bogdan's blog

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements - Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment.

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements - Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

Scaffolding and validation of bacterial genome assemblies using optical restriction maps - Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest.

A note on the false discovery rate and inconsistent comparisons between experiments

A note on the false discovery rate and inconsistent comparisons between experiments - Motivation: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies.

Exalign: a new method for comparative analysis of exon-intron gene structures

Exalign: a new method for comparative analysis of exon-intron gene structures - The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences.

Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA

Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA - The time course of polysome formation was studied in a long-term wheat germ cell-free translation system using sedimentation and electron microscopy techniques.

Exalign: a new method for comparative analysis of exon-intron gene structures

Exalign: a new method for comparative analysis of exon-intron gene structures - The evolution of genes is usually studied and reconstructed at the sequence level, that is, by comparing and aligning their genomic, transcript or protein sequences.

Detecting cis-regulatory binding sites for cooperatively binding proteins

Detecting cis-regulatory binding sites for cooperatively binding proteins - Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices.

A dual-tag microarray platform for high-performance nucleic acid and protein analyses

A dual-tag microarray platform for high-performance nucleic acid and protein analyses - DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve spec