Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna
leads to efficient filtration for
Web-based design and evaluation of T-cell vaccine candidates (2008)
Thurmond, James, Yoon, Hyejin, Kuiken, Carla, Yusim, Karina, Perkins, Simon, Theiler, James, ...
Summary: We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric....
The hepatitis C sequence database in Los Alamos (2008)
Kuiken, Carla, Hraber, Peter, Thurmond, James, Yusim, Karina
The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and...
Hraber, Peter T, Fischer, William, Bruno, William J, Leitner, Thomas, Kuiken, Carla
Abstract Background The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel...
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
Abstract Background Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1 (2006)
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
The Los Alamos hepatitis C sequence database (2005)
Kuiken, Carla, Yusim, Karina, Boykin, Laura, Richardson, Russell
Motivation: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for...
Zhang, Ming, Gaschen, Brian, Blay, Wendy, Foley, Brian, Haigwood, Nancy, Kuiken, Carla, ...
Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore Nlinked...
Zhang, Ming, Gaschen, Brian, Blay, Wendy, Foley, Brian, Haigwood, Nancy, Kuiken, Carla, ...
Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore N-linked...
The Los Alamos hepatitis C sequence database (2004)
Kuiken, Carla, Yusim, Karina, Boykin, Laura, Richardson, Russell
Motivation: The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for...
Zhang, Ming, Gaschen, Brian, Blay, Wendy, Foley, Brian, Haigwood, Nancy, Kuiken, Carla, ...
Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore Nlinked...
The Los Alamos hepatitis C sequence database (2004)
Kuiken, Carla, Yusim, Karina, Boykin, Laura, Richardson, Russell
Motivation: The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for...
Retrieval and on-the-fly alignment of sequence fragments from the HIV database (2001)
Gaschen, Brian, Kuiken, Carla, Korber, Bette, Foley, Brian
Motivation: The amount of HIV-1 sequence data generated (presently around 42000 sequences, of which more than 22000 are from the V3 region of the viral envelope) presents a challenge for anyone...
Genetic Analysis Reveals Epidemiologic Patterns in the Spread of Human Immunodeficiency Virus (2000)
Kuiken, Carla, Thakallapalli, Rama, Eskild, Anne, De Ronde, Anthony
The extreme variability of human immunodeficiency virus type 1 (HIV-1) makes it possible to conduct transmission studies on the basis of genetic analysis and to trace global and local patterns in the...
Van ’t Wout, Angélique B., Blaak, Hetty, Ran, Leonie J., Brouwer, Margreet, Kuiken, Carla, Schuitemaker, Hanneke
To investigate the temporal relationship between human immunodeficiency virus type 1 (HIV-1) replicative capacity and syncytium-inducing (SI) phenotype, biological and genetic characteristics of...
Kunstman, Kevin J., Puffer, Bridget, Korber, Bette T., Kuiken, Carla, Smith, Una R., Kunstman, Jennifer, ...
A chemokine receptor from the seven-transmembrane-domain G-protein-coupled receptor superfamily is an essential coreceptor for the cellular entry of human immunodeficiency virus type 1 (HIV-1) and...
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
Van ’t Wout, Angélique B., Blaak, Hetty, Ran, Leonie J., Brouwer, Margreet, Kuiken, Carla, Schuitemaker, Hanneke
To investigate the temporal relationship between human immunodeficiency virus type 1 (HIV-1) replicative capacity and syncytium-inducing (SI) phenotype, biological and genetic characteristics of...
Kunstman, Kevin J., Puffer, Bridget, Korber, Bette T., Kuiken, Carla, Smith, Una R., Kunstman, Jennifer, ...
A chemokine receptor from the seven-transmembrane-domain G-protein-coupled receptor superfamily is an essential coreceptor for the cellular entry of human immunodeficiency virus type 1 (HIV-1) and...
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
Schultz, Anne-Kathrin, Zhang, Ming, Leitner, Thomas, Kuiken, Carla, Korber, Bette, Morgenstern, Burkhard, ...
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, ...
Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for...
Lok, Anna S., Zoulim, Fabien, Locarnini, Stephen, Bartholomeusz, Angeline, Ghany, Marc G., Pawlotsky, Jean-Michel, ...
Substantial advances have been made in the treatment of chronic hepatitis B in the past decade. Approved treatments for chronic hepatitis B include 2 formulations of interferon and 4 nucleos(t)ide...
The hepatitis C sequence database in Los Alamos
Kuiken, Carla, Hraber, Peter, Thurmond, James, Yusim, Karina
The hepatitis C virus (HCV) is a significant public health threat worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and...