Jaap Heringa

According to our database, Jaap Heringa authored at least 79 papers between 1992 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph.

Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa

Bioinform., January, 2024

2022

PIPENN: protein interface prediction from sequence with an ensemble of neural nets.

Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou

Bioinform., 2022

2021

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs.

Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang

Health Inf. Sci. Syst., 2021

SeRenDIP-CE: sequence-based interface prediction for conformational epitopes.

Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra

Bioinform., 2021

2020

FAIR Principles: Interpretations and Implementation Considerations.

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

Data Intell., 2020

A framework for exhaustive modelling of genetic interaction patterns using Petri nets.

Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra

Bioinform., 2020

2019

Protein Three-Dimensional Structure Prediction.

Sanne Abeln, K. Anton Feenstra, Jaap Heringa

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

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.

Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren

PLoS Comput. Biol., 2019

Mining Inter-Relationships in Online Scientific Articles and its Visualization: Natural Language Processing for Systems Biology Modeling.

Nidheesh Melethadathil, Jaap Heringa, Bipin Nair, Shyam Diwakar

Int. J. Online Biomed. Eng., 2019

SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.

Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra

Bioinform., 2019

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.

Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa

Bioinform., 2019

Bioinformatics in the Netherlands: the value of a nationwide community.

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

Briefings Bioinform., 2019

2018

Motif-Aware PRALINE: Improving the alignment of motif regions.

Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa

PLoS Comput. Biol., 2018

Training for translation between disciplines: a philosophy for life and data sciences curricula.

K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa

Bioinform., 2018

Message from the eScience 2018 Program Committee Chairs for the Focused Session on Data Handling and Analytics for Health.

Jaap Heringa, Vincent T. van Hees

Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.

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

F1000Research, 2017

Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.

Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra

Bioinform., 2017

2016

Integration of EGA secure data access into Galaxy.

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

F1000Research, 2016

Editorial.

Jaap Heringa, Wentian Li, Jeffry D. Madura

Comput. Biol. Chem., 2016

metaModules identifies key functional subnetworks in microbiome-related disease.

Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln

Bioinform., 2016

ECCB 2016: The 15th European Conference on Computational Biology.

Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder

Bioinform., 2016

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa

Bioinform., 2016

SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences.

Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

2015

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt

Nucleic Acids Res., 2015

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case.

Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra

BMC Bioinform., 2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

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

Bioinform., 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.

Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau

Algorithms, 2015

SCRY: Enabling Quantitative Reasoning in SPARQL Queries.

Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

To SCRY Linked Data: Extending SPARQL the Easy Way.

Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa

Proceedings of the 1st International Diversity++ Workshop co-located with the 14th International Semantic Web Conference (ISWC 2015), 2015

Explaining disease using big data: How valid is your pathway?

Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa

Proceedings of the 2015 International Conference on High Performance Computing & Simulation, 2015

2014

A web server for protein-protein interaction network querying.

Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau

BMC Syst. Biol., 2014

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra

Bioinform., 2014

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.

Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt

Bioinform., 2014

Petri Nets Are a Biologist's Best Friend.

Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa

Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

2013

Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies.

Hannes Hettling, David J. C. Alders, Jaap Heringa, Thomas W. Binsl, A. B. Johan Groeneveld, Johannes H. G. M. van Beek

BMC Syst. Biol., 2013

Mapping proteins in the presence of paralogs using units of coevolution.

Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau

BMC Bioinform., 2013

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

Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens

Bioinform., 2013

Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.

Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa

Briefings Bioinform., 2013

2012

Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module.

René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra

J. Comput. Chem., 2012

2011

Protein analysis tools and services at IBIVU.

Bernd W. Brandt, Jaap Heringa

J. Integr. Bioinform., 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.

Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau

Proceedings of the Pattern Recognition in Bioinformatics, 2011

2010

Multi-Harmony: detecting functional specificity from sequence alignment.

Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa

Nucleic Acids Res., 2010

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density.

Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa

J. Chem. Inf. Model., 2010

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach.

Hannes Hettling, Jaap Heringa, Johannes H. G. M. van Beek

BMC Bioinform., 2010

Accurate confidence aware clustering of array CGH tumor profiles.

Bart P. P. van Houte, Jaap Heringa

Bioinform., 2010

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.

Bart P. P. van Houte, Thomas W. Binsl, Hannes Hettling, Jaap Heringa

Bioinform., 2010

Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.

Thomas W. Binsl, David J. C. Alders, Jaap Heringa, A. B. Johan Groeneveld, Johannes H. G. M. van Beek

Bioinform., 2010

2009

PhyloPars: estimation of missing parameter values using phylogeny.

Jorn Bruggeman, Jaap Heringa, Bernd W. Brandt

Nucleic Acids Res., 2009

webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Bernd W. Brandt, Jaap Heringa

Nucleic Acids Res., 2009

Structure and function analysis of flexible alignment regions in proteins.

Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa

BMC Bioinform., 2009

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development.

Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa

Bioinform., 2009

Executing multicellular differentiation: quantitative predictive modelling of <i>C.elegans</i> vulval development.

Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa

Bioinform., 2009

2008

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

Bernd W. Brandt, Jaap Heringa, Jack A. M. Leunissen

Nucleic Acids Res., 2008

The meaning of alignment: lessons from structural diversity.

Walter Pirovano, K. Anton Feenstra, Jaap Heringa

BMC Bioinform., 2008

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.

Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori

Bioinform., 2008

PRALINE^TM: a strategy for improved multiple alignment of transmembrane proteins.

Walter Pirovano, K. Anton Feenstra, Jaap Heringa

Bioinform., 2008

Dividing Protein Interaction Networks by Growing Orthologous Articulations.

Pavol Jancura, Jaap Heringa, Elena Marchiori

Proceedings of the Pattern Recognition in Bioinformatics, 2008

Design Issues for Qualitative Modelling of Biological Cells with Petri Nets.

Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa

Proceedings of the Formal Methods in Systems Biology, First International Workshop, 2008

Divide, Align and Full-Search for Discovering Conserved Protein Complexes.

Pavol Jancura, Jaap Heringa, Elena Marchiori

Proceedings of the Evolutionary Computation, 2008

2007

Sequence harmony: detecting functional specificity from alignments.

K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa

Nucleic Acids Res., 2007

Tools for computational processing of LC-MS datasets: A user's perspective.

Marius C. Codrea, Connie R. Jimenez, Jaap Heringa, Elena Marchiori

Comput. Methods Programs Biomed., 2007

Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data.

Marius C. Codrea, Connie R. Jimenez, Sander R. Piersma, Jaap Heringa, Elena Marchiori

Proceedings of the Evolutionary Computation, 2007

2006

AuberGene - a sensitive genome alignment tool.

Radek Szklarczyk, Jaap Heringa

Bioinform., 2006

A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding.

Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra

Proceedings of the Fifth International Conference on Machine Learning and Applications, 2006

2005

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

Victor A. Simossis, Jaap Heringa

Nucleic Acids Res., 2005

Scooby-domain: prediction of globular domains in protein sequence.

Richard A. George, Kuang Lin, Jaap Heringa

Nucleic Acids Res., 2005

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

Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa

Bioinform., 2005

2004

The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.

Victor A. Simossis, Jaap Heringa

Comput. Biol. Chem., 2004

Tracking repeats using significance and transitivity.

Radek Szklarczyk, Jaap Heringa

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

The PRALINE online server: optimising progressive multiple alignment on the web.

Victor A. Simossis, Jaap Heringa

Comput. Biol. Chem., 2003

Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.

Kuang Lin, Jens Kleinjung, William R. Taylor, Jaap Heringa

Comput. Biol. Chem., 2003

A Million-Fold Speed Improvement in Genomic Repeats Detection.

John W. Romein, Jaap Heringa, Henri E. Bal

Proceedings of the ACM/IEEE SC2003 Conference on High Performance Networking and Computing, 2003

2002

Local Weighting Schemes for Protein Multiple Sequence Alignment.

Jaap Heringa

Comput. Chem., 2002

Parallelized multiple alignment.

Jens Kleinjung, Nigel Douglas, Jaap Heringa

Bioinform., 2002

2001

Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages.

Jaap Heringa

Comput. Chem., 2001

2000

RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York.

David D. Pollock, Jaap Heringa

Comput. Chem., 2000

1999

Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment.

Jaap Heringa

Comput. Chem., 1999

1994

The Evolution and Recognition of Protein Sequence Repeats.

Jaap Heringa

Comput. Chem., 1994

1992

OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity.

Jaap Heringa, Hubert Sommerfeldt, Desmond G. Higgins, Patrick Argos

Comput. Appl. Biosci., 1992