Q&A: Nicola Ancona Compares Gene Set Enrichment Methods Head-to-Head

October 01, 2009

A number of methods are available for gene set enrichment analysis, but how should researchers determine which one to use in their studies?

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In this issue of BioInform

Young Investigator Profile

Elena Ezhkova

Postdoctoral Associate
Rockefeller University

Studying Stem Cells with Skin

Elena Ezhkova is using skin as a model system to analyze the processes behind stem cell differentiation. Specifically, Ezhkova is focused on understanding the role of epigenetic regulators, such as chromogen modifications, chromogen modelers, and DNA methylation enzymes, and how they control the commitment of stem cells to undergo differentiation or to self-renew. In addition, she is also looking at the impact of this alteration on the expression of epigenetic regulators of stem cell control and tissue development.
Blog

OpenCL + Python = CLyther

A new Python tool for OpenCL similar to Cython for C is coming down the pike.

March 12, 2010

The System Isn't Broken

Bloggers say researchers looking for NIH funding should quit complaining about the system and find a way to work with it.

March 12, 2010

Mixing Genes and Dieting

NPR's health blog takes a second look at a study linking people's genes to diet success.

March 12, 2010

'Impressed, but Puzzled'

Derek Lowe at In the Pipeline blogs about Rob Carlson's recent post on a garage lab in the Silicon Valley.

March 12, 2010
Papers of Note

Family-Based Whole-Genome Sequencing Reveals Candidates for Mendelian Disease
Roach, Glusman et al., Science
Researchers at the Institute for Systems Biology and Complete Genomics have identified candidate disease-causing genes for Miller syndrome and ciliary dyskinesia, both Mendelian disorders. They sequenced the genomes of a family of four, allowing them to determine recombination sites with precision (at 99.999 percent accuracy) and identify rare single-nucleotide polymorphisms. "Our results demonstrate the unique value of complete genome sequencing in families," the authors write.

Resequencing the Domestic Chicken Genome
Rubin, Zody et al., Nature
An international research team reports their resequencing efforts of the Gallus gallus domesticus — domestic chicken — genome. Using a massively parallel approach, they sequenced the chicken genome to 44.5-fold coverage and identified candidate mutations that may have played a role in the animal's domestication. The authors also suggest their results imply "the importance of the domestic chicken as a model organism for biomedical research."
People on the Move

Wellcome Trust Sanger Institute Professor Leena Peltonen-Palotie died this week of cancer at her home in Finland, according to the Sanger Institute. Peltonen-Palotie was head of human genetics at Wellcome Trust, and she held appointments at the Broad Institute at MIT and Harvard and the Institute for Molecular Medicine Finland.

Three leaders from the Human Genome Project — David Botstein, Francis Collins, and Eric Lander — have been named co-winners of the 2010 Albany Medical Center Prize in Medicine and Biomedical Research, which carries with it a purse of $500,000.

Adrian Dillon will resign from his job as executive VP of finance and administration and CFO of Agilent Technologies to become chief financial and administrative officer at Skype. He will be replaced at the beginning of April by Didier Hirsch, who currently is VP of corporate controllership and taxes and who will serve as acting CFO.
Upcoming Events

Conferences, Meetings & Deadlines

NHGRI Advanced Sequencing Technology Development Workshop
Mar. 10-11 / Chapel Hill, NC
National Human Genome Research Center, National Institutes of Health

Neuronal Circuits
Mar. 10-13 / Cold Spring Harbor, NY
CSHL

PTEN Pathways & Targets
Mar. 16-20 / Cold Spring Harbor, NY
CSHL

The Complex Life of mRNA: From Synthesis to Decay
Mar. 18-19 / Heidelberg, Germany
EMBL

Perspectives in Clinical Proteomics
Mar. 18-19 / Hinxton, UK
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Science
Researchers from the Institute for Systems Biology and elsewhere used Complete Genomics' sequencing service to identify mutations behind a Mendelian condition called Miller syndrome and an inherited lung disorder called ciliary dyskinesia in a family of four.
Business
Bruker will acquire certain mass spectrometry and chromatography product lines from Varian, clearing the way for Agilent to complete its $1.5 billion acquisition of Varian. The divestitures were part of conditions set by EU authorities for approval of the merger.
Funding
HHS expects that in 2010 NIH will spend another roughly $5.2 billion overall in stimulus funds that were left over from ARRA's first year. NIH still has more than $1.6 billion to spend in stimulus funds for lab construction and renovation, buildings and facilities, and shared instruments.
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Q&A: Nicola Ancona Compares Gene Set Enrichment Methods Head-to-Head

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