World's Best Scientists 2026 revealed!

D-Index & Metrics

Computer Science

D-Index
41
Citations
33788
World Ranking
8552
National Ranking
145

Overview

Jaap Heringa is affiliated with Vrije Universiteit Amsterdam in the Netherlands. Their research primarily focuses on biochemistry, genetics, molecular biology, and medicine, with a notable emphasis on molecular biology, cancer research, pathology and forensic medicine, genetics, and radiology, nuclear medicine, and imaging.

The scientist's work spans several key topics, including:

  • Cancer Genomics and Diagnostics
  • Genetic factors in colorectal cancer
  • RNA and protein synthesis mechanisms
  • Vaccines and immunoinformatics approaches
  • Monoclonal and Polyclonal Antibodies Research
  • Protein Structure and Dynamics
  • Computational Drug Discovery Methods

Heringa has published extensively in a range of scientific outlets. Frequent publication venues include Cancer Research, Bioinformatics, bioRxiv (Cold Spring Harbor Laboratory), npj Science of Food, and arXiv (Cornell University).

Recent papers demonstrate a focus on interface prediction and colorectal cancer research, with titles such as:

  • SeRenDIP-CE: sequence-based interface prediction for conformational epitopes, 2021, Bioinformatics
  • PIPENN: protein interface prediction from sequence with an ensemble of neural nets, 2022, Bioinformatics
  • Applying federated learning to combat food fraud in food supply chains, 2023, npj Science of Food
  • Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer, 2022, European Journal of Cancer
  • SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes, 2020, bioRxiv (Cold Spring Harbor Laboratory)

Co-authorship collaborations have been frequent with several researchers including Sanne Abeln, Remond J.A. Fijneman, Gerrit A. Meijer, Soufyan Lakbir, and Bas Stringer.

Best Publications

  • The FAIR Guiding Principles for scientific data management and stewardship

    Mark D Wilkinson;Michel Dumontier;IJsbrand Jan Aalbersberg;Gabrielle Appleton

  • T-Coffee: A novel method for fast and accurate multiple sequence alignment.

    Cédric Notredame;Cédric Notredame;Cédric Notredame;Desmond G Higgins;Jaap Heringa

  • Addendum: The FAIR Guiding Principles for scientific data management and stewardship

    Mark D. Wilkinson;Michel Dumontier;Ijsbrand Jan Aalbersberg;Gabrielle Appleton

  • PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.

    Victor A. Simossis;Jaap Heringa

  • FAIR principles : interpretations and implementation considerations

    Annika Jacobsen;Ricardo de Miranda Azevedo;Nick S. Juty;Dominique Batista

  • A simple and fast secondary structure prediction method using hidden neural networks

    Kuang Lin;Victor A. Simossis;Willam R. Taylor;Jaap Heringa

  • Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment.

    Jaap Heringa

  • Tracking repeats using significance and transitivity

    Radek Szklarczyk;Jaap Heringa

  • PhyloPars: estimation of missing parameter values using phylogeny

    Jorn Bruggeman;Jaap Heringa;Bernd W. Brandt

  • Protein secondary structure prediction.

    Walter Pirovano;Jaap Heringa

  • PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.

    Walter Pirovano;K. Anton Feenstra;Jaap Heringa

  • Homology-extended sequence alignment

    V. A. Simossis;J. Kleinjung;J. Heringa

  • SnapDRAGON: a method to delineate protein structural domains from sequence data.

    Richard A George;Jaap Heringa

  • Three-dimensional domain duplication, swapping and stealing

    Jaap Heringa;William R Taylor

  • Multi-RELIEF

    Kai Ye;K. Anton Feenstra;Jaap Heringa;Adriaan P. IJzerman

  • Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

    Nicola Bonzanni;Abhishek Garg;K Anton Feenstra;Judith Schütte

  • Detection of internal repeats: how common are they?

    Jaap Heringa

  • From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal

    Sandra Smit;Kristian Rother;Jaap Heringa;Rob Knight

  • The REPRO server: finding protein internal sequence repeats through the Web.

    Richard A. George;Jaap Heringa

  • Leveraging European infrastructures to access 1 million human genomes by 2022

    Gary Saunders;Michael Baudis;Regina Becker;Sergi Beltran

  • A method to recognize distant repeats in protein sequences

    Jaap Heringa;Patrick Argos

Frequent Co-Authors

Gunnar W. Klau
Gunnar W. Klau Heinrich Heine University Düsseldorf
Patrick Argos
Patrick Argos Purdue University West Lafayette
Wan Fokkink
Wan Fokkink Vrije Universiteit Amsterdam
Barend Mons
Barend Mons Leiden University Medical Center
Elena Marchiori
Elena Marchiori Radboud University
Bas E. Dutilh
Bas E. Dutilh Utrecht University
Henri E. Bal
Henri E. Bal Vrije Universiteit Amsterdam
Bengt Persson
Bengt Persson Science for Life Laboratory
Søren Brunak
Søren Brunak University of Copenhagen
Morris A. Swertz
Morris A. Swertz University Medical Center Groningen

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