Bette Korber, Brian Gaschen, Karina Yusim, Can Kesmir, Vincent Detours, Biophysics Los
Evolutionary modelling studies indicate less than a century has passed since the most recent common ancestor of the HIV-1 pandemic strains and, in that time frame, an extraordinarily diverse viral...
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...
Increased Sequence Diversity Coverage Improves Detection of HIV-Specific T Cell Responses (2007)
Frahm, Nicole, Kaufmann, Daniel E., Yusim, Karina, Muldoon, Mark, Kesmir, Can, Linde, Caitlyn H., ...
The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune...
Immunoinformatics Comes of Age (2006)
Bette Korber, Montiago LaBute, Karina Yusim
With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the...
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...
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...
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...
Karina Yusim, Can Kesmir, Brian Gaschen, Marylyn M. Addo, Marcus Altfeld, Søren Brunak, ...
The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published,...
Karina Yusim, Can Kesmir, Brian Gaschen, Marylyn M. Addo, Marcus Altfeld, Søren Brunak, ...
The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published,...
Yusim, Karina, Peters, Martine, Pybus, Oliver, Bhattacharya, Tanmoy, Delaporte, Eric, Mulanaga, Claire, ...
In earlier work, human immunodeficiency virus type 1 (HIV-1) sequences were analysed to estimate the timing of the ancestral sequence of the main group of HIV-1, the virus that is responsible for the...
Evolutionary and immunological implications of contemporary HIV-1 variation (2001)
Korber, Bette, Gaschen, Brian, Yusim, Karina, Thakallapally, Rama, Kesmir, Can, Detours, Vincent
Evolutionary modelling studies indicate less than a century has passed since the most recent common ancestor of the HIV-1 pandemic strains and, in that time frame, an extraordinarily diverse viral...
Yusim, Karina, Kesmir, Can, Gaschen, Brian, Addo, Marylyn M., Altfeld, Marcus, Brunak, Søren, ...
The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published,...
Immunoinformatics Comes of Age
Korber, Bette, LaBute, Montiago, Yusim, Karina
With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the...
Dickover, Ruth, Garratty, Eileen, Yusim, Karina, Miller, Catherine, Korber, Bette, Bryson, Yvonne
Perinatal human immunodeficiency virus type 1 (HIV-1) transmission is characterized by acquisition of a homogeneous viral quasispecies, yet the selective factors responsible for this genetic...
Yusim, Karina, Kesmir, Can, Gaschen, Brian, Addo, Marylyn M., Altfeld, Marcus, Brunak, Søren, ...
The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published,...
Immunoinformatics Comes of Age
Korber, Bette, LaBute, Montiago, Yusim, Karina
With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the...
Dickover, Ruth, Garratty, Eileen, Yusim, Karina, Miller, Catherine, Korber, Bette, Bryson, Yvonne
Perinatal human immunodeficiency virus type 1 (HIV-1) transmission is characterized by acquisition of a homogeneous viral quasispecies, yet the selective factors responsible for this genetic...
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...
Leslie, Alasdair, Kavanagh, Daniel, Honeyborne, Isobella, Pfafferott, Katja, Edwards, Charles, Pillay, Tilly, ...
Human immunodeficiency virus (HIV)-1 amino acid sequence polymorphisms associated with expression of specific human histocompatibility leukocyte antigen (HLA) class I alleles suggest sites of...
Goepfert, Paul A., Lumm, Wendy, Farmer, Paul, Matthews, Philippa, Prendergast, Andrew, Carlson, Jonathan M., ...
In a study of 114 epidemiologically linked Zambian transmission pairs, we evaluated the impact of human leukocyte antigen class I (HLA-I)–associated amino acid polymorphisms, presumed to reflect...