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The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations 27 Aug 2013 | 11:48 am
Motivation: In the noisy cellular environment, stochastic fluctuations at the molecular level manifest as cell–cell variability at the population level that is quantifiable using high-throughput singl...
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs 27 Aug 2013 | 11:48 am
Motivation: Alternative splicing and other processes that allow for different transcripts to be derived from the same gene are significant forces in the eukaryotic cell. RNA-Seq is a promising technol...
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference 27 Aug 2013 | 11:48 am
Motivation: Many human genes express multiple transcript isoforms through alternative splicing, which greatly increases diversity of protein function. Although RNA sequencing (RNA-Seq) technologies ha...
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server 27 Aug 2013 | 11:48 am
Motivation: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular st...
Naive binning improves phylogenomic analyses 27 Aug 2013 | 11:48 am
Motivation: Species tree estimation in the presence of incomplete lineage sorting (ILS) is a major challenge for phylogenomic analysis. Although many methods have been developed for this problem, litt...
LNETWORK: an efficient and effective method for constructing phylogenetic networks 27 Aug 2013 | 11:48 am
Motivation: The evolutionary history of species is traditionally represented with a rooted phylogenetic tree. Each tree comprises a set of clusters, i.e. subsets of the species that are descended from...
An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale 27 Aug 2013 | 11:48 am
Motivation: We present an integrated toolkit, BoBro2.0, for prediction and analysis of cis-regulatory motifs. This toolkit can (i) reliably identify statistically significant cis-regulatory motifs at ...
Scalable metagenomic taxonomy classification using a reference genome database 27 Aug 2013 | 11:48 am
Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prio...
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data 27 Aug 2013 | 11:48 am
Motivation: Haplotypes, defined as the sequence of alleles on one chromosome, are crucial for many genetic analyses. As experimental determination of haplotypes is extremely expensive, haplotypes are ...
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes 27 Aug 2013 | 11:48 am
Motivation: Gain-of-function mutations often cluster in specific protein regions, a signal that those mutations provide an adaptive advantage to cancer cells and consequently are positively selected d...
