The evolution of domain-content in bacterial genomes (2008)
Molina Nacho, Van Nimwegen Erik
Abstract Background Across all sequenced bacterial genomes, the number of domains nc in different functional categories c scales as a power-law in the total number of domains n, i.e....
Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis Dimos, Van Nimwegen Erik, Hausser Jean, Zavolan Mihaela
Abstract Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast,...
Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis Dimos, Van Nimwegen Erik, Hausser Jean, Zavolan Mihaela
Finding regulatory elements and regulatory motifs: a general probabilistic framework (2007)
Abstract Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding...
A simple physical model predicts small exon length variations. (2006)
Chern Tzu-Ming, Van Nimwegen Erik, Kai Chikatoshi, Kawai Jun, Carninci Piero, Hayashizaki Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
SPA: a probabilistic algorithm for spliced alignment. (2006)
Van Nimwegen Erik, Paul Nicodeme, Sheridan Robert, Zavolan Mihaela
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
Identification of clustered microRNAs using an ab initio prediction method (2005)
Sewer Alain, Paul Nicodème, Landgraf Pablo, Aravin Alexei, Pfeffer Sébastien, Brownstein Michael, ...
Abstract Background MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds...