Jaap Heringa

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Anton FeenstraAssistant professor of Bioinformatics, IBIVU Centre for Integrative Bioinformatics, VU UniversityVerified email at vu.nl
Sanne AbelnProfessor of AI Technology for Life, Utrecht UniversityVerified email at uu.nl
Walter PirovanoResearch project manager, gut-brain axis enthusiast, VU UniversityVerified email at vu.nl
des higginsUniversity College DublinVerified email at ucd.ie
Cedric NotredameCentre for Genomic Regulation, SpainVerified email at crg.eu
Punto BawonoThe Centre for Integrative Bioinformatics VU (IBIVU)Verified email at vu.nl
William R TaylorDivision head, Mathematical Biology, National Institute for Medical Research, UKVerified email at nimr.mrc.ac.uk
Mark D WilkinsonIsaac Peral Distinguished Researcher, UPMVerified email at upm.es
Gerrit A Meijerprofessor of oncologic pathology, Netherlands Cancer Institute, University Medical Center UtrechtVerified email at nki.nl
Nicola BonzanniVU University AmsterdamVerified email at vu.nl
Niklas BlombergDirector, ELIXIRVerified email at ebi.ac.uk
Michel DumontierDistinguished Professor of Data Science, Maastricht UniversityVerified email at maastrichtuniversity.nl
Kuang LinNDPH, Oxford UniversityVerified email at ndph.ox.ac.uk
Qingzhen Hou3BIO-BioInfo - BioModeling, BioInformatics & BioProcesses, Université Libre de BruxellesVerified email at ulb.ac.be
Jens KleinjungNxera TherapeuticsVerified email at jkleinj.eu
Remond J.A. FijnemanNetherlands Cancer Institute, Amsterdam, The NetherlandsVerified email at nki.nl
Wan FokkinkProfessor of Computer Science, Vrije Universiteit AmsterdamVerified email at vu.nl
Richard FinkersGenNovation B.V.Verified email at gennovation.nl
Jildau BouwmanTNOVerified email at tno.nl
Philip E. BourneUniversity of VirginiaVerified email at virginia.edu

Jaap Heringa

Professor of Bioinformatics, Vrije Universiteit Amsterdam

Verified email at vu.nl

Bioinformatics


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The FAIR Guiding Principles for scientific data management and stewardship MD Wilkinson, M Dumontier, IJJ Aalbersberg, G Appleton, M Axton, ... Scientific data 3 (1), 1-9, 2016	16666	2016
T-Coffee: A novel method for fast and accurate multiple sequence alignment C Notredame, DG Higgins, J Heringa Journal of molecular biology 302 (1), 205-217, 2000	8911	2000
’t Hoen MD Wilkinson, M Dumontier, IJ Aalbersberg, G Appleton, M Axton, A Baak, ... PAC, Hooft, R, Kuhn, T, Kok, R, Kok, J, Lusher, SJ, Martone, ME, Mons, A …, 2016	874	2016
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information VA Simossis, J Heringa Nucleic acids research 33 (suppl_2), W289-W294, 2005	584	2005
An analysis of protein domain linkers: their classification and role in protein folding RA George, J Heringa Protein engineering 15 (11), 871-879, 2002	550	2002
A simple and fast secondary structure prediction method using hidden neural networks K Lin, VA Simossis, WR Taylor, J Heringa Bioinformatics 21 (2), 152-159, 2005	366	2005
FAIR principles: interpretations and implementation considerations A Jacobsen, R de Miranda Azevedo, N Juty, D Batista, S Coles, R Cornet, ... Data intelligence 2 (1-2), 10-29, 2020	363	2020
The KH domain occurs in a diverse set of RNA‐binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid TJ Gibson, JD Thompson, J Heringa FEBS letters 324 (3), 361-366, 1993	268	1993
General secretion signal for the mycobacterial type VII secretion pathway MH Daleke, R Ummels, P Bawono, J Heringa, ... Proceedings of the National Academy of Sciences 109 (28), 11342-11347, 2012	235	2012
Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment J Heringa Computers & chemistry 23 (3-4), 341-364, 1999	201	1999
Interaction of transmembrane helices by a knobs‐into‐holes packing characteristic of soluble coiled coils D Langosch, J Heringa Proteins: Structure, Function, and Bioinformatics 31 (2), 150-159, 1998	190	1998
The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016) M Wilkinson, M Dumontier, I Aalbersberg, G Appleton, M Axton, A Baak, ...	180	2016
Tracking repeats using significance and transitivty. R Szklarczyk, J Heringa Bioinformatics 20 (Suppl 1), i311-i317, 2004	168	2004
Protein secondary structure prediction W Pirovano, J Heringa Data Mining Techniques for the Life Sciences, 327-348, 2010	165	2010
Homology-extended sequence alignment VA Simossis, J Kleinjung, J Heringa Nucleic acids research 33 (3), 816-824, 2005	144	2005
PRALINE™: a strategy for improved multiple alignment of transmembrane proteins W Pirovano, KA Feenstra, J Heringa Bioinformatics 24 (4), 492-497, 2008	141	2008
The ontogeny of a dominance hierarchy in colonies of the bumblebee Bombus terrestris (Hymenoptera, Apidae) A Van Doorn, J Heringa Insectes soc 33 (3), 25, 1986	141	1986
PhyloPars: estimation of missing parameter values using phylogeny J Bruggeman, J Heringa, BW Brandt Nucleic acids research 37 (suppl_2), W179-W184, 2009	134	2009
Side-chain clusters in protein structures and their role in protein folding J Heringa, P Argos Journal of molecular biology 220 (1), 151-171, 1991	129	1991
SnapDRAGON: a method to delineate protein structural domains from sequence data RA George, J Heringa Journal of molecular biology 316 (3), 839-851, 2002	123	2002

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