bogdan's blog

DensiTree: making sense of sets of phylogenetic trees

DensiTree: making sense of sets of phylogenetic trees - Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful m

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures - Summary: Multiple sequence alignment is an important tool in bioinformatics.

Tuning and controlling gene expression noise in synthetic gene networks

Tuning and controlling gene expression noise in synthetic gene networks - Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise.

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations - Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studie

ArchSchema: a tool for interactive graphing of related Pfam domain architectures

ArchSchema: a tool for interactive graphing of related Pfam domain architectures - Summary: ArchSchema is a Java Web Start application that generates a dynamic 2D network of related Pfam domain architectures.

HALO, a Java framework for precise transcript half-life determination

HALO--a Java framework for precise transcript half-life determination - Summary: Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives.

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data - Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision an

CoP: a database for characterizing co-expressed gene modules with biological information in plants

CoP: a database for characterizing co-expressed gene modules with biological information in plants - Summary: Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces - Protein–protein interactions (PPIs) are ubiquitous in Biology, and thus offer an enormous potential for the discovery of novel therapeutics.

Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities - Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing.