Prediction of effective genome size in metagenomic samples (2007)
Raes, Jeroen, Korbel, Jan O, Lercher, Martin J, Von Mering, Christian, Bork, Peer
Abstract We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses)...
Casneuf, Tineke, De Bodt, Stefanie, Raes, Jeroen, Maere, Steven, Van De Peer, Yves
Abstract Background Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide...
Investigating ancient duplication events in the Arabidopsis genome (2003)
Jeroen Raes, Klaas Vandepoele, Cedric Simillion, Yvan Saeys, Yves Van Peer
The complete genomic analysis of Arabidopsis thaliana has shown that a major fraction of the genome consists of paralogous genes that probably originated through one or more ancient large-scale gene...
Transcriptome analysis during cell division in plants
Breyne, Peter, Dreesen, Rozemarijn, Vandepoele, Klaas, De Veylder, Lieven, Van Breusegem, Frank, Callewaert, Lindy, ...
Using synchronized tobacco Bright Yellow-2 cells and cDNA-amplified fragment length polymorphism-based genomewide expression analysis, we built a comprehensive collection of plant cell...
Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis
Vandepoele, Klaas, Raes, Jeroen, De Veylder, Lieven, Rouzé, Pierre, Rombauts, Stephane, Inzé, Dirk
Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was...
Vandepoele, Klaas, Saeys, Yvan, Simillion, Cedric, Raes, Jeroen, Van De Peer, Yves
It is expected that one of the merits of comparative genomics lies in the transfer of structural and functional information from one genome to another. This is based on the observation that, although...
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w]
Raes, Jeroen, Rohde, Antje, Christensen, Jørgen Holst, Van De Peer, Yves, Boerjan, Wout
Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants,...
Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation...
Modeling gene and genome duplications in eukaryotes
Maere, Steven, De Bodt, Stefanie, Raes, Jeroen, Casneuf, Tineke, Van Montagu, Marc, Kuiper, Martin, ...
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the...
Casneuf, Tineke, De Bodt, Stefanie, Raes, Jeroen, Maere, Steven, Van De Peer, Yves
Analysis of expression data of duplicated genes in Arabidopsis thaliana shows that the mode of duplication, the time since duplication and the function of the duplicated genes play a role in the...
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
REHWINKEL, JAN, LETUNIC, IVICA, RAES, JEROEN, BORK, PEER, IZAURRALDE, ELISA
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not...
Transcriptome analysis during cell division in plants
Breyne, Peter, Dreesen, Rozemarijn, Vandepoele, Klaas, De Veylder, Lieven, Van Breusegem, Frank, Callewaert, Lindy, ...
Using synchronized tobacco Bright Yellow-2 cells and cDNA-amplified fragment length polymorphism-based genomewide expression analysis, we built a comprehensive collection of plant cell...
Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis
Vandepoele, Klaas, Raes, Jeroen, De Veylder, Lieven, Rouzé, Pierre, Rombauts, Stephane, Inzé, Dirk
Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was...
Vandepoele, Klaas, Saeys, Yvan, Simillion, Cedric, Raes, Jeroen, Van De Peer, Yves
It is expected that one of the merits of comparative genomics lies in the transfer of structural and functional information from one genome to another. This is based on the observation that, although...
Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis1[w]
Raes, Jeroen, Rohde, Antje, Christensen, Jørgen Holst, Van De Peer, Yves, Boerjan, Wout
Lignin, one of the most abundant terrestrial biopolymers, is indispensable for plant structure and defense. With the availability of the full genome sequence, large collections of insertion mutants,...
Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, ...
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation...
Modeling gene and genome duplications in eukaryotes
Maere, Steven, De Bodt, Stefanie, Raes, Jeroen, Casneuf, Tineke, Van Montagu, Marc, Kuiper, Martin, ...
Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the...
Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
REHWINKEL, JAN, LETUNIC, IVICA, RAES, JEROEN, BORK, PEER, IZAURRALDE, ELISA
Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that degrades mRNAs containing nonsense codons, and regulates the expression of naturally occurring transcripts. While NMD is not...
Casneuf, Tineke, De Bodt, Stefanie, Raes, Jeroen, Maere, Steven, Van De Peer, Yves
Analysis of expression data of duplicated genes in Arabidopsis thaliana shows that the mode of duplication, the time since duplication and the function of the duplicated genes play a role in the...
Cnops, Gerda, Neyt, Pia, Raes, Jeroen, Petrarulo, Marica, Nelissen, Hilde, Malenica, Nenad, ...
In multicellular organisms, patterning is a process that generates axes in the primary body plan, creates domains upon organ formation, and finally leads to differentiation into tissues and cell...
Prediction of effective genome size in metagenomic samples
Raes, Jeroen, Korbel, Jan O, Lercher, Martin J, Von Mering, Christian, Bork, Peer
A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads.
A Molecular Study of Microbe Transfer between Distant Environments
Hooper, Sean D., Raes, Jeroen, Foerstner, Konrad U., Harrington, Eoghan D., Dalevi, Daniel, Bork, Peer
Kunin, Victor, Raes, Jeroen, Harris, J Kirk, Spear, John R, Walker, Jeffrey J, Ivanova, Natalia, ...
To investigate the extent of genetic stratification in structured microbial communities, we compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from...