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For: McCarthy DJ, Campbell KR, Lun ATL, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 2017;33:1179-1186. [PMID: 28088763 PMCID: PMC5408845 DOI: 10.1093/bioinformatics/btw777] [Citation(s) in RCA: 910] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/07/2016] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
201
Wu SHS, Kim S, Lee H, Lee JH, Park SY, Bakonyi R, Teriyapirom I, Hallay N, Pilat-Carotta S, Theussl HC, Kim J, Lee JH, Simons BD, Kim JK, Colozza G, Koo BK. Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice. Nat Commun 2024;15:4963. [PMID: 38862535 PMCID: PMC11166929 DOI: 10.1038/s41467-024-49382-y] [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: 05/12/2023] [Accepted: 06/04/2024] [Indexed: 06/13/2024]  Open
202
Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.17.553679. [PMID: 37645841 PMCID: PMC10462127 DOI: 10.1101/2023.08.17.553679] [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]
203
Nassiri I, Kwok AJ, Bhandari A, Bull KR, Garner LC, Klenerman P, Webber C, Parkkinen L, Lee AW, Wu Y, Fairfax B, Knight JC, Buck D, Piazza P. Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression. BIOINFORMATICS ADVANCES 2024;4:vbae085. [PMID: 38911824 PMCID: PMC11193101 DOI: 10.1093/bioadv/vbae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024]
204
Hua H, Wang Y, Wang X, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z, Li C, Du Y, Deng H. Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived β cells. Cell Stem Cell 2024;31:850-865.e10. [PMID: 38697109 DOI: 10.1016/j.stem.2024.04.010] [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: 09/10/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
205
Guazzini M, Reisach AG, Weichwald S, Seiler C. spillR: spillover compensation in mass cytometry data. Bioinformatics 2024;40:btae337. [PMID: 38848472 PMCID: PMC11189660 DOI: 10.1093/bioinformatics/btae337] [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: 10/16/2023] [Revised: 04/29/2024] [Accepted: 06/05/2024] [Indexed: 06/09/2024]  Open
206
Benjamin KJM, Chen Q, Eagles NJ, Huuki-Myers LA, Collado-Torres L, Stolz JM, Pertea G, Shin JH, Paquola ACM, Hyde TM, Kleinman JE, Jaffe AE, Han S, Weinberger DR. Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry. Nat Neurosci 2024;27:1064-1074. [PMID: 38769152 PMCID: PMC11156587 DOI: 10.1038/s41593-024-01636-0] [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: 05/26/2023] [Accepted: 03/29/2024] [Indexed: 05/22/2024]
207
Lu DN, Zhang WC, Lin YZ, Jiang HY, He R, Li SL, Zhang YN, Shao CY, Zheng CM, Xu JJ, Ge MH. Single-cell and bulk RNA sequencing reveal heterogeneity and diagnostic markers in papillary thyroid carcinoma lymph-node metastasis. J Endocrinol Invest 2024;47:1513-1530. [PMID: 38146045 PMCID: PMC11143037 DOI: 10.1007/s40618-023-02262-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/26/2023] [Indexed: 12/27/2023]
208
Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024;43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024]  Open
209
Huuki-Myers LA, Spangler A, Eagles NJ, Montgomery KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR. A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex. Science 2024;384:eadh1938. [PMID: 38781370 PMCID: PMC11398705 DOI: 10.1126/science.adh1938] [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: 02/17/2023] [Accepted: 12/06/2023] [Indexed: 05/25/2024]
210
Wang W, Cen Y, Lu Z, Xu Y, Sun T, Xiao Y, Liu W, Li JJ, Wang C. scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data. Genome Biol 2024;25:136. [PMID: 38783325 PMCID: PMC11112958 DOI: 10.1186/s13059-024-03284-w] [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: 01/30/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024]  Open
211
Pilcher WC, Yao L, Gonzalez-Kozlova E, Pita-Juarez Y, Karagkouni D, Acharya CR, Michaud ME, Hamilton M, Nanda S, Song Y, Sato K, Wang JT, Satpathy S, Ma Y, Schulman J, D'Souza D, Jayasinghe RG, Cheloni G, Bakhtiari M, Pabustan N, Nie K, Foltz JA, Saldarriaga I, Alaaeldin R, Lepisto E, Chen R, Fiala MA, Thomas BE, Cook A, Dos Santos JV, Chiang IL, Figueiredo I, Fortier J, Slade M, Oh ST, Rettig MP, Anderson E, Li Y, Dasari S, Strausbauch MA, Simon VA, Immune Atlas Consortium, Rahman AH, Chen Z, Lagana A, DiPersio JF, Rosenblatt J, Kim-Schulze S, Dhodapkar MV, Lonial S, Kumar S, Bhasin SS, Kourelis T, Vij R, Avigan D, Cho HJ, Mulligan G, Ding L, Gnjatic S, Vlachos IS, Bhasin M. A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.593193. [PMID: 38798338 PMCID: PMC11118283 DOI: 10.1101/2024.05.15.593193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
212
Saxena R, Bushey RT, Campa MJ, Gottlin EB, Guo J, Patz EF, He YW. Promotion of an Antitumor Immune Program by a Tumor-specific, Complement-activating Antibody. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;212:1589-1601. [PMID: 38558134 DOI: 10.4049/jimmunol.2300728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
213
Mulè MP, Martins AJ, Cheung F, Farmer R, Sellers BA, Quiel JA, Jain A, Kotliarov Y, Bansal N, Chen J, Schwartzberg PL, Tsang JS. Integrating population and single-cell variations in vaccine responses identifies a naturally adjuvanted human immune setpoint. Immunity 2024;57:1160-1176.e7. [PMID: 38697118 DOI: 10.1016/j.immuni.2024.04.009] [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: 03/28/2023] [Revised: 01/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
214
O'Callaghan A, Eling N, Marioni JC, Vallejos CA. BASiCS workflow: a step-by-step analysis of expression variability using single cell RNA sequencing data. F1000Res 2024;11:59. [PMID: 38779464 PMCID: PMC11109695 DOI: 10.12688/f1000research.74416.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 05/25/2024]  Open
215
Ramnauth AD, Tippani M, Divecha HR, Papariello AR, Miller RA, Nelson ED, Pattie EA, Kleinman JE, Maynard KR, Collado-Torres L, Hyde TM, Martinowich K, Hicks SC, Page SC. Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567883. [PMID: 38045413 PMCID: PMC10690172 DOI: 10.1101/2023.11.20.567883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
216
Nguyen TH, Vicidomini R, Choudhury SD, Han TH, Maric D, Brody T, Serpe M. scRNA-seq data from the larval Drosophila ventral cord provides a resource for studying motor systems function and development. Dev Cell 2024;59:1210-1230.e9. [PMID: 38569548 PMCID: PMC11078614 DOI: 10.1016/j.devcel.2024.03.016] [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: 06/27/2023] [Revised: 12/05/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
217
Popp JM, Rhodes K, Jangi R, Li M, Barr K, Tayeb K, Battle A, Gilad Y. Cell-type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592174. [PMID: 38746382 PMCID: PMC11092595 DOI: 10.1101/2024.05.02.592174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
218
Vornholt E, Liharska LE, Cheng E, Hashemi A, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Thompson RC, Sullivan B, Moya E, Nadkarni GN, Sebra R, Schadt EE, Kopell BH, Charney AW, Beckmann ND. Characterizing cell type specific transcriptional differences between the living and postmortem human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306590. [PMID: 38746297 PMCID: PMC11092720 DOI: 10.1101/2024.05.01.24306590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
219
Renaut S, Saavedra Armero V, Boudreau DK, Gaudreault N, Desmeules P, Thériault S, Mathieu P, Joubert P, Bossé Y. Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights. PLoS Genet 2024;20:e1011301. [PMID: 38814983 PMCID: PMC11166281 DOI: 10.1371/journal.pgen.1011301] [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: 12/13/2023] [Revised: 06/11/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]  Open
220
Sharma G, Sharma A, Kim I, Cha DG, Kim S, Park ES, Noh JG, Lee J, Ku JH, Choi YH, Kong J, Lee H, Ko H, Lee J, Notaro A, Hong SH, Rhee JH, Kim SG, De Castro C, Molinaro A, Shin K, Kim S, Kim JK, Rudra D, Im SH. A dietary commensal microbe enhances antitumor immunity by activating tumor macrophages to sequester iron. Nat Immunol 2024;25:790-801. [PMID: 38664585 DOI: 10.1038/s41590-024-01816-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/13/2024] [Indexed: 05/04/2024]
221
Wei C, Jiang W, Wang R, Zhong H, He H, Gao X, Zhong S, Yu F, Guo Q, Zhang L, Schiffelers LDJ, Zhou B, Trepel M, Schmidt FI, Luo M, Shao F. Brain endothelial GSDMD activation mediates inflammatory BBB breakdown. Nature 2024;629:893-900. [PMID: 38632402 DOI: 10.1038/s41586-024-07314-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
222
Kerwin RE, Hart JE, Fiesel PD, Lou YR, Fan P, Jones AD, Last RL. Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster. SCIENCE ADVANCES 2024;10:eadn3991. [PMID: 38657073 PMCID: PMC11094762 DOI: 10.1126/sciadv.adn3991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
223
Lindeman I, Høydahl LS, Christophersen A, Risnes LF, Jahnsen J, Lundin KEA, Sollid LM, Iversen R. Generation of circulating autoreactive pre-plasma cells fueled by naive B cells in celiac disease. Cell Rep 2024;43:114045. [PMID: 38578826 DOI: 10.1016/j.celrep.2024.114045] [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: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024]  Open
224
Wang L, Liu Y, Tai J, Dou X, Yang H, Li Q, Liu J, Yan Z, Liu X. Transcriptome and single-cell analysis reveal disulfidptosis-related modification patterns of tumor microenvironment and prognosis in osteosarcoma. Sci Rep 2024;14:9186. [PMID: 38649690 PMCID: PMC11035678 DOI: 10.1038/s41598-024-59243-9] [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: 04/03/2023] [Accepted: 04/08/2024] [Indexed: 04/25/2024]  Open
225
Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024;12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [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: 04/20/2024]  Open
226
Lando D, Ma X, Cao Y, Jartseva A, Stevens TJ, Boucher W, Reynolds N, Montibus B, Hall D, Lackner A, Ragheb R, Leeb M, Hendrich BD, Laue ED. Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency. Mol Cell 2024;84:1406-1421.e8. [PMID: 38490199 PMCID: PMC7616059 DOI: 10.1016/j.molcel.2024.02.015] [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: 12/19/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
227
Wei Y, Lei J, Peng Y, Chang H, Luo T, Tang Y, Wang L, Wen H, Volpe G, Liu L, Han L. Expression characteristics and potential function of non-coding RNA in mouse cortical cells. Front Mol Neurosci 2024;17:1365978. [PMID: 38660385 PMCID: PMC11040102 DOI: 10.3389/fnmol.2024.1365978] [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: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]  Open
228
Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588105. [PMID: 38617294 PMCID: PMC11014536 DOI: 10.1101/2024.04.04.588105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
229
Wachter A, Woodbury ME, Lombardo S, Abdourahman A, Wuest C, McGlame E, Pastika T, Tamm J, Romanul N, Yanamandra K, Bennett R, Lin G, Kwon T, Liao F, Klein C, Grinberg Y, Jaisa-Aad M, Li H, Frosch MP, Kummer MP, Das S, Dellovade T, Karran EH, Langlois X, Ried JS, Serrano-Pozo A, Talanian RV, Biber K, Hyman BT. Landscape of brain myeloid cell transcriptome along the spatiotemporal progression of Alzheimer's disease reveals distinct sequential responses to Aβ and tau. Acta Neuropathol 2024;147:65. [PMID: 38557897 PMCID: PMC10984903 DOI: 10.1007/s00401-024-02704-2] [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: 09/05/2023] [Revised: 02/01/2024] [Accepted: 02/10/2024] [Indexed: 04/04/2024]
230
Mitra S, Malik R, Wong W, Rahman A, Hartemink AJ, Pritykin Y, Dey KK, Leslie CS. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nat Genet 2024;56:627-636. [PMID: 38514783 PMCID: PMC11018525 DOI: 10.1038/s41588-024-01689-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024]
231
Nielsen SSR, Pedersen JAZ, Sharma N, Wasehuus PK, Hansen MS, Møller AMJ, Borggaard XG, Rauch A, Frost M, Sondergaard TE, Søe K. Human osteoclasts in vitro are dose dependently both inhibited and stimulated by cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC). Bone 2024;181:117035. [PMID: 38342278 DOI: 10.1016/j.bone.2024.117035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
232
Ye X, Shih DJH, Ku Z, Hong J, Barrett DF, Rupp RE, Zhang N, Fu TM, Zheng WJ, An Z. Transcriptional signature of durable effector T cells elicited by a replication defective HCMV vaccine. NPJ Vaccines 2024;9:70. [PMID: 38561339 PMCID: PMC10984989 DOI: 10.1038/s41541-024-00860-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024]  Open
233
Choi C, Jeong YL, Park KM, Kim M, Kim S, Jo H, Lee S, Kim H, Choi G, Choi YH, Seong JK, Namgoong S, Chung Y, Jung YS, Granneman JG, Hyun YM, Kim JK, Lee YH. TM4SF19-mediated control of lysosomal activity in macrophages contributes to obesity-induced inflammation and metabolic dysfunction. Nat Commun 2024;15:2779. [PMID: 38555350 PMCID: PMC10981689 DOI: 10.1038/s41467-024-47108-8] [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: 10/17/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024]  Open
234
Smith JJ, Taylor SR, Blum JA, Feng W, Collings R, Gitler AD, Miller DM, Kratsios P. A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes. Cell Rep 2024;43:113857. [PMID: 38421866 PMCID: PMC11091551 DOI: 10.1016/j.celrep.2024.113857] [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: 08/18/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]  Open
235
Baker GJ, Novikov E, Zhao Z, Vallius T, Davis JA, Lin JR, Muhlich JL, Mittendorf EA, Santagata S, Guerriero JL, Sorger PK. Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.01.565120. [PMID: 37961235 PMCID: PMC10634977 DOI: 10.1101/2023.11.01.565120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
236
Tien JCY, Chang Y, Zhang Y, Chou J, Cheng Y, Wang X, Yang J, Mannan R, Shah P, Wang XM, Todd AJ, Eyunni S, Cheng C, Rebernick RJ, Xiao L, Bao Y, Neiswender J, Brough R, Pettitt SJ, Cao X, Miner SJ, Zhou L, Wu YM, Labanca E, Wang Y, Parolia A, Cieslik M, Robinson DR, Wang Z, Feng FY, Lord CJ, Ding K, Chinnaiyan AM. CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585990. [PMID: 38562774 PMCID: PMC10983964 DOI: 10.1101/2024.03.20.585990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
237
Fiesel PD, Kerwin RE, Daniel Jones A, Last RL. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.542877. [PMID: 37333341 PMCID: PMC10274652 DOI: 10.1101/2023.06.05.542877] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
238
Pothuri VS, Hogg GD, Conant L, Borcherding N, James CA, Mudd J, Williams G, Seo YD, Hawkins WG, Pillarisetty VG, DeNardo DG, Fields RC. Intratumoral T-cell receptor repertoire composition predicts overall survival in patients with pancreatic ductal adenocarcinoma. Oncoimmunology 2024;13:2320411. [PMID: 38504847 PMCID: PMC10950267 DOI: 10.1080/2162402x.2024.2320411] [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: 11/07/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024]  Open
239
Ciudad MT, Quevedo R, Lamorte S, Jin R, Nzirorera N, Koritzinsky M, McGaha TL. Dabrafenib Alters MDSC Differentiation and Function by Activation of GCN2. CANCER RESEARCH COMMUNICATIONS 2024;4:765-784. [PMID: 38421883 PMCID: PMC10936428 DOI: 10.1158/2767-9764.crc-23-0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
240
Waichman TV, Vercesi ML, Berardino AA, Beckel MS, Giacomini D, Rasetto NB, Herrero M, Di Bella DJ, Arlotta P, Schinder AF, Chernomoretz A. scX: A user-friendly tool for scRNA-seq exploration. ARXIV 2024:arXiv:2311.00012v2. [PMID: 37961742 PMCID: PMC10635291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
241
Hanhart D, Gossi F, Rapsomaniki MA, Kruithof-de Julio M, Chouvardas P. ScLinear predicts protein abundance at single-cell resolution. Commun Biol 2024;7:267. [PMID: 38438709 PMCID: PMC10912329 DOI: 10.1038/s42003-024-05958-4] [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: 08/04/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024]  Open
242
De Jesus DF, Zhang Z, Brown NK, Li X, Xiao L, Hu J, Gaffrey MJ, Fogarty G, Kahraman S, Wei J, Basile G, Rana TM, Mathews C, Powers AC, Parent AV, Atkinson MA, Dhe-Paganon S, Eizirik DL, Qian WJ, He C, Kulkarni RN. Redox regulation of m6A methyltransferase METTL3 in β-cells controls the innate immune response in type 1 diabetes. Nat Cell Biol 2024;26:421-437. [PMID: 38409327 PMCID: PMC11042681 DOI: 10.1038/s41556-024-01368-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
243
Brown DV, Anttila CJA, Ling L, Grave P, Baldwin TM, Munnings R, Farchione AJ, Bryant VL, Dunstone A, Biben C, Taoudi S, Weber TS, Naik SH, Hadla A, Barker HE, Vandenberg CJ, Dall G, Scott CL, Moore Z, Whittle JR, Freytag S, Best SA, Papenfuss AT, Olechnowicz SWZ, MacRaild SE, Wilcox S, Hickey PF, Amann-Zalcenstein D, Bowden R. A risk-reward examination of sample multiplexing reagents for single cell RNA-Seq. Genomics 2024;116:110793. [PMID: 38220132 DOI: 10.1016/j.ygeno.2024.110793] [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: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
244
Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. Nat Biotechnol 2024;42:470-483. [PMID: 37169965 PMCID: PMC10638471 DOI: 10.1038/s41587-023-01782-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023]
245
Yi F, Cohen T, Zimmerman N, Dündar F, Zumbo P, Eltilib R, Brophy EJ, Arkin H, Feucht J, Gormally MV, Hackett CS, Kropp KN, Etxeberria I, Chandran SS, Park JH, Hsu KC, Sadelain M, Betel D, Klebanoff CA. CAR-engineered lymphocyte persistence is governed by a FAS ligand/FAS auto-regulatory circuit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582108. [PMID: 38464085 PMCID: PMC10925151 DOI: 10.1101/2024.02.26.582108] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
246
Smyth LCD, Xu D, Okar SV, Dykstra T, Rustenhoven J, Papadopoulos Z, Bhasiin K, Kim MW, Drieu A, Mamuladze T, Blackburn S, Gu X, Gaitán MI, Nair G, Storck SE, Du S, White MA, Bayguinov P, Smirnov I, Dikranian K, Reich DS, Kipnis J. Identification of direct connections between the dura and the brain. Nature 2024;627:165-173. [PMID: 38326613 PMCID: PMC11254388 DOI: 10.1038/s41586-023-06993-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
247
Perez-Shibayama C, Gil-Cruz C, Cadosch N, Lütge M, Cheng HW, De Martin A, Frischmann K, Joachimbauer A, Onder L, Papadopoulou I, Papadopoulou C, Ring S, Krebs P, Vu VP, Nägele MP, Rossi VA, Parianos D, Zsilavecz VW, Cooper LT, Flammer A, Ruschitzka F, Rainer PP, Schmidt D, Ludewig B. Bone morphogenic protein-4 availability in the cardiac microenvironment controls inflammation and fibrosis in autoimmune myocarditis. NATURE CARDIOVASCULAR RESEARCH 2024;3:301-316. [PMID: 39196111 PMCID: PMC11358008 DOI: 10.1038/s44161-024-00432-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 01/19/2024] [Indexed: 08/29/2024]
248
Gillespie ER, Grice LF, Courtney IG, Lao HW, Jung W, Ramkomuth S, Xie J, Brown DA, Walsham J, Radford KJ, Nguyen QH, Ruitenberg MJ. Single-cell RNA sequencing reveals peripheral blood leukocyte responses to spinal cord injury in mice with humanised immune systems. J Neuroinflammation 2024;21:63. [PMID: 38429643 PMCID: PMC10908016 DOI: 10.1186/s12974-024-03048-0] [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: 07/24/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024]  Open
249
Zhang J, Zhang L, Gongol B, Hayes J, Borowsky A, Bailey-Serres J, Girke T. spatialHeatmap: visualizing spatial bulk and single-cell assays in anatomical images. NAR Genom Bioinform 2024;6:lqae006. [PMID: 38312938 PMCID: PMC10836942 DOI: 10.1093/nargab/lqae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 02/06/2024]  Open
250
Chousal JN, Morey R, Srinivasan S, Lee K, Zhang W, Yeo AL, To C, Cho K, Garzo VG, Parast MM, Laurent LC, Cook-Andersen H. Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential. Cell Rep 2024;43:113701. [PMID: 38277271 DOI: 10.1016/j.celrep.2024.113701] [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: 03/29/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/28/2024]  Open
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