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For: Bloom JD. Software for the analysis and visualization of deep mutational scanning data. BMC Bioinformatics 2015;16:168. [PMID: 25990960 DOI: 10.1186/s12859-015-0590-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Hong Z, Shimagaki KS, Barton JP. popDMS infers mutation effects from deep mutational scanning data. Bioinformatics 2024;40:btae499. [PMID: 39115383 PMCID: PMC11335369 DOI: 10.1093/bioinformatics/btae499] [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: 02/19/2024] [Revised: 07/10/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024]  Open
2
Álvarez-Rodríguez B, Velandia-Álvarez S, Toft C, Geller R. Mapping mutational fitness effects across the coxsackievirus B3 proteome reveals distinct profiles of mutation tolerability. PLoS Biol 2024;22:e3002709. [PMID: 39012844 PMCID: PMC11251597 DOI: 10.1371/journal.pbio.3002709] [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: 04/03/2024] [Accepted: 06/13/2024] [Indexed: 07/18/2024]  Open
3
Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, Brooke CB. Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin. Virus Evol 2024;10:veae046. [PMID: 38915760 PMCID: PMC11196192 DOI: 10.1093/ve/veae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 06/26/2024]  Open
4
Yu Y, Kass MA, Zhang M, Youssef N, Freije CA, Brock KP, Aguado LC, Seifert LL, Venkittu S, Hong X, Shlomai A, de Jong YP, Marks DS, Rice CM, Schneider WM. Deep mutational scanning of hepatitis B virus reveals a mechanism for cis-preferential reverse transcription. Cell 2024;187:2735-2745.e12. [PMID: 38723628 PMCID: PMC11127778 DOI: 10.1016/j.cell.2024.04.008] [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] [Received: 08/02/2023] [Revised: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
5
Claussnitzer M, Parikh VN, Wagner AH, Arbesfeld JA, Bult CJ, Firth HV, Muffley LA, Nguyen Ba AN, Riehle K, Roth FP, Tabet D, Bolognesi B, Glazer AM, Rubin AF. Minimum information and guidelines for reporting a multiplexed assay of variant effect. Genome Biol 2024;25:100. [PMID: 38641812 PMCID: PMC11027375 DOI: 10.1186/s13059-024-03223-9] [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] [Received: 06/18/2023] [Accepted: 03/25/2024] [Indexed: 04/21/2024]  Open
6
Liu T, Reiser WK, Tan TJC, Lv H, Rivera-Cardona J, Heimburger K, Wu NC, Brooke CB. Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585603. [PMID: 38562808 PMCID: PMC10983940 DOI: 10.1101/2024.03.18.585603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
7
Hong Z, Barton JP. popDMS infers mutation effects from deep mutational scanning data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577759. [PMID: 38352383 PMCID: PMC10862717 DOI: 10.1101/2024.01.29.577759] [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: 02/21/2024]
8
Kikawa C, Cartwright-Acar CH, Stuart JB, Contreras M, Levoir LM, Evans MJ, Bloom JD, Goo L. The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies. J Virol 2023;97:e0141423. [PMID: 37943046 PMCID: PMC10688354 DOI: 10.1128/jvi.01414-23] [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] [Received: 09/11/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]  Open
9
Li Y, Arcos S, Sabsay KR, te Velthuis AJW, Lauring AS. Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein. J Virol 2023;97:e0132923. [PMID: 37882522 PMCID: PMC10688322 DOI: 10.1128/jvi.01329-23] [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] [Received: 08/28/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023]  Open
10
Maes S, Deploey N, Peelman F, Eyckerman S. Deep mutational scanning of proteins in mammalian cells. CELL REPORTS METHODS 2023;3:100641. [PMID: 37963462 PMCID: PMC10694495 DOI: 10.1016/j.crmeth.2023.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
11
Zhang Y, Cui P, Shi J, Chen Y, Zeng X, Jiang Y, Tian G, Li C, Chen H, Kong H, Deng G. Key Amino Acid Residues That Determine the Antigenic Properties of Highly Pathogenic H5 Influenza Viruses Bearing the Clade 2.3.4.4 Hemagglutinin Gene. Viruses 2023;15:2249. [PMID: 38005926 PMCID: PMC10674173 DOI: 10.3390/v15112249] [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] [Received: 10/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]  Open
12
Schommers P, Kim DS, Schlotz M, Kreer C, Eggeling R, Hake A, Stecher M, Park J, Radford CE, Dingens AS, Ercanoglu MS, Gruell H, Odidika S, Dahlhaus M, Gieselmann L, Ahmadov E, Lawong RY, Heger E, Knops E, Wyen C, Kümmerle T, Römer K, Scholten S, Wolf T, Stephan C, Suárez I, Raju N, Adhikari A, Esser S, Streeck H, Duerr R, Nanfack AJ, Zolla-Pazner S, Geldmacher C, Geisenberger O, Kroidl A, William W, Maganga L, Ntinginya NE, Georgiev IS, Vehreschild JJ, Hoelscher M, Fätkenheuer G, Lavinder JJ, Bloom JD, Seaman MS, Lehmann C, Pfeifer N, Georgiou G, Klein F. Dynamics and durability of HIV-1 neutralization are determined by viral replication. Nat Med 2023;29:2763-2774. [PMID: 37957379 PMCID: PMC10667105 DOI: 10.1038/s41591-023-02582-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 09/07/2023] [Indexed: 11/15/2023]
13
Álvarez-Rodríguez B, Buceta J, Geller R. Comprehensive profiling of neutralizing polyclonal sera targeting coxsackievirus B3. Nat Commun 2023;14:6417. [PMID: 37828013 PMCID: PMC10570382 DOI: 10.1038/s41467-023-42144-2] [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] [Received: 01/28/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]  Open
14
Busia A, Listgarten J. MBE: model-based enrichment estimation and prediction for differential sequencing data. Genome Biol 2023;24:218. [PMID: 37784130 PMCID: PMC10544408 DOI: 10.1186/s13059-023-03058-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]  Open
15
Kikawa C, Cartwright-Acar CH, Stuart JB, Contreras M, Levoir LM, Evans MJ, Bloom JD, Goo L. The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557606. [PMID: 37808848 PMCID: PMC10557620 DOI: 10.1101/2023.09.13.557606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
16
Christensen S, Wernersson C, André I. Facile Method for High-throughput Identification of Stabilizing Mutations. J Mol Biol 2023;435:168209. [PMID: 37479080 DOI: 10.1016/j.jmb.2023.168209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
17
Smith MD, Case MA, Makowski EK, Tessier PM. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. Bioinformatics 2023;39:btad446. [PMID: 37478351 PMCID: PMC10477941 DOI: 10.1093/bioinformatics/btad446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/21/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023]  Open
18
Smith MD, Case MA, Makowski EK, Tessier PM. Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548448. [PMID: 37503142 PMCID: PMC10369870 DOI: 10.1101/2023.07.10.548448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
19
Hoskins I, Sun S, Cote A, Roth FP, Cenik C. satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect. Genome Biol 2023;24:82. [PMID: 37081510 PMCID: PMC10116734 DOI: 10.1186/s13059-023-02922-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/04/2023] [Indexed: 04/22/2023]  Open
20
Sun T, Rosenberg BR, Chung H, Rice CM. Identification of ADAR1 p150 and p110 Associated Edit Sites. Methods Mol Biol 2023;2651:285-294. [PMID: 36892775 DOI: 10.1007/978-1-0716-3084-6_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
21
Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annu Rev Genet 2022;56:441-465. [PMID: 36055970 DOI: 10.1146/annurev-genet-072920-032107] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
22
Azbukina N, Zharikova A, Ramensky V. Intragenic compensation through the lens of deep mutational scanning. Biophys Rev 2022;14:1161-1182. [PMID: 36345285 PMCID: PMC9636336 DOI: 10.1007/s12551-022-01005-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 12/20/2022]  Open
23
Ding D, Green AG, Wang B, Lite TLV, Weinstein EN, Marks DS, Laub MT. Co-evolution of interacting proteins through non-contacting and non-specific mutations. Nat Ecol Evol 2022;6:590-603. [PMID: 35361892 PMCID: PMC9090974 DOI: 10.1038/s41559-022-01688-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/31/2022] [Indexed: 01/08/2023]
24
Tareen A, Kooshkbaghi M, Posfai A, Ireland WT, McCandlish DM, Kinney JB. MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect. Genome Biol 2022;23:98. [PMID: 35428271 PMCID: PMC9011994 DOI: 10.1186/s13059-022-02661-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022]  Open
25
The endoplasmic reticulum proteostasis network profoundly shapes the protein sequence space accessible to HIV envelope. PLoS Biol 2022;20:e3001569. [PMID: 35180219 PMCID: PMC8906867 DOI: 10.1371/journal.pbio.3001569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 03/09/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]  Open
26
Guthmiller JJ, Han J, Utset HA, Li L, Lan LYL, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, de la Peña AT, Rosado V, Dugan HL, Zheng NY, Tepora ME, Bitar DJ, Changrob S, Strohmeier S, Huang M, García-Sastre A, Liedl KR, Bloom JD, Nachbagauer R, Palese P, Krammer F, Coughlan L, Ward AB, Wilson PC. Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Nature 2022;602:314-320. [PMID: 34942633 PMCID: PMC8828479 DOI: 10.1038/s41586-021-04356-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
27
Dubé AK, Dandage R, Dibyachintan S, Dionne U, Després PC, Landry CR. Deep Mutational Scanning of Protein-Protein Interactions Between Partners Expressed from Their Endogenous Loci In Vivo. Methods Mol Biol 2022;2477:237-259. [PMID: 35524121 DOI: 10.1007/978-1-0716-2257-5_14] [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: 06/14/2023]
28
Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021;43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
29
Intelligent host engineering for metabolic flux optimisation in biotechnology. Biochem J 2021;478:3685-3721. [PMID: 34673920 PMCID: PMC8589332 DOI: 10.1042/bcj20210535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
30
Youssef N, Susko E, Roger AJ, Bielawski JP. Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work. Protein Sci 2021;30:2009-2028. [PMID: 34322924 PMCID: PMC8442975 DOI: 10.1002/pro.4161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/08/2022]
31
Findlay GM. Linking genome variants to disease: scalable approaches to test the functional impact of human mutations. Hum Mol Genet 2021;30:R187-R197. [PMID: 34338757 PMCID: PMC8490018 DOI: 10.1093/hmg/ddab219] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022]  Open
32
McDonnell MM, Karvonen SC, Gaba A, Flath B, Chelico L, Emerman M. Highly-potent, synthetic APOBEC3s restrict HIV-1 through deamination-independent mechanisms. PLoS Pathog 2021;17:e1009523. [PMID: 34170969 PMCID: PMC8266076 DOI: 10.1371/journal.ppat.1009523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/08/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023]  Open
33
Burton TD, Eyre NS. Applications of Deep Mutational Scanning in Virology. Viruses 2021;13:1020. [PMID: 34071591 PMCID: PMC8227372 DOI: 10.3390/v13061020] [Citation(s) in RCA: 3] [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: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]  Open
34
Dingens AS, Pratap P, Malone K, Hilton SK, Ketas T, Cottrell CA, Overbaugh J, Moore JP, Klasse PJ, Ward AB, Bloom JD. High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination. eLife 2021;10:e64281. [PMID: 33438580 PMCID: PMC7864656 DOI: 10.7554/elife.64281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/12/2021] [Indexed: 01/01/2023]  Open
35
Mattenberger F, Latorre V, Tirosh O, Stern A, Geller R. Globally defining the effects of mutations in a picornavirus capsid. eLife 2021;10:64256. [PMID: 33432927 PMCID: PMC7861617 DOI: 10.7554/elife.64256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]  Open
36
Song H, Bremer BJ, Hinds EC, Raskutti G, Romero PA. Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning. Cell Syst 2020;12:92-101.e8. [PMID: 33212013 DOI: 10.1016/j.cels.2020.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 08/13/2020] [Accepted: 10/22/2020] [Indexed: 10/22/2022]
37
Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020;9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023]  Open
38
Identification of Antibodies Targeting the H3N2 Hemagglutinin Receptor Binding Site following Vaccination of Humans. Cell Rep 2020;29:4460-4470.e8. [PMID: 31875553 PMCID: PMC6953393 DOI: 10.1016/j.celrep.2019.11.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/26/2019] [Accepted: 11/20/2019] [Indexed: 11/26/2022]  Open
39
DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies. Genome Biol 2020;21:207. [PMID: 32799905 PMCID: PMC7429474 DOI: 10.1186/s13059-020-02091-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/05/2020] [Indexed: 12/30/2022]  Open
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Hilton SK, Huddleston J, Black A, North K, Dingens AS, Bedford T, Bloom JD. dms-view: Interactive visualization tool for deep mutational scanning data. JOURNAL OF OPEN SOURCE SOFTWARE 2020;5:2353. [PMID: 34189395 PMCID: PMC8237788 DOI: 10.21105/joss.02353] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Saad-Roy CM, Arinaminpathy N, Wingreen NS, Levin SA, Akey JM, Grenfell BT. Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans. PLoS Comput Biol 2020;16:e1007892. [PMID: 32584807 PMCID: PMC7316228 DOI: 10.1371/journal.pcbi.1007892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/21/2020] [Indexed: 01/01/2023]  Open
42
Wu NC, Thompson AJ, Lee JM, Su W, Arlian BM, Xie J, Lerner RA, Yen HL, Bloom JD, Wilson IA. Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses. Science 2020;368:1335-1340. [PMID: 32554590 PMCID: PMC7412937 DOI: 10.1126/science.aaz5143] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
43
Klesmith JR, Hackel BJ. Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit. Bioinformatics 2020;35:2707-2712. [PMID: 30590444 DOI: 10.1093/bioinformatics/bty1042] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/06/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]  Open
44
APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1. mBio 2020;11:mBio.00737-20. [PMID: 32345636 PMCID: PMC7188997 DOI: 10.1128/mbio.00737-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
45
Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ, Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD, Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schön A, Todd JP, Wang S, Wei H, Wu W, Mullikin JC, Bailer RT, Doria-Rose NA, Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS, Shapiro L, Kwong PD, Mascola JR. Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Cell 2020;178:567-584.e19. [PMID: 31348886 DOI: 10.1016/j.cell.2019.06.030] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/03/2019] [Accepted: 06/19/2019] [Indexed: 01/09/2023]
46
Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Viruses 2020;12:v12020241. [PMID: 32098152 PMCID: PMC7077290 DOI: 10.3390/v12020241] [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: 12/27/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 11/24/2022]  Open
47
Schommers P, Gruell H, Abernathy ME, Tran MK, Dingens AS, Gristick HB, Barnes CO, Schoofs T, Schlotz M, Vanshylla K, Kreer C, Weiland D, Holtick U, Scheid C, Valter MM, van Gils MJ, Sanders RW, Vehreschild JJ, Cornely OA, Lehmann C, Fätkenheuer G, Seaman MS, Bloom JD, Bjorkman PJ, Klein F. Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Cell 2020;180:471-489.e22. [PMID: 32004464 PMCID: PMC7042716 DOI: 10.1016/j.cell.2020.01.010] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/05/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023]
48
Building artificial genetic circuits to understand protein function. Methods Enzymol 2020;633:231-250. [DOI: 10.1016/bs.mie.2019.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Atkinson JT, Jones AM, Nanda V, Silberg JJ. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng Des Sel 2019;32:489-501. [PMID: 32626892 PMCID: PMC7462040 DOI: 10.1093/protein/gzaa012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 01/08/2023]  Open
50
Deep Mutational Scanning Comprehensively Maps How Zika Envelope Protein Mutations Affect Viral Growth and Antibody Escape. J Virol 2019;93:JVI.01291-19. [PMID: 31511387 DOI: 10.1128/jvi.01291-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022]  Open
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