Alessandro Sette

46 papers Journal 41Unranked 5
YearRankTypeTitle / Venue / Authors
2023 J jnl
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
BMC Bioinform.
Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum, Bjoern Peters
2023 J jnl
The Cancer Epitope Database and Analysis Resource (CEDAR).
Nucleic Acids Res.
Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters
2022 J jnl
A comprehensive analysis of the IEDB MHC class-I automated benchmark.
Briefings Bioinform.
Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters
2022 J jnl
Bioinformatic and Experimental Analysis of T Cell Immune Reactivity to SARS-CoV-2 and its Variants.
Frontiers Bioinform.
Alison Tarke, Alba Grifoni, Alessandro Sette
2021 J jnl
An immunologically friendly classification of non-peptidic ligands.
Database J. Biol. Databases Curation
Lindy Edwards, Rebecca C. Jackson, James A. Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette
2020 J jnl
A structured model for immune exposures.
Database J. Biol. Databases Curation
Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters
2020 J jnl
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system.
PLoS Comput. Biol.
Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters
2019 J jnl
Benchmark datasets of immune receptor-epitope structural complexes.
BMC Bioinform.
Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters
2019 J jnl
IEDB-AR: immune epitope database - analysis resource in 2019.
Nucleic Acids Res.
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, Bjoern Peters
2019 J jnl
The Immune Epitope Database (IEDB): 2018 update.
Nucleic Acids Res.
Randi Vita, Swapnil Mahajan, James A. Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R. Cantrell, Daniel K. Wheeler, Alessandro Sette, Bjoern Peters
2018 J jnl
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.
Database J. Biol. Databases Curation
Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters
2018 J jnl
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.
Bioinform.
Sandeep Kumar Dhanda, Randi Vita, Brendan Ha, Alba Grifoni, Bjoern Peters, Alessandro Sette
2018 J jnl
The SysteMHC Atlas project.
Nucleic Acids Res.
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, Bjoern Peters, Alessandro Sette, Tom H. M. Ottenhoff, Krista E. Meijgaarden, Natalie Nieuwenhuizen, Stefan H. E. Kaufmann, Ralph Schlapbach, John C. Castle, Alexey I. Nesvizhskii, Morten Nielsen, Eric W. Deutsch, David S. Campbell, Robert L. Moritz, Roman A. Zubarev, Anders Jimmy Ytterberg, Anthony W. Purcell, Miguel Marcilla, Alberto Paradela, Qi Wang, Catherine E. Costello, Nicola Ternette, Peter A. van Veelen, Cécile A. C. M. van Els, Albert J. R. Heck, Gustavo A. de Souza, Ludvig Magne Sollid, Arie Admon, Stefan Stevanovic, Hans-Georg Rammensee, Pierre Thibault, Claude Perreault, Michal Bassani-Sternberg, Ruedi Aebersold, Etienne Caron
2017 J jnl
Better living through ontologies at the Immune Epitope Database.
Database J. Biol. Databases Curation
Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters
2017 J jnl
Identifying specificity groups in the T cell receptor repertoire.
Nat.
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, Alessandro Sette, Scott D. Boyd, Thomas J. Scriba, Olivia M. Martinez, Mark M. Davis
2016 J jnl
An ontology for major histocompatibility restriction.
J. Biomed. Semant.
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
2015 J jnl
Automated benchmarking of peptide-MHC class I binding predictions.
Bioinform.
Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen
2015 J jnl
The immune epitope database (IEDB) 3.0.
Nucleic Acids Res.
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
2014 J jnl
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions.
BMC Bioinform.
Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters
2014 — conf
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes.
BCB
Sinu Paul, John Sidney, Bjoern Peters, Alessandro Sette
2014 — conf
The interplay of sequence conservation and T cell immune recognition.
BCB
Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters
2013 — conf
A Taxonomy for Immunologists.
ICBO
James A. Overton, Randi Vita, Jason Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters
2013 J jnl
Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation.
PLoS Comput. Biol.
Yohan Kim, Jonathan W. Yewdell, Alessandro Sette, Björn Peters
2013 J jnl
Properties of MHC Class I Presented Peptides That Enhance Immunogenicity.
PLoS Comput. Biol.
Jorg J. A. Calis, Matt Maybeno, Jason A. Greenbaum, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, Can Kesmir, Björn Peters
2013 J jnl
Query enhancement through the practical application of ontology: the IEDB and OBI.
J. Biomed. Semant.
Randi Vita, James A. Overton, Jason Greenbaum, Alessandro Sette, Björn Peters
2012 J jnl
Immune epitope database analysis resource.
Nucleic Acids Res.
Yohan Kim, Julia V. Ponomarenko, Zhanyang Zhu, Dorjee Tamang, Peng Wang, Jason Greenbaum, Claus Lundegaard, Alessandro Sette, Ole Lund, Philip E. Bourne, Morten Nielsen, Bjoern Peters
2011 J jnl
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation.
BMC Bioinform.
Emily Seymour, Rohini Damle, Alessandro Sette, Bjoern Peters
2011 J jnl
IEDB-3D: structural data within the immune epitope database.
Nucleic Acids Res.
Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne
2010 — conf
An automatic computational pipeline to display MHC binding motifs.
BCB
Peng Wang, Björn Peters, John Sidney, Alessandro Sette
2010 J jnl
Peptide binding predictions for HLA DR, DP and DQ molecules.
BMC Bioinform.
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters
2010 J jnl
The Immune Epitope Database 2.0.
Nucleic Acids Res.
Randi Vita, Laura Zarebski, Jason Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, Björn Peters
2009 J jnl
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior.
BMC Bioinform.
Yohan Kim, John Sidney, Clemencia Pinilla, Alessandro Sette, Björn Peters
2008 J jnl
A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach.
PLoS Comput. Biol.
Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Björn Peters
2008 J jnl
ElliPro: a new structure-based tool for the prediction of antibody epitopes.
BMC Bioinform.
Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters
2008 J jnl
Immune epitope database analysis resource (IEDB-AR).
Nucleic Acids Res.
Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters
2008 J jnl
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan.
PLoS Comput. Biol.
Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund
2007 J jnl
Automating document classification for the Immune Epitope Database.
BMC Bioinform.
Peng Wang, Alexander A. Morgan, Qing Zhang, Alessandro Sette, Björn Peters
2007 J jnl
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines.
BMC Bioinform.
Huynh-Hoa Bui, John Sidney, Wei Li, Nicholas Fusseder, Alessandro Sette
2006 J jnl
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules.
PLoS Comput. Biol.
Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S. Wilson, John Sidney, Ole Lund, Søren Buus, Alessandro Sette
2006 J jnl
Curation of complex, context-dependent immunological data.
BMC Bioinform.
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., Russell K. Chan, John Sidney, Stephen S. Wilson, Scott Stewart, Scott Way, Björn Peters, Alessandro Sette
2006 J jnl
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules.
Bioinform.
Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka
2006 J jnl
Predicting population coverage of T-cell epitope-based diagnostics and vaccines.
BMC Bioinform.
Huynh-Hoa Bui, John Sidney, Kenny Dinh, Scott Southwood, Mark J. Newman, Alessandro Sette
2006 — conf
The Immune Epitope Database and Analysis Resource.
PRIB
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, Scott Way, Stephen S. Wilson, Björn Peters
2005 J jnl
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method.
BMC Bioinform.
Björn Peters, Alessandro Sette
2003 J jnl
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules.
Bioinform.
Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng
1989 J jnl
A BASIC microcomputer program for data analysis of limiting dilution assays.
Comput. Appl. Biosci.
Alessandro Sette, Luciano Adorini, Camillo Mancini, Gino Doria