Conserved co-expression for candidate disease gene prioritization (2008)
Oti, Martin, Van Reeuwijk, Jeroen, Huynen, Martijn A, Brunner, Han G
Abstract Background Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The...
The [FeFe] hydrogenase of Nyctotherus ovalishas a chimeric origin (2007)
Boxma, Brigitte, Ricard, Guenola, Van Hoek, Angela HAM, Severing, Edouard, Van Der Staay, Georg WM, ...
Abstract Background The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an...
Toni Gabaldón, Martijn A. Huynen
Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the...
Van Noort, Vera, Snel, Berend, Huynen, Martijn A
Abstract Background In the post-genomic era various functional genomics, proteomics and computational techniques have been developed to elucidate the protein interaction network. While some of these...
Toni Gabaldón, Martijn A. Huynen
Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the...
Datson, Nicole A, Morsink, Maarten C, Atanasova, Srebrena, Armstrong, Victor W, Zischler, Hans, Schlumbohm, Christina, ...
Abstract Background The common marmoset monkey ( Callithrix jacchus ), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in...
Orthology prediction at scalable resolution by phylogenetic tree analysis (2007)
Van Der Heijden, René TJM, Snel, Berend, Van Noort, Vera, Huynen, Martijn A
Abstract Background Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an...
Datson, Nicole A., Morsink, Maarten C., Atanasova, Srebrena, Armstrong, Victor W., Zischler, Hans, Schlumbohm, Christina, ...
Background: The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in...
Benchmarking ortholog identification methods using functional genomics data (2006)
Hulsen, Tim, Huynen, Martijn A, De Vlieg, Jacob, Groenen, Peter MA
Abstract Background The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze...
Origin and evolution of the peroxisomal proteome (2006)
Gabaldón, Toni, Snel, Berend, Zimmeren, Frank Van, Hemrika, Wieger, Tabak, Henk, Huynen, Martijn A
Abstract Background Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import...
Ricard, Guénola, McEwan, Neil R, Dutilh, Bas E, Jouany, Jean-Pierre, Macheboeuf, Didier, Mitsumori, Makoto, ...
Abstract Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using...
Dutilh, Bas E, Huynen, Martijn A, Snel, Berend
Abstract Background The massive scale of microarray derived gene expression data allows for a global view of cellular function. Thus far, comparative studies of gene expression between species have...
An anaerobic mitochondrion that produces hydrogen (2005)
Boxma, Brigitte, Graaf, Rob M. De, Alen, Theo A. Van, Ricard, Guenola, Gabaldón, Toni, ...
Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these...
Automatic detection of conserved RNA structure elements in complete RNA virus genomes (2000)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Base Pairing Probabilities in a Complete HIV-1 RNA (1998)
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers (1998)
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes (1998)
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
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...
Martijn A. Huynen, Erik Van Nimwegen
We compare the frequency distribution of gene family sizes in the complete genomes of five Bacteria (Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae and...
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1995)
Martijn A. Huynen, Peter F. Stadler
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...
Base Pairing Probabilities in a Complete HIV-1 RNA (1995)
Martijn A. Huynen, Alan Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
Base Pairing Probabilities in a Complete HIV-1 RNA (1995)
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
Base Pairing Probabilities in a Complete HIV-1 RNA (1995)
Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler, Mailing Address, Martijn A. Huynen
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (McCaskill, 1990). By...
Base Pairing Probabilities in a Complete HIV-1 RNA (1995)
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base-pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill [33]. By analyzing...
Huynen, Martijn A., Bork, Peer
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to...
Ricard, Guénola, McEwan, Neil R, Dutilh, Bas E, Jouany, Jean-Pierre, Macheboeuf, Didier, Mitsumori, Makoto, ...
The identification of functional modules from the genomic association of genes
Snel, Berend, Bork, Peer, Huynen, Martijn A.
By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of...
Quantifying Modularity in the Evolution of Biomolecular Systems
Snel, Berend, Huynen, Martijn A.
Functional modules are considered the primary building blocks of biomolecular systems. Here we study to what extent functional modules behave cohesively across genomes:That is, are functional modules...
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
Snel, Berend, Van Noort, Vera, Huynen, Martijn A.
Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...
Von Mering, Christian, Jensen, Lars J., Snel, Berend, Hooper, Sean D., Krupp, Markus, Foglierini, Mathilde, ...
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical...
Correlation between sequence conservation and the genomic context after gene duplication
Notebaart, Richard A., Huynen, Martijn A., Teusink, Bas, Siezen, Roland J., Snel, Berend
A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze...
Van Noort, Vera, Snel, Berend, Huynen, Martijn A
We investigated the gene coexpression network in Saccharomyces cerevisiae, in which genes are linked when they are coregulated. This network is shown to have a scale-free, small-world architecture....
Correlation between sequence conservation and the genomic context after gene duplication
Notebaart, Richard A., Huynen, Martijn A., Teusink, Bas, Siezen, Roland J., Snel, Berend
Origin and evolution of the peroxisomal proteome
Gabaldón, Toni, Snel, Berend, Zimmeren, Frank Van, Hemrika, Wieger, Tabak, Henk, Huynen, Martijn A
Benchmarking ortholog identification methods using functional genomics data
Hulsen, Tim, Huynen, Martijn A, De Vlieg, Jacob, Groenen, Peter MA
A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.
Huynen, Martijn A., Bork, Peer
The determination of complete genome sequences provides us with an opportunity to describe and analyze evolution at the comprehensive level of genomes. Here we compare nine genomes with respect to...
The identification of functional modules from the genomic association of genes
Snel, Berend, Bork, Peer, Huynen, Martijn A.
By combining the pairwise interactions between proteins, as predicted by the conserved co-occurrence of their genes in operons, we obtain protein interaction networks. Here we study the properties of...
Quantifying Modularity in the Evolution of Biomolecular Systems
Snel, Berend, Huynen, Martijn A.
Functional modules are considered the primary building blocks of biomolecular systems. Here we study to what extent functional modules behave cohesively across genomes:That is, are functional modules...
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes
Snel, Berend, Van Noort, Vera, Huynen, Martijn A.
Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly...
Ettema, Thijs J. G., Makarova, Kira S., Jellema, Gera L., Gierman, Hinco J., Koonin, Eugene V., Huynen, Martijn A., ...
Despite the fact that phosphoenolpyruvate carboxylase (PEPC) activity has been measured and in some cases even purified from some Archaea, the gene responsible for this activity has not been...
Von Mering, Christian, Jensen, Lars J., Snel, Berend, Hooper, Sean D., Krupp, Markus, Foglierini, Mathilde, ...
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical...
Correlation between sequence conservation and the genomic context after gene duplication
Notebaart, Richard A., Huynen, Martijn A., Teusink, Bas, Siezen, Roland J., Snel, Berend
A key complication in comparative genomics for reliable gene function prediction is the existence of duplicated genes. To study the effect of gene duplication on function prediction, we analyze...
Van Noort, Vera, Snel, Berend, Huynen, Martijn A
We investigated the gene coexpression network in Saccharomyces cerevisiae, in which genes are linked when they are coregulated. This network is shown to have a scale-free, small-world architecture....
Correlation between sequence conservation and the genomic context after gene duplication
Notebaart, Richard A., Huynen, Martijn A., Teusink, Bas, Siezen, Roland J., Snel, Berend
Ricard, Guénola, McEwan, Neil R, Dutilh, Bas E, Jouany, Jean-Pierre, Macheboeuf, Didier, Mitsumori, Makoto, ...
Origin and evolution of the peroxisomal proteome
Gabaldón, Toni, Snel, Berend, Zimmeren, Frank Van, Hemrika, Wieger, Tabak, Henk, Huynen, Martijn A
Benchmarking ortholog identification methods using functional genomics data
Hulsen, Tim, Huynen, Martijn A, De Vlieg, Jacob, Groenen, Peter MA
A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.
Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, ...
We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and...
Power Laws in the Size Distribution of Gene Families in Complete Genomes: Biological Interpretations
Martijn A. Huynen, Erik Van Nimwegen
We compare the frequency distribution of gene family sizes in the complete genomes of five Bacteria ({\it Escherichia coli, Haemophilus influenzae, Mycoplasma genitalium, Mycoplasma pneumoniae,} and...
Orthology prediction at scalable resolution by phylogenetic tree analysis
Van Der Heijden, René TJM, Snel, Berend, Van Noort, Vera, Huynen, Martijn A
Datson, Nicole A, Morsink, Maarten C, Atanasova, Srebrena, Armstrong, Victor W, Zischler, Hans, Schlumbohm, Christina, ...
Reconstructing the evolution of the mitochondrial ribosomal proteome
Smits, Paulien, Smeitink, Jan A. M., Van Den Heuvel, Lambert P., Huynen, Martijn A., Ettema, Thijs J. G.
For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using...
Gabaldón, Toni, Huynen, Martijn A
Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the...
The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin
Boxma, Brigitte, Ricard, Guenola, Van Hoek, Angela HAM, Severing, Edouard, Van Der Staay, Georg WM, ...
Conserved co-expression for candidate disease gene prioritization
Oti, Martin, Van Reeuwijk, Jeroen, Huynen, Martijn A, Brunner, Han G
Van Noort, Vera, Snel, Berend, Huynen, Martijn A
By combining different types of large datasets that give evidence for protein-interactions, qualitative labels on the predicted protein interaction network of S. cerevisiae could be inferred,...
Signature, a web server for taxonomic characterization of sequence samples using signature genes
Dutilh, Bas E., He, Ying, Hekkelman, Maarten L., Huynen, Martijn A.
Signature genes are genes that are unique to a taxonomic clade and are common within it. They contain a wealth of information about clade-specific processes and hold a strong evolutionary signal that...
Signature Genes as a Phylogenomic Tool
Dutilh, Bas E., Snel, Berend, Ettema, Thijs J. G., Huynen, Martijn A.
Gene content has been shown to contain a strong phylogenetic signal, yet its usage for phylogenetic questions is hampered by horizontal gene transfer and parallel gene loss and until now required...
RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes
Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz
Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more...
Base Pairing Probabilities in a Complete HIV-1 RNA
Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, Peter F. Stadler
We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by MasCaskill (1990). By analyzing...
Lasonder, Edwin, Janse, Chris J., Van Gemert, Geert-Jan, Mair, Gunnar R., Vermunt, Adriaan M. W., Douradinha, Bruno G., ...
Plasmodium falciparum sporozoites that develop and mature inside an Anopheles mosquito initiate a malaria infection in humans. Here we report the first proteomic comparison of different parasite...