Literature DB >> 26678806

Reproducibility and conflicts in immune epitope data.

Randi Vita1, Nicole Vasilevsky2, Anita Bandrowski3, Melissa Haendel2, Alessandro Sette1, Bjoern Peters1.   

Abstract

The Immune Epitope Database is uniquely positioned to assess the body of research related to immune epitopes, we have manually curated all such published data. Thus, we are able to make observations on the state of these fields of research, as well as aggregate the individual data points to present a clearer picture of the immune response to specific antigens in all studied hosts. Additionally, we are able to identify where conflicts in the literature exist and where publications fall short in terms of identifiable methods and in reproducibility. Here we present guidelines to improve the quality of immune epitope data, which will benefit journals and researchers alike.
© 2015 John Wiley & Sons Ltd.

Keywords:  Immune Epitope Database; database; immune epitope; reproducibility

Mesh:

Substances:

Year:  2016        PMID: 26678806      PMCID: PMC4754615          DOI: 10.1111/imm.12566

Source DB:  PubMed          Journal:  Immunology        ISSN: 0019-2805            Impact factor:   7.397


  9 in total

1.  Meta-analysis of all immune epitope data in the Flavivirus genus: inventory of current immune epitope data status in the context of virus immunity and immunopathology.

Authors:  Kerrie Vaughan; Jason Greenbaum; Martin Blythe; Bjoern Peters; Alessandro Sette
Journal:  Viral Immunol       Date:  2010-06       Impact factor: 2.257

2.  The curation guidelines of the immune epitope database and analysis resource.

Authors:  R Vita; B Peters; A Sette
Journal:  Cytometry A       Date:  2008-11       Impact factor: 4.355

3.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.

Authors:  Chris F Taylor; Dawn Field; Susanna-Assunta Sansone; Jan Aerts; Rolf Apweiler; Michael Ashburner; Catherine A Ball; Pierre-Alain Binz; Molly Bogue; Tim Booth; Alvis Brazma; Ryan R Brinkman; Adam Michael Clark; Eric W Deutsch; Oliver Fiehn; Jennifer Fostel; Peter Ghazal; Frank Gibson; Tanya Gray; Graeme Grimes; John M Hancock; Nigel W Hardy; Henning Hermjakob; Randall K Julian; Matthew Kane; Carsten Kettner; Christopher Kinsinger; Eugene Kolker; Martin Kuiper; Nicolas Le Novère; Jim Leebens-Mack; Suzanna E Lewis; Phillip Lord; Ann-Marie Mallon; Nishanth Marthandan; Hiroshi Masuya; Ruth McNally; Alexander Mehrle; Norman Morrison; Sandra Orchard; John Quackenbush; James M Reecy; Donald G Robertson; Philippe Rocca-Serra; Henry Rodriguez; Heiko Rosenfelder; Javier Santoyo-Lopez; Richard H Scheuermann; Daniel Schober; Barry Smith; Jason Snape; Christian J Stoeckert; Keith Tipton; Peter Sterk; Andreas Untergasser; Jo Vandesompele; Stefan Wiemann
Journal:  Nat Biotechnol       Date:  2008-08       Impact factor: 54.908

4.  Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.

Authors:  Jason A Greenbaum; Maya F Kotturi; Yohan Kim; Carla Oseroff; Kerrie Vaughan; Nima Salimi; Randi Vita; Julia Ponomarenko; Richard H Scheuermann; Alessandro Sette; Bjoern Peters
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-16       Impact factor: 11.205

5.  A meta-analysis of the existing knowledge of immunoreactivity against hepatitis C virus (HCV).

Authors:  Yohan Kim; Kerrie Vaughan; Jason Greenbaum; Bjoern Peters; Mansun Law; Alessandro Sette
Journal:  PLoS One       Date:  2012-05-31       Impact factor: 3.240

6.  The IPD and IMGT/HLA database: allele variant databases.

Authors:  James Robinson; Jason A Halliwell; James D Hayhurst; Paul Flicek; Peter Parham; Steven G E Marsh
Journal:  Nucleic Acids Res       Date:  2014-11-20       Impact factor: 16.971

7.  The Resource Identification Initiative: A cultural shift in publishing.

Authors:  Anita Bandrowski; Matthew Brush; Jeffery S Grethe; Melissa A Haendel; David N Kennedy; Sean Hill; Patrick R Hof; Maryann E Martone; Maaike Pols; Serena Tan; Nicole Washington; Elena Zudilova-Seinstra; Nicole Vasilevsky
Journal:  F1000Res       Date:  2015-05-29

8.  On the reproducibility of science: unique identification of research resources in the biomedical literature.

Authors:  Nicole A Vasilevsky; Matthew H Brush; Holly Paddock; Laura Ponting; Shreejoy J Tripathy; Gregory M Larocca; Melissa A Haendel
Journal:  PeerJ       Date:  2013-09-05       Impact factor: 2.984

9.  The immune epitope database (IEDB) 3.0.

Authors:  Randi Vita; James A Overton; Jason A Greenbaum; Julia Ponomarenko; Jason D Clark; Jason R Cantrell; Daniel K Wheeler; Joseph L Gabbard; Deborah Hix; Alessandro Sette; Bjoern Peters
Journal:  Nucleic Acids Res       Date:  2014-10-09       Impact factor: 16.971

  9 in total
  2 in total

1.  T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal.

Authors:  Eddie A James; Roberto Mallone; Sally C Kent; Teresa P DiLorenzo
Journal:  Diabetes       Date:  2020-07       Impact factor: 9.461

2.  Minimal Information about MHC Multimers (MIAMM).

Authors:  Randi Vita; Apurva Mody; James A Overton; Soren Buus; Stephen T Haley; Alessandro Sette; Vamsee Mallajosyula; Mark M Davis; Dale L Long; Richard A Willis; Bjoern Peters; John D Altman
Journal:  J Immunol       Date:  2022-02-01       Impact factor: 5.426

  2 in total

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