Genetic Algorithms and Information Accumulation during the Evolution of Gene Regulation. - Martijn A. Huynen; Paulien Hogeweg (ICGA, 1989)

Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. - Ivo L. Hofacker; Martijn A. Huynen; Peter F. Stadler; Paul E. Stolorz (KDD, 1996)

Base Pairing Probabilities in a Complete HIV-1 RNA. - Martijn A. Huynen; Alan S. Perelson; W. A. Vieira; Peter F. Stadler (J. Comput. Biol., 1996)

Pathway alignment: Application in the comparative analysis of glycolysis. - Thomas Dandekar; Stefan Schuster; Martijn A. Huynen; Peer Bork (German Conference on Bioinformatics, 1998)

STRING: a database of predicted functional associations between proteins. - Christian von Mering; Martijn A. Huynen; Daniel Jaeggi; Steffen Schmidt; Peer Bork; Berend Snel (Nucleic Acids Res., 2003)

Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway. - Harm van Bakel; Martijn A. Huynen; Cisca Wijmenga (Bioinform., 2004)

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. - Toni Gabaldón; Martijn A. Huynen (ECCB/JBI, 2005)

The properties of protein family space depend on experimental design. - Victor Kunin; Sarah A. Teichmann; Martijn A. Huynen; Christos A. Ouzounis (Bioinform., 2005)

STRING: known and predicted protein-protein associations, integrated and transferred across organisms. - Christian von Mering; Lars Juhl Jensen; Berend Snel; Sean D. Hooper; Markus Krupp; Mathilde Foglierini; Nelly Jouffre; Martijn A. Huynen; Peer Bork (Nucleic Acids Res., 2005)

Optimized design and assessment of whole genome tiling arrays. - Stefan Gräf; Fiona G. G. Nielsen; Stefan Kurtz; Martijn A. Huynen; Ewan Birney; Henk Stunnenberg; Paul Flicek (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Assessment of phylogenomic and orthology approaches for phylogenetic inference. - Bas E. Dutilh; Vera van Noort; René T. J. M. van der Heijden; T. Boekhout; Berend Snel; Martijn A. Huynen (Bioinform., 2007)

Orthology prediction at scalable resolution by phylogenetic tree analysis. - René T. J. M. van der Heijden; Berend Snel; Vera van Noort; Martijn A. Huynen (BMC Bioinform., 2007)

Optimising oligonucleotide array design for ChIP-on-chip. - Fiona G. G. Nielsen; Stefan Gräf; Xinmin Zhang; Stefan Kurtz; Sergei Denissov; Roland Green; Ewan Birney; Paul Flicek; Martijn A. Huynen; Henk Stunnenberg (BMC Bioinform., 2007)

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism. - Toni Gabaldón; Martijn A. Huynen (PLoS Comput. Biol., 2007)

Conserved co-expression for candidate disease gene prioritization. - Martin Oti; Jeroen van Reeuwijk; Martijn A. Huynen; Han G. Brunner (BMC Bioinform., 2008)

Signature, a web server for taxonomic characterization of sequence samples using signature genes. - Bas E. Dutilh; Ying He; Maarten L. Hekkelman; Martijn A. Huynen (Nucleic Acids Res., 2008)

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. - Bas E. Dutilh; Martijn A. Huynen; Marc Strous (Bioinform., 2009)

Measuring the physical cohesiveness of proteins using physical interaction enrichment. - Iziah Edwin Sama; Martijn A. Huynen (Bioinform., 2010)

Flux Measurement Selection in Metabolic Networks. - Wout Megchelenbrink; Martijn A. Huynen; Elena Marchiori (PRIB, 2011)

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. - Jaime Huerta-Cepas; Joaquín Dopazo; Martijn A. Huynen; Toni Gabaldón (Briefings Bioinform., 2011)

FACIL: Fast and Accurate Genetic Code Inference and Logo. - Bas E. Dutilh; Rasa Jurgelenaite; Radek Szklarczyk; Sacha A. F. T. van Hijum; Harry R. Harhangi; Markus Schmid 002; Bart de Wild; Kees-Jan Françoijs; Henk Stunnenberg; Marc Strous; Mike S. M. Jetten; Huub J. M. Op den Camp; et al. (Bioinform., 2011)

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements. - Sergio Rossell; Martijn A. Huynen; Richard A. Notebaart (PLoS Comput. Biol., 2013)

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)

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. - Robin van der Lee; Qian Feng; Martijn A. Langereis; Rob ter Horst; Radek Szklarczyk; Mihai G. Netea; Arno C. Andeweg; Frank J. M. van Kuppeveld; Martijn A. Huynen (PLoS Comput. Biol., 2015)

WeGET: predicting new genes for molecular systems by weighted co-expression. - Radek Szklarczyk; Wout Megchelenbrink; Pavel Cizek; Marie Ledent; Gonny Velemans; Damian Szklarczyk; Martijn A. Huynen (Nucleic Acids Res., 2016)

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome. - Joeri van Strien; Sergio Guerrero-Castillo; Iliana A Chatzispyrou; Riekelt H. Houtkooper; Ulrich Brandt; Martijn A. Huynen (Bioinform., 2019)

Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies. - Lisette Meerstein-Kessel; Jeron Venhuizen; Daniel Garza; Nicolas Pröllochs; Emma J. Vos; Joshua M. Obiero; Philip L. Felgner; Robert W. Sauerwein; Marynthe Peters; Annie S. P. Yang; Martijn A. Huynen (PLoS Comput. Biol., 2021)

Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. - Joeri van Strien; Felix Evers; Madhurya Lutikurti; Stijn L. Berendsen; Alejandro Garanto; Geert-Jan van Gemert; Alfredo Cabrera-Orefice; Richard J. Rodenburg; Ulrich Brandt; Taco W. A. Kooij; Martijn A. Huynen (PLoS Comput. Biol., 2023)

The use of knowledge graphs for drug repurposing: From classical machine learning algorithms to graph neural networks. - Siqi Wei; Christo Sasi; Jelle Piepenbrock; Martijn A. Huynen; Peter A. C. 't Hoen (Comput. Biol. Medicine, 2025)