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ORCIDK. Anton Feenstra
Person information
- affiliation: Free University of Amsterdam, Netherlands
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Journal Articles
- 2024
[j27]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
- [j26]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) - [j25]Qingzhen Hou, Katharina Waury, Dea Gogishvili, K. Anton Feenstra:
Ten quick tips for sequence-based prediction of protein properties using machine learning. PLoS Comput. Biol. 18(12): 1010669 (2022) - 2021
- [j24]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) - [j23]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
- [j22]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) - 2019
- [j21]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) - [j20]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) - [j19]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) - 2018
- [j18]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) - [j17]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) - 2017
- [j16]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) - 2016
- [j15]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) - 2015
- [j14]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) - 2014
- [j13]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) - 2013
- [j12]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) - [j11]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) - 2012
- [j10]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) - 2010
- [j9]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) - 2009
- [j8]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) - [j7]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) - [j6]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) - 2008
- [j5]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) - [j4]Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinform. 24(4): 492-497 (2008) - [j3]Walter Pirovano, K. Anton Feenstra, Jaap Heringa:
The meaning of alignment: lessons from structural diversity. BMC Bioinform. 9 (2008) - 2007
- [j2]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) - 1999
- [j1]K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen:
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20(8): 786-798 (1999)
Conference and Workshop Papers
- 2015
- [c6]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 - 2014
- [c5]Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa:
Petri Nets Are a Biologist's Best Friend. FMMB 2014: 102-116 - 2013
- [c4]Timo Willemsen, K. Anton Feenstra, Paul Groth:
Building Executable Biological Pathway Models Automatically from BioPAX. LISC@ISWC 2013: 2-14 - 2009
- [c3]Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Elzbieta Krepska:
What Can Formal Methods Bring to Systems Biology? FM 2009: 16-22 - 2008
- [c2]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 - 2006
- [c1]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
Reference Works
- 2019
- [r1]Sanne Abeln, K. Anton Feenstra, Jaap Heringa:
Protein Three-Dimensional Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 497-511
Coauthor Index
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