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Jaap Heringa
Person information
- 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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