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List of works by Jaap Heringa

A Fourier analysis of symmetry in protein structure.

scientific article

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

scientific article published on 01 April 2020

A protein prioritization approach tailored for the FA/BRCA pathway

scientific article

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

scientific article published on 17 September 2004

Accurate confidence aware clustering of array CGH tumor profiles

scientific article published on 21 October 2009

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

article by Mark D Wilkinson et al published 19 March 2019 in Scientific Data

An analysis of protein domain linkers: their classification and role in protein folding

scientific article (publication date: November 2002)

An overview of multiple sequence alignment

scientific article

AuberGene--a sensitive genome alignment tool

scientific article published on 10 April 2006

Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer.

scientific article

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 01 November 2019

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

scientific article

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

scientific article published on 19 April 2013

Bioinformatics in the Netherlands: the value of a nationwide community

scientific article published on 01 March 2018

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

scientific article published on 15 September 2017

Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases

scientific article published on 3 February 2017

Bridging the translational innovation gap through good biomarker practice.

scientific article published on 28 April 2017

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

scientific article

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations

scientific article published on 26 August 2009

CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys.

scientific article

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

scientific article

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

scientific article

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

scientific article published on 22 January 2010

ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

scientific article

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling.

scientific article

Contact-based sequence alignment

scientific article

Correction: A Protein Prioritization Approach Tailored for the FA/BRCA Pathway

scientific article published on 15 October 2013

ECCB 2016: The 15th European Conference on Computational Biology

scientific article published on 01 September 2016

Editorial

Electron density fingerprints (EDprints): virtual screening using assembled information of electron density.

scientific article published in October 2010

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

scientific article

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

scientific article

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

scientific article (publication date: July 2015)

Exploring familial relationships using multiple sequence alignment

scientific article published on 01 January 2002

FAIR Principles: Interpretations and Implementation Considerations

scholarly article

From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal

scientific article published on 29 January 2008

General secretion signal for the mycobacterial type VII secretion pathway

scientific article

Global multiple-sequence alignment with repeats

scholarly article by Michael Sammeth published in April 2006

HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity.

scientific article published on 23 September 2013

HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag

scientific article

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

scientific article published on July 2013

Homology-extended sequence alignment

scientific article

Identifying foldable regions in protein sequence from the hydrophobic signal.

scientific article

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping

scientific article

Integration of EGA secure data access into Galaxy

scientific article

Lagrangian Relaxation Applied to Sparse Global Network Alignment

Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 27 August 2019

Local weighting schemes for protein multiple sequence alignment.

scientific article published in July 2002

Mapping proteins in the presence of paralogs using units of coevolution

scientific article

Motif-Aware PRALINE: Improving the alignment of motif regions

scientific article published on 01 November 2018

Multi-Harmony: detecting functional specificity from sequence alignment.

scientific article published on 4 June 2010

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

scientific article

Multiple Sequence Alignment

scientific article published in January 2017

Multiple alignment of transmembrane protein sequences

Multiple sequence alignment

scientific article published on 01 January 2008

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

scientific article published on 15 April 2015

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

NatalieQ: a web server for protein-protein interaction network querying

scientific article

On defining the dynamics of hydrophobic patches on protein surfaces

scientific article published on 01 July 2008

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

scientific article

PRALINE: a versatile multiple sequence alignment toolkit

scientific article published in January 2014

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

scientific article published on 02 January 2008

Parallelized multiple alignment.

scientific article published in September 2002

PhyloPars: estimation of missing parameter values using phylogeny

scientific article published on 13 May 2009

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

scientific article published on 24 November 2020

Protein Secondary Structure Prediction

Protein analysis tools and services at IBIVU

scientific article published on 08 September 2011

Protein domain identification and improved sequence similarity searching using PSI-BLAST.

scientific article published in September 2002

Quantifying the displacement of mismatches in multiple sequence alignment benchmarks

scientific article published on 19 May 2015

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function

scientific article

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

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

scientific article

Scooby-domain: prediction of globular domains in protein sequence

scientific article

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

scientific article published on 01 November 2019

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

scientific article published on 10 January 2017

Sequence comparison by sequence harmony identifies subtype-specific functional sites

scientific article

Sequence harmony: detecting functional specificity from alignments.

scientific article

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

scientific article

Side-chain clusters in protein structures and their role in protein folding

scientific article

SnapDRAGON: a method to delineate protein structural domains from sequence data

scientific article (publication date: 22 February 2002)

Structure and function analysis of flexible alignment regions in proteins.

scientific article published on 19 October 2009

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

scientific article

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

scientific article published on 01 December 2019

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

scientific article

The FAIR Guiding Principles for scientific data management and stewardship

scientific article (publication date: 15 March 2016)

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.

scientific article published on 13 May 2019

The meaning of alignment: lessons from structural diversity.

scientific article

The potential use of big data in oncology

scientific article published on 12 September 2019

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

scientific article published on 24 April 2007

Tracking repeats using significance and transitivity

scientific article published in August 2004

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

scientific article published in July 2018

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

scientific article

Yves Moreau and Jaap Heringa, on behalf of the ECCB10 organizing and steering committees ⬇️

scientific article published on September 15, 2010

metaModules identifies key functional subnetworks in microbiome-related disease

scientific article published on 5 September 2015

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

scientific article published on 6 May 2009

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

scientific article

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