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

Cited by (1,002)

Items 101–200 of 1,002

1. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets
   Zhen Miao, Michael S. Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, Rojesh Shrestha, Tamás Arányi, Amy Kwan, Ayano Kondo, Marco Pontoglio et al. · 2021 · Nature Communications
2. Osr2 functions as a biomechanical checkpoint to aggravate CD8+ T cell exhaustion in tumor
   Jinjia Zhang, Junhong Li, Yongqiang Hou, Yao Lin, Hao Zhao, Yiran Shi, Kaiyun Chen, Cheng Nian, Jiayu Tang, Lei Pan et al. · 2024 · Cell
3. Interrogation of human hematopoiesis at single-cell and single-variant resolution
   Ulirsch, Jacob C., Lareau, Caleb A., Bao, Erik L., Ludwig, Leif S., Guo, Michael H., Benner, Christian, Satpathy, Ansuman T., Kartha, Vinay K., Salem, Rany M., Hirschhorn, Joel N. et al. · 2019 · Nature Genetics
4. Chromatin accessibility profiling methods
   Minnoye, Liesbeth, Marinov, Georgi K., Krausgruber, Thomas, Pan, Lixia, Marand, Alexandre P., Secchia, Stefano, Greenleaf, William J., Furlong, Eileen E. M., Zhao, Keji, Schmitz, Robert J. et al. · 2021 · Nature Reviews Methods Primers
5. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression
   Wu, Steven J., Furlan, Scott N., Mihalas, Anca B., Kaya-Okur, Hatice S., Feroze, Abdullah H., Emerson, Samuel N., Zheng, Ye, Carson, Kalee, Cimino, Patrick J., Keene, C. Dirk et al. · 2021 · Nature Biotechnology
6. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
   Zhana Duren, Xi Xian Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman T. Satpathy, Howard Y. Chang, Yong Wang, Wing Hung Wong · 2018 · Proceedings of the National Academy of Sciences
7. Drivers of heterogeneity in synovial fibroblasts in rheumatoid arthritis
   Melanie H. Smith, Vianne Ran Gao, Preethi K. Periyakoil, Alejandro Kochen, Edward F. DiCarlo, Susan M. Goodman, Thomas M. Norman, Laura T. Donlin, Christina S. Leslie, Alexander Yu Rudensky · 2023 · Nature Immunology
8. Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
   Parker C. Wilson, Yoshiharu Muto, Hao Wu, Anil K. Karihaloo, Sushrut S. Waikar, Benjamin D. Humphreys · 2022 · Nature Communications
9. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory
   Timo Rückert, Caleb A. Lareau, Mir‐Farzin Mashreghi, Leif S. Ludwig, Chiara Romagnani · 2022 · Nature Immunology
10. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
    Mich, John K., Graybuck, Lucas T., Hess, Erik E., Mahoney, Joseph T., Kojima, Yoshiko, Ding, Yi, Somasundaram, Saroja, Miller, Jeremy A., Kalmbach, Brian E., Radaelli, Cristina et al. · 2021 · Cell Reports
11. HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice
    Huacheng Luo, Ganqian Zhu, Jianfeng Xu, Qian Lai, Bowen Yan, Ying Guo, Tsz Kan Fung, Bernd B. Zeisig, Ya Cui, Jie Zha et al. · 2019 · Cancer Cell
12. Chromatin Accessibility Dynamics and a Hierarchical Transcriptional Regulatory Network Structure for Plant Somatic Embryogenesis
    Fuxiang Wang, Guan-Dong Shang, Lian‐Yu Wu, Zhou-Geng Xu, Xinyan Zhao, Jiawei Wang · 2020 · Developmental Cell
13. Single Cell Multi-Omics Technology: Methodology and Application
    Youjin Hu, Qin An, Katherine M. Sheu, Brandon M. Trejo, Shuxin Fan, Ying Qing Guo · 2018 · Frontiers in Cell and Developmental Biology
14. Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk
    Joshua Chiou, Chun Zeng, Cheng Zhang, Jee Yun Han, Michael Schlichting, Michael Miller, Robert Mendez, Serina Huang, Jinzhao Wang, Yinghui Sui et al. · 2021 · Nature Genetics
15. Integrative analyses of single-cell transcriptome and regulome using MAESTRO
    Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jing‐Yu Fan, Xintao Qiu, Yingtian Xie et al. · 2020 · Genome biology
16. A genetic map of the mouse dorsal vagal complex and its role in obesity
    Ludwig, Mette Q., Cheng, Wenwen, Gordian, Desiree, Lee, Julie, Paulsen, Sarah J., Hansen, Stine N., Egerod, Kristoffer L., Barkholt, Pernille, Rhodes, Christopher J., Secher, Anna et al. · 2021 · Nature Metabolism
17. scPerturb: harmonized single-cell perturbation data
    Peidli, Stefan, Green, Tessa D., Shen, Ciyue, Gross, Torsten, Min, Joseph, Garda, Samuele, Yuan, Bo, Schumacher, Linus J., Taylor-King, Jake P., Marks, Debora S. et al. · 2024 · Nature Methods
18. An atlas of cells in the human tonsil
    Ramon Massoni-Badosa, Sergio Aguilar-Fernández, Juan Camilo Nieto, Paula Soler-Vila, Marc Elosua-Bayés, Doménica Marchese, Marta Kulis, Amaia Vilas‐Zornoza, Marco Matteo Bühler, Sonal Rashmi et al. · 2024 · Immunity
19. Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State
    Surya Nagaraja, Michael A. Quezada, Shawn M. Gillespie, Marlene Arzt, James Lennon, Pamelyn J. Woo, Volker Hovestadt, Madhuri Kambhampati, Mariella G. Filbin, Mario L. Suvà et al. · 2019 · Molecular Cell
20. Dissecting primate early post-implantation development using long-term in vitro embryo culture
    Yuyu Niu, Nianqin Sun, Chang Li, Ying Lei, Zhi‐Hao Huang, Jun Wu, Chenyang Si, Xi Dai, Chuanyu Liu, Jingkuan Wei et al. · 2019 · Science
21. Genomic, epigenomic, and biophysical cues controlling the emergence of the lung alveolus
    Jarod A. Zepp, Michael P. Morley, Claudia Loebel, Madison M. Kremp, Fatima N. Chaudhry, Maria Ciocca Basil, John P. Leach, Derek C. Liberti, Terren K. Niethamer, Yun Ying et al. · 2021 · Science
22. A genome-scale screen for synthetic drivers of T cell proliferation
    Mateusz Legut, Zoran Z. Gajic, Maria Guarino, Zharko Daniloski, Jahan A. Rahman, Xinhe Xue, Congyi Lu, Lu Lu, Eleni P. Mimitou, Stephanie Hao et al. · 2022 · Nature
23. Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia
    Lindsey E. Montefiori, Sonja Bendig, Zhaohui Gu, Xiaolong Chen, Petri Pölönen, Xiaotu Ma, Alex Murison, Andy G.X. Zeng, Laura García‐Prat, Kirsten M. Dickerson et al. · 2021 · Cancer Discovery
24. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
    Ku, Wai Lim, Nakamura, Kosuke, Gao, Weiwu, Cui, Kairong, Hu, Gangqing, Tang, Qingsong, Ni, Bing, Zhao, Keji · 2019 · Nature Methods
25. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation
    Zhou, Jingtian, Ma, Jianzhu, Chen, Yusi, Cheng, Chuankai, Bao, Bokan, Peng, Jian, Sejnowski, Terrence J., Dixon, Jesse R., Ecker, Joseph R. · 2019 · Proceedings of the National Academy of Sciences
26. scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles
    Suoqin Jin, Lihua Zhang, Qing Hua Nie · 2020 · Genome biology
27. CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data
    Kevin Troulé, Robert Petryszak, Batuhan Çakır, James J. Cranley, Alicia Harasty, Martin Prete, Zewen Kelvin Tuong, Sarah Amalia Teichmann, Luz García‐Alonso, Roser Vento-Tormo · 2025 · Nature Protocols
28. Cell-Type-Specific Gene Regulatory Networks Underlying Murine Neonatal Heart Regeneration at Single-Cell Resolution
    Zhaoning Wang, Miao Cui, Akansha M. Shah, Wei Hong Tan, Ning Liu, Rhonda Bassel‐Duby, Eric N. Olson · 2020 · Cell Reports
29. Developmental trajectory of prehematopoietic stem cell formation from endothelium
    Qin Zhu, Peng Gao, Joanna M. Tober, Laura F. Bennett, Changya Chen, Yasin Uzun, Yan Li, Elizabeth D. Howell, Melanie D. Mumau, Wenbao Yu et al. · 2020 · Blood
30. Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer
    Risom, Tyler, Langer, Ellen M., Chapman, Margaret P., Rantala, Juha, Fields, Andrew J., Boniface, Christopher, Alvarez, Mariano J., Kendsersky, Nicholas D., Pelz, Carl R., Johnson-Camacho, Katherine et al. · 2018 · Nature Communications
31. Inosine induces stemness features in CAR-T cells and enhances potency
    Dorota Danuta Klysz, Carley Fowler, Meena B. Malipatlolla, Lucille Stuani, Katherine A. Freitas, Yiyun Chen, Stefanie L. Meier, Bence Dániel, Katalin D. Sandor, Peng Xu et al. · 2024 · Cancer Cell
32. Cryptic activation of an Irf8 enhancer governs cDC1 fate specification
    Vivek Durai, Prachi Bagadia, Jeffrey M. Granja, Ansuman T. Satpathy, Devesha Hrishikesh Kulkarni, Jesse T. Davidson, Renee Wu, Swapneel J. Patel, Arifumi Iwata, Tiantian Liu et al. · 2019 · Nature Immunology
33. A comparative atlas of single-cell chromatin accessibility in the human brain
    Li, Yang Eric, Preissl, Sebastian, Miller, Michael, Johnson, Nicholas D., Wang, Zihan, Jiao, Henry, Zhu, Chenxu, Wang, Zhaoning, Xie, Yang, Poirion, Olivier et al. · 2023 · Science
34. Acoel genome reveals the regulatory landscape of whole-body regeneration
    Andrew R. Gehrke, Emily R Neverett, Yi‐Jyun Luo, Alexander Brandt, Lorenzo Ricci, Ryan E. Hulett, Annika D. Gompers, J. Graham Ruby, Daniel S. Rokhsar, Peter W. Reddien et al. · 2019 · Science
35. Molecular and cellular dynamics of the developing human neocortex
    Li Wang, Cheng Wang, Juan Moriano, Songcang Chen, Guolong Zuo, Arantxa Cebrián‐Silla, Shaobo Zhang, Tanzila Mukhtar, Shaohui Wang, Mengyi Song et al. · 2025 · Nature
36. Histone lactylation couples cellular metabolism with developmental gene regulatory networks
    Fjodor Merkuri, Megan Rothstein, Marcos Simões-Costa · 2024 · Nature Communications
37. Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes
    Evgeny Kiner, Elijah Willie, Brinda Vijaykumar, Kaitavjeet Chowdhary, Hugo Schmutz, Jodie S. Chandler, Alexandra Schnell, Pratiksha I. Thakore, Graham S Le Gros, Sara Mostafavi et al. · 2021 · Nature Immunology
38. A latent lineage potential in resident neural stem cells enables spinal cord repair
    Enric Llorens-Bobadilla, James M. Chell, Pierre Le Merre, Yi-Cheng Wu, Margherita Zamboni, J. Bergenstråhle, Moa Stenudd, E. Sopova, J. Lundeberg, O. Shupliakov et al. · 2020 · Science
39. Divergent transcriptional regulation of astrocyte reactivity across disorders
    Burda, Joshua E., O’Shea, Timothy M., Ao, Yan, Suresh, Keshav B., Wang, Shinong, Bernstein, Alexander M., Chandra, Ashu, Deverasetty, Sandeep, Kawaguchi, Riki, Kim, Jae H. et al. · 2022 · Nature
40. Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis
    Leif S. Ludwig, Caleb A. Lareau, Erik L. Bao, Satish Kumar Nandakumar, Christoph Muus, Jacob C. Ulirsch, Kaitavjeet Chowdhary, Jason D. Buenrostro, Narla Mohandas, Xiuli An et al. · 2019 · Cell Reports
41. 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
42. Aging disrupts circadian gene regulation and function in macrophages
    Eran Blacher, Connie A. Tsai, Lev Litichevskiy, Zohar Shipony, Chinyere Agbaegbu Iweka, Kai Markus Schneider, Bayarsaikhan Chuluun, Horace Craig Heller, Vilas Menon, Christoph A. Thaiss et al. · 2021 · Nature Immunology
43. Epigenetic Induction of Smooth Muscle Cell Phenotypic Alterations in Aortic Aneurysms and Dissections
    Abhijit Chakraborty, Yanming Li, Chen Zhang, Yang Li, Kimberly R. Rebello, Shengyu Li, Samantha Xu, Hernan G. Vasquez, Lin Zhang, Wei Luo et al. · 2023 · Circulation
44. Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos
    Yang Wang, Peng Yuan, Zhiqiang Yan, Ming Yang, Ying Huo, Yanli Nie, Xiaohui Zhu, Jie Qiao, Liying Yan · 2021 · Nature Communications
45. Therapy-induced APOBEC3A drives evolution of persistent cancer cells
    Hideko Isozaki, Ramin Sakhtemani, Ammal Abbasi, Naveed Nikpour, Marcello Stanzione, Sunwoo Oh, Adam Langenbucher, Susanna Monroe, Wenjia Su, Heidie Frisco Cabanos et al. · 2023 · Nature
46. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments
    Xin Sheng, Y. Guan, Ziyuan Ma, Jun-Nan Wu, Hong-Bo Liu, Cheng-Xiang Qiu, Steven Vitale, Zhen Miao, Matthew J. Seasock, Matthew B. Palmer et al. · 2021 · Nature Genetics
47. p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)
    Maya Maor-Nof, Zohar Shipony, Rodrigo Lopez-Gonzalez, Lisa Nakayama, Yong‐Jie Zhang, Julien Couthouis, Jacob A. Blum, Patricia A. Castruita, Gabriel R. Linares, Kai Ruan et al. · 2021 · Cell
48. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation
    Xuemei Liu, Xiao Min Bie, Xuelei Lin, Menglu Li, Hongzhe Wang, Xiaoyu Zhang, Yiman Yang, Xian Sheng Zhang, Xian Sheng Zhang, Jun Ying Xiao · 2023 · Nature Plants
49. Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk
    Adam W. Turner, Shengen Shawn Hu, José Verdezoto Mosquera, Wei Feng, Chani J. Hodonsky, Doris Wong, Gaelle E Auguste, Yipei Song, Katia Sol‐Church, Emily Farber et al. · 2022 · Nature Genetics
50. 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
51. Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia
    Christopher J. Ott, Alexander Joel Federation, Logan Sari Schwartz, Siddha N. Kasar, Josephine L. Klitgaard, Romina Lenci, Qiyuan Li, Matthew A. Lawlor, Stacey M. Fernandes, Amanda Souza et al. · 2018 · Cancer Cell
52. Innate immune memory after brain injury drives inflammatory cardiac dysfunction
    Alba Simats, Sijia Zhang, Denise Messerer, Faye Chong, Sude Beşkardeş, Aparna Sharma Chivukula, Jiayu Cao, Simon Besson‐Girard, Felipe A. Montellano, Caroline Morbach et al. · 2024 · Cell
53. 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
54. Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
    Baek, Seungbyn, Lee, Insuk · 2020 · Computational and Structural Biotechnology Journal
55. Deciphering cell states and genealogies of human haematopoiesis
    Chen Weng, Fulong Yu, Dian Yang, Michael Poeschla, L. Alexander Liggett, Matthew G. Jones, Xiaojie Qiu, Lara Wahlster, Alexis Caulier, Jeffrey A. Hussmann et al. · 2024 · Nature
56. Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA
    Jin Xu, Kevin A. Nuno, Ulrike M. Litzenburger, Yanyan Qi, M. Ryan Corces, Ravindra Majeti, Howard Y. Chang · 2019 · eLife
57. A map of cis-regulatory elements and 3D genome structures in zebrafish
    Hong-Bo Yang, Yu Luan, Ting-Ting Liu, H. Lee, Li Fang, Yan-Li Wang, Xiao-Tao Wang, Bo Zhang, Qiu-Shi Jin, K. Ang et al. · 2020 · Nature
58. Multimodal single-cell chromatin analysis with Signac
    Tim Stuart, Avi Srivastava, Caleb A. Lareau, Rahul Satija · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
59. High-throughput chromatin accessibility profiling at single-cell resolution
    Anja Mezger, Sandy L. Klemm, Ishminder K. Mann, Kara K. Brower, Alain A. Mir, Magnolia L. Bostick, Andrew A. Farmer, Polly Morrell Fordyce, Sten Linnarsson, William James Greenleaf · 2018 · Nature Communications
60. Ancestral perinatal obesogen exposure results in a transgenerational thrifty phenotype in mice
    Raquel Chamorro-García, Carlos Díaz-Castillo, Bassem M. Shoucri, Heidi Kaech, Ron Leavitt, Toshi Shioda, Bruce Blumberg · 2017 · Nature Communications
61. Single‐cell analyses reveal suppressive tumor microenvironment of human colorectal cancer
    Yan Mei, Weiwei Xiao, Hao Hu, Guanming Lu, Lingdan Chen, Zhun Sun, Mengdie Lü, Wenhui Ma, Ting Jiang, Yuanhong Gao et al. · 2021 · Clinical and Translational Medicine
62. A mixture-of-experts deep generative model for integrated analysis of single-cell multiomics data
    Kodai Minoura, Ko Abe, Hyunha Nam, Hiroyoshi Nishikawa, Teppei Shimamura · 2021 · Cell Reports Methods
63. 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
64. Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System
    S. Yachida, Y. Totoki, Michaël Noë, Y. Nakatani, Masafumi Horie, K. Kawasaki, Hiromi Nakamura, Mihoko Saito-Adachi, Masami Suzuki, Erina Takai et al. · 2021 · Cancer Discovery
65. HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia
    Huacheng Luo, Ganqian Zhu, Melanie A. Eshelman, Tsz Kan Fung, Qian Lai, Fei Wang, Bernd B. Zeisig, Julia Lesperance, Xiaoyan Ma, Chen Shi et al. · 2022 · Molecular Cell
66. Age-dependent alveolar epithelial plasticity orchestrates lung homeostasis and regeneration
    Ian J. Penkala, Derek C. Liberti, Josh Pankin, Aravind Sivakumar, Madison M. Kremp, Sowmya Jayachandran, Jeremy B. Katzen, John P. Leach, Rebecca Windmueller, Katharine Stolz et al. · 2021 · Cell stem cell
67. EpiScanpy: integrated single-cell epigenomic analysis
    Anna Danese, Maria Lucia Richter, Kridsadakorn Chaichoompu, David S. Fischer, Fabian Joachim Theis, Maria Colomé‐Tatché · 2021 · Nature Communications
68. Cardiac cell type–specific gene regulatory programs and disease risk association
    James D. Hocker, Olivier Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, Joshua Chiou, Tsui‐Min Wang, Qingquan Zhang, Xiaomeng Hou, Yang Eric Li et al. · 2021 · Science Advances
69. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation
    Nam, Anna S., Dusaj, Neville, Izzo, Franco, Murali, Rekha, Myers, Robert M., Mouhieddine, Tarek H., Sotelo, Jesus, Benbarche, Salima, Waarts, Michael, Gaiti, Federico et al. · 2022 · Nature Genetics
70. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells
    Chen, Amy F., Parks, Benjamin, Kathiria, Arwa S., Ober-Reynolds, Benjamin, Goronzy, Jorg J., Greenleaf, William J. · 2022 · Nature Methods
71. scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks
    Han Yuan, David R. Kelley · 2022 · Nature Methods
72. The type 2 cytokine Fc–IL-4 revitalizes exhausted CD8+ T cells against cancer
    Bing Feng, Zhiliang Bai, Xiaolei Zhou, Yang Zhao, Yuqing Xie, Xinyi Huang, Yang Liu, Tom Enbar, Rongrong Li, Yi Wang et al. · 2024 · Nature
73. A spatially resolved multi-omic single-cell atlas of soybean development
    Xuan Zhang, Ziliang Luo, Alexandre P. Marand, Haidong Yan, Hosung Jang, Sohyun Bang, John Pablo Mendieta, Mark A.A. Minow, Robert J. Schmitz · 2024 · Cell
74. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina
    Pin Lyu, Thanh V. Hoang, Clayton P. Santiago, Eric D. Thomas, Andrew E. Timms, Haley Appel, Megan Y. Gimmen, Nguyet Le, Lizhi Jiang, Dong Won Kim et al. · 2021 · Cell Reports
75. Epigenetic-sensitive pathways in personalized therapy of major cardiovascular diseases
    Concetta Schiano, Giuditta Benincasa, Monica Franzese, Nunzia Della Mura, Katia Pane, Marco Salvatore, Claudio Napoli A · 2020 · Pharmacology & Therapeutics
76. SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys
    Shikhar Aggarwal, Zhanxiang Wang, David Rincon Fernandez Pacheco, Anna Rinaldi, Alex C. Rajewski, Jasper Callemeyn, Elisabet Van Loon, Baptiste Lamarthée, Ambart E. Covarrubias, Jean Hou et al. · 2024 · Science
77. Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data
    Chunman Zuo, Luonan Chen · 2020 · Briefings in Bioinformatics
78. Hallmarks of CD8+ T cell dysfunction are established within hours of tumor antigen encounter before cell division
    Michael W. Rudloff, Paul Zumbo, Natalie R. Favret, Jessica J. Roetman, Carlos R. Detrés Román, Megan M. Erwin, Kristen A. Murray, Sriya T. Jonnakuti, Friederike Dündar, Doron Betel et al. · 2023 · Nature Immunology
79. An exhausted-like microglial population accumulates in aged and APOE4 genotype Alzheimer’s brains
    Millet, Alon, Ledo, Jose Henrique, Tavazoie, Sohail F. · 2024 · Immunity
80. Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction
    Li, Chen, Virgilio, Maria C., Collins, Kathleen L., Welch, Joshua D. · 2023 · Nature Biotechnology
81. Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells
    Feng Tian, Yuyan Cheng, Songlin Zhou, Qianbin Wang, Aboozar Monavarfeshani, Kun Gao, Weiqian Jiang, Riki Kawaguchi, Qing Wang, Mingjun Tang et al. · 2022 · Neuron
82. Recent advances in single-cell sequencing technologies
    Wen, Lu, Tang, Fuchou · 2022 · Precision Clinical Medicine
83. Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
    Zhijian Li, Christoph Kuppe, Susanne Maria Ziegler, Mingbo Cheng, Nazanin Kabgani, Sylvia Menzel, Martin Zenke, Rafael Kramann, Ivan G. Costa · 2021 · Nature Communications
84. Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis
    Mosquera, Jose Verdezoto, Auguste, Gaëlle, Wong, Doris, Turner, Adam W., Hodonsky, Chani J., Alvarez-Yela, Astrid Catalina, Song, Yipei, Cheng, Qi, Lino Cardenas, Christian L., Theofilatos, Konstantinos et al. · 2023 · Cell Reports
85. Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
    Fuqing Jiang, Xin Zhou, Yingying Qian, Miao Zhu, Lı Wang, Zhuxia Li, Qingmei Shen, Minhan Wang, Fangfang Qu, Guizhong Cui et al. · 2023 · Nature Methods
86. Single-cell and spatial atlases of spinal cord injury in the Tabulae Paralytica
    Michael A. Skinnider, Matthieu Gautier, Alan Yue Yang Teo, Claudia Kathe, Thomas Haynes Hutson, Achilleas Laskaratos, Alexandra de Coucy, Nicola Regazzi, Viviana Aureli, Nicholas D. James et al. · 2024 · Nature
87. Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission
    Zhiliang Bai, Bing Feng, Susan McClory, Beatriz Coutinho de Oliveira, Caroline J. Diorio, Céline Grégoire, Bo Tao, Luojia Yang, Ziran Zhao, Lei Peng et al. · 2024 · Nature
88. Unsupervised clustering and epigenetic classification of single cells
    Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, Xi Xian Chen, Zhana Duren, Alicia N. Schep, William James Greenleaf, Wing Hung Wong · 2018 · Nature Communications
89. 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
90. Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci
    Tiit Örd, Kadri Õunap, Lindsey K. Stolze, Rédouane Aherrahrou, Valtteri Nurminen, Anu Toropainen, Ilakya Selvarajan, Tapio Lönnberg, Einari Aavik, Seppo Ylä‐Herttuala et al. · 2021 · Circulation Research
91. Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19
    Maojun You, Liang Chen, Dawei Zhang, Peng Zhao, Zhu Chen, Enqiang Qin, Yanan Gao, Mark M. Davis, Pengyuan Yang · 2021 · Nature Cell Biology
92. TCR-independent CD137 (4-1BB) signaling promotes CD8+-exhausted T cell proliferation and terminal differentiation
    Andrea Pichler, Nadège Carrié, Marine Cuisinier, Samira Ghazali, Allison Voisin, Pierre‐Paul Axisa, Marie Tosolini, Céline Mazzotti, Dominic P. Golec, Sabrina Mahéo et al. · 2023 · Immunity
93. Multi-omic profiling of the developing human cerebral cortex at the single-cell level
    Kaiyi Zhu, Jaroslav M. Bendl, Samir Rahman, James M. Vicari, Claire Coleman, Tereza Clarence, Ovaun Latouche, Nadejda M. Tsankova, Aiqun Li, Kristen Brennand et al. · 2023 · Science Advances
94. Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis
    Yoshiharu Muto, Eryn E. Dixon, Yasuhiro Yoshimura, Hao Wu, Kohei Omachi, Nicolas Ledru, Parker C. Wilson, Andrew J. King, N. Eric Olson, Marvin G. Gunawan et al. · 2022 · Nature Communications
95. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank
    Eliah G. Overbey, JangKeun Kim, Braden T. Tierney, Jiwoon Park, Nadia Houerbi, Alexander G. Lucaci, S. Medina, Namita Damle, Deena Najjar, Kirill A. Grigorev et al. · 2024 · Nature
96. NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
    Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander et al. · 2021 · eLife
97. Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung
    Carla P. Concepcion, Sai Ma, Lindsay M. LaFave, Arjun J. Bhutkar, Manyuan Liu, Lydia P. DeAngelo, Jonathan Y. Kim, Isabella S. Del Priore, Adam Jacob Schoenfeld, Manon Miller et al. · 2021 · Cancer Discovery
98. BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors
    Kota Itahashi, Takuma Irie, Junichiro Yuda, Shogo Kumagai, Tokiyoshi Tanegashima, Yi-Tzu Lin, Sho Watanabe, Yasushi Goto, Jun Suzuki, Keiju Aokage et al. · 2022 · Science Immunology
99. Integration of spatial and single-cell data across modalities with weakly linked features
    Shuxiao Chen, Bokai Zhu, Sijia Huang, John W. Hickey, Kevin Z. Lin, Michael Snyder, William J. Greenleaf, Garry P. Nolan, Nancy R. Zhang, Zongming Ma · 2023 · Nature Biotechnology
100. Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System
     Shinichi Yachida, Yasushi Totoki, Michaël Noë, Yoichiro Nakatani, Masafumi Horie, Kenta Kawasaki, Hiromi K. Nakamura, Mihoko Saito-Adachi, Masami Suzuki, Erina Takai et al. · 2022 · Utrecht University Repository (Utrecht University)