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ORCIDJaap Heringa
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- affiliation: Free University of Amsterdam, Netherlands
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2020 – today
- 2024
[j63]Ting Liu
, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa:
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. Bioinform. 40(1) (2024)- 2022
- [j62]Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou:
PIPENN: protein interface prediction from sequence with an ensemble of neural nets. Bioinform. 38(8): 2111-2118 (2022) - 2021
- [j61]Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. Bioinform. 37(20): 3421-3427 (2021) - [j60]Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang:
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. Health Inf. Sci. Syst. 9(1): 3 (2021) - 2020
- [j59]Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra:
A framework for exhaustive modelling of genetic interaction patterns using Petri nets. Bioinform. 36(7): 2142-2149 (2020) - [j58]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, Karsten Kryger Hansen, Ali Hasnain, Kristina M. Hettne, Jaap Heringa, Rob W. W. Hooft, Melanie Imming, Keith G. Jeffery, Rajaram Kaliyaperumal, Martijn G. Kersloot, Christine R. Kirkpatrick, Tobias Kuhn, Ignasi Labastida, Barbara Magagna, Peter McQuilton, Natalie Meyers, Annalisa Montesanti, Mirjam van Reisen, Philippe Rocca-Serra, Robert Pergl, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Juliane Schneider, George O. Strawn, Mark Thompson, Andra Waagmeester, Tobias Weigel, Mark D. Wilkinson, Egon L. Willighagen, Peter Wittenburg, Marco Roos, Barend Mons, Erik Schultes:
FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2(1-2): 10-29 (2020)
2010 – 2019
- 2019
- [j57]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:
Bioinformatics in the Netherlands: the value of a nationwide community. Briefings Bioinform. 20(2): 540-550 (2019) - [j56]Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. Bioinform. 35(22): 4794-4796 (2019) - [j55]Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa:
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinform. 35(24): 5315-5317 (2019) - [j54]Nidheesh Melethadathil, Jaap Heringa, Bipin Nair, Shyam Diwakar:
Mining Inter-Relationships in Online Scientific Articles and its Visualization: Natural Language Processing for Systems Biology Modeling. Int. J. Online Biomed. Eng. 15(2): 39-59 (2019) - [j53]Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren:
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. 15(5) (2019) - [r1]Sanne Abeln, K. Anton Feenstra, Jaap Heringa:
Protein Three-Dimensional Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 497-511 - 2018
- [j52]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:
Bioinformatics in the Netherlands: the value of a nationwide community. Briefings Bioinform. 19(2): 359 (2018) - [j51]K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa:
Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinform. 34(13): i4-i12 (2018) - [j50]Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa:
Motif-Aware PRALINE: Improving the alignment of motif regions. PLoS Comput. Biol. 14(11) (2018) - [c14]Jaap Heringa, Vincent T. van Hees:
Message from the eScience 2018 Program Committee Chairs for the Focused Session on Data Handling and Analytics for Health. eScience 2018: 285 - 2017
- [j49]Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra:
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. Bioinform. 33(10): 1479-1487 (2017) - [i3]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, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino da Silva Santos, Jeroen Beliën, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond J. A. Fijneman, J. Dylan Spalding, Sanne Abeln:
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 6: 1488- (2017) - 2016
- [j48]Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln:
metaModules identifies key functional subnetworks in microbiome-related disease. Bioinform. 32(11): 1678-1685 (2016) - [j47]Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa:
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. Bioinform. 32(12): 60-69 (2016) - [j46]Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder:
ECCB 2016: The 15th European Conference on Computational Biology. Bioinform. 32(17): 389-392 (2016) - [j45]Jaap Heringa, Wentian Li, Jeffry D. Madura:
Editorial. Comput. Biol. Chem. 64: vii-viii (2016) - [c13]Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa:
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences. SWAT4LS 2016 - [i2]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, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln:
Integration of EGA secure data access into Galaxy. F1000Research 5: 2841 (2016) - 2015
- [j44]Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau:
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 8(4): 1035-1051 (2015) - [j43]Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau:
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 31(19): 3147-3155 (2015) - [j42]Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra:
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinform. 16: 325:1-325:12 (2015) - [j41]Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt:
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. Nucleic Acids Res. 43(Webserver-Issue): W301-W305 (2015) - [c12]Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa:
Explaining disease using big data: How valid is your pathway? HPCS 2015: 662-664 - [c11]Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa:
To SCRY Linked Data: Extending SPARQL the Easy Way. Diversity++@ISWC 2015: 8-14 - [c10]Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa:
SCRY: Enabling Quantitative Reasoning in SPARQL Queries. SWAT4LS 2015: 214-215 - 2014
- [j40]Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. Bioinform. 30(3): 326-334 (2014) - [j39]Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt:
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinform. 30(11): 1530-1538 (2014) - [j38]Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau:
A web server for protein-protein interaction network querying. BMC Syst. Biol. 8: 40 (2014) - [c9]Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa:
Petri Nets Are a Biologist's Best Friend. FMMB 2014: 102-116 - 2013
- [j37]Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa:
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings Bioinform. 14(5): 589-598 (2013) - [j36]Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens:
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinform. 29(13): 80-88 (2013) - [j35]Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau:
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14(S-15): S18 (2013) - [j34]Hannes Hettling, David J. C. Alders, Jaap Heringa, Thomas W. Binsl, A. B. Johan Groeneveld, Johannes H. G. M. van Beek:
Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies. BMC Syst. Biol. 7: 82 (2013) - 2012
- [j33]René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra:
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem. 33(12): 1207-1214 (2012) - 2011
- [j32]Bernd W. Brandt, Jaap Heringa:
Protein analysis tools and services at IBIVU. J. Integr. Bioinform. 8(2) (2011) - [c8]Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau:
Lagrangian Relaxation Applied to Sparse Global Network Alignment. PRIB 2011: 225-236 - [i1]Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau:
Lagrangian Relaxation Applied to Sparse Global Network Alignment. CoRR abs/1108.4358 (2011) - 2010
- [j31]Bart P. P. van Houte, Jaap Heringa:
Accurate confidence aware clustering of array CGH tumor profiles. Bioinform. 26(1): 6-14 (2010) - [j30]Thomas W. Binsl, David J. C. Alders, Jaap Heringa, A. B. Johan Groeneveld, Johannes H. G. M. van Beek:
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy. Bioinform. 26(5): 653-660 (2010) - [j29]Bart P. P. van Houte, Thomas W. Binsl, Hannes Hettling, Jaap Heringa:
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs. Bioinform. 26(10): 1366-1367 (2010) - [j28]Hannes Hettling, Jaap Heringa, Johannes H. G. M. van Beek:
Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach. BMC Bioinform. 11(S-10): O9 (2010) - [j27]Albert J. Kooistra, Thomas W. Binsl, Johannes H. G. M. van Beek, Chris de Graaf, Jaap Heringa:
Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density. J. Chem. Inf. Model. 50(10): 1772-1780 (2010) - [j26]Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa:
Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. 38(Web-Server-Issue): 35-40 (2010)
2000 – 2009
- 2009
- [j25]Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa:
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. Bioinform. 25(16): 2049-2056 (2009) - [j24]Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa:
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. Bioinform. 25(19): 2624 (2009) - [j23]Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa:
Structure and function analysis of flexible alignment regions in proteins. BMC Bioinform. 10(S-13): 0 (2009) - [j22]Bernd W. Brandt, Jaap Heringa:
webPRC: the Profile Comparer for alignment-based searching of public domain databases. Nucleic Acids Res. 37(Web-Server-Issue): 48-52 (2009) - [j21]Jorn Bruggeman, Jaap Heringa, Bernd W. Brandt:
PhyloPars: estimation of missing parameter values using phylogeny. Nucleic Acids Res. 37(Web-Server-Issue): 179-184 (2009) - 2008
- [j20]Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori:
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinform. 24(1): 18-25 (2008) - [j19]Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinform. 24(4): 492-497 (2008) - [j18]Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
The meaning of alignment: lessons from structural diversity. BMC Bioinform. 9 (2008) - [j17]Bernd W. Brandt, Jaap Heringa, Jack A. M. Leunissen:
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Res. 36(Web-Server-Issue): 255-259 (2008) - [c7]Pavol Jancura, Jaap Heringa, Elena Marchiori:
Divide, Align and Full-Search for Discovering Conserved Protein Complexes. EvoBIO 2008: 71-82 - [c6]Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa:
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. FMSB 2008: 48-62 - [c5]Pavol Jancura, Jaap Heringa, Elena Marchiori:
Dividing Protein Interaction Networks by Growing Orthologous Articulations. PRIB 2008: 187-200 - 2007
- [j16]Marius C. Codrea, Connie R. Jimenez, Jaap Heringa, Elena Marchiori:
Tools for computational processing of LC-MS datasets: A user's perspective. Comput. Methods Programs Biomed. 86(3): 281-290 (2007) - [j15]K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa:
Sequence harmony: detecting functional specificity from alignments. Nucleic Acids Res. 35(Web-Server-Issue): 495-498 (2007) - [c4]Marius C. Codrea, Connie R. Jimenez, Sander R. Piersma, Jaap Heringa, Elena Marchiori:
Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data. EvoBIO 2007: 35-46 - 2006
- [j14]Radek Szklarczyk, Jaap Heringa:
AuberGene - a sensitive genome alignment tool. Bioinform. 22(12): 1431-1436 (2006) - [c3]Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra:
A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. ICMLA 2006: 168-173 - 2005
- [j13]Kuang Lin, Victor A. Simossis, William R. Taylor, Jaap Heringa:
A simple and fast secondary structure prediction method using hidden neural networks. Bioinform. 21(2): 152-159 (2005) - [j12]Richard A. George, Kuang Lin, Jaap Heringa:
Scooby-domain: prediction of globular domains in protein sequence. Nucleic Acids Res. 33(Web-Server-Issue): 160-163 (2005) - [j11]Victor A. Simossis, Jaap Heringa:
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 33(Web-Server-Issue): 289-294 (2005) - 2004
- [j10]Victor A. Simossis, Jaap Heringa:
The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods. Comput. Biol. Chem. 28(5-6): 351-366 (2004) - [c2]Radek Szklarczyk, Jaap Heringa:
Tracking repeats using significance and transitivity. ISMB/ECCB (Supplement of Bioinformatics) 2004: 311-317 - 2003
- [j9]Kuang Lin, Jens Kleinjung, William R. Taylor, Jaap Heringa:
Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. Comput. Biol. Chem. 27(2): 93-102 (2003) - [j8]Victor A. Simossis, Jaap Heringa:
The PRALINE online server: optimising progressive multiple alignment on the web. Comput. Biol. Chem. 27(4-5): 511-519 (2003) - [c1]John W. Romein, Jaap Heringa, Henri E. Bal:
A Million-Fold Speed Improvement in Genomic Repeats Detection. SC 2003: 20 - 2002
- [j7]Jens Kleinjung, Nigel Douglas, Jaap Heringa:
Parallelized multiple alignment. Bioinform. 18(9): 1270-1271 (2002) - [j6]Jaap Heringa:
Local Weighting Schemes for Protein Multiple Sequence Alignment. Comput. Chem. 26(5): 459-477 (2002) - 2001
- [j5]Jaap Heringa:
Post-genome Informatics: Minoru Kanehisa, Oxford University Press, Oxford, 2000, 148 pages. Comput. Chem. 25(4): 425-426 (2001) - 2000
- [j4]David D. Pollock, Jaap Heringa:
RECOMB98. Computational Molecular Biology: Pre- and Post-genomics, March 22-25, 1998, New York. Comput. Chem. 24(1): 133-134 (2000)
1990 – 1999
- 1999
- [j3]Jaap Heringa:
Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment. Comput. Chem. 23(3-4): 341-364 (1999) - 1994
- [j2]Jaap Heringa:
The Evolution and Recognition of Protein Sequence Repeats. Comput. Chem. 18(3): 233-243 (1994) - 1992
- [j1]Jaap Heringa, Hubert Sommerfeldt, Desmond G. Higgins, Patrick Argos:
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. Comput. Appl. Biosci. 8(6): 599-600 (1992)
Coauthor Index
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