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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

Antiviral drug-resistant HBV: Standardization of nomenclature and assays and recommendations for management

Anna S. Lok, Fabien Zoulim, Stephen Locarnini, Angeline Bartholomeusz, Marc G. Ghany, Jean-Michel Pawlotsky, Yun-Fan Liaw, Masashi Mizokami, Carla Kuiken

Journal:

Year:

2007

Language:

english

File:

PDF, 231 KB

english, 2007

3

Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource

Smith, Donald B., Bukh, Jens, Kuiken, Carla, Muerhoff, A. Scott, Rice, Charles M., Stapleton, Jack T., Simmonds, Peter

Journal:

Year:

2014

Language:

english

File:

PDF, 712 KB

english, 2014

4

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

Brister, James Rodney, Bao, Yiming, Kuiken, Carla, Lefkowitz, Elliot J., Mercier, Philippe Le, Leplae, Raphael, Madupu, Ramana, Scheuermann, Richard H., Schobel, Seth, Seto, Donald, Shrivastava, Susmi

Journal:

Year:

2010

Language:

english

File:

PDF, 81 KB

english, 2010

5

A set of reference sequences for the hepatitis C genotypes 4d, 4f, and 4k covering the full open reading frame

Thomas Kuntzen, Andrew Berical, Jean Ndjomou, Phil Bennett, Arne Schneidewind, Niall Lennon, Bruce W. Birren, Carla Kuiken, Matthew R. Henn, Peter Simmonds, Todd M. Allen

Journal:

Journal of Medical Virology

Year:

2008

Language:

english

File:

PDF, 635 KB

english, 2008

6

Sequence Note Sequence Features Downstream of the Primer-Binding Site of HIV Type 1 Subtype E Shared by Subtype G and a Subset of Subtype A

Chang, Sui-Yuan, Apichartpiyakul, Chatchaw Ann, Kuiken, Carla L., Essex, Max, Lee1, Tun-Hou

Journal:

AIDS Research and Human Retroviruses

Year:

1999

Language:

english

File:

PDF, 211 KB

english, 1999

7

Genomic Analysis of HIV Type 1 Strains Derived from a Mother and Child Pair of Long-Term Nonprogressors

Reinis, Milan, Weiser, Barbara, Kuiken, Carla, Dong, Tao, Lang, Dorothy, Nachman, Sharon, Zhang, Yonghong, Rowland-Jones, Sarah, Burger, Harold

Journal:

AIDS Research and Human Retroviruses

Year:

2007

Language:

english

File:

PDF, 107 KB

english, 2007

8

Ancient co-speciation of simian foamy viruses and primates

Switzer, William M., Salemi, Marco, Shanmugam, Vedapuri, Gao, Feng, Cong, Mian-er, Kuiken, Carla, Bhullar, Vinod, Beer, Brigitte E., Vallet, Dominique, Gautier-Hion, Annie

Journal:

Year:

2005

Language:

english

File:

PDF, 553 KB

english, 2005

9

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: A problem of ancient DNA and molecular phylogenies

Antoinette C. Kuyl, Carla L. Kuiken, John T. Dekker, Wladimir R. K. Perizonius, Jaap Goudsmit

Journal:

Journal of Molecular Evolution

Year:

1995

Language:

english

File:

PDF, 623 KB

english, 1995

10

Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants

Fischer, Will, Perkins, Simon, Theiler, James, Bhattacharya, Tanmoy, Yusim, Karina, Funkhouser, Robert, Kuiken, Carla, Haynes, Barton, Letvin, Norman L, Walker, Bruce D

Journal:

Nature Medicine

Year:

2006

Language:

english

File:

PDF, 442 KB

english, 2006

11

WITHDRAWN: 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

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

Journal:

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

12

Linear versus conformational variation of V3 neutralization domains of HIV-1 during experimental and natural infection

Goudsmit, Jaap, Kuiken, Carla L., Nara, Peter L.

Journal:

Year:

1989

File:

PDF, 435 KB

1989

13

Los Alamos hepatitis C virus sequence and human immunology databases: An expanding resource for antiviral research

Hraber, Peter T., Leach, Robert W., Reilly, Lee P., Thurmond, James, Yusim, Karina, Kuiken, Carla

Journal:

Antiviral Chemistry & Chemotherapy

Year:

2007

Language:

english

File:

PDF, 168 KB

english, 2007

14

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

15

HIV-1 V3 domain variation in brain and spleen of children with AIDS: Tissue-specific evolution within host-determined quasispecies

Leon G. Epstein, Carla Kuiken, Benjamin M. Blumberg, Susan Hartman, Leroy R. Sharer, Marjon Clement, Jaap Goudsmit

Journal:

Year:

1991

Language:

english

File:

PDF, 915 KB

english, 1991

16

Hepatitis C Virus Genotype 1a NS5A Pretreatment Sequence Variation and Viral Kinetics in African American and White Patients

Layden‐Almer, Jennifer E., Kuiken, Carla, Ribeiro, Ruy M., Kunstman, Kevin J., Perelson, Alan S., Layden, Thomas J., Wolinsky, Steven M.

Journal:

The Journal of Infectious Diseases

Year:

2005

Language:

english

File:

PDF, 682 KB

english, 2005

17

Antibody Responses to HIV-1 Envelope and GAG Epitopes in HIV-1 Seroconverters with Rapid versus Slow Disease Progression

Gabriël Zwart, Lia van der Hoek, Margreeth Valk, Marlon T.E. Cornelissen, Elly Baan, John Dekker, Maarten Koot, Carla L. Kuiken, Jaap Goudsmit

Journal:

Year:

1994

File:

PDF, 502 KB

1994

18

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

19

Characterization of the African HIV-1 isolate CBL-4 (RUT) by partial sequence analysis and virus neutralization with peptide antibody and antisense phosphate-methylated DNA

Goudsmit, Jaap, Geelen, Jan, Keulen, Wilco, Notermans, Daan, Kuiken, Carla, Ramautarsing, Chitra, Smit, Lia, Koole, Leo, van Genderen, Marcel, Buck, Henk, Sninsky, John, Krone, Willy

Journal:

Year:

1990

File:

PDF, 529 KB

1990

20

Characterization of the African HIV-1 isolate CBL-4 (RUT) by partial sequence analysis and virus neutralization with peptide antibody and antisense phosphate-methylated DNA

Goudsmit, Jaap, Geelen, Jan, Keulen, Wilco, Notermans, Daan, Kuiken, Carla, Ramautarsing, Chitra, Smit, Lia, Koole, Leo, van Genderen, Marcel, Buck, Henk, Sninsky, John, Krone, Willy

Journal:

Year:

1990

File:

PDF, 48 KB

1990

21

Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences

Antoinette C. Kuyl, Carla L. Kuiken, John T. Dekker, Jaap Goudsmit

Journal:

Journal of Molecular Evolution

Year:

1995

Language:

english

File:

PDF, 778 KB

english, 1995

22

Sequence Note : HIV Type 1 Subtypes in The Netherlands Circulating among Women Originating from AIDS-Endemic Regions

LUKASHOV, VLADIMIR V., KUIKEN, CARLA L., BOER, KEES, GOUDSMIT, JAAP

Journal:

AIDS Research and Human Retroviruses

Year:

1996

Language:

english

File:

PDF, 343 KB

english, 1996

23

Gross Defects in the vpr and vpu Genes of HIV Type 1 Cannot Explain the Differences in RNA Copy Number between Long-Term Asymptomatics and Progressors

CORNELISSEN, MARION, KUIKEN, CARLA, ZORGDRAGER, FOKLA, HARTMAN, SUSAN, GOUDSMIT, JAAP

Journal:

AIDS Research and Human Retroviruses

Year:

1997

Language:

english

File:

PDF, 1.03 MB

english, 1997

24

Long‐Term Survivors in Nairobi: Complete HIV‐1 RNA Sequences and Immunogenetic Associations

Fang, Guowei, Kuiken, Carla, Weiser, Barbara, Rowland‐Jones, Sarah, Plummer, Francis, Chen, Chih‐Hsiung, Kaul, Rupert, Omu Anzala, Aggrey, Bwayo, Job, Kimani, Joshua, Philpott, Sean M., Kitchen, Chris

Journal:

The Journal of Infectious Diseases

Year:

2004

Language:

english

File:

PDF, 242 KB

english, 2004

25

A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes

Carla Kuiken, Christophe Combet, Jens Bukh, Tadasu Shin-I, Gilbert Deleage, Masashi Mizokami, Russell Richardson, Erwin Sablon, Karina Yusim, Jean-Michel Pawlotsky, Peter Simmonds, Los Alamos HIV data

Journal:

Year:

2006

Language:

english

File:

PDF, 2.32 MB

english, 2006

26

HIV Type 1 Subtype C in Addis Ababa, Ethiopia

ABEBE, ALMAZ, KUIKEN, CARLA L., GOUDSMIT, JAAP, VALK, MARGREETH, MESSELE, TSEHAYNESH, SAHLU, TEFERA, YENENEH, HAILU, FONTANET, ARNAUD, DE WOLF, FRANK, DE WIT, TOBIAS F. RINKE

Journal:

AIDS Research and Human Retroviruses

Year:

1997

Language:

english

File:

PDF, 582 KB

english, 1997

27

Transition From Long-Term Nonprogression to HIV-1 Disease Associated With Escape From Cellular Immune Control

Kemal, Kimdar Sherefa, Beattie, Tara, Dong, Tao, Weiser, Barbara, Kaul, Rupert, Kuiken, Carla, Sutton, Julian, Lang, Dorothy, Yang, Hongbing, Peng, Yan Chun, Collman, Ronald, Philpott, Sean, Rowland-J

Journal:

JAIDS Journal of Acquired Immune Deficiency Syndromes

Year:

2008

Language:

english

File:

PDF, 353 KB

english, 2008

28

Evidence for limited within-person evolution of the V3 domain of the HIV-1 envelope in the Amsterdam population

Kuiken, Carla L., Lukashov, Vladimir V., Baan, Elly, Dekker, John, Leunissen, Jack A.M., Goudsmit, Jaap

Journal:

Year:

1996

File:

PDF, 1.02 MB

1996

29

Conserved V3 Loop Sequences and Transmission of Human Immunodeficiency Virus Type 1

SHPAER, EUGENE G., DELWART, ERIC L., KUIKEN, CARLA L., GOUDSMIT, JAAP, BACHMANN, MICHAEL H., MULLINS, JAMES I.

Journal:

AIDS Research and Human Retroviruses

Year:

1994

Language:

english

File:

PDF, 1.10 MB

english, 1994

30

Greater diversity of the HIV-1 V3 neutralization domain in Tanzania compared with The Netherlands

Zwart, Gabriël, Wolfs, Tom F.W., Bookelman, Raymond, Hartman, Susan, Bakker, Margreet, Boucher, Charles A. B., Kuiken, Carla, Goudsmit, Jaap

Journal:

Year:

1993

File:

PDF, 764 KB

1993

31

Molecular and epidemiological profiles of hepatitis C virus genotype 4 in Denmark

Mette Brandt Eriksen, Louise Bruun Jørgensen, Henrik Krarup, Alex Lund Laursen, Peer Brehm Christensen, Axel Møller, Poul Schlichting, Carla Kuiken, Jens Bukh, Nina Weis

Journal:

Journal of Medical Virology

Year:

2010

Language:

english

File:

PDF, 245 KB

english, 2010

32

Recombination following superinfection by HIV-1

Fang, Guowei, Weiser, Barbara, Kuiken, Carla, Philpott, Sean M, Rowland-Jones, Sarah, Plummer, Francis, Kimani, Joshua, Shi, Binshan, Kaul, Rupert, Bwayo, Job, Anzala, Omu, Burger, Harold

Journal:

Year:

2004

Language:

english

File:

PDF, 270 KB

english, 2004

33

Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes

Peter Simmonds, Jens Bukh, Christophe Combet, Gilbert Deléage, Nobuyuki Enomoto, Stephen Feinstone, Phillippe Halfon, Geneviève Inchauspé, Carla Kuiken, Geert Maertens, Masashi Mizokami, Donald G. Mur

Journal:

Year:

2005

Language:

english

File:

PDF, 276 KB

english, 2005

34

Kaposi's sarcoma and AIDS

REISS, PETER, LANGE, JOEP M. A., KUIKEN, CARLA L., GOUDSMIT, JAAP

Journal:

Year:

1990

File:

PDF, 145 KB

1990

35

Increasing Antigenic and Genetic Diversity of the V3 Variable Domain of the Human Immunodeficiency Virus Envelope Protein in the Course of the AIDS Epidemic

Carla L. Kuiken, Gabriel Zwart, Elly Baan, Roel A. Coutinho, J. Anneke van Den Hoek and Jaap Goudsmit

Journal:

Proceedings of the National Academy of Sciences

Year:

1993

Language:

english

File:

PDF, 1018 KB

english, 1993

36

Characterization of the Specificity of the Human Antibody Response to the V3 Neutralization Domain of HIV-1

ZWART, GABRIËL, WOLFS, TOM F.W., VALK, MARGREETH, VAN DER HOEK, LIA, KUIKEN, CARLA L., GOUDSMIT, JAAP

Journal:

AIDS Research and Human Retroviruses

Year:

1992

Language:

english

File:

PDF, 1.72 MB

english, 1992

37

Evidence for HIV Type 1 Strains of U.S. Intravenous Drug Users as Founders of AIDS Epidemic among Intravenous Drug Users in Northern Europe

LUKASHOV, VLADIMIR V., KUIKEN, CARLA L., VLAHOV, DAVID, COUTINHO, ROEL A., GOUDSMIT, JAAP

Journal:

AIDS Research and Human Retroviruses

Year:

1996

Language:

english

File:

PDF, 732 KB

english, 1996

38

HIV-1 subtype C syncytium- and non-syncytium-inducing phenotypes and coreceptor usage among Ethiopian patients with AIDS

Abebe, Almaz, Demissie, Dereje, Goudsmit, Jaap, Brouwer, Margreet, Kuiken, Carla L., Pollakis, Georgios, Schuitemaker, Hanneke, Fontanet, Arnaud L., Rinke de Wit, Tobias F.

Journal:

Year:

1999

Language:

english

File:

PDF, 171 KB

english, 1999

39

AIDS prognosis based on HIV-1 RNA, CD4+ T-cell count and function

de Wolf, Frank, Spijkerman, Ingrid, Schellekens, Peter Th., Langendam, Miranda, Kuiken, Carla, Bakker, Margreet, Roos, Marijke, Coutinho, Roel, Miedema, Frank, Goudsmit, Jaap

Journal:

Year:

1997

Language:

english

File:

PDF, 534 KB

english, 1997

40

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

41

Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection

Peter Hraber, Carla Kuiken, Karina Yusim

Journal:

Year:

2007

Language:

english

File:

PDF, 181 KB

english, 2007

42

Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino acid substitution

Tom F.W. Wolfs, Gabriël Zwart, Margreet Bakker, Margreeth Valk, Carla L. Kuiken, Jaap Goudsmit

Journal:

Year:

1991

Language:

english

File:

PDF, 713 KB

english, 1991

43

Silent Mutation Pattern in V3 Sequences Distinguishes Virus according to Risk Group in Europe

KUIKEN, CARLA L., GOUDSMIT, JAAP

Journal:

AIDS Research and Human Retroviruses

Year:

1994

Language:

english

File:

PDF, 274 KB

english, 1994

44

Designing a low-cost drug resistance database for viral hepatitis

Journal:

Antiviral Therapy

Year:

2010

Language:

english

File:

PDF, 117 KB

english, 2010

45

Hepatitis C databases, principles and utility to researchers

Carla Kuiken, Masashi Mizokami, Gilbert Deleage, Karina Yusim, Francois Penin, Tadasu Shin-I, Céline Charavay, Ning Tao, Daniel Crisan, Delphine Grando, Anita Dalwani, Christophe Geourjon, Ashish Agra

Journal:

Year:

2006

Language:

english

File:

PDF, 677 KB

english, 2006

46

Construction of an Infectious HIV Type 1 Molecular Clone from an African Patient with a Subtype D/C Recombinant Virus

Shi, Binshan, Philpott, Sean M., Weiser, Barbara, Kuiken, Carla, Brunner, Cheryl, Fang, Guowei, Fowke, Keith R., Plummer, Francis A., Rowland-Jones, Sarah, Bwayo, Job, Anzala, Aggrey O., Kimani, Joshu

Journal:

AIDS Research and Human Retroviruses

Year:

2004

Language:

english

File:

PDF, 883 KB

english, 2004

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