FACIL: Fast and Accurate Genetic Code Inference and Logo

Motivation: The intensification of DNA sequencing will increasingly unveil uncharacterized species with potential alternative genetic codes. A total of 0.65% of the DNA sequences currently in Genbank encode their proteins with a variant genetic code, and these exceptions occur in many unrelated taxa. Results: We introduce FACIL (Fast and Accurate genetic Code Inference and Logo), a fast and reliable tool to evaluate nucleic acid sequences for their genetic code that detects alternative codes even in species distantly related to known organisms. To illustrate this, we apply FACIL to a set of mitochondrial genomic contigs of Globobulimina pseudospinescens. This foraminifer does not have any sequenced close relative in the databases, yet we infer its alternative genetic code with high confidence values. Results are intuitively visualized in a Genetic Code Logo

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

The molecular mechanisms underlying transcriptional regulation in apicomplexan parasites remain poorly understood. Recently, the Apicomplexan AP2 (ApiAP2) family of DNA binding proteins was identified as a major class of transcriptional regulators that are found across all Apicomplexa. To gain insight into the regulatory role of these proteins in the malaria parasite, we have comprehensively surveyed the DNA-binding specificities of all 27 members of the ApiAP2 protein family from Plasmodium falciparum revealing unique binding preferences for the majority of these DNA binding proteins. In addition to high affinity primary motif interactions, we also observe interactions with secondary motifs. The ability of a number of ApiAP2 proteins to bind multiple, distinct motifs significantly increases the potential complexity of the transcriptional regulatory networks governed by the ApiAP2 family. Using these newly identified sequence motifs, we infer the trans-factors associated with previously reported plasmodial cis-elements and provide evidence that ApiAP2 proteins modulate key regulatory decisions at all stages of parasite development. Our results offer a detailed view of ApiAP2 DNA binding specificity and take the first step toward inferring comprehensive gene regulatory networks for P. falciparum

Parameter Estimation in Large Causal Models

Contains fulltext : 60099.pdf (preprint version ) (Open Access

Symmetric Causal Independence Models for Classification

Contains fulltext : 35323.pdf (preprint version ) (Open Access

Exploring the Noisy Threshold Function in Designing Bayesian Networks

Contains fulltext : 32495.pdf (preprint version ) (Open Access

Using symmetric causal independence models to predict gene expression from sequence data

Contains fulltext : 36663.pdf (preprint version ) (Open Access

Noisy Threshold Functions for Modelling Causal Independence in Bayesian Networks

Contains fulltext : 35578.pdf (preprint version ) (Open Access)19 p p

Symmetric causal independence models

Contains fulltext : 65549_symmcainm.pdf (publisher's version ) (Open Access)Radboud Universiteit Nijmegen, 19 januari 2009Promotor : Heskes, T.M.151 p