Jaap Heringa

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 23

Top Topics

Protein Interaction

Multiple Sequence Alignments

Top Venues

Briefings Bioinform.

PLoS Comput. Biol.

Publications

Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. Bioinform. 40 (1) (2024)
Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
PIPENN: protein interface prediction from sequence with an ensemble of neural nets. Bioinform. 38 (8) (2022)
Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. Bioinform. 37 (20) (2021)
Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. Health Inf. Sci. Syst. 9 (1) (2021)
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
FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2 (1-2) (2020)
Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra
A framework for exhaustive modelling of genetic interaction patterns using Petri nets. Bioinform. 36 (7) (2020)
Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. Bioinform. 35 (22) (2019)
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
Bioinformatics in the Netherlands: the value of a nationwide community. Briefings Bioinform. 20 (2) (2019)
Nidheesh Melethadathil, Jaap Heringa, Bipin Nair, Shyam Diwakar
Mining Inter-Relationships in Online Scientific Articles and its Visualization: Natural Language Processing for Systems Biology Modeling. Int. J. Online Biomed. Eng. 15 (2) (2019)
Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinform. 35 (24) (2019)
Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren
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. 15 (5) (2019)
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinform. 34 (13) (2018)
Jaap Heringa, Vincent T. van Hees
Message from the eScience 2018 Program Committee Chairs for the Focused Session on Data Handling and Analytics for Health. eScience (2018)
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
Bioinformatics in the Netherlands: the value of a nationwide community. Briefings Bioinform. 19 (2) (2018)
Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
Motif-Aware PRALINE: Improving the alignment of motif regions. PLoS Comput. Biol. 14 (11) (2018)
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
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 6 (2017)
Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. Bioinform. 33 (10) (2017)
Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder
ECCB 2016: The 15th European Conference on Computational Biology. Bioinform. 32 (17) (2016)
Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences. SWAT4LS (2016)
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
Integration of EGA secure data access into Galaxy. F1000Research 5 (2016)
Jaap Heringa, Wentian Li, Jeffry D. Madura
Editorial. Comput. Biol. Chem. 64 (2016)
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
metaModules identifies key functional subnetworks in microbiome-related disease. Bioinform. 32 (11) (2016)
Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. Bioinform. 32 (12) (2016)
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
To SCRY Linked Data: Extending SPARQL the Easy Way. Diversity++@ISWC (2015)
Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
Explaining disease using big data: How valid is your pathway? HPCS (2015)
Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinform. 16 (2015)
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
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 31 (19) (2015)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 8 (4) (2015)
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
SCRY: Enabling Quantitative Reasoning in SPARQL Queries. SWAT4LS (2015)
Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. Bioinform. 30 (3) (2014)
Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinform. 30 (11) (2014)
Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau
A web server for protein-protein interaction network querying. BMC Syst. Biol. 8 (2014)
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
Petri Nets Are a Biologist's Best Friend. FMMB (2014)
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14 (S-15) (2013)
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings Bioinform. 14 (5) (2013)
Hannes Hettling, David J. C. Alders, Jaap Heringa, Thomas W. Binsl, A. B. Johan Groeneveld, Johannes H. G. M. van Beek
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies. BMC Syst. Biol. 7 (2013)
Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinform. 29 (13) (2013)
René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem. 33 (12) (2012)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Lagrangian Relaxation Applied to Sparse Global Network Alignment CoRR (2011)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Lagrangian Relaxation Applied to Sparse Global Network Alignment. PRIB (2011)
Bernd W. Brandt, Jaap Heringa
Protein analysis tools and services at IBIVU. J. Integr. Bioinform. 8 (2) (2011)
Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa
Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Bart P. P. van Houte, Jaap Heringa
Accurate confidence aware clustering of array CGH tumor profiles. Bioinform. 26 (1) (2010)
Thomas W. Binsl, David J. C. Alders, Jaap Heringa, A. B. Johan Groeneveld, Johannes H. G. M. van Beek
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy. Bioinform. 26 (5) (2010)
Hannes Hettling, Jaap Heringa, Johannes H. G. M. van Beek
Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach. BMC Bioinform. 11 (S-10) (2010)
Bart P. P. van Houte, Thomas W. Binsl, Hannes Hettling, Jaap Heringa
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. Bioinform. 26 (10) (2010)
Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa
Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density. J. Chem. Inf. Model. 50 (10) (2010)
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
vulval development. Bioinform. 25 (16) (2009)
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. Bioinform. 25 (19) (2009)
Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa
Structure and function analysis of flexible alignment regions in proteins. BMC Bioinform. 10 (S-13) (2009)
Jorn Bruggeman, Jaap Heringa, Bernd W. Brandt
PhyloPars: estimation of missing parameter values using phylogeny. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Bernd W. Brandt, Jaap Heringa
webPRC: the Profile Comparer for alignment-based searching of public domain databases. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. FMSB (2008)
Pavol Jancura, Jaap Heringa, Elena Marchiori
Dividing Protein Interaction Networks by Growing Orthologous Articulations. PRIB (2008)
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
The meaning of alignment: lessons from structural diversity. BMC Bioinform. 9 (2008)
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
: a strategy for improved multiple alignment of transmembrane proteins. Bioinform. 24 (4) (2008)
Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinform. 24 (1) (2008)
Bernd W. Brandt, Jaap Heringa, Jack A. M. Leunissen
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Pavol Jancura, Jaap Heringa, Elena Marchiori
Divide, Align and Full-Search for Discovering Conserved Protein Complexes. EvoBIO (2008)
K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa
Sequence harmony: detecting functional specificity from alignments. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Marius C. Codrea, Connie R. Jimenez, Jaap Heringa, Elena Marchiori
Tools for computational processing of LC-MS datasets: A user's perspective. Comput. Methods Programs Biomed. 86 (3) (2007)
Marius C. Codrea, Connie R. Jimenez, Sander R. Piersma, Jaap Heringa, Elena Marchiori
Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data. EvoBIO (2007)
Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra
A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. ICMLA (2006)
Radek Szklarczyk, Jaap Heringa
AuberGene - a sensitive genome alignment tool. Bioinform. 22 (12) (2006)
Richard A. George, Kuang Lin, Jaap Heringa
Scooby-domain: prediction of globular domains in protein sequence. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Victor A. Simossis, Jaap Heringa
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa
A simple and fast secondary structure prediction method using hidden neural networks. Bioinform. 21 (2) (2005)
Victor A. Simossis, Jaap Heringa
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. Comput. Biol. Chem. 28 (5-6) (2004)
Radek Szklarczyk, Jaap Heringa
Tracking repeats using significance and transitivity. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Victor A. Simossis, Jaap Heringa
The PRALINE online server: optimising progressive multiple alignment on the web. Comput. Biol. Chem. 27 (4-5) (2003)
Kuang Lin, Jens Kleinjung, William R. Taylor, Jaap Heringa
Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. Comput. Biol. Chem. 27 (2) (2003)
John W. Romein, Jaap Heringa, Henri E. Bal
A Million-Fold Speed Improvement in Genomic Repeats Detection. SC (2003)
Jens Kleinjung, Nigel Douglas, Jaap Heringa
Parallelized multiple alignment. Bioinform. 18 (9) (2002)
Jaap Heringa
Local Weighting Schemes for Protein Multiple Sequence Alignment. Comput. Chem. 26 (5) (2002)
Jaap Heringa
Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages. Comput. Chem. 25 (4) (2001)
David D. Pollock, Jaap Heringa
RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York. Comput. Chem. 24 (1) (2000)
Jaap Heringa
Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment. Comput. Chem. 23 (3-4) (1999)
Jaap Heringa
The Evolution and Recognition of Protein Sequence Repeats. Comput. Chem. 18 (3) (1994)
Jaap Heringa, Hubert Sommerfeldt, Desmond G. Higgins, Patrick Argos
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput. Appl. Biosci. 8 (6) (1992)