bogdan's blog

Sequence-specific reconstruction from fragmentary databases using seed sequences

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data - Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple se

OCTOPUS: improving topology prediction by two-track ANN-based scores and topological grammar

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar - Motivation: As -helical transmembrane proteins constitute roughly 25% of a typical genome and are vital parts of many essential biological processes, structural knowledge of these pr

Modeling promoter grammars with evolving hidden Markov models

Modeling promoter grammars with evolving hidden Markov models - Motivation: Describing and modeling biological features of eukaryotic promoters remains an important and challenging problem within computational biology.

On correcting the overestimation of the permutation-based false discovery rate estimator

On correcting the overestimation of the permutation-based false discovery rate estimator - Motivation: Recent attempts to account for multiple testing in the analysis of microarray data have focused on controlling the false discovery rate (FDR), which is defined as the expected percentage of the num

Predicting protein function from domain content

Predicting protein function from domain content - Motivation: Computational assignment of protein function may be the single most vital application of bioinformatics in the post-genome era.

Minimally invasive determination of mRNA concentration in single living bacteria

Minimally invasive determination of mRNA concentration in single living bacteria - Fluorescence correlation spectroscopy (FCS) has permitted the characterization of high concentrations of noncoding RNAs in a single living bacterium.

Inversing the natural hydrogen bonding rule to selectively amplify GC-rich ADAR-edited RNAs

Inversing the natural hydrogen bonding rule to selectively amplify GC-rich ADAR-edited RNAs - DNA complementarity is expressed by way of three hydrogen bonds for a G:C base pair and two for A:T. As a result, careful control of the denaturation temperature of PCR allows selective amplification of AT-rich alleles.

Single-molecule imaging of full protein synthesis by immobilized ribosomes

Single-molecule imaging of full protein synthesis by immobilized ribosomes - How folding of proteins is coupled to their synthesis remains poorly understood. Here, we apply single-molecule fluorescence imaging to full protein synthesis in vitro.

Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA

Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA - Fluorescent microscopy experiments show that when 2'-O-methyl-modified molecular beacons (MBs) are introduced into NIH/3T3 cells, they elicit a nonspecific signal in the nucleus.

Using inferred residue contacts to distinguish between correct and incorrect protein models

Using inferred residue contacts to distinguish between correct and incorrect protein models - Motivation: The de novo prediction of 3D protein structure is enjoying a period of dramatic improvements.