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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)
701
Fehlmann T, Lehallier B, Schaum N, Hahn O, Kahraman M, Li Y, Grammes N, Geffers L, Backes C, Balling R, Kern F, Krüger R, Lammert F, Ludwig N, Meder B, Fromm B, Maetzler W, Berg D, Brockmann K, Deuschle C, von Thaler AK, Eschweiler GW, Milman S, Barziliai N, Reichert M, Wyss-Coray T, Meese E, Keller A. Common diseases alter the physiological age-related blood microRNA profile. Nat Commun 2020;11:5958. [PMID: 33235214 PMCID: PMC7686493 DOI: 10.1038/s41467-020-19665-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023]  Open
702
Mižíková I, Thébaud B. Looking at the developing lung in single-cell resolution. Am J Physiol Lung Cell Mol Physiol 2020;320:L680-L687. [PMID: 33205990 DOI: 10.1152/ajplung.00385.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
703
Prompsy P, Kirchmeier P, Marsolier J, Deloger M, Servant N, Vallot C. Interactive analysis of single-cell epigenomic landscapes with ChromSCape. Nat Commun 2020;11:5702. [PMID: 33177523 PMCID: PMC7658988 DOI: 10.1038/s41467-020-19542-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023]  Open
704
Single-Cell RNA Sequencing Unravels Heterogeneity of the Stromal Niche in Cutaneous Melanoma Heterogeneous Spheroids. Cancers (Basel) 2020;12:cancers12113324. [PMID: 33182777 PMCID: PMC7697260 DOI: 10.3390/cancers12113324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022]  Open
705
Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat Commun 2020;11:5650. [PMID: 33159064 PMCID: PMC7648640 DOI: 10.1038/s41467-020-19015-1] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/16/2020] [Indexed: 01/05/2023]  Open
706
The bone marrow microenvironment of pre-B acute lymphoblastic leukemia at single-cell resolution. Sci Rep 2020;10:19173. [PMID: 33154494 PMCID: PMC7645756 DOI: 10.1038/s41598-020-76157-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023]  Open
707
Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults. Front Immunol 2020;11:580373. [PMID: 33250895 PMCID: PMC7672042 DOI: 10.3389/fimmu.2020.580373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]  Open
708
Chung NC. Statistical significance of cluster membership for unsupervised evaluation of cell identities. Bioinformatics 2020;36:3107-3114. [PMID: 32142108 PMCID: PMC7214036 DOI: 10.1093/bioinformatics/btaa087] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 01/05/2020] [Accepted: 03/03/2020] [Indexed: 01/09/2023]  Open
709
Lotto J, Drissler S, Cullum R, Wei W, Setty M, Bell EM, Boutet SC, Nowotschin S, Kuo YY, Garg V, Pe'er D, Church DM, Hadjantonakis AK, Hoodless PA. Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages. Cell 2020;183:702-716.e14. [PMID: 33125890 PMCID: PMC7643810 DOI: 10.1016/j.cell.2020.09.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 02/08/2023]
710
Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Tumor Profiler Consortium, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2020;9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 07/20/2023]  Open
711
Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, Moreno P, Mautner S, Papatheodorou I, Nekrutenko A, Taylor J, Blankenberg D, Backofen R, Grüning B. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. Gigascience 2020;9:5931798. [PMID: 33079170 PMCID: PMC7574357 DOI: 10.1093/gigascience/giaa102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/30/2020] [Indexed: 11/25/2022]  Open
712
Stary V, Pandey RV, Strobl J, Kleissl L, Starlinger P, Pereyra D, Weninger W, Fischer GF, Bock C, Farlik M, Stary G. A discrete subset of epigenetically primed human NK cells mediates antigen-specific immune responses. Sci Immunol 2020;5:eaba6232. [PMID: 33067380 PMCID: PMC7615005 DOI: 10.1126/sciimmunol.aba6232] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
713
Huang R, Soneson C, Ernst FG, Rue-Albrecht KC, Yu G, Hicks SC, Robinson MD. TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Res 2020;9:1246. [PMID: 33274053 PMCID: PMC7684683 DOI: 10.12688/f1000research.26669.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 09/12/2023]  Open
714
Huang R, Soneson C, Ernst FG, Rue-Albrecht KC, Yu G, Hicks SC, Robinson MD. TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Res 2020;9:1246. [PMID: 33274053 PMCID: PMC7684683 DOI: 10.12688/f1000research.26669.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/04/2021] [Indexed: 12/26/2022]  Open
715
Ravenscroft TA, Janssens J, Lee PT, Tepe B, Marcogliese PC, Makhzami S, Holmes TC, Aerts S, Bellen HJ. Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains. J Neurosci 2020;40:7999-8024. [PMID: 32928889 PMCID: PMC7574647 DOI: 10.1523/jneurosci.0142-20.2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/15/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022]  Open
716
Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during clinical latency. Nat Commun 2020;11:4977. [PMID: 33020483 PMCID: PMC7536220 DOI: 10.1038/s41467-020-18701-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 09/03/2020] [Indexed: 02/07/2023]  Open
717
Penkava F, Velasco-Herrera MDC, Young MD, Yager N, Nwosu LN, Pratt AG, Lara AL, Guzzo C, Maroof A, Mamanova L, Cole S, Efremova M, Simone D, Filer A, Brown CC, Croxford AL, Isaacs JD, Teichmann S, Bowness P, Behjati S, Hussein Al-Mossawi M. Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis. Nat Commun 2020;11:4767. [PMID: 32958743 PMCID: PMC7505844 DOI: 10.1038/s41467-020-18513-6] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/27/2020] [Indexed: 11/08/2022]  Open
718
Zhang AW, Campbell KR. Computational modelling in single-cell cancer genomics: methods and future directions. Phys Biol 2020;17:061001. [DOI: 10.1088/1478-3975/abacfe] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
719
Frost HR. Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring. Nucleic Acids Res 2020;48:e94. [PMID: 32633778 PMCID: PMC7498348 DOI: 10.1093/nar/gkaa582] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 12/26/2022]  Open
720
Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR. Methodologies for Following EMT In Vivo at Single Cell Resolution. Methods Mol Biol 2020;2179:303-314. [PMID: 32939729 DOI: 10.1007/978-1-0716-0779-4_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
721
Sayols S, Klassek J, Werner C, Möckel S, Ritz S, Mendez-Lago M, Soshnikova N. Signalling codes for the maintenance and lineage commitment of embryonic gastric epithelial progenitors. Development 2020;147:dev.188839. [PMID: 32878924 DOI: 10.1242/dev.188839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022]
722
Perez-Shibayama C, Islander U, Lütge M, Cheng HW, Onder L, Ring SS, De Martin A, Novkovic M, Colston J, Gil-Cruz C, Ludewig B. Type I interferon signaling in fibroblastic reticular cells prevents exhaustive activation of antiviral CD8+ T cells. Sci Immunol 2020;5:5/51/eabb7066. [PMID: 32917792 DOI: 10.1126/sciimmunol.abb7066] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022]
723
Ando Y, Kwon ATJ, Shin JW. An era of single-cell genomics consortia. Exp Mol Med 2020;52:1409-1418. [PMID: 32929222 PMCID: PMC8080593 DOI: 10.1038/s12276-020-0409-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/24/2020] [Accepted: 02/10/2020] [Indexed: 12/24/2022]  Open
724
Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Pinaud S, Nicholls A, Ros XR, Su J, Eldridge MD, Riedel A, Serrao EM, Rodewald HR, Mack M, Shields JD, Cohen ES, McKenzie ANJ, Goodwin RJA, Brindle KM, Marioni JC, Halim TYF. ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung. Nat Immunol 2020;21:998-1009. [PMID: 32747815 PMCID: PMC7116357 DOI: 10.1038/s41590-020-0745-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/23/2020] [Indexed: 12/23/2022]
725
Lee M, Lee E, Han SK, Choi YH, Kwon DI, Choi H, Lee K, Park ES, Rha MS, Joo DJ, Shin EC, Kim S, Kim JK, Lee YJ. Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells. Nat Commun 2020;11:4367. [PMID: 32868763 PMCID: PMC7459300 DOI: 10.1038/s41467-020-18155-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/09/2020] [Indexed: 12/19/2022]  Open
726
Centonze A, Lin S, Tika E, Sifrim A, Fioramonti M, Malfait M, Song Y, Wuidart A, Van Herck J, Dannau A, Bouvencourt G, Dubois C, Dedoncker N, Sahay A, de Maertelaer V, Siebel CW, Van Keymeulen A, Voet T, Blanpain C. Heterotypic cell-cell communication regulates glandular stem cell multipotency. Nature 2020;584:608-613. [PMID: 32848220 DOI: 10.1038/s41586-020-2632-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/20/2020] [Indexed: 12/15/2022]
727
Raimundo F, Vallot C, Vert JP. Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis. Genome Biol 2020;21:212. [PMID: 32831127 PMCID: PMC7444048 DOI: 10.1186/s13059-020-02128-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]  Open
728
Yin C, Chen Z. Developing Sustainable Classification of Diseases via Deep Learning and Semi-Supervised Learning. Healthcare (Basel) 2020;8:E291. [PMID: 32846941 PMCID: PMC7551840 DOI: 10.3390/healthcare8030291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 01/07/2023]  Open
729
Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V. Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans. Immunity 2020;53:353-370.e8. [PMID: 32735845 PMCID: PMC7447982 DOI: 10.1016/j.immuni.2020.07.003] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 12/27/2019] [Accepted: 07/02/2020] [Indexed: 01/10/2023]
730
Friedrich S, Sonnhammer ELL. Fusion transcript detection using spatial transcriptomics. BMC Med Genomics 2020;13:110. [PMID: 32753032 PMCID: PMC7437936 DOI: 10.1186/s12920-020-00738-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/11/2020] [Indexed: 12/20/2022]  Open
731
Wiseman DH, Baker SM, Dongre AV, Gurashi K, Storer JA, Somervaille TC, Batta K. Chronic myelomonocytic leukaemia stem cell transcriptomes anticipate disease morphology and outcome. EBioMedicine 2020;58:102904. [PMID: 32763828 PMCID: PMC7403890 DOI: 10.1016/j.ebiom.2020.102904] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023]  Open
732
Paik DT, Cho S, Tian L, Chang HY, Wu JC. Single-cell RNA sequencing in cardiovascular development, disease and medicine. Nat Rev Cardiol 2020;17:457-473. [PMID: 32231331 PMCID: PMC7528042 DOI: 10.1038/s41569-020-0359-y] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
733
Ramachandran P, Matchett KP, Dobie R, Wilson-Kanamori JR, Henderson NC. Single-cell technologies in hepatology: new insights into liver biology and disease pathogenesis. Nat Rev Gastroenterol Hepatol 2020;17:457-472. [PMID: 32483353 DOI: 10.1038/s41575-020-0304-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 12/19/2022]
734
Zhang Y, Li W, Zhou Y. Identification of hub genes in diabetic kidney disease via multiple-microarray analysis. ANNALS OF TRANSLATIONAL MEDICINE 2020;8:997. [PMID: 32953797 PMCID: PMC7475500 DOI: 10.21037/atm-20-5171] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
735
Brann DH, Tsukahara T, Weinreb C, Lipovsek M, Van den Berge K, Gong B, Chance R, Macaulay IC, Chou HJ, Fletcher RB, Das D, Street K, de Bezieux HR, Choi YG, Risso D, Dudoit S, Purdom E, Mill J, Hachem RA, Matsunami H, Logan DW, Goldstein BJ, Grubb MS, Ngai J, Datta SR. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. SCIENCE ADVANCES 2020;6:eabc5801. [PMID: 32937591 PMCID: PMC10715684 DOI: 10.1126/sciadv.abc5801] [Citation(s) in RCA: 722] [Impact Index Per Article: 144.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
736
Aragona M, Sifrim A, Malfait M, Song Y, Van Herck J, Dekoninck S, Gargouri S, Lapouge G, Swedlund B, Dubois C, Baatsen P, Vints K, Han S, Tissir F, Voet T, Simons BD, Blanpain C. Mechanisms of stretch-mediated skin expansion at single-cell resolution. Nature 2020;584:268-273. [PMID: 32728211 DOI: 10.1038/s41586-020-2555-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/19/2020] [Indexed: 02/06/2023]
737
Jacob F, Pather SR, Huang WK, Wong SZH, Zhou H, Zhang F, Cubitt B, Chen CZ, Xu M, Pradhan M, Zhang DY, Zheng W, Bang AG, Song H, de A Torre JC, Ming GL. Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.28.225151. [PMID: 32766575 PMCID: PMC7402032 DOI: 10.1101/2020.07.28.225151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
738
Ramos TAR, Maracaja-Coutinho V, Ortega JM, do Rêgo TG. CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles. BMC Res Notes 2020;13:338. [PMID: 32665017 PMCID: PMC7359491 DOI: 10.1186/s13104-020-05171-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/03/2020] [Indexed: 01/12/2023]  Open
739
Ireland AS, Micinski AM, Kastner DW, Guo B, Wait SJ, Spainhower KB, Conley CC, Chen OS, Guthrie MR, Soltero D, Qiao Y, Huang X, Tarapcsák S, Devarakonda S, Chalishazar MD, Gertz J, Moser JC, Marth G, Puri S, Witt BL, Spike BT, Oliver TG. MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. Cancer Cell 2020;38:60-78.e12. [PMID: 32473656 PMCID: PMC7393942 DOI: 10.1016/j.ccell.2020.05.001] [Citation(s) in RCA: 319] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/23/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
740
Zhong R, Chen D, Cao S, Li J, Han B, Zhong H. Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq. Clin Transl Oncol 2020;23:405-417. [PMID: 32656582 DOI: 10.1007/s12094-020-02435-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
741
Liu J, Liu S, Gao H, Han L, Chu X, Sheng Y, Shou W, Wang Y, Liu Y, Wan J, Yang L. Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells. Genome Biol 2020;21:169. [PMID: 32646524 PMCID: PMC7350744 DOI: 10.1186/s13059-020-02082-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]  Open
742
Cole MB, Risso D, Wagner A, DeTomaso D, Ngai J, Purdom E, Dudoit S, Yosef N. Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq. Cell Syst 2020;8:315-328.e8. [PMID: 31022373 DOI: 10.1016/j.cels.2019.03.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/07/2019] [Accepted: 03/15/2019] [Indexed: 01/17/2023]
743
Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Res 2020;48:W395-W402. [PMID: 32479607 PMCID: PMC7319590 DOI: 10.1093/nar/gkaa434] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022]  Open
744
Rath JA, Bajwa G, Carreres B, Hoyer E, Gruber I, Martínez-Paniagua MA, Yu YR, Nouraee N, Sadeghi F, Wu M, Wang T, Hebeisen M, Rufer N, Varadarajan N, Ho PC, Brenner MK, Gfeller D, Arber C. Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4+ T cells. SCIENCE ADVANCES 2020;6:eaaz7809. [PMID: 32923584 PMCID: PMC7455496 DOI: 10.1126/sciadv.aaz7809] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
745
Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3. Nat Cell Biol 2020;22:767-778. [PMID: 32601371 PMCID: PMC7610380 DOI: 10.1038/s41556-020-0536-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/24/2020] [Indexed: 01/24/2023]
746
Liang P, Yang W, Chen X, Long C, Zheng L, Li H, Zuo Y. Machine Learning of Single-Cell Transcriptome Highly Identifies mRNA Signature by Comparing F-Score Selection with DGE Analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2020;20:155-163. [PMID: 32169803 PMCID: PMC7066034 DOI: 10.1016/j.omtn.2020.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/27/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022]
747
Graf C, Wilgenbus P, Pagel S, Pott J, Marini F, Reyda S, Kitano M, Macher-Göppinger S, Weiler H, Ruf W. Myeloid cell-synthesized coagulation factor X dampens antitumor immunity. Sci Immunol 2020;4:4/39/eaaw8405. [PMID: 31541031 DOI: 10.1126/sciimmunol.aaw8405] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/02/2019] [Accepted: 08/06/2019] [Indexed: 12/20/2022]
748
Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clément O, Simmons RK, Lister R, Forrest ARR. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol 2020;21:130. [PMID: 32487174 PMCID: PMC7265231 DOI: 10.1186/s13059-020-02048-6] [Citation(s) in RCA: 361] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022]  Open
749
Xiong Z, Yang Q, Li X. Effect of intra- and inter-tumoral heterogeneity on molecular characteristics of primary IDH-wild type glioblastoma revealed by single-cell analysis. CNS Neurosci Ther 2020;26:981-989. [PMID: 32488994 PMCID: PMC7415209 DOI: 10.1111/cns.13396] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023]  Open
750
Barbar L, Jain T, Zimmer M, Kruglikov I, Sadick JS, Wang M, Kalpana K, Rose IVL, Burstein SR, Rusielewicz T, Nijsure M, Guttenplan KA, di Domenico A, Croft G, Zhang B, Nobuta H, Hébert JM, Liddelow SA, Fossati V. CD49f Is a Novel Marker of Functional and Reactive Human iPSC-Derived Astrocytes. Neuron 2020;107:436-453.e12. [PMID: 32485136 DOI: 10.1016/j.neuron.2020.05.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/05/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022]
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