Peggs, Coleen M D; Yan, Jun; Jing, Yangwode; Burdine, Rebecca D; Adamson, Britt; Toettcher, Jared E; Myhrvold, Cameron; Jain, Piyush K | bioRxiv : the preprint server for biology | 39026836 | 2024 Jul 10 |
| SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. | Yu, Hongyu; Wu, Daiqing; Mishra, Shreya; Shen, Guning; Sun, Huaigu; Hu, Ming; Li, Yun | Communications biology | 38982263 | 2024 Jul 09 |
| Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome. | Wang, Sung Eun; Cheng, Yubao; Lim, Jaechul; Jang, Mi-Ae; Forrest, Emily N; Kim, Yuna; Donahue, Meaghan; Qiao, Sheng-Nan; Xiong, Yan; Jin, Jian; Wang, Siyuan; Jiang, Yong-Hui | Research square | 39011107 | 2024 Jul 03 |
| Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. | Boe, Ryan H; Triandafillou, Catherine G; Lazcano, Rossana; Wargo, Jennifer A; Raj, Arjun | bioRxiv : the preprint server for biology | 39005406 | 2024 Jul 02 |
| CTCF is essential for proper mitotic spindle structure and anaphase segregation. | Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D | Chromosoma | 37728741 | 2024 Jul |
| From feulgen to modern methods: marking a century of DNA imaging advances. | Lakadamyali, Melike | Histochemistry and cell biology | 38753186 | 2024 Jul |
| Dynamic chromosome association with nuclear organelles in living cells. | Phan, Lam Minh Uyen; Yeo, Wei-Hong; Zhang, Hao F; Huang, Sui | Histochemistry and cell biology | 38811432 | 2024 Jul |
| Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus. | Girard, Martin; de la Cruz, Monica Olvera; Marko, John F; Erbaş, Aykut | Physical review. E | 39160964 | 2024 Jul |
| Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning. | Niu, Zijian; O'Farrell, Aoife; Li, Jingxin; Reffsin, Sam; Jain, Naveen; Dardani, Ian; Goyal, Yogesh; Raj, Arjun | bioRxiv : the preprint server for biology | 38352551 | 2024 Jan 31 |
| Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development. | Kaplan, Harris S; Logeman, Brandon L; Zhang, Kai; Santiago, Celine; Sohail, Noor; Naumenko, Serhiy; Ho Sui, Shannan J; Ginty, David D; Ren, Bing; Dulac, Catherine | bioRxiv : the preprint server for biology | 38328205 | 2024 Jan 23 |
| Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. | Hao, Qinyu; Liu, Minxue; Daulatabad, Swapna Vidhur; Gaffari, Saba; Song, You Jin; Srivastava, Rajneesh; Bhaskar, Shivang; Moitra, Anurupa; Mangan, Hazel; Tseng, Elizabeth; Gilmore, Rachel B; Frier, Susan M; Chen, Xin; Wang, Chengliang; Huang, Sui; Chamberlain, Stormy; Jin, Hong; Korlach, Jonas; McStay, Brian; Sinha, Saurabh; Janga, Sarath Chandra; Prasanth, Supriya G; Prasanth, Kannanganattu V | eLife | 38240312 | 2024 Jan 19 |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed, Ellen H; Aoki, Kazuhiro; Toettcher, Jared E | bioRxiv : the preprint server for biology | 38293146 | 2024 Jan 17 |
| SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. | Yu, Hongyu; Wu, Daiqing; Shen, Guning; Hu, Ming; Li, Yun | bioRxiv : the preprint server for biology | 38293083 | 2024 Jan 15 |
| mRNA initiation and termination are spatially coordinated. | Calvo-Roitberg, Ezequiel; Carroll, Christine L; Venev, Sergey V; Kim, GyeungYun; Mick, Steven T; Dekker, Job; Fiszbein, Ana; Pai, Athma A | bioRxiv : the preprint server for biology | 38260419 | 2024 Jan 07 |
| 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. | Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie | Nature structural & molecular biology | 38053013 | 2024 Jan |
| Emergence of replication timing during early mammalian development. | Nakatani, Tsunetoshi; Schauer, Tamas; Altamirano-Pacheco, Luis; Klein, Kyle N; Ettinger, Andreas; Pal, Mrinmoy; Gilbert, David M; Torres-Padilla, Maria-Elena | Nature | 38123678 | 2024 Jan |
| RNA-mediated symmetry breaking enables singular olfactory receptor choice. | Pourmorady, Ariel D; Bashkirova, Elizaveta V; Chiariello, Andrea M; Belagzhal, Houda; Kodra, Albana; Duffié, Rachel; Kahiapo, Jerome; Monahan, Kevin; Pulupa, Joan; Schieren, Ira; Osterhoudt, Alexa; Dekker, Job; Nicodemi, Mario; Lomvardas, Stavros | Nature | 38123679 | 2024 Jan |
| Toward a common standard for data and specimen provenance in life sciences. | Wittner, Rudolf; Holub, Petr; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Plass, Markus; Allocca, Clare; Betsou, Fay; Burdett, Tony; Cancio, Ibon; Chapman, Adriane; Chapman, Martin; Courtot, Mélanie; Curcin, Vasa; Eder, Johann; Elliot, Mark; Exter, Katrina; Goble, Carole; Golebiewski, Martin; Kisler, Bron; Kremer, Andreas; Leo, Simone; Lin-Gibson, Sheng; Marsano, Anna; Mattavelli, Marco; Moore, Josh; Nakae, Hiroki; Perseil, Isabelle; Salman, Ayat; Sluka, James; Soiland-Reyes, Stian; Strambio-De-Castillia, Caterina; Sussman, Michael; Swedlow, Jason R; Zatloukal, Kurt; Geiger, Jörg | Learning health systems | 38249839 | 2024 Jan |
| SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML. | Zhao, Rongwei; Xu, Meng; Wondisford, Anne R; Lackner, Rachel M; Salsman, Jayme; Dellaire, Graham; Chenoweth, David M; O'Sullivan, Roderick J; Zhao, Xiaolan; Zhang, Huaiying | bioRxiv : the preprint server for biology | 38463993 | 2024 Feb 29 |
| A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations. | Chandrashekar, Harshini; Simandi, Zoltan; Choi, Heesun; Ryu, Han-Seul; Waldman, Abraham J; Nikish, Alexandria; Muppidi, Srikar S; Gong, Wanfeng; Paquet, Dominik; Phillips-Cremins, Jennifer E | bioRxiv : the preprint server for biology | 38463966 | 2024 Feb 27 |
| Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain, Naveen; Goyal, Yogesh; Dunagin, Margaret C; Cote, Christopher J; Mellis, Ian A; Emert, Benjamin; Jiang, Connie L; Dardani, Ian P; Reffsin, Sam; Arnett, Miles; Yang, Wenli; Raj, Arjun | Cell systems | 38335955 | 2024 Feb 21 |
| Phase separation of YAP-MAML2 differentially regulates the transcriptome. | Chung, Chan-I; Yang, Junjiao; Yang, Xiaoyu; Liu, Hongjiang; Ma, Zhimin; Szulzewsky, Frank; Holland, Eric C; Shen, Yin; Shu, Xiaokun | Proceedings of the National Academy of Sciences of the United States of America | 38315854 | 2024 Feb 13 |
| Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types. | Hamazaki, Nobuhiko; Yang, Wei; Kubo, Connor; Qiu, Chengxiang; Martin, Beth K; Garge, Riddhiman K; Regalado, Samuel G; Nichols, Eva; Lee, Choli; Daza, Riza M; Srivatsan, Sanjay; Shendure, Jay | bioRxiv : the preprint server for biology | 38405970 | 2024 Feb 12 |
| Bigtools: a high-performance BigWig and BigBed library in Rust. | Huey, Jack D; Abdennur, Nezar | bioRxiv : the preprint server for biology | 38370777 | 2024 Feb 08 |
| DNA density is a better indicator of a nuclear bleb than lamin B loss. | Bunner, Samantha; Prince, Kelsey; Srikrishna, Karan; Pujadas, Emily Marie; McCarthy, Antonia Amonu; Kuklinski, Anna; Jackson, Olivia; Pellegrino, Pedro; Jagtap, Shrushti; Eweka, Imuetiyan; Lawlor, Colman; Eastin, Emma; Yas, Griffin; Aiello, Julianna; LaPointe, Nathan; von Blucher, Isabelle Schramm; Hardy, Jillian; Chen, Jason; Backman, Vadim; Janssen, Anne; Packard, Mary; Dorfman, Katherine; Almassalha, Luay; Bahiru, Michael Seifu; Stephens, A D | bioRxiv : the preprint server for biology | 38370828 | 2024 Feb 07 |
| Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. | Stein, Johannes; Ericsson, Maria; Nofal, Michel; Magni, Lorenzo; Aufmkolk, Sarah; McMillan, Ryan B; Breimann, Laura; Herlihy, Conor P; Lee, S Dean; Willemin, Andréa; Wohlmann, Jens; Arguedas-Jimenez, Laura; Yin, Peng; Pombo, Ana; Church, George M; Wu, Chao-Kng | bioRxiv : the preprint server for biology | 38370628 | 2024 Feb 05 |
| Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. | Aguilar, Robin; Camplisson, Conor K; Lin, Qiaoyi; Miga, Karen H; Noble, William S; Beliveau, Brian J | Nature communications | 38310092 | 2024 Feb 03 |
| Actin contraction controls nuclear blebbing and rupture independent of actin confinement. | Pho, Mai; Berrada, Yasmin; Gunda, Aachal; Lavallee, Anya; Chiu, Katherine; Padam, Arimita; Currey, Marilena L; Stephens, Andrew D | Molecular biology of the cell | 38088876 | 2024 Feb 01 |
| Bioframe: operations on genomic intervals in Pandas dataframes. | Open2C; Abdennur, Nezar; Fudenberg, Geoffrey; Flyamer, Ilya M; Galitsyna, Aleksandra A; Goloborodko, Anton; Imakaev, Maxim; Venev, Sergey | Bioinformatics (Oxford, England) | 38402507 | 2024 Feb 01 |
| Epigenetic regulatory layers in the 3D nucleus. | Willemin, Andréa; Szabó, Dominik; Pombo, Ana | Molecular cell | 38242127 | 2024 Feb 01 |
| Role of H3K4 monomethylation in gene regulation. | Wang, Zhaoning; Ren, Bing | Current opinion in genetics & development | 38278054 | 2024 Feb |
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| A single-cell time-lapse of mouse prenatal development from gastrula to birth. | Qiu, Chengxiang; Martin, Beth K; Welsh, Ian C; Daza, Riza M; Le, Truc-Mai; Huang, Xingfan; Nichols, Eva K; Taylor, Megan L; Fulton, Olivia; O'Day, Diana R; Gomes, Anne Roshella; Ilcisin, Saskia; Srivatsan, Sanjay; Deng, Xinxian; Disteche, Christine M; Noble, William Stafford; Hamazaki, Nobuhiko; Moens, Cecilia B; Kimelman, David; Cao, Junyue; Schier, Alexander F; Spielmann, Malte; Murray, Stephen A; Trapnell, Cole; Shendure, Jay | Nature | 38355799 | 2024 Feb |
| A fast, scalable and versatile tool for analysis of single-cell omics data. | Zhang, Kai; Zemke, Nathan R; Armand, Ethan J; Ren, Bing | Nature methods | 38191932 | 2024 Feb |
| What are tethering elements? | Li, Xiao; Levine, Michael | Current opinion in genetics & development | 38237456 | 2024 Feb |
| The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. | Makeyev, Eugene V; Huang, Sui | Nucleus (Austin, Tex.) | 38281066 | 2024 Dec |
| A molecular proximity sensor based on an engineered, dual-component guide RNA. | Choi, Junhong; Chen, Wei; Liao, Hanna; Li, Xiaoyi; Shendure, Jay | bioRxiv : the preprint server for biology | 37645782 | 2024 Aug 27 |
| CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. | Kaplan, Samuel Joseph; Wong, Wilfred; Yan, Jielin; Pulecio, Julian; Cho, Hyein S; Li, Qianzi; Zhao, Jiahui; Leslie-Iyer, Jayanti; Kazakov, Jonathan; Murphy, Dylan; Luo, Renhe; Dey, Kushal K; Apostolou, Effie; Leslie, Christina S; Huangfu, Danwei | Cell reports | 39163202 | 2024 Aug 27 |
| HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA. | Saunders, Hayden S; Chio, Un Seng; Moore, Camille M; Ramani, Vijay; Cheng, Yifan; Narlikar, Geeta J | bioRxiv : the preprint server for biology | 39229246 | 2024 Aug 24 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden, Nicholas G; Lam, Jessica C; Goel, Viraat Y; Wang, Siqing; Wang, Xiaokang; Midla, Susannah C; Quijano, Alma; Keller, Cheryl A; Giardine, Belinda M; Hardison, Ross C; Zhang, Haoyue; Hansen, Anders S; Blobel, Gerd A | bioRxiv : the preprint server for biology | 39229045 | 2024 Aug 24 |
| SUMO promotes DNA repair protein collaboration to support alternative telomere lengthening in the absence of PML. | Zhao, Rongwei; Xu, Meng; Yu, Xiaoyang; Wondisford, Anne R; Lackner, Rachel M; Salsman, Jayme; Dellaire, Graham; Chenoweth, David M; O'Sullivan, Roderick J; Zhao, Xiaolan; Zhang, Huaiying | Genes & development | 39038850 | 2024 Aug 20 |
| Retinoic acid induces human gastruloids with posterior embryo-like structures. | Hamazaki, Nobuhiko; Yang, Wei; Kubo, Connor A; Qiu, Chengxiang; Martin, Beth K; Garge, Riddhiman K; Regalado, Samuel G; Nichols, Eva K; Pendyala, Sriram; Bradley, Nicholas; Fowler, Douglas M; Lee, Choli; Daza, Riza M; Srivatsan, Sanjay; Shendure, Jay | Nature cell biology | 39164488 | 2024 Aug 20 |
| Interpretable representation learning for 3D multi-piece intracellular structures using point clouds. | Vasan, Ritvik; Ferrante, Alexandra J; Borensztejn, Antoine; Frick, Christopher L; Gaudreault, Nathalie; Mogre, Saurabh S; Morris, Benjamin; Pires, Guilherme G; Rafelski, Susanne M; Theriot, Julie A; Viana, Matheus P | bioRxiv : the preprint server for biology | 39091871 | 2024 Aug 13 |
| YAP charge patterning mediates signal integration through transcriptional co-condensates. | Meyer, Kirstin; Yserentant, Klaus; Cheloor-Kovilakam, Rasmi; Ruff, Kiersten M; Chung, Chan-I; Shu, Xiaokun; Huang, Bo; Weiner, Orion D | bioRxiv : the preprint server for biology | 39149273 | 2024 Aug 10 |
| Transcription factor clusters as information transfer agents. | Munshi, Rahul; Ling, Jia; Ryabichko, Sergey; Wieschaus, Eric F; Gregor, Thomas | ArXiv | 38495568 | 2024 Aug 08 |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed, Ellen H; Gao, Yang; Aoki, Kazuhiro; Toettcher, Jared E | Nature communications | 39112465 | 2024 Aug 07 |
| Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. | Bing, Xinyang; Ke, Wenfan; Fujioka, Miki; Kurbidaeva, Amina; Levitt, Sarah; Levine, Mike; Schedl, Paul; Jaynes, James B | eLife | 39110499 | 2024 Aug 07 |
| Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. | Chen, Valerie; Yang, Muyu; Cui, Wenbo; Kim, Joon Sik; Talwalkar, Ameet; Ma, Jian | Nature methods | 39122941 | 2024 Aug |
| Symbolic recording of signalling and cis-regulatory element activity to DNA. | Chen, Wei; Choi, Junhong; Li, Xiaoyi; Nathans, Jenny F; Martin, Beth; Yang, Wei; Hamazaki, Nobuhiko; Qiu, Chengxiang; Lalanne, Jean-Benoît; Regalado, Samuel; Kim, Haedong; Agarwal, Vikram; Nichols, Eva; Leith, Anh; Lee, Choli; Shendure, Jay | Nature | 39020177 | 2024 Aug |
| GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. | Zhou, Tianming; Zhang, Ruochi; Jia, Deyong; Doty, Raymond T; Munday, Adam D; Gao, Daniel; Xin, Li; Abkowitz, Janis L; Duan, Zhijun; Ma, Jian | Nature genetics | 38744973 | 2024 Aug |
| Rules of engagement for condensins and cohesins guide mitotic chromosome formation. | Samejima, Kumiko; Gibcus, Johan H; Abraham, Sameer; Cisneros-Soberanis, Fernanda; Samejima, Itaru; Beckett, Alison J; Pučeková, Nina; Abad, Maria Alba; Medina-Pritchard, Bethan; Paulson, James R; Xie, Linfeng; Jeyaprakash, A Arockia; Prior, Ian A; Mirny, Leonid A; Dekker, Job; Goloborodko, Anton; Earnshaw, William C | bioRxiv : the preprint server for biology | 38659940 | 2024 Apr 30 |
| Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells. | Chang, Lei; Xie, Yang; Taylor, Brett; Wang, Zhaoning; Sun, Jiachen; Tan, Tuyet R; Bejar, Rafael; Chen, Clark C; Furnari, Frank B; Hu, Ming; Ren, Bing | bioRxiv : the preprint server for biology | 38712075 | 2024 Apr 22 |
| Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. | Hildebrand, Erica M; Polovnikov, Kirill; Dekker, Bastiaan; Liu, Yu; Lafontaine, Denis L; Fox, A Nicole; Li, Ying; Venev, Sergey V; Mirny, Leonid A; Dekker, Job | Molecular cell | 38521067 | 2024 Apr 18 |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene. | Coté, Allison; O'Farrell, Aoife; Dardani, Ian; Dunagin, Margaret; Coté, Chris; Wan, Yihan; Bayatpour, Sareh; Drexler, Heather L; Alexander, Katherine A; Chen, Fei; Wassie, Asmamaw T; Patel, Rohan; Pham, Kenneth; Boyden, Edward S; Berger, Shelly; Phillips-Cremins, Jennifer; Churchman, L Stirling; Raj, Arjun | eLife | 38577979 | 2024 Apr 05 |
| Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. | Guo, Jimmy K; Blanco, Mario R; Walkup 4th, Ward G; Bonesteele, Grant; Urbinati, Carl R; Banerjee, Abhik K; Chow, Amy; Ettlin, Olivia; Strehle, Mackenzie; Peyda, Parham; Amaya, Enrique; Trinh, Vickie; Guttman, Mitchell | Molecular cell | 38387462 | 2024 Apr 04 |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. | Andronov, Leonid; Han, Mengting; Zhu, Yanyu; Balaji, Ashwin; Roy, Anish R; Barentine, Andrew E S; Patel, Puja; Garhyan, Jaishree; Qi, Lei S; Moerner, W E | bioRxiv : the preprint server for biology | 37986994 | 2024 Apr 01 |
| Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. | Oomen, Marlies E; Torres-Padilla, Maria-Elena | EMBO reports | 38528171 | 2024 Apr |
| Single-cell multiplex chromatin and RNA interactions in ageing human brain. | Wen, Xingzhao; Luo, Zhifei; Zhao, Wenxin; Calandrelli, Riccardo; Nguyen, Tri C; Wan, Xueyi; Charles Richard, John Lalith; Zhong, Sheng | Nature | 38538789 | 2024 Apr |
| Toward a comprehensive view of gene architecture during transcription. | Woodworth, Marcus A; Lakadamyali, Melike | Current opinion in genetics & development | 38309073 | 2024 Apr |
| Contribution of CENP-F to FOXM1-Mediated Discordant Centromere and Kinetochore Transcriptional Regulation. | Khurana, Sakshi; Varma, Dileep; Foltz, Daniel R | Molecular and cellular biology | 38779933 | 2024 |
| Nuclear shape is affected differentially by loss of lamin A, lamin C, or both lamin A and C. | Pho, Mai; Berrada, Yasmin; Gunda, Aachal; Stephens, Andrew D | microPublication biology | 38440331 | 2024 |
| HybriSeq: Probe-based Device-free Single-cell RNA Profiling. | Foyt, Daniel; Brown, David; Zhou, Shuqin; Huang, Bo | bioRxiv : the preprint server for biology | 37808850 | 2023 Sep 29 |
| Alu transposable elements rewire enhancer-promoter network through RNA pairing. | Wen, Xingzhao; Zhong, Sheng | Molecular cell | 37738962 | 2023 Sep 21 |
| SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. | Lee, Lindsay; Yu, Miao; Li, Xiaoqi; Zhu, Chenxu; Zhang, Yanxiao; Yu, Hongyu; Chen, Ziyin; Mishra, Shreya; Ren, Bing; Li, Yun; Hu, Ming | Briefings in bioinformatics | 37649383 | 2023 Sep 20 |
| CTCF is essential for proper mitotic spindle structure and anaphase segregation. | Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D | Chromosoma | 37728741 | 2023 Sep 20 |
| Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. | Bashkirova, Elizaveta V; Klimpert, Nell; Monahan, Kevin; Campbell, Christine E; Osinski, Jason M; Tan, Longzhi; Schieren, Ira; Pourmorady, Ariel; Stecky, Beka; Barnea, Gilad; Xie, X Sunnie; Abdus-Saboor, Ishmail; Shykind, Benjamin; Jones-Marlin, Bianca; Gronostajski, Richard M; Fleischmann, Alexander; Lomvardas, Stavros | bioRxiv : the preprint server for biology | 36993168 | 2023 Sep 19 |
| Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. | Deshpande, Rajashree A; Marin-Gonzalez, Alberto; Barnes, Hannah K; Woolley, Phillip R; Ha, Taekjip; Paull, Tanya T | Nature communications | 37717054 | 2023 Sep 16 |
| Community-developed checklists for publishing images and image analyses. | Schmied, Christopher; Nelson, Michael S; Avilov, Sergiy; Bakker, Gert-Jan; Bertocchi, Cristina; Bischof, Johanna; Boehm, Ulrike; Brocher, Jan; Carvalho, Mariana; Chiritescu, Catalin; Christopher, Jana; Cimini, Beth A; Conde-Sousa, Eduardo; Ebner, Michael; Ecker, Rupert; Eliceiri, Kevin; Fernandez-Rodriguez, Julia; Gaudreault, Nathalie; Gelman, Laurent; Grunwald, David; Gu, Tingting; Halidi, Nadia; Hammer, Mathias; Hartley, Matthew; Held, Marie; Jug, Florian; Kapoor, Varun; Koksoy, Ayse Aslihan; Lacoste, Judith; Dévédec, Sylvia Le; Guyader, Sylvie Le; Liu, Penghuan; Martins, Gabriel G; Mathur, Aastha; Miura, Kota; Montero Llopis, Paula; Nitschke, Roland; North, Alison; Parslow, Adam C; Payne-Dwyer, Alex; Plantard, Laure; Ali, Rizwan; Schroth-Diez, Britta; Schütz, Lucas; Scott, Ryan T; Seitz, Arne; Selchow, Olaf; Sharma, Ved P; Spitaler, Martin; Srinivasan, Sathya; Strambio-De-Castillia, Caterina; Taatjes, Douglas; Tischer, Christian; Jambor, Helena Klara | ArXiv | 36824427 | 2023 Sep 14 |
| Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. | Chang, Li-Hsin; Ghosh, Sourav; Papale, Andrea; Luppino, Jennifer M; Miranda, Mélanie; Piras, Vincent; Degrouard, Jéril; Edouard, Joanne; Poncelet, Mallory; Lecouvreur, Nathan; Bloyer, Sébastien; Leforestier, Amélie; Joyce, Eric F; Holcman, David; Noordermeer, Daan | Nature communications | 37699887 | 2023 Sep 12 |
| SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. | Zhang, Meng; Ehmann, Mary Elisabeth; Matukumalli, Srija; Boob, Aashutosh Girish; Gilbert, David M; Zhao, Huimin | Nature communications | 37699958 | 2023 Sep 12 |
| Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M | eLife | 37695017 | 2023 Sep 11 |
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| Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. | Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E | Development (Cambridge, England) | 37602510 | 2023 Sep 01 |
| Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. | Cheng, Li-Chun; Zhang, Xi; Baboo, Sabyasachi; Nguyen, Julie A; Martinez-Bartolomé, Salvador; Loose, Esther; Diedrich, Jolene; Yates 3rd, John R; Gerace, Larry | Life science alliance | 37433644 | 2023 Sep |
| Perturbations in 3D genome organization can promote acquired drug resistance. | Manjón, Anna G; Manzo, Stefano Giustino; Prekovic, Stefan; Potgeter, Leon; van Schaik, Tom; Liu, Ning Qing; Flach, Koen; Peric-Hupkes, Daniel; Joosten, Stacey; Teunissen, Hans; Friskes, Anoek; Ilic, Mila; Hintzen, Dorine; Franceschini-Santos, Vinícius H; Zwart, Wilbert; de Wit, Elzo; van Steensel, Bas; Medema, René H | Cell reports | 37733591 | 2023 Oct 31 |
| Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. | Kuang, Shuzhen; Pollard, Katherine S | bioRxiv : the preprint server for biology | 37961712 | 2023 Oct 24 |
| Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. | Calandrelli, Riccardo; Wen, Xingzhao; Charles Richard, John Lalith; Luo, Zhifei; Nguyen, Tri C; Chen, Chien-Ju; Qi, Zhijie; Xue, Shuanghong; Chen, Weizhong; Yan, Zhangming; Wu, Weixin; Zaleta-Rivera, Kathia; Hu, Rong; Yu, Miao; Wang, Yuchuan; Li, Wenbo; Ma, Jian; Ren, Bing; Zhong, Sheng | Nature communications | 37845234 | 2023 Oct 16 |
| Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. | Berg, Isabel K; Currey, Marilena L; Gupta, Sarthak; Berrada, Yasmin; Nguyen, Bao V; Pho, Mai; Patteson, Alison E; Schwarz, J M; Banigan, Edward J; Stephens, Andrew D | Journal of cell science | 37756607 | 2023 Oct 15 |
| The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. | Sinha, Joydeb; Nickels, Jan F; Thurm, Abby R; Ludwig, Connor H; Archibald, Bella N; Hinks, Michaela M; Wan, Jun; Fang, Dong; Bintu, Lacramioara | bioRxiv : the preprint server for biology | 37873347 | 2023 Oct 14 |
| In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. | Gunsalus, Laura M; Keiser, Michael J; Pollard, Katherine S | Cell genomics | 37868032 | 2023 Oct 11 |
| Single-cell chromatin state transitions during epigenetic memory formation. | Fujimori, Taihei; Rios-Martinez, Carolina; Thurm, Abby R; Hinks, Michaela M; Doughty, Benjamin R; Sinha, Joydeb; Le, Derek; Hafner, Antonina; Greenleaf, William J; Boettiger, Alistair N; Bintu, Lacramioara | bioRxiv : the preprint server for biology | 37873344 | 2023 Oct 05 |
| Gene Activity as the Predictive Indicator for Transcriptional Bursting Dynamics. | Chen, Po-Ta; Zoller, Benjamin; Levo, Michal; Gregor, Thomas | ArXiv | 37131882 | 2023 Oct 02 |
| PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. | Deng, Yihe; Zhang, Ruochi; Xu, Pan; Ma, Jian; Gu, Quanquan | bioRxiv : the preprint server for biology | 37873233 | 2023 Oct 02 |
| Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity. | Pal, Mrinmoy; Altamirano-Pacheco, Luis; Schauer, Tamas; Torres-Padilla, Maria-Elena | Genes & development | 37914351 | 2023 Oct 01 |
| Probing neural circuit mechanisms in Alzheimer's disease using novel technologies. | Grieco, Steven F; Holmes, Todd C; Xu, Xiangmin | Molecular psychiatry | 36959497 | 2023 Oct |
| Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. | Goldman, Naomi; Chandra, Aditi; Johnson, Isabelle; Sullivan, Matthew A; Patil, Abhijeet R; Vanderbeck, Ashley; Jay, Atishay; Zhou, Yeqiao; Ferrari, Emily K; Mayne, Leland; Aguilan, Jennifer; Xue, Hai-Hui; Faryabi, Robert B; John Wherry, E; Sidoli, Simone; Maillard, Ivan; Vahedi, Golnaz | Nature immunology | 37592014 | 2023 Oct |
| Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. | Abdulhay, Nour J; Hsieh, Laura J; McNally, Colin P; Ostrowski, Megan S; Moore, Camille M; Ketavarapu, Mythili; Kasinathan, Sivakanthan; Nanda, Arjun S; Wu, Ke; Chio, Un Seng; Zhou, Ziling; Goodarzi, Hani; Narlikar, Geeta J; Ramani, Vijay | Nature structural & molecular biology | 37696956 | 2023 Oct |
| Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. | Karlow, Jennifer A; Pehrsson, Erica C; Xing, Xiaoyun; Watson, Mark; Devarakonda, Siddhartha; Govindan, Ramaswamy; Wang, Ting | Genomics, proteomics & bioinformatics | 37742993 | 2023 Oct |
| HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials. | Wei, Xiaolin; Tran, Duc; Diao, Yarui | Current protocols | 37818863 | 2023 Oct |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. | Andronov, Leonid; Han, Mengting; Zhu, Yanyu; Roy, Anish R; Barentine, Andrew E S; Garhyan, Jaishree; Qi, Lei S; Moerner, W E | bioRxiv : the preprint server for biology | 37986994 | 2023 Nov 29 |
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| Genome folding principles revealed in condensin-depleted mitotic chromosomes. | Zhao, Han; Lin, Yinzhi; Lin, En; Liu, Fuhai; Shu, Lirong; Jing, Dannan; Wang, Baiyue; Wang, Manzhu; Shan, Fengnian; Zhang, Lin; Lam, Jessica C; Midla, Susannah C; Giardine, Belinda M; Keller, Cheryl A; Hardison, Ross C; Blobel, Gerd A; Zhang, Haoyue | bioRxiv : the preprint server for biology | 38014261 | 2023 Nov 13 |
| Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. | Southerland, Kevin W; Xu, Yueyuan; Peters, Derek T; Lin, Xin; Wei, Xiaolin; Xiang, Yu; Fei, Kaileen; Olivere, Lindsey A; Morowitz, Jeremy M; Otto, James; Dai, Qunsheng; Kontos, Christopher D; Diao, Yarui | Genome medicine | 37950327 | 2023 Nov 10 |
| Proteostasis governs differential temperature sensitivity across embryonic cell types. | Dorrity, Michael W; Saunders, Lauren M; Duran, Madeleine; Srivatsan, Sanjay R; Barkan, Eliza; Jackson, Dana L; Sattler, Sydney M; Ewing, Brent; Queitsch, Christine; Shendure, Jay; Raible, David W; Kimelman, David; Trapnell, Cole | Cell | 37949057 | 2023 Nov 09 |
| FOXO1 is a master regulator of CAR T memory programming. | Doan, Alexander; Mueller, Katherine P; Chen, Andy; Rouin, Geoffrey T; Daniel, Bence; Lattin, John; Chen, Yingshi; Mozarsky, Brett; Markovska, Martina; Arias-Umana, Jose; Hapke, Robert; Jung, Inyoung; Xu, Peng; Klysz, Dorota; Bashti, Malek; Quinn, Patrick J; Sandor, Katalin; Zhang, Wenxi; Hall, Junior; Lareau, Caleb; Grupp, Stephan A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W | Research square | 37986944 | 2023 Nov 07 |
| Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. | Liu, Zhi; Lee, Dong-Sung; Liang, Yuqiong; Zheng, Ye; Dixon, Jesse R | Nature communications | 37932264 | 2023 Nov 06 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni, Ketrin; Pollard, Katherine S | bioRxiv : the preprint server for biology | 37961123 | 2023 Nov 05 |
| Nucleolar structure connects with global nuclear organization. | Wang, Chen; Ma, Hanhui; Baserga, Susan J; Pederson, Thoru; Huang, Sui | Molecular biology of the cell | 37610836 | 2023 Nov 01 |
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| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong, Kyle; Zhang, Ruochi; Ma, Jian | bioRxiv : the preprint server for biology | 37292994 | 2023 May 25 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus, Laura; McArthur, Evonne; Gjoni, Ketrin; Kuang, Shuzhen; Pittman, Maureen; Capra, John; Pollard, Katherine | Research square | 37292728 | 2023 May 23 |
| Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. | Xiong, Xiong; Tasan, Ipek; Yang, Che; Zhang, Meng; Hernandez Gonzalez, Gabriela A; Liu, Shuting; Chaturvedi, Pankaj; Belmont, Andrew S; Zhao, Huimin | ACS synthetic biology | 37058298 | 2023 May 19 |
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| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu, Tian; Ang, Cheen Euong; Zhuang, Xiaowei | Cell | 37172568 | 2023 May 11 |
| Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche. | Haensel, Daniel; Daniel, Bence; Gaddam, Sadhana; Pan, Cory; Fabo, Tania; Bjelajac, Jeremy; Jussila, Anna R; Gonzalez, Fernanda; Li, Nancy Yanzhe; Chen, Yun; Hou, JinChao; Patel, Tiffany; Aasi, Sumaira; Satpathy, Ansuman T; Oro, Anthony E | Nature communications | 37164949 | 2023 May 10 |
| Interpreting non-coding disease-associated human variants using single-cell epigenomics. | Gaulton, Kyle J; Preissl, Sebastian; Ren, Bing | Nature reviews. Genetics | 37161089 | 2023 May 09 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hart | bioRxiv : the preprint server for biology | 36865282 | 2023 May 07 |
| Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. | Chen, Liang-Fu; Long, Hannah Katherine; Park, Minhee; Swigut, Tomek; Boettiger, Alistair Nicol; Wysocka, Joanna | Molecular cell | 36996812 | 2023 May 04 |
| GAGA-associated factor fosters loop formation in the Drosophila genome. | Li, Xiao; Tang, Xiaona; Bing, Xinyang; Catalano, Christopher; Li, Taibo; Dolsten, Gabriel; Wu, Carl; Levine, Michael | Molecular cell | 37003261 | 2023 May 04 |
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| Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. | Lareau, Caleb A; Liu, Vincent; Muus, Christoph; Praktiknjo, Samantha D; Nitsch, Lena; Kautz, Pauline; Sandor, Katalin; Yin, Yajie; Gutierrez, Jacob C; Pelka, Karin; Satpathy, Ansuman T; Regev, Aviv; Sankaran, Vijay G; Ludwig, Leif S | Nature protocols | 36792778 | 2023 May |
| Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. | Zou, Roger S; Liu, Yang; Gaido, Oscar E Reyes; Konig, Maximilian F; Mog, Brian J; Shen, Leo L; Aviles-Vazquez, Franklin; Marin-Gonzalez, Alberto; Ha, Taekjip | Nature methods | 37024653 | 2023 May |
| Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser. | Zhuo, Xiaoyu; Hsu, Silas; Purushotham, Deepak; Kuntala, Prashant Kumar; Harrison, Jessica K; Du, Alan Y; Chen, Samuel; Li, Daofeng; Wang, Ting | Genome research | 37156621 | 2023 May |
| Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. | Patil, Abhijeet R; Schug, Jonathan; Naji, Ali; Kaestner, Klaus H; Faryabi, Robert B; Vahedi, Golnaz | Nature metabolism | 37188822 | 2023 May |
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| Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. | Pecori, Federico; Torres-Padilla, Maria-Elena | Developmental cell | 36977375 | 2023 Mar 27 |
| Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. | Liu, Zhi; Lee, Dong-Sung; Liang, Yuqiong; Zheng, Ye; Dixon, Jesse | bioRxiv : the preprint server for biology | 36865315 | 2023 Mar 21 |
| Transcription shapes 3D chromatin organization by interacting with loop extrusion. | Banigan, Edward J; Tang, Wen; van den Berg, Aafke A; Stocsits, Roman R; Wutz, Gordana; Brandão, Hugo B; Busslinger, Georg A; Peters, Jan-Michael; Mirny, Leonid A | Proceedings of the National Academy of Sciences of the United States of America | 36897969 | 2023 Mar 14 |
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| Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. | Ho, Emily K; Oatman, Harrison R; McFann, Sarah E; Yang, Liu; Johnson, Heath E; Shvartsman, Stanislav Y; Toettcher, Jared E | bioRxiv : the preprint server for biology | 36945584 | 2023 Mar 10 |
| High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling. | Booth, Gregory T; Daza, Riza M; Srivatsan, Sanjay R; McFaline-Figueroa, Jos L; Gladden, Rula Green; Furlan, Scott N; Shendure, Jay; Trapnell, Cole | bioRxiv : the preprint server for biology | 36945538 | 2023 Mar 06 |
| Phase Separation in Biology and Disease; Current Perspectives and Open Questions. | Boeynaems, Steven; Chong, Shasha; Gsponer, Jörg; Holt, Liam; Milovanovic, Dragomir; Mitrea, Diana M; Mueller-Cajar, Oliver; Portz, Bede; Reilly, John F; Reinkemeier, Christopher D; Sabari, Benjamin R; Sanulli, Serena; Shorter, James; Sontag, Emily; Strader, Lucia; Stachowiak, Jeanne; Weber, Stephanie C; White, Michael; Zhang, Huaiying; Zweckstetter, Markus; Elbaum-Garfinkle, Shana; Kriwacki, Richard | Journal of molecular biology | 36690068 | 2023 Mar 01 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner, David B; Chen, Hongtao; Barinov, Lev; Zoller, Benjamin; Gregor, Thomas | Science (New York, N.Y.) | 37384691 | 2023 Jun 30 |
| UNADON: transformer-based model to predict genome-wide chromosome spatial position. | Yang, Muyu; Ma, Jian | Bioinformatics (Oxford, England) | 37387176 | 2023 Jun 30 |
| Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. | Luo, Zhifei; Wen, Xingzhao; Zhao, Wenxin; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng | bioRxiv : the preprint server for biology | 37425846 | 2023 Jun 28 |
| Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. | Catta-Preta, Rinaldo; Lindtner, Susan; Ypsilanti, Athena; Price, James; Abnousi, Armen; Su-Feher, Linda; Wang, Yurong; Juric, Ivan; Jones, Ian R; Akiyama, Jennifer A; Hu, Ming; Shen, Yin; Visel, Axel; Pennacchio, Len A; Dickel, Diane; Rubenstein, John L R; Nord, Alex S | bioRxiv : the preprint server for biology | 37425940 | 2023 Jun 28 |
| Deep learning enables fast, gentle STED microscopy. | Ebrahimi, Vahid; Stephan, Till; Kim, Jiah; Carravilla, Pablo; Eggeling, Christian; Jakobs, Stefan; Han, Kyu Young | Communications biology | 37369761 | 2023 Jun 27 |
| SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. | Wolin, Erica; Guo, Jimmy K; Blanco, Mario R; Perez, Andrew A; Goronzy, Isabel N; Abdou, Ahmed A; Gorhe, Darvesh; Guttman, Mitchell; Jovanovic, Marko | bioRxiv : the preprint server for biology | 37333139 | 2023 Jun 07 |
| Epiphany: predicting Hi-C contact maps from 1D epigenomic signals. | Yang, Rui; Das, Arnav; Gao, Vianne R; Karbalayghareh, Alireza; Noble, William S; Bilmes, Jeffery A; Leslie, Christina S | Genome biology | 37280678 | 2023 Jun 06 |
| Recording morphogen signals reveals origins of gastruloid symmetry breaking. | McNamara, Harold M; Solley, Sabrina C; Adamson, Britt; Chan, Michelle M; Toettcher, Jared E | bioRxiv : the preprint server for biology | 37333235 | 2023 Jun 05 |
| Light-switchable transcription factors obtained by direct screening in mammalian cells. | Zhu, Liyuan; McNamara, Harold M; Toettcher, Jared E | Nature communications | 37268649 | 2023 Jun 02 |
| Genome folding dynamics during the M-to-G1-phase transition. | Zhang, Haoyue; Blobel, Gerd A | Current opinion in genetics & development | 37099832 | 2023 Jun |
| Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. | Goel, Viraat Y; Huseyin, Miles K; Hansen, Anders S | Nature genetics | 37157000 | 2023 Jun |
| Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. | Van Buren, Eric; Radicioni, Giorgia; Lester, Sarah; O'Neal, Wanda K; Dang, Hong; Kasela, Silva; Garudadri, Suresh; Curtis, Jeffrey L; Han, MeiLan K; Krishnan, Jerry A; Wan, Emily S; Silverman, Edwin K; Hastie, Annette; Ortega, Victor E; Lappalainen, Tuuli; Nawijn, Martijn C; Berge, Maarten van den; Christenson, Stephanie A; Li, Yun; Cho, Michael H; Kesimer, Mehmet; Kelada, Samir N P | PLoS genetics | 37352370 | 2023 Jun |
| ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. | Gao, Vianne R; Yang, Rui; Das, Arnav; Luo, Renhe; Luo, Hanzhi; McNally, Dylan R; Karagiannidis, Ioannis; Rivas, Martin A; Wang, Zhong-Min; Barisic, Darko; Karbalayghareh, Alireza; Wong, Wilfred; Zhan, Yingqian A; Chin, Christopher R; Noble, William; Bilmes, Jeff A; Apostolou, Effie; Kharas, Michael G; Béguelin, Wendy; Viny, Aaron D; Huangfu, Danwei; Rudensky, Alexander Y; Melnick, Ari M; Leslie, Christina S | bioRxiv : the preprint server for biology | 37546906 | 2023 Jul 28 |
| Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. | Chiariello, Andrea M; Abraham, Alex; Bianco, Simona; Esposito, Andrea; Vercellone, Francesca; Conte, Mattia; Fontana, Andrea; Nicodemi, Mario | bioRxiv : the preprint server for biology | 37546924 | 2023 Jul 28 |
| Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. | Chung, Chan-I; Yang, Junjiao; Shu, Xiaokun | ACS central science | 37521779 | 2023 Jul 26 |
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| Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. | Chiliński, Mateusz; Lipiński, Jakub; Agarwal, Abhishek; Ruan, Yijun; Plewczynski, Dariusz | Scientific reports | 37474564 | 2023 Jul 20 |
| Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. | Murphy, Dylan; Salataj, Eralda; Di Giammartino, Dafne Campigli; Rodriguez-Hernaez, Javier; Kloetgen, Andreas; Garg, Vidur; Char, Erin; Uyehara, Christopher M; Ee, Ly-Sha; Lee, UkJin; Stadtfeld, Matthias; Hadjantonakis, Anna-Katerina; Tsirigos, Aristotelis; Polyzos, Alexander; Apostolou, Effie | bioRxiv : the preprint server for biology | 37577543 | 2023 Jul 19 |
| Phase separation of ecDNA aggregates establishes in-trans contact domains boosting selective MYC regulatory interactions. | Conte, Mattia; Matteuzzi, Tommaso; Esposito, Andrea; Chiariello, Andrea M; Bianco, Simona; Vercellone, Francesca; Nicodemi, Mario | bioRxiv : the preprint server for biology | 37503084 | 2023 Jul 17 |
| High throughput PRIME editing screens identify functional DNA variants in the human genome. | Ren, Xingjie; Yang, Han; Nierenberg, Jovia L; Sun, Yifan; Chen, Jiawen; Beaman, Cooper; Pham, Thu; Nobuhara, Mai; Takagi, Maya Asami; Narayan, Vivek; Li, Yun; Ziv, Elad; Shen, Yin | bioRxiv : the preprint server for biology | 37502948 | 2023 Jul 12 |
| Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. | Chandra, Aditi; Yoon, Sora; Michieletto, Michaël F; Goldman, Naomi; Ferrari, Emily K; Abedi, Maryam; Johnson, Isabelle; Fasolino, Maria; Pham, Kenneth; Joannas, Leonel; Kee, Barbara L; Henao-Mejia, Jorge; Vahedi, Golnaz | Immunity | 37263273 | 2023 Jul 11 |
| Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis. | He, Shuonan; Shao, Wanqing; Chen, Shiyuan Cynthia; Wang, Ting; Gibson, Matthew C | Current biology : CB | 37315559 | 2023 Jul 10 |
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| Deep learning enables fast, gentle STED microscopy. | Ebrahimi, Vahid; Stephan, Till; Kim, Jiah; Carravilla, Pablo; Eggeling, Christian; Jakobs, Stefan; Han, Kyu Young | bioRxiv : the preprint server for biology | 36747618 | 2023 Jan 27 |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah, Parisha P; Keough, Kathleen C; Gjoni, Ketrin; Santini, Garrett T; Abdill, Richard J; Wickramasinghe, Nadeera M; Dundes, Carolyn E; Karnay, Ashley; Chen, Angela; Salomon, Rachel E A; Walsh, Patrick J; Nguyen, Son C; Whalen, Sean; Joyce, Eric F; Loh, Kyle M; Dubois, Nicole; Pollard, Katherine S; Jain, Rajan | Genome biology | 36691074 | 2023 Jan 23 |
| Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. | Mahadevan, Jyothi; Jha, Asmita; Rudolph, Johannes; Bowerman, Samuel; Narducci, Domenic; Hansen, Anders S; Luger, Karolin | iScience | 36594010 | 2023 Jan 20 |
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| ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. | Chai, Haoxi; Tjong, Harianto; Li, Peng; Liao, Wei; Wang, Ping; Wong, Chee Hong; Ngan, Chew Yee; Leonard, Warren J; Wei, Chia-Lin; Ruan, Yijun | Nature communications | 36639381 | 2023 Jan 13 |
| Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation. | Alavattam, Kris G; Mitzelfelt, Katie A; Bonora, Giancarlo; Fields, Paul A; Yang, Xiulan; Chiu, Han Sheng; Pabon, Lil; Bertero, Alessandro; Palpant, Nathan J; Noble, William S; Murry, Charles E | Stem cell reports | 36493778 | 2023 Jan 10 |
| Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis. | He, Shuonan; Shao, Wanqing; Chen, Shiyuan Cynthia; Wang, Ting; Gibson, Matthew C | bioRxiv : the preprint server for biology | 36711919 | 2023 Jan 10 |
| CTCF is essential for proper mitotic spindle structure and anaphase segregation. | Chiu, Katherine; Berrada, Yasmin; Eskndir, Nebiyat; Song, Dasol; Fong, Claire; Naughton, Sarah; Chen, Tina; Moy, Savanna; Gyurmey, Sarah; James, Liam; Ezeiruaku, Chimere; Capistran, Caroline; Lowey, Daniel; Diwanji, Vedang; Peterson, Samantha; Parakh, Harshini; Burgess, Ayanna R; Probert, Cassandra; Zhu, Annie; Anderson, Bryn; Levi, Nehora; Gerlitz, Gabi; Packard, Mary C; Dorfman, Katherine A; Bahiru, Michael Seifu; Stephens, Andrew D | bioRxiv : the preprint server for biology | 36712070 | 2023 Jan 10 |
| Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. | Daniel, Bence; Belk, Julia A; Meier, Stefanie L; Chen, Andy Y; Sandor, Katalin; Czimmerer, Zsolt; Varga, Zsofia; Bene, Krisztian; Buquicchio, Frank A; Qi, Yanyan; Kitano, Hugo; Wheeler, Joshua R; Foster, Deshka S; Januszyk, Michael; Longaker, Michael T; Chang, Howard Y; Satpathy, Ansuman T | Molecular cell | 36521490 | 2023 Jan 05 |
| Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. | Shi, Tuo; Beaulieu, Marielle O; Saunders, Lauren M; Fabian, Peter; Trapnell, Cole; Segil, Neil; Crump, J Gage; Raible, David W | eLife | 36598134 | 2023 Jan 04 |
| A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. | Jia, Bojing Blair; Jussila, Adam; Kern, Colin; Zhu, Quan; Ren, Bing | Nature biotechnology | 36593410 | 2023 Jan 02 |
| Inference of 3D genome architecture by modeling overdispersion of Hi-C data. | Varoquaux, Nelle; Noble, William S; Vert, Jean-Philippe | Bioinformatics (Oxford, England) | 36594573 | 2023 Jan 01 |
| Gos: a declarative library for interactive genomics visualization in Python. | Manz, Trevor; L'Yi, Sehi; Gehlenborg, Nils | Bioinformatics (Oxford, England) | 36688709 | 2023 Jan 01 |
| Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. | Michieletto, Michaël F; Tello-Cajiao, John J; Mowel, Walter K; Chandra, Aditi; Yoon, Sora; Joannas, Leonel; Clark, Megan L; Jimenez, Monica T; Wright, Jasmine M; Lundgren, Patrick; Williams, Adam; Thaiss, Christoph A; Vahedi, Golnaz; Henao-Mejia, Jorge | Nature immunology | 36050414 | 2023 Jan |
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| Advances in CRISPR therapeutics. | Chavez, Michael; Chen, Xinyi; Finn, Paul B; Qi, Lei S | Nature reviews. Nephrology | 36280707 | 2023 Jan |
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| Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. | Spracklin, George; Abdennur, Nezar; Imakaev, Maxim; Chowdhury, Neil; Pradhan, Sriharsa; Mirny, Leonid A; Dekker, Job | Nature structural & molecular biology | 36550219 | 2023 Jan |
| SPICEMIX enables integrative single-cell spatial modeling of cell identity. | Chidester, Benjamin; Zhou, Tianming; Alam, Shahul; Ma, Jian | Nature genetics | 36624346 | 2023 Jan |
| Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function. | Zhan, Yuxiang; Yildirim, Asli; Boninsegna, Lorenzo; Alber, Frank | bioRxiv : the preprint server for biology | 36824908 | 2023 Feb 19 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner, David B; Chen, Hongtao; Barinov, Lev; Zoller, Benjamin; Gregor, Thomas | bioRxiv : the preprint server for biology | 36711618 | 2023 Feb 13 |
| Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain, Naveen; Goyal, Yogesh; Dunagin, Margaret C; Cote, Christopher J; Mellis, Ian A; Emert, Benjamin; Jiang, Connie L; Dardani, Ian P; Reffsin, Sam; Raj, Arjun | bioRxiv : the preprint server for biology | 36798299 | 2023 Feb 10 |
| Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. | Choudhary, Mayank N K; Quaid, Kara; Xing, Xiaoyun; Schmidt, Heather; Wang, Ting | Nature communications | 36746940 | 2023 Feb 06 |
| Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. | Heo, Su-Jin; Thakur, Shreyasi; Chen, Xingyu; Loebel, Claudia; Xia, Boao; McBeath, Rowena; Burdick, Jason A; Shenoy, Vivek B; Mauck, Robert L; Lakadamyali, Melike | Nature biomedical engineering | 35996026 | 2023 Feb |
| Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation. | Khurana, Sakshi; Foltz, Daniel R | bioRxiv : the preprint server for biology | 38234763 | 2023 Dec 27 |
| Machine learning reveals the diversity of human 3D chromatin contact patterns. | Gilbertson, Erin N; Brand, Colin M; McArthur, Evonne; Rinker, David C; Kuang, Shuzhen; Pollard, Katherine S; Capra, John A | bioRxiv : the preprint server for biology | 38187606 | 2023 Dec 23 |
| Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. | Malachowski, Thomas; Chandradoss, Keerthivasan Raanin; Boya, Ravi; Zhou, Linda; Cook, Ashley L; Su, Chuanbin; Pham, Kenneth; Haws, Spencer A; Kim, Ji Hun; Ryu, Han-Seul; Ge, Chunmin; Luppino, Jennifer M; Nguyen, Son C; Titus, Katelyn R; Gong, Wanfeng; Wallace, Owen; Joyce, Eric F; Wu, Hao; Rojas, Luis Alejandro; Phillips-Cremins, Jennifer E | Cell | 38134876 | 2023 Dec 21 |
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