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For: Garcia V, Feldman MW, Regoes RR. Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection. PLoS Comput Biol 2016;12:e1004721. [PMID: 26829720 PMCID: PMC4735108 DOI: 10.1371/journal.pcbi.1004721] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Muzquiz R, Jamshidi C, Conroy DW, Jaroniec CP, Foster MP. Insights into Ligand-Mediated Activation of an Oligomeric Ring-Shaped Gene-Regulatory Protein from Solution- and Solid-State NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593404. [PMID: 38798368 PMCID: PMC11118279 DOI: 10.1101/2024.05.10.593404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
2
Dupic T, Phillips AM, Desai MM. Protein sequence landscapes are not so simple: on reference-free versus reference-based inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577800. [PMID: 38352387 PMCID: PMC10862727 DOI: 10.1101/2024.01.29.577800] [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: 02/23/2024]
3
Pinto SR, Uchida N. Tonic dopamine and biases in value learning linked through a biologically inspired reinforcement learning model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566580. [PMID: 38014087 PMCID: PMC10680794 DOI: 10.1101/2023.11.10.566580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
4
Weaver DT, King ES, Maltas J, Scott JG. Reinforcement Learning informs optimal treatment strategies to limit antibiotic resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523765. [PMID: 36711676 PMCID: PMC9882109 DOI: 10.1101/2023.01.12.523765] [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: 01/15/2023]
5
Ahn JC, Coyle SM. Comparative profiling of cellular gait on adhesive micropatterns defines statistical patterns of activity that underlie native and cancerous cell dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564389. [PMID: 37961146 PMCID: PMC10634873 DOI: 10.1101/2023.10.27.564389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
6
Hassani SA, Womelsdorf T. Noradrenergic alpha-2a Receptor Stimulation Enhances Prediction Error Signaling in Anterior Cingulate Cortex and Striatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564052. [PMID: 37961384 PMCID: PMC10634832 DOI: 10.1101/2023.10.25.564052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
7
Kleinman M, Wang T, Xiao D, Feghhi E, Lee K, Carr N, Li Y, Hadidi N, Chandrasekaran C, Kao JC. A cortical information bottleneck during decision-making. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548742. [PMID: 37502862 PMCID: PMC10369960 DOI: 10.1101/2023.07.12.548742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
8
Amin MR, Hasan M, Arnab SP, DeGiorgio M. Tensor decomposition based feature extraction and classification to detect natural selection from genomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.527731. [PMID: 37034767 PMCID: PMC10081272 DOI: 10.1101/2023.03.27.527731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
9
Vahidi P, Sani OG, Shanechi MM. Modeling and dissociation of intrinsic and input-driven neural population dynamics underlying behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532554. [PMID: 36993213 PMCID: PMC10055042 DOI: 10.1101/2023.03.14.532554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
10
Rife Magalis B, Autissier P, Williams KC, Chen X, Browne C, Salemi M. Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host. Front Immunol 2021;12:709962. [PMID: 34691023 PMCID: PMC8527182 DOI: 10.3389/fimmu.2021.709962] [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: 05/14/2021] [Accepted: 09/21/2021] [Indexed: 01/18/2023]  Open
11
Andriamandimby SF, Brook CE, Razanazatovo N, Rakotondramanga JM, Rasambainarivo F, Raharimanga V, Razanajatovo IM, Mangahasimbola R, Razafindratsimandresy R, Randrianarisoa S, Bernardson B, Rabarison JH, Randrianarisoa M, Nasolo FS, Rabetombosoa RM, Randremanana R, Héraud JM, Dussart P. Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.06.21259473. [PMID: 34268517 PMCID: PMC8282106 DOI: 10.1101/2021.07.06.21259473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
12
Walsh C, Tafforeau P, Wagner WL, Jafree DJ, Bellier A, Werlein C, Kühnel MP, Boller E, Walker-Samuel S, Robertus JL, Long DA, Jacob J, Marussi S, Brown E, Holroyd N, Jonigk DD, Ackermann M, Lee PD. Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429481. [PMID: 33564772 PMCID: PMC7872374 DOI: 10.1101/2021.02.03.429481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
13
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection. PLoS Pathog 2020;16:e1008171. [PMID: 32492061 PMCID: PMC7295245 DOI: 10.1371/journal.ppat.1008171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 06/15/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022]  Open
14
Garcia V, Glassberg EC, Harpak A, Feldman MW. Clonal interference can cause wavelet-like oscillations of multilocus linkage disequilibrium. J R Soc Interface 2019;15:rsif.2017.0921. [PMID: 29563246 DOI: 10.1098/rsif.2017.0921] [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: 12/07/2017] [Accepted: 02/23/2018] [Indexed: 11/12/2022]  Open
15
Baral S, Raja R, Sen P, Dixit NM. Towards multiscale modeling of the CD8+ T cell response to viral infections. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019;11:e1446. [PMID: 30811096 PMCID: PMC6614031 DOI: 10.1002/wsbm.1446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/22/2022]
16
Zinger T, Gelbart M, Miller D, Pennings PS, Stern A. Inferring population genetics parameters of evolving viruses using time-series data. Virus Evol 2019;5:vez011. [PMID: 31191979 PMCID: PMC6555871 DOI: 10.1093/ve/vez011] [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] [Indexed: 12/16/2022]  Open
17
Conway JM, Ribeiro RM. Modeling the immune response to HIV infection. ACTA ACUST UNITED AC 2018;12:61-69. [PMID: 31463420 DOI: 10.1016/j.coisb.2018.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
18
Ganusov VV. Time Intervals in Sequence Sampling, Not Data Modifications, Have a Major Impact on Estimates of HIV Escape Rates. Viruses 2018;10:v10030099. [PMID: 29495443 PMCID: PMC5869492 DOI: 10.3390/v10030099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/20/2018] [Accepted: 02/22/2018] [Indexed: 12/31/2022]  Open
19
Yang Y, Ganusov VV. Kinetics of HIV-Specific CTL Responses Plays a Minimal Role in Determining HIV Escape Dynamics. Front Immunol 2018;9:140. [PMID: 29472921 PMCID: PMC5810297 DOI: 10.3389/fimmu.2018.00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/16/2018] [Indexed: 11/13/2022]  Open
20
Reeves DB, Peterson CW, Kiem HP, Schiffer JT. Autologous Stem Cell Transplantation Disrupts Adaptive Immune Responses during Rebound Simian/Human Immunodeficiency Virus Viremia. J Virol 2017;91:e00095-17. [PMID: 28404854 PMCID: PMC5469274 DOI: 10.1128/jvi.00095-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]  Open
21
Garcia V, Feldman MW. Within-Epitope Interactions Can Bias CTL Escape Estimation in Early HIV Infection. Front Immunol 2017;8:423. [PMID: 28507544 PMCID: PMC5410659 DOI: 10.3389/fimmu.2017.00423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/27/2017] [Indexed: 01/03/2023]  Open
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