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For: Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci 2015;370:20140235. [PMID: 26194749 PMCID: PMC4528412 DOI: 10.1098/rstb.2014.0235] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 01/05/2023]  Open
Number Cited by Other Article(s)
1
Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023;44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
2
Steiner MC, Novembre J. Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution. PLoS Genet 2022;18:e1010391. [PMID: 36137003 PMCID: PMC9498967 DOI: 10.1371/journal.pgen.1010391] [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] [Indexed: 11/18/2022]  Open
3
Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022;2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
4
Matsen FA, Ralph PL. Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency. J Comput Biol 2022;29:802-824. [PMID: 35776513 PMCID: PMC9419934 DOI: 10.1089/cmb.2021.0644] [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] [Indexed: 11/12/2022]  Open
5
Lupo C, Spisak N, Walczak AM, Mora T. Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies. PLoS Comput Biol 2022;18:e1010167. [PMID: 35653375 PMCID: PMC9197026 DOI: 10.1371/journal.pcbi.1010167] [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: 12/15/2021] [Revised: 06/14/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022]  Open
6
Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints. Proc Natl Acad Sci U S A 2022;119:2113512119. [PMID: 35177475 PMCID: PMC8872716 DOI: 10.1073/pnas.2113512119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/15/2022]  Open
7
Swiatczak B. Struggle within: evolution and ecology of somatic cell populations. Cell Mol Life Sci 2021;78:6797-6806. [PMID: 34477897 PMCID: PMC11073125 DOI: 10.1007/s00018-021-03931-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/31/2021] [Accepted: 08/25/2021] [Indexed: 12/19/2022]
8
Sheng J, Wang S. Coevolutionary transitions emerging from flexible molecular recognition and eco-evolutionary feedback. iScience 2021;24:102861. [PMID: 34401660 PMCID: PMC8353512 DOI: 10.1016/j.isci.2021.102861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/16/2021] [Accepted: 07/13/2021] [Indexed: 01/16/2023]  Open
9
Burmeister AR, Hansen E, Cunningham JJ, Rego EH, Turner PE, Weitz JS, Hochberg ME. Fighting microbial pathogens by integrating host ecosystem interactions and evolution. Bioessays 2020;43:e2000272. [PMID: 33377530 DOI: 10.1002/bies.202000272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022]
10
Spisak N, Walczak AM, Mora T. Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data. Nucleic Acids Res 2020;48:10702-10712. [PMID: 33035336 PMCID: PMC7641750 DOI: 10.1093/nar/gkaa825] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 01/23/2023]  Open
11
Sachdeva V, Husain K, Sheng J, Wang S, Murugan A. Tuning environmental timescales to evolve and maintain generalists. Proc Natl Acad Sci U S A 2020;117:12693-12699. [PMID: 32457160 PMCID: PMC7293598 DOI: 10.1073/pnas.1914586117] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
12
Zelner J, Petrie JG, Trangucci R, Martin ET, Monto AS. Effects of Sequential Influenza A(H1N1)pdm09 Vaccination on Antibody Waning. J Infect Dis 2020;220:12-19. [PMID: 30722022 DOI: 10.1093/infdis/jiz055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/30/2019] [Indexed: 12/17/2022]  Open
13
Bradt V, Malafa S, von Braun A, Jarmer J, Tsouchnikas G, Medits I, Wanke K, Karrer U, Stiasny K, Heinz FX. Pre-existing yellow fever immunity impairs and modulates the antibody response to tick-borne encephalitis vaccination. NPJ Vaccines 2019;4:38. [PMID: 31508246 PMCID: PMC6731309 DOI: 10.1038/s41541-019-0133-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/19/2019] [Indexed: 12/29/2022]  Open
14
Adams RM, Kinney JB, Walczak AM, Mora T. Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy. Cell Syst 2019;8:86-93.e3. [PMID: 30611676 PMCID: PMC6487650 DOI: 10.1016/j.cels.2018.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/12/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022]
15
Balelli I, Milišić V, Wainrib G. Random walks on binary strings applied to the somatic hypermutation of B-cells. Math Biosci 2018;300:168-186. [DOI: 10.1016/j.mbs.2018.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/19/2018] [Indexed: 11/29/2022]
16
Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front Immunol 2018;9:224. [PMID: 29515569 PMCID: PMC5826328 DOI: 10.3389/fimmu.2018.00224] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022]  Open
17
Mora T. [IGoR: a tool for learning and simulating the random generation of antigen receptors]. Biol Aujourdhui 2018;211:229-231. [PMID: 29412133 DOI: 10.1051/jbio/2017033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Indexed: 06/08/2023]
18
Kulp DW, Steichen JM, Pauthner M, Hu X, Schiffner T, Liguori A, Cottrell CA, Havenar-Daughton C, Ozorowski G, Georgeson E, Kalyuzhniy O, Willis JR, Kubitz M, Adachi Y, Reiss SM, Shin M, de Val N, Ward AB, Crotty S, Burton DR, Schief WR. Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding. Nat Commun 2017;8:1655. [PMID: 29162799 PMCID: PMC5698488 DOI: 10.1038/s41467-017-01549-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022]  Open
19
Khavrutskii IV, Chaudhury S, Stronsky SM, Lee DW, Benko JG, Wallqvist A, Bavari S, Cooper CL. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses. Front Immunol 2017;8:910. [PMID: 28855898 PMCID: PMC5557726 DOI: 10.3389/fimmu.2017.00910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022]  Open
20
Carter MJ, Mitchell RM, Meyer Sauteur PM, Kelly DF, Trück J. The Antibody-Secreting Cell Response to Infection: Kinetics and Clinical Applications. Front Immunol 2017;8:630. [PMID: 28620385 PMCID: PMC5451496 DOI: 10.3389/fimmu.2017.00630] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/12/2017] [Indexed: 01/15/2023]  Open
21
Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development. Cell Rep 2017;19:1467-1478. [DOI: 10.1016/j.celrep.2017.04.054] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 03/21/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022]  Open
22
Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol 2017;22:105-111. [PMID: 28088686 DOI: 10.1016/j.coviro.2016.12.004] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/25/2022]
23
Varki A. Biological roles of glycans. Glycobiology 2017;27:3-49. [PMID: 27558841 PMCID: PMC5884436 DOI: 10.1093/glycob/cww086] [Citation(s) in RCA: 1693] [Impact Index Per Article: 211.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023]  Open
24
Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections. PLoS Genet 2016;12:e1006171. [PMID: 27442127 PMCID: PMC4956326 DOI: 10.1371/journal.pgen.1006171] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023]  Open
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