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1

Integrated sequence and immunology filovirus database at Los Alamos

Yusim, Karina, Yoon, Hyejin, Foley, Brian, Feng, Shihai, Macke, Jennifer, Dimitrijevic, Mira, Abfalterer, Werner, Szinger, James, Fischer, Will, Kuiken, Carla, Korber, Bette

Journal:

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

2

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

Hraber, Peter, Korber, Bette, Wagh, Kshitij, Giorgi, Elena, Bhattacharya, Tanmoy, Gnanakaran, S., Lapedes, Alan, Learn, Gerald, Kreider, Edward, Li, Yingying, Shaw, George, Hahn, Beatrice, Montefiori,

Journal:

Year:

2015

Language:

english

File:

PDF, 2.81 MB

english, 2015

3

Killer cell immunoglobulin-like receptors (KIR) of the African-origin sabaeus monkey: evidence for recombination events in the evolution of KIR

Karen L. Hershberger, Jessica Kurian, Bette T. Korber, Norman L. Letvin

Journal:

European Journal of Immunology

Year:

2005

Language:

english

File:

PDF, 838 KB

english, 2005

4

HIV-1 intra-subtype superinfection rates: estimates using a structured coalescent with recombination

Jesse E. Taylor, Bette T. Korber

Journal:

Infection, Genetics and Evolution

Year:

2005

Language:

english

File:

PDF, 186 KB

english, 2005

5

The KIR and CD94/NKG2 families of molecules in the rhesus monkey

Michelle L. LaBonte, Karen L. Hershberger, Bette Korber, Norman L. Letvin

Journal:

Immunological Reviews

Year:

2001

Language:

english

File:

PDF, 599 KB

english, 2001

6

Recent Evolutionary History of Human Immunodeficiency Virus Type 1 Subtype B—Response

Una R. Smith, Carla R. Kuiken, Bette T. Korber

Journal:

Journal of Molecular Evolution

Year:

2003

Language:

english

File:

PDF, 53 KB

english, 2003

7

10.1038/35400

Ho, David D., Zhu, Tuofu, Korber, Bette T., Nahmias, Andre J., Hooper, Edward, Sharp, Paul M.

Journal:

Year:

1998

Language:

english

File:

PDF, 233 KB

english, 1998

8

10.1038/88656

Walker, Bruce D., Korber, Bette T.

Journal:

Nature Immunology

Year:

2001

Language:

english

File:

PDF, 398 KB

english, 2001

9

HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus

Altfeld, Marcus, Allen, Todd M., Yu, Xu G., Johnston, Mary N., Agrawal, Deepak, Korber, Bette T., Montefiori, David C., O'Connor, David H., Davis, Ben T., Lee, Paul K.

Journal:

Year:

2002

Language:

english

File:

PDF, 524 KB

english, 2002

10

addendum: HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus

Altfeld, Marcus, Allen, Todd M., Yu, Xu G., Johnston, Mary N., Agrawal, Deepak, Korber, Bette T., Montefiori, David C., O'Connor, David H., Davis, Ben T., Lee, Paul K.

Journal:

Year:

2003

Language:

english

File:

PDF, 85 KB

english, 2003

11

Maternal HIV-1 viral load and vertical transmission of infection: The Ariel Project for the prevention of HIV transmission from mother to infant

Cao, Yunzhen, Krogstad, Paul, Korber, Bette T., Koup, Richard A., Muldoon, Mark, Macken, Catherine, Song, Jia-Li, Jin, Zhanqun, Zhao, Jla-Qi, Clapp, Sheila

Journal:

Nature Medicine

Year:

1997

File:

PDF, 548 KB

1997

12

Advantage of rare HLA supertype in HIV disease progression

Trachtenberg, Elizabeth, Korber, Bette, Sollars, Cristina, Kepler, Thomas B, Hraber, Peter T, Hayes, Elizabeth, Funkhouser, Robert, Fugate, Michael, Theiler, James, Hsu, Yen S

Journal:

Nature Medicine

Year:

2003

Language:

english

File:

PDF, 136 KB

english, 2003

13

Liver transplantation with hepatitis C virus-infected graft: Interaction between donor and recipient viral strains

Xiaofeng Fan, Dorothy M. Lang, Yanjuan Xu, Andre C. Lyra, Karina Yusim, James E. Everhart, Bette T.M. Korber, Alan S. Perelson, Adrian M. Di Bisceglie

Journal:

Year:

2003

Language:

english

File:

PDF, 195 KB

english, 2003

14

Expression and evolutionary analysis of West Nile virus (Merion Strain)

Mathura P. Ramanathan, Jerome A. Chambers, Jesse Taylor, Bette T. Korber, Mark D. Lee, Aysegul Nalca, Kesan Dang, Panyupa Pankhong, Watcharee Attatippaholkun, David B. Weiner

Journal:

Journal of NeuroVirology

Year:

2005

Language:

english

File:

PDF, 960 KB

english, 2005

15

The Sequential Introduction of HIV-1 Subtype B and CRF01 AE in Singapore by Sexual Transmission: Accelerated V3 Region Evolution in a Subpopulation of Asian CRF01 Viruses

Marcia L. Kalish, Bette T. Korber, Satish Pillai, Kenneth E. Robbins, Yee Sin Leo, Ae Saekhou, Iris Verghese, Phillip Gerrish, Chee Leok Goh, Davis Lupo, Boon Huan Tan, Teresa M. Brown, Roy Chan

Journal:

Year:

2002

Language:

english

File:

PDF, 577 KB

english, 2002

16

Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes

Christine M. Rousseau, Brian A. Birditt, Angela R. McKay, Julia N. Stoddard, Tsan Chun Lee, Sherry McLaughlin, Sarah W. Moore, Nice Shindo, Gerald H. Learn, Bette T. Korber, Christian Brander, Philip

Journal:

Journal of Virological Methods

Year:

2006

Language:

english

File:

PDF, 301 KB

english, 2006

17

Mycobacterium tuberculosis – Heterogeneity revealed through whole genome sequencing

Chris Ford, Karina Yusim, Tom Ioerger, Shihai Feng, Michael Chase, Mary Greene, Bette Korber, Sarah Fortune

Journal:

Year:

2012

Language:

english

File:

PDF, 913 KB

english, 2012

18

The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4

Pavel Pugach, Shawn E Kuhmann, Joann Taylor, Andre J Marozsan, Amy Snyder, Thomas Ketas, Steven M Wolinsky, Bette T Korber, John P Moore

Journal:

Year:

2004

Language:

english

File:

PDF, 555 KB

english, 2004

19

Analysis of HIV-1 subtype B third variable region peptide motifs for induction of neutralizing antibodies against HIV-1 primary isolates

Barton F. Haynes, Benjiang Ma, David C. Montefiori, Terri Wrin, Christos J. Petropoulos, Laura L. Sutherland, Richard M. Scearce, Cathrine Denton, Shi-Mao Xia, Bette T. Korber, Hua-Xin Liao

Journal:

Year:

2006

Language:

english

File:

PDF, 655 KB

english, 2006

20

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

Elena E Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S Perelson, Bette T Korber, Tanmoy Bhattacharya

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 785 KB

english, 2010

21

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette Korber, Burkhard Morgenstern, Mario Stanke

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 893 KB

english, 2006

22

The role of recombination in the emergence of a complex and dynamic HIV epidemic

Ming Zhang, Brian Foley, Anne-Kathrin Schultz, Jennifer P Macke, Ingo Bulla, Mario Stanke, Burkhard Morgenstern, Bette Korber, Thomas Leitner

Journal:

Year:

2010

Language:

english

File:

PDF, 1.94 MB

english, 2010

23

Extensive HLA class I binding promiscuity among EBV- and HIV- derived cytotoxic T lymphocyte epitopes

Nicole Frahm, Karina Yusim, Peter Hraber, Sharon Adams, Franco Marincola, Bette Korber, Christian Brander

Journal:

Human Immunology

Year:

2004

Language:

english

File:

PDF, 21 KB

english, 2004

24

Association of HLA class I supertypes with HIV-1 disease progression in the Chicago MACS: evidence for frequency-dependent selection

Elizabeth Trachtenberg, Bette Korber, Cristina Sollars, Elizabeth Hayes, Robert Funkhouser, Tom Kepler, Peter Hraber, Michael Hsu, Henry Erlich, Steven Wolinsky

Journal:

Human Immunology

Year:

2002

Language:

english

File:

PDF, 33 KB

english, 2002

25

The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data

Irina Maljkovic Berry, Gayathri Athreya, Moulik Kothari, Marcus Daniels, William J. Bruno, Bette Korber, Carla Kuiken, Ruy M. Ribeiro, Thomas Leitner

Journal:

Year:

2009

Language:

english

File:

PDF, 820 KB

english, 2009

26

Evolution of hepatitis C viral quasispecies after liver transplantation

Andre C. Lyra, Xiaofeng Fan, Dorothy M. Lang, Karina Yusim, Sanjay Ramrakhiani, Elizabeth M. Brunt, Bette Korber, Alan S. Perelson, Adrian M. Di Bisceglie

Journal:

Gastroenterology

Year:

2002

Language:

english

File:

PDF, 263 KB

english, 2002

27

HIV-1 Reverse Transcriptase: A Diversity Generator and Quasispecies Regulator

JOSÉ L. MUNOZ, WADE P. PARKS, STEVEN M. WOLINSKY, BETTE T. M. KORBER, CECELIA HUTTO

Journal:

Annals of the New York Academy of Sciences

Year:

1993

Language:

english

File:

PDF, 372 KB

english, 1993

28

Quantifying Residual HIV-1 Replication in Patients Receiving Combination Antiretroviral Therapy

Zhang, Linqi, Ramratnam, Bharat, Tenner-Racz, Klara, He, Yuxian, Vesanen, Mika, Lewin, Sharon, Talal, Andrew, Racz, Paul, Perelson, Alan S., Korber, Bette T., Markowitz, Martin, Guo, Yong, Duran, Marg

Journal:

Boston Medical and Surgical Journal

Year:

1999

Language:

english

File:

PDF, 304 KB

english, 1999

29

Modeling sequence evolution in HIV-1 infection with recombination

Giorgi, Elena E., Korber, Bette T., Perelson, Alan S., Bhattacharya, Tanmoy

Journal:

Journal of Theoretical Biology

Year:

2013

Language:

english

File:

PDF, 608 KB

english, 2013

30

HIV-1 Vaccine Development After STEP

Barouch, Dan H., Korber, Bette

Journal:

Annual Review of Medicine

Year:

2010

Language:

english

File:

PDF, 371 KB

english, 2010

31

A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling

Imholte, Greg C., Sauteraud, Renan, Korber, Bette, Bailer, Robert T., Turk, Ellen T., Shen, Xiaoying, Tomaras, Georgia D., Mascola, John R., Koup, Richard A., Montefiori, David C., Gottardo, Raphael

Journal:

Journal of Immunological Methods

Year:

2013

Language:

english

File:

PDF, 3.84 MB

english, 2013

32

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Brodin, Johanna, Krishnamoorthy, Mohan, Athreya, Gayathri, Fischer, Will, Hraber, Peter, Gleasner, Cheryl, Green, Lance, Korber, Bette, Leitner, Thomas

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 437 KB

english, 2013

33

Cross-reactive potential of human T-lymphocyte responses in HIV-1 infection

Giorgi, Elena E., Balachandran, Harikrishnan, Muldoon, Mark, Letvin, Norman L., Haynes, Barton F., Korber, Bette T., Santra, Sampa

Journal:

Year:

2014

Language:

english

File:

PDF, 680 KB

english, 2014

34

Network Analysis of the Communication Pathways in HIV-1 Envelope Proteins For Mechanistic Understanding of Immune Escape

Sethi, Anurag, Derdeyn, Cynthia, Korber, Bette, Gnanakaran, S.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 51 KB

english, 2011

35

Regulation of Murine Class I Genes by Interferons is Controlled by Regions Located Both 5′and 3′to the Transcription Initiation Site

Bette Korber, Leroy Hood and Iwona Stroynowski

Journal:

Proceedings of the National Academy of Sciences

Year:

1987

Language:

english

File:

PDF, 987 KB

english, 1987

36

Association between Maternal and Infant Class I and II HLA Alleles and of Their Concordance with the Risk of Perinatal HIV Type 1 Transmission

Polycarpou, Anastasia, Ntais, Christos, Korber, Bette T., Elrich, Henry A., Winchester, Robert, Krogstad, Paul, Wolinsky, Steven, Rostron, Timothy, Rowland-Jones, Sarah L., Ammann, Arthur J., Ioannidi

Journal:

AIDS Research and Human Retroviruses

Year:

2002

Language:

english

File:

PDF, 114 KB

english, 2002

37

The World Health Organization Global Programme on AIDS Proposal for Standardization of HIV Sequence Nomenclature

KORBER, BETTE T.M., OSMANOV, SALADIN, ESPARZA, JOSE, MYERS, GERALD

Journal:

AIDS Research and Human Retroviruses

Year:

1994

Language:

english

File:

PDF, 610 KB

english, 1994

38

The Emergence of Simian/Human Immunodeficiency Viruses

MYERS, GERALD, MacINNES, KERSTI, KORBER, BETTE

Journal:

AIDS Research and Human Retroviruses

Year:

1992

Language:

english

File:

PDF, 2.42 MB

english, 1992

39

Comment to the Letter to the Editor

Brander, Christian, Walker, Bruce D., Korber, Bette

Journal:

AIDS Research and Human Retroviruses

Year:

1998

Language:

english

File:

PDF, 287 KB

english, 1998

40

HIV-1 Sequence Variation Between Isolates from Mother-Infant Transmission Pairs

WIKE, CARLA M., KORBER, BETTE T.M., DANIELS, MICHAEL R., HUTTO, CECELIA, MUÑOZ, JOSE, FURTADO, MANOHAR, PARKS, WADE, SAAH, ALFRED, BULTERYS, MARC, KURAWIGE, JEAN-BAPTISTE, WOLINSKY, STEVEN M.

Journal:

AIDS Research and Human Retroviruses

Year:

1992

Language:

english

File:

PDF, 650 KB

english, 1992

41

HIV Type 1 V3 Region Primer-Induced Antibody Suppression Is Overcome by Administration of C4-V3 Peptides as a Polyvalent Immunogen

HAYNES, BARTON F., MOODY, M. ANTHONY, HEINLEY, CRAIG S., KORBER, BETTE, MILLARD, WILLIAM A., SCEARCE, RICHARD M.

Journal:

AIDS Research and Human Retroviruses

Year:

1995

Language:

english

File:

PDF, 1.47 MB

english, 1995

42

A Computer Program Designed to Screen Rapidly for HIV Type 1 Intersubtype Recombinant Sequences

SIEPEL, ADAM C., HALPERN, AARON L., MACKEN, CATHERINE, KORBER, BETTE T.M.

Journal:

AIDS Research and Human Retroviruses

Year:

1995

Language:

english

File:

PDF, 510 KB

english, 1995

43

Mother-to-Child Transmission in the United States of Subtypes D and A/G Human Immunodeficiency Virus Type 1

Krogstad, Paul, Eshleman, Susan H., Geng, Yongzhi, Jackson, J. Brooks, Wantman, Michael, Korber, Bette, Lang, Dorothy, Wiznia, Andrew, Johnson, George, Nachman, Sharon, Palumbo, Paul

Journal:

AIDS Research and Human Retroviruses

Year:

2002

Language:

english

File:

PDF, 106 KB

english, 2002

44

AIDS Research Pioneer Gerry Myers Dies

Korber, Bette, Foley, Brian

Journal:

AIDS Research and Human Retroviruses

Year:

2011

Language:

english

File:

PDF, 91 KB

english, 2011

45

Molecular Characterization of a Highly Divergent HIV Type 1 Isolate Obtained Early in the AIDS Epidemic from the Democratic Republic of Congo

Gao, Feng, Trask, Stanley A., Hui, Huxong, Mamaeva, Olga, Chen, Yalu, Theodore, Theodore S., Foley, Brian T., Korber, Bette T., Shaw, George M., Hahn, Beatrice H.

Journal:

AIDS Research and Human Retroviruses

Year:

2001

Language:

english

File:

PDF, 313 KB

english, 2001

46

Associations between Amino Acids in the Evolution of HIV Type 1 Protease Sequences under Indinavir Therapy

Brown, Andrew J. Leigh, Korber, Bette T., Condra, Jon H.

Journal:

AIDS Research and Human Retroviruses

Year:

1999

Language:

english

File:

PDF, 346 KB

english, 1999

47

Detection of HIV-1 p24 Gag in plasma by a nanoparticle-based bio-barcode-amplification method

Kim, Eun-Young, Stanton, Jennifer, Korber, Bette TM, Krebs, Kendall, Bogdan, Derek, Kunstman, Kevin, Wu, Samuel, Phair, John P, Mirkin, Chad A, Wolinsky, Steven M

Journal:

Year:

2008

Language:

english

File:

PDF, 4.51 MB

english, 2008

48

HIV Type 1 Molecular Clones Able to Use the Bonzo/STRL-33 Coreceptor for Virus Entry

Zhang, Yi-Jun, Zhang, Linqi, Ketas, Tom, Korber, Bette T.M., Moore, John P.

Journal:

AIDS Research and Human Retroviruses

Year:

2001

Language:

english

File:

PDF, 258 KB

english, 2001

49

Diversity of V3 Region Sequences of Human Immunodeficiency Viruses Type 1 from the Central African Republic

MURPHY, ELLEN, KORBER, BETTE, GEORGES-COURBOT, MARIE-CLAUDE, YOU, BRUNO, PINTER, ABRAHAM, COOK, DEBRA, KIENY, MARIE-PAULE, GEORGES, ALAIN, MATHIOT, CHRISTIAN, BARRÉ-SINOUSSI, FRANCOISE, GIRARD, MARC

Journal:

AIDS Research and Human Retroviruses

Year:

1993

Language:

english

File:

PDF, 1.63 MB

english, 1993

50

Signature Pattern Analysis: A Method for Assessing Viral Sequence Relatedness

KORBER, BETTE, MYERS, GERALD

Journal:

AIDS Research and Human Retroviruses

Year:

1992

Language:

english

File:

PDF, 1.91 MB

english, 1992

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