Bayesian learning of biological pathways on genomic data assimilation

Bayesian learning of biological pathways on genomic data assimilation - Motivation: Mathematical modeling and simulation, based on biochemical rate equations, provide us a rigorous tool for unraveling complex mechanisms of biological pathways.

Gene set enrichment analysis using linear models and diagnostics

Gene set enrichment analysis using linear models and diagnostics - Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques.

Phylogenetic distances are encoded in networks of interacting pathways

Phylogenetic distances are encoded in networks of interacting pathways - Motivation: Although metabolic reactions are unquestionably shaped by evolutionary processes, the degree to which the overall structure and complexity of their interconnections are linked to the phylogeny of species has not bee

Genome annotation in the presence of insertional RNA editing

Genome annotation in the presence of insertional RNA editing - Motivation: Insertional RNA editing renders gene prediction very difficult compared to organisms without such RNA editing.

Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon

Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon - We present a simple and novel assay—employing a universal molecular beacon (MB) in the presence of Hg2+—for the detection of single nucleotide polymorphisms (SNPs) based on Hg2+–DNA c

Direct mapping and alignment of protein sequences onto genomic sequence

Direct mapping and alignment of protein sequences onto genomic sequence - Motivation: Finding protein-coding genes in a newly determined genomic sequence is the first step toward understanding the content written in the genome.

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification

INTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification - Motivation: Identification of functionally important residues in proteins plays a significant role in biological discovery.

Prioritization of candidate cancer genes--an aid to oncogenomic studies

Prioritization of candidate cancer genes--an aid to oncogenomic studies - The development of techniques for oncogenomic analyses such as array comparative genomic hybridization, messenger RNA expression arrays and mutational screens have come to the fore in modern cancer research.

Seeder: discriminative seeding DNA motif discovery

Seeder: discriminative seeding DNA motif discovery - Motivation: The computational identification of transcription factor binding sites is a major challenge in bioinformatics and an important complement to experimental approaches.

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison - Motivation: Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information.