Publications by authors named "Jaap Heringa"

84Publications

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

Bioinformatics 2020 04;36(7):2142-2149

Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz917DOI Listing
April 2020

The potential use of big data in oncology.

Oral Oncol 2019 11 12;98:8-12. Epub 2019 Sep 12.

Department of Head and Neck Oncology and Surgery, Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1016/j.oraloncology.2019.09.003DOI Listing
November 2019

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

Bioinformatics 2019 12;35(24):5315-5317

Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954659PMC
December 2019

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

Bioinformatics 2019 11;35(22):4794-4796

IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz428DOI Listing
November 2019

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

PLoS Comput Biol 2018 11 1;14(11):e1006547. Epub 2018 Nov 1.

Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.1006547
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http://dx.doi.org/10.1371/journal.pcbi.1006547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233922PMC
November 2018

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

Bioinformatics 2018 07;34(13):i4-i12

Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022589PMC
July 2018

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

Bioinformatics 2017 May;33(10):1479-1487

Center for Integrative Bioinformatics VU (IBIVU), Amsterdam, HV, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btx005DOI Listing
May 2017

Editorial.

Comput Biol Chem 2016 10;64:vii-viii

Duquesne University, Pittsburgh, PA, USA.

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http://dx.doi.org/10.1016/S1476-9271(16)30509-6DOI Listing
October 2016

Multiple Sequence Alignment.

Methods Mol Biol 2017 ;1525:167-189

Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_8DOI Listing
January 2018

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping.

Sci Rep 2016 10 21;6:35436. Epub 2016 Oct 21.

School of Medicine, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, UK.

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http://dx.doi.org/10.1038/srep35436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073228PMC
October 2016

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

Bioinformatics 2016 09;32(17):i389-i392

University Medical Centre Utrecht, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw481DOI Listing
September 2016

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

Bioinformatics 2016 06;32(12):i60-i69

Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908334PMC
June 2016

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

PLoS One 2016 11;11(5):e0155251. Epub 2016 May 11.

Center for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155251PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864233PMC
July 2017

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

Nucleic Acids Res 2016 05 31;44(8):e72. Epub 2015 Dec 31.

Centre for Integrative Bioinformatics VU, VU University Amsterdam, Amsterdam 1081 HV, The Netherlands Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands ENPICOM, Eindhoven 5632 CW, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv1518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856970PMC
May 2016

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

BMC Bioinformatics 2015 Oct 8;16:325. Epub 2015 Oct 8.

Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s12859-015-0758-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599308PMC
October 2015

metaModules identifies key functional subnetworks in microbiome-related disease.

Bioinformatics 2016 06 5;32(11):1678-85. Epub 2015 Sep 5.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv526DOI Listing
June 2016

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

Bioinformatics 2015 Oct 27;31(19):3147-55. Epub 2015 May 27.

Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands, Erable Team, INRIA, Lyon, France.

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http://bioinformatics.oxfordjournals.org/content/31/19/3147.
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv316DOI Listing
October 2015

Quantifying the displacement of mismatches in multiple sequence alignment benchmarks.

PLoS One 2015 19;10(5):e0127431. Epub 2015 May 19.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands; Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127431PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438059PMC
April 2016

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

Nucleic Acids Res 2015 Jul 15;43(W1):W301-5. Epub 2015 Apr 15.

Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489229PMC
July 2015

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

BMC Syst Biol 2014 Apr 1;8:40. Epub 2014 Apr 1.

Life Sciences, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1752-0509-8-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998945PMC
April 2014

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

Bioinformatics 2014 Jun 10;30(11):1530-8. Epub 2014 Feb 10.

Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu085DOI Listing
June 2014

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

PLoS One 2013 5;8(12):e81235. Epub 2013 Dec 5.

Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081235PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855271PMC
March 2015

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

Bioinformatics 2014 Feb 22;30(3):326-34. Epub 2013 Nov 22.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/30/3/326.fu
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt675DOI Listing
February 2014

PRALINE: a versatile multiple sequence alignment toolkit.

Methods Mol Biol 2014 ;1079:245-62

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/978-1-62703-646-7_16DOI Listing
May 2014

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

Retrovirology 2013 Sep 23;10:102. Epub 2013 Sep 23.

Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1742-4690-10-102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849187PMC
September 2013

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

BMC Syst Biol 2013 Aug 21;7:82. Epub 2013 Aug 21.

Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, de Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1752-0509-7-82DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765389PMC
August 2013

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

Bioinformatics 2013 Jul;29(13):i80-8

IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, De Boelelaan 1081, NKI-AVL The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btt243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694641PMC
July 2013

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

Brief Bioinform 2013 Sep 19;14(5):589-98. Epub 2013 Apr 19.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands. Tel.: +31 20 59 87816; Fax: +31 20 59 87653;

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http://dx.doi.org/10.1093/bib/bbt023DOI Listing
September 2013

General secretion signal for the mycobacterial type VII secretion pathway.

Proc Natl Acad Sci U S A 2012 Jul 25;109(28):11342-7. Epub 2012 Jun 25.

Department of Medical Microbiology and Infection Control, VU University Medical Centre, 1081 BT Amsterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1119453109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396530PMC
July 2012

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

J Comput Chem 2012 May 28;33(12):1207-14. Epub 2012 Feb 28.

Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands; Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands.

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http://doi.wiley.com/10.1002/jcc.22947
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http://dx.doi.org/10.1002/jcc.22947DOI Listing
May 2012

Protein analysis tools and services at IBIVU.

J Integr Bioinform 2011 Sep 8;8(2):168. Epub 2011 Sep 8.

Centre for Integrative Bioinformatics, IBIVU, VU University Amsterdam, De Boelelaan 1081A, Amsterdam, The Netherlands.

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http://dx.doi.org/10.2390/biecoll-jib-2011-168DOI Listing
September 2011

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

J Chem Inf Model 2010 Oct;50(10):1772-80

Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Leiden/Amsterdam Center for Drug Research, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/ci1002608DOI Listing
October 2010

Multi-Harmony: detecting functional specificity from sequence alignment.

Nucleic Acids Res 2010 Jul 4;38(Web Server issue):W35-40. Epub 2010 Jun 4.

Centre for Integrative Bioinformatics, VU University Amsterdam, De Boelelaan 1081A, 1081HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkq415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896201PMC
July 2010

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

Bioinformatics 2010 May 23;26(10):1366-7. Epub 2010 Apr 23.

Centre for Integrative Bioinformatics VU, VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq155DOI Listing
May 2010

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

Bioinformatics 2010 Mar 22;26(5):653-60. Epub 2010 Jan 22.

Centre for Integrative Bioinformatics, VU University Amsterdam, 1081HV Amsterdam, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq018DOI Listing
March 2010

Accurate confidence aware clustering of array CGH tumor profiles.

Bioinformatics 2010 Jan 21;26(1):6-14. Epub 2009 Oct 21.

Centre for Integrative Bioinformatics VU (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btp603DOI Listing
January 2010

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

BMC Genomics 2009 Aug 26;10:401. Epub 2009 Aug 26.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-10-401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748095PMC
August 2009

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

Bioinformatics 2009 Aug 10;25(16):2049-56. Epub 2009 Jun 10.

Centre for Integrative Bioinformatics and Department of Computer Science, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btp355DOI Listing
August 2009

PhyloPars: estimation of missing parameter values using phylogeny.

Nucleic Acids Res 2009 Jul 13;37(Web Server issue):W179-84. Epub 2009 May 13.

Department of Theoretical Biology, Faculty of Earth & Life Sciences, VU University Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkp370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703881PMC
July 2009

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

Nucleic Acids Res 2009 Jul 6;37(Web Server issue):W48-52. Epub 2009 May 6.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkp279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703954PMC
July 2009

The meaning of alignment: lessons from structural diversity.

BMC Bioinformatics 2008 Dec 23;9:556. Epub 2008 Dec 23.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081HV Amsterdam, the Netherlands.

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http://dx.doi.org/10.1186/1471-2105-9-556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2630330PMC
December 2008

Multiple sequence alignment.

Methods Mol Biol 2008 ;452:143-61

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/978-1-60327-159-2_7DOI Listing
July 2008

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

Nucleic Acids Res 2008 Jul 7;36(Web Server issue):W255-9. Epub 2008 May 7.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkn237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447787PMC
July 2008

An overview of multiple sequence alignment.

Curr Protoc Bioinformatics 2003 Nov;Chapter 3:Unit 3.7

Integrative Bioinformatics Institute (IBIVU), Free University, Amsterdam, The Netherlands.

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http://www.wseas.us/e-library/conferences/2013/Dubrovnik/TEL
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http://downloads.hindawi.com/journals/isrn/2013/615630.pdf
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http://doi.wiley.com/10.1002/0471250953.bi0307s03
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http://dx.doi.org/10.1002/0471250953.bi0307s03DOI Listing
November 2003

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

RNA 2008 Mar 29;14(3):410-6. Epub 2008 Jan 29.

Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1261/rna.881308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248259PMC
March 2008

On defining the dynamics of hydrophobic patches on protein surfaces.

Proteins 2008 Jul;72(1):105-14

Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.

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http://dx.doi.org/10.1002/prot.21924DOI Listing
July 2008

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.

Bioinformatics 2008 Feb 2;24(4):492-7. Epub 2008 Jan 2.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btm636DOI Listing
February 2008

Identifying foldable regions in protein sequence from the hydrophobic signal.

Nucleic Acids Res 2008 Feb 1;36(2):578-88. Epub 2007 Dec 1.

Structural & Computational Biology Program, Victor Chang Cardiac Research Institute, Sydney, Australia.

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http://nar.oxfordjournals.org/content/36/2/578.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkm1070
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http://dx.doi.org/10.1093/nar/gkm1070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2241846PMC
February 2008

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

Bioinformatics 2008 Jan 17;24(1):18-25. Epub 2007 Nov 17.

Division of Medical Chemistry, LACDR, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btm537DOI Listing
January 2008

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

Proc Natl Acad Sci U S A 2007 Jul 24;104(31):12807-12. Epub 2007 Jul 24.

Centre for Integrative Bioinformatics, Vrije University, De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.0703238104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1937548PMC
July 2007

Sequence harmony: detecting functional specificity from alignments.

Nucleic Acids Res 2007 Jul 21;35(Web Server issue):W495-8. Epub 2007 Jun 21.

Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkm406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933219PMC
July 2007

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

Comput Methods Programs Biomed 2007 Jun 24;86(3):281-90. Epub 2007 Apr 24.

Centre for Integrative Bioinformatics VU, Department of Computer Science, Free University De Boelelaan 1081a, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.cmpb.2007.03.001DOI Listing
June 2007

Sequence comparison by sequence harmony identifies subtype-specific functional sites.

Nucleic Acids Res 2006 27;34(22):6540-8. Epub 2006 Nov 27.

Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkl901DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1702503PMC
January 2007

Global multiple-sequence alignment with repeats.

Proteins 2006 Jul;64(1):263-74

Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, Amsterdam, The Netherlands.

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http://doi.wiley.com/10.1002/prot.20957
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http://dx.doi.org/10.1002/prot.20957DOI Listing
July 2006

AuberGene--a sensitive genome alignment tool.

Bioinformatics 2006 Jun 10;22(12):1431-6. Epub 2006 Apr 10.

Centre for Integrative Bioinformatics VU (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl112DOI Listing
June 2006

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

Nucleic Acids Res 2005 Jul;33(Web Server issue):W160-3

Inpharmatica Ltd, 60 Charlotte Street, London W1T 2NU, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gki381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160142PMC
July 2005

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

Bioinformatics 2005 Jan 17;21(2):152-9. Epub 2004 Sep 17.

Division of Mathematical Biology, The National Institute for Medical Research The Ridgeway, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1093/bioinformatics/bth487DOI Listing
January 2005

Tracking repeats using significance and transitivity.

Bioinformatics 2004 Aug;20 Suppl 1:i311-7

Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081A, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bth911DOI Listing
August 2004

Contact-based sequence alignment.

Nucleic Acids Res 2004 30;32(8):2464-73. Epub 2004 Apr 30.

Bioinformatics Unit, Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit, De Boelelaan 1081A, 1081HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkh566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419454PMC
May 2004

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

Comput Biol Chem 2003 May;27(2):93-102

Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, NW7 1AA, London, UK.

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http://dx.doi.org/10.1016/s1476-9271(03)00022-7DOI Listing
May 2003

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

Protein Eng 2002 Nov;15(11):871-9

Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill NW7 1AA, UK.

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http://dx.doi.org/10.1093/protein/15.11.871DOI Listing
November 2002

Parallelized multiple alignment.

Bioinformatics 2002 Sep;18(9):1270-1

Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1093/bioinformatics/18.9.1270DOI Listing
September 2002

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

Proteins 2002 Sep;48(4):672-81

Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, United Kingdom.

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http://dx.doi.org/10.1002/prot.10175DOI Listing
September 2002

Local weighting schemes for protein multiple sequence alignment.

Authors:
Jaap Heringa

Comput Chem 2002 Jul;26(5):459-77

Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK.

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http://dx.doi.org/10.1016/s0097-8485(02)00008-6DOI Listing
July 2002

A Fourier analysis of symmetry in protein structure.

Protein Eng 2002 Feb;15(2):79-89

Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1093/protein/15.2.79DOI Listing
February 2002

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

J Mol Biol 2002 Feb;316(3):839-51

Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

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http://dx.doi.org/10.1006/jmbi.2001.5387DOI Listing
February 2002

Exploring familial relationships using multiple sequence alignment.

Methods Mol Biol 2002 ;173:231-53

Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.

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http://dx.doi.org/10.1385/1-59259-184-1:231DOI Listing
August 2002