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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Feb 1, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The recommender, Anuj Kumar, is an assistant professor in molecular, cellular, and developmental biology at the Universityof Michigan. This installment was reported and written by Meredith Salisbury, Genome Technology editor.

 

For a complete list of recommended papers, read Genome Technology, a GenomeWeb News sister publication.


"In silico simulation of biological network dynamics," Lukasz Salwinski and David Eisenberg. Nature Biotechnology. 2004; 22 (9): 1017-1019.

 

"In this paper, the authors describe an approach to simulating biological networks using field programmable gate arrays, whose parallel architecture allows for more realistic simulation of the reaction steps in biological networks, according to the paper's abstract. They say that in the past such large-scale simulations have been limited both by data availability and by the vast computational demands for the stochastic algorithms needed to model the networks.

 

"'With the rise of various -omics approaches, the limitation of experimental data is being lifted, but the computational demands remain staggering for simulating networks of thousands of reactions involving thousands of reactants,' the authors note. 'The problem stems from the sequential nature of microprocessor architecture and the highly parallel nature of biological systems, with the result that simulation times become prohibitively long.' The authors say using FPGAs can improve simulation run times by 'at least an order of magnitude' over what conventional microprocessors can achieve."

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.