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For: Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Bioinformatics 2018;33:2314-2321. [PMID: 28379368 PMCID: PMC5860123 DOI: 10.1093/bioinformatics/btx194] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/02/2017] [Indexed: 01/17/2023]  Open
Number Cited by Other Article(s)
101
Ventre E, Herbach U, Espinasse T, Benoit G, Gandrillon O. One model fits all: Combining inference and simulation of gene regulatory networks. PLoS Comput Biol 2023;19:e1010962. [PMID: 36972296 PMCID: PMC10079230 DOI: 10.1371/journal.pcbi.1010962] [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: 07/19/2022] [Revised: 04/06/2023] [Accepted: 02/17/2023] [Indexed: 03/29/2023]  Open
102
Oubounyt M, Elkjaer ML, Laske T, Grønning AB, Moeller M, Baumbach J. De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters. NAR Genom Bioinform 2023;5:lqad018. [PMID: 36879901 PMCID: PMC9985332 DOI: 10.1093/nargab/lqad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 03/07/2023]  Open
103
van der Sande M, Frölich S, van Heeringen SJ. Computational approaches to understand transcription regulation in development. Biochem Soc Trans 2023;51:1-12. [PMID: 36695505 PMCID: PMC9988001 DOI: 10.1042/bst20210145] [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: 10/28/2022] [Revised: 01/07/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
104
Song Q, Ruffalo M, Bar-Joseph Z. Using single cell atlas data to reconstruct regulatory networks. Nucleic Acids Res 2023;51:e38. [PMID: 36762475 PMCID: PMC10123116 DOI: 10.1093/nar/gkad053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023]  Open
105
Khozyainova AA, Valyaeva AA, Arbatsky MS, Isaev SV, Iamshchikov PS, Volchkov EV, Sabirov MS, Zainullina VR, Chechekhin VI, Vorobev RS, Menyailo ME, Tyurin-Kuzmin PA, Denisov EV. Complex Analysis of Single-Cell RNA Sequencing Data. BIOCHEMISTRY. BIOKHIMIIA 2023;88:231-252. [PMID: 37072324 PMCID: PMC10000364 DOI: 10.1134/s0006297923020074] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 03/12/2023]
106
Juan H, Huang H. Quantitative analysis of high‐throughput biological data. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
107
Zhang Y, Wang M, Wang Z, Liu Y, Xiong S, Zou Q. MetaSEM: Gene Regulatory Network Inference from Single-Cell RNA Data by Meta-Learning. Int J Mol Sci 2023;24:2595. [PMID: 36768917 PMCID: PMC9916710 DOI: 10.3390/ijms24032595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023]  Open
108
Lin Z, Ou-Yang L. Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning. Brief Bioinform 2023;24:6965907. [PMID: 36585783 DOI: 10.1093/bib/bbac586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 01/01/2023]  Open
109
Caranica C, Lu M. A data-driven optimization method for coarse-graining gene regulatory networks. iScience 2023;26:105927. [PMID: 36698721 PMCID: PMC9868542 DOI: 10.1016/j.isci.2023.105927] [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: 08/09/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]  Open
110
Koumadorakis DE, Krokidis MG, Dimitrakopoulos GN, Vrahatis AG. A Consensus Gene Regulatory Network for Neurodegenerative Diseases Using Single-Cell RNA-Seq Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023;1423:215-224. [PMID: 37525047 DOI: 10.1007/978-3-031-31978-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
111
Huang L, Clauss B, Lu M. What Makes a Functional Gene Regulatory Network? A Circuit Motif Analysis. J Phys Chem B 2022;126:10374-10383. [PMID: 36471236 PMCID: PMC9896654 DOI: 10.1021/acs.jpcb.2c05412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
112
Coulier A, Singh P, Sturrock M, Hellander A. Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation. PLoS Comput Biol 2022;18:e1010683. [PMID: 36520957 PMCID: PMC9799300 DOI: 10.1371/journal.pcbi.1010683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 12/29/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]  Open
113
Chuwdhury GS, Ng IOL, Ho DWH. scAnalyzeR: A Comprehensive Software Package With Graphical User Interface for Single-Cell RNA Sequencing Analysis and its Application on Liver Cancer. Technol Cancer Res Treat 2022;21:15330338221142729. [PMID: 36476060 PMCID: PMC9742707 DOI: 10.1177/15330338221142729] [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] [Indexed: 12/13/2022]  Open
114
Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022;9:68. [PMID: 36461064 PMCID: PMC9716519 DOI: 10.1186/s40779-022-00434-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]  Open
115
Chen Z, King WC, Hwang A, Gerstein M, Zhang J. DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. SCIENCE ADVANCES 2022;8:eabq3745. [PMID: 36449617 PMCID: PMC9710871 DOI: 10.1126/sciadv.abq3745] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
116
Guan J, Wang Y, Wang Y, Zhuang Y, Ji G. SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference. BMC Genomics 2022;23:782. [PMID: 36451086 PMCID: PMC9710113 DOI: 10.1186/s12864-022-09020-7] [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: 05/10/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]  Open
117
Mao G, Zeng R, Peng J, Zuo K, Pang Z, Liu J. Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons. BMC Bioinformatics 2022;23:503. [PMID: 36434499 PMCID: PMC9700916 DOI: 10.1186/s12859-022-05055-5] [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: 07/16/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022]  Open
118
Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022;22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
119
Xu Y, Chen J, Lyu A, Cheung WK, Zhang L. dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data. Brief Bioinform 2022;23:6720420. [PMID: 36168811 DOI: 10.1093/bib/bbac424] [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: 03/23/2022] [Revised: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]  Open
120
Ferrari C, Manosalva Pérez N, Vandepoele K. MINI-EX: Integrative inference of single-cell gene regulatory networks in plants. MOLECULAR PLANT 2022;15:1807-1824. [PMID: 36307979 DOI: 10.1016/j.molp.2022.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 05/26/2023]
121
Majumder S, Thakran Y, Pal V, Singh K. Fuzzy and Rough Set Theory Based Computational Framework for Mining Genetic Interaction Triplets From Gene Expression Profiles for Lung Adenocarcinoma. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3469-3481. [PMID: 34665736 DOI: 10.1109/tcbb.2021.3120844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
122
Jiang J, Lyu P, Li J, Huang S, Tao J, Blackshaw S, Qian J, Wang J. IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles. iScience 2022;25:105359. [PMID: 36325073 PMCID: PMC9619378 DOI: 10.1016/j.isci.2022.105359] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/19/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022]  Open
123
Bocci F, Zhou P, Nie Q. spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data. Mol Syst Biol 2022;18:e11176. [PMID: 36321549 PMCID: PMC9627675 DOI: 10.15252/msb.202211176] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022]  Open
124
Chen G, Liu ZP. Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data. Bioinformatics 2022;38:4522-4529. [PMID: 35961023 DOI: 10.1093/bioinformatics/btac559] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/18/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022]  Open
125
Subramanian A, Zakeri P, Mousa M, Alnaqbi H, Alshamsi FY, Bettoni L, Damiani E, Alsafar H, Saeys Y, Carmeliet P. Angiogenesis goes computational - The future way forward to discover new angiogenic targets? Comput Struct Biotechnol J 2022;20:5235-5255. [PMID: 36187917 PMCID: PMC9508490 DOI: 10.1016/j.csbj.2022.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022]  Open
126
Shu H, Ding F, Zhou J, Xue Y, Zhao D, Zeng J, Ma J. Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data. Brief Bioinform 2022;23:6693602. [PMID: 36070863 DOI: 10.1093/bib/bbac389] [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: 05/30/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022]  Open
127
Zheng H, Wang S, Li X, Hu H. INSISTC: Incorporating network structure information for single-cell type classification. Genomics 2022;114:110480. [PMID: 36075505 DOI: 10.1016/j.ygeno.2022.110480] [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: 07/24/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/27/2022]
128
Zhao X, Lan Y, Chen D. Exploring long non-coding RNA networks from single cell omics data. Comput Struct Biotechnol J 2022;20:4381-4389. [PMID: 36051880 PMCID: PMC9403499 DOI: 10.1016/j.csbj.2022.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]  Open
129
Bulbul Ahmed M, Humayan Kabir A. Understanding of the various aspects of gene regulatory networks related to crop improvement. Gene 2022;833:146556. [PMID: 35609798 DOI: 10.1016/j.gene.2022.146556] [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] [Received: 11/30/2021] [Revised: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 12/30/2022]
130
Dinh K, Wang Q. A probabilistic Boolean model on hair follicle cell fate regulation by TGF-β. Biophys J 2022;121:2638-2652. [PMID: 35714600 PMCID: PMC9300639 DOI: 10.1016/j.bpj.2022.05.035] [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: 08/03/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022]  Open
131
Ellis D, Wu D, Datta S. SAREV: A review on statistical analytics of single-cell RNA sequencing data. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL STATISTICS 2022;14:e1558. [PMID: 36034329 PMCID: PMC9400796 DOI: 10.1002/wics.1558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/09/2021] [Indexed: 06/15/2023]
132
Yang B, Bao W, Chen B, Song D. Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data. BioData Min 2022;15:13. [PMID: 35690842 PMCID: PMC9188720 DOI: 10.1186/s13040-022-00297-8] [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: 02/09/2022] [Accepted: 05/22/2022] [Indexed: 11/30/2022]  Open
133
Gan Y, Hu X, Zou G, Yan C, Xu G. Inferring Gene Regulatory Networks From Single-Cell Transcriptomic Data Using Bidirectional RNN. Front Oncol 2022;12:899825. [PMID: 35692809 PMCID: PMC9178250 DOI: 10.3389/fonc.2022.899825] [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: 03/19/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]  Open
134
Sonawane AR, Aikawa E, Aikawa M. Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases. Front Cardiovasc Med 2022;9:873582. [PMID: 35665246 PMCID: PMC9160390 DOI: 10.3389/fcvm.2022.873582] [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: 02/11/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023]  Open
135
Caligola S, De Sanctis F, Canè S, Ugel S. Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. Front Genet 2022;13:867880. [PMID: 35651929 PMCID: PMC9149246 DOI: 10.3389/fgene.2022.867880] [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: 02/01/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022]  Open
136
Inference of Molecular Regulatory Systems Using Statistical Path-Consistency Algorithm. ENTROPY 2022;24:e24050693. [PMID: 35626576 PMCID: PMC9142129 DOI: 10.3390/e24050693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]
137
Hang Y, Burns J, Shealy BT, Pauly R, Ficklin SP, Feltus FA. Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue. BMC Genomics 2022;23:350. [PMID: 35524179 PMCID: PMC9077899 DOI: 10.1186/s12864-022-08591-9] [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: 06/28/2021] [Accepted: 04/25/2022] [Indexed: 12/24/2022]  Open
138
Liu R, Pisco AO, Braun E, Linnarsson S, Zou J. Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation. J Mol Biol 2022;434:167606. [PMID: 35489382 DOI: 10.1016/j.jmb.2022.167606] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022]
139
SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes. Commun Biol 2022;5:351. [PMID: 35414121 PMCID: PMC9005655 DOI: 10.1038/s42003-022-03319-7] [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: 07/07/2021] [Accepted: 03/24/2022] [Indexed: 11/08/2022]  Open
140
Zhang Y, He Y, Chen Q, Yang Y, Gong M. Fusion prior gene network for high reliable single-cell gene regulatory network inference. Comput Biol Med 2022;143:105279. [PMID: 35134605 DOI: 10.1016/j.compbiomed.2022.105279] [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: 10/26/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 11/03/2022]
141
Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022;17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022]  Open
142
Single-Cell Transcriptome and Network Analyses Unveil Key Transcription Factors Regulating Mesophyll Cell Development in Maize. Genes (Basel) 2022;13:genes13020374. [PMID: 35205426 PMCID: PMC8872562 DOI: 10.3390/genes13020374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/17/2022]  Open
143
Su EY, Spangler A, Bian Q, Kasamoto JY, Cahan P. Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification. Stem Cell Reports 2022;17:427-442. [PMID: 35090587 PMCID: PMC8828556 DOI: 10.1016/j.stemcr.2021.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/21/2021] [Accepted: 12/26/2021] [Indexed: 11/17/2022]  Open
144
Deshpande A, Chu LF, Stewart R, Gitter A. Network inference with Granger causality ensembles on single-cell transcriptomics. Cell Rep 2022;38:110333. [PMID: 35139376 PMCID: PMC9093087 DOI: 10.1016/j.celrep.2022.110333] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/19/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022]  Open
145
Sekula M, Gaskins J, Datta S. Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models. Front Genet 2022;12:810816. [PMID: 35186014 PMCID: PMC8855158 DOI: 10.3389/fgene.2021.810816] [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: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022]  Open
146
Clark NM, Elmore JM, Walley JW. To the proteome and beyond: advances in single-cell omics profiling for plant systems. PLANT PHYSIOLOGY 2022;188:726-737. [PMID: 35235661 PMCID: PMC8825333 DOI: 10.1093/plphys/kiab429] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 05/19/2023]
147
Swift J, Greenham K, Ecker JR, Coruzzi GM, McClung CR. The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022;109:764-778. [PMID: 34797944 PMCID: PMC9215356 DOI: 10.1111/tpj.15589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 05/26/2023]
148
Zhao M, He W, Tang J, Zou Q, Guo F. A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data. Brief Bioinform 2022;23:6513730. [DOI: 10.1093/bib/bbab568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/21/2022]  Open
149
Shrivastava H, Zhang X, Song L, Aluru S. GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks. J Comput Biol 2022;29:27-44. [PMID: 35050715 DOI: 10.1089/cmb.2021.0437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
150
Erbe R, Gore J, Gemmill K, Gaykalova DA, Fertig EJ. The use of machine learning to discover regulatory networks controlling biological systems. Mol Cell 2022;82:260-273. [PMID: 35016036 PMCID: PMC8905511 DOI: 10.1016/j.molcel.2021.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/22/2023]
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