Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Genome Biology: Apr 1, 2009

A minireview by EBI's Paul Flicek checks in on Bowtie, a short-read aligner that's ultrafast and can align more than 25 million human genome reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Because DNA sequence data are coming in at record amounts, the "Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation," Flicek writes in the abstract.

In this paper, scientists made the first computational model of the budding yeast ubiquitin system to look at the entire system as a whole, especially the function and interaction of various parts. Among other things, they found there to be functional diversification of SUMO-dependent Ub-ligases and identified novel components of SCF (Skp1-cullin-F-box) -dependent complexes, receptors in the ERAD (endoplasmic reticulum associated degradation) system, and a key role for Sus1 in chromatin dynamics. They also show a "major impact of the Ub-system on large parts of the proteome via its interaction with the transcription regulatory network."

Work led by Scripps' Kelly Frazer and Olivier Harismendy and JCVI's Samuel Levy evaluated the current next-gen sequencing platforms for their performance in targeted sequencing for sequence-based association studies. They found that all three platforms have high sensitivity in generating greater than 95 percent of base calls when compared to Sanger results, and that at higher coverage depth, base calling errors are both systematic and depend on local sequence characteristics.

In collaboration with researchers at LBNL, scientists have mapped sub-networks in the EGFR-MAPK pathway in 30 different breast cancer cell lines, showing that PAK1 may be a marker for sensitivity to MEK inhibitors. Mapping genomic, transcriptional, and proteomic data onto a model of EGFR-MEK signaling comprised of 539 molecular states and 396 active state signaling rules, they were able to come up with a functional test for breast cancer cells lines against three MEK inhibitors. They found that cell lines overexpressing PAK1 are "significantly more sensitive to MEK inhibition as compared to those that express PAK1 at low levels."

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.