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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Mar 15, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The recommender, Toshimori Kitami, is a graduate student in the department of genetics at CaseWestern ReserveUniversity.

 

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


Dynamics of cellular level function and regulation derived from murine expression array data. de Bivort B, Huang S, Bar-Yam Y. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51)17687-17692.

 

In contrast to most experimental work investigating regulatory mechanisms in small networks of genes, Yaneer Bar-Yam at Harvard University and his co-authors chose a larger-scale study in an effort to observe the cumulative effects of all gene interactions in terms of cellular-level function. By organizing groups of genes into large groups with related behaviors, called megamodules, the authors were able to determine the effective aggregate regulatory influences among 12 major gene groups in murine B lymphocytes over a variety of time steps, as they write in the abstract.

 

Applying systems biology to humans and mice is typically slow and expensive, but Bar-Yam and his co-authors overcome cost and complexity issues by reducing complex data into smaller numbers of profiles and identifying the interactions between these profiles, says Toshimori Kitami, a biologist at CaseWestern ReserveUniversity. While this method may omit some details, it provides a stepping ground for more feasible systems biology research in higher eukaryotes, Kitami adds.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

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EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.