Characterization and potential functional significance of human-chimpanzee large INDEL variation.

Background: Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species.

Did natural selection for increased cognitive ability in humans lead to an elevated risk of cancer?

Despite the overall genetic similarity that exists between humans and chimpanzees, the species are phenotypically distinct. Among the most notable distinctions are differences in brain size and cognitive abilities. Previous studies have shown that significant differences in gene expression exist between the human and chimpanzee brain.

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.

Background: The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements encode gene regulatory functions. This fact has important evolutionary implications, since repetitive DNA is the most dynamic part of the genome.

Endogenous retroviruses of the chicken genome.

We analyzed the chicken (Gallus gallus) genome sequence to search for previously uncharacterized endogenous retrovirus (ERV) sequences using ab initio and combined evidence approaches. We discovered 11 novel families of ERVs that occupy more than 21 million base pairs, approximately 2%, of the chicken genome. These novel families include a number of recently active full-length elements possessing identical long terminal repeats (LTRs) as well as intact gag and pol open reading frames.

Exonization of the LTR transposable elements in human genome.

Background: Retrotransposons have been shown to contribute to evolution of both structure and regulation of protein coding genes. It has been postulated that the primary mechanism by which retrotransposons contribute to structural gene evolution is through insertion into an intron or a gene flanking region, and subsequent incorporation into an exon.

Results: We found that Long Terminal Repeat (LTR) retrotransposons are associated with 1,057 human genes (5.

Identification of candidate methylation-responsive genes in ovarian cancer.

Background: Aberrant methylation of gene promoter regions has been linked to changes in gene expression in cancer development and progression. Genes associated with CpG islands (CGIs) are especially prone to methylation, but not all CGI-associated genes display changes in methylation patterns in cancers.

Results: In order to identify genes subject to regulation by methylation, we conducted gene expression profile analyses of an ovarian cancer cell line (OVCAR-3) before and after treatment with the demethylating agent 5-aza-deoxycytidine (5-aza-dC).

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

Background: Retrotransposons, the most abundant and widespread class of eukaryotic transposable elements, are believed to play a significant role in mutation and disease and to have contributed significantly to the evolution of genome structure and function. The recent sequencing of the chimpanzee genome is providing an unprecedented opportunity to study the functional significance of these elements in two closely related primate species and to better evaluate their role in primate evolution.

Results: We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified.

Investigation into biomedical literature classification using support vector machines.

Specific topic search in the PubMed Database, one of the most important information resources for scientific community, presents a big challenge to the users. The researcher typically formulates boolean queries followed by scanning the retrieved records for relevance, which is very time consuming and error prone. We applied Support Vector Machines (SVM) for automatic retrieval of PubMed articles related to Human genome epidemiological research at CDC (Center for disease Control and Prevention).