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126
Li Y, Liu D, Li T, Zhu Y. Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations. BMC Bioinformatics 2020;21:12. [PMID: 31918656 PMCID: PMC6953167 DOI: 10.1186/s12859-019-3314-3] [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: 05/07/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022]  Open
127
Zhang P, Chen JS, Li QY, Sheng LX, Gao YX, Lu BZ, Zhu WB, Zhan XY, Li Y, Yuan ZB, Xu G, Qiu BT, Yan M, Guo CX, Wang YQ, Huang YJ, Zhang JX, Liu FY, Tang ZW, Lin SZ, Cooper DN, Yang HM, Wang J, Gao YQ, Yin W, Zhang GJ, Yan GM. Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys. Zool Res 2020;41:3-19. [PMID: 31840949 PMCID: PMC6956719 DOI: 10.24272/j.issn.2095-8137.2020.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
128
Alasady MJ, Mendillo ML. The Multifaceted Role of HSF1 in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020;1243:69-85. [PMID: 32297212 DOI: 10.1007/978-3-030-40204-4_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
129
Poos AM, Kordaß T, Kolte A, Ast V, Oswald M, Rippe K, König R. Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 2019;20:737. [PMID: 31888467 PMCID: PMC6937852 DOI: 10.1186/s12859-019-3323-2] [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] [Received: 11/12/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023]  Open
130
Martínez-Bartolomé M, Range RC. A biphasic role of non-canonical Wnt16 signaling during early anterior-posterior patterning and morphogenesis of the sea urchin embryo. Development 2019;146:dev168799. [PMID: 31822478 PMCID: PMC6955209 DOI: 10.1242/dev.168799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 11/26/2019] [Indexed: 12/28/2022]
131
Poorebrahim M, Sadeghi S, Ghanbarian M, Kalhor H, Mehrtash A, Teimoori-Toolabi L. Identification of candidate genes and miRNAs for sensitizing resistant colorectal cancer cells to oxaliplatin and irinotecan. Cancer Chemother Pharmacol 2019;85:153-171. [PMID: 31781855 DOI: 10.1007/s00280-019-03975-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/05/2019] [Indexed: 12/16/2022]
132
Schubert M, Colomé-Tatché M, Foijer F. Gene networks in cancer are biased by aneuploidies and sample impurities. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019;1863:194444. [PMID: 31654805 DOI: 10.1016/j.bbagrm.2019.194444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/05/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022]
133
Liu L, Liu J. A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps. J Bioinform Comput Biol 2019;17:1950023. [PMID: 31617458 DOI: 10.1142/s0219720019500239] [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: 01/09/2023]
134
Colgan W, Leanza A, Hwang A, DeBiasse MB, Llosa I, Rodrigues D, Adhikari H, Barreto Corona G, Bock S, Carillo-Perez A, Currie M, Darkoa-Larbi S, Dellal D, Gutow H, Hokama P, Kibby E, Linhart N, Moody S, Naganuma A, Nguyen D, Stanton R, Stark S, Tumey C, Velleca A, Ryan JF, Davidson B. Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. EvoDevo 2019;10:24. [PMID: 31632631 PMCID: PMC6790052 DOI: 10.1186/s13227-019-0137-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/29/2022]  Open
135
Antoneli F, Golubitsky M, Stewart I. Homeostasis in a feed forward loop gene regulatory motif. J Theor Biol 2019;445:103-109. [PMID: 29477558 DOI: 10.1016/j.jtbi.2018.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/13/2018] [Accepted: 02/22/2018] [Indexed: 12/19/2022]
136
Díaz-Montaña JJ, Díaz-Díaz N, Barranco CD, Ponzoni I. Development and use of a Cytoscape app for GRNCOP2. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019;177:211-218. [PMID: 31319950 DOI: 10.1016/j.cmpb.2019.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 05/05/2019] [Accepted: 05/29/2019] [Indexed: 06/10/2023]
137
Patel H, Hodges AK, Curtis C, Lee SH, Troakes C, Dobson RJB, Newhouse SJ. Transcriptomic analysis of probable asymptomatic and symptomatic alzheimer brains. Brain Behav Immun 2019;80:644-656. [PMID: 31063847 DOI: 10.1016/j.bbi.2019.05.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022]  Open
138
Hamilton AR, Traniello IM, Ray AM, Caldwell AS, Wickline SA, Robinson GE. Division of labor in honey bees is associated with transcriptional regulatory plasticity in the brain. J Exp Biol 2019;222:jeb200196. [PMID: 31138635 PMCID: PMC6679348 DOI: 10.1242/jeb.200196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
139
Deyell M, Ameta S, Nghe P. Large scale control and programming of gene expression using CRISPR. Semin Cell Dev Biol 2019;96:124-132. [PMID: 31181342 DOI: 10.1016/j.semcdb.2019.05.013] [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] [Received: 12/21/2018] [Accepted: 05/14/2019] [Indexed: 12/22/2022]
140
Haliki E, Alpagut Keskin N, Masalci O. Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. J Biol Phys 2019;45:235-251. [PMID: 31175490 DOI: 10.1007/s10867-019-09526-4] [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: 10/16/2018] [Accepted: 05/09/2019] [Indexed: 10/26/2022]  Open
141
Unsupervised GRN Ensemble. Methods Mol Biol 2019;1883:283-302. [PMID: 30547405 DOI: 10.1007/978-1-4939-8882-2_12] [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: 02/04/2023]
142
Grzegorczyk M, Aderhold A, Husmeier D. Overview and Evaluation of Recent Methods for Statistical Inference of Gene Regulatory Networks from Time Series Data. Methods Mol Biol 2019;1883:49-94. [PMID: 30547396 DOI: 10.1007/978-1-4939-8882-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
143
García-Nieto J, Nebro AJ, Aldana-Montes JF. Inference of gene regulatory networks with multi-objective cellular genetic algorithm. Comput Biol Chem 2019;80:409-418. [PMID: 31128452 DOI: 10.1016/j.compbiolchem.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/26/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
144
Ruklisa D, Brazma A, Cerans K, Schlitt T, Viksna J. Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ. BMC Bioinformatics 2019;20:296. [PMID: 31151381 PMCID: PMC6544977 DOI: 10.1186/s12859-019-2909-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] [Received: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 11/10/2022]  Open
145
Stingl K, Koraimann G. Prokaryotic Information Games: How and When to Take up and Secrete DNA. Curr Top Microbiol Immunol 2019. [PMID: 29536355 DOI: 10.1007/978-3-319-75241-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
146
Souferi B, Emerson MM. Quantitative analysis of the ThrbCRM1-centered gene regulatory network. Biol Open 2019;8:bio.039115. [PMID: 30971410 PMCID: PMC6504004 DOI: 10.1242/bio.039115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
147
Whole mount in situ hybridization techniques for analysis of the spatial distribution of mRNAs in sea urchin embryos and early larvae. Methods Cell Biol 2019. [PMID: 30948007 DOI: 10.1016/bs.mcb.2019.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
148
Mrázek J, Karls AC. In silico simulations of occurrence of transcription factor binding sites in bacterial genomes. BMC Evol Biol 2019;19:67. [PMID: 30823869 PMCID: PMC6397444 DOI: 10.1186/s12862-019-1381-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/01/2019] [Indexed: 11/16/2022]  Open
149
Approximate kernel reconstruction for time-varying networks. BioData Min 2019;12:5. [PMID: 30774716 PMCID: PMC6364395 DOI: 10.1186/s13040-019-0192-1] [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: 08/10/2018] [Accepted: 01/14/2019] [Indexed: 11/10/2022]  Open
150
Cussat-Blanc S, Harrington K, Banzhaf W. Artificial Gene Regulatory Networks-A Review. ARTIFICIAL LIFE 2019;24:296-328. [PMID: 30681915 DOI: 10.1162/artl_a_00267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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