A BASIC microcomputer program for data analysis of limiting dilution assays. - Alessandro Sette; Luciano Adorini; Camillo Mancini; Gino Doria (Comput. Appl. Biosci., 1989)

Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. - Björn Peters; Weiwei Tong; John Sidney; Alessandro Sette; Zhiping Weng (Bioinform., 2003)

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. - Björn Peters; Alessandro Sette (BMC Bioinform., 2005)

The Immune Epitope Database and Analysis Resource. - Alessandro Sette; Huynh-Hoa Bui; John Sidney; Philip E. Bourne; Søren Buus; Ward Fleri; R. Kubo; Ole Lund; D. Nemazee; Julia V. Ponomarenko; Muthu Sathiamurthy; Scott Stewart; et al. (PRIB, 2006)

Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. - Shanfeng Zhu; Keiko Udaka; John Sidney; Alessandro Sette; Kiyoko F. Aoki-Kinoshita; Hiroshi Mamitsuka (Bioinform., 2006)

Predicting population coverage of T-cell epitope-based diagnostics and vaccines. - Huynh-Hoa Bui; John Sidney; Kenny Dinh; Scott Southwood; Mark J. Newman; Alessandro Sette (BMC Bioinform., 2006)

Curation of complex, context-dependent immunological data. - Randi Vita; Kerrie Vaughan; Laura Zarebski; Nima Salimi; Ward Fleri; Howard Grey; Muthu Sathiamurthy; John Mokili; Huynh-Hoa Bui; Philip E. Bourne; Julia V. Ponomarenko; Romulo de Castro Jr.; et al. (BMC Bioinform., 2006)

A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. - Bjoern Peters; Huynh-Hoa Bui; Sune Frankild; Morten Nielsen 001; Claus Lundegaard; Emrah Kostem; Derek Basch; Kasper Lamberth; Mikkel Harndahl; Ward Fleri; Stephen S. Wilson; John Sidney; et al. (PLoS Comput. Biol., 2006)

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. - Huynh-Hoa Bui; John Sidney; Wei Li; Nicholas Fusseder; Alessandro Sette (BMC Bioinform., 2007)

Automating document classification for the Immune Epitope Database. - Peng Wang 014; Alexander A. Morgan; Qing Zhang; Alessandro Sette; Björn Peters (BMC Bioinform., 2007)

ElliPro: a new structure-based tool for the prediction of antibody epitopes. - Julia V. Ponomarenko; Huynh-Hoa Bui; Wei Li; Nicholas Fusseder; Philip E. Bourne; Alessandro Sette; Björn Peters (BMC Bioinform., 2008)

Immune epitope database analysis resource (IEDB-AR). - Qing Zhang; Peng Wang 014; Yohan Kim; Pernille Haste-Andersen; John E. Beaver; Philip E. Bourne; Huynh-Hoa Bui; Søren Buus; Sune Frankild; Jason Greenbaum; Ole Lund; Claus Lundegaard; et al. (Nucleic Acids Res., 2008)

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan. - Morten Nielsen 001; Claus Lundegaard; Thomas Blicher; Bjoern Peters; Alessandro Sette; Sune Justesen; Søren Buus; Ole Lund (PLoS Comput. Biol., 2008)

A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach. - Peng Wang 014; John Sidney; Courtney Dow; Bianca Mothé; Alessandro Sette; Björn Peters (PLoS Comput. Biol., 2008)

Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. - Yohan Kim; John Sidney; Clemencia Pinilla; Alessandro Sette; Björn Peters (BMC Bioinform., 2009)

An automatic computational pipeline to display MHC binding motifs. - Peng Wang 014; Björn Peters; John Sidney; Alessandro Sette (BCB, 2010)

Peptide binding predictions for HLA DR, DP and DQ molecules. - Peng Wang 014; John Sidney; Yohan Kim; Alessandro Sette; Ole Lund; Morten Nielsen 001; Björn Peters (BMC Bioinform., 2010)

The Immune Epitope Database 2.0. - Randi Vita; Laura Zarebski; Jason Greenbaum; Hussein Emami; Ilka Hoof; Nima Salimi; Rohini Damle; Alessandro Sette; Björn Peters (Nucleic Acids Res., 2010)

Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. - Emily Seymour; Rohini Damle; Alessandro Sette; Bjoern Peters (BMC Bioinform., 2011)

IEDB-3D: structural data within the immune epitope database. - Julia V. Ponomarenko; Nikitas Papangelopoulos; Dirk M. Zajonc; Björn Peters; Alessandro Sette; Philip E. Bourne (Nucleic Acids Res., 2011)

Immune epitope database analysis resource. - Yohan Kim; Julia V. Ponomarenko; Zhanyang Zhu; Dorjee Tamang; Peng Wang 014; Jason Greenbaum; Claus Lundegaard; Alessandro Sette; Ole Lund; Philip E. Bourne; Morten Nielsen 001; Bjoern Peters (Nucleic Acids Res., 2012)

A Taxonomy for Immunologists. - James A. Overton; Randi Vita; Jason Greenbaum; Heiko Dietze; Alessandro Sette; Bjoern Peters (ICBO, 2013)

Query enhancement through the practical application of ontology: the IEDB and OBI. - Randi Vita; James A. Overton; Jason Greenbaum; Alessandro Sette; Björn Peters (J. Biomed. Semant., 2013)

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity. - Jorg J. A. Calis; Matt Maybeno; Jason A. Greenbaum; Daniela Weiskopf; Aruna D. De Silva; Alessandro Sette; Can Kesmir; Björn Peters (PLoS Comput. Biol., 2013)

Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation. - Yohan Kim; Jonathan W. Yewdell; Alessandro Sette; Björn Peters (PLoS Comput. Biol., 2013)

The interplay of sequence conservation and T cell immune recognition. - Anne Bresciani; Jason Greenbaum; Cecilia S. Lindestam Arlehamn; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (BCB, 2014)

Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. - Sinu Paul; John Sidney; Bjoern Peters; Alessandro Sette (BCB, 2014)

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. - Yohan Kim; John Sidney; Søren Buus; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (BMC Bioinform., 2014)

Automated benchmarking of peptide-MHC class I binding predictions. - Thomas Trolle; Imir G. Metushi; Jason A. Greenbaum; Yohan Kim; John Sidney; Ole Lund; Alessandro Sette; Bjoern Peters; Morten Nielsen 001 (Bioinform., 2015)

The immune epitope database (IEDB) 3.0. - Randi Vita; James A. Overton; Jason A. Greenbaum; Julia V. Ponomarenko; Jason D. Clark; Jason R. Cantrell; Daniel K. Wheeler; Joseph L. Gabbard; Deborah Hix; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2015)

An ontology for major histocompatibility restriction. - Randi Vita; James A. Overton; Emily Seymour; John Sidney; Jim Kaufman; Rebecca L. Tallmadge; Shirley Ellis; John Hammond; Geoff W. Butcher; Alessandro Sette; Bjoern Peters (J. Biomed. Semant., 2016)

Better living through ontologies at the Immune Epitope Database. - Randi Vita; James A. Overton; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2017)

Identifying specificity groups in the T cell receptor repertoire. - Jacob Glanville; Huang Huang; Allison Nau; Olivia Hatton; Lisa E. Wagar; Florian Rubelt; Xuhuai Ji; Arnold Han; Sheri M. Krams; Christina Pettus; Nikhil Haas; Cecilia S. Lindestam Arlehamn; et al. (Nat., 2017)

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. - Randi Vita; James A. Overton; Christopher J. Mungall; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2018)

ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins. - Sandeep Kumar Dhanda; Randi Vita; Brendan Ha; Alba Grifoni; Bjoern Peters; Alessandro Sette (Bioinform., 2018)

The SysteMHC Atlas project. - Wenguang Shao; Patrick G. A. Pedrioli; Witold Wolski; Christian Scurtescu; Emanuel Schmid; Juan Antonio Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S. Lindestam Arlehamn; Kerrie Vaughan; et al. (Nucleic Acids Res., 2018)

Benchmark datasets of immune receptor-epitope structural complexes. - Swapnil Mahajan; Zhen Yan; Martin Closter Jespersen; Kamilla Kjærgaard Jensen; Paolo Marcatili; Morten Nielsen 001; Alessandro Sette; Bjoern Peters (BMC Bioinform., 2019)

IEDB-AR: immune epitope database - analysis resource in 2019. - Sandeep Kumar Dhanda; Swapnil Mahajan; Sinu Paul; Zhen Yan; Haeuk Kim; Martin Closter Jespersen; Vanessa Isabell Jurtz; Massimo Andreatta; Jason A. Greenbaum; Paolo Marcatili; Alessandro Sette; Morten Nielsen 001; et al. (Nucleic Acids Res., 2019)

The Immune Epitope Database (IEDB): 2018 update. - Randi Vita; Swapnil Mahajan; James A. Overton; Sandeep Kumar Dhanda; Sheridan Martini; Jason R. Cantrell; Daniel K. Wheeler; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2019)

A structured model for immune exposures. - Randi Vita; James A. Overton; Patrick Dunn; Kei-Hoi Cheung; Steven H. Kleinstein; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2020)

Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. - Sinu Paul; Nathan P. Croft; Anthony W. Purcell; David C. Tscharke; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (PLoS Comput. Biol., 2020)

An immunologically friendly classification of non-peptidic ligands. - Lindy Edwards; Rebecca C. Jackson; James A. Overton; Randi Vita; Nina Blazeska; Bjoern Peters; Alessandro Sette (Database J. Biol. Databases Curation, 2021)

A comprehensive analysis of the IEDB MHC class-I automated benchmark. - Raphael Trevizani; Zhen Yan; Jason A. Greenbaum; Alessandro Sette; Morten Nielsen 001; Bjoern Peters (Briefings Bioinform., 2022)

Bioinformatic and Experimental Analysis of T Cell Immune Reactivity to SARS-CoV-2 and its Variants. - Alison Tarke; Alba Grifoni; Alessandro Sette (Frontiers Bioinform., 2022)

The Cancer Epitope Database and Analysis Resource (CEDAR). - Zeynep Kosaloglu-Yalçin; Nina Blazeska; Randi Vita; Hannah Carter; Morten Nielsen 001; Stephen Schoenberger; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2023)

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. - Daniel Marrama; William D. Chronister; Luise Westernberg; Randi Vita; Zeynep Kosaloglu-Yalçin; Alessandro Sette; Morten Nielsen 001; Jason A. Greenbaum; Bjoern Peters (BMC Bioinform., 2023)