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For: Gitter A, Carmi M, Barkai N, Bar-Joseph Z. Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Res 2012;23:365-76. [PMID: 23064748 PMCID: PMC3561877 DOI: 10.1101/gr.138628.112] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Number Cited by Other Article(s)
1
Marques I, Hu H. Molecular Insight of Plants Response to Drought Stress: Perspectives and New Insights towards Food Security. Int J Mol Sci 2024;25:4988. [PMID: 38732211 PMCID: PMC11084910 DOI: 10.3390/ijms25094988] [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: 04/17/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]  Open
2
Martini L, Baek SH, Lo I, Raby BA, Silverman E, Weiss S, Glass K, Halu A. Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions. Nucleic Acids Res 2024;52:e5. [PMID: 37953325 PMCID: PMC10783515 DOI: 10.1093/nar/gkad1035] [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: 10/28/2022] [Revised: 06/27/2023] [Accepted: 10/23/2023] [Indexed: 11/14/2023]  Open
3
Yin L, Zander M, Huang SSC, Xie M, Song L, Saldierna Guzmán JP, Hann E, Shanbhag BK, Ng S, Jain S, Janssen BJ, Clark NM, Walley JW, Beddoe T, Bar-Joseph Z, Lewsey MG, Ecker JR. Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531630. [PMID: 36945593 PMCID: PMC10028877 DOI: 10.1101/2023.03.07.531630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
4
Singh A, Kandi AR, Jayaprakashappa D, Thuery G, Purohit DJ, Huelsmeier J, Singh R, Pothapragada SS, Ramaswami M, Bakthavachalu B. The transcriptional response to oxidative stress is independent of stress-granule formation. Mol Biol Cell 2022;33:ar25. [PMID: 34985933 PMCID: PMC9250384 DOI: 10.1091/mbc.e21-08-0418] [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] [Received: 08/25/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 11/11/2022]  Open
5
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]
6
Ding J, Lugo-Martinez J, Yuan Y, Huang J, Hume AJ, Suder EL, Mühlberger E, Kotton DN, Bar-Joseph Z. Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.06.01.127589. [PMID: 33083801 PMCID: PMC7574259 DOI: 10.1101/2020.06.01.127589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
7
Han M, Liu X, Zhang W, Wang M, Bu W, Chang C, Yu M, Li Y, Tian C, Yang X, Zhu Y, He F. TSMiner: a novel framework for generating time-specific gene regulatory networks from time-series expression profiles. Nucleic Acids Res 2021;49:e108. [PMID: 34313778 PMCID: PMC8502000 DOI: 10.1093/nar/gkab629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 12/03/2022]  Open
8
Ma CZ, Brent MR. Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. Bioinformatics 2021;37:1234-1245. [PMID: 33135076 PMCID: PMC8189679 DOI: 10.1093/bioinformatics/btaa947] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/26/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]  Open
9
Treveil A, Bohar B, Sudhakar P, Gul L, Csabai L, Olbei M, Poletti M, Madgwick M, Andrighetti T, Hautefort I, Modos D, Korcsmaros T. ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Comput Biol 2021;17:e1008685. [PMID: 33534793 PMCID: PMC7886129 DOI: 10.1371/journal.pcbi.1008685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/16/2021] [Accepted: 01/10/2021] [Indexed: 12/21/2022]  Open
10
Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice (Oryza sativa L.). Genes (Basel) 2020;11:genes11101124. [PMID: 32987927 PMCID: PMC7650634 DOI: 10.3390/genes11101124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022]  Open
11
Jiang Y, Liang Y, Wang D, Xu D, Joshi T. A dynamic programing approach to integrate gene expression data and network information for pathway model generation. Bioinformatics 2020;36:169-176. [PMID: 31168616 DOI: 10.1093/bioinformatics/btz467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 05/15/2019] [Accepted: 05/31/2019] [Indexed: 11/13/2022]  Open
12
Cardner M, Meyer-Schaller N, Christofori G, Beerenwinkel N. Inferring signalling dynamics by integrating interventional with observational data. Bioinformatics 2020;35:i577-i585. [PMID: 31510686 PMCID: PMC6612850 DOI: 10.1093/bioinformatics/btz325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
13
Nagpal S, Baksi KD, Kuntal BK, Mande SS. NetConfer: a web application for comparative analysis of multiple biological networks. BMC Biol 2020;18:53. [PMID: 32430035 PMCID: PMC7236966 DOI: 10.1186/s12915-020-00781-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/14/2020] [Indexed: 12/29/2022]  Open
14
Chiang S, Shinohara H, Huang JH, Tsai HK, Okada M. Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Lett 2020;594:1477-1496. [PMID: 32052437 DOI: 10.1002/1873-3468.13757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/26/2019] [Accepted: 01/20/2020] [Indexed: 11/10/2022]
15
IMPRes-Pro: A high dimensional multiomics integration method for in silico hypothesis generation. Methods 2020;173:16-23. [DOI: 10.1016/j.ymeth.2019.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/18/2023]  Open
16
Deep learning for inferring gene relationships from single-cell expression data. Proc Natl Acad Sci U S A 2019;116:27151-27158. [PMID: 31822622 DOI: 10.1073/pnas.1911536116] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
17
Marshall-Colón A, Kliebenstein DJ. Plant Networks as Traits and Hypotheses: Moving Beyond Description. TRENDS IN PLANT SCIENCE 2019;24:840-852. [PMID: 31300195 DOI: 10.1016/j.tplants.2019.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
18
Ruffalo M, Bar-Joseph Z. Protein interaction disruption in cancer. BMC Cancer 2019;19:370. [PMID: 31014259 PMCID: PMC6823625 DOI: 10.1186/s12885-019-5532-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/27/2019] [Indexed: 12/18/2022]  Open
19
Del Sol A, Okawa S, Ravichandran S. Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy. Trends Biotechnol 2019;37:687-696. [PMID: 30782480 DOI: 10.1016/j.tibtech.2019.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/28/2022]
20
Siahpirani AF, Chasman D, Roy S. Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks. Methods Mol Biol 2019;1883:161-194. [PMID: 30547400 DOI: 10.1007/978-1-4939-8882-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
21
Dash M, Yordanov YS, Georgieva T, Wei H, Busov V. Gene network analysis of poplar root transcriptome in response to drought stress identifies a PtaJAZ3PtaRAP2.6-centered hierarchical network. PLoS One 2018;13:e0208560. [PMID: 30540849 PMCID: PMC6291141 DOI: 10.1371/journal.pone.0208560] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/19/2018] [Indexed: 12/02/2022]  Open
22
Franks AM, Markowetz F, Airoldi EM. REFINING CELLULAR PATHWAY MODELS USING AN ENSEMBLE OF HETEROGENEOUS DATA SOURCES. Ann Appl Stat 2018;12:1361-1384. [PMID: 36506698 PMCID: PMC9733905 DOI: 10.1214/16-aoas915] [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] [Indexed: 12/15/2022]
23
Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. Sci Rep 2018;8:7949. [PMID: 29785040 PMCID: PMC5962585 DOI: 10.1038/s41598-018-26170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023]  Open
24
Mertins P, Przybylski D, Yosef N, Qiao J, Clauser K, Raychowdhury R, Eisenhaure TM, Maritzen T, Haucke V, Satoh T, Akira S, Carr SA, Regev A, Hacohen N, Chevrier N. An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling. Cell Rep 2018;19:2853-2866. [PMID: 28658630 DOI: 10.1016/j.celrep.2017.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 04/11/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]  Open
25
Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLoS Comput Biol 2018. [PMID: 29538379 PMCID: PMC5868853 DOI: 10.1371/journal.pcbi.1006019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
26
Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z. Reconstructing cancer drug response networks using multitask learning. BMC SYSTEMS BIOLOGY 2017;11:96. [PMID: 29017547 PMCID: PMC5635550 DOI: 10.1186/s12918-017-0471-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023]
27
Jain S, Arrais J, Venkatachari NJ, Ayyavoo V, Bar-Joseph Z. Reconstructing the temporal progression of HIV-1 immune response pathways. Bioinformatics 2017;32:i253-i261. [PMID: 27307624 PMCID: PMC4908338 DOI: 10.1093/bioinformatics/btw254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
28
Ahn H, Jung I, Shin SJ, Park J, Rhee S, Kim JK, Jung W, Kwon HB, Kim S. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice. FRONTIERS IN PLANT SCIENCE 2017;8:1044. [PMID: 28663756 PMCID: PMC5471331 DOI: 10.3389/fpls.2017.01044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
29
Sychev ZE, Hu A, DiMaio TA, Gitter A, Camp ND, Noble WS, Wolf-Yadlin A, Lagunoff M. Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PLoS Pathog 2017;13:e1006256. [PMID: 28257516 PMCID: PMC5352148 DOI: 10.1371/journal.ppat.1006256] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 03/15/2017] [Accepted: 02/22/2017] [Indexed: 12/22/2022]  Open
30
Korla K, Chandra N. A Systems Perspective of Signalling Networks in Host–Pathogen Interactions. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
31
Kleyman M, Sefer E, Nicola T, Espinoza C, Chhabra D, Hagood JS, Kaminski N, Ambalavanan N, Bar-Joseph Z. Selecting the most appropriate time points to profile in high-throughput studies. eLife 2017;6:e18541. [PMID: 28124972 PMCID: PMC5319842 DOI: 10.7554/elife.18541] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 01/23/2017] [Indexed: 12/25/2022]  Open
32
Gil DP, Law JN, Murali TM. The PathLinker app: Connect the dots in protein interaction networks. F1000Res 2017;6:58. [PMID: 28413614 PMCID: PMC5365231 DOI: 10.12688/f1000research.9909.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/14/2016] [Indexed: 11/20/2022]  Open
33
He FQ, Ollert M. Network-Guided Key Gene Discovery for a Given Cellular Process. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016. [PMID: 27783134 DOI: 10.1007/10_2016_39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
34
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PLoS Comput Biol 2016;12:e1005013. [PMID: 27403523 PMCID: PMC4942116 DOI: 10.1371/journal.pcbi.1005013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/06/2016] [Indexed: 12/17/2022]  Open
35
Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J. Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. Nucleic Acids Res 2016;44:5529-39. [PMID: 27216817 PMCID: PMC4937331 DOI: 10.1093/nar/gkw462] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 05/16/2016] [Indexed: 12/22/2022]  Open
36
Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae. mBio 2016;7:mBio.00559-16. [PMID: 27143390 PMCID: PMC4959655 DOI: 10.1128/mbio.00559-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
37
Tuncbag N, Gosline SJC, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PLoS Comput Biol 2016;12:e1004879. [PMID: 27096930 PMCID: PMC4838263 DOI: 10.1371/journal.pcbi.1004879] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/23/2016] [Indexed: 02/07/2023]  Open
38
Horowitz M. Epigenetics and cytoprotection with heat acclimation. J Appl Physiol (1985) 2016;120:702-10. [DOI: 10.1152/japplphysiol.00552.2015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/05/2015] [Indexed: 01/19/2023]  Open
39
Wise A, Bar-Joseph Z. cDREM: inferring dynamic combinatorial gene regulation. J Comput Biol 2016;22:324-33. [PMID: 25844671 DOI: 10.1089/cmb.2015.0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
40
Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016;1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
41
Gitter A, Bar-Joseph Z. The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. Methods Mol Biol 2016;1303:493-506. [PMID: 26235087 DOI: 10.1007/978-1-4939-2627-5_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
42
Acharya L, Reynolds R, Zhu D. Network inference through synergistic subnetwork evolution. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2015;2015:12. [PMID: 26640480 PMCID: PMC4662719 DOI: 10.1186/s13637-015-0027-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/21/2015] [Indexed: 12/02/2022]
43
Venkatachari NJ, Zerbato JM, Jain S, Mancini AE, Chattopadhyay A, Sluis-Cremer N, Bar-Joseph Z, Ayyavoo V. Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. Retrovirology 2015;12:85. [PMID: 26438393 PMCID: PMC4594640 DOI: 10.1186/s12977-015-0211-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/25/2015] [Indexed: 12/27/2022]  Open
44
Terfve CDA, Wilkes EH, Casado P, Cutillas PR, Saez-Rodriguez J. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data. Nat Commun 2015;6:8033. [PMID: 26354681 PMCID: PMC4579397 DOI: 10.1038/ncomms9033] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/09/2015] [Indexed: 12/27/2022]  Open
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Tripathi S, Flobak Å, Chawla K, Baudot A, Bruland T, Thommesen L, Kuiper M, Lægreid A. The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC SYSTEMS BIOLOGY 2015. [PMID: 26205660 PMCID: PMC4513977 DOI: 10.1186/s12918-015-0181-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Li Y, Varala K, Coruzzi GM. From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks. Trends Genet 2015;31:509-15. [PMID: 26072453 DOI: 10.1016/j.tig.2015.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 12/17/2022]
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Ho YH, Gasch AP. Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 2015;61:503-11. [PMID: 25957506 DOI: 10.1007/s00294-015-0491-0] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/24/2022]
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Jain S, Gitter A, Bar-Joseph Z. Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput Biol 2014;10:e1003943. [PMID: 25522349 PMCID: PMC4270428 DOI: 10.1371/journal.pcbi.1003943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/28/2014] [Indexed: 01/04/2023]  Open
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TimeXNet: identifying active gene sub-networks using time-course gene expression profiles. BMC SYSTEMS BIOLOGY 2014;8 Suppl 4:S2. [PMID: 25522063 PMCID: PMC4290689 DOI: 10.1186/1752-0509-8-s4-s2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Wise A, Bar-Joseph Z. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. ACTA ACUST UNITED AC 2014;31:1250-7. [PMID: 25480376 DOI: 10.1093/bioinformatics/btu800] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 11/26/2014] [Indexed: 02/02/2023]
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