K. Anton Feenstra

35 papers B 1C 1Journal 27Unranked 5

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. Bioinform. Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa
2022	—	`conf`	Computational Prediction Approaches for Predicting Mutation Impact on Protein-Protein Interactions. ICATCI (2) Yi Ping, Laura Hoekstra, K. Anton Feenstra
2022	J	`jnl`	PIPENN: protein interface prediction from sequence with an ensemble of neural nets. Bioinform. Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
2022	J	`jnl`	Ten quick tips for sequence-based prediction of protein properties using machine learning. PLoS Comput. Biol. Qingzhen Hou, Katharina Waury, Dea Gogishvili, K. Anton Feenstra
2021	J	`jnl`	Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. Health Inf. Sci. Syst. Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang
2021	J	`jnl`	SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. Bioinform. Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2020	J	`jnl`	A framework for exhaustive modelling of genetic interaction patterns using Petri nets. Bioinform. Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra
2019	—	`ch.`	Protein Three-Dimensional Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) Sanne Abeln, K. Anton Feenstra, Jaap Heringa
2019	J	`jnl`	SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. Bioinform. Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2019	J	`jnl`	Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinform. Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
2019	J	`jnl`	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. Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren
2018	J	`jnl`	Motif-Aware PRALINE: Improving the alignment of motif regions. PLoS Comput. Biol. Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2018	J	`jnl`	Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinform. K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
2017	J	`jnl`	Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. Bioinform. Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra
2016	J	`jnl`	BioASF: a framework for automatically generating executable pathway models specified in BioPAX. Bioinform. Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015	—	`conf`	Explaining disease using big data: How valid is your pathway? HPCS Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015	J	`jnl`	Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinform. Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra
2014	J	`jnl`	Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. Bioinform. Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2014	—	`conf`	Petri Nets Are a Biologist's Best Friend. FMMB Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2013	J	`jnl`	Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings Bioinform. Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
2013	—	`conf`	Building Executable Biological Pathway Models Automatically from BioPAX. LISC@ISWC Timo Willemsen, K. Anton Feenstra, Paul Groth
2013	J	`jnl`	Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. Bioinform. Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens
2012	J	`jnl`	Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem. René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
2010	J	`jnl`	Multi-Harmony: detecting functional specificity from sequence alignment. Nucleic Acids Res. Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa
2009	J	`jnl`	Executing multicellular differentiation: quantitative predictive modelling of Bioinform. Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009	J	`jnl`	Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. Bioinform. Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009	J	`jnl`	Structure and function analysis of flexible alignment regions in proteins. BMC Bioinform. Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa
2009	B	`conf`	What Can Formal Methods Bring to Systems Biology? FM Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Elzbieta Krepska
2008	—	`conf`	Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. FMSB Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2008	J	`jnl`	Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinform. Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
2008	J	`jnl`	PRALINE Bioinform. Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2008	J	`jnl`	The meaning of alignment: lessons from structural diversity. BMC Bioinform. Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2007	J	`jnl`	Sequence harmony: detecting functional specificity from alignments. Nucleic Acids Res. K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa
2006	C	`conf`	A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. ICMLA Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra
1999	J	`jnl`	Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen