Bjoern Peters

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 34

Top Topics

Development Kit

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Publications

Eve Richardson, Raphael Trevizani, Jason A. Greenbaum, Hannah Carter, Morten Nielsen, Bjoern Peters
The receiver operating characteristic curve accurately assesses imbalanced datasets. Patterns 5 (6) (2024)
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) (2023)
Jarjapu Mahita, Brendan Ha, Anais Gambiez, Sharon L. Schendel, Haoyang Li, Kathryn M. Hastie, S. Moses Dennison, Kan Li, Natalia Kuzmina, Sivakumar Periasamy, Alexander Bukreyev, Jennifer E. Munt, Mary Osei-Twum, Caroline Atyeo, James A. Overton, Randi Vita, Hector Guzman-Orozco, Marcus Mendes, Mari Kojima, Peter J. Halfmann, Yoshihiro Kawaoka, Galit Alter, Luc Gagnon, Ralph S. Baric, Georgia D. Tomaras, Tim Germann, Daniel Bedinger, Jason A. Greenbaum, Erica Ollmann Saphire, Bjoern Peters
Coronavirus Immunotherapeutic Consortium Database. Database J. Biol. Databases Curation 2023 (2023)
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) (2023)
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR (2022)
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022 (2022) (2022)
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)
Paul F. Zierep, Randi Vita, Nina Blazeska, Aurélien F. A. Moumbock, Jason A. Greenbaum, Bjoern Peters, Stefan Günther
Towards the prediction of non-peptidic epitopes. PLoS Comput. Biol. 18 (2) (2022)
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022 (2022) (2022)
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR (2021)
Jason Bennett, Mikhail Pomaznoy, Akul Singhania, Bjoern Peters
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PLoS Comput. Biol. 17 (10) (2021)
Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
Randi Vita, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021)
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)
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)
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)
Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Scott Christley, Ademar Aguiar, George Blanck, Felix Breden, Syed Ahmad Chan Bukhari, Christian E. Busse, Jerome Jaglale, Srilakshmy L. Harikrishnan, Uri Laserson, Bjoern Peters, Artur Rocha, Chaim A. Schramm, Sarah Taylor, Jason A. Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell
The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Frontiers Big Data 3 (2020)
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) (2019)
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) (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, Bjoern Peters
IEDB-AR: immune epitope database - analysis resource in 2019. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl, Bjoern Peters
Reporting and connecting cell type names and gating definitions through ontologies. BMC Bioinform. (5) (2019)
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 (2018)
Mikhail Pomaznoy, Brendan Ha, Bjoern Peters
GOnet: a tool for interactive Gene Ontology analysis. BMC Bioinform. 19 (1) (2018)
Massimo Andreatta, Thomas Trolle, Zhen Yan, Jason A. Greenbaum, Bjoern Peters, Morten Nielsen
An automated benchmarking platform for MHC class II binding prediction methods. Bioinform. 34 (9) (2018)
Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein
Formalizing the Representation of Immune Exposures for Human Immunology Studies. ICBO (2018)
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 M. 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) (2018)
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) (2018)
Randi Vita, James A. Overton, Bjoern Peters
Identification of errors in the IEDB using ontologies. Database J. Biol. Databases Curation 2018 (2018)
Bjoern Peters, Steven E. Brenner, Edwin Wang, Donna K. Slonim, Maricel G. Kann
Putting benchmarks in their rightful place: The heart of computational biology. PLoS Comput. Biol. 14 (11) (2018)
Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters
Better living through ontologies at the Immune Epitope Database. Database J. Biol. Databases Curation 2017 (2017)
Gully A. Burns, Randi Vita, James A. Overton, Ward Fleri, Bjoern Peters
Semantic Modeling for Accelerated Immune Epitope Database (IEDB) Biocuration. K-CAP Workshops (2017)
Martin Closter Jespersen, Bjoern Peters, Morten Nielsen, Paolo Marcatili
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
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 (2016)
Inbal Sela-Culang, Shaul Ashkenazi, Bjoern Peters, Yanay Ofran
PEASE: predicting B-cell epitopes utilizing antibody sequence. Bioinform. 31 (8) (2015)
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) (2015)
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) (2015)
Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
CLO: The cell line ontology. J. Biomed. Semant. 5 (2014)
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)
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)
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 (2014)
James A. Overton, Randi Vita, Jason Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters
A Taxonomy for Immunologists. ICBO (2013)
Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. ICBO (2013)
Vered Kunik, Bjoern Peters, Yanay Ofran
Structural Consensus among Antibodies Defines the Antigen Binding Site. PLoS Comput. Biol. 8 (2) (2012)
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) (2012)
Yohan Kim, Jonathan W. Yewdell, Bjoern Peters
Determining positional bias of MHC class I restricted T-cell epitopes in viral antigens. BCB (2011)
Emily Seymour, Rohini Damle, Alessandro Sette, Bjoern Peters
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. BMC Bioinform. 12 (2011)
Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters
Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 6 (1) (2011)
Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuermann, Q. Alison Yao, Martin S. Zand, Christopher J. Mungall
Hematopoietic cell types: Prototype for a revised cell ontology. J. Biomed. Informatics 44 (1) (2011)
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)
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)