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For: Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol 2006;7:R36. [PMID: 16686963 PMCID: PMC1779511 DOI: 10.1186/gb-2006-7-5-r36] [Citation(s) in RCA: 334] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 02/13/2006] [Accepted: 03/30/2006] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Segura-Ortiz A, García-Nieto J, Aldana-Montes JF, Navas-Delgado I. Multi-objective context-guided consensus of a massive array of techniques for the inference of Gene Regulatory Networks. Comput Biol Med 2024;179:108850. [PMID: 39013340 DOI: 10.1016/j.compbiomed.2024.108850] [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: 02/08/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
2
Yu J, Leng J, Yuan F, Sun D, Wu LY. Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae435. [PMID: 38963312 PMCID: PMC11236096 DOI: 10.1093/bioinformatics/btae435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024]
3
Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024;46:e2300210. [PMID: 38715516 DOI: 10.1002/bies.202300210] [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: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
4
Kion-Crosby W, Barquist L. Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders. BIOINFORMATICS ADVANCES 2024;4:vbae066. [PMID: 39027639 PMCID: PMC11256956 DOI: 10.1093/bioadv/vbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/05/2024] [Accepted: 05/02/2024] [Indexed: 07/20/2024]
5
Tjärnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R. Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference. Genome Biol 2024;25:24. [PMID: 38238840 PMCID: PMC10797903 DOI: 10.1186/s13059-023-03134-1] [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: 02/28/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024]  Open
6
Raja R, Khanum S, Aboulmouna L, Maurya MR, Gupta S, Subramaniam S, Ramkrishna D. Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach. Biophys J 2024;123:221-234. [PMID: 38102827 PMCID: PMC10808046 DOI: 10.1016/j.bpj.2023.12.010] [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: 02/20/2023] [Revised: 09/18/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]  Open
7
Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Del Rio-Tsonis K. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. Development 2024;151:dev202249. [PMID: 38180241 PMCID: PMC10906490 DOI: 10.1242/dev.202249] [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: 08/09/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
8
Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data. NAR Genom Bioinform 2023;5:lqad106. [PMID: 38094309 PMCID: PMC10716740 DOI: 10.1093/nargab/lqad106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023]  Open
9
Wu Y, Qian B, Wang A, Dong H, Zhu E, Ma B. iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion. Bioinformatics 2023;39:btad619. [PMID: 37851379 PMCID: PMC10589915 DOI: 10.1093/bioinformatics/btad619] [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: 04/17/2023] [Revised: 10/04/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]  Open
10
Shojaee A, Huang SSC. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions. Brief Bioinform 2023;24:bbad370. [PMID: 37897702 PMCID: PMC10612495 DOI: 10.1093/bib/bbad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]  Open
11
Peterson EJR, Brooks AN, Reiss DJ, Kaur A, Do J, Pan M, Wu WJ, Morrison R, Srinivas V, Carter W, Arrieta-Ortiz ML, Ruiz RA, Bhatt A, Baliga NS. MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance. Cell Rep 2023;42:112875. [PMID: 37542718 PMCID: PMC10480492 DOI: 10.1016/j.celrep.2023.112875] [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: 08/16/2021] [Revised: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]  Open
12
Li R, Rozum JC, Quail MM, Qasim MN, Sindi SS, Nobile CJ, Albert R, Hernday AD. Inferring gene regulatory networks using transcriptional profiles as dynamical attractors. PLoS Comput Biol 2023;19:e1010991. [PMID: 37607190 PMCID: PMC10473541 DOI: 10.1371/journal.pcbi.1010991] [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: 03/02/2023] [Revised: 09/01/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023]  Open
13
Marku M, Pancaldi V. From time-series transcriptomics to gene regulatory networks: A review on inference methods. PLoS Comput Biol 2023;19:e1011254. [PMID: 37561790 PMCID: PMC10414591 DOI: 10.1371/journal.pcbi.1011254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]  Open
14
Kernfeld E, Yang Y, Weinstock JS, Battle A, Cahan P. A systematic comparison of computational methods for expression forecasting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551039. [PMID: 37577640 PMCID: PMC10418073 DOI: 10.1101/2023.07.28.551039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
15
Tangeman JA, Rebull SM, Grajales-Esquivel E, Weaver JM, Bendezu-Sayas S, Robinson ML, Lachke SA, Rio-Tsonis KD. Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548451. [PMID: 37502967 PMCID: PMC10369908 DOI: 10.1101/2023.07.10.548451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
16
Mbebi AJ, Nikoloski Z. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput Biol 2023;19:e1010832. [PMID: 37523414 PMCID: PMC10414675 DOI: 10.1371/journal.pcbi.1010832] [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: 12/21/2022] [Revised: 08/10/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]  Open
17
Pan TC, Chockalingam SP, Aluru M, Aluru S. MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework. Bioinformatics 2023;39:btad373. [PMID: 37289522 PMCID: PMC10287961 DOI: 10.1093/bioinformatics/btad373] [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: 04/29/2022] [Revised: 04/06/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023]  Open
18
Shen B, Coruzzi G, Shasha D. EnsInfer: a simple ensemble approach to network inference outperforms any single method. BMC Bioinformatics 2023;24:114. [PMID: 36964499 PMCID: PMC10037858 DOI: 10.1186/s12859-023-05231-1] [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: 12/12/2022] [Accepted: 03/15/2023] [Indexed: 03/26/2023]  Open
19
Abid D, Brent MR. NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration. Bioinformatics 2023;39:7000334. [PMID: 36692138 PMCID: PMC9912366 DOI: 10.1093/bioinformatics/btad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023]  Open
20
Tjärnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R. Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526909. [PMID: 36778259 PMCID: PMC9915715 DOI: 10.1101/2023.02.02.526909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
21
Escorcia-Rodríguez JM, Gaytan-Nuñez E, Hernandez-Benitez EM, Zorro-Aranda A, Tello-Palencia MA, Freyre-González JA. Improving gene regulatory network inference and assessment: The importance of using network structure. Front Genet 2023;14:1143382. [PMID: 36926589 PMCID: PMC10012345 DOI: 10.3389/fgene.2023.1143382] [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: 01/16/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]  Open
22
Galindez G, Sadegh S, Baumbach J, Kacprowski T, List M. Network-based approaches for modeling disease regulation and progression. Comput Struct Biotechnol J 2022;21:780-795. [PMID: 36698974 PMCID: PMC9841310 DOI: 10.1016/j.csbj.2022.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]  Open
23
A Framework for Comparison and Assessment of Synthetic RNA-Seq Data. Genes (Basel) 2022;13:genes13122362. [PMID: 36553629 PMCID: PMC9778097 DOI: 10.3390/genes13122362] [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: 11/09/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/16/2022]  Open
24
Hao Y, Lu L, Liu A, Lin X, Xiao L, Kong X, Li K, Liang F, Xiong J, Qu L, Li Y, Li J. Integrating bioinformatic strategies in spatial life science research. Brief Bioinform 2022;23:bbac415. [PMID: 36198665 PMCID: PMC9677476 DOI: 10.1093/bib/bbac415] [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: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/27/2022] [Indexed: 12/14/2022]  Open
25
Hawe JS, Saha A, Waldenberger M, Kunze S, Wahl S, Müller-Nurasyid M, Prokisch H, Grallert H, Herder C, Peters A, Strauch K, Theis FJ, Gieger C, Chambers J, Battle A, Heinig M. Network reconstruction for trans acting genetic loci using multi-omics data and prior information. Genome Med 2022;14:125. [PMID: 36344995 PMCID: PMC9641770 DOI: 10.1186/s13073-022-01124-9] [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: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]  Open
26
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: 2] [Impact Index Per Article: 1.0] [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]
27
Cummins B, Motta FC, Moseley RC, Deckard A, Campione S, Gameiro M, Gedeon T, Mischaikow K, Haase SB. Experimental guidance for discovering genetic networks through hypothesis reduction on time series. PLoS Comput Biol 2022;18:e1010145. [PMID: 36215333 PMCID: PMC9584434 DOI: 10.1371/journal.pcbi.1010145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/20/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022]  Open
28
Perkel JM. Smart software untangles gene regulation in cells. Nature 2022;609:428-431. [PMID: 36064802 DOI: 10.1038/d41586-022-02826-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
29
You Y, Sun X, Ma M, He J, Li L, Porto FW, Lin S. Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton. Nat Commun 2022;13:4022. [PMID: 35821503 PMCID: PMC9276738 DOI: 10.1038/s41467-022-31802-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/05/2022] [Indexed: 11/30/2022]  Open
30
Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nat Methods 2022;19:812-822. [PMID: 35710610 PMCID: PMC10460539 DOI: 10.1038/s41592-022-01522-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
31
Jansen JE, Aschenbrenner D, Uhlig HH, Coles MC, Gaffney EA. A method for the inference of cytokine interaction networks. PLoS Comput Biol 2022;18:e1010112. [PMID: 35731827 PMCID: PMC9216621 DOI: 10.1371/journal.pcbi.1010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/15/2022] [Indexed: 11/19/2022]  Open
32
Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJ, Baliga NS, Stoeger T, Ruffin F, Richardson RA, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR. Mathematical models to study the biology of pathogens and the infectious diseases they cause. iScience 2022;25:104079. [PMID: 35359802 PMCID: PMC8961237 DOI: 10.1016/j.isci.2022.104079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
33
Niu P, Soto MJ, Yoon BJ, Dougherty ER, Alexander FJ, Blaby I, Qian X. Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline. STAR Protoc 2022;3:101184. [PMID: 35243375 PMCID: PMC8866898 DOI: 10.1016/j.xpro.2022.101184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
34
Gibbs CS, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, Bonneau R. High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0. Bioinformatics 2022;38:2519-2528. [PMID: 35188184 PMCID: PMC9048651 DOI: 10.1093/bioinformatics/btac117] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/08/2021] [Accepted: 02/17/2022] [Indexed: 12/04/2022]  Open
35
Zorro-Aranda A, Escorcia-Rodríguez JM, González-Kise JK, Freyre-González JA. Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor. Sci Rep 2022;12:2840. [PMID: 35181703 PMCID: PMC8857197 DOI: 10.1038/s41598-022-06658-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022]  Open
36
Aluru M, Shrivastava H, Chockalingam SP, Shivakumar S, Aluru S. EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. Bioinformatics 2022;38:1312-1319. [PMID: 34888624 DOI: 10.1093/bioinformatics/btab829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 01/05/2023]  Open
37
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: 3] [Impact Index Per Article: 1.5] [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]
38
Qin G, Knijnenburg TA, Gibbs DL, Moser R, Monnat RJ, Kemp CJ, Shmulevich I. A functional module states framework reveals transcriptional states for drug and target prediction. Cell Rep 2022;38:110269. [PMID: 35045296 DOI: 10.1016/j.celrep.2021.110269] [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: 02/18/2021] [Revised: 08/24/2021] [Accepted: 12/23/2021] [Indexed: 11/03/2022]  Open
39
Zheng L, Liu Z, Yang Y, Shen HB. Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning. Bioinformatics 2022;38:746-753. [PMID: 34664632 DOI: 10.1093/bioinformatics/btab718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/19/2021] [Accepted: 10/15/2021] [Indexed: 02/03/2023]  Open
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Emerging Machine Learning Techniques for Modelling Cellular Complex Systems in Alzheimer's Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1338:199-208. [PMID: 34973026 DOI: 10.1007/978-3-030-78775-2_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer. Drug Resist Updat 2022;60:100811. [DOI: 10.1016/j.drup.2022.100811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/07/2023]
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Immanuel SRC, Arrieta-Ortiz ML, Ruiz RA, Pan M, Lopez Garcia de Lomana A, Peterson EJR, Baliga NS. Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME. NPJ Syst Biol Appl 2021;7:43. [PMID: 34873198 PMCID: PMC8648758 DOI: 10.1038/s41540-021-00205-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 11/02/2021] [Indexed: 12/04/2022]  Open
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Niu P, Soto MJ, Yoon BJ, Dougherty ER, Alexander FJ, Blaby I, Qian X. TRIMER: Transcription Regulation Integrated with Metabolic Regulation. iScience 2021;24:103218. [PMID: 34761179 PMCID: PMC8567008 DOI: 10.1016/j.isci.2021.103218] [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: 04/19/2021] [Revised: 08/22/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023]  Open
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Saint-André V. Computational biology approaches for mapping transcriptional regulatory networks. Comput Struct Biotechnol J 2021;19:4884-4895. [PMID: 34522292 PMCID: PMC8426465 DOI: 10.1016/j.csbj.2021.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]  Open
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Ghosh Roy G, Geard N, Verspoor K, He S. PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data. Bioinformatics 2021;36:5187-5193. [PMID: 32697830 DOI: 10.1093/bioinformatics/btaa651] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/06/2020] [Accepted: 07/16/2020] [Indexed: 02/01/2023]  Open
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_15] [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: 11/19/2023]
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Tripathi RK, Wilkins O. Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience. PLANT, CELL & ENVIRONMENT 2021;44:2006-2017. [PMID: 33522607 PMCID: PMC8359182 DOI: 10.1111/pce.14012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
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Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma. NPJ Precis Oncol 2021;5:60. [PMID: 34183722 PMCID: PMC8239045 DOI: 10.1038/s41698-021-00185-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 05/13/2021] [Indexed: 01/19/2023]  Open
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Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021;12:652189. [PMID: 34249082 PMCID: PMC8264776 DOI: 10.3389/fgene.2021.652189] [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: 01/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022]  Open
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Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Identifying the combinatorial control of signal-dependent transcription factors. PLoS Comput Biol 2021;17:e1009095. [PMID: 34166361 PMCID: PMC8263068 DOI: 10.1371/journal.pcbi.1009095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/07/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022]  Open
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