An efficient method to identify differentially expressed genes in microarray experiments

An efficient method to identify differentially expressed genes in microarray experiments - Motivation: Microarray experiments typically analyze thousands to tens of thousands of genes from small numbers of biological replicates.

Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification

Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification - Motivation: Modern high-throughput sequencing technologies enable the simultaneous analysis of organisms in an environment.

Retroviral promoters in the human genome

Retroviral promoters in the human genome - Motivation: Endogenous retrovirus (ERV) elements have been shown to contribute promoter sequences that can initiate transcription of adjacent human genes.

Predicting failure rate of PCR in large genomes

Predicting failure rate of PCR in large genomes - We have developed statistical models for estimating the failure rate of polymerase chain reaction (PCR) primers using 236 primer sequence-related factors. The model involved 1314 primer pairs and is based on more than 80 000 PCR experiments.

POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors

POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors - Motivation: At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences.

The effectiveness of position- and composition-specific gap costs for protein similarity searches

The effectiveness of position- and composition-specific gap costs for protein similarity searches - Motivation: The flexibility in gap cost enjoyed by hidden Markov models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs).

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles - Motivation: More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required.

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis - The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution.