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ORCIDBibTeX records: Jaap Heringa
@article{DBLP:journals/bioinformatics/LiuFHH24,
author = {Ting Liu and
K. Anton Feenstra and
Zhisheng Huang and
Jaap Heringa},
title = {Mining literature and pathway data to explore the relations of ketamine
with neurotransmitters and gut microbiota using a knowledge-graph},
journal = {Bioinform.},
volume = {40},
number = {1},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btad771},
doi = {10.1093/BIOINFORMATICS/BTAD771},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LiuFHH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StringerFAHFH22,
author = {Bas Stringer and
Hans de Ferrante and
Sanne Abeln and
Jaap Heringa and
K. Anton Feenstra and
Reza Haydarlou},
title = {{PIPENN:} protein interface prediction from sequence with an ensemble
of neural nets},
journal = {Bioinform.},
volume = {38},
number = {8},
pages = {2111--2118},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac071},
doi = {10.1093/BIOINFORMATICS/BTAC071},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/StringerFAHFH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouSWCHXAHF21,
author = {Qingzhen Hou and
Bas Stringer and
Katharina Waury and
Henriette Capel and
Reza Haydarlou and
Fuzhong Xue and
Sanne Abeln and
Jaap Heringa and
K. Anton Feenstra},
title = {SeRenDIP-CE: sequence-based interface prediction for conformational
epitopes},
journal = {Bioinform.},
volume = {37},
number = {20},
pages = {3421--3427},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab321},
doi = {10.1093/BIOINFORMATICS/BTAB321},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouSWCHXAHF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/hisas/LiuPWFHH21,
author = {Ting Liu and
Xueli Pan and
Xu Wang and
K. Anton Feenstra and
Jaap Heringa and
Zhisheng Huang},
title = {Predicting the relationships between gut microbiota and mental disorders
with knowledge graphs},
journal = {Health Inf. Sci. Syst.},
volume = {9},
number = {1},
pages = {3},
year = {2021},
url = {https://doi.org/10.1007/s13755-020-00128-2},
doi = {10.1007/S13755-020-00128-2},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/hisas/LiuPWFHH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JacobsenIAHKF20,
author = {Annika Jacobsen and
Olga Ivanova and
Saman Amini and
Jaap Heringa and
Patrick Kemmeren and
K. Anton Feenstra},
title = {A framework for exhaustive modelling of genetic interaction patterns
using Petri nets},
journal = {Bioinform.},
volume = {36},
number = {7},
pages = {2142--2149},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz917},
doi = {10.1093/BIOINFORMATICS/BTZ917},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JacobsenIAHKF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dint/JacobsenAJBCCCC20,
author = {Annika Jacobsen and
Ricardo de Miranda Azevedo and
Nick S. Juty and
Dominique Batista and
Simon J. Coles and
Ronald Cornet and
M{\'{e}}lanie Courtot and
Merc{\`{e}} Crosas and
Michel Dumontier and
Chris T. A. Evelo and
Carole A. Goble and
Giancarlo Guizzardi and
Karsten Kryger Hansen and
Ali Hasnain and
Kristina M. Hettne and
Jaap Heringa and
Rob W. W. Hooft and
Melanie Imming and
Keith G. Jeffery and
Rajaram Kaliyaperumal and
Martijn G. Kersloot and
Christine R. Kirkpatrick and
Tobias Kuhn and
Ignasi Labastida and
Barbara Magagna and
Peter McQuilton and
Natalie Meyers and
Annalisa Montesanti and
Mirjam van Reisen and
Philippe Rocca{-}Serra and
Robert Pergl and
Susanna{-}Assunta Sansone and
Luiz Olavo Bonino da Silva Santos and
Juliane Schneider and
George O. Strawn and
Mark Thompson and
Andra Waagmeester and
Tobias Weigel and
Mark D. Wilkinson and
Egon L. Willighagen and
Peter Wittenburg and
Marco Roos and
Barend Mons and
Erik Schultes},
title = {{FAIR} Principles: Interpretations and Implementation Considerations},
journal = {Data Intell.},
volume = {2},
number = {1-2},
pages = {10--29},
year = {2020},
url = {https://doi.org/10.1162/dint\_r\_00024},
doi = {10.1162/DINT\_R\_00024},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dint/JacobsenAJBCCCC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GelderHRBKRMH19,
author = {Celia W. G. van Gelder and
Rob W. W. Hooft and
Merlijn N. van Rijswijk and
Linda van den Berg and
Ruben G. Kok and
Marcel J. T. Reinders and
Barend Mons and
Jaap Heringa},
title = {Bioinformatics in the Netherlands: the value of a nationwide community},
journal = {Briefings Bioinform.},
volume = {20},
number = {2},
pages = {540--550},
year = {2019},
url = {https://doi.org/10.1093/bib/bbx087},
doi = {10.1093/BIB/BBX087},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GelderHRBKRMH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouGGAHF19,
author = {Qingzhen Hou and
Paul F. G. De Geest and
Christian J. Griffioen and
Sanne Abeln and
Jaap Heringa and
K. Anton Feenstra},
title = {SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate
predictions of {PPI} interface positions},
journal = {Bioinform.},
volume = {35},
number = {22},
pages = {4794--4796},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz428},
doi = {10.1093/BIOINFORMATICS/BTZ428},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouGGAHF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DijkstraPFFAH19,
author = {Maurits J. J. Dijkstra and
Atze van der Ploeg and
K. Anton Feenstra and
Wan J. Fokkink and
Sanne Abeln and
Jaap Heringa},
title = {Tailor-made multiple sequence alignments using the {PRALINE} 2 alignment
toolkit},
journal = {Bioinform.},
volume = {35},
number = {24},
pages = {5315--5317},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz572},
doi = {10.1093/BIOINFORMATICS/BTZ572},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DijkstraPFFAH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijoe/MelethadathilHN19,
author = {Nidheesh Melethadathil and
Jaap Heringa and
Bipin Nair and
Shyam Diwakar},
title = {Mining Inter-Relationships in Online Scientific Articles and its Visualization:
Natural Language Processing for Systems Biology Modeling},
journal = {Int. J. Online Biomed. Eng.},
volume = {15},
number = {2},
pages = {39--59},
year = {2019},
url = {https://doi.org/10.3991/ijoe.v15i02.9432},
doi = {10.3991/IJOE.V15I02.9432},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijoe/MelethadathilHN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/AminiJILHHFK19,
author = {Saman Amini and
Annika Jacobsen and
Olga Ivanova and
Philip Lijnzaad and
Jaap Heringa and
Frank C. P. Holstege and
K. Anton Feenstra and
Patrick Kemmeren},
title = {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},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {5},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007061},
doi = {10.1371/JOURNAL.PCBI.1007061},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/AminiJILHHFK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/bioinf/AbelnFH19,
author = {Sanne Abeln and
K. Anton Feenstra and
Jaap Heringa},
editor = {Shoba Ranganathan and
Michael Gribskov and
Kenta Nakai and
Christian Sch{\"{o}}nbach},
title = {Protein Three-Dimensional Structure Prediction},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology - Volume
2},
pages = {497--511},
publisher = {Elsevier},
year = {2019},
url = {https://doi.org/10.1016/b978-0-12-809633-8.20505-0},
doi = {10.1016/B978-0-12-809633-8.20505-0},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/bioinf/AbelnFH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GelderHRBKRMH18,
author = {Celia W. G. van Gelder and
Rob W. W. Hooft and
Merlijn N. van Rijswijk and
Linda van den Berg and
Ruben G. Kok and
Marcel J. T. Reinders and
Barend Mons and
Jaap Heringa},
title = {Bioinformatics in the Netherlands: the value of a nationwide community},
journal = {Briefings Bioinform.},
volume = {19},
number = {2},
pages = {359},
year = {2018},
url = {https://doi.org/10.1093/bib/bbx171},
doi = {10.1093/BIB/BBX171},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GelderHRBKRMH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FeenstraAWSMTHH18,
author = {K. Anton Feenstra and
Sanne Abeln and
Johan A. Westerhuis and
Filipe Brancos dos Santos and
Douwe Molenaar and
Bas Teusink and
Huub C. J. Hoefsloot and
Jaap Heringa},
title = {Training for translation between disciplines: a philosophy for life
and data sciences curricula},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i4--i12},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty233},
doi = {10.1093/BIOINFORMATICS/BTY233},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FeenstraAWSMTHH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DijkstraBAFFH18,
author = {Maurits J. J. Dijkstra and
Punto Bawono and
Sanne Abeln and
K. Anton Feenstra and
Wan J. Fokkink and
Jaap Heringa},
title = {Motif-Aware {PRALINE:} Improving the alignment of motif regions},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {11},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006547},
doi = {10.1371/JOURNAL.PCBI.1006547},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DijkstraBAFFH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eScience/HeringaH18,
author = {Jaap Heringa and
Vincent T. van Hees},
title = {Message from the eScience 2018 Program Committee Chairs for the Focused
Session on Data Handling and Analytics for Health},
booktitle = {14th {IEEE} International Conference on e-Science, e-Science 2018,
Amsterdam, The Netherlands, October 29 - November 1, 2018},
pages = {285},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.org/10.1109/eScience.2018.00052},
doi = {10.1109/ESCIENCE.2018.00052},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eScience/HeringaH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouGVHF17,
author = {Qingzhen Hou and
Paul F. G. De Geest and
Wim F. Vranken and
Jaap Heringa and
K. Anton Feenstra},
title = {Seeing the trees through the forest: sequence-based homo- and heteromeric
protein-protein interaction sites prediction using random forest},
journal = {Bioinform.},
volume = {33},
number = {10},
pages = {1479--1487},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx005},
doi = {10.1093/BIOINFORMATICS/BTX005},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouGVHF17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/ZhangBSSEHSHRPB17,
author = {Chao Zhang and
Jochem Bijlard and
Christine Staiger and
Serena A. Scollen and
David van Enckevort and
Youri Hoogstrate and
Alexander Senf and
Saskia D. Hiltemann and
Susanna Repo and
Wibo Pipping and
Mariska Bierkens and
Stefan Payralbe and
Bas Stringer and
Jaap Heringa and
Andrew Stubbs and
Luiz Olavo Bonino da Silva Santos and
Jeroen Beli{\"{e}}n and
Ward Weistra and
Rita Azevedo and
Kees van Bochove and
Gerrit Meijer and
Jan{-}Willem Boiten and
Jordi Rambla and
Remond J. A. Fijneman and
J. Dylan Spalding and
Sanne Abeln},
title = {Systematically linking tranSMART, Galaxy and {EGA} for reusing human
translational research data},
journal = {F1000Research},
volume = {6},
pages = {1488},
year = {2017},
url = {https://doi.org/10.12688/f1000research.12168.1},
doi = {10.12688/F1000RESEARCH.12168.1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/ZhangBSSEHSHRPB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayBEKZCHA16,
author = {Ali May and
Bernd W. Brandt and
Mohammed El{-}Kebir and
Gunnar W. Klau and
Egija Zaura and
Wim Crielaard and
Jaap Heringa and
Sanne Abeln},
title = {metaModules identifies key functional subnetworks in microbiome-related
disease},
journal = {Bioinform.},
volume = {32},
number = {11},
pages = {1678--1685},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv526},
doi = {10.1093/BIOINFORMATICS/BTV526},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayBEKZCHA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaydarlouJBFAH16,
author = {Reza Haydarlou and
Annika Jacobsen and
Nicola Bonzanni and
K. Anton Feenstra and
Sanne Abeln and
Jaap Heringa},
title = {BioASF: a framework for automatically generating executable pathway
models specified in BioPAX},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {60--69},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw250},
doi = {10.1093/BIOINFORMATICS/BTW250},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaydarlouJBFAH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeringaRAR16,
author = {Jaap Heringa and
Marcel J. T. Reinders and
Sanne Abeln and
Jeroen de Ridder},
title = {{ECCB} 2016: The 15th European Conference on Computational Biology},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {389--392},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw481},
doi = {10.1093/BIOINFORMATICS/BTW481},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeringaRAR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/HeringaLM16,
author = {Jaap Heringa and
Wentian Li and
Jeffry D. Madura},
title = {Editorial},
journal = {Comput. Biol. Chem.},
volume = {64},
pages = {vii--viii},
year = {2016},
url = {https://doi.org/10.1016/S1476-9271(16)30509-6},
doi = {10.1016/S1476-9271(16)30509-6},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/HeringaLM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat4ls/StringerMAHH16,
author = {Bas Stringer and
Albert Mero{\~{n}}o{-}Pe{\~{n}}uela and
Sanne Abeln and
Frank van Harmelen and
Jaap Heringa},
editor = {Adrian Paschke and
Albert Burger and
Andrea Splendiani and
M. Scott Marshall and
Paolo Romano},
title = {{SCRY:} Extending {SPARQL} with Custom Data Processing Methods for
the Life Sciences},
booktitle = {Proceedings of the 9th International Conference Semantic Web Applications
and Tools for Life Sciences, Amsterdam, The Netherlands, December
5-8, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1795},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1795/paper30.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/swat4ls/StringerMAHH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/HoogstrateZSBHERHJFBMSRSA16,
author = {Youri Hoogstrate and
Chao Zhang and
Alexander Senf and
Jochem Bijlard and
Saskia D. Hiltemann and
David van Enckevort and
Susanna Repo and
Jaap Heringa and
Guido Jenster and
Remond J. A. Fijneman and
Jan{-}Willem Boiten and
Gerrit A. Meijer and
Andrew Stubbs and
Jordi Rambla and
J. Dylan Spalding and
Sanne Abeln},
title = {Integration of {EGA} secure data access into Galaxy},
journal = {F1000Research},
volume = {5},
pages = {2841},
year = {2016},
url = {https://doi.org/10.12688/f1000research.10221.1},
doi = {10.12688/F1000RESEARCH.10221.1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/HoogstrateZSBHERHJFBMSRSA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/El-KebirHK15,
author = {Mohammed El{-}Kebir and
Jaap Heringa and
Gunnar W. Klau},
title = {Natalie 2.0: Sparse Global Network Alignment as a Special Case of
Quadratic Assignment},
journal = {Algorithms},
volume = {8},
number = {4},
pages = {1035--1051},
year = {2015},
url = {https://doi.org/10.3390/a8041035},
doi = {10.3390/A8041035},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/El-KebirHK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/El-KebirSHBDMBH15,
author = {Mohammed El{-}Kebir and
Hayssam Soueidan and
Thomas Hume and
Daniela Beisser and
Marcus T. Dittrich and
Tobias M{\"{u}}ller and
Guillaume Blin and
Jaap Heringa and
Macha Nikolski and
Lodewyk F. A. Wessels and
Gunnar W. Klau},
title = {xHeinz: an algorithm for mining cross-species network modules under
a flexible conservation model},
journal = {Bioinform.},
volume = {31},
number = {19},
pages = {3147--3155},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv316},
doi = {10.1093/BIOINFORMATICS/BTV316},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/El-KebirSHBDMBH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HouDHHF15,
author = {Qingzhen Hou and
Bas E. Dutilh and
Martijn A. Huynen and
Jaap Heringa and
K. Anton Feenstra},
title = {Sequence specificity between interacting and non-interacting homologs
identifies interface residues - a homodimer and monomer use case},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {325:1--325:12},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0758-y},
doi = {10.1186/S12859-015-0758-Y},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HouDHHF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MayABHCB15,
author = {Ali May and
Sanne Abeln and
Mark J. Buijs and
Jaap Heringa and
Wim Crielaard and
Bernd W. Brandt},
title = {NGS-eval: {NGS} Error analysis and novel sequence VAriant detection
tooL},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Webserver-Issue},
pages = {W301--W305},
year = {2015},
url = {https://doi.org/10.1093/nar/gkv346},
doi = {10.1093/NAR/GKV346},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MayABHCB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ieeehpcs/StringerDFAH15,
author = {Bas Stringer and
Maurits J. J. Dijkstra and
K. Anton Feenstra and
Sanne Abeln and
Jaap Heringa},
title = {Explaining disease using big data: How valid is your pathway?},
booktitle = {2015 International Conference on High Performance Computing {\&}
Simulation, {HPCS} 2015, Amsterdam, Netherlands, July 20-24, 2015},
pages = {662--664},
publisher = {{IEEE}},
year = {2015},
url = {https://doi.org/10.1109/HPCSim.2015.7237114},
doi = {10.1109/HPCSIM.2015.7237114},
timestamp = {Wed, 16 Oct 2019 14:14:54 +0200},
biburl = {https://dblp.org/rec/conf/ieeehpcs/StringerDFAH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/semweb/StringerMLAH15,
author = {Bas Stringer and
Albert Mero{\~{n}}o{-}Pe{\~{n}}uela and
Antonis Loizou and
Sanne Abeln and
Jaap Heringa},
editor = {Claudia d'Amato and
Freddy L{\'{e}}cu{\'{e}} and
Raghava Mutharaju and
Tom Narock and
Fabian Wirth},
title = {To {SCRY} Linked Data: Extending {SPARQL} the Easy Way},
booktitle = {Proceedings of the 1st International Diversity++ Workshop co-located
with the 14th International Semantic Web Conference {(ISWC} 2015),
Bethlehem, Pennsylvania, USA, October 12, 2015},
series = {{CEUR} Workshop Proceedings},
volume = {1501},
pages = {8--14},
publisher = {CEUR-WS.org},
year = {2015},
url = {https://ceur-ws.org/Vol-1501/Diversity2015-paper\_2.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:04 +0100},
biburl = {https://dblp.org/rec/conf/semweb/StringerMLAH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat4ls/StringerMLAH15,
author = {Bas Stringer and
Albert Mero{\~{n}}o{-}Pe{\~{n}}uela and
Antonis Loizou and
Sanne Abeln and
Jaap Heringa},
editor = {James Malone and
Robert Stevens and
Kerstin Forsberg and
Andrea Splendiani},
title = {{SCRY:} Enabling Quantitative Reasoning in {SPARQL} Queries},
booktitle = {Proceedings of the 8th Semantic Web Applications and Tools for Life
Sciences International Conference, Cambridge UK, December 7-10, 2015},
series = {{CEUR} Workshop Proceedings},
volume = {1546},
pages = {214--215},
publisher = {CEUR-WS.org},
year = {2015},
url = {https://ceur-ws.org/Vol-1546/poster\_60.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:03 +0100},
biburl = {https://dblp.org/rec/conf/swat4ls/StringerMLAH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayPDBAHF14,
author = {Ali May and
Ren{\'{e}} Pool and
Erik van Dijk and
Jochem Bijlard and
Sanne Abeln and
Jaap Heringa and
K. Anton Feenstra},
title = {Coarse-grained versus atomistic simulations: realistic interaction
free energies for real proteins},
journal = {Bioinform.},
volume = {30},
number = {3},
pages = {326--334},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt675},
doi = {10.1093/BIOINFORMATICS/BTT675},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayPDBAHF14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MayACHB14,
author = {Ali May and
Sanne Abeln and
Wim Crielaard and
Jaap Heringa and
Bernd W. Brandt},
title = {Unraveling the outcome of 16S rDNA-based taxonomy analysis through
mock data and simulations},
journal = {Bioinform.},
volume = {30},
number = {11},
pages = {1530--1538},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu085},
doi = {10.1093/BIOINFORMATICS/BTU085},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MayACHB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/El-KebirBHK14,
author = {Mohammed El{-}Kebir and
Bernd W. Brandt and
Jaap Heringa and
Gunnar W. Klau},
title = {A web server for protein-protein interaction network querying},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {40},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-40},
doi = {10.1186/1752-0509-8-40},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/El-KebirBHK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fmmb/BonzanniFFH14,
author = {Nicola Bonzanni and
K. Anton Feenstra and
Wan J. Fokkink and
Jaap Heringa},
editor = {Fran{\c{c}}ois Fages and
Carla Piazza},
title = {Petri Nets Are a Biologist's Best Friend},
booktitle = {Formal Methods in Macro-Biology - First International Conference,
{FMMB} 2014, Noum{\'{e}}a, New Caledonia, September 22-24, 2014.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8738},
pages = {102--116},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-10398-3\_8},
doi = {10.1007/978-3-319-10398-3\_8},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fmmb/BonzanniFFH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AbelnMFHTH13,
author = {Sanne Abeln and
Douwe Molenaar and
K. Anton Feenstra and
Huub C. J. Hoefsloot and
Bas Teusink and
Jaap Heringa},
title = {Bioinformatics and Systems Biology: bridging the gap between heterogeneous
student backgrounds},
journal = {Briefings Bioinform.},
volume = {14},
number = {5},
pages = {589--598},
year = {2013},
url = {https://doi.org/10.1093/bib/bbt023},
doi = {10.1093/BIB/BBT023},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AbelnMFHTH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BonzanniGFSKMHXG13,
author = {Nicola Bonzanni and
Abhishek Garg and
K. Anton Feenstra and
Judith Sch{\"{u}}tte and
Sarah Kinston and
Diego Miranda{-}Saavedra and
Jaap Heringa and
Ioannis Xenarios and
Berthold G{\"{o}}ttgens},
title = {Hard-wired heterogeneity in blood stem cells revealed using a dynamic
regulatory network model},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {80--88},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt243},
doi = {10.1093/BIOINFORMATICS/BTT243},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BonzanniGFSKMHXG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/El-KebirMWPHSK13,
author = {Mohammed El{-}Kebir and
Tobias Marschall and
Inken Wohlers and
Murray Patterson and
Jaap Heringa and
Alexander Sch{\"{o}}nhuth and
Gunnar W. Klau},
title = {Mapping proteins in the presence of paralogs using units of coevolution},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-15}},
pages = {S18},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S15-S18},
doi = {10.1186/1471-2105-14-S15-S18},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/El-KebirMWPHSK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/HettlingAHBGB13,
author = {Hannes Hettling and
David J. C. Alders and
Jaap Heringa and
Thomas W. Binsl and
A. B. Johan Groeneveld and
Johannes H. G. M. van Beek},
title = {Computational estimation of tricarboxylic acid cycle fluxes using
noisy {NMR} data from cardiac biopsies},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {82},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-82},
doi = {10.1186/1752-0509-7-82},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/HettlingAHBGB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/PoolHHSSF12,
author = {Ren{\'{e}} Pool and
Jaap Heringa and
Martin Hoefling and
Roland Schulz and
Jeremy C. Smith and
K. Anton Feenstra},
title = {Enabling grand-canonical Monte Carlo: Extending the flexibility of
{GROMACS} through the GromPy python interface module},
journal = {J. Comput. Chem.},
volume = {33},
number = {12},
pages = {1207--1214},
year = {2012},
url = {https://doi.org/10.1002/jcc.22947},
doi = {10.1002/JCC.22947},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/PoolHHSSF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/BrandtH11,
author = {Bernd W. Brandt and
Jaap Heringa},
title = {Protein analysis tools and services at {IBIVU}},
journal = {J. Integr. Bioinform.},
volume = {8},
number = {2},
year = {2011},
url = {https://doi.org/10.2390/biecoll-jib-2011-168},
doi = {10.2390/BIECOLL-JIB-2011-168},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/BrandtH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/El-KebirHK11,
author = {Mohammed El{-}Kebir and
Jaap Heringa and
Gunnar W. Klau},
editor = {Marco Loog and
Lodewyk F. A. Wessels and
Marcel J. T. Reinders and
Dick de Ridder},
title = {Lagrangian Relaxation Applied to Sparse Global Network Alignment},
booktitle = {Pattern Recognition in Bioinformatics - 6th {IAPR} International Conference,
{PRIB} 2011, Delft, The Netherlands, November 2-4, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7036},
pages = {225--236},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-24855-9\_20},
doi = {10.1007/978-3-642-24855-9\_20},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/El-KebirHK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1108-4358,
author = {Mohammed El{-}Kebir and
Jaap Heringa and
Gunnar W. Klau},
title = {Lagrangian Relaxation Applied to Sparse Global Network Alignment},
journal = {CoRR},
volume = {abs/1108.4358},
year = {2011},
url = {http://arxiv.org/abs/1108.4358},
eprinttype = {arXiv},
eprint = {1108.4358},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1108-4358.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouteH10,
author = {Bart P. P. van Houte and
Jaap Heringa},
title = {Accurate confidence aware clustering of array {CGH} tumor profiles},
journal = {Bioinform.},
volume = {26},
number = {1},
pages = {6--14},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btp603},
doi = {10.1093/BIOINFORMATICS/BTP603},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouteH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BinslAHGB10,
author = {Thomas W. Binsl and
David J. C. Alders and
Jaap Heringa and
A. B. Johan Groeneveld and
Johannes H. G. M. van Beek},
title = {Computational quantification of metabolic fluxes from a single isotope
snapshot: application to an animal biopsy},
journal = {Bioinform.},
volume = {26},
number = {5},
pages = {653--660},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq018},
doi = {10.1093/BIOINFORMATICS/BTQ018},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BinslAHGB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HouteBHH10,
author = {Bart P. P. van Houte and
Thomas W. Binsl and
Hannes Hettling and
Jaap Heringa},
title = {CGHnormaliter: a Bioconductor package for normalization of array {CGH}
data with many CNAs},
journal = {Bioinform.},
volume = {26},
number = {10},
pages = {1366--1367},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq155},
doi = {10.1093/BIOINFORMATICS/BTQ155},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HouteBHH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HettlingHB10,
author = {Hannes Hettling and
Jaap Heringa and
Johannes H. G. M. van Beek},
title = {Analysis of the functional properties of the creatine kinase system
using a multiscale 'sloppy' modeling approach},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-10}},
pages = {O9},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S10-O9},
doi = {10.1186/1471-2105-11-S10-O9},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HettlingHB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KooistraBBGH10,
author = {Albert J. Kooistra and
Thomas W. Binsl and
Johannes H. G. M. van Beek and
Chris de Graaf and
Jaap Heringa},
title = {Electron Density Fingerprints (EDprints): Virtual Screening Using
Assembled Information of Electron Density},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {10},
pages = {1772--1780},
year = {2010},
url = {https://doi.org/10.1021/ci1002608},
doi = {10.1021/CI1002608},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KooistraBBGH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrandtFH10,
author = {Bernd W. Brandt and
K. Anton Feenstra and
Jaap Heringa},
title = {Multi-Harmony: detecting functional specificity from sequence alignment},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Web-Server-Issue},
pages = {35--40},
year = {2010},
url = {https://doi.org/10.1093/nar/gkq415},
doi = {10.1093/NAR/GKQ415},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrandtFH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BonzanniKFFKBH09,
author = {Nicola Bonzanni and
Elzbieta Krepska and
K. Anton Feenstra and
Wan J. Fokkink and
Thilo Kielmann and
Henri E. Bal and
Jaap Heringa},
title = {Executing multicellular differentiation: quantitative predictive modelling
of \emph{C.elegans} vulval development},
journal = {Bioinform.},
volume = {25},
number = {16},
pages = {2049--2056},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp355},
doi = {10.1093/BIOINFORMATICS/BTP355},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BonzanniKFFKBH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BonzanniKFFKBH09a,
author = {Nicola Bonzanni and
Elzbieta Krepska and
K. Anton Feenstra and
Wan J. Fokkink and
Thilo Kielmann and
Henri E. Bal and
Jaap Heringa},
title = {Executing multicellular differentiation: quantitative predictive modelling
of C.elegans vulval development},
journal = {Bioinform.},
volume = {25},
number = {19},
pages = {2624},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp509},
doi = {10.1093/BIOINFORMATICS/BTP509},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BonzanniKFFKBH09a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PirovanoRFH09,
author = {Walter Pirovano and
Anneke van der Reijden and
K. Anton Feenstra and
Jaap Heringa},
title = {Structure and function analysis of flexible alignment regions in proteins},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-13}},
pages = {0},
year = {2009},
url = {http://www.biomedcentral.com/1471-2105/10/S13/P6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PirovanoRFH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrandtH09,
author = {Bernd W. Brandt and
Jaap Heringa},
title = {webPRC: the Profile Comparer for alignment-based searching of public
domain databases},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Web-Server-Issue},
pages = {48--52},
year = {2009},
url = {https://doi.org/10.1093/nar/gkp279},
doi = {10.1093/NAR/GKP279},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrandtH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BruggemanHB09,
author = {Jorn Bruggeman and
Jaap Heringa and
Bernd W. Brandt},
title = {PhyloPars: estimation of missing parameter values using phylogeny},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Web-Server-Issue},
pages = {179--184},
year = {2009},
url = {https://doi.org/10.1093/nar/gkp370},
doi = {10.1093/NAR/GKP370},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BruggemanHB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YeFHIM08,
author = {Kai Ye and
K. Anton Feenstra and
Jaap Heringa and
Adriaan P. IJzerman and
Elena Marchiori},
title = {Multi-RELIEF: a method to recognize specificity determining residues
from multiple sequence alignments using a Machine-Learning approach
for feature weighting},
journal = {Bioinform.},
volume = {24},
number = {1},
pages = {18--25},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm537},
doi = {10.1093/BIOINFORMATICS/BTM537},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YeFHIM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PirovanoFH08,
author = {Walter Pirovano and
K. Anton Feenstra and
Jaap Heringa},
title = {PRALINE\({}^{\mbox{TM}}\): a strategy for improved multiple alignment
of transmembrane proteins},
journal = {Bioinform.},
volume = {24},
number = {4},
pages = {492--497},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm636},
doi = {10.1093/BIOINFORMATICS/BTM636},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PirovanoFH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PirovanoFH08,
author = {Walter Pirovano and
K. Anton Feenstra and
Jaap Heringa},
title = {The meaning of alignment: lessons from structural diversity},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-556},
doi = {10.1186/1471-2105-9-556},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PirovanoFH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrandtHL08,
author = {Bernd W. Brandt and
Jaap Heringa and
Jack A. M. Leunissen},
title = {{SEQATOMS:} a web tool for identifying missing regions in {PDB} in
sequence context},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Web-Server-Issue},
pages = {255--259},
year = {2008},
url = {https://doi.org/10.1093/nar/gkn237},
doi = {10.1093/NAR/GKN237},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrandtHL08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/evoW/JancuraHM08,
author = {Pavol Jancura and
Jaap Heringa and
Elena Marchiori},
editor = {Elena Marchiori and
Jason H. Moore},
title = {Divide, Align and Full-Search for Discovering Conserved Protein Complexes},
booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics,
6th European Conference, EvoBIO 2008, Naples, Italy, March 26-28,
2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4973},
pages = {71--82},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-78757-0\_7},
doi = {10.1007/978-3-540-78757-0\_7},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/evoW/JancuraHM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fmsb/KrepskaBFFKBH08,
author = {Elzbieta Krepska and
Nicola Bonzanni and
K. Anton Feenstra and
Wan J. Fokkink and
Thilo Kielmann and
Henri E. Bal and
Jaap Heringa},
editor = {Jasmin Fisher},
title = {Design Issues for Qualitative Modelling of Biological Cells with Petri
Nets},
booktitle = {Formal Methods in Systems Biology, First International Workshop, {FMSB}
2008, Cambridge, UK, June 4-5, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5054},
pages = {48--62},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-68413-8\_4},
doi = {10.1007/978-3-540-68413-8\_4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fmsb/KrepskaBFFKBH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/prib/JancuraHM08,
author = {Pavol Jancura and
Jaap Heringa and
Elena Marchiori},
editor = {Madhu Chetty and
Alioune Ngom and
Shandar Ahmad},
title = {Dividing Protein Interaction Networks by Growing Orthologous Articulations},
booktitle = {Pattern Recognition in Bioinformatics, Third {IAPR} International
Conference, {PRIB} 2008, Melbourne, Australia, October 15-17, 2008.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5265},
pages = {187--200},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-88436-1\_17},
doi = {10.1007/978-3-540-88436-1\_17},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/prib/JancuraHM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmpb/CodreaJHM07,
author = {Marius C. Codrea and
Connie R. Jimenez and
Jaap Heringa and
Elena Marchiori},
title = {Tools for computational processing of {LC-MS} datasets: {A} user's
perspective},
journal = {Comput. Methods Programs Biomed.},
volume = {86},
number = {3},
pages = {281--290},
year = {2007},
url = {https://doi.org/10.1016/j.cmpb.2007.03.001},
doi = {10.1016/J.CMPB.2007.03.001},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cmpb/CodreaJHM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FeenstraPKH07,
author = {K. Anton Feenstra and
Walter Pirovano and
Klaas Krab and
Jaap Heringa},
title = {Sequence harmony: detecting functional specificity from alignments},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {495--498},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm406},
doi = {10.1093/NAR/GKM406},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FeenstraPKH07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/evoW/CodreaJPHM07,
author = {Marius C. Codrea and
Connie R. Jimenez and
Sander R. Piersma and
Jaap Heringa and
Elena Marchiori},
editor = {Elena Marchiori and
Jason H. Moore and
Jagath C. Rajapakse},
title = {Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry
Data},
booktitle = {Evolutionary Computation,Machine Learning and Data Mining in Bioinformatics,
5th European Conference, EvoBIO 2007, Valencia, Spain, April 11-13,
2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4447},
pages = {35--46},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71783-6\_4},
doi = {10.1007/978-3-540-71783-6\_4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/evoW/CodreaJPHM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SzklarczykH06,
author = {Radek Szklarczyk and
Jaap Heringa},
title = {AuberGene - a sensitive genome alignment tool},
journal = {Bioinform.},
volume = {22},
number = {12},
pages = {1431--1436},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl112},
doi = {10.1093/BIOINFORMATICS/BTL112},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SzklarczykH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icmla/MarchioriPHF06,
author = {Elena Marchiori and
Walter Pirovano and
Jaap Heringa and
K. Anton Feenstra},
editor = {M. Arif Wani and
Tao Li and
Lukasz A. Kurgan and
Jieping Ye and
Ying Liu},
title = {A Feature Selection Algorithm for Detecting Subtype Specific Functional
Sites from Protein Sequences for Smad Receptor Binding},
booktitle = {The Fifth International Conference on Machine Learning and Applications,
{ICMLA} 2006, Orlando, Florida, USA, 14-16 December 2006},
pages = {168--173},
publisher = {{IEEE} Computer Society},
year = {2006},
url = {https://doi.org/10.1109/ICMLA.2006.7},
doi = {10.1109/ICMLA.2006.7},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icmla/MarchioriPHF06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LinSTH05,
author = {Kuang Lin and
Victor A. Simossis and
William R. Taylor and
Jaap Heringa},
title = {A simple and fast secondary structure prediction method using hidden
neural networks},
journal = {Bioinform.},
volume = {21},
number = {2},
pages = {152--159},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bth487},
doi = {10.1093/BIOINFORMATICS/BTH487},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LinSTH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GeorgeLH05,
author = {Richard A. George and
Kuang Lin and
Jaap Heringa},
title = {Scooby-domain: prediction of globular domains in protein sequence},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {160--163},
year = {2005},
url = {https://doi.org/10.1093/nar/gki381},
doi = {10.1093/NAR/GKI381},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GeorgeLH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SimossisH05,
author = {Victor A. Simossis and
Jaap Heringa},
title = {{PRALINE:} a multiple sequence alignment toolbox that integrates homology-extended
and secondary structure information},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {289--294},
year = {2005},
url = {https://doi.org/10.1093/nar/gki390},
doi = {10.1093/NAR/GKI390},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SimossisH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/SimossisH04,
author = {Victor A. Simossis and
Jaap Heringa},
title = {The influence of gapped positions in multiple sequence alignments
on secondary structure prediction methods},
journal = {Comput. Biol. Chem.},
volume = {28},
number = {5-6},
pages = {351--366},
year = {2004},
url = {https://doi.org/10.1016/j.compbiolchem.2004.09.005},
doi = {10.1016/J.COMPBIOLCHEM.2004.09.005},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/SimossisH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SzklarczykH04,
author = {Radek Szklarczyk and
Jaap Heringa},
title = {Tracking repeats using significance and transitivity},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {311--317},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth911},
doi = {10.1093/BIOINFORMATICS/BTH911},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/SzklarczykH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/LinKTH03,
author = {Kuang Lin and
Jens Kleinjung and
William R. Taylor and
Jaap Heringa},
title = {Testing homology with Contact Accepted mutatiOn {(CAO):} a contact-based
Markov model of protein evolution},
journal = {Comput. Biol. Chem.},
volume = {27},
number = {2},
pages = {93--102},
year = {2003},
url = {https://doi.org/10.1016/S1476-9271(03)00022-7},
doi = {10.1016/S1476-9271(03)00022-7},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/LinKTH03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/SimossisH03,
author = {Victor A. Simossis and
Jaap Heringa},
title = {The {PRALINE} online server: optimising progressive multiple alignment
on the web},
journal = {Comput. Biol. Chem.},
volume = {27},
number = {4-5},
pages = {511--519},
year = {2003},
url = {https://doi.org/10.1016/j.compbiolchem.2003.09.002},
doi = {10.1016/J.COMPBIOLCHEM.2003.09.002},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/SimossisH03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/RomeinHB03,
author = {John W. Romein and
Jaap Heringa and
Henri E. Bal},
title = {A Million-Fold Speed Improvement in Genomic Repeats Detection},
booktitle = {Proceedings of the {ACM/IEEE} {SC2003} Conference on High Performance
Networking and Computing, 15-21 November 2003, Phoenix, AZ, USA, CD-Rom},
pages = {20},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/1048935.1050171},
doi = {10.1145/1048935.1050171},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sc/RomeinHB03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KleinjungDH02,
author = {Jens Kleinjung and
Nigel Douglas and
Jaap Heringa},
title = {Parallelized multiple alignment},
journal = {Bioinform.},
volume = {18},
number = {9},
pages = {1270--1271},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.9.1270},
doi = {10.1093/BIOINFORMATICS/18.9.1270},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KleinjungDH02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Heringa02,
author = {Jaap Heringa},
title = {Local Weighting Schemes for Protein Multiple Sequence Alignment},
journal = {Comput. Chem.},
volume = {26},
number = {5},
pages = {459--477},
year = {2002},
url = {https://doi.org/10.1016/S0097-8485(02)00008-6},
doi = {10.1016/S0097-8485(02)00008-6},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/Heringa02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Heringa01,
author = {Jaap Heringa},
title = {Post-genome Informatics: Minoru Kanehisa, Oxford University Press,
Oxford, 2000, 148 pages},
journal = {Comput. Chem.},
volume = {25},
number = {4},
pages = {425--426},
year = {2001},
url = {https://doi.org/10.1016/S0097-8485(01)00078-X},
doi = {10.1016/S0097-8485(01)00078-X},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/Heringa01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/PollockH00,
author = {David D. Pollock and
Jaap Heringa},
title = {{RECOMB98.} Computational Molecular Biology: Pre- and Post-genomics,
March 22-25, 1998, New York},
journal = {Comput. Chem.},
volume = {24},
number = {1},
pages = {133--134},
year = {2000},
url = {https://doi.org/10.1016/S0097-8485(00)80013-3},
doi = {10.1016/S0097-8485(00)80013-3},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/PollockH00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Heringa99,
author = {Jaap Heringa},
title = {Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary
Structure-induced Multiple Alignment},
journal = {Comput. Chem.},
volume = {23},
number = {3-4},
pages = {341--364},
year = {1999},
url = {https://doi.org/10.1016/S0097-8485(99)00012-1},
doi = {10.1016/S0097-8485(99)00012-1},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/Heringa99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Heringa94,
author = {Jaap Heringa},
title = {The Evolution and Recognition of Protein Sequence Repeats},
journal = {Comput. Chem.},
volume = {18},
number = {3},
pages = {233--243},
year = {1994},
url = {https://doi.org/10.1016/0097-8485(94)85018-6},
doi = {10.1016/0097-8485(94)85018-6},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/Heringa94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HeringaSHA92,
author = {Jaap Heringa and
Hubert Sommerfeldt and
Desmond G. Higgins and
Patrick Argos},
title = {{OBSTRUCT:} a program to obtain largest cliques from a protein sequence
set according to structural resolution and sequence similarity},
journal = {Comput. Appl. Biosci.},
volume = {8},
number = {6},
pages = {599--600},
year = {1992},
url = {https://doi.org/10.1093/bioinformatics/8.6.599},
doi = {10.1093/BIOINFORMATICS/8.6.599},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HeringaSHA92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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