Martijn A. Huynen

发表

Reliable and specific protein function prediction by combining homology with genomic(s) context

Toni Gabaldón, Berend Snel, Martijn A. Huynen, 2006 .

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Martijn A. Huynen, Sergio Rossell, Richard A. Notebaart, 2013, PLoS Comput. Biol..

Pathway alignment: Application in the comparative analysis of glycolysis

Peer Bork, Stefan Schuster, Martijn A. Huynen, 1998, German Conference on Bioinformatics.

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes

Martijn A. Huynen, Toni Gabaldón, M. Huynen, 2005, ECCB/JBI.

Orthology prediction at scalable resolution by phylogenetic tree analysis

Berend Snel, Vera van Noort, Martijn A. Huynen, 2007, BMC Bioinformatics.

Assessment of phylogenomic and orthology approaches for phylogenetic inference

Bas E. Dutilh, Berend Snel, Vera van Noort, 2007, Bioinform..

Iterative read mapping and assembly allows the use of a more distant reference in metagenome assembly

Bas E. Dutilh, Martijn A. Huynen, Jolein Gloerich, 2011 .

Genetic Algorithms and Information Accumulation during the Evolution of Gene Regulation

Paulien Hogeweg, Martijn A. Huynen, 1989, ICGA.

STRING: known and predicted protein–protein associations, integrated and transferred across organisms

Christian von Mering, Peer Bork, Sean D. Hooper, 2004, Nucleic Acids Res..

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Bas E. Dutilh, Martijn A. Huynen, Marc Strous, 2009, Bioinform..

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response

Qian Feng, Martijn A. Huynen, Robin van der Lee, 2015, PLoS Comput. Biol..

FACIL: Fast and Accurate Genetic Code Inference and Logo

Bas E. Dutilh, Martijn A. Huynen, Sacha A. F. T. van Hijum, 2011, Bioinform..

CEDAR, an online resource for the reporting and exploration of complexome profiling data

Uwe Schulte, Mercedes Pardo, Jyoti S. Choudhary, 2020, bioRxiv.

Optimized design and assessment of whole genome tiling arrays

Paul Flicek, Ewan Birney, Martijn A. Huynen, 2007, ISMB/ECCB.

Sequence specificity between interacting and non-interacting homologs identifies interface residues – a homodimer and monomer use case

Jaap Heringa, Bas E. Dutilh, Martijn A. Huynen, 2015, BMC Bioinformatics.

Optimising oligonucleotide array design for ChIP-on-chip

Paul Flicek, Ewan Birney, Martijn A. Huynen, 2007, BMC Bioinformatics.

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome

Martijn A. Huynen, Riekelt H. Houtkooper, Sergio Guerrero-Castillo, 2019, Bioinform..

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism

Martijn A. Huynen, Toni Gabaldón, M. Huynen, 2007, PLoS Comput. Biol..

Flux Measurement Selection in Metabolic Networks

Elena Marchiori, Martijn A. Huynen, Wout Megchelenbrink, 2011, PRIB.

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

Joaquín Dopazo, Jaime Huerta-Cepas, Martijn A. Huynen, 2011, Briefings Bioinform..

Base Pairing Probabilities in a Complete HIV-1 RNA

Alan S. Perelson, Peter F. Stadler, Martijn A. Huynen, 1996, J. Comput. Biol..

WeGET: predicting new genes for molecular systems by weighted co-expression

Damian Szklarczyk, Martijn A. Huynen, Radek Szklarczyk, 2015, Nucleic Acids Res..

Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway

Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga, 2004, Bioinform..

Measuring the physical cohesiveness of proteins using physical interaction enrichment

Martijn A. Huynen, Iziah Edwin Sama, M. Huynen, 2010, Bioinform..

STRING: a database of predicted functional associations between proteins

Christian von Mering, Peer Bork, Berend Snel, 2003, Nucleic Acids Res..

Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers

Peter F. Stadler, Ivo L. Hofacker, Martijn A. Huynen, 1996, KDD.

The properties of protein family space depend on experimental design

Christos A. Ouzounis, Sarah A. Teichmann, Martijn A. Huynen, 2005, Bioinform..

Signature, a web server for taxonomic characterization of sequence samples using signature genes

Ying He, Bas E. Dutilh, Martijn A. Huynen, 2008, Nucleic Acids Res..

Conserved co-expression for candidate disease gene prioritization

Martijn A. Huynen, Han G. Brunner, Martin Oti, 2008, BMC Bioinformatics.

Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism

Martijn A. Huynen, Kira S. Makarova, Eugene V. Koonin, 2004, Journal of bacteriology.

Iterative read mapping and assembly allows the use of a more distant reference in metagenome assembly

Bas E. Dutilh, Martijn A. Huynen, Jolein Gloerich, 2011 .

Power Laws in the Size Distribution of Gene Families in Complete Genomes: Biological Interpretations

Martijn A. Huynen, Erik van Nimwegen, 1997 .

Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum

Martijn A. Huynen, Ulrich Brandt, Alfredo Cabrera-Orefice, 2020, Nature Communications.

The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise

Bas E. Dutilh, Berend Snel, Martijn A. Huynen, 2004, Journal of Molecular Evolution.

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Dmitrij Frishman, Markus Schmid, Bas E. Dutilh, 2006, Nature.

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts

Martijn A. Huynen, Laurens Wiel, M. Huynen, 2017, bioRxiv.

ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

Martijn A. Huynen, Adam Eyre-Walker, M. Huynen, 2013, PloS one.

Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes

Peer Bork, Berend Snel, Martijn A. Huynen, 1999 .

Proteomic Profiling of Plasmodium Sporozoite Maturation Identifies New Proteins Essential for Parasite Development and Infectivity

Martijn A. Huynen, Robert W. Sauerwein, Matthias Mann, 2008, PLoS pathogens.

Exploitation of gene context to infer evolution and to predict function

Peer Bork, Berend Snel, Martijn A. Huynen, 2000 .

Conservation of gene co-regulation in prokaryotes and eukaryotes

Peer Bork, Berend Snel, Martijn A. Huynen, 2002 .

Clustering of Codons with Rare Cognate tRNAs in Human Genes Suggests an Extra Level of Expression Regulation

Martijn A. Huynen, M. Huynen, Joanna L. Parmley, 2009, PLoS genetics.

TEFM (c17orf42) is necessary for transcription of human mtDNA

Martijn A. Huynen, Michal Minczuk, Thijs J. G. Ettema, 2011, Nucleic acids research.

Correlation between sequence conservation and the genomic context after gene duplication

Berend Snel, Martijn A. Huynen, Bas Teusink, 2005, Nucleic Acids Research.

Constructing a minimal genome

Martijn A. Huynen, M. Huynen, 2000 .

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

Bas E. Dutilh, Alexander Hoischen, Martijn A. Huynen, 2010, PLoS genetics.

Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system

Martijn A. Huynen, Rutger O. Vogel, Radek Szklarczyk, 2015, BMC Genomics.

Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets

Martijn A. Huynen, Richard A. Notebaart, Xiaowen Lu, 2013, Nature Communications.

Comparative Genome Analysis: Exploiting the Context of Genes to Infer Evolution and Predict Function

Berend Snel, Martijn A. Huynen, Thomas Dandekar, 2000 .

Evolutionary Dynamics of RNA and the Neutral Theory

Walter Fontana, Peter F. Stadler, Martijn A. Huynen, 1995 .

Predicting Human Genetic Interactions from Cancer Genome Evolution

Martijn A. Huynen, Richard A. Notebaart, Wout Megchelenbrink, 2015, PloS one.

Reconstructing the evolution of the mitochondrial ribosomal proteome

Martijn A. Huynen, Thijs J. G. Ettema, M. Huynen, 2007, Nucleic acids research.

Evolutionary Diversity of Vertebrate Small Heat Shock Proteins

Martijn A. Huynen, Wilfried W. de Jong, M. Huynen, 2004, Journal of Molecular Evolution.