K. Anton Feenstra

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 13

Top Topics

Protein Interaction

Multiple Sequence Alignments

Top Venues

PLoS Comput. Biol.

Publications

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)
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) (2022)
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) (2022)
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) (2021)
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) (2021)
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) (2020)
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) (2019)
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) (2019)
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)
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) (2018)
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)
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) (2017)
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) (2016)
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)
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 (2015)
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) (2014)
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
Petri Nets Are a Biologist's Best Friend. FMMB (2014)
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) (2013)
Timo Willemsen, K. Anton Feenstra, Paul Groth
Building Executable Biological Pathway Models Automatically from BioPAX. LISC@ISWC (2013)
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) (2013)
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) (2012)
Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa
Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Elzbieta Krepska
What Can Formal Methods Bring to Systems Biology? FM (2009)
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
vulval development. Bioinform. 25 (16) (2009)
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) (2009)
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) (2009)
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)
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
The meaning of alignment: lessons from structural diversity. BMC Bioinform. 9 (2008)
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
: a strategy for improved multiple alignment of transmembrane proteins. Bioinform. 24 (4) (2008)
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) (2008)
K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa
Sequence harmony: detecting functional specificity from alignments. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
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)
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) (1999)