Jaap Heringa

82 papers A 1C 1Journal 67Unranked 12
YearRankTypeTitle / Venue / Authors
2024 J jnl
CIBRA identifies genomic alterations with a system-wide impact on tumor biology.
Bioinform.
Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer, Jaap Heringa, Remond J. A. Fijneman, Sanne Abeln
2024 J jnl
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.
Bioinform.
Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa
2022 J jnl
PIPENN: protein interface prediction from sequence with an ensemble of neural nets.
Bioinform.
Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
2021 J jnl
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs.
Health Inf. Sci. Syst.
Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang
2021 J jnl
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes.
Bioinform.
Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2020 J jnl
A framework for exhaustive modelling of genetic interaction patterns using Petri nets.
Bioinform.
Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra
2020 J jnl
FAIR Principles: Interpretations and Implementation Considerations.
Data Intell.
Annika Jacobsen, Ricardo de Miranda Azevedo, Nick S. Juty, Dominique Batista, Simon J. Coles, Ronald Cornet, Mélanie Courtot, Mercè Crosas, Michel Dumontier, Chris T. A. Evelo, Carole A. Goble, Giancarlo Guizzardi, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes
2019 J jnl
Bioinformatics in the Netherlands: the value of a nationwide community.
Briefings Bioinform.
Celia W. G. van Gelder, Rob W. W. Hooft, Merlijn N. van Rijswijk, Linda van den Berg, Ruben G. Kok, Marcel J. T. Reinders, Barend Mons, Jaap Heringa
2019 J jnl
Mining Inter-Relationships in Online Scientific Articles and its Visualization: Natural Language Processing for Systems Biology Modeling.
Int. J. Online Biomed. Eng.
Nidheesh Melethadathil, Jaap Heringa, Bipin Nair, Shyam Diwakar
2019 — ch.
Protein Three-Dimensional Structure Prediction.
Encyclopedia of Bioinformatics and Computational Biology (2)
Sanne Abeln, K. Anton Feenstra, Jaap Heringa
2019 J jnl
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.
Bioinform.
Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2019 J jnl
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.
Bioinform.
Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
2019 J jnl
The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern.
PLoS Comput. Biol.
Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren
2018 J jnl
Bioinformatics in the Netherlands: the value of a nationwide community.
Briefings Bioinform.
Celia W. G. van Gelder, Rob W. W. Hooft, Merlijn N. van Rijswijk, Linda van den Berg, Ruben G. Kok, Marcel J. T. Reinders, Barend Mons, Jaap Heringa
2018 — conf
Message from the eScience 2018 Program Committee Chairs for the Focused Session on Data Handling and Analytics for Health.
eScience
Jaap Heringa, Vincent T. van Hees
2018 J jnl
Motif-Aware PRALINE: Improving the alignment of motif regions.
PLoS Comput. Biol.
Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2018 J jnl
Training for translation between disciplines: a philosophy for life and data sciences curricula.
Bioinform.
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
2017 J jnl
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.
Bioinform.
Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra
2017 J jnl
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
F1000Research
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena A. Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia D. Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino da Silva Santos, Jeroen Beliën, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond J. A. Fijneman, J. Dylan Spalding, Sanne Abeln
2016 J jnl
BioASF: a framework for automatically generating executable pathway models specified in BioPAX.
Bioinform.
Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2016 J jnl
ECCB 2016: The 15th European Conference on Computational Biology.
Bioinform.
Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder
2016 J jnl
Editorial.
Comput. Biol. Chem.
Jaap Heringa, Wentian Li, Jeffry D. Madura
2016 J jnl
Integration of EGA secure data access into Galaxy.
F1000Research
Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia D. Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J. A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln
2016 — conf
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences.
SWAT4LS
Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa
2016 J jnl
metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform.
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
2015 — conf
Explaining disease using big data: How valid is your pathway?
HPCS
Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015 J jnl
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.
Nucleic Acids Res.
Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt
2015 J jnl
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2015 — conf
SCRY: Enabling Quantitative Reasoning in SPARQL Queries.
SWAT4LS
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
2015 J jnl
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case.
BMC Bioinform.
Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra
2015 — conf
To SCRY Linked Data: Extending SPARQL the Easy Way.
Diversity++@ISWC
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
2015 J jnl
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform.
Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau
2014 J jnl
A web server for protein-protein interaction network querying.
BMC Syst. Biol.
Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau
2014 J jnl
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.
Bioinform.
Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2014 — conf
Petri Nets Are a Biologist's Best Friend.
FMMB
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2014 J jnl
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.
Bioinform.
Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt
2013 J jnl
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.
Briefings Bioinform.
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
2013 J jnl
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies.
BMC Syst. Biol.
Hannes Hettling, David J. C. Alders, Jaap Heringa, Thomas W. Binsl, A. B. Johan Groeneveld, Johannes H. G. M. van Beek
2013 J jnl
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.
Bioinform.
Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens
2013 J jnl
Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform.
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
2012 J jnl
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module.
J. Comput. Chem.
René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
2011 J jnl
Lagrangian Relaxation Applied to Sparse Global Network Alignment
CoRR
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2011 — conf
Lagrangian Relaxation Applied to Sparse Global Network Alignment.
PRIB
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2011 J jnl
Protein analysis tools and services at IBIVU.
J. Integr. Bioinform.
Bernd W. Brandt, Jaap Heringa
2010 J jnl
Accurate confidence aware clustering of array CGH tumor profiles.
Bioinform.
Bart P. P. van Houte, Jaap Heringa
2010 J jnl
Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach.
BMC Bioinform.
Hannes Hettling, Jaap Heringa, Johannes H. G. M. van Beek
2010 J jnl
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.
Bioinform.
Bart P. P. van Houte, Thomas W. Binsl, Hannes Hettling, Jaap Heringa
2010 J jnl
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.
Bioinform.
Thomas W. Binsl, David J. C. Alders, Jaap Heringa, A. B. Johan Groeneveld, Johannes H. G. M. van Beek
2010 J jnl
Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density.
J. Chem. Inf. Model.
Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa
2010 J jnl
Multi-Harmony: detecting functional specificity from sequence alignment.
Nucleic Acids Res.
Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa
2009 J jnl
Executing multicellular differentiation: quantitative predictive modelling of
Bioinform.
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009 J jnl
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development.
Bioinform.
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009 J jnl
PhyloPars: estimation of missing parameter values using phylogeny.
Nucleic Acids Res.
Jorn Bruggeman, Jaap Heringa, Bernd W. Brandt
2009 J jnl
Structure and function analysis of flexible alignment regions in proteins.
BMC Bioinform.
Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa
2009 J jnl
webPRC: the Profile Comparer for alignment-based searching of public domain databases.
Nucleic Acids Res.
Bernd W. Brandt, Jaap Heringa
2008 — conf
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets.
FMSB
Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2008 — conf
Divide, Align and Full-Search for Discovering Conserved Protein Complexes.
EvoBIO
Pavol Jancura, Jaap Heringa, Elena Marchiori
2008 — conf
Dividing Protein Interaction Networks by Growing Orthologous Articulations.
PRIB
Pavol Jancura, Jaap Heringa, Elena Marchiori
2008 J jnl
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
Bioinform.
Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
2008 J jnl
PRALINE
Bioinform.
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2008 J jnl
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.
Nucleic Acids Res.
Bernd W. Brandt, Jaap Heringa, Jack A. M. Leunissen
2008 J jnl
The meaning of alignment: lessons from structural diversity.
BMC Bioinform.
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2007 — conf
Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data.
EvoBIO
Marius C. Codrea, Connie R. Jimenez, Sander R. Piersma, Jaap Heringa, Elena Marchiori
2007 J jnl
Sequence harmony: detecting functional specificity from alignments.
Nucleic Acids Res.
K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa
2007 J jnl
Tools for computational processing of LC-MS datasets: A user's perspective.
Comput. Methods Programs Biomed.
Marius C. Codrea, Connie R. Jimenez, Jaap Heringa, Elena Marchiori
2006 C conf
A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding.
ICMLA
Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra
2006 J jnl
AuberGene - a sensitive genome alignment tool.
Bioinform.
Radek Szklarczyk, Jaap Heringa
2005 J jnl
A simple and fast secondary structure prediction method using hidden neural networks.
Bioinform.
Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa
2005 J jnl
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information.
Nucleic Acids Res.
Victor A. Simossis, Jaap Heringa
2005 J jnl
Scooby-domain: prediction of globular domains in protein sequence.
Nucleic Acids Res.
Richard A. George, Kuang Lin, Jaap Heringa
2004 J jnl
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.
Comput. Biol. Chem.
Victor A. Simossis, Jaap Heringa
2004 — conf
Tracking repeats using significance and transitivity.
ISMB/ECCB (Supplement of Bioinformatics)
Radek Szklarczyk, Jaap Heringa
2003 A conf
A Million-Fold Speed Improvement in Genomic Repeats Detection.
SC
John W. Romein, Jaap Heringa, Henri E. Bal
2003 J jnl
Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.
Comput. Biol. Chem.
Kuang Lin, Jens Kleinjung, William R. Taylor, Jaap Heringa
2003 J jnl
The PRALINE online server: optimising progressive multiple alignment on the web.
Comput. Biol. Chem.
Victor A. Simossis, Jaap Heringa
2002 J jnl
Local Weighting Schemes for Protein Multiple Sequence Alignment.
Comput. Chem.
Jaap Heringa
2002 J jnl
Parallelized multiple alignment.
Bioinform.
Jens Kleinjung, Nigel Douglas, Jaap Heringa
2001 J jnl
Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages.
Comput. Chem.
Jaap Heringa
2000 J jnl
RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York.
Comput. Chem.
David D. Pollock, Jaap Heringa
1999 J jnl
Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment.
Comput. Chem.
Jaap Heringa
1994 J jnl
The Evolution and Recognition of Protein Sequence Repeats.
Comput. Chem.
Jaap Heringa
1992 J jnl
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity.
Comput. Appl. Biosci.
Jaap Heringa, Hubert Sommerfeldt, Desmond G. Higgins, Patrick Argos