Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Cited by (269)

Items 101–200 of 269

1. Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF
   Delacher, Michael, Imbusch, Charles D., Hotz-Wagenblatt, Agnes, Mallm, Jan-Philipp, Bauer, Katharina, Simon, Malte, Riegel, Dania, Rendeiro, André F., Bittner, Sebastian, Sanderink, Lieke et al. · 2020 · Immunity
2. Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer
   Parolia, Abhijit, Cieslik, Marcin, Chu, Shih-Chun, Xiao, Lanbo, Ouchi, Takahiro, Zhang, Yuping, Wang, Xiaoju, Vats, Pankaj, Cao, Xuhong, Pitchiaya, Sethuramasundaram et al. · 2019 · Nature
3. WILDS: A Benchmark of in-the-Wild Distribution Shifts
   Koh, Pang Wei, Sagawa, Shiori, Marklund, Henrik, Xie, Sang Michael, Zhang, Marvin, Balsubramani, Akshay, Hu, Weihua, Yasunaga, Michihiro, Phillips, Richard Lanas, Gao, Irena et al. · 2020 · arXiv
4. Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses
   Xu, Heping, Ding, Jiarui, Porter, Caroline B.M., Wallrapp, Antonia, Tabaka, Marcin, Ma, Sai, Fu, Shujie, Guo, Xuanxuan, Riesenfeld, Samantha J., Su, Chienwen et al. · 2019 · Immunity
5. Decoding enhancers using massively parallel reporter assays
   Inoue, Fumitaka, Ahituv, Nadav · 2015 · Genomics
6. Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
   Sabbagh, Mark F, Heng, Jacob S, Luo, Chongyuan, Castanon, Rosa G, Nery, Joseph R, Rattner, Amir, Goff, Loyal A, Ecker, Joseph R, Nathans, Jeremy · 2018 · eLife
7. Multiplexed analysis of chromosome conformation at vastly improved sensitivity
   Davies, James O J, Telenius, Jelena M, McGowan, Simon J, Roberts, Nigel A, Taylor, Stephen, Higgs, Douglas R, Hughes, Jim R · 2016 · Nature Methods
8. Resolving <i>TYK2</i> locus genotype-to-phenotype differences in autoimmunity
   Dendrou, Calliope A., Cortes, Adrian, Shipman, Lydia, Evans, Hayley G., Attfield, Kathrine E., Jostins, Luke, Barber, Thomas, Kaur, Gurman, Kuttikkatte, Subita Balaram, Leach, Oliver A. et al. · 2016 · Science Translational Medicine
9. Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
   Zhao, Tongtong, Chiang, Zachary D., Morriss, Julia W., LaFave, Lindsay M., Murray, Evan M., Del Priore, Isabella, Meli, Kevin, Lareau, Caleb A., Nadaf, Naeem M., Li, Jilong et al. · 2022 · Nature
10. Epigenomics of human CD8 T cell differentiation and aging
    Moskowitz, David M., Zhang, David W., Hu, Bin, Le Saux, Sabine, Yanes, Rolando E., Ye, Zhongde, Buenrostro, Jason D., Weyand, Cornelia M., Greenleaf, William J., Goronzy, Jörg J. · 2017 · Science Immunology
11. AP-1 imprints a reversible transcriptional programme of senescent cells.
    Martínez-Zamudio, Ricardo Iván, Roux, Pierre-François, de Freitas, José Américo N.L.F., Robinson, Lucas, Doré, Gregory, Sun, Bin, Belenki, Dimitri, Milanovic, Maja, Herbig, Utz, Schmitt, Clemens A. et al. · 2020 · Nature Cell Biology
12. A CD4+ T cell population expanded in lupus blood provides B cell help through interleukin-10 and succinate
    Caielli, Simone, Veiga, Diogo Troggian, Balasubramanian, Preetha, Athale, Shruti, Domic, Bojana, Murat, Elise, Banchereau, Romain, Xu, Zhaohui, Chandra, Manjari, Chung, Cheng-Han et al. · 2019 · Nature Medicine
13. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
    Liu, Longqi, Liu, Chuanyu, Quintero, Andrés, Wu, Liang, Yuan, Yue, Wang, Mingyue, Cheng, Mengnan, Leng, Lizhi, Xu, Liqin, Dong, Guoyi et al. · 2019 · Nature Communications
14. Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes
    Novikova, Gloriia, Kapoor, Manav, TCW, Julia, Abud, Edsel M., Efthymiou, Anastasia G., Chen, Steven X., Cheng, Haoxiang, Fullard, John F., Bendl, Jaroslav, Liu, Yiyuan et al. · 2021 · Nature Communications
15. Epigenetic variation between human induced pluripotent stem cell lines is an indicator of differentiation capacity
    Nishizawa, Masatoshi, Chonabayashi, Kazuhisa, Nomura, Masaki, Tanaka, Azusa, Nakamura, Masahiro, Inagaki, Azusa, Nishikawa, Misato, Takei, Ikue, Oishi, Akiko, Tanabe, Koji et al. · 2016 · Cell stem cell
16. Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer’s patients
    Mertens, Jerome, Herdy, Joseph R., Traxler, Larissa, Schafer, Simon T., Schlachetzki, Johannes C.M., Böhnke, Lena, Reid, Dylan A., Lee, Hyungjun, Zangwill, Dina, Fernandes, Diana P. et al. · 2021 · Cell Stem Cell
17. An Organoid Biobank of Neuroendocrine Neoplasms Enables Genotype-Phenotype Mapping
    Kawasaki, Kenta, Toshimitsu, Kohta, Matano, Mami, Fujita, Masashi, Fujii, Masayuki, Togasaki, Kazuhiro, Ebisudani, Toshiki, Shimokawa, Mariko, Takano, Ai, Takahashi, Sirirat et al. · 2020 · Cell
18. Sex reversal following deletion of a single distal enhancer of <i>Sox9</i>
    Gonen, Nitzan, Futtner, Chris R., Wood, Sophie, Garcia-Moreno, S. Alexandra, Salamone, Isabella M., Samson, Shiela C., Sekido, Ryohei, Poulat, Francis, Maatouk, Danielle M., Lovell-Badge, Robin · 2018 · Science
19. TCR Transgenic Mice Reveal Stepwise, Multi-site Acquisition of the Distinctive Fat-Treg Phenotype
    Li, Chaoran, DiSpirito, Joanna R., Zemmour, David, Spallanzani, Raul German, Kuswanto, Wilson, Benoist, Christophe, Mathis, Diane · 2018 · Cell
20. Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons
    Liu, Elaine Y., Russ, Jenny, Cali, Christopher P., Phan, Jessica M., Amlie-Wolf, Alexandre, Lee, Edward B. · 2019 · Cell Reports
21. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy
    Lee, Jaecheol, Termglinchan, Vittavat, Diecke, Sebastian, Itzhaki, Ilanit, Lam, Chi Keung, Garg, Priyanka, Lau, Edward, Greenhaw, Matthew, Seeger, Timon, Wu, Haodi et al. · 2019 · Nature
22. Neuronal enhancers are hotspots for DNA single-strand break repair
    Wu, Wei, Kargbo-Hill, Sarah E., Nathan, William J., Paiano, Jacob, Callen, Elsa, Wang, Dongpeng, Shinoda, Kenta, van Wietmarschen, Niek, Colón-Mercado, Jennifer M., Zong, Dali et al. · 2021 · Nature
23. Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells
    Johnson, John L., Georgakilas, Georgios, Petrovic, Jelena, Kurachi, Makoto, Cai, Stanley, Harly, Christelle, Pear, Warren S., Bhandoola, Avinash, Wherry, E. John, Vahedi, Golnaz · 2018 · Immunity
24. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function
    Arda, H. Efsun, Li, Lingyu, Tsai, Jennifer, Torre, Eduardo A., Rosli, Yenny, Peiris, Heshan, Spitale, Robert C., Dai, Chunhua, Gu, Xueying, Qu, Kun et al. · 2016 · Cell Metabolism
25. Molecular and functional variation in iPSC-derived sensory neurons
    HIPSCI Consortium, Schwartzentruber, Jeremy, Foskolou, Stefanie, Kilpinen, Helena, Rodrigues, Julia, Alasoo, Kaur, Knights, Andrew J., Patel, Minal, Goncalves, Angela, Ferreira, Rita et al. · 2018 · Nature Genetics
26. SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data
    Persad, Sitara, Choo, Zi-Ning, Dien, Christine, Sohail, Noor, Masilionis, Ignas, Chaligné, Ronan, Nawy, Tal, Brown, Chrysothemis C., Sharma, Roshan, Pe’er, Itsik et al. · 2023 · Nature Biotechnology
27. Trained Immunity-Promoting Nanobiologic Therapy Suppresses Tumor Growth and Potentiates Checkpoint Inhibition
    Priem, Bram, van Leent, Mandy M.T., Teunissen, Abraham J.P., Sofias, Alexandros Marios, Mourits, Vera P., Willemsen, Lisa, Klein, Emma D., Oosterwijk, Roderick S., Meerwaldt, Anu E., Munitz, Jazz et al. · 2020 · Cell
28. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk
    Rajarajan, Prashanth, Borrman, Tyler, Liao, Will, Schrode, Nadine, Flaherty, Erin, Casiño, Charlize, Powell, Samuel, Yashaswini, Chittampalli, LaMarca, Elizabeth A., Kassim, Bibi et al. · 2018 · Science
29. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
    Hanssen, Lars L. P., Kassouf, Mira T., Oudelaar, A. Marieke, Biggs, Daniel, Preece, Chris, Downes, Damien J., Gosden, Matthew, Sharpe, Jacqueline A., Sloane-Stanley, Jacqueline A., Hughes, Jim R. et al. · 2017 · Nature Cell Biology
30. Decline in IGF1 in the bone marrow microenvironment initiates hematopoietic stem cell aging
    Young, Kira, Eudy, Elizabeth, Bell, Rebecca, Loberg, Matthew A., Stearns, Tim, Sharma, Devyani, Velten, Lars, Haas, Simon, Filippi, Marie-Dominique, Trowbridge, Jennifer J. · 2021 · Cell Stem Cell
31. Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids
    Artegiani, Benedetta, van Voorthuijsen, Lisa, Lindeboom, Rik G.H., Seinstra, Daniëlle, Heo, Inha, Tapia, Pablo, López-Iglesias, Carmen, Postrach, Daniel, Dayton, Talya, Oka, Rurika et al. · 2019 · Cell Stem Cell
32. Genetic determinants of co-accessible chromatin regions in activated T cells across humans
    Gate, Rachel E., Cheng, Christine S., Aiden, Aviva P., Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M. Grace, Subramaniam, Meena, Shamim, Muhammad et al. · 2018 · Nature Genetics
33. Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity
    Karmaus, Peer W. F., Chen, Xiang, Lim, Seon Ah, Herrada, Andrés A., Nguyen, Thanh-Long M., Xu, Beisi, Dhungana, Yogesh, Rankin, Sherri, Chen, Wenan, Rosencrance, Celeste et al. · 2019 · Nature
34. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function
    Link, Verena M., Duttke, Sascha H., Chun, Hyun B., Holtman, Inge R., Westin, Emma, Hoeksema, Marten A., Abe, Yohei, Skola, Dylan, Romanoski, Casey E., Tao, Jenhan et al. · 2018 · Cell
35. Developments in stem cell-derived islet replacement therapy for treating type 1 diabetes
    Hogrebe, Nathaniel J., Ishahak, Matthew, Millman, Jeffrey R. · 2023 · Cell Stem Cell
36. Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF
    Kang, Kyuho, Park, Sung Ho, Chen, Janice, Qiao, Yu, Giannopoulou, Eugenia, Berg, Karen, Hanidu, Adedayo, Li, Jun, Nabozny, Gerald, Kang, Keunsoo et al. · 2017 · Immunity
37. Increased post-mitotic senescence in aged human neurons is a pathological feature of Alzheimer’s disease
    Herdy, Joseph R., Traxler, Larissa, Agarwal, Ravi K., Karbacher, Lukas, Schlachetzki, Johannes C.M., Boehnke, Lena, Zangwill, Dina, Galasko, Doug, Glass, Christopher K., Mertens, Jerome et al. · 2022 · Cell Stem Cell
38. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
    Smith, Zachary D., Shi, Jiantao, Gu, Hongcang, Donaghey, Julie, Clement, Kendell, Cacchiarelli, Davide, Gnirke, Andreas, Michor, Franziska, Meissner, Alexander · 2017 · Nature
39. Fate-Mapping of GM-CSF Expression Identifies a Discrete Subset of Inflammation-Driving T Helper Cells Regulated by Cytokines IL-23 and IL-1β
    Komuczki, Juliana, Tuzlak, Selma, Friebel, Ekaterina, Hartwig, Tom, Spath, Sabine, Rosenstiel, Philip, Waisman, Ari, Opitz, Lennart, Oukka, Mohammed, Schreiner, Bettina et al. · 2019 · Immunity
40. The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis-Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation
    Wang, Dapeng, Diao, Huitian, Getzler, Adam J., Rogal, Walter, Frederick, Megan A., Milner, Justin, Yu, Bingfei, Crotty, Shane, Goldrath, Ananda W., Pipkin, Matthew E. · 2018 · Immunity
41. The chromatin accessibility signature of human immune aging stems from CD8+ T cells
    Ucar, Duygu, Márquez, Eladio J., Chung, Cheng-Han, Marches, Radu, Rossi, Robert J., Uyar, Asli, Wu, Te-Chia, George, Joshy, Stitzel, Michael L., Palucka, A. Karolina et al. · 2017 · Journal of Experimental Medicine
42. High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human
    Wang, Xinchen, He, Liang, Goggin, Sarah M., Saadat, Alham, Wang, Li, Sinnott-Armstrong, Nasa, Claussnitzer, Melina, Kellis, Manolis · 2018 · Nature Communications
43. Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism
    Miro-Blanch, Joan, Yanes, Oscar · 2019 · Frontiers in Genetics
44. Single-cell sequencing to multi-omics: technologies and applications
    Wu, Xiangyu, Yang, Xin, Dai, Yunhan, Zhao, Zihan, Zhu, Junmeng, Guo, Hongqian, Yang, Rong · 2024 · Biomarker Research
45. Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia
    Bryois, Julien, Garrett, Melanie E., Song, Lingyun, Safi, Alexias, Giusti-Rodriguez, Paola, Johnson, Graham D., Shieh, Annie W., Buil, Alfonso, Fullard, John F., Roussos, Panos et al. · 2018 · Nature Communications
46. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration
    Wang, Jie, Zibetti, Cristina, Shang, Peng, Sripathi, Srinivasa R., Zhang, Pingwu, Cano, Marisol, Hoang, Thanh, Xia, Shuli, Ji, Hongkai, Merbs, Shannath L. et al. · 2018 · Nature Communications
47. An atlas of gene regulatory elements in adult mouse cerebrum
    Li, Yang Eric, Preissl, Sebastian, Hou, Xiaomeng, Zhang, Ziyang, Zhang, Kai, Qiu, Yunjiang, Poirion, Olivier B., Li, Bin, Chiou, Joshua, Liu, Hanqing et al. · 2021 · Nature
48. Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells
    Delacher, Michael, Simon, Malte, Sanderink, Lieke, Hotz-Wagenblatt, Agnes, Wuttke, Marina, Schambeck, Kathrin, Schmidleithner, Lisa, Bittner, Sebastian, Pant, Asmita, Ritter, Uwe et al. · 2021 · Immunity
49. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
    Bao, Xiaomin, Rubin, Adam J., Qu, Kun, Zhang, Jiajing, Giresi, Paul G., Chang, Howard Y., Khavari, Paul A. · 2015 · Genome Biology
50. Decoding gene regulation in the fly brain
    Janssens, Jasper, Aibar, Sara, Taskiran, Ibrahim Ihsan, Ismail, Joy N., Spanier, Katina I., Bravo González-Blas, Carmen, Quan, Xiao Jiang, Papasokrati, Dafni, Hulselmans, Gert, Makhzami, Samira et al. · 2021
51. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility
    Lio, Chan-Wang, Zhang, Jiayuan, González-Avalos, Edahí, Hogan, Patrick G, Chang, Xing, Rao, Anjana · 2016 · eLife
52. Decoding gene regulation in the fly brain
    Janssens, Jasper, Aibar, Sara, Taskiran, Ibrahim Ihsan, Ismail, Joy N., Gomez, Alicia Estacio, Aughey, Gabriel, Spanier, Katina I., De Rop, Florian V., González-Blas, Carmen Bravo, Dionne, Marc et al. · 2022 · Nature
53. Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D
    Viñuela, Ana, Varshney, Arushi, van de Bunt, Martijn, Prasad, Rashmi B., Asplund, Olof, Bennett, Amanda, Boehnke, Michael, Brown, Andrew A., Erdos, Michael R., Fadista, João et al. · 2020 · Nature Communications
54. Epigenetic regulation: A new frontier for biomedical engineers
    Chen, Zhen, Li, Shuai, Subramaniam, Shankar, Shyy, John Y.-J., Chien, Shu · 2017 · Annual Review of Biomedical Engineering
55. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions
    Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay · 2017 · The American Journal of Human Genetics
56. Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus
    Fernandez-Albert, Jordi, Lipinski, Michal, Lopez-Cascales, María T., Rowley, M. Jordan, Martin-Gonzalez, Ana M., del Blanco, Beatriz, Corces, Victor G., Barco, Angel · 2019 · Nature Neuroscience
57. FoxO maintains a genuine muscle stem-cell quiescent state until geriatric age
    García-Prat, Laura, Perdiguero, Eusebio, Alonso-Martín, Sonia, Dell’Orso, Stefania, Ravichandran, Srikanth, Brooks, Stephen R., Juan, Aster H., Campanario, Silvia, Jiang, Kan, Hong, Xiaotong et al. · 2020 · Nature Cell Biology
58. 5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes
    Mellén, Marian, Ayata, Pinar, Heintz, Nathaniel · 2017 · Proceedings of the National Academy of Sciences
59. Long-range single-molecule mapping of chromatin accessibility in eukaryotes
    Shipony, Zohar, Marinov, Georgi K., Swaffer, Matthew P., Sinnott-Armstrong, Nicholas A., Skotheim, Jan M., Kundaje, Anshul, Greenleaf, William J. · 2020 · Nature Methods
60. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble
    Marco, Asaf, Meharena, Hiruy S., Dileep, Vishnu, Raju, Ravikiran M., Davila-Velderrain, Jose, Zhang, Amy Letao, Adaikkan, Chinnakkaruppan, Young, Jennie Z., Gao, Fan, Kellis, Manolis et al. · 2020 · Nature Neuroscience
61. Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function
    Yucel, Nora, Wang, Yu Xin, Mai, Thach, Porpiglia, Ermelinda, Lund, Peder J., Markov, Glenn, Garcia, Benjamin A., Bendall, Sean C., Angelo, Michael, Blau, Helen M. · 2019 · Cell Reports
62. Dual Requirement of CHD8 for Chromatin Landscape Establishment and Histone Methyltransferase Recruitment to Promote CNS Myelination and Repair
    Zhao, Chuntao, Dong, Chen, Frah, Magali, Deng, Yaqi, Marie, Corentine, Zhang, Feng, Xu, Lingli, Ma, Zhixing, Dong, Xinran, Lin, Yifeng et al. · 2018 · Developmental Cell
63. The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes
    Jacobs, Jelle, Atkins, Mardelle, Davie, Kristofer, Imrichova, Hana, Romanelli, Lucia, Christiaens, Valerie, Hulselmans, Gert, Potier, Delphine, Wouters, Jasper, Taskiran, Ibrahim I. et al. · 2018 · Nature Genetics
64. High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer
    Pierce, Sarah E., Granja, Jeffrey M., Greenleaf, William J. · 2021 · Nature Communications
65. Transcript-indexed ATAC-seq for precision immune profiling
    Satpathy, Ansuman T., Saligrama, Naresha, Buenrostro, Jason D., Wei, Yuning, Wu, Beijing, Rubin, Adam J., Granja, Jeffrey M., Lareau, Caleb A., Li, Rui, Qi, Yanyan et al. · 2018 · Nature Medicine
66. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
    Baek, Seungbyn, Lee, Insuk · 2020 · Computational and Structural Biotechnology Journal
67. GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler
    Takaku, Motoki, Grimm, Sara A., Shimbo, Takashi, Perera, Lalith, Menafra, Roberta, Stunnenberg, Hendrik G., Archer, Trevor K., Machida, Shinichi, Kurumizaka, Hitoshi, Wade, Paul A. · 2016 · Genome Biology
68. Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)
    Carter, Benjamin, Ku, Wai Lim, Kang, Jee Youn, Hu, Gangqing, Perrie, Jonathan, Tang, Qingsong, Zhao, Keji · 2019 · Nature Communications
69. Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks
    Rendeiro, André F., Schmidl, Christian, Strefford, Jonathan C., Walewska, Renata, Davis, Zadie, Farlik, Matthias, Oscier, David, Bock, Christoph · 2016 · Nature Communications
70. Recent advances in single-cell sequencing technologies
    Wen, Lu, Tang, Fuchou · 2022 · Precision Clinical Medicine
71. 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. et al. · 2017 · Cell Stem Cell
72. Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development
    Ngan, Chew Yee, Wong, Chee Hong, Tjong, Harianto, Wang, Wenbo, Goldfeder, Rachel L., Choi, Cindy, He, Hao, Gong, Liang, Lin, Junyan, Urban, Barbara et al. · 2020 · Nature Genetics
73. A comprehensive transcriptome signature of murine hematopoietic stem cell aging
    Flohr Svendsen, Arthur, Yang, Daozheng, Kim, KyungMok, Lazare, Seka, Skinder, Natalia, Zwart, Erik, Mura-Meszaros, Anna, Ausema, Albertina, von Eyss, Björn, de Haan, Gerald et al. · 2021 · Blood
74. <i>Dnmt3a</i> restrains mast cell inflammatory responses
    Leoni, Cristina, Montagner, Sara, Rinaldi, Andrea, Bertoni, Francesco, Polletti, Sara, Balestrieri, Chiara, Monticelli, Silvia · 2017 · Proceedings of the National Academy of Sciences
75. Functional assessment of human enhancer activities using whole-genome STARR-sequencing
    Liu, Yuwen, Yu, Shan, Dhiman, Vineet K., Brunetti, Tonya, Eckart, Heather, White, Kevin P. · 2017 · Genome Biology
76. Genetically Defined Syngeneic Mouse Models of Ovarian Cancer as Tools for the Discovery of Combination Immunotherapy
    Iyer, Sonia, Zhang, Shuang, Yucel, Simge, Horn, Heiko, Smith, Sean G., Reinhardt, Ferenc, Hoefsmit, Esmee, Assatova, Bimarzhan, Casado, Julia, Meinsohn, Marie-Charlotte et al. · 2021 · Cancer Discovery
77. FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer
    Arruabarrena-Aristorena, Amaia, Maag, Jesper L.V., Kittane, Srushti, Cai, Yanyan, Karthaus, Wouter R., Ladewig, Erik, Park, Jane, Kannan, Srinivasaraghavan, Ferrando, Lorenzo, Cocco, Emiliano et al. · 2020 · Cancer Cell
78. A Specific ChREBP and PPARα Cross-Talk Is Required for the Glucose-Mediated FGF21 Response
    Iroz, Alison, Montagner, Alexandra, Benhamed, Fadila, Levavasseur, Françoise, Polizzi, Arnaud, Anthony, Elodie, Régnier, Marion, Fouché, Edwin, Lukowicz, Céline, Cauzac, Michèle et al. · 2017 · Cell Reports
79. Promoter or enhancer, what’s the difference? Deconstruction of established distinctions and presentation of a unifying model
    Andersson, Robin · 2015 · BioEssays
80. Single-cell epigenomic variability reveals functional cancer heterogeneity
    Litzenburger, Ulrike M., Buenrostro, Jason D., Wu, Beijing, Shen, Ying, Sheffield, Nathan C., Kathiria, Arwa, Greenleaf, William J., Chang, Howard Y. · 2017 · Genome Biology
81. A NPAS4–NuA4 complex couples synaptic activity to DNA repair
    Pollina, Elizabeth A., Gilliam, Daniel T., Landau, Andrew T., Lin, Cindy, Pajarillo, Naomi, Davis, Christopher P., Harmin, David A., Yap, Ee-Lynn, Vogel, Ian R., Griffith, Eric C. et al. · 2023 · Nature
82. Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding
    Hosokawa, Hiroyuki, Ungerbäck, Jonas, Wang, Xun, Matsumoto, Masaki, Nakayama, Keiichi I., Cohen, Sarah M., Tanaka, Tomoaki, Rothenberg, Ellen V. · 2018 · Immunity
83. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons
    Reid, Dylan A., Reed, Patrick J., Schlachetzki, Johannes C. M., Nitulescu, Ioana I., Chou, Grace, Tsui, Enoch C., Jones, Jeffrey R., Chandran, Sahaana, Lu, Ake T., McClain, Claire A. et al. · 2021 · Science
84. MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
    Juric, Ivan, Yu, Miao, Abnousi, Armen, Raviram, Ramya, Fang, Rongxin, Zhao, Yuan, Zhang, Yanxiao, Qiu, Yunjiang, Yang, Yuchen, Li, Yun et al. · 2019 · PLOS Computational Biology
85. Dynamics of the 4D Genome during in Vivo Lineage Specification and Differentiation
    Oudelaar, A. Marieke, Beagrie, Robert A., Gosden, Matthew, de Ornellas, Sara, Georgiades, Emily, Kerry, Jon, Hidalgo, Daniel, Carrelha, Joana, Shivalingam, Arun, El-Sagheer, Afaf H. et al. · 2020 · Nature Communications
86. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF
    Berest, Ivan, Arnold, Christian, Reyes-Palomares, Armando, Palla, Giovanni, Rasmussen, Kasper Dindler, Giles, Holly, Bruch, Peter-Martin, Huber, Wolfgang, Dietrich, Sascha, Helin, Kristian et al. · 2019 · Cell Reports
87. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data
    Yuan, Qiuyue, Duren, Zhana · 2025 · Nature Biotechnology
88. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination
    Choi, Jinmi, Lysakovskaia, Kseniia, Stik, Gregoire, Demel, Carina, Söding, Johannes, Tian, Tian V, Graf, Thomas, Cramer, Patrick · 2021 · eLife
89. IL-33-PU.1 Transcriptome Reprogramming Drives Functional State Transition and Clearance Activity of Microglia in Alzheimer’s Disease
    Lau, Shun-Fat, Chen, Congping, Fu, Wing-Yu, Qu, Jianan Y., Cheung, Tom H., Fu, Amy K.Y., Ip, Nancy Y. · 2020 · Cell Reports
90. Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility
    Koester, Janis, Miroshnikova, Yekaterina A., Ghatak, Sushmita, Chacón-Martínez, Carlos Andrés, Morgner, Jessica, Li, Xinping, Atanassov, Ilian, Altmüller, Janine, Birk, David E., Koch, Manuel et al. · 2021 · Nature Cell Biology
91. Cross-species analysis of enhancer logic using deep learning
    Minnoye, Liesbeth, Taskiran, Ibrahim Ihsan, Mauduit, David, Fazio, Maurizio, Van Aerschot, Linde, Hulselmans, Gert, Christiaens, Valerie, Makhzami, Samira, Seltenhammer, Monika, Karras, Panagiotis et al. · 2020 · Genome Research
92. Genetic risk for Alzheimer’s disease is concentrated in specific macrophage and microglial transcriptional networks
    Tansey, Katherine E., Cameron, Darren, Hill, Matthew J. · 2018 · Genome Medicine
93. Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa
    Povoleri, Giovanni A. M., Nova-Lamperti, Estefania, Scottà, Cristiano, Fanelli, Giorgia, Chen, Yun-Ching, Becker, Pablo D., Boardman, Dominic, Costantini, Benedetta, Romano, Marco, Pavlidis, Polychronis et al. · 2018 · Nature Immunology
94. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis
    Gillespie, Mark A., Palii, Carmen G., Sanchez-Taltavull, Daniel, Shannon, Paul, Longabaugh, William J.R., Downes, Damien J., Sivaraman, Karthi, Espinoza, Herbert M., Hughes, Jim R., Price, Nathan D. et al. · 2020 · Molecular Cell
95. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence
    Parry, Aled J., Hoare, Matthew, Bihary, Dóra, Hänsel-Hertsch, Robert, Smith, Stephen, Tomimatsu, Kosuke, Mannion, Elizabeth, Smith, Amy, D’Santos, Paula, Russell, I. Alasdair et al. · 2018 · Nature Communications
96. Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens
    Liscovitch-Brauer, Noa, Montalbano, Antonino, Deng, Jiale, Méndez-Mancilla, Alejandro, Wessels, Hans-Hermann, Moss, Nicholas G., Kung, Chia-Yu, Sookdeo, Akash, Guo, Xinyi, Geller, Evan et al. · 2021 · Nature Biotechnology
97. Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors
    Meharena, Hiruy S., Marco, Asaf, Dileep, Vishnu, Lockshin, Elana R., Akatsu, Grace Y., Mullahoo, James, Watson, L. Ashley, Ko, Tak, Guerin, Lindsey N., Abdurrob, Fatema et al. · 2022 · Cell Stem Cell
98. Bhlhe40 and Bhlhe41 Transcription Factors Regulate Alveolar Macrophage Self‐renewal and Identity
    Rauschmeier, René, Gustafsson, Charlotte, Reinhardt, Annika, A‐Gonzalez, Noelia, Tortola, Luigi, Cansever, Dilay, Subramanian, Sethuraman, Taneja, Reshma, Rossner, Moritz J, Sieweke, Michael H et al. · 2019 · The EMBO Journal
99. Aged hematopoietic stem cells are refractory to bloodborne systemic rejuvenation interventions
    Ho, Theodore T., Dellorusso, Paul V., Verovskaya, Evgenia V., Bakker, Sietske T., Flach, Johanna, Smith, Lucas K., Ventura, Patrick B., Lansinger, Olivia M., Hérault, Aurélie, Zhang, Si Yi et al. · 2021 · Journal of Experimental Medicine
100. IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation
     Park, Sun-Mi, Cho, Hyunwoo, Thornton, Angela M., Barlowe, Trevor S., Chou, Timothy, Chhangawala, Sagar, Fairchild, Lauren, Taggart, James, Chow, Arthur, Schurer, Alexandria et al. · 2019 · Cell Stem Cell