Interactive HIV-Host Genome-to-Genome map

Bartha,Istvan

Publication date

October 2013

DOI

Abstract

Schematic representation of the HLA class I genes and of the SNPs associated with HIV-1 amino acid variants in the region. The association between human SNP's and viral amino acid variations are projected on the HIV-1 proteome

Extracted data

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Data Protection

Interactive HIV-Host Genome-to-Genome map

Bartha,Istvan

Open link

Publication date

October 2013

DOI

10.5281/zenodo.7138

Abstract

Extracted data

Morgane Rolland (25957)
Jonathan M. Carlson (117346)
Siriphan Manocheewa (361985)
J. Victor Swain (361987)
Erinn Lanxon-Cookson (361989)
Wenjie Deng (25960)
Christine M. Rousseau (83291)
Dana N. Raugi (135530)
Gerald H. Learn (64221)
Brandon S. Maust (361990)
Hoosen Coovadia (83292)
Thumbi Ndung'u (104433)
Philip J. R. Goulder (83293)
Bruce D. Walker (64224)
Christian Brander (64220)
David E. Heckerman (226479)
James I. Mullins (30582)

February 2013

Associations are depicted with a circular map: AA interactions among residues are represented wit...

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans

McLaren, Paul J
Ripke, Stephan
Pelak, Kimberly
Weintrob, Amy C
Patsopoulos, Nikolaos A
Jia, Xiaoming
Erlich, Rachel L
Lennon, Niall J
Kadie, Carl M
Heckerman, David
Gupta, Namrata
Haas, David W
Deeks, Steven G
Pereyra, Florencia
Walker, Bruce D
de Bakker, Paul IW

October 2012

A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 cont...

Kuan-Hsiang Gary Huang (210002)
Dominique Goedhals (302234)
Jonathan M. Carlson (117346)
Mark A. Brockman (260732)
Swati Mishra (352839)
Zabrina L. Brumme (178788)
Stephen Hickling (352843)
Christopher S. W. Tang (352846)
Toshiyuki Miura (147628)
Chris Seebregts (165522)
David Heckerman (25962)
Thumbi Ndung'u (104433)
Bruce Walker (39038)
Paul Klenerman (33807)
Dewald Steyn (302236)
Philip Goulder (87977)
Rodney Phillips (76846)
Cloete van Vuuren (302238)
John Frater (236996)

February 2013

The table shows the results of the association analysis between HLA ...

Interactive HIV-Host Genome-to-Genome map

Bartha,Istvan (5265865)

May 2018

Schematic representation of the HLA class I genes and of the SNPs associated with HIV-1 amino acid v...

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Bartha, István
Carlson, Jonathan M
Brumme, Chanson J
McLaren, Paul J
Brumme, Zabrina L
John, Mina
Haas, David W
Martinez-Picado, Javier
Dalmau, Judith
López-Galíndez, Cecilio
Casado, Concepción
Rauch, Andri
Günthard, Huldrych F
Bernasconi, Enos
Vernazza, Pietro
Klimkait, Thomas
Yerly Ferrillo, Sabine
O'Brien, Stephen J
Listgarten, Jennifer
Pfeifer, Nico
Lippert, Christoph
Fusi, Nicolo
Kutalik, Zoltán
Allen, Todd M
Müller, Viktor
Harrigan, P Richard
Heckerman, David
Telenti, Amalio
Fellay, Jacques

January 2013

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using...

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

Pereyra, F.
Jia, X.
McLaren, P.J.
Telenti, A.
de Bakker, P.I.W.
Walker, B.D.
Ripke, S.
Brumme, C.J.
Pulit, S.L.
Carrington, M.
Kadie, C.M.
Carlson, J.M.
Heckerman, D.
Graham, R.R.
Plenge, R.M.
Deeks, S.G.
Gianniny, L.
Crawford, G.
Sullivan, J.
Gonzalez, E.
Davies, L.
Camargo, A.
Moore, J.M
Beattie, N.
Gupta, S.
Crenshaw, A.
Burtt, N.P.
Guiducci, C.
Gupta, N.
Gao, X.
Qi, Y.
Yuki, Y.
Piechocka-Trocha, A.
Cutrell, E.
Rosenberg, R.
Moss, K.L.
Lemay, P.
O'Leary, J.
Schaefer, T.
Verma, P.
Tóth, I.
Block, B.
Baker, B.
Rothchild, A.
Lian, J.
Proudfoot, J.
Alvino, D.M.L.
Vine, S.
Addo, M.M.
Allen, T.M.
Altfeld, M.
Henn, M.R.
Le Gall, S.
Streeck, H.
Haas, D.W.
Kuritzkes, D.R.
Robbins, G.K.
Shafer, R.W.
Gulick, R.M.
Shikuma, C.M.
Haubrich, R.
Riddler, S.
Sax, P.E.
Daar, E.S.
Ribaudo, H.J.
Agan, B.
Agarwal, S.
Ahern, R.L.
Allen, B.L.
Altidor, S.
Altschuler, E.L.
Ambardar, S.
Anastos, K.
Anderson, B.
Anderson, V.
Andrady, U.
Antoniskis, D.
Bangsberg, D.
Barbaro, D.
Barrie, W.
Bartczak, J.
Barton, S.
Basden, P.
Basgoz, N.
Bazner, S.
Bellos, N.C.
Benson, A.M.
Berger, J.
Bernard, N.F.
Bernard, A.M.
Birch, C.
Bodner, S.J.
Bolan, R.K.
Boudreaux, E.T.
Bradley, M.
Braun, J.F.
Brndjar, J.E.
Brown, S.J.
Brown, K.
Brown, S.T.
Burack, J.
Bush, L.M.
Cafaro, V.
Campbell, O.
Campbell, J.
Carlson, R.H.
Carmichael, J.K.
Casey, K.K.
Cavacuiti, C.
Celestin, G.
Chambers, S.T.
Chez, N.
Chirch, L.M.
Cimoch, P.J.
Cohen, D.
Cohn, L.E.
Conway, B.
Cooper, D.A.
Cornelson, B.
Cox, D.T.
Cristofano, M.V.
Cuchural, G.
Czartoski, J.L.
Dahman, J.M.
Daly, J.S.
Davis, B.T.
Davis, K.
Davod, S.M.
DeJesus, E.
Dietz, C.A.
Dunham, E.
Dunn, M.E.
Ellerin, T.B.
Eron, J.J.
Fangman, J.J.W.
Farel, C.E.
Ferlazzo, H.
Fidler, S.
Fleenor-Ford, A.
Frankel, R.
Freedberg, K.A.
French, N.K.
Fuchs, J.D.
Fuller, J.D.
Gaberman, J.
Gallant, J.E.
Gandhi, R.T.
García, E.
Garmon, D.
Gathe, J.C.
Gaultier, C.R.
Gebre, W.
Gilman, F.D.
Gilson, I.
Goepfert, P.A.
Gottlieb, M.S.
Goulston, C.
Groger, R.K.
Gurley, T.D.
Haber, S.
Hardwicke, R.
Hardy, W.D.
Harrigan, P.R.
Hawkins, T.N.
Heath, S.
Hecht, F.M.
Henry, W.K.
Hladek, M.
Hoffman, R.P.
Horton, J.M.
Hsu, R.K.
Huhn, G.D.
Hunt, P.
Hupert, M.J.
Illeman, M.L.
Jaeger, H.
Jellinger, R.M.
John, M.
Johnson, J.A.
Johnson, K.L.
Johnson, H.
Johnson, K.
Joly, J.
Jordan, W.C.
Kauffman, C.A.
Khanlou, H.
Killian, R.K.
Kim, A.Y.
Kim, D.D.
Kinder, C.A.
Kirchner, J.T.
Kogelman, L.
Kojic, E.M.
Korthuis, P.T.
Kurisu, W.
Kwon, D.S.
LaMar, M.
Lampiris, H.
Lanzafame, M.
Lederman, M.M.
Lee, D.M.
Lee, J.M.L.
Lee, M.J.
Lee, E.T.Y.
Lemoine, J.
Levy, J.A.
Llibre, J.M.
Liguori, M.A.
Little, S.J.
Liu, A.Y.
Lopez, A.J.
Loutfy, M.R.
Loy, D.
Mohammed, D.Y.
Man, A.
Mansour, M.K.
Marconi, V.C.
Markowitz, M.
Marques, R.
Martin, J.N.
Martin, H.L.
Mayer, K.H.
McElrath, M.J.
McGhee, T.A.
McGovern, B.H.
McGowan, K.
McIntyre, D.
Mcleod, G.X.
Menezes, P.
Mesa, G.
Metroka, C.E.
Meyer-Olson, D.
Miller, A.O.
Montgomery, K.
Mounzer, K.C.
Nagami, E.H.
Nagin, I.
Nahass, R.G.
Nelson, M.O.
Nielsen, C.
Norene, D.L.
O'Connor, D.H.
Ojikutu, B.O.
Okulicz, J.
Oladehin, O.O.
Oldfield, E.C.
Olender, S.A.
Ostrowski, M.
Owen, W.F.
Pae, E.
Parsonnet, J.
Pavlatos, A.M.
Perlmutter, A.M.
Pierce, M.N.
Pincus, J.M.
Pisani, L.
Price, L.J.
Proia, L.
Prokesch, R.C.
Pujet, H.C.
Ramgopal, M.
Rathod, A.
Rausch, M.
Ravishankar, J.
Rhame, F.S.
Richards, C.S.
Richman, D.D.
Rodes, B.
Rodriguez, M.
Rose, R.C.
Rosenberg, E.S.
Rosenthal, D.
Ross, P.E.
Rubin, D.S.
Rumbaugh, E.
Saenz, L.
Salvaggio, M.R.
Sanchez, W.C.
Sanjana, V.M.
Santiago, S.
Schmidt, W.
Schuitemaker, H.
Sestak, P.M.
Shalit, P.
Shay, W.
Shirvani, V.N.
Silebi, V.I.
Sizemore, J.M.
Skolnik, P.R.
Sokol-Anderson, M.
Sosman, J.M.
Stabile, P.
Stapleton, J.T.
Starrett, S.
Stein, F.
Stellbrink, H-J
Sterman, F.L.
Stone, V.E.
Stone, D.R.
Tambussi, G.
Taplitz, R.A.
Tedaldi, E.M.
Telenti, A.
Theisen, W.
Torres, R.
Tosiello, L.
Tremblay, C.
Tribble, M.A.
Trinh, P.D.
Tsao, A.
Ueda, P.
Vaccaro, A.
Valadas, E.
Vanig, T.J.
Vecino, I.
Vega, V.M.
Veikley, W.
Wade, B.H.
Walworth, C.
Wanidworanun, C.
Ward, D.J.
Warner, D.A.
Weber, R.D.
Webster, D.
Weis, S.
Wheeler, D.A.
White, D.J.
Wilkins, E.
Winston, A.
Wlodaver, C.G.
van't Wout, A.
Wright, D.P.
Yang, O.O.
Yurdin, D.L.
Zabukovic, B.W.
Zachary, K.C.
Zeeman, B.
Zhao, M.

December 2010

Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the ma...

A whole-genome association study of major determinants for host control of HIV-1

FELLAY J
SHIANNA K. V
GE D
COLOMBO S
LEDERGERBER B
WEALE M
ZHANG K
GUMBS C
CASTAGNA A
COSSARIZZA, Andrea
COZZI LEPRI A
DE LUCA A
EASTERBROOK P
FRANCIOLI P
MALLAL S
MARTINEZ PICADO J
MIR J. M
OBEL N
SMITH J. P
WYNIGER J
DESCOMBES P
ANTONARAKIS S. E
LETVIN N. L
MCMICHAEL A. J
HAYNES B. F
TELENTI A
GOLDSTEIN D. B.

January 2007

Understanding why some people establish and maintain effective control of HIV-1 and others do not is...

A Genome-To-Genome Analysis of Associations between Human Genetic Variation, HIV-1 Sequence Diversity, and Viral Control

Bartha, Istvan
Carlson, Jonathan M.
Brumme, Chanson J.
McLaren, Paul J.
Brumme, Zabrina L.
John, Mina
Haas, David W.
Martinez-Picado, Javier
Dalmau, Judith
Lopez-Galindez, Cecilio
Casado, Concepcion
Rauch, Andri
Gunthard, Huldrych F.
Bernasconi, Enos
Vernazza, Pietro
Klimkait, Thomas
Yerly, Sabine
O\u27Brien, Stephen J.
Listgarten, Jennifer
Pfeifer, Nico
Lippert, Christoph
Fusi, Nicolo
Kutalik, Zoltan
Allen, Todd M.
Muller, Viktor
Harrigan, P. Richard
Heckerman, David
Telenti, Amalio
Fellay, Jacques

October 2013

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using...

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

Bartha, I.
Carlson, J.M.
Brumme, C.J.
McLaren, P.J.
Brumme, Z.L.
John, M.
Haas, D.W.
Martinez-Picado, J.
Dalmau, J.
López-Galíndez, C.
Casado, C.
Rauch, A.
Günthard, H.F.
Bernasconi, E.
Vernazza, P.
Klimkait, T.
Yerly, S.
O'Brien, S.J.
Listgarten, J.
Pfeifer, N.
Lippert, C.
Fusi, N.
Kutalik, Z.
Allen, T.M.
Müller, V.
Harrigan, P.R.
Heckerman, D.
Telenti, A.
Fellay, J.

January 2013

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using...

A whole-genome association study of major determinants for host control of HIV-1.

Fellay, J
Shianna, K
Ge, D
Colombo, S
Ledergerber, B
Weale, M
Zhang, K
Gumbs, C
Castagna, A
Cossarizza, A
Cozzi-Lepri, A
De Luca, A
Easterbrook, P
Francioli, P
Mallal, S
Martinez-Picado, J
Miro, J
Obel, N
Smith, J
Wyniger, J
Descombes, P
Antonarakis, SE
Letvin, N
Mcmichael, A
Haynes, B

January 2007

Understanding why some people establish and maintain effective control of HIV-1 and others do not is...

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.

Luo, Y.
Kanai, M.
Choi, W.
Li, X.
Sakaue, S.
Yamamoto, K.
Ogawa, K.
Gutierrez-Arcelus, M.
Gregersen, P.K.
Stuart, P.E.
Elder, J.T.
Forer, L.
Schönherr, S.
Fuchsberger, C.
Smith, A.V.
Fellay, J.
Carrington, M.
Haas, D.W.
Guo, X.
Palmer, N.D.
Chen, Y.I.
Rotter, J.I.
Taylor, K.D.
Rich, S.S.
Correa, A.
Wilson, J.G.
Kathiresan, S.
Cho, M.H.
Metspalu, A.
Esko, T.
Okada, Y.
Han, B.
McLaren, P.J.
Raychaudhuri, S.

October 2021

Fine-mapping to plausible causal variation may be more effective in multi-ancestry cohorts, particul...

Common DNA variants within the MHC region that are associated with HIV-1 acquisition comparing 6,334 HIV-1 infected patients to 7,247 population controls are driven by HIV-1 controllers and not maintained when restricting to patients with known dates of seroconversion.

Paul J. McLaren (151463)
Cédric Coulonges (76755)
Stephan Ripke (156076)
Leonard van den Berg (437389)
Susan Buchbinder (31646)
Mary Carrington (64679)
Andrea Cossarizza (295123)
Judith Dalmau (180283)
Steven G. Deeks (131630)
Olivier Delaneau (76754)
Andrea De Luca (132288)
James J. Goedert (199127)
David Haas (437390)
Joshua T. Herbeck (214670)
Sekar Kathiresan (60585)
Gregory D. Kirk (199129)
Olivier Lambotte (252533)
Ma Luo (153573)
Simon Mallal (75844)
Daniëlle van Manen (85698)
Javier Martinez-Picado (91236)
Laurence Meyer (130347)
José M. Miro (255427)
James I. Mullins (30582)
Niels Obel (135891)
Stephen J. O'Brien (53045)
Florencia Pereyra (178819)
Francis A. Plummer (149579)
Guido Poli (164113)
Ying Qi (59980)
Pierre Rucart (437391)
Manj S. Sandhu (200068)
Patrick R. Shea (437392)
Hanneke Schuitemaker (85702)
Ioannis Theodorou (157932)
Fredrik Vannberg (437393)
Jan Veldink (187567)
Bruce D. Walker (64224)
Amy Weintrob (299466)
Cheryl A. Winkler (115868)
Steven Wolinsky (437394)
Amalio Telenti (25361)
David B. Goldstein (194563)
Paul I. W. de Bakker (61332)
Jean-François Zagury (76757)
Jacques Fellay (192975)

July 2013

A) Regional association plot of the locus containing genome-wide significant SNPs after meta-anal...

Amino Acid associations in HIV-1 subtype C Gag.

Morgane Rolland (25957)
Jonathan M. Carlson (117346)
Siriphan Manocheewa (361985)
J. Victor Swain (361987)
Erinn Lanxon-Cookson (361989)
Wenjie Deng (25960)
Christine M. Rousseau (83291)
Dana N. Raugi (135530)
Gerald H. Learn (64221)
Brandon S. Maust (361990)
Hoosen Coovadia (83292)
Thumbi Ndung'u (104433)
Philip J. R. Goulder (83293)
Bruce D. Walker (64224)
Christian Brander (64220)
David E. Heckerman (226479)
James I. Mullins (30582)

February 2013

Associations are depicted with a circular map: AA interactions among residues are represented wit...

Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans

McLaren, Paul J
Ripke, Stephan
Pelak, Kimberly
Weintrob, Amy C
Patsopoulos, Nikolaos A
Jia, Xiaoming
Erlich, Rachel L
Lennon, Niall J
Kadie, Carl M
Heckerman, David
Gupta, Namrata
Haas, David W
Deeks, Steven G
Pereyra, Florencia
Walker, Bruce D
de Bakker, Paul IW

October 2012

A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 cont...

Kuan-Hsiang Gary Huang (210002)
Dominique Goedhals (302234)
Jonathan M. Carlson (117346)
Mark A. Brockman (260732)
Swati Mishra (352839)
Zabrina L. Brumme (178788)
Stephen Hickling (352843)
Christopher S. W. Tang (352846)
Toshiyuki Miura (147628)
Chris Seebregts (165522)
David Heckerman (25962)
Thumbi Ndung'u (104433)
Bruce Walker (39038)
Paul Klenerman (33807)
Dewald Steyn (302236)
Philip Goulder (87977)
Rodney Phillips (76846)
Cloete van Vuuren (302238)
John Frater (236996)

February 2013

The table shows the results of the association analysis between HLA ...

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Bartha, István
Carlson, Jonathan M
Brumme, Chanson J
McLaren, Paul J
Brumme, Zabrina L
John, Mina
Haas, David W
Martinez-Picado, Javier
Dalmau, Judith
López-Galíndez, Cecilio
Casado, Concepción
Rauch, Andri
Günthard, Huldrych F
Bernasconi, Enos
Vernazza, Pietro
Klimkait, Thomas
Yerly Ferrillo, Sabine
O'Brien, Stephen J
Listgarten, Jennifer
Pfeifer, Nico
Lippert, Christoph
Fusi, Nicolo
Kutalik, Zoltán
Allen, Todd M
Müller, Viktor
Harrigan, P Richard
Heckerman, David
Telenti, Amalio
Fellay, Jacques

January 2013

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using...

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation

Pereyra, F.
Jia, X.
McLaren, P.J.
Telenti, A.
de Bakker, P.I.W.
Walker, B.D.
Ripke, S.
Brumme, C.J.
Pulit, S.L.
Carrington, M.
Kadie, C.M.
Carlson, J.M.
Heckerman, D.
Graham, R.R.
Plenge, R.M.
Deeks, S.G.
Gianniny, L.
Crawford, G.
Sullivan, J.
Gonzalez, E.
Davies, L.
Camargo, A.
Moore, J.M
Beattie, N.
Gupta, S.
Crenshaw, A.
Burtt, N.P.
Guiducci, C.
Gupta, N.
Gao, X.
Qi, Y.
Yuki, Y.
Piechocka-Trocha, A.
Cutrell, E.
Rosenberg, R.
Moss, K.L.
Lemay, P.
O'Leary, J.
Schaefer, T.
Verma, P.
Tóth, I.
Block, B.
Baker, B.
Rothchild, A.
Lian, J.
Proudfoot, J.
Alvino, D.M.L.
Vine, S.
Addo, M.M.
Allen, T.M.
Altfeld, M.
Henn, M.R.
Le Gall, S.
Streeck, H.
Haas, D.W.
Kuritzkes, D.R.
Robbins, G.K.
Shafer, R.W.
Gulick, R.M.
Shikuma, C.M.
Haubrich, R.
Riddler, S.
Sax, P.E.
Daar, E.S.
Ribaudo, H.J.
Agan, B.
Agarwal, S.
Ahern, R.L.
Allen, B.L.
Altidor, S.
Altschuler, E.L.
Ambardar, S.
Anastos, K.
Anderson, B.
Anderson, V.
Andrady, U.
Antoniskis, D.
Bangsberg, D.
Barbaro, D.
Barrie, W.
Bartczak, J.
Barton, S.
Basden, P.
Basgoz, N.
Bazner, S.
Bellos, N.C.
Benson, A.M.
Berger, J.
Bernard, N.F.
Bernard, A.M.
Birch, C.
Bodner, S.J.
Bolan, R.K.
Boudreaux, E.T.
Bradley, M.
Braun, J.F.
Brndjar, J.E.
Brown, S.J.
Brown, K.
Brown, S.T.
Burack, J.
Bush, L.M.
Cafaro, V.
Campbell, O.
Campbell, J.
Carlson, R.H.
Carmichael, J.K.
Casey, K.K.
Cavacuiti, C.
Celestin, G.
Chambers, S.T.
Chez, N.
Chirch, L.M.
Cimoch, P.J.
Cohen, D.
Cohn, L.E.
Conway, B.
Cooper, D.A.
Cornelson, B.
Cox, D.T.
Cristofano, M.V.
Cuchural, G.
Czartoski, J.L.
Dahman, J.M.
Daly, J.S.
Davis, B.T.
Davis, K.
Davod, S.M.
DeJesus, E.
Dietz, C.A.
Dunham, E.
Dunn, M.E.
Ellerin, T.B.
Eron, J.J.
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Zachary, K.C.
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Zhao, M.

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SHIANNA K. V
GE D
COLOMBO S
LEDERGERBER B
WEALE M
ZHANG K
GUMBS C
CASTAGNA A
COSSARIZZA, Andrea
COZZI LEPRI A
DE LUCA A
EASTERBROOK P
FRANCIOLI P
MALLAL S
MARTINEZ PICADO J
MIR J. M
OBEL N
SMITH J. P
WYNIGER J
DESCOMBES P
ANTONARAKIS S. E
LETVIN N. L
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HAYNES B. F
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Dalmau, Judith
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Casado, Concepcion
Rauch, Andri
Gunthard, Huldrych F.
Bernasconi, Enos
Vernazza, Pietro
Klimkait, Thomas
Yerly, Sabine
O\u27Brien, Stephen J.
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Lippert, Christoph
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Abstract

Extracted data

Interactive HIV-Host Genome-to-Genome map

Abstract

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