Jaap Heringa

According to our database1, Jaap Heringa authored at least 74 papers between 1992 and 2021.

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Bibliography

2021
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs.
Health Inf. Sci. Syst., 2021

2020
FAIR Principles: Interpretations and Implementation Considerations.
Data Intell., 2020

A framework for exhaustive modelling of genetic interaction patterns using Petri nets.
Bioinform., 2020

2019
Protein Three-Dimensional Structure Prediction.
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.
PLoS Comput. Biol., 2019

Mining Inter-Relationships in Online Scientific Articles and its Visualization: Natural Language Processing for Systems Biology Modeling.
Int. J. Online Biomed. Eng., 2019

SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.
Bioinform., 2019

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.
Bioinform., 2019

2018
Motif-Aware PRALINE: Improving the alignment of motif regions.
PLoS Comput. Biol., 2018

Training for translation between disciplines: a philosophy for life and data sciences curricula.
Bioinform., 2018

Bioinformatics in the Netherlands: the value of a nationwide community.
Briefings Bioinform., 2018

Message from the eScience 2018 Program Committee Chairs for the Focused Session on Data Handling and Analytics for Health.
Proceedings of the 14th IEEE International Conference on e-Science, 2018

2017
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest.
Bioinform., 2017

2016
Editorial.
Comput. Biol. Chem., 2016

metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform., 2016

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

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.
Bioinform., 2016

SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences.
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.
Nucleic Acids Res., 2015

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case.
BMC Bioinform., 2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform., 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms, 2015

SCRY: Enabling Quantitative Reasoning in SPARQL Queries.
Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

To SCRY Linked Data: Extending SPARQL the Easy Way.
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?
Proceedings of the 2015 International Conference on High Performance Computing & Simulation, 2015

2014
A web server for protein-protein interaction network querying.
BMC Syst. Biol., 2014

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.
Bioinform., 2014

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.
Bioinform., 2014

Petri Nets Are a Biologist's Best Friend.
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.
BMC Syst. Biol., 2013

Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform., 2013

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.
Bioinform., 2013

Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.
Briefings Bioinform., 2013

2012
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module.
J. Comput. Chem., 2012

2011
Protein analysis tools and services at IBIVU.
J. Integr. Bioinform., 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.
Proceedings of the Pattern Recognition in Bioinformatics, 2011

2010
Multi-Harmony: detecting functional specificity from sequence alignment.
Nucleic Acids Res., 2010

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density.
J. Chem. Inf. Model., 2010

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach.
BMC Bioinform., 2010

Accurate confidence aware clustering of array CGH tumor profiles.
Bioinform., 2010

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.
Bioinform., 2010

Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.
Bioinform., 2010

2009
PhyloPars: estimation of missing parameter values using phylogeny.
Nucleic Acids Res., 2009

webPRC: the Profile Comparer for alignment-based searching of public domain databases.
Nucleic Acids Res., 2009

Structure and function analysis of flexible alignment regions in proteins.
BMC Bioinform., 2009

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development.
Bioinform., 2009

Executing multicellular differentiation: quantitative predictive modelling of <i>C.elegans</i> vulval development.
Bioinform., 2009

2008
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.
Nucleic Acids Res., 2008

The meaning of alignment: lessons from structural diversity.
BMC Bioinform., 2008

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.
Bioinform., 2008

PRALINE<sup>TM</sup>: a strategy for improved multiple alignment of transmembrane proteins.
Bioinform., 2008

Dividing Protein Interaction Networks by Growing Orthologous Articulations.
Proceedings of the Pattern Recognition in Bioinformatics, 2008

Design Issues for Qualitative Modelling of Biological Cells with Petri Nets.
Proceedings of the Formal Methods in Systems Biology, First International Workshop, 2008

Divide, Align and Full-Search for Discovering Conserved Protein Complexes.
Proceedings of the Evolutionary Computation, 2008

2007
Sequence harmony: detecting functional specificity from alignments.
Nucleic Acids Res., 2007

Tools for computational processing of LC-MS datasets: A user's perspective.
Comput. Methods Programs Biomed., 2007

Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data.
Proceedings of the Evolutionary Computation, 2007

2006
AuberGene - a sensitive genome alignment tool.
Bioinform., 2006

A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding.
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.
Nucleic Acids Res., 2005

Scooby-domain: prediction of globular domains in protein sequence.
Nucleic Acids Res., 2005

A simple and fast secondary structure prediction method using hidden neural networks.
Bioinform., 2005

2004
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods.
Comput. Biol. Chem., 2004

Tracking repeats using significance and transitivity.
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.
Comput. Biol. Chem., 2003

Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.
Comput. Biol. Chem., 2003

A Million-Fold Speed Improvement in Genomic Repeats Detection.
Proceedings of the ACM/IEEE SC2003 Conference on High Performance Networking and Computing, 2003

2002
Local Weighting Schemes for Protein Multiple Sequence Alignment.
Comput. Chem., 2002

Parallelized multiple alignment.
Bioinform., 2002

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

2000
RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York.
Comput. Chem., 2000

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

1994
The Evolution and Recognition of Protein Sequence Repeats.
Comput. Chem., 1994

1992
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity.
Comput. Appl. Biosci., 1992


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