-
1
-
-
84924253559
-
High-throughput profiling of point mutations across the HIV-1 genome
-
PMID: 25522661
-
Al-Mawsawi LQ, Wu NC, Olson CA, Shi VC, Qi H, Zheng X, Wu TT, Sun R. 2014. High-throughput profiling of point mutations across the HIV-1 genome. Retrovirology 11:124. DOI: https://doi.org/10.1186/s12977-014-0124-6, PMID: 25522661
-
(2014)
Retrovirology
, vol.11
, pp. 124
-
-
Al-Mawsawi, LQ1
Wu, NC2
Olson, CA3
Shi, VC4
Qi, H5
Zheng, X6
Wu, TT7
Sun, R.8
-
2
-
-
0025267919
-
Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera
-
PMID: 2328092
-
Albert J, Abrahamsson B, Nagy K, Aurelius E, Gaines H, Nyström G, Fenyö EM. 1990. Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera. Aids 4:107-112. DOI: https://doi.org/10.1097/00002030-199002000-00002, PMID: 2328092
-
(1990)
Aids
, vol.4
, pp. 107-112
-
-
Albert, J1
Abrahamsson, B2
Nagy, K3
Aurelius, E4
Gaines, H5
Nyström, G6
Fenyö, EM.7
-
3
-
-
77954191991
-
Structural conservation predominates over sequence variability in the crown of HIV type 1‘s V3 loop
-
PMID: 20560796
-
Almond D, Kimura T, Kong X, Swetnam J, Zolla-Pazner S, Cardozo T. 2010. Structural conservation predominates over sequence variability in the crown of HIV type 1‘s V3 loop. AIDS Research and Human Retroviruses 26:717-723. DOI: https://doi.org/10.1089/aid.2009.0254, PMID: 20560796
-
(2010)
AIDS Research and Human Retroviruses
, vol.26
, pp. 717-723
-
-
Almond, D1
Kimura, T2
Kong, X3
Swetnam, J4
Zolla-Pazner, S5
Cardozo, T.6
-
4
-
-
84891364264
-
Mutational effects on stability are largely conserved during protein evolution
-
PMID: 24324165
-
Ashenberg O, Gong LI, Bloom JD. 2013. Mutational effects on stability are largely conserved during protein evolution. PNAS 110:21071-21076. DOI: https://doi.org/10.1073/pnas.1314781111, PMID: 24324165
-
(2013)
PNAS
, vol.110
, pp. 21071-21076
-
-
Ashenberg, O1
Gong, LI2
Bloom, JD.3
-
5
-
-
84923166404
-
Scaling laws describe memories of host-pathogen riposte in the HIV population
-
PMID: 25646424
-
Barton JP, Kardar M, Chakraborty AK. 2015. Scaling laws describe memories of host-pathogen riposte in the HIV population. PNAS 112:1965-1970. DOI: https://doi.org/10.1073/pnas.1415386112, PMID: 25646424
-
(2015)
PNAS
, vol.112
, pp. 1965-1970
-
-
Barton, JP1
Kardar, M2
Chakraborty, AK.3
-
6
-
-
84943806240
-
Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins
-
PMID: 26445980
-
Bazykin GA. 2015. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins. Biology Letters 11:20150315. DOI: https://doi.org/10.1098/rsbl.2015.0315, PMID: 26445980
-
(2015)
Biology Letters
, vol.11
, pp. 20150315
-
-
Bazykin, GA.1
-
7
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B:289-300.
-
(1995)
Journal of the Royal Statistical Society, Series B
, pp. 289-300
-
-
Benjamini, Y1
Hochberg, Y.2
-
8
-
-
0033985999
-
A recombinant human immunodeficiency virus type 1 envelope glycoprotein complex stabilized by an intermolecular disulfide bond between the gp120 and gp41 subunits is an antigenic mimic of the trimeric virion-associated structure
-
PMID: 10623724
-
Binley JM, Sanders RW, Clas B, Schuelke N, Master A, Guo Y, Kajumo F, Anselma DJ, Maddon PJ, Olson WC, Moore JP. 2000. A recombinant human immunodeficiency virus type 1 envelope glycoprotein complex stabilized by an intermolecular disulfide bond between the gp120 and gp41 subunits is an antigenic mimic of the trimeric virion-associated structure. Journal of Virology 74:627-643. DOI: https://doi.org/10.1128/JVI.74.2.627-643.2000, PMID: 10623724
-
(2000)
Journal of Virology
, vol.74
, pp. 627-643
-
-
Binley, JM1
Sanders, RW2
Clas, B3
Schuelke, N4
Master, A5
Guo, Y6
Kajumo, F7
Anselma, DJ8
Maddon, PJ9
Olson, WC10
Moore, JP.11
-
9
-
-
33645811495
-
Protein stability promotes evolvability
-
PMID: 16581913
-
Bloom JD, Labthavikul ST, Otey CR, Arnold FH. 2006. Protein stability promotes evolvability. PNAS 103:5869-5874. DOI: https://doi.org/10.1073/pnas.0510098103, PMID: 16581913
-
(2006)
PNAS
, vol.103
, pp. 5869-5874
-
-
Bloom, JD1
Labthavikul, ST2
Otey, CR3
Arnold, FH.4
-
10
-
-
84905001681
-
An experimentally determined evolutionary model dramatically improves phylogenetic fit
-
PMID: 24859245
-
Bloom JD. 2014a. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Molecular Biology and Evolution 31:1956-1978. DOI: https://doi.org/10.1093/molbev/msu173, PMID: 24859245
-
(2014)
Molecular Biology and Evolution
, vol.31
, pp. 1956-1978
-
-
Bloom, JD.1
-
11
-
-
84923357744
-
An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs
-
PMID: 25063439
-
Bloom JD. 2014b. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Molecular Biology and Evolution 31:2753-2769. DOI: https://doi.org/10.1093/molbev/msu220, PMID: 25063439
-
(2014)
Molecular Biology and Evolution
, vol.31
, pp. 2753-2769
-
-
Bloom, JD.1
-
12
-
-
84930207201
-
Software for the analysis and visualization of deep mutational scanning data
-
PMID: 25990960
-
Bloom JD. 2015. Software for the analysis and visualization of deep mutational scanning data. BMC Bioinformatics 16:168. DOI: https://doi.org/10.1186/s12859-015-0590-4, PMID: 25990960
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 168
-
-
Bloom, JD.1
-
13
-
-
85011382314
-
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
-
PMID: 28095902
-
Bloom JD. 2017. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biology Direct 12:1. DOI: https://doi.org/10.1186/s13062-016-0172-z, PMID: 28095902
-
(2017)
Biology Direct
, vol.12
, pp. 1
-
-
Bloom, JD.1
-
14
-
-
84920771763
-
Mutations in HIV-1 envelope that enhance entry with the macaque CD4 receptor alter antibody recognition by disrupting quaternary interactions within the trimer
-
PMID: 25378497
-
Boyd DF, Peterson D, Haggarty BS, Jordan AP, Hogan MJ, Goo L, Hoxie JA, Overbaugh J. 2015. Mutations in HIV-1 envelope that enhance entry with the macaque CD4 receptor alter antibody recognition by disrupting quaternary interactions within the trimer. Journal of Virology 89:894-907. DOI: https://doi.org/10.1128/JVI.02680-14, PMID: 25378497
-
(2015)
Journal of Virology
, vol.89
, pp. 894-907
-
-
Boyd, DF1
Peterson, D2
Haggarty, BS3
Jordan, AP4
Hogan, MJ5
Goo, L6
Hoxie, JA7
Overbaugh, J.8
-
15
-
-
27244460793
-
Antibody vs. HIV in a clash of evolutionary titans
-
PMID: 16219699
-
Burton DR, Stanfield RL, Wilson IA. 2005. Antibody vs. HIV in a clash of evolutionary titans. PNAS 102:14943-14948. DOI: https://doi.org/10.1073/pnas.0505126102, PMID: 16219699
-
(2005)
PNAS
, vol.102
, pp. 14943-14948
-
-
Burton, DR1
Stanfield, RL2
Wilson, IA.3
-
16
-
-
84875613641
-
Match criteria for human cell line authentication: where do we draw the line?
-
PMID: 23136038
-
Capes-Davis A, Reid YA, Kline MC, Storts DR, Strauss E, Dirks WG, Drexler HG, MacLeod RA, Sykes G, Kohara A, Nakamura Y, Elmore E, Nims RW, Alston-Roberts C, Barallon R, Los GV, Nardone RM, Price PJ, Steuer A, Thomson J, et al. 2013. Match criteria for human cell line authentication: where do we draw the line? International Journal of Cancer 132:2510-2519. DOI: https://doi.org/10.1002/ijc.27931, PMID: 23136038
-
(2013)
International Journal of Cancer
, vol.132
, pp. 2510-2519
-
-
Capes-Davis, A1
Reid, YA2
Kline, MC3
Storts, DR4
Strauss, E5
Dirks, WG6
Drexler, HG7
MacLeod, RA8
Sykes, G9
Kohara, A10
Nakamura, Y11
Elmore, E12
Nims, RW13
Alston-Roberts, C14
Barallon, R15
Los, GV16
Nardone, RM17
Price, PJ18
Steuer, A19
Thomson, J20
more..
-
17
-
-
0024421757
-
The cytoplasmic domain of simian immunodeficiency virus transmembrane protein modulates infectivity
-
PMID: 2778881
-
Chakrabarti L, Emerman M, Tiollais P, Sonigo P. 1989. The cytoplasmic domain of simian immunodeficiency virus transmembrane protein modulates infectivity. Journal of Virology 63:4395-4403. PMID: 2778881
-
(1989)
Journal of Virology
, vol.63
, pp. 4395-4403
-
-
Chakrabarti, L1
Emerman, M2
Tiollais, P3
Sonigo, P.4
-
18
-
-
0030970693
-
Core structure of gp41 from the HIV envelope glycoprotein
-
PMID: 9108481
-
Chan DC, Fass D, Berger JM, Kim PS. 1997. Core structure of gp41 from the HIV envelope glycoprotein. Cell 89: 263-273. DOI: https://doi.org/10.1016/S0092-8674(00)80205-6, PMID: 9108481
-
(1997)
Cell
, vol.89
, pp. 263-273
-
-
Chan, DC1
Fass, D2
Berger, JM3
Kim, PS.4
-
19
-
-
85014702390
-
Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints
-
PMID: 28262665
-
Chan YH, Venev SV, Zeldovich KB, Matthews CR. 2017. Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints. Nature Communications 8:14614. DOI: https://doi.org/10.1038/ncomms14614, PMID: 28262665
-
(2017)
Nature Communications
, vol.8
, pp. 14614
-
-
Chan, YH1
Venev, SV2
Zeldovich, KB3
Matthews, CR.4
-
20
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
PMID: 3709526
-
Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. The EMBO Journal 5:823. PMID: 3709526
-
(1986)
The EMBO Journal
, vol.5
, pp. 823
-
-
Chothia, C1
Lesk, AM.2
-
21
-
-
2142738304
-
WebLogo: a sequence logo generator
-
PMID: 15173120
-
Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Research 14:1188-1190. DOI: https://doi.org/10.1101/gr.849004, PMID: 15173120
-
(2004)
Genome Research
, vol.14
, pp. 1188-1190
-
-
Crooks, GE1
Hon, G2
Chandonia, JM3
Brenner, SE.4
-
22
-
-
77956641491
-
Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region
-
PMID: 20157005
-
da Silva J, Coetzer M, Nedellec R, Pastore C, Mosier DE. 2010. Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185:293-303. DOI: https://doi.org/10.1534/genetics.109.112458, PMID: 20157005
-
(2010)
Genetics
, vol.185
, pp. 293-303
-
-
da Silva, J1
Coetzer, M2
Nedellec, R3
Pastore, C4
Mosier, DE.5
-
23
-
-
84886011849
-
Isolate-specific differences in the conformational dynamics and antigenicity of HIV-1 gp120
-
PMID: 23903848
-
Davenport TM, Guttman M, Guo W, Cleveland B, Kahn M, Hu SL, Lee KK. 2013. Isolate-specific differences in the conformational dynamics and antigenicity of HIV-1 gp120. Journal of Virology 87:10855-10873. DOI: https://doi.org/10.1128/JVI.01535-13, PMID: 23903848
-
(2013)
Journal of Virology
, vol.87
, pp. 10855-10873
-
-
Davenport, TM1
Guttman, M2
Guo, W3
Cleveland, B4
Kahn, M5
Hu, SL6
Lee, KK.7
-
24
-
-
84950267324
-
Immunogenicity of Stabilized HIV-1 envelope trimers with reduced exposure of non-neutralizing epitopes
-
PMID: 26687358
-
de Taeye SW, Ozorowski G, Torrents de la Peña A, Guttman M, Julien JP, van den Kerkhof TL, Burger JA, Pritchard LK, Pugach P, Yasmeen A, Crampton J, Hu J, Bontjer I, Torres JL, Arendt H, DeStefano J, Koff WC, Schuitemaker H, Eggink D, Berkhout B, et al. 2015. Immunogenicity of Stabilized HIV-1 envelope trimers with reduced exposure of non-neutralizing epitopes. Cell 163:1702-1715. DOI: https://doi.org/10.1016/j.cell.2015.11.056, PMID: 26687358
-
(2015)
Cell
, vol.163
, pp. 1702-1715
-
-
de Taeye, SW1
Ozorowski, G2
Torrents de la Peña, A3
Guttman, M4
Julien, JP5
van den Kerkhof, TL6
Burger, JA7
Pritchard, LK8
Pugach, P9
Yasmeen, A10
Crampton, J11
Hu, J12
Bontjer, I13
Torres, JL14
Arendt, H15
DeStefano, J16
Koff, WC17
Schuitemaker, H18
Eggink, D19
Berkhout, B20
more..
-
25
-
-
85020234897
-
Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody
-
PMID: 28579254
-
Dingens AS, Haddox HK, Overbaugh J, Bloom JD. 2017. Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody. Cell Host & Microbe 21:777-787. DOI: https://doi.org/10.1016/j.chom.2017.05.003, PMID: 28579254
-
(2017)
Cell Host & Microbe
, vol.21
, pp. 777-787
-
-
Dingens, AS1
Haddox, HK2
Overbaugh, J3
Bloom, JD.4
-
26
-
-
84946144214
-
Site-specific amino acid preferences are mostly conserved in two closely related protein homologs
-
PMID: 26226986
-
Doud MB, Ashenberg O, Bloom JD. 2015. Site-specific amino acid preferences are mostly conserved in two closely related protein homologs. Molecular Biology and Evolution 32:2944-2960. DOI: https://doi.org/10.1093/molbev/msv167, PMID: 26226986
-
(2015)
Molecular Biology and Evolution
, vol.32
, pp. 2944-2960
-
-
Doud, MB1
Ashenberg, O2
Bloom, JD.3
-
27
-
-
84973131100
-
Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin
-
Doud M, Bloom J. 2016. Accurate measurement of the effects of all amino-acid mutations on influenza hemagglutinin. Viruses 8:155. DOI: https://doi.org/10.3390/v8060155
-
(2016)
Viruses
, vol.8
, pp. 155
-
-
Doud, M1
Bloom, J.2
-
28
-
-
85001967895
-
Saturation mutagenesis of the HIV-1 envelope CD4 binding loop reveals residues controlling distinct trimer conformations
-
PMID: 27820858
-
Duenas-Decamp M, Jiang L, Bolon D, Clapham PR. 2016. Saturation mutagenesis of the HIV-1 envelope CD4 binding loop reveals residues controlling distinct trimer conformations. PLOS Pathogens 12:e1005988. DOI: https://doi.org/10.1371/journal.ppat.1005988, PMID: 27820858
-
(2016)
PLOS Pathogens
, vol.12
, pp. e1005988
-
-
Duenas-Decamp, M1
Jiang, L2
Bolon, D3
Clapham, PR.4
-
29
-
-
84907518965
-
HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations
-
PMID: 25278604
-
Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P. 2014. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science 346:56-61. DOI: https://doi.org/10.1126/science.1256739, PMID: 25278604
-
(2014)
Science
, vol.346
, pp. 56-61
-
-
Faria, NR1
Rambaut, A2
Suchard, MA3
Baele, G4
Bedford, T5
Ward, MJ6
Tatem, AJ7
Sousa, JD8
Arinaminpathy, N9
Pépin, J10
Posada, D11
Peeters, M12
Pybus, OG13
Lemey, P.14
-
30
-
-
84875546274
-
Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
-
PMID: 23521886
-
Ferguson AL, Mann JK, Omarjee S, Ndung’u T, Walker BD, Chakraborty AK. 2013. Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38: 606-617. DOI: https://doi.org/10.1016/j.immuni.2012.11.022, PMID: 23521886
-
(2013)
Immunity
, vol.38
, pp. 606-617
-
-
Ferguson, AL1
Mann, JK2
Omarjee, S3
Ndung’u, T4
Walker, BD5
Chakraborty, AK.6
-
31
-
-
84879064073
-
Stability-mediated epistasis constrains the evolution of an influenza protein
-
PMID: 23682315
-
Gong LI, Suchard MA, Bloom JD. 2013. Stability-mediated epistasis constrains the evolution of an influenza protein. eLife 2:e00631. DOI: https://doi.org/10.7554/eLife.00631, PMID: 23682315
-
(2013)
eLife
, vol.2
, pp. e00631
-
-
Gong, LI1
Suchard, MA2
Bloom, JD.3
-
32
-
-
84902131373
-
Early development of broadly neutralizing antibodies in HIV-1-infected infants
-
PMID: 24859529
-
Goo L, Chohan V, Nduati R, Overbaugh J. 2014. Early development of broadly neutralizing antibodies in HIV-1-infected infants. Nature Medicine 20:655-658. DOI: https://doi.org/10.1038/nm.3565, PMID: 24859529
-
(2014)
Nature Medicine
, vol.20
, pp. 655-658
-
-
Goo, L1
Chohan, V2
Nduati, R3
Overbaugh, J.4
-
33
-
-
85028970031
-
Analysis of Large-Scale mutagenesis data to assess the impact of single amino acid substitutions
-
PMID: 28751422
-
Gray VE, Hause RJ, Fowler DM. 2017. Analysis of Large-Scale mutagenesis data to assess the impact of single amino acid substitutions. Genetics 207:53-61. DOI: https://doi.org/10.1534/genetics.117.300064, PMID: 28751422
-
(2017)
Genetics
, vol.207
, pp. 53-61
-
-
Gray, VE1
Hause, RJ2
Fowler, DM.3
-
34
-
-
84987652813
-
Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site
-
PMID: 27617431
-
Gristick HB, von Boehmer L, West AP, Schamber M, Gazumyan A, Golijanin J, Seaman MS, Fätkenheuer G, Klein F, Nussenzweig MC, Bjorkman PJ. 2016. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nature Structural & Molecular Biology 23:906-915. DOI: https://doi.org/10.1038/nsmb.3291, PMID: 27617431
-
(2016)
Nature Structural & Molecular Biology
, vol.23
, pp. 906-915
-
-
Gristick, HB1
von Boehmer, L2
West, AP3
Schamber, M4
Gazumyan, A5
Golijanin, J6
Seaman, MS7
Fätkenheuer, G8
Klein, F9
Nussenzweig, MC10
Bjorkman, PJ.11
-
35
-
-
84904127504
-
CD4-induced activation in a soluble HIV-1 Env trimer
-
PMID: 24931470
-
Guttman M, Garcia NK, Cupo A, Matsui T, Julien JP, Sanders RW, Wilson IA, Moore JP, Lee KK. 2014. CD4-induced activation in a soluble HIV-1 Env trimer. Structure 22:974-984. DOI: https://doi.org/10.1016/j.str.2014.05.001, PMID: 24931470
-
(2014)
Structure
, vol.22
, pp. 974-984
-
-
Guttman, M1
Garcia, NK2
Cupo, A3
Matsui, T4
Julien, JP5
Sanders, RW6
Wilson, IA7
Moore, JP8
Lee, KK.9
-
36
-
-
84923164032
-
Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env
-
PMID: 25652336
-
Guttman M, Cupo A, Julien JP, Sanders RW, Wilson IA, Moore JP, Lee KK. 2015. Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env. Nature Communications 6:6144. DOI: https://doi.org/10.1038/ncomms7144, PMID: 25652336
-
(2015)
Nature Communications
, vol.6
, pp. 6144
-
-
Guttman, M1
Cupo, A2
Julien, JP3
Sanders, RW4
Wilson, IA5
Moore, JP6
Lee, KK.7
-
37
-
-
85008164772
-
Experimental estimation of the effects of all amino-acid mutations to hiv’s envelope protein on viral replication in cell culture
-
PMID: 27959955
-
Haddox HK, Dingens AS, Bloom JD. 2016. Experimental estimation of the effects of all amino-acid mutations to hiv’s envelope protein on viral replication in cell culture. PLOS Pathogens 12:e1006114. DOI: https://doi.org/10.1371/journal.ppat.1006114, PMID: 27959955
-
(2016)
PLOS Pathogens
, vol.12
, pp. e1006114
-
-
Haddox, HK1
Dingens, AS2
Bloom, JD.3
-
38
-
-
85117697820
-
Computer code for ‘Mapping mutational effects along the evolutionary landscape of HIV envelope’
-
da9c939
-
Haddox HK, Dingens AS, Hilton SK, Overbaugh J, Bloom JD. 2018. Computer code for ‘Mapping mutational effects along the evolutionary landscape of HIV envelope’. Github. da9c939. https://github.com/jbloomlab/
-
(2018)
Github
-
-
Haddox, HK1
Dingens, AS2
Hilton, SK3
Overbaugh, J4
Bloom, JD.5
-
39
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies
-
PMID: 9656490
-
EnvMutationalShiftsPaper Halpern AL, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Molecular Biology and Evolution 15:910-917. DOI: https://doi.org/10.1093/oxfordjournals.molbev.a025995, PMID: 9656490
-
(1998)
Molecular Biology and Evolution
, vol.15
, pp. 910-917
-
-
EnvMutationalShiftsPaper Halpern, AL1
Bruno, WJ.2
-
40
-
-
84906217983
-
Historical contingency and its biophysical basis in glucocorticoid receptor evolution
-
PMID: 24930765
-
Harms MJ, Thornton JW. 2014. Historical contingency and its biophysical basis in glucocorticoid receptor evolution. Nature 512:203-207. DOI: https://doi.org/10.1038/nature13410, PMID: 24930765
-
(2014)
Nature
, vol.512
, pp. 203-207
-
-
Harms, MJ1
Thornton, JW.2
-
41
-
-
33751381461
-
TimeTree: a public knowledge-base of divergence times among organisms
-
PMID: 17021158
-
Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972. DOI: https://doi.org/10.1093/bioinformatics/btl505, PMID: 17021158
-
(2006)
Bioinformatics
, vol.22
, pp. 2971-2972
-
-
Hedges, SB1
Dudley, J2
Kumar, S.3
-
42
-
-
85026452162
-
phydms: software for phylogenetic analyses informed by deep mutational scanning
-
PMID: 28785526
-
Hilton SK, Doud MB, Bloom JD. 2017. phydms: software for phylogenetic analyses informed by deep mutational scanning. PeerJ 5:e3657. DOI: https://doi.org/10.7717/peerj.3657, PMID: 28785526
-
(2017)
PeerJ
, vol.5
, pp. e3657
-
-
Hilton, SK1
Doud, MB2
Bloom, JD.3
-
43
-
-
84921607768
-
Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface
-
PMID: 25186731
-
Huang J, Kang BH, Pancera M, Lee JH, Tong T, Feng Y, Imamichi H, Georgiev IS, Chuang GY, Druz A, Doria-Rose NA, Laub L, Sliepen K, van Gils MJ, de la Peña AT, Derking R, Klasse PJ, Migueles SA, Bailer RT, Alam M, et al. 2014. Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface. Nature 515:138-142. DOI: https://doi.org/10.1038/nature13601, PMID: 25186731
-
(2014)
Nature
, vol.515
, pp. 138-142
-
-
Huang, J1
Kang, BH2
Pancera, M3
Lee, JH4
Tong, T5
Feng, Y6
Imamichi, H7
Georgiev, IS8
Chuang, GY9
Druz, A10
Doria-Rose, NA11
Laub, L12
Sliepen, K13
van Gils, MJ14
de la Peña, AT15
Derking, R16
Klasse, PJ17
Migueles, SA18
Bailer, RT19
Alam, M20
more..
-
44
-
-
0033960641
-
Frequent microsatellite instability and BAX mutations in T cell acute lymphoblastic leukemia cell lines
-
PMID: 10739008
-
Inoue K, Kohno T, Takakura S, Hayashi Y, Mizoguchi H, Yokota J. 2000. Frequent microsatellite instability and BAX mutations in T cell acute lymphoblastic leukemia cell lines. Leukemia Research 24:255-262. DOI: https://doi.org/10.1016/S0145-2126(99)00182-4, PMID: 10739008
-
(2000)
Leukemia Research
, vol.24
, pp. 255-262
-
-
Inoue, K1
Kohno, T2
Takakura, S3
Hayashi, Y4
Mizoguchi, H5
Yokota, J.6
-
45
-
-
84890858459
-
Crystal structure of a soluble cleaved HIV-1 envelope trimer
-
PMID: 24179159
-
Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. 2013. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 342:1477-1483. DOI: https://doi.org/10.1126/science.1245625, PMID: 24179159
-
(2013)
Science
, vol.342
, pp. 1477-1483
-
-
Julien, JP1
Cupo, A2
Sok, D3
Stanfield, RL4
Lyumkis, D5
Deller, MC6
Klasse, PJ7
Burton, DR8
Sanders, RW9
Moore, JP10
Ward, AB11
Wilson, IA.12
-
46
-
-
84942856317
-
Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens
-
PMID: 26372963
-
Julien JP, Lee JH, Ozorowski G, Hua Y, Torrents de la Peña A, de Taeye SW, Nieusma T, Cupo A, Yasmeen A, Golabek M, Pugach P, Klasse PJ, Moore JP, Sanders RW, Ward AB, Wilson IA. 2015. Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens. PNAS 112: 11947-11952. DOI: https://doi.org/10.1073/pnas.1507793112, PMID: 26372963
-
(2015)
PNAS
, vol.112
, pp. 11947-11952
-
-
Julien, JP1
Lee, JH2
Ozorowski, G3
Hua, Y4
Torrents de la Peña, A5
de Taeye, SW6
Nieusma, T7
Cupo, A8
Yasmeen, A9
Golabek, M10
Pugach, P11
Klasse, PJ12
Moore, JP13
Sanders, RW14
Ward, AB15
Wilson, IA.16
-
47
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
PMID: 6667333
-
Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637. DOI: https://doi.org/10.1002/bip.360221211, PMID: 6667333
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W1
Sander, C.2
-
48
-
-
85026676132
-
Parallel evolution of metazoan mitochondrial proteins
-
PMID: 28595327
-
Klink GV, Bazykin GA. 2017. Parallel evolution of metazoan mitochondrial proteins. Genome Biology and Evolution 9:1341-1350. DOI: https://doi.org/10.1093/gbe/evx025, PMID: 28595327
-
(2017)
Genome Biology and Evolution
, vol.9
, pp. 1341-1350
-
-
Klink, GV1
Bazykin, GA.2
-
49
-
-
0001720445
-
Numbering positions in HIV relative to HXB2CG
-
Korber B, Foley BT, Kuiken C, Pillai SK, Sodroski JG. 1998. Numbering positions in HIV relative to HXB2CG. Human Retroviruses and AIDS 3:102-111.
-
(1998)
Human Retroviruses and AIDS
, vol.3
, pp. 102-111
-
-
Korber, B1
Foley, BT2
Kuiken, C3
Pillai, SK4
Sodroski, JG.5
-
50
-
-
78049359630
-
Correcting the bias of empirical frequency parameter estimators in codon models
-
PMID: 20689581
-
Kosakovsky Pond S, Delport W, Muse SV, Scheffler K. 2010. Correcting the bias of empirical frequency parameter estimators in codon models. PLoS ONE 5:e11230. DOI: https://doi.org/10.1371/journal.pone.0011230, PMID: 20689581
-
(2010)
PLoS ONE
, vol.5
, pp. e11230
-
-
Kosakovsky Pond, S1
Delport, W2
Muse, SV3
Scheffler, K.4
-
51
-
-
17744396121
-
Not so different after all: a comparison of methods for detecting amino acid sites under selection
-
PMID: 15703242
-
Kosakovsky Pond SL, Frost SD. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Molecular Biology and Evolution 22:1208-1222. DOI: https://doi.org/10.1093/molbev/msi105, PMID: 15703242
-
(2005)
Molecular Biology and Evolution
, vol.22
, pp. 1208-1222
-
-
Kosakovsky Pond, SL1
Frost, SD.2
-
52
-
-
84859257158
-
Exploring the complexity of the HIV-1 fitness landscape
-
PMID: 22412384
-
Kouyos RD, Leventhal GE, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Bonhoeffer S. 2012. Exploring the complexity of the HIV-1 fitness landscape. PLoS Genetics 8:e1002551. DOI: https://doi.org/10.1371/journal.pgen.1002551, PMID: 22412384
-
(2012)
PLoS Genetics
, vol.8
, pp. e1002551
-
-
Kouyos, RD1
Leventhal, GE2
Hinkley, T3
Haddad, M4
Whitcomb, JM5
Petropoulos, CJ6
Bonhoeffer, S.7
-
53
-
-
85019124285
-
Stability-mediated epistasis restricts accessible mutational pathways in the functional evolution of avian hemoglobin
-
PMID: 28201714
-
Kumar A, Natarajan C, Moriyama H, Witt CC, Weber RE, Fago A, Storz JF. 2017. Stability-mediated epistasis restricts accessible mutational pathways in the functional evolution of avian hemoglobin. Molecular Biology and Evolution 34:1240-1251. DOI: https://doi.org/10.1093/molbev/msx085, PMID: 28201714
-
(2017)
Molecular Biology and Evolution
, vol.34
, pp. 1240-1251
-
-
Kumar, A1
Natarajan, C2
Moriyama, H3
Witt, CC4
Weber, RE5
Fago, A6
Storz, JF.7
-
54
-
-
0034482696
-
Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates
-
PMID: 11188697
-
Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson WA. 2000. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 8:1329-1339. DOI: https://doi.org/10.1016/S0969-2126(00)00547-5, PMID: 11188697
-
(2000)
Structure
, vol.8
, pp. 1329-1339
-
-
Kwong, PD1
Wyatt, R2
Majeed, S3
Robinson, J4
Sweet, RW5
Sodroski, J6
Hendrickson, WA.7
-
55
-
-
0037069682
-
HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites
-
PMID: 12478295
-
Kwong PD, Doyle ML, Casper DJ, Cicala C, Leavitt SA, Majeed S, Steenbeke TD, Venturi M, Chaiken I, Fung M, Katinger H, Parren PW, Robinson J, Van Ryk D, Wang L, Burton DR, Freire E, Wyatt R, Sodroski J, Hendrickson WA, et al. 2002. HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420:678-682. DOI: https://doi.org/10.1038/nature01188, PMID: 12478295
-
(2002)
Nature
, vol.420
, pp. 678-682
-
-
Kwong, PD1
Doyle, ML2
Casper, DJ3
Cicala, C4
Leavitt, SA5
Majeed, S6
Steenbeke, TD7
Venturi, M8
Chaiken, I9
Fung, M10
Katinger, H11
Parren, PW12
Robinson, J13
Van Ryk, D14
Wang, L15
Burton, DR16
Freire, E17
Wyatt, R18
Sodroski, J19
Hendrickson, WA20
more..
-
56
-
-
85019040760
-
A broadly neutralizing antibody targets the dynamic hiv envelope trimer apex via a long, rigidified, and anionic b-hairpin structure
-
PMID: 28423342
-
Lee JH, Andrabi R, Su CY, Yasmeen A, Julien JP, Kong L, Wu NC, McBride R, Sok D, Pauthner M, Cottrell CA, Nieusma T, Blattner C, Paulson JC, Klasse PJ, Wilson IA, Burton DR, Ward AB. 2017. A broadly neutralizing antibody targets the dynamic hiv envelope trimer apex via a long, rigidified, and anionic b-hairpin structure. Immunity 46:690-702. DOI: https://doi.org/10.1016/j.immuni.2017.03.017, PMID: 28423342
-
(2017)
Immunity
, vol.46
, pp. 690-702
-
-
Lee, JH1
Andrabi, R2
Su, CY3
Yasmeen, A4
Julien, JP5
Kong, L6
Wu, NC7
McBride, R8
Sok, D9
Pauthner, M10
Cottrell, CA11
Nieusma, T12
Blattner, C13
Paulson, JC14
Klasse, PJ15
Wilson, IA16
Burton, DR17
Ward, AB.18
-
57
-
-
0028022110
-
Control of expression, glycosylation, and secretion of HIV-1 gp120 by homologous and heterologous signal sequences
-
PMID: 8091657
-
Li Y, Luo L, Thomas DY, Kang CY. 1994. Control of expression, glycosylation, and secretion of HIV-1 gp120 by homologous and heterologous signal sequences. Virology 204:266-278. DOI: https://doi.org/10.1006/viro.1994.1531, PMID: 8091657
-
(1994)
Virology
, vol.204
, pp. 266-278
-
-
Li, Y1
Luo, L2
Thomas, DY3
Kang, CY.4
-
58
-
-
85040867141
-
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies
-
PMID: 29311326
-
Louie RHY, Kaczorowski KJ, Barton JP, Chakraborty AK, McKay MR. 2018. Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies. PNAS 115:E564-E573. DOI: https://doi.org/10.1073/pnas.1717765115, PMID: 29311326
-
(2018)
PNAS
, vol.115
, pp. E564-E573
-
-
Louie, RHY1
Kaczorowski, KJ2
Barton, JP3
Chakraborty, AK4
McKay, MR.5
-
59
-
-
65449188351
-
Appreciating HIV type 1 diversity: subtype differences in Env
-
PMID: 19327047
-
Lynch RM, Shen T, Gnanakaran S, Derdeyn CA. 2009. Appreciating HIV type 1 diversity: subtype differences in Env. AIDS Research and Human Retroviruses 25:237-248. DOI: https://doi.org/10.1089/aid.2008.0219, PMID: 19327047
-
(2009)
AIDS Research and Human Retroviruses
, vol.25
, pp. 237-248
-
-
Lynch, RM1
Shen, T2
Gnanakaran, S3
Derdeyn, CA.4
-
60
-
-
84890859441
-
Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer
-
PMID: 24179160
-
Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB. 2013. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 342:1484-1490. DOI: https://doi.org/10.1126/science.1245627, PMID: 24179160
-
(2013)
Science
, vol.342
, pp. 1484-1490
-
-
Lyumkis, D1
Julien, JP2
de Val, N3
Cupo, A4
Potter, CS5
Klasse, PJ6
Burton, DR7
Sanders, RW8
Moore, JP9
Carragher, B10
Wilson, IA11
Ward, AB.12
-
61
-
-
84923177364
-
The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing
-
PMID: 25102049
-
Mann JK, Barton JP, Ferguson AL, Omarjee S, Walker BD, Chakraborty A, Ndung’u T. 2014. The fitness landscape of HIV-1 gag: advanced modeling approaches and validation of model predictions by in vitro testing. PLoS Computational Biology 10:e1003776. DOI: https://doi.org/10.1371/journal.pcbi.1003776, PMID: 25102049
-
(2014)
PLoS Computational Biology
, vol.10
, pp. e1003776
-
-
Mann, JK1
Barton, JP2
Ferguson, AL3
Omarjee, S4
Walker, BD5
Chakraborty, A6
Ndung’u, T.7
-
62
-
-
84905454017
-
Modeling evolution using the probability of fixation: history and implications
-
PMID: 25195318
-
McCandlish DM, Stoltzfus A. 2014. Modeling evolution using the probability of fixation: history and implications. The Quarterly Review of Biology 89:225-252. DOI: https://doi.org/10.1086/677571, PMID: 25195318
-
(2014)
The Quarterly Review of Biology
, vol.89
, pp. 225-252
-
-
McCandlish, DM1
Stoltzfus, A.2
-
63
-
-
69549126129
-
Specificity of the autologous neutralizing antibody response
-
PMID: 20048698
-
Moore PL, Gray ES, Morris L. 2009. Specificity of the autologous neutralizing antibody response. Current Opinion in HIV and AIDS 4:358-363. DOI: https://doi.org/10.1097/COH.0b013e32832ea7e8, PMID: 20048698
-
(2009)
Current Opinion in HIV and AIDS
, vol.4
, pp. 358-363
-
-
Moore, PL1
Gray, ES2
Morris, L.3
-
64
-
-
84909606387
-
Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions
-
PMID: 25298114
-
Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR, Smith AB, Kwong PD, Blanchard SC, Mothes W. 2014. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 346:759-763. DOI: https://doi.org/10.1126/science.1254426, PMID: 25298114
-
(2014)
Science
, vol.346
, pp. 759-763
-
-
Munro, JB1
Gorman, J2
Ma, X3
Zhou, Z4
Arthos, J5
Burton, DR6
Koff, WC7
Courter, JR8
Smith, AB9
Kwong, PD10
Blanchard, SC11
Mothes, W.12
-
65
-
-
84864605220
-
Detecting individual sites subject to episodic diversifying selection
-
PMID: 22807683
-
Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genetics 8:e1002764. DOI: https://doi.org/10.1371/journal.pgen.1002764, PMID: 22807683
-
(2012)
PLoS Genetics
, vol.8
, pp. e1002764
-
-
Murrell, B1
Wertheim, JO2
Moola, S3
Weighill, T4
Scheffler, K5
Kosakovsky Pond, SL.6
-
66
-
-
84929648750
-
Gene-wide identification of episodic selection
-
PMID: 25701167
-
Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. 2015. Gene-wide identification of episodic selection. Molecular Biology and Evolution 32:1365-1371. DOI: https://doi.org/10.1093/molbev/msv035, PMID: 25701167
-
(2015)
Molecular Biology and Evolution
, vol.32
, pp. 1365-1371
-
-
Murrell, B1
Weaver, S2
Smith, MD3
Wertheim, JO4
Murrell, S5
Aylward, A6
Eren, K7
Pollner, T8
Martin, DP9
Smith, DM10
Scheffler, K11
Kosakovsky Pond, SL.12
-
67
-
-
84878935899
-
Epistasis among adaptive mutations in deer mouse hemoglobin
-
PMID: 23766324
-
Natarajan C, Inoguchi N, Weber RE, Fago A, Moriyama H, Storz JF. 2013. Epistasis among adaptive mutations in deer mouse hemoglobin. Science 340:1324-1327. DOI: https://doi.org/10.1126/science.1236862, PMID: 23766324
-
(2013)
Science
, vol.340
, pp. 1324-1327
-
-
Natarajan, C1
Inoguchi, N2
Weber, RE3
Fago, A4
Moriyama, H5
Storz, JF.6
-
68
-
-
0034161409
-
Effect of breastfeeding and formula feeding on transmission of HIV-1: a randomized clinical trial
-
PMID: 10703779
-
Nduati R, John G, Mbori-Ngacha D, Richardson B, Overbaugh J, Mwatha A, Ndinya-Achola J, Bwayo J, Onyango FE, Hughes J, Kreiss J. 2000. Effect of breastfeeding and formula feeding on transmission of HIV-1: a randomized clinical trial. Jama 283:1167-1174. DOI: https://doi.org/10.1001/jama.283.9.1167, PMID: 10703779
-
(2000)
Jama
, vol.283
, pp. 1167-1174
-
-
Nduati, R1
John, G2
Mbori-Ngacha, D3
Richardson, B4
Overbaugh, J5
Mwatha, A6
Ndinya-Achola, J7
Bwayo, J8
Onyango, FE9
Hughes, J10
Kreiss, J.11
-
69
-
-
0025253819
-
Identification of individual human immunodeficiency virus type 1 gp120 amino acids important for CD4 receptor binding
-
PMID: 2243375
-
Olshevsky U, Helseth E, Furman C, Li J, Haseltine W, Sodroski J. 1990. Identification of individual human immunodeficiency virus type 1 gp120 amino acids important for CD4 receptor binding. Journal of Virology 64: 5701-5707. PMID: 2243375
-
(1990)
Journal of Virology
, vol.64
, pp. 5701-5707
-
-
Olshevsky, U1
Helseth, E2
Furman, C3
Li, J4
Haseltine, W5
Sodroski, J.6
-
70
-
-
85025476641
-
Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike
-
PMID: 28700571
-
Ozorowski G, Pallesen J, de Val N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA, Ward AB. 2017. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature 547:360-363. DOI: https://doi.org/10.1038/nature23010, PMID: 28700571
-
(2017)
Nature
, vol.547
, pp. 360-363
-
-
Ozorowski, G1
Pallesen, J2
de Val, N3
Lyumkis, D4
Cottrell, CA5
Torres, JL6
Copps, J7
Stanfield, RL8
Cupo, A9
Pugach, P10
Moore, JP11
Wilson, IA12
Ward, AB.13
-
71
-
-
84909640954
-
Structure and immune recognition of trimeric pre-fusion HIV-1 Env
-
PMID: 25296255
-
Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, Stewart-Jones GB, Stuckey J, Bailer RT, Joyce MG, Louder MK, Tumba N, Yang Y, Zhang B, Cohen MS, Haynes BF, et al. 2014. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 514:455-461. DOI: https://doi.org/10.1038/nature13808, PMID: 25296255
-
(2014)
Nature
, vol.514
, pp. 455-461
-
-
Pancera, M1
Zhou, T2
Druz, A3
Georgiev, IS4
Soto, C5
Gorman, J6
Huang, J7
Acharya, P8
Chuang, GY9
Ofek, G10
Stewart-Jones, GB11
Stuckey, J12
Bailer, RT13
Joyce, MG14
Louder, MK15
Tumba, N16
Yang, Y17
Zhang, B18
Cohen, MS19
Haynes, BF20
more..
-
72
-
-
84876867850
-
Phenotypic properties of transmitted founder HIV-1
-
PMID: 23542380
-
Parrish NF, Gao F, Li H, Giorgi EE, Barbian HJ, Parrish EH, Zajic L, Iyer SS, Decker JM, Kumar A, Hora B, Berg A, Cai F, Hopper J, Denny TN, Ding H, Ochsenbauer C, Kappes JC, Galimidi RP, West AP, et al. 2013. Phenotypic properties of transmitted founder HIV-1. PNAS 110:6626-6633. DOI: https://doi.org/10.1073/pnas.1304288110, PMID: 23542380
-
(2013)
PNAS
, vol.110
, pp. 6626-6633
-
-
Parrish, NF1
Gao, F2
Li, H3
Giorgi, EE4
Barbian, HJ5
Parrish, EH6
Zajic, L7
Iyer, SS8
Decker, JM9
Kumar, A10
Hora, B11
Berg, A12
Cai, F13
Hopper, J14
Denny, TN15
Ding, H16
Ochsenbauer, C17
Kappes, JC18
Galimidi, RP19
West, AP20
more..
-
73
-
-
0026318224
-
Changes in growth properties on passage in tissue culture of viruses derived from infectious molecular clones of HIV-1LAI, HIV-1MAL, and HIV-1ELI
-
PMID: 1683726
-
Peden K, Emerman M, Montagnier L. 1991. Changes in growth properties on passage in tissue culture of viruses derived from infectious molecular clones of HIV-1LAI, HIV-1MAL, and HIV-1ELI. Virology 185:661-672. DOI: https://doi.org/10.1016/0042-6822(91)90537-L, PMID: 1683726
-
(1991)
Virology
, vol.185
, pp. 661-672
-
-
Peden, K1
Emerman, M2
Montagnier, L.3
-
74
-
-
84922439802
-
Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface
-
PMID: 25657251
-
Podgornaia AI, Laub MT. 2015. Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface. Science 347:673-677. DOI: https://doi.org/10.1126/science.1257360, PMID: 25657251
-
(2015)
Science
, vol.347
, pp. 673-677
-
-
Podgornaia, AI1
Laub, MT.2
-
75
-
-
84861422981
-
Amino acid coevolution induces an evolutionary Stokes shift
-
PMID: 22547823
-
Pollock DD, Thiltgen G, Goldstein RA. 2012. Amino acid coevolution induces an evolutionary Stokes shift. PNAS 109:E1352-E1359. DOI: https://doi.org/10.1073/pnas.1120084109, PMID: 22547823
-
(2012)
PNAS
, vol.109
, pp. E1352-E1359
-
-
Pollock, DD1
Thiltgen, G2
Goldstein, RA.3
-
76
-
-
9644301241
-
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
-
PMID: 15545256
-
Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Systematic Biology 53:793-808. DOI: https://doi.org/10.1080/10635150490522304, PMID: 15545256
-
(2004)
Systematic Biology
, vol.53
, pp. 793-808
-
-
Posada, D1
Buckley, TR.2
-
77
-
-
0032992212
-
Variants from the diverse virus population identified at seroconversion of a clade A human immunodeficiency virus type 1-infected woman have distinct biological properties
-
PMID: 10364271
-
Poss M, Overbaugh J. 1999. Variants from the diverse virus population identified at seroconversion of a clade A human immunodeficiency virus type 1-infected woman have distinct biological properties. Journal of Virology 73:5255-5264. PMID: 10364271
-
(1999)
Journal of Virology
, vol.73
, pp. 5255-5264
-
-
Poss, M1
Overbaugh, J.2
-
78
-
-
1642377363
-
The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4
-
PMID: 15033560
-
Pugach P, Kuhmann SE, Taylor J, Marozsan AJ, Snyder A, Ketas T, Wolinsky SM, Korber BT, Moore JP. 2004. The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4. Virology 321:8-22. DOI: https://doi.org/10.1016/j.virol.2003.12.012, PMID: 15033560
-
(2004)
Virology
, vol.321
, pp. 8-22
-
-
Pugach, P1
Kuhmann, SE2
Taylor, J3
Marozsan, AJ4
Snyder, A5
Ketas, T6
Wolinsky, SM7
Korber, BT8
Moore, JP.9
-
79
-
-
85117710629
-
A
-
Pugach P, Ozorowski G, Cupo A, Ringe R, Yasmeen A, de Val N, Derking R, Kim HJ, Korzun J, Golabek M, de Los Reyes K, Ketas TJ, Julien JP, Burton DR, Wilson IA, Sanders RW, Klasse PJ, Ward AB, Moore JP. 2015. A
-
(2015)
-
-
Pugach, P1
Ozorowski, G2
Cupo, A3
Ringe, R4
Yasmeen, A5
de Val, N6
Derking, R7
Kim, HJ8
Korzun, J9
Golabek, M10
de Los Reyes, K11
Ketas, TJ12
Julien, JP13
Burton, DR14
Wilson, IA15
Sanders, RW16
Klasse, PJ17
Ward, AB18
Moore, JP.19
-
80
-
-
84923172318
-
native-like SOSIP.664 trimer based on an HIV-1 subtype B env gene
-
PMID: 25589637
-
native-like SOSIP.664 trimer based on an HIV-1 subtype B env gene. Journal of Virology 89:3380-3395. DOI: https://doi.org/10.1128/JVI.03473-14, PMID: 25589637
-
Journal of Virology
, vol.89
, pp. 3380-3395
-
-
-
81
-
-
85020906366
-
Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity
-
PMID: 28446609
-
Rathore U, Saha P, Kesavardhana S, Kumar AA, Datta R, Devanarayanan S, Das R, Mascola JR, Varadarajan R. 2017. Glycosylation of the core of the HIV-1 envelope subunit protein gp120 is not required for native trimer formation or viral infectivity. Journal of Biological Chemistry 292:10197-10219. DOI: https://doi.org/10.1074/jbc.M117.788919, PMID: 28446609
-
(2017)
Journal of Biological Chemistry
, vol.292
, pp. 10197-10219
-
-
Rathore, U1
Saha, P2
Kesavardhana, S3
Kumar, AA4
Datta, R5
Devanarayanan, S6
Das, R7
Mascola, JR8
Varadarajan, R.9
-
82
-
-
0037389643
-
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
-
PMID: 12644702
-
Richman DD, Wrin T, Little SJ, Petropoulos CJ. 2003. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. PNAS 100:4144-4149. DOI: https://doi.org/10.1073/pnas.0630530100, PMID: 12644702
-
(2003)
PNAS
, vol.100
, pp. 4144-4149
-
-
Richman, DD1
Wrin, T2
Little, SJ3
Petropoulos, CJ.4
-
83
-
-
84988239865
-
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history
-
PMID: 25392342
-
Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM. 2015. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution 32:440-455. DOI: https://doi.org/10.1093/molbev/msu312, PMID: 25392342
-
(2015)
Molecular Biology and Evolution
, vol.32
, pp. 440-455
-
-
Risso, VA1
Manssour-Triedo, F2
Delgado-Delgado, A3
Arco, R4
Barroso-delJesus, A5
Ingles-Prieto, A6
Godoy-Ruiz, R7
Gavira, JA8
Gaucher, EA9
Ibarra-Molero, B10
Sanchez-Ruiz, JM.11
-
84
-
-
84983146295
-
HIV transmission biology: translation for HIV prevention
-
PMID: 26418086
-
Ronen K, Sharma A, Overbaugh J. 2015. HIV transmission biology: translation for HIV prevention. Aids 29:2219-2227. DOI: https://doi.org/10.1097/QAD.0000000000000845, PMID: 26418086
-
(2015)
Aids
, vol.29
, pp. 2219-2227
-
-
Ronen, K1
Sharma, A2
Overbaugh, J.3
-
85
-
-
33748925430
-
Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity
-
PMID: 16973562
-
Sagar M, Wu X, Lee S, Overbaugh J. 2006. Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity. Journal of Virology 80:9586-9598. DOI: https://doi.org/10.1128/JVI.00141-06, PMID: 16973562
-
(2006)
Journal of Virology
, vol.80
, pp. 9586-9598
-
-
Sagar, M1
Wu, X2
Lee, S3
Overbaugh, J.4
-
86
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
PMID: 2017436
-
Sander C, Schneider R. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins: Structure, Function, and Genetics 9:56-68. DOI: https://doi.org/10.1002/prot.340090107, PMID: 2017436
-
(1991)
Proteins: Structure, Function, and Genetics
, vol.9
, pp. 56-68
-
-
Sander, C1
Schneider, R.2
-
87
-
-
0036333661
-
Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1
-
PMID: 12163607
-
Sanders RW, Vesanen M, Schuelke N, Master A, Schiffner L, Kalyanaraman R, Paluch M, Berkhout B, Maddon PJ, Olson WC, Lu M, Moore JP. 2002. Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1. Journal of Virology 76:8875-8889. DOI: https://doi.org/10.1128/JVI.76.17.8875-8889.2002, PMID: 12163607
-
(2002)
Journal of Virology
, vol.76
, pp. 8875-8889
-
-
Sanders, RW1
Vesanen, M2
Schuelke, N3
Master, A4
Schiffner, L5
Kalyanaraman, R6
Paluch, M7
Berkhout, B8
Maddon, PJ9
Olson, WC10
Lu, M11
Moore, JP.12
-
88
-
-
84884678235
-
A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies
-
PMID: 24068931
-
Sanders RW, Derking R, Cupo A, Julien JP, Yasmeen A, de Val N, Kim HJ, Blattner C, de la Peña AT, Korzun J, Golabek M, de Los Reyes K, Ketas TJ, van Gils MJ, King CR, Wilson IA, Ward AB, Klasse PJ, Moore JP. 2013. A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathogens 9:e1003618. DOI: https://doi.org/10.1371/journal.ppat.1003618, PMID: 24068931
-
(2013)
PLoS Pathogens
, vol.9
, pp. e1003618
-
-
Sanders, RW1
Derking, R2
Cupo, A3
Julien, JP4
Yasmeen, A5
de Val, N6
Kim, HJ7
Blattner, C8
de la Peña, AT9
Korzun, J10
Golabek, M11
de Los Reyes, K12
Ketas, TJ13
van Gils, MJ14
King, CR15
Wilson, IA16
Ward, AB17
Klasse, PJ18
Moore, JP.19
-
89
-
-
84937469192
-
HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers
-
PMID: 26089353
-
Sanders RW, van Gils MJ, Derking R, Sok D, Ketas TJ, Burger JA, Ozorowski G, Cupo A, Simonich C, Goo L, Arendt H, Kim HJ, Lee JH, Pugach P, Williams M, Debnath G, Moldt B, van Breemen MJ, Isik G, Medina-Ramírez M, et al. 2015. HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers. Science 349:aac4223. DOI: https://doi.org/10.1126/science.aac4223, PMID: 26089353
-
(2015)
Science
, vol.349
, pp. aac4223
-
-
Sanders, RW1
van Gils, MJ2
Derking, R3
Sok, D4
Ketas, TJ5
Burger, JA6
Ozorowski, G7
Cupo, A8
Simonich, C9
Goo, L10
Arendt, H11
Kim, HJ12
Lee, JH13
Pugach, P14
Williams, M15
Debnath, G16
Moldt, B17
van Breemen, MJ18
Isik, G19
Medina-Ramírez, M20
more..
-
90
-
-
84934908389
-
Contingency and entrenchment in protein evolution under purifying selection
-
PMID: 26056312
-
Shah P, McCandlish DM, Plotkin JB. 2015. Contingency and entrenchment in protein evolution under purifying selection. PNAS 112:E3226-E3235. DOI: https://doi.org/10.1073/pnas.1412933112, PMID: 26056312
-
(2015)
PNAS
, vol.112
, pp. E3226-E3235
-
-
Shah, P1
McCandlish, DM2
Plotkin, JB.3
-
91
-
-
84886705258
-
Origins of HIV and the AIDS pandemic
-
PMID: 22229120
-
Sharp PM, Hahn BH. 2011. Origins of HIV and the AIDS pandemic. Cold Spring Harbor Perspectives in Medicine 1:a006841. DOI: https://doi.org/10.1101/cshperspect.a006841, PMID: 22229120
-
(2011)
Cold Spring Harbor Perspectives in Medicine
, vol.1
, pp. a006841
-
-
Sharp, PM1
Hahn, BH.2
-
92
-
-
84976608123
-
HIV-1 Neutralizing Antibodies with Limited Hypermutation from an Infant
-
PMID: 27345369
-
Simonich CA, Williams KL, Verkerke HP, Williams JA, Nduati R, Lee KK, Overbaugh J. 2016. HIV-1 Neutralizing Antibodies with Limited Hypermutation from an Infant. Cell 166:77-87. DOI: https://doi.org/10.1016/j.cell.2016.05.055, PMID: 27345369
-
(2016)
Cell
, vol.166
, pp. 77-87
-
-
Simonich, CA1
Williams, KL2
Verkerke, HP3
Williams, JA4
Nduati, R5
Lee, KK6
Overbaugh, J.7
-
93
-
-
84899553363
-
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
-
PMID: 24451623
-
Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313. DOI: https://doi.org/10.1093/bioinformatics/btu033, PMID: 24451623
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
94
-
-
0022459886
-
Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS
-
PMID: 2423250
-
Starcich BR, Hahn BH, Shaw GM, McNeely PD, Modrow S, Wolf H, Parks ES, Parks WP, Josephs SF, Gallo RC. 1986. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell 45:637-648. DOI: https://doi.org/10.1016/0092-8674(86)90778-6, PMID: 2423250
-
(1986)
Cell
, vol.45
, pp. 637-648
-
-
Starcich, BR1
Hahn, BH2
Shaw, GM3
McNeely, PD4
Modrow, S5
Wolf, H6
Parks, ES7
Parks, WP8
Josephs, SF9
Gallo, RC.10
-
95
-
-
85094300278
-
Pervasive contingency and entrenchment in a billion years of Hsp90 evolution
-
Starr TN, Flynn JM, Mishra P, Bolon DN, Thornton JW. 2017. Pervasive contingency and entrenchment in a billion years of Hsp90 evolution. bioRxiv. DOI: https://doi.org/10.1101/189803
-
(2017)
bioRxiv
-
-
Starr, TN1
Flynn, JM2
Mishra, P3
Bolon, DN4
Thornton, JW.5
-
96
-
-
84976553126
-
Epistasis in protein evolution
-
PMID: 26833806
-
Starr TN, Thornton JW. 2016. Epistasis in protein evolution. Protein Science 25:1204-1218. DOI: https://doi.org/10.1002/pro.2897, PMID: 26833806
-
(2016)
Protein Science
, vol.25
, pp. 1204-1218
-
-
Starr, TN1
Thornton, JW.2
-
97
-
-
84963936310
-
Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G
-
PMID: 27114034
-
Stewart-Jones GB, Soto C, Lemmin T, Chuang GY, Druz A, Kong R, Thomas PV, Wagh K, Zhou T, Behrens AJ, Bylund T, Choi CW, Davison JR, Georgiev IS, Joyce MG, Kwon YD, Pancera M, Taft J, Yang Y, Zhang B, et al. 2016. Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell 165:813-826. DOI: https://doi.org/10.1016/j.cell.2016.04.010, PMID: 27114034
-
(2016)
Cell
, vol.165
, pp. 813-826
-
-
Stewart-Jones, GB1
Soto, C2
Lemmin, T3
Chuang, GY4
Druz, A5
Kong, R6
Thomas, PV7
Wagh, K8
Zhou, T9
Behrens, AJ10
Bylund, T11
Choi, CW12
Davison, JR13
Georgiev, IS14
Joyce, MG15
Kwon, YD16
Pancera, M17
Taft, J18
Yang, Y19
Zhang, B20
more..
-
98
-
-
0030780614
-
Atomic structure of a thermostable subdomain of HIV-1 gp41
-
PMID: 9356444
-
Tan K, Liu J, Wang J, Shen S, Lu M. 1997. Atomic structure of a thermostable subdomain of HIV-1 gp41. PNAS 94:12303-12308. DOI: https://doi.org/10.1073/pnas.94.23.12303, PMID: 9356444
-
(1997)
PNAS
, vol.94
, pp. 12303-12308
-
-
Tan, K1
Liu, J2
Wang, J3
Shen, S4
Lu, M.5
-
99
-
-
84888331478
-
Maximum allowed solvent accessibilites of residues in proteins
-
PMID: 24278298
-
Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. 2013. Maximum allowed solvent accessibilites of residues in proteins. PLoS ONE 8:e80635. DOI: https://doi.org/10.1371/journal.pone.0080635, PMID: 24278298
-
(2013)
PLoS ONE
, vol.8
, pp. e80635
-
-
Tien, MZ1
Meyer, AG2
Sydykova, DK3
Spielman, SJ4
Wilke, CO.5
-
100
-
-
57349153146
-
Only five of 10 strictly conserved disulfide bonds are essential for folding and eight for function of the HIV-1 envelope glycoprotein
-
PMID: 18653472
-
van Anken E, Sanders RW, Liscaljet IM, Land A, Bontjer I, Tillemans S, Nabatov AA, Paxton WA, Berkhout B, Braakman I. 2008. Only five of 10 strictly conserved disulfide bonds are essential for folding and eight for function of the HIV-1 envelope glycoprotein. Molecular Biology of the Cell 19:4298-4309. DOI: https://doi.org/10.1091/mbc.E07-12-1282, PMID: 18653472
-
(2008)
Molecular Biology of the Cell
, vol.19
, pp. 4298-4309
-
-
van Anken, E1
Sanders, RW2
Liscaljet, IM3
Land, A4
Bontjer, I5
Tillemans, S6
Nabatov, AA7
Paxton, WA8
Berkhout, B9
Braakman, I.10
-
101
-
-
84990046310
-
Epitope-independent purification of native-like envelope trimers from diverse HIV-1 isolates
-
PMID: 27512064
-
Verkerke HP, Williams JA, Guttman M, Simonich CA, Liang Y, Filipavicius M, Hu SL, Overbaugh J, Lee KK. 2016. Epitope-independent purification of native-like envelope trimers from diverse HIV-1 isolates. Journal of Virology 90:9471-9482. DOI: https://doi.org/10.1128/JVI.01351-16, PMID: 27512064
-
(2016)
Journal of Virology
, vol.90
, pp. 9471-9482
-
-
Verkerke, HP1
Williams, JA2
Guttman, M3
Simonich, CA4
Liang, Y5
Filipavicius, M6
Hu, SL7
Overbaugh, J8
Lee, KK.9
-
102
-
-
85034456376
-
ggseqlogo: a versatile R package for drawing sequence logos
-
PMID: 29036507
-
Wagih O. 2017. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33:3645-3647. DOI: https://doi.org/10.1093/bioinformatics/btx469, PMID: 29036507
-
(2017)
Bioinformatics
, vol.33
, pp. 3645-3647
-
-
Wagih, O.1
-
103
-
-
0036295508
-
Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs
-
PMID: 12079336
-
Wang X, Minasov G, Shoichet BK. 2002. Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs. Journal of Molecular Biology 320:85-95. DOI: https://doi.org/10.1016/S0022-2836(02)00400-X, PMID: 12079336
-
(2002)
Journal of Molecular Biology
, vol.320
, pp. 85-95
-
-
Wang, X1
Minasov, G2
Shoichet, BK.3
-
104
-
-
84873255997
-
A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization
-
PMID: 23384254
-
Wang W, Nie J, Prochnow C, Truong C, Jia Z, Wang S, Chen XS, Wang Y. 2013. A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization. Retrovirology 10:14. DOI: https://doi.org/10.1186/1742-4690-10-14, PMID: 23384254
-
(2013)
Retrovirology
, vol.10
, pp. 14
-
-
Wang, W1
Nie, J2
Prochnow, C3
Truong, C4
Jia, Z5
Wang, S6
Chen, XS7
Wang, Y.8
-
105
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
PMID: 12466850
-
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562. DOI: https://doi.org/10.1038/nature01262, PMID: 12466850
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, RH1
Lindblad-Toh, K2
Birney, E3
Rogers, J4
Abril, JF5
Agarwal, P6
Agarwala, R7
Ainscough, R8
Alexandersson, M9
An, P10
Antonarakis, SE11
Attwood, J12
Baertsch, R13
Bailey, J14
Barlow, K15
Beck, S16
Berry, E17
Birren, B18
Bloom, T19
Bork, P20
more..
-
106
-
-
0037456827
-
Antibody neutralization and escape by HIV-1
-
PMID: 12646921
-
Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, Komarova NL, Nowak MA, Hahn BH, Kwong PD, Shaw GM. 2003. Antibody neutralization and escape by HIV-1. Nature 422:307-312. DOI: https://doi.org/10.1038/nature01470, PMID: 12646921
-
(2003)
Nature
, vol.422
, pp. 307-312
-
-
Wei, X1
Decker, JM2
Wang, S3
Hui, H4
Kappes, JC5
Wu, X6
Salazar-Gonzalez, JF7
Salazar, MG8
Kilby, JM9
Saag, MS10
Komarova, NL11
Nowak, MA12
Hahn, BH13
Kwong, PD14
Shaw, GM.15
-
107
-
-
0030962291
-
Atomic structure of the ectodomain from HIV-1 gp41
-
PMID: 9163431
-
Weissenhorn W, Dessen A, Harrison SC, Skehel JJ, Wiley DC. 1997. Atomic structure of the ectodomain from HIV-1 gp41. Nature 387:426-430. DOI: https://doi.org/10.1038/387426a0, PMID: 9163431
-
(1997)
Nature
, vol.387
, pp. 426-430
-
-
Weissenhorn, W1
Dessen, A2
Harrison, SC3
Skehel, JJ4
Wiley, DC.5
-
108
-
-
78651241895
-
Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure
-
PMID: 21203482
-
White TA, Bartesaghi A, Borgnia MJ, Meyerson JR, de la Cruz MJ, Bess JW, Nandwani R, Hoxie JA, Lifson JD, Milne JL, Subramaniam S. 2010. Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS Pathogens 6:e1001249. DOI: https://doi.org/10.1371/journal.ppat.1001249, PMID: 21203482
-
(2010)
PLoS Pathogens
, vol.6
, pp. e1001249
-
-
White, TA1
Bartesaghi, A2
Borgnia, MJ3
Meyerson, JR4
de la Cruz, MJ5
Bess, JW6
Nandwani, R7
Hoxie, JA8
Lifson, JD9
Milne, JL10
Subramaniam, S.11
-
109
-
-
80052302577
-
Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins
-
PMID: 21715507
-
Wilen CB, Parrish NF, Pfaff JM, Decker JM, Henning EA, Haim H, Petersen JE, Wojcechowskyj JA, Sodroski J, Haynes BF, Montefiori DC, Tilton JC, Shaw GM, Hahn BH, Doms RW. 2011. Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins. Journal of Virology 85: 8514-8527. DOI: https://doi.org/10.1128/JVI.00736-11, PMID: 21715507
-
(2011)
Journal of Virology
, vol.85
, pp. 8514-8527
-
-
Wilen, CB1
Parrish, NF2
Pfaff, JM3
Decker, JM4
Henning, EA5
Haim, H6
Petersen, JE7
Wojcechowskyj, JA8
Sodroski, J9
Haynes, BF10
Montefiori, DC11
Tilton, JC12
Shaw, GM13
Hahn, BH14
Doms, RW.15
-
110
-
-
53349127137
-
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
-
PMID: 18833279
-
Worobey M, Gemmel M, Teuwen DE, Haselkorn T, Kunstman K, Bunce M, Muyembe JJ, Kabongo JM, Kalengayi RM, Van Marck E, Gilbert MT, Wolinsky SM. 2008. Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455:661-664. DOI: https://doi.org/10.1038/nature07390, PMID: 18833279
-
(2008)
Nature
, vol.455
, pp. 661-664
-
-
Worobey, M1
Gemmel, M2
Teuwen, DE3
Haselkorn, T4
Kunstman, K5
Bunce, M6
Muyembe, JJ7
Kabongo, JM8
Kalengayi, RM9
Van Marck, E10
Gilbert, MT11
Wolinsky, SM.12
-
111
-
-
30344485709
-
Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant
-
PMID: 16378985
-
Wu X, Parast AB, Richardson BA, Nduati R, John-Stewart G, Mbori-Ngacha D, Rainwater SM, Overbaugh J. 2006. Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. Journal of Virology 80:835-844. DOI: https://doi.org/10.1128/JVI.80.2.835-844.2006, PMID: 16378985
-
(2006)
Journal of Virology
, vol.80
, pp. 835-844
-
-
Wu, X1
Parast, AB2
Richardson, BA3
Nduati, R4
John-Stewart, G5
Mbori-Ngacha, D6
Rainwater, SM7
Overbaugh, J.8
-
112
-
-
84900431101
-
High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
-
PMID: 24820965
-
Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, Chen SH, Lu IH, Lin CY, Chin RG, Luan HH, Nguyen N, Nelson SF, Li X, Wu TT, Sun R. 2014. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Scientific reports 4:4942. DOI: https://doi.org/10.1038/srep04942, PMID: 24820965
-
(2014)
Scientific reports
, vol.4
, pp. 4942
-
-
Wu, NC1
Young, AP2
Al-Mawsawi, LQ3
Olson, CA4
Feng, J5
Qi, H6
Chen, SH7
Lu, IH8
Lin, CY9
Chin, RG10
Luan, HH11
Nguyen, N12
Nelson, SF13
Li, X14
Wu, TT15
Sun, R.16
-
113
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
-
PMID: 7932792
-
Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306-314. DOI: https://doi.org/10.1007/BF00160154, PMID: 7932792
-
(1994)
Journal of Molecular Evolution
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
114
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
PMID: 10790415
-
Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449. PMID: 10790415
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z1
Nielsen, R2
Goldman, N3
Pedersen, AM.4
-
115
-
-
2942661340
-
Modulation of Env content in virions of simian immunodeficiency virus: correlation with cell surface expression and virion infectivity
-
PMID: 15194752
-
Yuste E, Reeves JD, Doms RW, Desrosiers RC. 2004. Modulation of Env content in virions of simian immunodeficiency virus: correlation with cell surface expression and virion infectivity. Journal of Virology 78: 6775-6785. DOI: https://doi.org/10.1128/JVI.78.13.6775-6785.2004, PMID: 15194752
-
(2004)
Journal of Virology
, vol.78
, pp. 6775-6785
-
-
Yuste, E1
Reeves, JD2
Doms, RW3
Desrosiers, RC.4
-
116
-
-
84925558761
-
Quantifying selection against synonymous mutations in HIV-1 env evolution
-
PMID: 23986591
-
Zanini F, Neher RA. 2013. Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of Virology 87:11843-11850. DOI: https://doi.org/10.1128/JVI.01529-13, PMID: 23986591
-
(2013)
Journal of Virology
, vol.87
, pp. 11843-11850
-
-
Zanini, F1
Neher, RA.2
-
117
-
-
77954100808
-
Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design
-
PMID: 20577269
-
Zolla-Pazner S, Cardozo T. 2010. Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design. Nature Reviews Immunology 10:527-535. DOI: https://doi.org/10.1038/nri2801, PMID: 20577269
-
(2010)
Nature Reviews Immunology
, vol.10
, pp. 527-535
-
-
Zolla-Pazner, S1
Cardozo, T.2
|