Works matching AU Vita, Randi

Results: 30

Query enhancement through the practical application of ontology: the IEDB and OBI.

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. Suppl 1, p. 1, doi. 10.1186/2041-1480-4-S1-S6

By:

Vita, Randi;
Overton, James A.;
Greenbaum, Jason A.;
Sette, Alessandro;
consortium, OBI;
Peters, Bjoern

Publication type:

Article

A curated collection of human vaccination response signatures.

Published in:

Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01558-1

By:

Smith, Kenneth C.;
Chawla, Daniel G.;
Dhillon, Bhavjinder K.;
Ji, Zhou;
Vita, Randi;
van der Leest, Eva C.;
Weng, Jing Yi Jessica;
Tang, Ernest;
Abid, Amani;
The Human Immunology Project Consortium (HIPC);
Peters, Bjoern;
Hancock, Robert E. W.;
Floratos, Aris;
Kleinstein, Steven H.

Publication type:

Article

The Immune Epitope Database 2.0.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D854, doi. 10.1093/nar/gkp1004

By:

Vita, Randi;
Zarebski, Laura;
Greenbaum, Jason A.;
Emami, Hussein;
Hoof, Ilka;
Salimi, Nima;
Damle, Rohini;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database.

Published in:

Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.02688

By:

Mahajan, Swapnil;
Vita, Randi;
Shackelford, Deborah;
Lane, Jerome;
Schulten, Veronique;
Zarebski, Laura;
Jespersen, Martin Closter;
Marcatili, Paolo;
Nielsen, Morten;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Reporting and connecting cell type names and gating definitions through ontologies.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 259, doi. 10.1186/s12859-019-2725-5

By:

Overton, James A.;
Vita, Randi;
Dunn, Patrick;
Burel, Julie G.;
Bukhari, Syed Ahmad Chan;
Cheung, Kei-Hoi;
Kleinstein, Steven H.;
Diehl, Alexander D.;
Peters, Bjoern

Publication type:

Article

Towards the prediction of non-peptidic epitopes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009151

By:

Zierep, Paul F.;
Vita, Randi;
Blazeska, Nina;
Moumbock, Aurélien F. A.;
Greenbaum, Jason A.;
Peters, Bjoern;
Günther, Stefan

Publication type:

Article

The Biocurator: Connecting and Enhancing Scientific Data.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 10, p. 1190, doi. 10.1371/journal.pcbi.0020125

By:

Salimi, Nima;
Vita, Randi

Publication type:

Article

ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins.

Published in:

Bioinformatics, 2018, v. 34, n. 22, p. 3931, doi. 10.1093/bioinformatics/bty463

By:

Dhanda, Sandeep Kumar;
Vita, Randi;
Ha, Brendan;
Grifoni, Alba;
Peters, Bjoern;
Sette, Alessandro

Publication type:

Article

A behind‐the‐scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts.

Published in:

Immunology, 2020, v. 161, n. 2, p. 139, doi. 10.1111/imm.13234

By:

Salimi, Nima;
Edwards, Lindy;
Foos, Gabriele;
Greenbaum, Jason A.;
Martini, Sheridan;
Reardon, Brian;
Shackelford, Deborah;
Vita, Randi;
Zalman, Leora;
Peters, Bjoern;
Sette, Alessandro

Publication type:

Article

The Immune Epitope Database: How Data Are Entered and Retrieved.

Published in:

2017

By:

Fleri, Ward;
Vaughan, Kerrie;
Salimi, Nima;
Vita, Randi;
Peters, Bjoern;
Sette, Alessandro

Publication type:

journal article

Standardizing free-text data exemplified by two fields from the Immune Epitope Database.

Published in:

Journal of Biomedical Semantics, 2025, v. 16, n. 1, p. 1, doi. 10.1186/s13326-025-00324-7

By:

Duesing, Sebastian;
Bennett, Jason;
Overton, James A.;
Vita, Randi;
Peters, Bjoern

Publication type:

Article

An ontology for major histocompatibility restriction.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0045-5

By:

Vita, Randi;
Overton, James A.;
Seymour, Emily;
Sidney, John;
Kaufman, Jim;
Tallmadge, Rebecca L.;
Ellis, Shirley;
Hammond, John;
Butcher, Geoff W.;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Reproducibility and conflicts in immune epitope data.

Published in:

Immunology, 2016, v. 147, n. 3, p. 349, doi. 10.1111/imm.12566

By:

Vita, Randi;
Vasilevsky, Nicole;
Bandrowski, Anita;
Haendel, Melissa;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Curation of complex, context-dependent immunological data.

Published in:

BMC Bioinformatics, 2006, v. 7, p. 341, doi. 10.1186/1471-2105-7-341

By:

Vita, Randi;
Vaughan, Kerrie;
Zarebski, Laura;
Salimi, Nima;
Fleri, Ward;
Grey, Howard;
Sathiamurthy, Muthu;
Mokili, John;
Huynh-Hoa Bui;
Bourne, Philip E;
Ponomarenko, Julia;
de Castro Jr, Romulo;
Chan, Russell K;
Sidney, John;
Wilson, Stephen S;
Stewart, Scott;
Way, Scott;
Peters, Bjoern;
Sette, Alessandro

Publication type:

Article

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.

Published in:

Frontiers in Immunology, 2021, v. 11, p. N.PAG, doi. 10.3389/fimmu.2021.640725

By:

Chronister, William D.;
Crinklaw, Austin;
Mahajan, Swapnil;
Vita, Randi;
Koşaloğlu-Yalçın, Zeynep;
Yan, Zhen;
Greenbaum, Jason A.;
Jessen, Leon E.;
Nielsen, Morten;
Christley, Scott;
Cowell, Lindsay G.;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

The Immune Epitope Database (IEDB): 2024 update.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D436, doi. 10.1093/nar/gkae1092

By:

Vita, Randi;
Blazeska, Nina;
Marrama, Daniel;
Members, IEDB Curation Team;
Duesing, Sebastian;
Bennett, Jason;
Greenbaum, Jason;
De Almeida Mendes, Marcus;
Mahita, Jarjapu;
Wheeler, Daniel K;
Cantrell, Jason R;
Overton, James A;
Natale, Darren A;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Cancer Epitope Database and Analysis Resource (CEDAR).

Published in:

Nucleic Acids Research, 2023, v. 51, n. D1, p. D845, doi. 10.1093/nar/gkac902

By:

Koşaloğlu-Yalçın, Zeynep;
Blazeska, Nina;
Vita, Randi;
Carter, Hannah;
Nielsen, Morten;
Schoenberger, Stephen;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

The Immune Epitope Database (IEDB): 2018 update.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D339, doi. 10.1093/nar/gky1006

By:

Vita, Randi;
Mahajan, Swapnil;
Overton, James A;
Dhanda, Sandeep Kumar;
Martini, Sheridan;
Cantrell, Jason R;
Wheeler, Daniel K;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

The immune epitope database (IEDB) 3.0.

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D405, doi. 10.1093/nar/gku938

By:

Vita, Randi;
Overton, James A.;
Greenbaum, Jason A.;
Ponomarenko, Julia;
Clark, Jason D.;
Cantrell, Jason R.;
Wheeler, Daniel K.;
Gabbard, Joseph L.;
Hix, Deborah;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

SPAK kinase is a substrate and target of PKC? in T-cell receptor-induced AP-1 activation pathway.

Published in:

EMBO Journal, 2004, v. 23, n. 5, p. 1112, doi. 10.1038/sj.emboj.7600125

By:

Li, Vingqiu;
Hu, Junru;
Vita, Randi;
Sun, Binggang;
Tabata, Hiroki;
Altman, Amnon

Publication type:

Article

PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05606-4

By:

Marrama, Daniel;
Chronister, William D.;
Westernberg, Luise;
Vita, Randi;
Koşaloğlu-Yalçın, Zeynep;
Sette, Alessandro;
Nielsen, Morten;
Greenbaum, Jason A.;
Peters, Bjoern

Publication type:

Article

Coronavirus Immunotherapeutic Consortium Database.

Published in:

Database: The Journal of Biological Databases & Curation, 2023, v. 2023, p. 1, doi. 10.1093/database/baac112

By:

Mahita, Jarjapu;
Ha, Brendan;
Gambiez, Anais;
Schendel, Sharon L;
Li, Haoyang;
Hastie, Kathryn M;
Dennison, S Moses;
Li, Kan;
Kuzmina, Natalia;
Periasamy, Sivakumar;
Bukreyev, Alexander;
Munt, Jennifer E;
Osei-Twum, Mary;
Atyeo, Caroline;
Overton, James A;
Vita, Randi;
Guzman-Orozco, Hector;
Mendes, Marcus;
Kojima, Mari;
Halfmann, Peter J

Publication type:

Article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069

By:

Jackson, Rebecca;
Matentzoglu, Nicolas;
Overton, James A;
Vita, Randi;
Balhoff, James P;
Buttigieg, Pier Luigi;
Carbon, Seth;
Courtot, Melanie;
Diehl, Alexander D;
Dooley, Damion M;
Duncan, William D;
Harris, Nomi L;
Haendel, Melissa A;
Lewis, Suzanna E;
Natale, Darren A;
Osumi-Sutherland, David;
Ruttenberg, Alan;
Schriml, Lynn M;
Smith, Barry;
Stoeckert Jr., Christian J

Publication type:

Article

Standardization of assay representation in the Ontology for Biomedical Investigations.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab040

By:

Vita, Randi;
Zheng, Jie;
Jackson, Rebecca;
Dooley, Damion;
Overton, James A;
Miller, Mark A;
Berrios, Daniel C;
Scheuermann, Richard H;
He, Yongqun;
McGinty, Hande Küçük;
Brochhausen, Mathias;
Lin, Aisyah Yu;
Jain, Sagar B;
Chibucos, Marcus C;
Judkins, John;
Giglio, Michelle G;
Feng, Irene Y;
Burns, Gully;
Brush, Matthew H;
Peters, Bjoern

Publication type:

Article

immunologically friendly classification of non-peptidic ligands.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab014

By:

Edwards, Lindy;
Jackson, Rebecca;
Overton, James A;
Vita, Randi;
Blazeska, Nina;
Peters, Bjoern;
Sette, Alessandro

Publication type:

Article

A structured model for immune exposures.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baaa016

By:

Vita, Randi;
Overton, James A;
Dunn, Patrick;
Cheung, Kei-Hoi;
Kleinstein, Steven H;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Identification of errors in the IEDB using ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay005

By:

Vita, Randi;
Overton, James A;
Peters, Bjoern

Publication type:

Article

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

Published in:

Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bax105

By:

Vita, Randi;
Overton, James A;
Mungall, Christopher J;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Better living through ontologies at the Immune Epitope Database.

Published in:

Database: The Journal of Biological Databases & Curation, 2017, v. 2017, n. 1, p. 1, doi. 10.1093/database/bax014

By:

Vita, Randi;
Overton, James A.;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Towards Defining Molecular Determinants Recognized by Adaptive Immunity in Allergic Disease: An Inventory of the Available Data.

Published in:

Journal of Allergy, 2010, p. 1, doi. 10.1155/2010/628026

By:

Vaughan, Kerrie;
Greenbaum, Jason;
Kim, Yohan;
Vita, Randi;
Jo Chung;
Peters, Bjoern;
Broide, David;
Goodman, Richard;
Grey, Howard;
Sette, Alessandro

Publication type:

Article