chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

Cited by (1,002)

Items 401–500 of 1,002

1. Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex
   Ying Lei, Mengnan Cheng, Zihao Li, Zhenkun Zhuang, Liang Li Wu, Yunong Sun, Lei Han, Zhi‐Hao Huang, Yuzhou Wang, Zifei Wang et al. · 2022 · Nature Communications
2. Embryologic Origin Influences Smooth Muscle Cell Phenotypic Modulation Signatures in Murine Marfan Syndrome Aortic Aneurysm
   Albert J Pedroza, Alex R. Dalal, Rohan Shad, Nobu Yokoyama, Ken Nakamura, Paul P. Cheng, Robert C. Wirka, Olivia R. Mitchel, Michael Baiocchi, William Hiesinger et al. · 2022 · Arteriosclerosis Thrombosis and Vascular Biology
3. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
   Tareian A. Cazares, Faiz W. Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T. Bejjani, Joseph A. Wayman, Omer A. Donmez, Benjamin Wronowski, Sreeja Parameswaran et al. · 2023 · PLoS Computational Biology
4. Complex Analysis of Single-Cell RNA Sequencing Data
   Anna A. Khozyainova, Anna A. Valyaeva, Mikhail S. Arbatsky, Sergey V. Isaev, Pavel S. Iamshchikov, Egor Volchkov, Marat S. Sabirov, Viktoria R. Zainullina, Vadim I. Chechekhin, R. S. Vorobev et al. · 2023 · Biochemistry (Moscow)
5. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation
   Alan Selewa, Kaixuan Luo, Michael Wasney, Linsin A. Smith, Xiaotong Sun, Chenwei Tang, Heather Eckart, Ivan P. G. Moskowitz, Anindita Basu, Xin He et al. · 2023 · Nature Communications
6. Essential transcription factors for induced neuron differentiation
   Congyi Lu, Görkem Garipler, Chao Dai, Timothy Roush, Jose Salome-Correa, Alex Martin, Noa Liscovitch‐Brauer, Esteban O. Mazzoni, Neville E. Sanjana · 2023 · Nature Communications
7. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis
   Kathryn Weinand, Saori Sakaue, Aparna Nathan, Anna Helena Jonsson, Fan Zhang, Gerald F. M. Watts, Majd Al Suqri, Zhu Zhu, Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, Jennifer Albrecht et al. · 2024 · Nature Communications
8. Integration of single-cell transcriptomes and chromatin landscapes reveals regulatory programs driving pharyngeal organ development
   Margaret E. Magaletta, Macrina Lobo, Eric M. Kernfeld, Hananeh Aliee, Jack D. Huey, Teagan J. Parsons, Fabian Joachim Theis, René Maehr · 2022 · Nature Communications
9. Single-cell RNA-seq and chromatin accessibility profiling decipher the heterogeneity of mouse γδ T cells
   Zhenhua Li, Quanli Yang, Xin Tang, Yiming Chen, Shanshan Wang, Xiaojie Qi, Yawen Zhang, Zonghua Liu, Jing Luo, Hui Liu et al. · 2021 · 中国科学通报：英文版
10. Chemokines form nanoparticles with DNA and can superinduce TLR-driven immune inflammation
    Yong Du, Marie Dominique Ah Kioon, Paôline Laurent, Vidyanath Chaudhary, Michael Pierides, Chao Yang, David Oliver, Lionel B. Ivashkiv, Franck J. Barrat · 2022 · The Journal of Experimental Medicine
11. Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes
    Haofei Wang, Benjamin Keepers, Yunzhe Qian, Yifang Xie, Marazzano Colon, Jiandong Liu, Qian Li · 2022 · Cell stem cell
12. Transcriptome and chromatin landscape of iNKT cells are shaped by subset differentiation and antigen exposure
    Mallory Paynich Murray, Isaac Engel, Grégory Seumois, Sara Herrera de la Mata, Sandy Lisette Rosales, Ashu Sethi, Ashmitaa Logandha Ramamoorthy Premlal, Goo‐Young Seo, Jason Greenbaum, Pandurangan Vijayanand et al. · 2021 · Nature Communications
13. Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity
    Tala Shahin, Hye Sun Kuehn, Mohamed R. Shoeb, Lisa M. Gawriyski, Sarah Giuliani, Peter Repiščák, Birgit Hoeger, Özlem Yüce Petronczki, Sevgi Köstel Bal, Samaneh Zoghi et al. · 2021 · Science Immunology
14. Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression
    Amin Abedini, Jonathan L. Levinsohn, Konstantin A. Klötzer, Bernhard Dumoulin, Ziyuan Ma, Julia Frederick, Poonam Dhillon, Michael S. Balzer, Rojesh Shrestha, Hongbo Liu et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
15. Single-molecule states link transcription factor binding to gene expression
    Doughty, Benjamin R., Hinks, Michaela M., Schaepe, Julia M., Marinov, Georgi K., Thurm, Abby R., Rios-Martinez, Carolina, Parks, Benjamin E., Tan, Yingxuan, Marklund, Emil, Dubocanin, Danilo et al. · 2024 · Nature
16. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer
    Giacomo Grillo, Tina Keshavarzian, Simon Linder, Christopher Arlidge, Lisanne Mout, Ankita Nand, Mona Teng, Aditi Qamra, Stanley Zhou, Ken J. Kron et al. · 2023 · Cancer Discovery
17. Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas
    Jingyi Wu, L. Nicolas Gonzalez Castro, Sofia Battaglia, Chadi A. El Farran, Joshua P. D’Antonio, Tyler E. Miller, Mario L. Suvà, B Bernstein · 2024 · Nature Cancer
18. CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation
    Sabina Sood, Christopher M. Weber, H. Courtney Hodges, A. Krokhotin, Aryaman Shalizi, Gerald R. Crabtree · 2020 · Proceedings of the National Academy of Sciences
19. AgeAnno: a knowledgebase of single-cell annotation of aging in human
    Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim, Xiaobo Zhou · 2022 · Nucleic Acids Research
20. Computational Methods for Single-Cell Imaging and Omics Data Integration
    Ebony Rose Watson, Atefeh Taherian Fard, Jessica C. Mar · 2022 · Frontiers in Molecular Biosciences
21. Massively Parallel CRISPR‐Based Genetic Perturbation Screening at Single‐Cell Resolution
    Junyun Cheng, Gaole Lin, Tianhao Wang, Yunzhu Wang, Wenbo Guo, Jie Liao, Penghui Yang, Jie Chen, Xin Shao, Xiaoyan Lu et al. · 2022 · Advanced Science
22. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages
    Michael D. Iglesia, Reyka G. Jayasinghe, Siqi Chen, Nadezhda V. Terekhanova, John M. Herndon, Erik P. Storrs, Alla Y. Karpova, Daniel Cui Zhou, Nataly Naser Al Deen, Andrew T. Shinkle et al. · 2024 · Nature Cancer
23. Chromatin accessibility associates with protein-RNA correlation in human cancer
    Akshay Sanghi, Joshua James Gruber, Ahmed A. Metwally, Lihua Jiang, Warren D. Reynolds, John B. Sunwoo, Lisa Ann Orloff, Howard Y. Chang, Maya M. Kasowski, Michael P. Snyder · 2021 · Nature Communications
24. Increased ACTL6A occupancy within mSWI/SNF chromatin remodelers drives human squamous cell carcinoma
    Chiung-Ying Chang, Zohar Shipony, Sherry G. Lin, Ann Kuo, Xiaochen Xiong, Kyle M. Loh, William James Greenleaf, Gerald R. Crabtree · 2021 · Molecular Cell
25. scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference
    Zhijian Li, James Shiniti Nagai, Christoph Kuppe, Rafael Kramann, Ivan G. Costa · 2023 · Bioinformatics Advances
26. BACH1 deficiency prevents neointima formation and maintains the differentiated phenotype of vascular smooth muscle cells by regulating chromatin accessibility
    Jieyu Guo, Jingjing Qiu, Mengping Jia, Qinhan Li, Xiangxiang Wei, Liliang Li, Qi Pan, Jiayu Jin, Fei Ge, Siyu Ma et al. · 2023 · Nucleic Acids Research
27. Single-Cell Multiomics
    Emily Flynn, Ana Almonte-Loya, Gabriela K. Fragiadakis · 2023 · Annual Review of Biomedical Data Science
28. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
    Parker C. Wilson, Amit K. Verma, Yasuhiro Yoshimura, Yoshiharu Muto, Haikuo Li, Nicole P. Malvin, Eryn E. Dixon, Benjamin D. Humphreys · 2024 · Genome biology
29. simATAC: a single-cell ATAC-seq simulation framework
    Zeinab Navidi, Lin Zhang, Bo Wang · 2021 · Genome biology
30. Nonparametric single-cell multiomic characterization of trio relationships between transcription factors, target genes, and cis-regulatory regions
    Yuchao Jiang, Yuriko Harigaya, Zhaojun Zhang, Hongpan Zhang, Chongzhi Zang, Nancy Ruonan Zhang · 2022 · Cell Systems
31. Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogramming
    Surag Nair, Mohamed Ameen, Laksshman Sundaram, Anusri Pampari, Jacob Matthew Schreiber, Akshay Balsubramani, Yu Xin Wang, David Burns, Helen M. Blau, Ioannis Karakikes et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
32. Single cell epigenomic and transcriptomic analysis uncovers potential transcription factors regulating mitotic/meiotic switch
    Fa‐Li Zhang, Yanqin Feng, Jing-Ya Wang, Kexin Zhu, Lu Wang, Jiamao Yan, Xiu‐Xiu Li, Junjie Wang, Wei Ge, Massimo De Felici et al. · 2023 · Cell Death and Disease
33. Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress
    Brian T. Do, Peggy P. Hsu, Sidney Y. Vermeulen, Zhishan Wang, Taghreed Hirz, Keene L. Abbott, Najihah Aziz, Joseph M. Replogle, Stefan Bjelosevic, Jonathan D. Paolino et al. · 2024 · Developmental Cell
34. Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells
    Kaitlin P. McCreery, Aki Stubb, Rebecca K. Stephens, Nadezda A. Fursova, Andrew Cook, Kai Kruse, Anja Michelbach, Leah C. Biggs, Adib Keikhosravi, Sonja Nykänen et al. · 2025 · Nature Cell Biology
35. Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices
    Claudia Racioppi, Keira Wiechecki, Lionel Christiaen · 2019 · eLife
36. Discovering How Heme Controls Genome Function Through Heme-omics
    Ruiqi Liao, Ye Zheng, Xin Liu, Yuannyu Zhang, Gretchen L. Seim, Nobuyuki Tanimura, Gary M. Wilson, Peiman Hematti, Joshua J. Coon, Jing Fan et al. · 2020 · Cell Reports
37. Integrated single-cell transcriptomic and epigenetic study of cell state transition and lineage commitment in embryonic mouse cerebellum
    Nagham Khouri‐Farah, Qiuxia Guo, Kerry Morgan, Jihye Shin, James Y. H. Li · 2022 · Science Advances
38. Epigenetic regulation of HBV-specific tumor-infiltrating T cells in HBV-related HCC
    Maojun You, Yanan Gao, Junliang Fu, Runze Xie, Zhenyu Zhu, Zhixian Hong, Lingzhan Meng, Shunda Du, Junliang Liu, Fu‐Sheng Wang et al. · 2023 · Hepatology
39. Tumor heterogeneity and tumor-microglia interactions in primary and recurrent IDH1-mutant gliomas
    Enrique Blanco-Carmona, Ashwin Narayanan, Inmaculada Hernandez, Juan Camilo Nieto, Marc Elosua-Bayés, Xueyuan Sun, Claudia S. Schmidt, Mustafa Necmettin Pamir, Koray Özduman, Christel C. Herold‐Mende et al. · 2023 · Cell Reports Medicine
40. Distinct epicardial gene regulatory programs drive development and regeneration of the zebrafish heart
    Michael Weinberger, Filipa Costa Simões, Trishalee Gungoosingh, Tatjana Sauka‐Spengler, Paul Richard Riley · 2024 · Developmental Cell
41. Functional mapping of androgen receptor enhancer activity
    Chia-Chi Flora Huang, Shreyas Lingadahalli, Tunç Morova, Doğancan Özturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar et al. · 2021 · Genome biology
42. Functional analysis of structural variants in single cells using Strand-seq
    Hyobin Jeong, Karen Grimes, Kerstin Katharina Rauwolf, Peter‐Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, Tobias Roider, Radhakrishnan Sabarinathan, David Porubskỳ et al. · 2022 · Nature Biotechnology
43. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
    Longqi Liu, Chuanyu Liu, Andrés Quintero, Liang Li Wu, Yue Yuan, Mingyue Wang, Mengnan Cheng, Lizhi Leng, Liqin Xu, Guoyi Dong et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
44. Advancing biological understanding of cellular senescence with computational multiomics
    Li, Sheng, Agudelo Garcia, Paula A., Aliferis, Constantin, Becich, Michael J., Calyeca, Jazmin, Cosgrove, Benjamin D., Elisseeff, Jennifer, Farzad, Negin, Fertig, Elana J., Glass, Carolyn et al. · 2025 · Nature Genetics
45. scAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data
    Qinran Zhang, Suoqin Jin, Xiufen Zou · 2022 · Nucleic Acids Research
46. Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma
    Nianping Liu, Chen Jiang, Xinfeng Yao, Minghao Fang, Xiaolong Qiao, Lin Zhu, Zongcheng Yang, Xuyuan Gao, Ying Ji, Chaoshi Niu et al. · 2023 · Cell Discovery
47. Repression of Latent NF-κB Enhancers by PDX1 Regulates β-cell Functional Heterogeneity
    Benjamin J. Weidemann, Biliana Marcheva, Mikoto Kobayashi, Chiaki Omura, M. Newman, Yumiko Kobayashi, Nathan J Waldeck, Mark Perelis, Louise Lantier, Owen P. McGuinness et al. · 2024 · Cell Metabolism
48. Epigenetic Heritability of Cell Plasticity Drives Cancer Drug Resistance through a One-to-Many Genotype-to-Phenotype Paradigm
    Erica Aparecida de Oliveira, Salvatore Milite, Javier Fernández-Mateos, George D. Cresswell, Erika Yara Romero, Georgios Vlachogiannis, Bingjie Chen, Chela T. James, Lucrezia Patruno, Gianluca Ascolani et al. · 2025 · Cancer Research
49. Single-nucleus chromatin accessibility profiling identifies cell types and functional variants contributing to major depression
    Anjali Chawla, Doruk Cakmakci, Laura M. Fiori, Wenmin Zang, Malosree Maitra, Jennie Yang, Dariusz Żurawek, Gabriella Frosi, Reza Rahimian, Haruka Mitsuhashi et al. · 2025 · Nature Genetics
50. Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity
    Rebecca A. Leylek, Marcela Alcántara‐Hernández, Jeffrey M. Granja, Michael Chavez, Kimberly Perez, Oscar R. Diaz, Rui Li, Ansuman T. Satpathy, Howard Y. Chang, Juliana Idoyaga · 2020 · Cell Reports
51. Chromatin accessibility maps provide evidence of multilineage gene priming in hematopoietic stem cells
    Eric W. Martin, Jana Krietsch, Roman E. Reggiardo, Rebekah Sousae, Daniel H. Kim, E. Camilla Forsberg · 2021 · Epigenetics & Chromatin
52. Heme-stress activated NRF2 skews fate trajectories of bone marrow cells from dendritic cells towards red pulp-like macrophages in hemolytic anemia
    Florence Vallelian, Raphael M. Buzzi, Marc Pfefferlé, Ayla Yalamanoglu, Irina L. Dubach, Andreas Wassmer, Thomas Gentinetta, Kerstin Hansen, Rok Humar, Nadja Schulthess et al. · 2022 · Cell Death and Differentiation
53. The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma
    Hayley J. Zullow, Akshay Sankar, Davis R. Ingram, Daniel D. Samé Guerra, Andrew R. D’Avino, Clayton K. Collings, Rossana Lazcano, Wei‐Lien Wang, Yu Liang, Jun Qi et al. · 2022 · Molecular Cell
54. The molecular consequences of androgen activity in the human breast
    Florian Raths, Mehran Karimzadeh, Nathan Ing, Andrew Martinez, Yoona Yang, Ying Qu, Tian-Yu Lee, Brianna Mulligan, Suzanne Devkota, Wayne T. Tilley et al. · 2023 · Cell Genomics
55. A single-cell based precision medicine approach using glioblastoma patient-specific models
    James Hugh Park, Abdullah Hamid Feroze, Samuel Emerson, Anca B. Mihalas, Christopher Dirk Keene, Patrick Joseph Cimino, Adrián López García de Lomana, Kavya Kannamma Kannan, Wei‐Ju Wu, Serdar Turkarslan et al. · 2022 · npj Precision Oncology
56. Single-cell chromatin accessibility and transcriptome atlas of mouse embryos
    Shan Jiang, Zheng Huang, Yun Li, Chengwei Yu, Hao Yu, Yuwen Ke, Lan Jiang, Jiang Liu · 2023 · Cell Reports
57. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing
    Amanda J. Craig, Maruhen Amir Datsch Silveira, Lichun Ma, Mahler Revsine, Limin Wang, Sophia Heinrich, Zachary Rae, Allison J. Ruchinskas, Kimia Dadkhah, Whitney Do et al. · 2023 · Cell Reports
58. Epigenetic reprogramming shapes the cellular landscape of schwannoma
    Siyuan John Liu, Tim Casey-Clyde, Nam Woo Cho, Jason T. Swinderman, Melike Pekmezci, Mark C. Dougherty, Kyla J. Foster, William Chen, Javier E. Villanueva-Meyer, Danielle L. Swaney et al. · 2024 · Nature Communications
59. SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions
    Qing Deng, Priya Lakra, Panhong Gou, Haopeng Yang, Cem Meydan, Matt R. Teater, Christopher R. Chin, Wenchao Zhang, Tommy Dinh, Usama Khamis Hussein et al. · 2024 · Cancer Cell
60. Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells
    Malte Simon, Philipp Stüve, Lisa Schmidleithner, Sebastian Bittner, Niklas Beumer, Nicholas Strieder, Christian Schmidl, Asmita Pant, Claudia Gebhard, Andreas Eigenberger et al. · 2024 · Immunity
61. Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development
    Sunghyun Kim, Kari A. Koppitch, Riana K. Parvez, Jinjin Guo, MaryAnne A. Achieng, Jack Schnell, Nils O. Lindström, Andrew P. McMahon · 2024 · Developmental Cell
62. scImmOmics: a manually curated resource of single-cell multi-omics immune data
    Yanyu Li, Li‐Wei Zhou, Fengcui Qian, Qiao-Li Fang, Zhengmin Yu, Ting Cui, Fu-Juan Dong, Fu-Hong Cai, Tingting Yu, Lidong Li et al. · 2024 · Nucleic Acids Research
63. TCR-mimicking STAR conveys superior sensitivity over CAR in targeting tumors with low-density neoantigens
    Daosheng Huang, Yi Li, Wei Rui, Keyong Sun, Zhixiao Zhou, Xiachen Lv, Yu Li, Junfan Chen, Jing Zhou, Vincent Liu et al. · 2024 · Cell Reports
64. CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks
    Leyla Abbasova, Paulina Urbanaviciute, Di Hu, Joy N. Ismail, Brian M. Schilder, Alexi Nott, Nathan Skene, Sarah J. Marzi · 2025 · Nature Communications
65. A pancreatic cancer organoid biobank links multi-omics signatures to therapeutic response and clinical evaluation of statin combination therapy
    Yunguang Li, Shijie Tang, Huan Wang, Hongwen Zhu, Yurun Lu, Yehan Zhang, Shiwei Guo, Juan He, Yikai Li, Ying Zhang et al. · 2025 · Cell stem cell
66. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility
    Kaile Wang, Zhenna Xiao, Yun Yan, Rui Ye, Min Shan Hu, Shanshan Bai, Emi Sei, Yawei Qiao, Hui Chen, Bora Lim et al. · 2021 · Molecular Cell
67. An epigenome atlas of neural progenitors within the embryonic mouse forebrain
    Christopher T. Rhodes, Joyce J. Thompson, Apratim Mitra, Dhanya Asokumar, Dongjin R. Lee, Daniel J. Lee, Yajun Zhang, Eva Jason, Ryan Dale, Pedro P. Rocha et al. · 2022 · Nature Communications
68. Taz protects hematopoietic stem cells from an aging-dependent decrease in PU.1 activity
    Kyung Mok Kim, Anna Mura-Mészáros, Marie Tollot, Murali Shyam Krishnan, Marco Gründl, Laura Neubert, Marco Groth, Alejo Rodriguez-Fraticelli, Arthur Flohr Svendsen, Stefano Campaner et al. · 2022 · Nature Communications
69. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses
    Sean M. Gross, Mark A. Dane, Rebecca Lee Smith, Kaylyn L. Devlin, Ian C. McLean, Daniel S. Derrick, Caitlin E. Mills, Kartik Subramanian, Alexandra B. London, Denis Torre et al. · 2022 · Communications Biology
70. Depletion of exhausted alloreactive T cells enables targeting of stem-like memory T cells to generate tumor-specific immunity
    Simone A. Minnie, Olivia G. Waltner, Kathleen S. Ensbey, Nicole S Nemychenkov, Christine R. Schmidt, Shruti S. Bhise, Samuel R.W. Legg, Gabriela Campoy, Luke D. Samson, Rachel D. Kuns et al. · 2022 · Science Immunology
71. Inferring and perturbing cell fate regulomes in human cerebral organoids
    Jonas Simon Fleck, Sophie Martina Johanna Jansen, Damian Wollny, Makiko Seimiya, Fides Lea Zenk, Małgorzata Santel, Zhisong He, J. Gray Camp, Barbara Treutlein · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
72. Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity
    Eleanor Valenzi, Harinath Bahudhanapati, Jiangning Tan, Tracy Tabib, Daniel I. Sullivan, Mehdi syed Nouraie, John Sembrat, Li Fan, Kong Chen, Silvia Liu et al. · 2023 · European Respiratory Journal
73. Single cell epigenomic atlas of the developing human brain and organoids
    Ziffra, Ryan S., Kim, Chang N., Wilfert, Amy, Turner, Tychele N., Haeussler, Maximilian, Casella, Alex M., Przytycki, Pawel F., Kreimer, Anat, Pollard, Katherine S., Ament, Seth A. et al. · 2019
74. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
    Zhenyu Liu, Yuqiong Hu, Haoling Xie, Kexuan Chen, Lu Wen, Wei Fu, Xin Zhou, Fuchou Tang · 2024 · Cancer Discovery
75. Single-cell insights: pioneering an integrated atlas of chromatin accessibility and transcriptomic landscapes in diabetic cardiomyopathy
    Qiang Su, Wanzhong Huang, Yu‐An Huang, Rixin Dai, Chang Chen, Qiuyan Li, Hao Liu, Zhenhao Li, Yuxiang Zhao, Qiang Wu et al. · 2024 · Cardiovascular Diabetology
76. Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice
    Yuvarani Masarapu, Egle Cekanaviciute, Žaneta Andrusivová, Jakub Orzechowski Westholm, Åsa K. Björklund, Robin Fallegger, Pau Badia-i-Mompel, Valery Boyko, Shubha Vasisht, Amanda Saravia-Butler et al. · 2024 · Nature Communications
77. Single-cell multiome and spatial profiling reveals pancreas cell type–specific gene regulatory programs of type 1 diabetes progression
    Rebecca L. Melton, Sara Jiménez, Weston S. Elison, Luca Tucciarone, Abigail Howell, Gaowei Wang, Denise A. Berti, Elisha Beebe, Michael Miller, Chun Zeng et al. · 2025 · Science Advances
78. Interactive analysis of single-cell epigenomic landscapes with ChromSCape
    Pacôme Prompsy, Pia Kirchmeier, Justine Marsolier, Marc Deloger, Nicolas Servant, Céline Vallot · 2020 · Nature Communications
79. The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State
    Karthik Arumugam, William Shin, Valentina Schiavone, Lukas J. Vlahos, Xiaochuan Tu, Davide Carnevali, Jordan S. Kesner, Evan Paull, Neus Romo, Prem S. Subramaniam et al. · 2020 · Cell Reports
80. Mammary gland development from a single cell ‘omics view
    Alecia‐Jane Twigger, Walid T. Khaled · 2021 · Seminars in Cell and Developmental Biology
81. Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning
    Wolfgang Kopp, Altuna Akalin, Uwe Ohler · 2022 · Nature Machine Intelligence
82. Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
    Paola Benaglio, Han Zhu, Mei-Lin Okino, Jian Yan, Ruth M. Elgamal, Naoki Nariai, Elisha Beebe, Katha Korgaonkar, Yunjiang Qiu, Margaret K. R. Donovan et al. · 2022 · Cell Genomics
83. Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets
    Deepshika Ramanan, Kaitavjeet Chowdhary, Serge M. Candéias, Martina Sassone‐Corsi, Adélaïde Gélineau, Diane J. Mathis, Christophe O. Benoist · 2023 · Proceedings of the National Academy of Sciences
84. Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
    Yingshu Li, Yongjie Liu, Hang Yang, Ting Zhang, Kiyoshi Naruse, Qiang Tu · 2020 · Genome Research
85. Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors
    Rohit Singh, Alexander P. Wu, Anish Mudide, Bonnie Berger · 2024 · Cell Systems
86. scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution
    Johannes Hingerl, Laura D. Martens, Alexander Karollus, Trevor Manz, Jason D. Buenrostro, Fabian Joachim Theis, Julien Gagneur · 2025 · Nature Methods
87. Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells
    Dania Riegel, Elena Romero-Fernández, Malte Simon, Akinbami Adenugba, Katrin Singer, Roman Mayr, Florian Weber, Mark Kleemann, Charles David Imbusch, Marina P Kreutz et al. · 2023 · Molecular Cell
88. Loss of PBAF promotes expansion and effector differentiation of CD8+ T cells during chronic viral infection and cancer
    Arjun Kharel, Jian Shen, Ryan J. Brown, Yao Chen, Christine P. Nguyen, Donia Alson, Theresa Bluemn, Jie Fan, Kexin Gai, Bin Zhang et al. · 2023 · Cell Reports
89. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
    Xi Xian Chen, Yuan Wang, Antonio Cappuccio, Wan-Sze Cheng, Frederique Murielle Ruf-Zamojski, Venugopalan D. Nair, Clare M. Miller, Aliza B. Rubenstein, German Nudelman, Alicja Tadych et al. · 2023 · Nature Computational Science
90. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag
    Derek H. Janssens, Jacob E. Greene, Steven J. Wu, Christine A. Codomo, Samuel S. Minot, Scott N. Furlan, Kami Ahmad, Steven Henikoff · 2023 · Nature Protocols
91. Cholesterol lowering depletes atherosclerotic lesions of smooth muscle cell-derived fibromyocytes and chondromyocytes
    Laura Carramolino, Julián Albarrán-Juárez, Anton Markov, Esther Hernández‐SanMiguel, Diana Sharysh, Vanessa Cumbicus, Daniel Morales‐Cano, Verónica Labrador-Cantarero, Peter Loof Møller, Paula Nogales et al. · 2024 · Nature Cardiovascular Research
92. An integrated transcription factor framework for Treg identity and diversity
    Kaitavjeet Chowdhary, Juliette Léon, Deepshika Ramanan, Diane Mathis, Christophe O. Benoist · 2024 · Proceedings of the National Academy of Sciences
93. Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation
    Ziyuan He, Marla C. Glass, Pravina Venkatesan, Marie L. Feser, Leander Lazaro, Lauren Y. Okada, Nhung T. T. Tran, Yudong D. He, Samir Rachid Zaim, Christy Bennett et al. · 2025 · Science Translational Medicine
94. Epigenetic memory of colitis promotes tumour growth
    Surya Nagaraja, Lety Ojeda-Miron, Ruochi Zhang, Ena Oreskovic, Conrad Hock, Hu Yan, Daniel Zeve, Karina Sharma, Roni R. Hyman, Qiming Zhang et al. · 2026 · Nature
95. Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation
    Qian Li, Yahui Wang, Xin Hu, Yapeng Zhang, Hongwei Li, Qi Zhang, Wentao Cai, Zezhao Wang, Bo Zhu, Lingyang Xu et al. · 2022 · Cell Proliferation
96. Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse
    Muya Shu, Danni Hong, Hongli Lin, Jixiang Zhang, Zhengnan Luo, Yi Du, Zheng Sun, Man Yin, Yanyun Yin, Lifang Liu et al. · 2022 · Developmental Cell
97. Hnf4 activates mimetic-cell enhancers to recapitulate gut and liver development within the thymus
    Daniel A. Michelson, Chong Zuo, Michael Paul Verzi, Christophe O. Benoist, Diane J. Mathis · 2023 · The Journal of Experimental Medicine
98. Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms
    Andrew Jeffrey Dunbar, Robert L. Bowman, Young C. Park, Kavi O’Connor, Franco Izzo, Robert M. Myers, Abdul Karzai, Zachary Zaroogian, Won Jun Kim, Inés Fernández-Maestre et al. · 2024 · Cancer Discovery
99. Organoid culture promotes dedifferentiation of mouse myoblasts into stem cells capable of complete muscle regeneration
    Feodor D. Price, Mark N. Matyas, Andrew R. Gehrke, William Chen, Erica Wolin, Kristina M. Holton, Rebecca M. Gibbs, Alice E. Lee, Pooja S Singu, Jeffrey S Sakakeeny et al. · 2024 · Nature Biotechnology
100. Phenotypic heterogeneity and plasticity in colorectal cancer metastasis
     Samuel Ogden, Nasrine Metic, Ozen Leylek, Elise A. Smith, Alison Berner, Ann‐Marie Baker, Imran Uddin, Marta Buzzetti, Marco Gerlinger, Trevor A. Graham et al. · 2025 · Cell Genomics