BioMed

An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems - Motivation: Distribution analysis is one of the most basic forms of statistical analysis.

A statistical framework for protein quantitation in bottom-up MS-based proteomics - Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures.

Efficient silencing of gene expression with modular trimeric Pol II expression cassettes comprising microRNA shuttles - Expressed polycistronic microRNA (miR) cassettes have useful properties that can be utilized for RNA interference (RNAi)-based gene silencing.

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships - Transcriptional regulation is mediated by the collective binding of proteins called transcription factors to cis-regulatory elements.

Visual and statistical comparison of metagenomes - Background: Metagenomics is the study of the genomic content of an environmental sample of microbes.

UTGB toolkit for personalized genome browsers - The advent of high-throughput DNA sequencers has increased the pace of collecting enormous amounts of genomic information, yielding billions of nucleotides on a weekly basis.

CORAL: aligning conserved core regions across domain families - Motivation: Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences - Motivation: The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemic

Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains - Motivation: We have previously demonstrated that proteins may be aligned not only by sequence or structural homology, but also using their dynamical properties.

p53-dependent antiviral RNA-interference facilitates tumor-selective viral replication - RNA-interference (RNAi) is a potent tool for specific gene silencing.