Horizontal gene transfer and recombination play a major role in microbial evolution and have been detected in diverse groups, including many of medical relevance such as HIV and dengue virus. In the absence of mechanistic barriers, the evolutionary success of a particular recombination event is determined by whether the recombinant genotype suffers a fitness cost through the disruption of favor...

-The understanding of the speciation process can best be achieved by a knowledge of the genic differences between two closely related species and the correlation of such differences with the characteristics which demarcate the two species. D. persimilis and D. pseudoobscura are two sibling species differing from each other in morphology, ecological preferences, and behavior, and no hybrids exis...

HE present study is based on the analysis of the recessive mutator gene T (MAMPELL 1945). This mutator is located to the right of cinnabar in the second chromosome of Drosophila pseudoobscura, race B (D. persimilis Dobzhansky and Epling). When males are homozygous for this gene, mutations (usually belonging to the “Minute” phenotype) are induced in those males as well as in their offspring, no ...

We describe here the context of the LLL challenge of Genic Interaction extraction, the background of its organization and the data sets. We discuss then the results of the participating systems.

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid asse...

We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequentl...

While exome sequencing is readily amenable to single-nucleotide variant discovery, the sparse and nonuniform nature of the exome capture reaction has hindered exome-based detection and characterization of genic copy number variation. We developed a novel method using singular value decomposition (SVD) normalization to discover rare genic copy number variants (CNVs) as well as genotype copy numb...

Maize exhibits a high degree of intraspecific variation in genome structure, most of which is due to intergenic retrotransposon polymorphsisms among unrelated varieties. For example, a comparison of eight haplotypes of the bronze1 (bz1) locus, which contains numerous retrotransposons, showed that sequence similarity between any two haplotypes ranged from 25 to 84% (Wang and Dooner, 2006). In th...

We explore here the application of Gleaner, an Inductive Logic Programming approach to learning in highly-skewed domains, to the Learning Language in Logic 2005 biomedical information-extraction challenge task. We create and describe a large number of background knowledge predicates suited for this task. We find that Gleaner outperforms standard Aleph theories with respect to recall and that ad...