bogdan's blog

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization - DNA microarray measurements are susceptible to error caused by non-specific hybridization between a probe and a target (cross-hybridization), or between two targets (bulk-hybridization).

A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides

A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides - We have determined diversities exceeding 1012 different sequences in an annealing and melting assay using synthetic randomized oligonucleotides as a standard.

Validation of double digest selective label database for sequenced prokaryotic genomes

Validation of double digest selective label database for sequenced prokaryotic genomes - Summary: A database for simulation of double digest selective label (DDSL) typing technique has been created and validated against a sequenced strain (Salmonella enterica serovar Typhimurium strain LT2).

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data - Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage.

PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches

Fortunately, R package developers finally got to the problem of parallel computations. An excerpt (below) from a recent Bioinformatics article is a good illustration.

webMGR: an online tool for the multiple genome rearrangement problem

webMGR: an online tool for the multiple genome rearrangement problem - Summary: The algorithm MGR enables the reconstruction of rearrangement phylogenies based on gene or synteny block order in multiple genomes.

Tmod: toolbox of motif discovery

Tmod: toolbox of motif discovery - Summary: Motif discovery is an important topic in computational transcriptional regulation studies.

Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes

Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes - We present a new computational method for solving a classical problem, the identification problem of cis-regulatory motifs in a given set of promoter sequences, based on one key new idea.

MATICCE: mapping transitions in continuous character evolution

MATICCE: mapping transitions in continuous character evolution - Summary: MATICCE is a new software package in the R language for mapping phylogenetic transitions in organismal traits that have continuous distributions.