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For: Likhoshvai VA, Khlebodarova TM, Bazhan SI, Gainova IA, Chereshnev VA, Bocharov GA. Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components. BMC Genomics 2014;15 Suppl 12:S1. [PMID: 25564443 PMCID: PMC4303933 DOI: 10.1186/1471-2164-15-s12-s1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Giaretta A. Frequency response in splicing regulation under mRNA auto-depletion control. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022;2022:2248-2253. [PMID: 36083926 DOI: 10.1109/embc48229.2022.9871147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
2
Giaretta A. Stochasticity in transcriptional, splicing and translational regulations in time and frequency domains. Biosystems 2022;212:104595. [DOI: 10.1016/j.biosystems.2021.104595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/13/2021] [Accepted: 12/22/2021] [Indexed: 11/02/2022]
3
Giaretta A. Frequency analysis of splicing regulation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021;2021:4487-4492. [PMID: 34892215 DOI: 10.1109/embc46164.2021.9629722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
4
Markov Chain-Based Stochastic Modelling of HIV-1 Life Cycle in a CD4 T Cell. MATHEMATICS 2021. [DOI: 10.3390/math9172025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
5
Likhoshvai VA, Khlebodarova TM. Evolution and extinction can occur rapidly: a modeling approach. PeerJ 2021;9:e11130. [PMID: 33954033 PMCID: PMC8051336 DOI: 10.7717/peerj.11130] [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: 11/04/2020] [Accepted: 02/27/2021] [Indexed: 11/25/2022]  Open
6
Orlov YL, Galieva ER, Tatarinova TV. Bioinformatics research at SBB-2019. BMC Bioinformatics 2020;21:366. [PMID: 32921301 PMCID: PMC7489004 DOI: 10.1186/s12859-020-03712-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
7
Viral Infection Dynamics Model Based on a Markov Process with Time Delay between Cell Infection and Progeny Production. MATHEMATICS 2020. [DOI: 10.3390/math8081207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
8
Giaretta A. A Minimal Stochastic Model of Transcriptional and Splicing Regulation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020;2020:2357-2360. [PMID: 33018480 DOI: 10.1109/embc44109.2020.9176735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
9
Modeling of the HIV-1 Life Cycle in Productively Infected Cells to Predict Novel Therapeutic Targets. Pathogens 2020;9:pathogens9040255. [PMID: 32244421 PMCID: PMC7238236 DOI: 10.3390/pathogens9040255] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022]  Open
10
DeMarino C, Cowen M, Pleet ML, Pinto DO, Khatkar P, Erickson J, Docken SS, Russell N, Reichmuth B, Phan T, Kuang Y, Anderson DM, Emelianenko M, Kashanchi F. Differences in Transcriptional Dynamics Between T-cells and Macrophages as Determined by a Three-State Mathematical Model. Sci Rep 2020;10:2227. [PMID: 32042107 PMCID: PMC7010665 DOI: 10.1038/s41598-020-59008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/17/2020] [Indexed: 12/18/2022]  Open
11
Orlov YL, Galieva ER, Melerzanov AV. Computer genomics research at the bioinformatics conference series in Novosibirsk. BMC Genomics 2019;20:537. [PMID: 31291908 PMCID: PMC6620193 DOI: 10.1186/s12864-019-5846-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
12
Orlov YL, Kochetov AV, Li G, Kolchanov NA. Genomics research at Bioinformatics of Genome Regulation and Structure\ Systems Biology (BGRS\SB) conferences in Novosibirsk. BMC Genomics 2019;20:322. [PMID: 32039700 PMCID: PMC7227187 DOI: 10.1186/s12864-019-5707-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
13
Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Sci Rep 2019;9:5139. [PMID: 30914719 PMCID: PMC6435700 DOI: 10.1038/s41598-019-41582-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/05/2019] [Indexed: 11/12/2022]  Open
14
Bocharov G, Meyerhans A, Bessonov N, Trofimchuk S, Volpert V. Interplay between reaction and diffusion processes in governing the dynamics of virus infections. J Theor Biol 2018;457:221-236. [PMID: 30170043 DOI: 10.1016/j.jtbi.2018.08.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 08/22/2018] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
15
Towards a Multiscale Model of Acute HIV Infection. COMPUTATION 2017. [DOI: 10.3390/computation5010006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
16
Bocharov G, Meyerhans A, Bessonov N, Trofimchuk S, Volpert V. Spatiotemporal Dynamics of Virus Infection Spreading in Tissues. PLoS One 2016;11:e0168576. [PMID: 27997613 PMCID: PMC5173377 DOI: 10.1371/journal.pone.0168576] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/03/2016] [Indexed: 12/21/2022]  Open
17
Jackson PE, Tebit DM, Rekosh D, Hammarskjold ML. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates. AIDS Res Hum Retroviruses 2016;32:923-34. [PMID: 27147495 DOI: 10.1089/aid.2016.0047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
18
Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016;7:470-86. [PMID: 26929078 DOI: 10.1002/wrna.1342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/28/2023]
19
Distinct promoter activation mechanisms modulate noise-driven HIV gene expression. Sci Rep 2015;5:17661. [PMID: 26666681 PMCID: PMC4678399 DOI: 10.1038/srep17661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/30/2015] [Indexed: 12/11/2022]  Open
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