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For: Chen S, Rivaud P, Park JH, Tsou T, Charles E, Haliburton JR, Pichiorri F, Thomson M. Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign. Proc Natl Acad Sci U S A 2020;117:28784-28794. [PMID: 33127759 PMCID: PMC7682438 DOI: 10.1073/pnas.2005990117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE. Cell Syst 2025:101294. [PMID: 40378843 DOI: 10.1016/j.cels.2025.101294] [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: 08/26/2024] [Revised: 02/20/2025] [Accepted: 04/22/2025] [Indexed: 05/19/2025]
2
Liu Y, Li C, Shen LC, Yan H, Wei G, Gasser RB, Hu X, Song J, Yu DJ. scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data. Comput Biol Med 2025;190:110068. [PMID: 40158457 DOI: 10.1016/j.compbiomed.2025.110068] [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: 04/07/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 04/02/2025]
3
Li X, Liu Y, Zhou F, Guo W, Chen G, Tao J, Huang J, Qiu J, Chen H, Ren B, You L, Shi Y, Yang G, Zhang T, Gu J, Zhao Y. Decipher the single-cell level responses to chemotherapy in pancreatic ductal adenocarcinoma by a cross-time context graph model. Cancer Lett 2025;626:217751. [PMID: 40294840 DOI: 10.1016/j.canlet.2025.217751] [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: 03/13/2025] [Revised: 04/24/2025] [Accepted: 04/26/2025] [Indexed: 04/30/2025]
4
Sukys A, Grima R. Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data. Nucleic Acids Res 2025;53:gkaf295. [PMID: 40240003 PMCID: PMC12000877 DOI: 10.1093/nar/gkaf295] [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: 01/24/2024] [Revised: 03/22/2025] [Accepted: 03/28/2025] [Indexed: 04/18/2025]  Open
5
Ramirez A, Orcutt-Jahns BT, Pascoe S, Abraham A, Remigio B, Thomas N, Meyer AS. Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.07.29.605698. [PMID: 39131377 PMCID: PMC11312543 DOI: 10.1101/2024.07.29.605698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
6
Guo W, Li X, Wang D, Yan N, Hu Q, Yang F, Zhang X, Yao J, Gu J. scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes. Genome Biol 2024;25:297. [PMID: 39574111 PMCID: PMC11583649 DOI: 10.1186/s13059-024-03436-y] [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: 03/14/2024] [Accepted: 11/15/2024] [Indexed: 11/24/2024]  Open
7
Chari T, Gorin G, Pachter L. Biophysically interpretable inference of cell types from multimodal sequencing data. NATURE COMPUTATIONAL SCIENCE 2024;4:677-689. [PMID: 39317762 DOI: 10.1038/s43588-024-00689-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 08/08/2024] [Indexed: 09/26/2024]
8
Sadria M, Layton A, Goyal S, Bader GD. Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. CELL REPORTS METHODS 2024;4:100819. [PMID: 38986613 PMCID: PMC11294839 DOI: 10.1016/j.crmeth.2024.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 11/20/2023] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
9
Chari T, Gorin G, Pachter L. Stochastic Modeling of Biophysical Responses to Perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602131. [PMID: 39005347 PMCID: PMC11245117 DOI: 10.1101/2024.07.04.602131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
10
Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M. D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.19.537364. [PMID: 37131803 PMCID: PMC10153191 DOI: 10.1101/2023.04.19.537364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
11
Bunne C, Stark SG, Gut G, Del Castillo JS, Levesque M, Lehmann KV, Pelkmans L, Krause A, Rätsch G. Learning single-cell perturbation responses using neural optimal transport. Nat Methods 2023;20:1759-1768. [PMID: 37770709 PMCID: PMC10630137 DOI: 10.1038/s41592-023-01969-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/23/2023] [Indexed: 09/30/2023]
12
Pool AH, Poldsam H, Chen S, Thomson M, Oka Y. Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references. Nat Methods 2023;20:1506-1515. [PMID: 37697162 DOI: 10.1038/s41592-023-02003-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/15/2023] [Indexed: 09/13/2023]
13
Chari T, Gorin G, Pachter L. Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.17.558131. [PMID: 37745403 PMCID: PMC10516047 DOI: 10.1101/2023.09.17.558131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
14
Chari T, Pachter L. The specious art of single-cell genomics. PLoS Comput Biol 2023;19:e1011288. [PMID: 37590228 PMCID: PMC10434946 DOI: 10.1371/journal.pcbi.1011288] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]  Open
15
Sun L, Wang G, Zhang Z. SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level. Brief Bioinform 2023;24:6961608. [PMID: 36575569 DOI: 10.1093/bib/bbac590] [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: 07/25/2022] [Revised: 11/08/2022] [Accepted: 12/02/2022] [Indexed: 12/29/2022]  Open
16
Bing X, Bunea F, Strimas-Mackey S, Wegkamp M. Likelihood estimation of sparse topic distributions in topic models and its applications to Wasserstein document distance calculations. Ann Stat 2022. [DOI: 10.1214/22-aos2229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
17
Gandhi M, Bakhai V, Trivedi J, Mishra A, De Andrés F, LLerena A, Sharma R, Nair S. Current perspectives on interethnic variability in multiple myeloma: Single cell technology, population pharmacogenetics and molecular signal transduction. Transl Oncol 2022;25:101532. [PMID: 36103755 PMCID: PMC9478452 DOI: 10.1016/j.tranon.2022.101532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/15/2022]  Open
18
Sohail A, Jiang X, Wahid A, Wang H, Cao C, Xiao H. Free-flow zone electrophoresis facilitated proteomics analysis of heterogeneous subpopulations in H1299 lung cancer cells. Anal Chim Acta 2022;1227:340306. [DOI: 10.1016/j.aca.2022.340306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/30/2022] [Accepted: 08/21/2022] [Indexed: 11/01/2022]
19
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]
20
Chari T, Weissbourd B, Gehring J, Ferraioli A, Leclère L, Herl M, Gao F, Chevalier S, Copley RR, Houliston E, Anderson DJ, Pachter L. Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types. SCIENCE ADVANCES 2021;7:eabh1683. [PMID: 34826233 PMCID: PMC8626072 DOI: 10.1126/sciadv.abh1683] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 10/06/2021] [Indexed: 05/12/2023]
21
Sozen B, Jorgensen V, Weatherbee BAT, Chen S, Zhu M, Zernicka-Goetz M. Reconstructing aspects of human embryogenesis with pluripotent stem cells. Nat Commun 2021;12:5550. [PMID: 34548496 PMCID: PMC8455697 DOI: 10.1038/s41467-021-25853-4] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 02/01/2023]  Open
22
Ji Y, Lotfollahi M, Wolf FA, Theis FJ. Machine learning for perturbational single-cell omics. Cell Syst 2021;12:522-537. [PMID: 34139164 DOI: 10.1016/j.cels.2021.05.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 12/18/2022]
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