REVIEW Predicting Function: From Genes to Genomes (2008)
Peer Bork, Thomas D, E Diaz-lazcoz, Frank Eisenhaber, Martijn Huynen, ...
Genomes and function prediction Prediction of protein function using computational tools becomes more and more important as the gap between the increasing amount of sequences and the experimental...
Martijn Huynen, Peter Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
Optimising oligonucleotide array design for ChIP-on-chip (2007)
Nielsen, Fiona, Graef, Stefan, Zhang, Xinmin, Kurtz, Stefan, Denissov, Sergei, Green, Roland, ...
No abstract available.
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway (2004)
Van Bakel, Harm, Huynen, Martijn, Wijmenga, Cisca
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be...
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway (2004)
Van Bakel, Harm, Huynen, Martijn, Wijmenga, Cisca
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be...
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway (2004)
Van Bakel, Harm, Huynen, Martijn, Wijmenga, Cisca
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be...
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway (2004)
Van Bakel, Harm, Huynen, Martijn, Wijmenga, Cisca
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be...
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway (2004)
Van Bakel, Harm, Huynen, Martijn, Wijmenga, Cisca
Motivation: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be...
STRING: a database of predicted functional associations between proteins (2003)
Mering, Christian Von, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2 (2002)
Voncken, Frank G.J., Boxma, Brigitte, Akhmanova, Anna S., Vogels, Godfried D., Huynen, Martijn, ...
The presence of a [Fe]-hydrogenase in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2 has been demonstrated by immunocytochemistry, subcellular fractionation,...
Voncken, Frank, Boxma, Brigitte, Tjaden, Joachim, Akhmanova, Anna, Huynen, Martijn, Verbeek, Fons, ...
A mitochondrial-type ADP/ATP carrier (AAC) has been identified in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2. Biochemical and immunocytochemical studies revealed...
Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments (2001)
Hackstein, Johannes H.P., Akhmanova, Anna, Voncken, Frank, Hoek, Angela Van, Alen, Theo Van, Boxma, Brigitte, ...
Hydrogenosomes are membrane-bound organelles that compartmentalise the final steps of energy metabolism in a number of anaerobic eukaryotes. They produce hydrogen and ATP. Here we will review the...
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
Pathway alignment : application to the comparative analysis of glycolytic enzymes (1999)
Dandekar, Thomas, Schuster, Stefan, Snel, Berend, Huynen, Martijn, Bork, Peer
Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on...
Neutral Evolution of Mutational Robustness (1999)
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely...
Neutral evolution of mutational robustness (1999)
Nimwegen, Erik Van, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the populations limit distribution on the neutral network is solely...
Enzymes Thomas Dandekar, Thomas Dandekar, Stefan Schuster, Berend Snel, Martijn Huynen, Peer Bork
INTRODUCTION Sequence alignment is a well-established tool for investigating and comparing nucleic acids from di#erent species and for identifying characteristic gaps, insertions and dissimilarities....
The Frequency Distribution of Gene Family Sizes in Complete Genomes. (1998)
Martijn A. Huynen, Erik Van Nimwegen, Martijn Huynen
We compare the frequency distribution of gene family sizes in the complete genomes of six Bacteria (Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Mycoplasma genitalium, Mycoplasma...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1996)
Martijn Huynen, Peter Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1996)
Martijn Huynen, Peter F. Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
Neutral evolution of mutational robustness
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population’s limit distribution on the neutral network is solely...
Zheng, Zhi Ming, Huynen, Martijn, Baker, Carl C.
The bovine papillomavirus type 1 (BPV-1) exonic splicing suppressor (ESS) is juxtaposed immediately downstream of BPV-1 splicing enhancer 1 and negatively modulates selection of a suboptimal 3′...
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
STRING: a database of predicted functional associations between proteins
Von Mering, Christian, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
Huynen, Martijn, Snel, Berend, Lathe, Warren, Bork, Peer
Various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. The types of genomic context that they use are Type I: the...
Neutral evolution of mutational robustness
Van Nimwegen, Erik, Crutchfield, James P., Huynen, Martijn
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population’s limit distribution on the neutral network is solely...
Zheng, Zhi Ming, Huynen, Martijn, Baker, Carl C.
The bovine papillomavirus type 1 (BPV-1) exonic splicing suppressor (ESS) is juxtaposed immediately downstream of BPV-1 splicing enhancer 1 and negatively modulates selection of a suboptimal 3′...
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
STRING: a database of predicted functional associations between proteins
Von Mering, Christian, Huynen, Martijn, Jaeggi, Daniel, Schmidt, Steffen, Bork, Peer, Snel, Berend
Functional links between proteins can often be inferred from genomic associations between the genes that encode them: groups of genes that are required for the same function tend to show similar...
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
Huynen, Martijn, Snel, Berend, Lathe, Warren, Bork, Peer
Various new methods have been proposed to predict functional interactions between proteins based on the genomic context of their genes. The types of genomic context that they use are Type I: the...
Neutral Evolution of Mutational Robustness
Eric Van Nimwegen, James P. Crutchfield, Martijn Huynen
We introduce and analyze a general model of a population evolving over a network of selectively neutral genotypes. We show that the population's limit distribution on the neutral network is solely...
Assessing the Reliability of RNA folding Using Statistical Mechanics
Martijn Huynen, Robin Gutell, Danielle Konings
We have analyzed the base-pair probability distribution of 16S and 16S-like and 23S and 23S-like ribosomal RNAs of Archaea, Bacteria, chloroplasts, mitochondria and Eukarya, as predicted by the...
Evolutionary Dynamics of RNA and the Neutral Theory
Martijn Huynen, Peter Stadler, Walter Fontana
Understanding the relationship between genotype and phenotype is essential for understanding evolutionary dynamics. RNA is an extremely simple yet highly instructive case: both genotype (sequence)...