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For: Delaney C, Schnell A, Cammarata LV, Yao-Smith A, Regev A, Kuchroo VK, Singer M. Combinatorial prediction of marker panels from single-cell transcriptomic data. Mol Syst Biol 2020;15:e9005. [PMID: 31657111 PMCID: PMC6811728 DOI: 10.15252/msb.20199005] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 01/10/2023]  Open
Number Cited by Other Article(s)
1
Miller TE, El Farran CA, Couturier CP, Chen Z, D'Antonio JP, Verga J, Villanueva MA, Gonzalez Castro LN, Tong YE, Saadi TA, Chiocca AN, Zhang Y, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE. Programs, origins and immunomodulatory functions of myeloid cells in glioma. Nature 2025;640:1072-1082. [PMID: 40011771 PMCID: PMC12018266 DOI: 10.1038/s41586-025-08633-8] [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: 10/09/2023] [Accepted: 01/10/2025] [Indexed: 02/28/2025]
2
Chen H, Zhang X, Cheng Q, Shen X, Zeng L, Wang Y, Fan L, Jiang W. snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses. Sci Data 2024;11:1434. [PMID: 39725704 DOI: 10.1038/s41597-024-04323-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024]  Open
3
Kuemmerle LB, Luecken MD, Firsova AB, Barros de Andrade E Sousa L, Straßer L, Mekki II, Campi F, Heumos L, Shulman M, Beliaeva V, Hediyeh-Zadeh S, Schaar AC, Mahbubani KT, Sountoulidis A, Balassa T, Kovacs F, Horvath P, Piraud M, Ertürk A, Samakovlis C, Theis FJ. Probe set selection for targeted spatial transcriptomics. Nat Methods 2024;21:2260-2270. [PMID: 39558096 PMCID: PMC11621025 DOI: 10.1038/s41592-024-02496-z] [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: 07/19/2022] [Accepted: 09/30/2024] [Indexed: 11/20/2024]
4
Sun Y, Qiu P. Hierarchical marker genes selection in scRNA-seq analysis. PLoS Comput Biol 2024;20:e1012643. [PMID: 39666603 PMCID: PMC11637363 DOI: 10.1371/journal.pcbi.1012643] [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: 11/21/2023] [Accepted: 11/16/2024] [Indexed: 12/14/2024]  Open
5
Gardner AL, Jost TA, Morgan D, Brock A. Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations. NPJ Syst Biol Appl 2024;10:120. [PMID: 39420005 PMCID: PMC11487074 DOI: 10.1038/s41540-024-00441-6] [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: 05/29/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024]  Open
6
Xie Y, Yang J, Ouyang JF, Petretto E. scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets. Brief Bioinform 2024;25:bbae482. [PMID: 39350339 PMCID: PMC11442147 DOI: 10.1093/bib/bbae482] [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: 03/25/2024] [Revised: 08/30/2024] [Accepted: 09/12/2024] [Indexed: 10/04/2024]  Open
7
Fesneau O, Thevin V, Pinet V, Goldsmith C, Vieille B, M'Homa Soudja S, Lattanzio R, Hahne M, Dardalhon V, Hernandez-Vargas H, Benech N, Marie JC. An intestinal TH17 cell-derived subset can initiate cancer. Nat Immunol 2024;25:1637-1649. [PMID: 39060651 PMCID: PMC11362008 DOI: 10.1038/s41590-024-01909-7] [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: 06/15/2023] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
8
Ji L, Wang A, Sonthalia S, Naiman DQ, Younes L, Colantuoni C, Geman D. CellCover Captures Neural Stem Cell Progression in Mammalian Neocortical Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.06.535943. [PMID: 37383947 PMCID: PMC10299349 DOI: 10.1101/2023.04.06.535943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
9
Jia Y, Ma P, Yao Q. CellMarkerPipe: cell marker identification and evaluation pipeline in single cell transcriptomes. Sci Rep 2024;14:13151. [PMID: 38849445 PMCID: PMC11161599 DOI: 10.1038/s41598-024-63492-z] [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: 02/13/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]  Open
10
Gardner AL, Jost TA, Brock A. Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596337. [PMID: 38854060 PMCID: PMC11160629 DOI: 10.1101/2024.05.28.596337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
11
Su EY, Fread K, Goggin S, Zunder ER, Cahan P. Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells. Sci Data 2024;11:559. [PMID: 38816402 PMCID: PMC11139855 DOI: 10.1038/s41597-024-03399-6] [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: 03/31/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024]  Open
12
Lee EJ, Suh M, Choi H, Choi Y, Hwang DW, Bae S, Lee DS. Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy on specific regional brain cells in a mouse dementia model. BMC Genomics 2024;25:516. [PMID: 38796425 PMCID: PMC11128132 DOI: 10.1186/s12864-024-10434-8] [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: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]  Open
13
Zhou X, Seow WY, Ha N, Cheng TH, Jiang L, Boonruangkan J, Goh JJL, Prabhakar S, Chou N, Chen KH. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nat Commun 2024;15:2342. [PMID: 38491027 PMCID: PMC10943009 DOI: 10.1038/s41467-024-46669-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: 08/11/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024]  Open
14
Nechanitzky R, Ramachandran P, Nechanitzky D, Li WY, Wakeham AC, Haight J, Saunders ME, Epelman S, Mak TW. CaSSiDI: novel single-cell "Cluster Similarity Scoring and Distinction Index" reveals critical functions for PirB and context-dependent Cebpb repression. Cell Death Differ 2024;31:265-279. [PMID: 38383888 PMCID: PMC10923835 DOI: 10.1038/s41418-024-01268-8] [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: 05/16/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]  Open
15
Minutti CM, Piot C, Pereira da Costa M, Chakravarty P, Rogers N, Huerga Encabo H, Cardoso A, Loong J, Bessou G, Mionnet C, Langhorne J, Bonnet D, Dalod M, Tomasello E, Reis e Sousa C. Distinct ontogenetic lineages dictate cDC2 heterogeneity. Nat Immunol 2024;25:448-461. [PMID: 38351322 PMCID: PMC10907303 DOI: 10.1038/s41590-024-01745-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/08/2024] [Indexed: 03/03/2024]
16
Pullin JM, McCarthy DJ. A comparison of marker gene selection methods for single-cell RNA sequencing data. Genome Biol 2024;25:56. [PMID: 38409056 PMCID: PMC10895860 DOI: 10.1186/s13059-024-03183-0] [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: 09/13/2022] [Accepted: 02/07/2024] [Indexed: 02/28/2024]  Open
17
Gregory W, Sarwar N, Kevrekidis G, Villar S, Dumitrascu B. MarkerMap: nonlinear marker selection for single-cell studies. NPJ Syst Biol Appl 2024;10:17. [PMID: 38351188 PMCID: PMC10864304 DOI: 10.1038/s41540-024-00339-3] [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: 04/26/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024]  Open
18
Dawson A, Zarou MM, Prasad B, Bittencourt-Silvestre J, Zerbst D, Himonas E, Hsieh YC, van Loon I, Blanco GR, Ianniciello A, Kerekes Z, Krishnan V, Agarwal P, Almasoudi H, McCluskey L, Hopcroft LEM, Scott MT, Baquero P, Dunn K, Vetrie D, Copland M, Bhatia R, Coffelt SB, Tiong OS, Wheadon H, Zanivan S, Kirschner K, Helgason GV. Leukaemia exposure alters the transcriptional profile and function of BCR::ABL1 negative macrophages in the bone marrow niche. Nat Commun 2024;15:1090. [PMID: 38316788 PMCID: PMC10844594 DOI: 10.1038/s41467-024-45471-0] [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: 04/29/2022] [Accepted: 01/25/2024] [Indexed: 02/07/2024]  Open
19
Arigoni M, Ratto ML, Riccardo F, Balmas E, Calogero L, Cordero F, Beccuti M, Calogero RA, Alessandri L. A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity. Sci Data 2024;11:159. [PMID: 38307867 PMCID: PMC10837414 DOI: 10.1038/s41597-024-03002-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024]  Open
20
Yao Q, Jia Y, Ma P. cellMarkerPipe: Cell Marker Identification and Evaluation Pipeline in Single Cell Transcriptomes. RESEARCH SQUARE 2024:rs.3.rs-3844718. [PMID: 38313296 PMCID: PMC10836098 DOI: 10.21203/rs.3.rs-3844718/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
21
Cai M, Zhou J, McKennan C, Wang J. scMD facilitates cell type deconvolution using single-cell DNA methylation references. Commun Biol 2024;7:1. [PMID: 38168620 PMCID: PMC10762261 DOI: 10.1038/s42003-023-05690-5] [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: 08/14/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]  Open
22
Maden SK, Kwon SH, Huuki-Myers LA, Collado-Torres L, Hicks SC, Maynard KR. Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets. Genome Biol 2023;24:288. [PMID: 38098055 PMCID: PMC10722720 DOI: 10.1186/s13059-023-03123-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]  Open
23
Brockmann L, Tran A, Huang Y, Edwards M, Ronda C, Wang HH, Ivanov II. Intestinal microbiota-specific Th17 cells possess regulatory properties and suppress effector T cells via c-MAF and IL-10. Immunity 2023;56:2719-2735.e7. [PMID: 38039966 PMCID: PMC10964950 DOI: 10.1016/j.immuni.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/04/2023] [Accepted: 11/05/2023] [Indexed: 12/03/2023]
24
Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023;147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
25
Miller TE, El Farran CA, Couturier CP, Chen Z, D’Antonio JP, Verga J, Villanueva MA, Castro LNG, Tong YE, Saadi TA, Chiocca AN, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE. Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563466. [PMID: 37961527 PMCID: PMC10634776 DOI: 10.1101/2023.10.24.563466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
26
Ng GYL, Tan SC, Ong CS. On the use of QDE-SVM for gene feature selection and cell type classification from scRNA-seq data. PLoS One 2023;18:e0292961. [PMID: 37856458 PMCID: PMC10586655 DOI: 10.1371/journal.pone.0292961] [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: 04/10/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023]  Open
27
Tansey M, Boles J, Uriarte Huarte O. Microfluidics-free single-cell genomics reveals complex central-peripheral immune crosstalk in the mouse brain during peripheral inflammation. RESEARCH SQUARE 2023:rs.3.rs-3428910. [PMID: 37886510 PMCID: PMC10602178 DOI: 10.21203/rs.3.rs-3428910/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
28
Ouyang JF, Mishra K, Xie Y, Park H, Huang KY, Petretto E, Behmoaras J. Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis. eLife 2023;12:e85530. [PMID: 37706477 PMCID: PMC10547479 DOI: 10.7554/elife.85530] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 09/13/2023] [Indexed: 09/15/2023]  Open
29
Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023;20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
30
Tang Y, Li X, Shi M. LIDER: cell embedding based deep neural network classifier for supervised cell type identification. PeerJ 2023;11:e15862. [PMID: 37601262 PMCID: PMC10439717 DOI: 10.7717/peerj.15862] [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: 04/14/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]  Open
31
Cai M, Zhou J, McKennan C, Wang J. scMD: cell type deconvolution using single-cell DNA methylation references. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551733. [PMID: 37577715 PMCID: PMC10418231 DOI: 10.1101/2023.08.03.551733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
32
Hong Y, Song K, Zhang Z, Deng Y, Zhang X, Zhao J, Jiang J, Zhang Q, Guo C, Peng C. The spatiotemporal dynamics of spatially variable genes in developing mouse brain revealed by a novel computational scheme. Cell Death Discov 2023;9:264. [PMID: 37500639 PMCID: PMC10374563 DOI: 10.1038/s41420-023-01569-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]  Open
33
Bod L, Kye YC, Shi J, Torlai Triglia E, Schnell A, Fessler J, Ostrowski SM, Von-Franque MY, Kuchroo JR, Barilla RM, Zaghouani S, Christian E, Delorey TM, Mohib K, Xiao S, Slingerland N, Giuliano CJ, Ashenberg O, Li Z, Rothstein DM, Fisher DE, Rozenblatt-Rosen O, Sharpe AH, Quintana FJ, Apetoh L, Regev A, Kuchroo VK. B-cell-specific checkpoint molecules that regulate anti-tumour immunity. Nature 2023;619:348-356. [PMID: 37344597 PMCID: PMC10795478 DOI: 10.1038/s41586-023-06231-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
34
Maden SK, Kwon SH, Huuki-Myers LA, Collado-Torres L, Hicks SC, Maynard KR. Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single cell RNA-sequencing datasets. ARXIV 2023:arXiv:2305.06501v1. [PMID: 37214135 PMCID: PMC10197733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
35
Baran Y, Doğan B. scMAGS: Marker gene selection from scRNA-seq data for spatial transcriptomics studies. Comput Biol Med 2023;155:106634. [PMID: 36774895 DOI: 10.1016/j.compbiomed.2023.106634] [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: 11/05/2022] [Revised: 01/28/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
36
Using "Galaxy-rCASC": A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis. Methods Mol Biol 2022;2584:311-335. [PMID: 36495458 DOI: 10.1007/978-1-0716-2756-3_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
37
Identifying Gene Markers Associated with Cell Subpopulations. Methods Mol Biol 2022;2584:251-268. [PMID: 36495455 DOI: 10.1007/978-1-0716-2756-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
38
Haensel D, Gaddam S, Li NY, Gonzalez F, Patel T, Cloutier JM, Sarin KY, Tang JY, Rieger KE, Aasi SZ, Oro AE. LY6D marks pre-existing resistant basosquamous tumor subpopulations. Nat Commun 2022;13:7520. [PMID: 36473848 PMCID: PMC9726704 DOI: 10.1038/s41467-022-35020-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]  Open
39
Zamani M, Cheng YH, Charbonier F, Gupta VK, Mayer AT, Trevino AE, Quertermous T, Chaudhuri O, Cahan P, Huang NF. Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis. ADVANCED FUNCTIONAL MATERIALS 2022;32:2203069. [PMID: 36816792 PMCID: PMC9937733 DOI: 10.1002/adfm.202203069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 05/28/2023]
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Ferrall-Fairbanks MC, Dhawan A, Johnson B, Newman H, Volpe V, Letson C, Ball M, Hunter AM, Balasis ME, Kruer T, Ben-Crentsil NA, Kroeger JL, Balderas R, Komrokji RS, Sallman DA, Zhang J, Bejar R, Altrock PM, Padron E. Progenitor Hierarchy of Chronic Myelomonocytic Leukemia Identifies Inflammatory Monocytic-Biased Trajectory Linked to Worse Outcomes. Blood Cancer Discov 2022;3:536-553. [PMID: 36053528 PMCID: PMC9627238 DOI: 10.1158/2643-3230.bcd-21-0217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/16/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]  Open
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Gómez‐Escolar C, Serrano‐Navarro A, Benguria A, Dopazo A, Sánchez‐Cabo F, Ramiro AR. Single cell clonal analysis identifies an AID-dependent pathway of plasma cell differentiation. EMBO Rep 2022;23:e55000. [PMID: 36205653 PMCID: PMC9724673 DOI: 10.15252/embr.202255000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/07/2022]  Open
42
Keenan BP, McCarthy EE, Ilano A, Yang H, Zhang L, Allaire K, Fan Z, Li T, Lee DS, Sun Y, Cheung A, Luong D, Chang H, Chen B, Marquez J, Sheldon B, Kelley RK, Ye CJ, Fong L. Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis. Cell Rep 2022;40:111384. [PMID: 36130508 PMCID: PMC10060099 DOI: 10.1016/j.celrep.2022.111384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 01/17/2023]  Open
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Li R, Banjanin B, Schneider RK, Costa IG. Detection of cell markers from single cell RNA-seq with sc2marker. BMC Bioinformatics 2022;23:276. [PMID: 35831796 PMCID: PMC9281170 DOI: 10.1186/s12859-022-04817-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/28/2022] [Indexed: 11/12/2022]  Open
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Murphy M, Jegelka S, Fraenkel E. Self-supervised learning of cell type specificity from immunohistochemical images. Bioinformatics 2022;38:i395-i403. [PMID: 35758799 PMCID: PMC9235491 DOI: 10.1093/bioinformatics/btac263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
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Chen X, Chen S, Thomson M. Minimal gene set discovery in single-cell mRNA-seq datasets with ActiveSVM. NATURE COMPUTATIONAL SCIENCE 2022;2:387-398. [PMID: 38177588 PMCID: PMC10766518 DOI: 10.1038/s43588-022-00263-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/17/2022] [Indexed: 01/06/2024]
46
Collier A, Liu A, Torkelson J, Pattison J, Gaddam S, Zhen H, Patel T, McCarthy K, Ghanim H, Oro AE. Gibbin mesodermal regulation patterns epithelial development. Nature 2022;606:188-196. [PMID: 35585237 PMCID: PMC9202145 DOI: 10.1038/s41586-022-04727-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/05/2022] [Indexed: 02/04/2023]
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Lu Y, Wu CT, Parker SJ, Cheng Z, Saylor G, Van Eyk JE, Yu G, Clarke R, Herrington DM, Wang Y. COT: an efficient and accurate method for detecting marker genes among many subtypes. BIOINFORMATICS ADVANCES 2022;2:vbac037. [PMID: 35673616 PMCID: PMC9163574 DOI: 10.1093/bioadv/vbac037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/10/2022] [Accepted: 05/16/2022] [Indexed: 01/27/2023]
48
Ahmadi S, Sukprasert P, Vegesna R, Sinha S, Schischlik F, Artzi N, Khuller S, Schäffer AA, Ruppin E. The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective. Nat Commun 2022;13:1613. [PMID: 35338126 PMCID: PMC8956718 DOI: 10.1038/s41467-022-29154-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/22/2022] [Indexed: 02/08/2023]  Open
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Pauken KE, Lagattuta KA, Lu BY, Lucca LE, Daud AI, Hafler DA, Kluger HM, Raychaudhuri S, Sharpe AH. TCR-sequencing in cancer and autoimmunity: barcodes and beyond. Trends Immunol 2022;43:180-194. [PMID: 35090787 PMCID: PMC8882139 DOI: 10.1016/j.it.2022.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/21/2023]
50
A Sight of the Diagnostic Value of Aberrant Cell-Free DNA Methylation in Lung Cancer. DISEASE MARKERS 2022;2022:9619357. [PMID: 35126793 PMCID: PMC8814721 DOI: 10.1155/2022/9619357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/12/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
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