Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. - K. Anton Feenstra; Berk Hess; Herman J. C. Berendsen (J. Comput. Chem., 1999)

A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. - Elena Marchiori; Walter Pirovano; Jaap Heringa; K. Anton Feenstra (ICMLA, 2006)

Sequence harmony: detecting functional specificity from alignments. - K. Anton Feenstra; Walter Pirovano; Klaas Krab; Jaap Heringa (Nucleic Acids Res., 2007)

Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. - Elzbieta Krepska; Nicola Bonzanni; K. Anton Feenstra; Wan J. Fokkink; Thilo Kielmann; Henri E. Bal; Jaap Heringa (FMSB, 2008)

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (Bioinform., 2008)

Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. - Kai Ye 001; K. Anton Feenstra; Jaap Heringa; Adriaan P. IJzerman; Elena Marchiori (Bioinform., 2008)

The meaning of alignment: lessons from structural diversity. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (BMC Bioinform., 2008)

What Can Formal Methods Bring to Systems Biology? - Nicola Bonzanni; K. Anton Feenstra; Wan J. Fokkink; Elzbieta Krepska (FM, 2009)

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. - Nicola Bonzanni; Elzbieta Krepska; K. Anton Feenstra; Wan J. Fokkink; Thilo Kielmann; Henri E. Bal; Jaap Heringa (Bioinform., 2009)

Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development. - Nicola Bonzanni; Elzbieta Krepska; K. Anton Feenstra; Wan J. Fokkink; Thilo Kielmann; Henri E. Bal; Jaap Heringa (Bioinform., 2009)

Structure and function analysis of flexible alignment regions in proteins. - Walter Pirovano; Anneke van der Reijden; K. Anton Feenstra; Jaap Heringa (BMC Bioinform., 2009)

Multi-Harmony: detecting functional specificity from sequence alignment. - Bernd W. Brandt; K. Anton Feenstra; Jaap Heringa (Nucleic Acids Res., 2010)

Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. - René Pool; Jaap Heringa; Martin Hoefling; Roland Schulz; Jeremy C. Smith; K. Anton Feenstra (J. Comput. Chem., 2012)

Building Executable Biological Pathway Models Automatically from BioPAX. - Timo Willemsen; K. Anton Feenstra; Paul Groth (LISC@ISWC, 2013)

Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. - Sanne Abeln; Douwe Molenaar; K. Anton Feenstra; Huub C. J. Hoefsloot; Bas Teusink; Jaap Heringa (Briefings Bioinform., 2013)

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model. - Nicola Bonzanni; Abhishek Garg; K. Anton Feenstra; Judith Schütte; Sarah Kinston; Diego Miranda-Saavedra; Jaap Heringa; Ioannis Xenarios; Berthold Göttgens (Bioinform., 2013)

Petri Nets Are a Biologist's Best Friend. - Nicola Bonzanni; K. Anton Feenstra; Wan J. Fokkink; Jaap Heringa (FMMB, 2014)

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. - Ali May; René Pool; Erik van Dijk; Jochem Bijlard; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2014)

Explaining disease using big data: How valid is your pathway? - Bas Stringer; Maurits J. J. Dijkstra; K. Anton Feenstra; Sanne Abeln; Jaap Heringa (HPCS, 2015)

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. - Qingzhen Hou; Bas E. Dutilh; Martijn A. Huynen; Jaap Heringa; K. Anton Feenstra (BMC Bioinform., 2015)

BioASF: a framework for automatically generating executable pathway models specified in BioPAX. - Reza Haydarlou; Annika Jacobsen; Nicola Bonzanni; K. Anton Feenstra; Sanne Abeln; Jaap Heringa (Bioinform., 2016)

Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest. - Qingzhen Hou; Paul F. G. De Geest; Wim F. Vranken; Jaap Heringa; K. Anton Feenstra (Bioinform., 2017)

Training for translation between disciplines: a philosophy for life and data sciences curricula. - K. Anton Feenstra; Sanne Abeln; Johan A. Westerhuis; Filipe Brancos dos Santos; Douwe Molenaar; Bas Teusink; Huub C. J. Hoefsloot; Jaap Heringa (Bioinform., 2018)

Motif-Aware PRALINE: Improving the alignment of motif regions. - Maurits J. J. Dijkstra; Punto Bawono; Sanne Abeln; K. Anton Feenstra; Wan J. Fokkink; Jaap Heringa (PLoS Comput. Biol., 2018)

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. - Maurits J. J. Dijkstra; Atze van der Ploeg; K. Anton Feenstra; Wan J. Fokkink; Sanne Abeln; Jaap Heringa (Bioinform., 2019)

SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. - Qingzhen Hou; Paul F. G. De Geest; Christian J. Griffioen; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2019)

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. - Saman Amini; Annika Jacobsen; Olga Ivanova; Philip Lijnzaad; Jaap Heringa; Frank C. P. Holstege; K. Anton Feenstra; Patrick Kemmeren (PLoS Comput. Biol., 2019)

Protein Three-Dimensional Structure Prediction. - Sanne Abeln; K. Anton Feenstra; Jaap Heringa (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

A framework for exhaustive modelling of genetic interaction patterns using Petri nets. - Annika Jacobsen; Olga Ivanova; Saman Amini; Jaap Heringa; Patrick Kemmeren; K. Anton Feenstra (Bioinform., 2020)

SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. - Qingzhen Hou; Bas Stringer; Katharina Waury; Henriette Capel; Reza Haydarlou; Fuzhong Xue; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2021)

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. - Ting Liu; Xueli Pan; Xu Wang 032; K. Anton Feenstra; Jaap Heringa; Zhisheng Huang (Health Inf. Sci. Syst., 2021)

PIPENN: protein interface prediction from sequence with an ensemble of neural nets. - Bas Stringer; Hans de Ferrante; Sanne Abeln; Jaap Heringa; K. Anton Feenstra; Reza Haydarlou (Bioinform., 2022)

Ten quick tips for sequence-based prediction of protein properties using machine learning. - Qingzhen Hou; Katharina Waury; Dea Gogishvili; K. Anton Feenstra (PLoS Comput. Biol., 2022)

Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. - Ting Liu; K. Anton Feenstra; Zhisheng Huang; Jaap Heringa (Bioinform., 2024)