Martijn A. Huynen

29 papers A* 1Journal 23Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
The use of knowledge graphs for drug repurposing: From classical machine learning algorithms to graph neural networks.
Comput. Biol. Medicine
Siqi Wei, Christo Sasi, Jelle Piepenbrock, Martijn A. Huynen, Peter A. C. 't Hoen
2023 J jnl
Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution.
PLoS Comput. Biol.
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
2021 J jnl
Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies.
PLoS Comput. Biol.
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
2019 J jnl
COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome.
Bioinform.
Joeri van Strien, Sergio Guerrero-Castillo, Iliana A. Chatzispyrou, Riekelt H. Houtkooper, Ulrich Brandt, Martijn A. Huynen
2016 J jnl
WeGET: predicting new genes for molecular systems by weighted co-expression.
Nucleic Acids Res.
Radek Szklarczyk, Wout Megchelenbrink, Pavel Cizek, Marie Ledent, Gonny Velemans, Damian Szklarczyk, Martijn A. Huynen
2015 J jnl
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response.
PLoS Comput. Biol.
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
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
2013 J jnl
Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements.
PLoS Comput. Biol.
Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart
2011 J jnl
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings Bioinform.
Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón
2011 J jnl
FACIL: Fast and Accurate Genetic Code Inference and Logo.
Bioinform.
Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A. F. T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Henk Stunnenberg, Marc Strous, Mike S. M. Jetten, Huub J. M. Op den Camp, Martijn A. Huynen
2011 — conf
Flux Measurement Selection in Metabolic Networks.
PRIB
Wout Megchelenbrink, Martijn A. Huynen, Elena Marchiori
2010 J jnl
Measuring the physical cohesiveness of proteins using physical interaction enrichment.
Bioinform.
Iziah Edwin Sama, Martijn A. Huynen
2009 J jnl
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
Bioinform.
Bas E. Dutilh, Martijn A. Huynen, Marc Strous
2008 J jnl
Conserved co-expression for candidate disease gene prioritization.
BMC Bioinform.
Martin Oti, Jeroen van Reeuwijk, Martijn A. Huynen, Han G. Brunner
2008 J jnl
Signature, a web server for taxonomic characterization of sequence samples using signature genes.
Nucleic Acids Res.
Bas E. Dutilh, Ying He, Maarten L. Hekkelman, Martijn A. Huynen
2007 J jnl
Assessment of phylogenomic and orthology approaches for phylogenetic inference.
Bioinform.
Bas E. Dutilh, Vera van Noort, René T. J. M. van der Heijden, T. Boekhout, Berend Snel, Martijn A. Huynen
2007 J jnl
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism.
PLoS Comput. Biol.
Toni Gabaldón, Martijn A. Huynen
2007 J jnl
Optimising oligonucleotide array design for ChIP-on-chip.
BMC Bioinform.
Fiona G. G. Nielsen, Stefan Gräf, Xinmin Zhang, Stefan Kurtz, Sergei Denissov, Roland Green, Ewan Birney, Paul Flicek, Martijn A. Huynen, Henk Stunnenberg
2007 — conf
Optimized design and assessment of whole genome tiling arrays.
ISMB/ECCB (Supplement of Bioinformatics)
Stefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, Paul Flicek
2007 J jnl
Orthology prediction at scalable resolution by phylogenetic tree analysis.
BMC Bioinform.
René T. J. M. van der Heijden, Berend Snel, Vera van Noort, Martijn A. Huynen
2005 — conf
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
ECCB/JBI
Toni Gabaldón, Martijn A. Huynen
2005 J jnl
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res.
Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork
2005 J jnl
The properties of protein family space depend on experimental design.
Bioinform.
Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis
2004 J jnl
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
Bioinform.
Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga
2003 J jnl
STRING: a database of predicted functional associations between proteins.
Nucleic Acids Res.
Christian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel
1998 — conf
Pathway alignment: Application in the comparative analysis of glycolysis.
German Conference on Bioinformatics
Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork
1996 J jnl
Base Pairing Probabilities in a Complete HIV-1 RNA.
J. Comput. Biol.
Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler
1996 A* conf
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers.
KDD
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
1989 — conf
Genetic Algorithms and Information Accumulation during the Evolution of Gene Regulation.
ICGA
Martijn A. Huynen, Paulien Hogeweg