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)

The Evolution and Recognition of Protein Sequence Repeats. - Jaap Heringa (Comput. Chem., 1994)

Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment. - Jaap Heringa (Comput. Chem., 1999)

RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York. - David D. Pollock; Jaap Heringa (Comput. Chem., 2000)

Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages. - Jaap Heringa (Comput. Chem., 2001)

Parallelized multiple alignment. - Jens Kleinjung; Nigel Douglas; Jaap Heringa (Bioinform., 2002)

Local Weighting Schemes for Protein Multiple Sequence Alignment. - Jaap Heringa (Comput. Chem., 2002)

A Million-Fold Speed Improvement in Genomic Repeats Detection. - John W. Romein; Jaap Heringa; Henri E. Bal (SC, 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)

The PRALINE online server: optimising progressive multiple alignment on the web. - Victor A. Simossis; Jaap Heringa (Comput. Biol. Chem., 2003)

Tracking repeats using significance and transitivity. - Radek Szklarczyk; Jaap Heringa (ISMB/ECCB (Supplement of Bioinformatics), 2004)

The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. - Victor A. Simossis; Jaap Heringa (Comput. Biol. Chem., 2004)

A simple and fast secondary structure prediction method using hidden neural networks. - Kuang Lin; Victor A. Simossis; William R. Taylor; Jaap Heringa (Bioinform., 2005)

Scooby-domain: prediction of globular domains in protein sequence. - Richard A. George; Kuang Lin; Jaap Heringa (Nucleic Acids Res., 2005)

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. - Victor A. Simossis; Jaap Heringa (Nucleic Acids Res., 2005)

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 (ICMLA, 2006)

AuberGene - a sensitive genome alignment tool. - Radek Szklarczyk; Jaap Heringa (Bioinform., 2006)

Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data. - Marius C. Codrea; Connie R. Jimenez; Sander R. Piersma; Jaap Heringa; Elena Marchiori (EvoBIO, 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)

Sequence harmony: detecting functional specificity from alignments. - K. Anton Feenstra; Walter Pirovano; Klaas Krab; Jaap Heringa (Nucleic Acids Res., 2007)

Divide, Align and Full-Search for Discovering Conserved Protein Complexes. - Pavol Jancura; Jaap Heringa; Elena Marchiori (EvoBIO, 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 (FMSB, 2008)

Dividing Protein Interaction Networks by Growing Orthologous Articulations. - Pavol Jancura; Jaap Heringa; Elena Marchiori (PRIB, 2008)

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (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 001; K. Anton Feenstra; Jaap Heringa; Adriaan P. IJzerman; Elena Marchiori (Bioinform., 2008)

The meaning of alignment: lessons from structural diversity. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (BMC Bioinform., 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)

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 C.elegans vulval development. - Nicola Bonzanni; Elzbieta Krepska; K. Anton Feenstra; Wan J. Fokkink; Thilo Kielmann; Henri E. Bal; Jaap Heringa (Bioinform., 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)

webPRC: the Profile Comparer for alignment-based searching of public domain databases. - Bernd W. Brandt; Jaap Heringa (Nucleic Acids Res., 2009)

PhyloPars: estimation of missing parameter values using phylogeny. - Jorn Bruggeman; Jaap Heringa; Bernd W. Brandt (Nucleic Acids Res., 2009)

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)

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)

Accurate confidence aware clustering of array CGH tumor profiles. - Bart P. P. van Houte; Jaap Heringa (Bioinform., 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)

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)

Multi-Harmony: detecting functional specificity from sequence alignment. - Bernd W. Brandt; K. Anton Feenstra; Jaap Heringa (Nucleic Acids Res., 2010)

Lagrangian Relaxation Applied to Sparse Global Network Alignment. - Mohammed El-Kebir; Jaap Heringa; Gunnar W. Klau (PRIB, 2011)

Protein analysis tools and services at IBIVU. - Bernd W. Brandt; Jaap Heringa (J. Integr. Bioinform., 2011)

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)

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)

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)

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)

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)

Petri Nets Are a Biologist's Best Friend. - Nicola Bonzanni; K. Anton Feenstra; Wan J. Fokkink; Jaap Heringa (FMMB, 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)

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)

A web server for protein-protein interaction network querying. - Mohammed El-Kebir; Bernd W. Brandt; Jaap Heringa; Gunnar W. Klau (BMC Syst. Biol., 2014)

Explaining disease using big data: How valid is your pathway? - Bas Stringer; Maurits J. J. Dijkstra; K. Anton Feenstra; Sanne Abeln; Jaap Heringa (HPCS, 2015)

To SCRY Linked Data: Extending SPARQL the Easy Way. - Bas Stringer; Albert Meroño-Peñuela; Antonis Loizou; Sanne Abeln; Jaap Heringa (Diversity++@ISWC, 2015)

SCRY: Enabling Quantitative Reasoning in SPARQL Queries. - Bas Stringer; Albert Meroño-Peñuela; Antonis Loizou; Sanne Abeln; Jaap Heringa (SWAT4LS, 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)

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 001; Guillaume Blin; Jaap Heringa; Macha Nikolski; Lodewyk F. A. Wessels; Gunnar W. Klau (Bioinform., 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)

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)

SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences. - Bas Stringer; Albert Meroño-Peñuela; Sanne Abeln; Frank van Harmelen; Jaap Heringa (SWAT4LS, 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)

ECCB 2016: The 15th European Conference on Computational Biology. - Jaap Heringa; Marcel J. T. Reinders; Sanne Abeln; Jeroen de Ridder (Bioinform., 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)

Editorial. - Jaap Heringa; Wentian Li; Jeffry D. Madura (Comput. Biol. Chem., 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; et al. (F1000Research, 2016)

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)

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; et al. (F1000Research, 2017)

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 (eScience, 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)

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)

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)

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)

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)

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)

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)

Protein Three-Dimensional Structure Prediction. - Sanne Abeln; K. Anton Feenstra; Jaap Heringa (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

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)

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; et al. (Data Intell., 2020)

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)

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. - Ting Liu; Xueli Pan; Xu Wang 032; K. Anton Feenstra; Jaap Heringa; Zhisheng Huang (Health Inf. Sci. Syst., 2021)

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)

CIBRA identifies genomic alterations with a system-wide impact on tumor biology. - Soufyan Lakbir; Caterina Buranelli; Gerrit A. Meijer; Jaap Heringa; Remond J. A. Fijneman; Sanne Abeln (Bioinform., 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., 2024)