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For: Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A 2014;111:E5643-50. [PMID: 25512504 DOI: 10.1073/pnas.1408993111] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
Number Cited by Other Article(s)
1
Liarou M, Matthes T, Marchand-Maillet S. TimeFlow: A Density-Driven Pseudotime Method for Flow Cytometry Data Analysis. Cytometry A 2025;107:233-247. [PMID: 40111028 DOI: 10.1002/cyto.a.24928] [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: 07/25/2024] [Revised: 01/15/2025] [Accepted: 02/27/2025] [Indexed: 03/22/2025]
2
He R, Sarwal V, Qiu X, Zhuang Y, Zhang L, Liu Y, Chiang J. Generative AI Models in Time-Varying Biomedical Data: Scoping Review. J Med Internet Res 2025;27:e59792. [PMID: 40063929 PMCID: PMC11933772 DOI: 10.2196/59792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/08/2024] [Accepted: 11/15/2024] [Indexed: 03/28/2025]  Open
3
Chen X, Ma Y, Shi Y, Zhang B, Wu H, Gao J. Fuzzy-Based Identification of Transition Cells to Infer Cell Trajectory for Single-Cell Transcriptomics. J Comput Biol 2025;32:253-273. [PMID: 39670822 DOI: 10.1089/cmb.2023.0432] [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] [Indexed: 12/14/2024]  Open
4
Zhang Z, Zhu Y, Lai Z, Zhou M, Chen X, Tang R, Alaynick W, Cho SH, Lo YH. Predicting cell properties with AI from 3D imaging flow cytometer data. Sci Rep 2025;15:5715. [PMID: 39962067 PMCID: PMC11833109 DOI: 10.1038/s41598-024-80722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Accepted: 11/21/2024] [Indexed: 02/20/2025]  Open
5
Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025;68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [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: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
6
Lee S, Lee DY, So I, Chun JN, Jeon JH. Chromatin accessibility is associated with therapeutic response in prostate cancer. Oncol Lett 2024;28:605. [PMID: 39483964 PMCID: PMC11525612 DOI: 10.3892/ol.2024.14738] [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: 03/11/2024] [Accepted: 09/12/2024] [Indexed: 11/03/2024]  Open
7
Sun R, Cao W, Li S, Jiang J, Shi Y, Zhang B. scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy. PLoS Comput Biol 2024;20:e1012638. [PMID: 39585902 PMCID: PMC11627384 DOI: 10.1371/journal.pcbi.1012638] [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: 07/08/2024] [Revised: 12/09/2024] [Accepted: 11/12/2024] [Indexed: 11/27/2024]  Open
8
Iida K, Okada M. Identifying Key Regulatory Genes in Drug Resistance Acquisition: Modeling Pseudotime Trajectories of Breast Cancer Single-Cell Transcriptome. Cancers (Basel) 2024;16:1884. [PMID: 38791962 PMCID: PMC11119661 DOI: 10.3390/cancers16101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]  Open
9
Cui Z, Wei H, Goding C, Cui R. Stem cell heterogeneity, plasticity, and regulation. Life Sci 2023;334:122240. [PMID: 37925141 DOI: 10.1016/j.lfs.2023.122240] [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: 09/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
10
Zou X, Liu Y, Wang M, Zou J, Shi Y, Su X, Xu J, Tong HHY, Ji Y, Gui L, Hao J. scCURE identifies cell types responding to immunotherapy and enables outcome prediction. CELL REPORTS METHODS 2023;3:100643. [PMID: 37989083 PMCID: PMC10694528 DOI: 10.1016/j.crmeth.2023.100643] [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: 01/17/2023] [Revised: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
11
Daniels BC, Wang Y, Page RE, Amdam GV. Identifying a developmental transition in honey bees using gene expression data. PLoS Comput Biol 2023;19:e1010704. [PMID: 37733808 PMCID: PMC10547183 DOI: 10.1371/journal.pcbi.1010704] [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: 11/03/2022] [Revised: 10/03/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]  Open
12
Yang T, Hathcock D, Chen Y, McEuen PL, Sethna JP, Cohen I, Griniasty I. Bifurcation instructed design of multistate machines. Proc Natl Acad Sci U S A 2023;120:e2300081120. [PMID: 37579174 PMCID: PMC10450659 DOI: 10.1073/pnas.2300081120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/23/2023] [Indexed: 08/16/2023]  Open
13
Proverbio D, Skupin A, Gonçalves J. Systematic analysis and optimization of early warning signals for critical transitions using distribution data. iScience 2023;26:107156. [PMID: 37456849 PMCID: PMC10338236 DOI: 10.1016/j.isci.2023.107156] [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: 11/04/2022] [Revised: 04/21/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]  Open
14
Multi-Objective Genetic Algorithm for Cluster Analysis of Single-Cell Transcriptomes. J Pers Med 2023;13:jpm13020183. [PMID: 36836417 PMCID: PMC9960600 DOI: 10.3390/jpm13020183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]  Open
15
Ao C, Jiao S, Wang Y, Yu L, Zou Q. Biological Sequence Classification: A Review on Data and General Methods. RESEARCH (WASHINGTON, D.C.) 2022;2022:0011. [PMID: 39285948 PMCID: PMC11404319 DOI: 10.34133/research.0011] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/25/2022] [Indexed: 09/19/2024]
16
Giri R, Brady S, Papadopoulos DK, Carthew RW. Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate. iScience 2022;25:105097. [PMID: 36157584 PMCID: PMC9494244 DOI: 10.1016/j.isci.2022.105097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]  Open
17
Sáez M, Briscoe J, Rand DA. Dynamical landscapes of cell fate decisions. Interface Focus 2022;12:20220002. [PMID: 35860004 PMCID: PMC9184965 DOI: 10.1098/rsfs.2022.0002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022]  Open
18
Cho H, Kuo YH, Rockne RC. Comparison of cell state models derived from single-cell RNA sequencing data: graph versus multi-dimensional space. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022;19:8505-8536. [PMID: 35801475 PMCID: PMC9308174 DOI: 10.3934/mbe.2022395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
19
Zhu M, Lai Y. Improvements Achieved by Multiple Imputation for Single-Cell RNA-Seq Data in Clustering Analysis and Differential Expression Analysis. J Comput Biol 2022;29:634-649. [PMID: 35575729 DOI: 10.1089/cmb.2021.0597] [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: 11/12/2022]  Open
20
Dai C, Jiang Y, Yin C, Su R, Zeng X, Zou Q, Nakai K, Wei L. scIMC: a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods. Nucleic Acids Res 2022;50:4877-4899. [PMID: 35524568 PMCID: PMC9122610 DOI: 10.1093/nar/gkac317] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022]  Open
21
Single Cell Self-Paced Clustering with Transcriptome Sequencing Data. Int J Mol Sci 2022;23:ijms23073900. [PMID: 35409258 PMCID: PMC8999118 DOI: 10.3390/ijms23073900] [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: 03/06/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022]  Open
22
A design principle of spindle oscillations in mammalian sleep. iScience 2022;25:103873. [PMID: 35243235 PMCID: PMC8861656 DOI: 10.1016/j.isci.2022.103873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/22/2022]  Open
23
Anchang B, Mendez-Giraldez R, Xu X, Archer TK, Chen Q, Hu G, Plevritis SK, Motsinger-Reif AA, Li JL. Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures. Brief Bioinform 2022;23:6534382. [PMID: 35192692 PMCID: PMC8921621 DOI: 10.1093/bib/bbac017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022]  Open
24
Ding J, Sharon N, Bar-Joseph Z. Temporal modelling using single-cell transcriptomics. Nat Rev Genet 2022;23:355-368. [PMID: 35102309 DOI: 10.1038/s41576-021-00444-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/16/2022]
25
Rams M, Conrad TOF. Dictionary learning allows model-free pseudotime estimation of transcriptomic data. BMC Genomics 2022;23:56. [PMID: 35033004 PMCID: PMC8760643 DOI: 10.1186/s12864-021-08276-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/22/2021] [Indexed: 11/10/2022]  Open
26
OUP accepted manuscript. Brief Funct Genomics 2022;21:159-176. [DOI: 10.1093/bfgp/elac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022]  Open
27
Jeong H, Shin S, Yeom HG. Accurate Single-Cell Clustering through Ensemble Similarity Learning. Genes (Basel) 2021;12:genes12111670. [PMID: 34828276 PMCID: PMC8623803 DOI: 10.3390/genes12111670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022]  Open
28
Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 2021;13:83-102.e6. [PMID: 34626539 DOI: 10.1016/j.cels.2021.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
29
Wang X, Zheng J. Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction. BMC Bioinformatics 2021;22:419. [PMID: 34479487 PMCID: PMC8414693 DOI: 10.1186/s12859-021-04330-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022]  Open
30
Li H. Single-cell RNA sequencing in Drosophila: Technologies and applications. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2021;10:e396. [PMID: 32940008 PMCID: PMC7960577 DOI: 10.1002/wdev.396] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
31
Wei Z, Zhang S. CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data. Bioinformatics 2021;37:i51-i58. [PMID: 34252936 PMCID: PMC8686678 DOI: 10.1093/bioinformatics/btab286] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 12/13/2022]  Open
32
Mondal PK, Saha US, Mukhopadhyay I. PseudoGA: cell pseudotime reconstruction based on genetic algorithm. Nucleic Acids Res 2021;49:7909-7924. [PMID: 34244782 PMCID: PMC8661435 DOI: 10.1093/nar/gkab457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/03/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023]  Open
33
Zhao C, Xiu W, Hua Y, Zhang N, Zhang Y. CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data. Bioinformatics 2021;37:3774-3780. [PMID: 34196686 DOI: 10.1093/bioinformatics/btab488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022]  Open
34
Bartlett T. Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development. BMC Bioinformatics 2021;22:301. [PMID: 34088262 PMCID: PMC8176738 DOI: 10.1186/s12859-021-04201-9] [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: 11/05/2020] [Accepted: 05/12/2021] [Indexed: 11/10/2022]  Open
35
Camacho-Aguilar E, Warmflash A, Rand DA. Quantifying cell transitions in C. elegans with data-fitted landscape models. PLoS Comput Biol 2021;17:e1009034. [PMID: 34061834 PMCID: PMC8195438 DOI: 10.1371/journal.pcbi.1009034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/11/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022]  Open
36
Penalized Latent Dirichlet Allocation Model in Single-Cell RNA Sequencing. STATISTICS IN BIOSCIENCES 2021. [DOI: 10.1007/s12561-021-09304-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
37
Dai Y, Xu A, Li J, Wu L, Yu S, Chen J, Zhao W, Sun XJ, Huang J. CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. BMC Bioinformatics 2021;22:138. [PMID: 33752602 PMCID: PMC7983272 DOI: 10.1186/s12859-021-04054-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/26/2021] [Indexed: 01/20/2023]  Open
38
Kopf A, Claassen M. Latent representation learning in biology and translational medicine. PATTERNS (NEW YORK, N.Y.) 2021;2:100198. [PMID: 33748792 PMCID: PMC7961186 DOI: 10.1016/j.patter.2021.100198] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
39
Revealing lineage-related signals in single-cell gene expression using random matrix theory. Proc Natl Acad Sci U S A 2021;118:1913931118. [PMID: 33836557 PMCID: PMC7980374 DOI: 10.1073/pnas.1913931118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
40
Pretschner A, Pabel S, Haas M, Heiner M, Marwan W. Regulatory Dynamics of Cell Differentiation Revealed by True Time Series From Multinucleate Single Cells. Front Genet 2021;11:612256. [PMID: 33488676 PMCID: PMC7820898 DOI: 10.3389/fgene.2020.612256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022]  Open
41
Lieberman B, Kusi M, Hung CN, Chou CW, He N, Ho YY, Taverna JA, Huang THM, Chen CL. Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2021;5:1-21. [PMID: 34322662 PMCID: PMC8315474 DOI: 10.20517/jtgg.2020.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
42
Goodwin K, Nelson CM. Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. Curr Top Dev Biol 2020;143:239-280. [PMID: 33820623 DOI: 10.1016/bs.ctdb.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
43
Chen X, Chen S, Jiang R. EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes. BMC Bioinformatics 2020;21:392. [PMID: 32938367 PMCID: PMC7496207 DOI: 10.1186/s12859-020-03679-z] [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] [Indexed: 11/10/2022]  Open
44
Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle. Nat Med 2020;26:1644-1653. [PMID: 32929266 DOI: 10.1038/s41591-020-1040-z] [Citation(s) in RCA: 314] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
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Lin C, Bar-Joseph Z. Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. Bioinformatics 2020;35:4707-4715. [PMID: 31038684 DOI: 10.1093/bioinformatics/btz296] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/11/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022]  Open
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Unsupervised generative and graph representation learning for modelling cell differentiation. Sci Rep 2020;10:9790. [PMID: 32555334 PMCID: PMC7300092 DOI: 10.1038/s41598-020-66166-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/10/2020] [Indexed: 12/22/2022]  Open
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Chen Z, An S, Bai X, Gong F, Ma L, Wan L. DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data. Bioinformatics 2020;35:2593-2601. [PMID: 30535348 DOI: 10.1093/bioinformatics/bty1009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 12/16/2022]  Open
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Klimovskaia A, Lopez-Paz D, Bottou L, Nickel M. Poincaré maps for analyzing complex hierarchies in single-cell data. Nat Commun 2020;11:2966. [PMID: 32528075 PMCID: PMC7290024 DOI: 10.1038/s41467-020-16822-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/25/2020] [Indexed: 01/23/2023]  Open
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Liao J, Lu X, Shao X, Zhu L, Fan X. Uncovering an Organ's Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics. Trends Biotechnol 2020;39:43-58. [PMID: 32505359 DOI: 10.1016/j.tibtech.2020.05.006] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 01/17/2023]
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Ding J, Bar-Joseph Z. Analysis of time-series regulatory networks. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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