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For: Buenrostro JD, Corces MR, Lareau CA, Wu B, Schep AN, Aryee MJ, Majeti R, Chang HY, Greenleaf WJ. Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell 2018;173:1535-1548.e16. [PMID: 29706549 PMCID: PMC5989727 DOI: 10.1016/j.cell.2018.03.074] [Citation(s) in RCA: 390] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/03/2018] [Accepted: 03/27/2018] [Indexed: 12/26/2022]
Number Cited by Other Article(s)
51
Cai S, Li H, Tie R, Shan W, Luo Q, Wang S, Feng C, Chen H, Zhang M, Xu Y, Li X, Chen M, Lu J, Qian P, Huang H. Nlrc3 signaling is indispensable for hematopoietic stem cell emergence via Notch signaling in vertebrates. Nat Commun 2024;15:226. [PMID: 38172511 PMCID: PMC10764762 DOI: 10.1038/s41467-023-44251-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/06/2023] [Indexed: 01/05/2024]  Open
52
Zhang Y, Liu F. The evolving views of hematopoiesis: from embryo to adulthood and from in vivo to in vitro. J Genet Genomics 2024;51:3-15. [PMID: 37734711 DOI: 10.1016/j.jgg.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
53
Gayoso A, Weiler P, Lotfollahi M, Klein D, Hong J, Streets A, Theis FJ, Yosef N. Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells. Nat Methods 2024;21:50-59. [PMID: 37735568 PMCID: PMC10776389 DOI: 10.1038/s41592-023-01994-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/23/2023]
54
Lambo S, Trinh DL, Ries RE, Jin D, Setiadi A, Ng M, Leblanc VG, Loken MR, Brodersen LE, Dai F, Pardo LM, Ma X, Vercauteren SM, Meshinchi S, Marra MA. A longitudinal single-cell atlas of treatment response in pediatric AML. Cancer Cell 2023;41:2117-2135.e12. [PMID: 37977148 DOI: 10.1016/j.ccell.2023.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
55
Wang K, Zhang X, Cheng H, Ma W, Bao G, Dong L, Gou Y, Yang J, Cai H. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. BMC Bioinformatics 2023;24:463. [PMID: 38062357 PMCID: PMC10704760 DOI: 10.1186/s12859-023-05590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]  Open
56
Li K, Chen X, Song S, Hou L, Chen S, Jiang R. Cofea: correlation-based feature selection for single-cell chromatin accessibility data. Brief Bioinform 2023;25:bbad458. [PMID: 38113078 PMCID: PMC10782922 DOI: 10.1093/bib/bbad458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]  Open
57
Akhtyamov P, Shaheen L, Raevskiy M, Stupnikov A, Medvedeva YA. scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting. Brief Bioinform 2023;25:bbad447. [PMID: 38084919 PMCID: PMC10714317 DOI: 10.1093/bib/bbad447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/29/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023]  Open
58
Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. Transposable Elements Are Co-opted as Oncogenic Regulatory Elements by Lineage-Specific Transcription Factors in Prostate Cancer. Cancer Discov 2023;13:2470-2487. [PMID: 37694973 PMCID: PMC10618745 DOI: 10.1158/2159-8290.cd-23-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/30/2023] [Accepted: 09/08/2023] [Indexed: 09/12/2023]
59
Chang Y, Hummel SN, Jung J, Jin G, Deng Q, Bao X. Engineered hematopoietic and immune cells derived from human pluripotent stem cells. Exp Hematol 2023;127:14-27. [PMID: 37611730 PMCID: PMC10615717 DOI: 10.1016/j.exphem.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
60
Subramanian S, Thoms JAI, Huang Y, Cornejo-Páramo P, Koch FC, Jacquelin S, Shen S, Song E, Joshi S, Brownlee C, Woll PS, Chacon-Fajardo D, Beck D, Curtis DJ, Yehson K, Antonenas V, O'Brien T, Trickett A, Powell JA, Lewis ID, Pitson SM, Gandhi MK, Lane SW, Vafaee F, Wong ES, Göttgens B, Alinejad-Rokny H, Wong JWH, Pimanda JE. Genome-wide transcription factor-binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs. Blood 2023;142:1448-1462. [PMID: 37595278 PMCID: PMC10651876 DOI: 10.1182/blood.2023021120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]  Open
61
Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. Genome Biol 2023;24:236. [PMID: 37858253 PMCID: PMC10588049 DOI: 10.1186/s13059-023-03067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]  Open
62
Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023;14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]  Open
63
Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023;10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023]  Open
64
Arenas-Mena C, Akin S. Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 2023;225:iyad145. [PMID: 37551428 PMCID: PMC10789315 DOI: 10.1093/genetics/iyad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]  Open
65
Phan QM, Salz L, Kindl SS, Lopez JS, Thompson SM, Makkar J, Driskell IM, Driskell RR. Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation. EMBO J 2023;42:e113880. [PMID: 37602956 PMCID: PMC10548174 DOI: 10.15252/embj.2023113880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]  Open
66
Li W, Gurdziel K, Pitchaikannu A, Gupta N, Hazlett LD, Xu S. The miR-183/96/182 cluster is a checkpoint for resident immune cells and shapes the cellular landscape of the cornea. Ocul Surf 2023;30:17-41. [PMID: 37536656 PMCID: PMC10834862 DOI: 10.1016/j.jtos.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
67
Vallelonga V, Gandolfi F, Ficara F, Della Porta MG, Ghisletti S. Emerging Insights into Molecular Mechanisms of Inflammation in Myelodysplastic Syndromes. Biomedicines 2023;11:2613. [PMID: 37892987 PMCID: PMC10603842 DOI: 10.3390/biomedicines11102613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023]  Open
68
Athaya T, Ripan RC, Li X, Hu H. Multimodal deep learning approaches for single-cell multi-omics data integration. Brief Bioinform 2023;24:bbad313. [PMID: 37651607 PMCID: PMC10516349 DOI: 10.1093/bib/bbad313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]  Open
69
Zhang K, Zemke NR, Armand EJ, Ren B. SnapATAC2: a fast, scalable and versatile tool for analysis of single-cell omics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557221. [PMID: 37745443 PMCID: PMC10515871 DOI: 10.1101/2023.09.11.557221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
70
Carbonetto P, Luo K, Sarkar A, Hung A, Tayeb K, Pott S, Stephens M. GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.03.531029. [PMID: 36945441 PMCID: PMC10028846 DOI: 10.1101/2023.03.03.531029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
71
Liu S, Wu W, Du Y, Yin H, Chen Q, Yu W, Wang W, Yu J, Liu L, Lou W, Pu N. The evolution and heterogeneity of neutrophils in cancers: origins, subsets, functions, orchestrations and clinical applications. Mol Cancer 2023;22:148. [PMID: 37679744 PMCID: PMC10483725 DOI: 10.1186/s12943-023-01843-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023]  Open
72
Korzhenevich J, Janowska I, van der Burg M, Rizzi M. Human and mouse early B cell development: So similar but so different. Immunol Lett 2023;261:1-12. [PMID: 37442242 DOI: 10.1016/j.imlet.2023.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
73
Wong M, Wei Y, Ho YC. Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. Curr Opin HIV AIDS 2023;18:246-256. [PMID: 37535039 PMCID: PMC10442869 DOI: 10.1097/coh.0000000000000809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
74
Liang KL, Laurenti E, Taghon T. Circulating IRF8-expressing CD123+CD127+ lymphoid progenitors: key players in human hematopoiesis. Trends Immunol 2023;44:678-692. [PMID: 37591714 PMCID: PMC7614993 DOI: 10.1016/j.it.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
75
Guo X, He C, Xin S, Gao H, Wang B, Liu X, Zhang S, Gong F, Yu X, Pan L, Sun F, Xu J. Current perspective on biological properties of plasmacytoid dendritic cells and dysfunction in gut. Immun Inflamm Dis 2023;11:e1005. [PMID: 37773693 PMCID: PMC10510335 DOI: 10.1002/iid3.1005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]  Open
76
Cheong JG, Ravishankar A, Sharma S, Parkhurst CN, Grassmann SA, Wingert CK, Laurent P, Ma S, Paddock L, Miranda IC, Karakaslar EO, Nehar-Belaid D, Thibodeau A, Bale MJ, Kartha VK, Yee JK, Mays MY, Jiang C, Daman AW, Martinez de Paz A, Ahimovic D, Ramos V, Lercher A, Nielsen E, Alvarez-Mulett S, Zheng L, Earl A, Yallowitz A, Robbins L, LaFond E, Weidman KL, Racine-Brzostek S, Yang HS, Price DR, Leyre L, Rendeiro AF, Ravichandran H, Kim J, Borczuk AC, Rice CM, Jones RB, Schenck EJ, Kaner RJ, Chadburn A, Zhao Z, Pascual V, Elemento O, Schwartz RE, Buenrostro JD, Niec RE, Barrat FJ, Lief L, Sun JC, Ucar D, Josefowicz SZ. Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. Cell 2023;186:3882-3902.e24. [PMID: 37597510 PMCID: PMC10638861 DOI: 10.1016/j.cell.2023.07.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/20/2023] [Accepted: 07/12/2023] [Indexed: 08/21/2023]
77
Rhee C, Scadden EW, Wong LP, Schiroli G, Mazzola MC, Chea PL, Kato H, Hoyer FF, Mistry M, Lee BK, Kim J, Nahrendorf M, Mansour MK, Sykes DB, Sadreyev RI, Scadden DT. Limited plasticity of monocyte fate and function associated with epigenetic scripting at the level of progenitors. Blood 2023;142:658-674. [PMID: 37267513 PMCID: PMC10447620 DOI: 10.1182/blood.2023020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023]  Open
78
Selewa A, Luo K, Wasney M, Smith L, Sun X, Tang C, Eckart H, Moskowitz IP, Basu A, He X, Pott S. Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation. Nat Commun 2023;14:4999. [PMID: 37591828 PMCID: PMC10435551 DOI: 10.1038/s41467-023-40505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023]  Open
79
Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553315. [PMID: 37645872 PMCID: PMC10462003 DOI: 10.1101/2023.08.15.553315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
80
Jassinskaja M, Gonka M, Kent DG. Resolving the hematopoietic stem cell state by linking functional and molecular assays. Blood 2023;142:543-552. [PMID: 36735913 PMCID: PMC10644060 DOI: 10.1182/blood.2022017864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 02/05/2023]  Open
81
Ghersi JJ, Baldissera G, Hintzen J, Luff SA, Cheng S, Xia IF, Sturgeon CM, Nicoli S. Haematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic endothelium. Nat Cell Biol 2023;25:1135-1145. [PMID: 37460694 PMCID: PMC10415179 DOI: 10.1038/s41556-023-01187-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/09/2023] [Indexed: 08/12/2023]
82
Li C, Chen X, Chen S, Jiang R, Zhang X. simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data. Bioinformatics 2023;39:btad453. [PMID: 37494428 PMCID: PMC10394124 DOI: 10.1093/bioinformatics/btad453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]  Open
83
Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 2023;6:765. [PMID: 37479893 PMCID: PMC10362028 DOI: 10.1038/s42003-023-05120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]  Open
84
Otto D, Jordan C, Dury B, Dien C, Setty M. Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes using Mellon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.09.548272. [PMID: 37502954 PMCID: PMC10369887 DOI: 10.1101/2023.07.09.548272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
85
Yashar WM, Curtiss BM, Coleman DJ, VanCampen J, Kong G, Macaraeg J, Estabrook J, Demir E, Long N, Bottomly D, McWeeney SK, Tyner JW, Druker BJ, Maxson JE, Braun TP. Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia. Mol Cancer Res 2023;21:631-647. [PMID: 36976323 PMCID: PMC10330306 DOI: 10.1158/1541-7786.mcr-22-0745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
86
Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat Genet 2023;55:1198-1209. [PMID: 37386249 PMCID: PMC10548551 DOI: 10.1038/s41588-023-01433-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
87
Steimle JD, Kim C, Rowton M, Nadadur RD, Wang Z, Stocker M, Hoffmann AD, Hanson E, Kweon J, Sinha T, Choi K, Black BL, Cunningham JM, Moskowitz IP, Ikegami K. ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment. Cell Rep 2023;42:112665. [PMID: 37330911 PMCID: PMC10592526 DOI: 10.1016/j.celrep.2023.112665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 03/14/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]  Open
88
Bobbitt JR, Seachrist DD, Keri RA. Chromatin Organization and Transcriptional Programming of Breast Cancer Cell Identity. Endocrinology 2023;164:bqad100. [PMID: 37394919 PMCID: PMC10370366 DOI: 10.1210/endocr/bqad100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023]
89
Gibellini L, Borella R, Santacroce E, Serattini E, Boraldi F, Quaglino D, Aramini B, De Biasi S, Cossarizza A. Circulating and Tumor-Associated Neutrophils in the Era of Immune Checkpoint Inhibitors: Dynamics, Phenotypes, Metabolism, and Functions. Cancers (Basel) 2023;15:3327. [PMID: 37444436 DOI: 10.3390/cancers15133327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]  Open
90
Kim Y, Greenleaf WJ, Bendall SC. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol 2023;82:102323. [PMID: 37028221 PMCID: PMC10330158 DOI: 10.1016/j.coi.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
91
Zhang S, Pyne S, Pietrzak S, Halberg S, McCalla SG, Siahpirani AF, Sridharan R, Roy S. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 2023;14:3064. [PMID: 37244909 PMCID: PMC10224950 DOI: 10.1038/s41467-023-38637-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023]  Open
92
Gong W, Dsouza N, Garry DJ. SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors. Genome Biol 2023;24:125. [PMID: 37218013 DOI: 10.1186/s13059-023-02954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/27/2023] [Indexed: 05/24/2023]  Open
93
Tognon M, Giugno R, Pinello L. A survey on algorithms to characterize transcription factor binding sites. Brief Bioinform 2023;24:bbad156. [PMID: 37099664 PMCID: PMC10422928 DOI: 10.1093/bib/bbad156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023]  Open
94
Salemme V, Centonze G, Avalle L, Natalini D, Piccolantonio A, Arina P, Morellato A, Ala U, Taverna D, Turco E, Defilippi P. The role of tumor microenvironment in drug resistance: emerging technologies to unravel breast cancer heterogeneity. Front Oncol 2023;13:1170264. [PMID: 37265795 PMCID: PMC10229846 DOI: 10.3389/fonc.2023.1170264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]  Open
95
Hu N, Wang J, Ju B, Li Y, Fan P, Jin X, Kang X, Wu S. Recent advances of osteoimmunology research in rheumatoid arthritis: From single-cell omics approach. Chin Med J (Engl) 2023:00029330-990000000-00608. [PMID: 37166215 DOI: 10.1097/cm9.0000000000002678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Indexed: 05/12/2023]  Open
96
Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023;30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
97
Salma M, Andrieu-Soler C, Deleuze V, Soler E. High-throughput methods for the analysis of transcription factors and chromatin modifications: Low input, single cell and spatial genomic technologies. Blood Cells Mol Dis 2023;101:102745. [PMID: 37121019 DOI: 10.1016/j.bcmd.2023.102745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
98
Ueda K. Review: MDMX plays a central role in leukemic transformation and may be a promising target for leukemia prevention strategies. Exp Hematol 2023:S0301-472X(23)00161-3. [PMID: 37086813 DOI: 10.1016/j.exphem.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/24/2023]
99
Montalban-Bravo G, Ma F, Thongon N, Yang H, Gomez IG, Rodriguez-Sevilla JJ, Adema V, Wildeman B, Lockyer P, Kim YJ, Tanaka T, Darbaniyan F, Pancholy S, Zhang G, Al-Atrash G, Dwyer K, Takahashi K, Garcia-Manero G, Kantarjian H, Colla S. Targeting MCL1-driven anti-apoptotic pathways to overcome hypomethylating agent resistance in RAS -mutated chronic myelomonocytic leukemia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.535928. [PMID: 37066354 PMCID: PMC10104149 DOI: 10.1101/2023.04.07.535928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
100
Pregizer S, Vreven T, Mathur M, Robinson LN. Multi-omic single cell sequencing: Overview and opportunities for kidney disease therapeutic development. Front Mol Biosci 2023;10:1176856. [PMID: 37091871 PMCID: PMC10113659 DOI: 10.3389/fmolb.2023.1176856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023]  Open
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