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2020 – today
- 2023
[j41]Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen
, Jason A. Greenbaum, Bjoern Peters:
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. BMC Bioinform. 24(1): 485 (2023)- [j40]Zeynep Kosaloglu-Yalçin, Nina Blazeska, Randi Vita, Hannah Carter, Morten Nielsen, Stephen Schoenberger, Alessandro Sette, Bjoern Peters:
The Cancer Epitope Database and Analysis Resource (CEDAR). Nucleic Acids Res. 51(D1): 845-852 (2023) - 2022
- [j39]Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters:
A comprehensive analysis of the IEDB MHC class-I automated benchmark. Briefings Bioinform. 23(4) (2022) - [j38]Alison Tarke, Alba Grifoni, Alessandro Sette:
Bioinformatic and Experimental Analysis of T Cell Immune Reactivity to SARS-CoV-2 and its Variants. Frontiers Bioinform. 2 (2022) - 2021
- [j37]Lindy Edwards, Rebecca C. Jackson, James A. Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette:
An immunologically friendly classification of non-peptidic ligands. Database J. Biol. Databases Curation 2021 (2021) - 2020
- [j36]Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters:
A structured model for immune exposures. Database J. Biol. Databases Curation 2020 (2020) - [j35]Sinu Paul, Nathan P. Croft, Anthony W. Purcell, David C. Tscharke, Alessandro Sette, Morten Nielsen, Bjoern Peters:
Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput. Biol. 16(5) (2020)
2010 – 2019
- 2019
- [j34]Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters:
Benchmark datasets of immune receptor-epitope structural complexes. BMC Bioinform. 20(1): 490:1-490:7 (2019) - [j33]Randi Vita, Swapnil Mahajan, James A. Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R. Cantrell, Daniel K. Wheeler, Alessandro Sette, Bjoern Peters:
The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47(Database-Issue): D339-D343 (2019) - [j32]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:
IEDB-AR: immune epitope database - analysis resource in 2019. Nucleic Acids Res. 47(Webserver-Issue): W502-W506 (2019) - 2018
- [j31]Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters:
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 2018: bax105 (2018) - [j30]Sandeep Kumar Dhanda, Randi Vita, Brendan Ha, Alba Grifoni, Bjoern Peters, Alessandro Sette:
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins. Bioinform. 34(22): 3931-3933 (2018) - [j29]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:
The SysteMHC Atlas project. Nucleic Acids Res. 46(Database-Issue): D1237-D1247 (2018) - 2017
- [j28]Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters:
Better living through ontologies at the Immune Epitope Database. Database J. Biol. Databases Curation 2017: bax014 (2017) - [j27]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:
Identifying specificity groups in the T cell receptor repertoire. Nat. 547(7661): 94-98 (2017) - 2016
- [j26]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:
An ontology for major histocompatibility restriction. J. Biomed. Semant. 7: 1 (2016) - 2015
- [j25]Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen:
Automated benchmarking of peptide-MHC class I binding predictions. Bioinform. 31(13): 2174-2181 (2015) - [j24]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:
The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 43(Database-Issue): 405-412 (2015) - 2014
- [j23]Yohan Kim, John Sidney, Søren Buus, Alessandro Sette, Morten Nielsen, Bjoern Peters:
Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions. BMC Bioinform. 15: 241 (2014) - [c5]Sinu Paul, John Sidney, Bjoern Peters, Alessandro Sette:
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. BCB 2014: 733-738 - [c4]Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen, Bjoern Peters:
The interplay of sequence conservation and T cell immune recognition. BCB 2014: 739-743 - 2013
- [j22]Randi Vita, James A. Overton, Jason Greenbaum, Alessandro Sette, Björn Peters:
Query enhancement through the practical application of ontology: the IEDB and OBI. J. Biomed. Semant. 4(S-1): S6 (2013) - [j21]Yohan Kim, Jonathan W. Yewdell, Alessandro Sette, Björn Peters:
Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation. PLoS Comput. Biol. 9(1) (2013) - [j20]Jorg J. A. Calis, Matt Maybeno, Jason A. Greenbaum, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, Can Kesmir, Björn Peters:
Properties of MHC Class I Presented Peptides That Enhance Immunogenicity. PLoS Comput. Biol. 9(10) (2013) - [c3]James A. Overton, Randi Vita, Jason Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters:
A Taxonomy for Immunologists. ICBO 2013: 124 - 2012
- [j19]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:
Immune epitope database analysis resource. Nucleic Acids Res. 40(Web-Server-Issue): 525-530 (2012) - 2011
- [j18]Emily Seymour, Rohini Damle, Alessandro Sette, Bjoern Peters:
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. BMC Bioinform. 12: 482 (2011) - [j17]Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne:
IEDB-3D: structural data within the immune epitope database. Nucleic Acids Res. 39(Database-Issue): 1164-1170 (2011) - 2010
- [j16]Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Björn Peters:
Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinform. 11: 568 (2010) - [j15]Randi Vita, Laura Zarebski, Jason Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, Björn Peters:
The Immune Epitope Database 2.0. Nucleic Acids Res. 38(Database-Issue): 854-862 (2010) - [c2]Peng Wang, Björn Peters, John Sidney, Alessandro Sette:
An automatic computational pipeline to display MHC binding motifs. BCB 2010: 634-641
2000 – 2009
- 2009
- [j14]Yohan Kim, John Sidney, Clemencia Pinilla, Alessandro Sette, Björn Peters:
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. BMC Bioinform. 10: 394 (2009) - 2008
- [j13]Julia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters:
ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinform. 9 (2008) - [j12]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:
Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res. 36(Web-Server-Issue): 513-518 (2008) - [j11]Peng Wang, John Sidney, Courtney Dow, Bianca Mothé, Alessandro Sette, Björn Peters:
A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach. PLoS Comput. Biol. 4(4) (2008) - [j10]Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund:
Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan. PLoS Comput. Biol. 4(7) (2008) - 2007
- [j9]Huynh-Hoa Bui, John Sidney, Wei Li, Nicholas Fusseder, Alessandro Sette:
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinform. 8 (2007) - [j8]Peng Wang, Alexander A. Morgan, Qing Zhang, Alessandro Sette, Björn Peters:
Automating document classification for the Immune Epitope Database. BMC Bioinform. 8 (2007) - 2006
- [j7]Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka:
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinform. 22(13): 1648-1655 (2006) - [j6]Huynh-Hoa Bui, John Sidney, Kenny Dinh, Scott Southwood, Mark J. Newman, Alessandro Sette:
Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinform. 7: 153 (2006) - [j5]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:
Curation of complex, context-dependent immunological data. BMC Bioinform. 7: 341 (2006) - [j4]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:
A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules. PLoS Comput. Biol. 2(6) (2006) - [c1]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:
The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132 - 2005
- [j3]Björn Peters, Alessandro Sette:
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinform. 6: 132 (2005) - 2003
- [j2]Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng:
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinform. 19(14): 1765-1772 (2003)
1980 – 1989
- 1989
- [j1]Alessandro Sette, Luciano Adorini, Camillo Mancini, Gino Doria:
A BASIC microcomputer program for data analysis of limiting dilution assays. Comput. Appl. Biosci. 5(2): 161 (1989)
Coauthor Index
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