Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates (2009)
Bjoern Peters, Alan Ruttenberg, Jason Greenbaum, Melanie Courtot, Ryan Brinkman, Patricia Whetzel, ...
The developers of the Ontology of Biomedical Investigations (OBI) primarily use Protégé for editing. However, adding many classes with similar patterns of logical definition is time...
Hematopoietic Cell Types: Prototype for a Revised Cell Ontology (2009)
Alexander D. Diehl, Alison D. Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, ...
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology. A recent workshop sponsored by NIAID on hematopoietic cell types in the...
Hematopoietic Cell Types: Prototype for a Revised Cell Ontology (2009)
Alexander D. Diehl, Alison D. Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, ...
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision...
Ontology for Biomedical Investigations (2009)
Bjoern Peters, The OBI Consortium
The goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made...
Yongqun He, Lindsay Cowell, Alexander D. Diehl, Harry Mobley, Bjoern Peters, Alan Ruttenberg, ...
Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein...
Yongqun He, Lindsay Cowell, Alexander D. Diehl, Harry Mobley, Bjoern Peters, Alan Ruttenberg, ...
The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects...
Of mice and humans: how good are HLA transgenic mice as a model of human immune responses? (2009)
Kotturi, Maya F, Assarsson, Erika, Peters, Bjoern, Grey, Howard, Oseroff, Carla, Pasquetto, Valerie, ...
Abstract Background Previous studies have defined vaccinia virus (VACV)-derived T cell epitopes in VACV-infected human leukocyte antigen-A*0201 (HLA-A2.1) transgenic (Tg) mice and A2.1-positive human...
ElliPro: a new structure-based tool for the prediction of antibody epitopes (2008)
Ponomarenko, Julia, Bui, Huynh-Hoa, Li, Wei, Fusseder, Nicholas, Bourne, Philip E, Sette, Alessandro, ...
Abstract Background Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity,...
DOI 10.1007/s00251-005-0803-5 ORIGINAL PAPER (2008)
Bjoern Peters, John Sidney, Phil Bourne, Huynh-hoa Bui, Soeren Buus, David Nemazee, ...
The design and implementation of the immune epitope database and analysis resource
Sidney, John, Assarsson, Erika, Moore, Carrie, Ngo, Sandy, Pinilla, Clemencia, Sette, Alessandro, ...
Abstract Background It has been previously shown that combinatorial peptide libraries are a useful tool to characterize the binding specificity of class I MHC molecules. Compared to other...
HLA class I supertypes: a revised and updated classification (2008)
Sidney, John, Peters, Bjoern, Frahm, Nicole, Brander, Christian, Sette, Alessandro
Abstract Background Class I major histocompatibility complex (MHC) molecules bind, and present to T cells, short peptides derived from intracellular processing of proteins. The peptide repertoire of...
HLA class I supertypes: a revised and updated classification (2008)
John Sidney, Bjoern Peters, Nicole Frahm, Christian Brander, Alessandro Sette
Background: Class I major histocompatibility complex (MHC) molecules bind, and present to T cells, short peptides derived from intracellular processing of proteins. The peptide repertoire of a...
John Sidney, Erika Assarsson, Carrie Moore, Y Ngo, Clemencia Pinilla, Ro Sette, ...
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries
Immune epitope database analysis resource (IEDB-AR) (2008)
Zhang, Qing, Wang, Peng, Kim, Yohan, Haste-Andersen, Pernille, Beaver, John, Bourne, Philip E., ...
We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune...
An analysis of the epitope knowledge related to Mycobacteria (2007)
Blythe, Martin J, Zhang, Qing, Vaughan, Kerrie, De Castro, Romulo, Salimi, Nima, Bui, Huynh-Hoa, ...
Abstract Background Tuberculosis, caused by the bacterium Mycobacterium tuberculosis , remains a leading cause of infectious disease morbidity and mortality, and is responsible for more than 2...
Automating document classification for the Immune Epitope Database (2007)
Wang, Peng, Morgan, Alexander A, Zhang, Qing, Sette, Alessandro, Peters, Bjoern
Abstract Background The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant...
Curation of complex, context-dependent immunological data (2006)
Vita, Randi, Vaughan, Kerrie, Zarebski, Laura, Salimi, Nima, Fleri, Ward, Grey, Howard, ...
Abstract Background The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org ....
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules (2006)
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, ...
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide...
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules (2006)
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, ...
Recognition of peptides bound to MHC class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be...
I Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, ...
© 2006 Vita et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Sathiamurthy, Muthuraman, Peters, Bjoern, Bui, Huynh-Hoa, Sidney, John, Mokili, John, Wilson, Stephen S, ...
Abstract Background Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource...
Peters, Bjoern, Sette, Alessandro
Abstract Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility...
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint (2005)
Bjoern Peters, John Sidney, Phil Bourne, Huynh-Hoa Bui, Soeren Buus, Grace Doh, ...
A planned repository of immune epitope data with associated analysis tools should be a boon to vaccine development.
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint (2005)
Bjoern Peters, John Sidney, Phil Bourne, Huynh-Hoa Bui, Soeren Buus, Grace Doh, ...
Peters, Bjoern, Hentschel, Juliane, Mau, Harald, Halle, Elke, Witte, Wolfgang, Obladen, Michael
The course of infection in a 3-week-old premature newborn suffering from extensive dermatitis with flaccid blisters is described. Staphylococcus aureus was recovered from a local wound infection...
Oseroff, Carla, Kos, Ferdynand, Bui, Huynh-Hoa, Peters, Bjoern, Pasquetto, Valerie, Glenn, Jean, ...
We have analyzed by ex vivo ELISPOT the anti-vaccinia cytotoxic T lymphocyte responses of peripheral blood mononuclear cells from humans vaccinated with Dryvax vaccine. More than 6,000 peptides from...
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
Peters, Bjoern, Sidney, John, Bourne, Phil, Bui, Huynh-Hoa, Buus, Soeren, Doh, Grace, ...
A planned repository of immune epitope data with associated analysis tools should be a boon to vaccine development
Sathiamurthy, Muthuraman, Peters, Bjoern, Bui, Huynh-Hoa, Sidney, John, Mokili, John, Wilson, Stephen S, ...
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules
Peters, Bjoern, Bui, Huynh-Hoa, Frankild, Sune, Nielsen, Morten, Lundegaard, Claus, Kostem, Emrah, ...
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide...
Curation of complex, context-dependent immunological data
Vita, Randi, Vaughan, Kerrie, Zarebski, Laura, Salimi, Nima, Fleri, Ward, Grey, Howard, ...
Peters, Bjoern, Hentschel, Juliane, Mau, Harald, Halle, Elke, Witte, Wolfgang, Obladen, Michael
The course of infection in a 3-week-old premature newborn suffering from extensive dermatitis with flaccid blisters is described. Staphylococcus aureus was recovered from a local wound infection...
The Immune Epitope Database and Analysis Resource: From Vision to Blueprint
Peters, Bjoern, Sidney, John, Bourne, Phil, Bui, Huynh-Hoa, Buus, Soeren, Doh, Grace, ...
A planned repository of immune epitope data with associated analysis tools should be a boon to vaccine development
Oseroff, Carla, Kos, Ferdynand, Bui, Huynh-Hoa, Peters, Bjoern, Pasquetto, Valerie, Glenn, Jean, ...
We have analyzed by ex vivo ELISPOT the anti-vaccinia cytotoxic T lymphocyte responses of peripheral blood mononuclear cells from humans vaccinated with Dryvax vaccine. More than 6,000 peptides from...
Sathiamurthy, Muthuraman, Peters, Bjoern, Bui, Huynh-Hoa, Sidney, John, Mokili, John, Wilson, Stephen S, ...
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules
Peters, Bjoern, Bui, Huynh-Hoa, Frankild, Sune, Nielsen, Morten, Lundegaard, Claus, Kostem, Emrah, ...
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide...
Curation of complex, context-dependent immunological data
Vita, Randi, Vaughan, Kerrie, Zarebski, Laura, Salimi, Nima, Fleri, Ward, Grey, Howard, ...
Identification of Protective Lassa Virus Epitopes That Are Restricted by HLA-A2
Botten, Jason, Alexander, Jeff, Pasquetto, Valerie, Sidney, John, Barrowman, Polly, Ting, Joey, ...
Recovery from Lassa virus (LASV) infection usually precedes the appearance of neutralizing antibodies, indicating that cellular immunity plays a primary role in viral clearance. To date, the role of...
Ab and T cell epitopes of influenza A virus, knowledge and opportunities
Bui, Huynh-Hoa, Peters, Bjoern, Assarsson, Erika, Mbawuike, Innocent, Sette, Alessandro
The Immune Epitope Database and Analysis Resources (IEDB) (www.immuneepitope.org) was recently developed to capture epitope related data. IEDB also hosts various bioinformatics tools that can be used...
Nielsen, Morten, Lundegaard, Claus, Blicher, Thomas, Lamberth, Kasper, Harndahl, Mikkel, Justesen, Sune, ...
Kotturi, Maya F., Peters, Bjoern, Buendia-Laysa, Fernando, Sidney, John, Oseroff, Carla, Botten, Jason, ...
CD8+ T-cell responses control lymphocytic choriomeningitis virus (LCMV) infection in H-2b mice. Although antigen-specific responses against LCMV infection are well studied, we found that a...
Automating document classification for the Immune Epitope Database
Wang, Peng, Morgan, Alexander A, Zhang, Qing, Sette, Alessandro, Peters, Bjoern
An analysis of the epitope knowledge related to Mycobacteria
Blythe, Martin J, Zhang, Qing, Vaughan, Kerrie, De Castro, Romulo, Salimi, Nima, Bui, Huynh-Hoa, ...
HLA class I supertypes: a revised and updated classification
Sidney, John, Peters, Bjoern, Frahm, Nicole, Brander, Christian, Sette, Alessandro
Sidney, John, Assarsson, Erika, Moore, Carrie, Ngo, Sandy, Pinilla, Clemencia, Sette, Alessandro, ...
Wang, Peng, Sidney, John, Dow, Courtney, Mothé, Bianca, Sette, Alessandro, Peters, Bjoern
The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. A number of computational tools have been developed for this purpose, but there is a...
A Detailed Analysis of the Murine TAP Transporter Substrate Specificity
Burgevin, Anne, Saveanu, Loredana, Kim, Yohan, Barilleau, Émilie, Kotturi, Maya, Sette, Alessandro, ...
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan
Nielsen, Morten, Lundegaard, Claus, Blicher, Thomas, Peters, Bjoern, Sette, Alessandro, Justesen, Sune, ...
CD4 positive T helper cells control many aspects of specific immunity. These cells are specific for peptides derived from protein antigens and presented by molecules of the extremely polymorphic...
Immune epitope database analysis resource (IEDB-AR)
Zhang, Qing, Wang, Peng, Kim, Yohan, Haste-Andersen, Pernille, Beaver, John, Bourne, Philip E., ...
We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune...
Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes
Assarsson, Erika, Greenbaum, Jason A., Sundström, Magnus, Schaffer, Lana, Hammond, Jennifer A., Pasquetto, Valerie, ...
Vaccinia virus is the prototypic orthopoxvirus and was the vaccine used to eradicate smallpox, yet the expression profiles of many of its genes remain unknown. Using a genome tiling array approach,...
ElliPro: a new structure-based tool for the prediction of antibody epitopes
Ponomarenko, Julia, Bui, Huynh-Hoa, Li, Wei, Fusseder, Nicholas, Bourne, Philip E, Sette, Alessandro, ...
Reply to Satheshkumar and Moss: Poxvirus transcriptome analysis
Assarsson, Erika, Greenbaum, Jason A., Sundström, Magnus, Schaffer, Lana, Hammond, Jennifer A., Pasquetto, Valerie, ...
Lymphocytic Choriomeningitis Virus Infection Yields Overlapping CD4+ and CD8+ T-Cell Responses▿
Dow, Courtney, Oseroff, Carla, Peters, Bjoern, Nance-Sotelo, Courtney, Sidney, John, Buchmeier, Michael, ...
Activation of CD4+ T cells helps establish and sustain other immune responses. We have previously shown that responses against a broad set of nine CD4+ T-cell epitopes were present in the setting of...