Monday, August 29, 2011

New Roles Emerge For Non-Coding RNAs In Directing Embryonic Development

Scientists at the Broad Institute of MIT and Harvard have discovered that a mysterious class of large RNAs plays a central role in embryonic development, contrary to the dogma that proteins alone are the master regulators of this process. The research, published online August 28 in the journal Nature, reveals that these RNAs orchestrate the fate of embryonic stem (ES) cells by keeping them in their fledgling state or directing them along the path to cell specialization.
Broad scientists discovered several years ago that the human and mouse genomes encode thousands of unusual RNAs — termed large, intergenic non-coding RNAs (lincRNAs) —but their role was almost entirely unknown. By studying more than 100 lincRNAs in ES cells, the researchers now show that these RNAs help regulate development by physically interacting with proteins to coordinate gene expression and suggest that lincRNAs may play similar roles in most cells.

Monday, August 22, 2011

Comparative analysis of algorithms for next-generation sequencing read alignment


Motivation: The advent of next-generation sequencing (NGS) techniques presents many novel opportunities for many applications in life sciences. The vast number of short reads produced by these techniques, however, pose significant computational challenges. The first step in many types of genomic analysis is the mapping of short reads to a reference genome, and several groups have developed dedicated algorithms and software packages to perform this function. As the developers of these packages optimize their algorithms with respect to various considerations, the relative merits of different software packages remain unclear. However, for scientists who generate and use NGS data for their specific research projects, an important consideration is choosing the software that is most suitable for their application.
Results: With a view to comparing existing short read alignment software, we develop a simulation and evaluation suite, SEAL, which simulates NGS runs for different configurations of various factors, including sequencing error, indels, and coverage. We also develop criteria to compare the performances of software with disparate output structure (e.g., some packages return a single alignment while some return multiple possible alignments). Using these criteria, we comprehensively evaluate the performances of Bowtie, BWA, mr- and mrsFAST, Novoalign, SHRiMP and SOAPv2, with regard to accuracy and runtime.

Monday, August 15, 2011

Can the false-discovery rate be misleading?

"The decoy-database approach is currently the gold standard for assessing the confidence of identifications in shotgun proteomic experiments. Here we demonstrate that what might appear to be a good result under the decoy-database approach for a given false-discovery rate could be, in fact, the product of overfitting. This problem has been overlooked until now and could lead to obtaining boosted identification numbers whose reliability does not correspond to the expected false-discovery rate. To remedy this, we are introducing a modified version of the method, termed a semi-labeled decoy approach, which enables the statistical determination of an overfitted result."


Comments: Dr. Pavel Pevzner published some paper with similar idea, if my memory services me correct.

Monday, August 8, 2011

Bioinformatics for Cancer Genomics (BiCG)

Workshop Details
Date: August 29 - September 2, 2011
Location: MaRS Building, Downtown Toronto
Lead Faculty (2011): John McPherson, Francis Ouellette, Paul Boutros, Michael Brudno, Sohrab Shah, Gary Bader and Anna Lapuk
Registration Fee for Applications received before July 29, 2011: $950 + HST
Registration Fee for Applications received after July 29, 2011: $1150 + HST
Awards available for 2011.

Course Objectives
Cancer research has rapidly embraced high throughput technologies into its research, using various microarray, tissue array, and next generation sequencing platforms. The result has been a rapid increase in cancer data output and data types. Now more than ever, having the informatic skills and knowledge of available bioinformatic resources specific to cancer is critical.
The CBW will host a 5-day workshop covering the key bioinformatics concepts and tools required to analyze cancer genomic data sets. Participants will gain experience in genomic data visualization tools which will be applied throughout the development of the skills required to analyze cancer -omic data for gene expression, genome rearrangement, somatic mutations and copy number variation. The workshop will conclude with analyzing and conducting pathway analysis on the resultant cancer gene list and integration of clinical data.

Monday, August 1, 2011

Ontario Institute for Cancer Research Receives $420 Million Over Five Years for Important Cancer Research in Ontario Read more: Ontario Institute for Cancer Research Receives $420 Million Over Five Years for Important Cancer Research in Ontario

TORONTO, July 26, 2011 /PRNewswire/ -- The Ontario Institute for Cancer Research (OICR) will receive $420 million over five years from the Government of Ontario to continue its research into the prevention, early detection, diagnosis and treatment of cancer. The Institute will also occupy two floors of Phase II of the MaRS Centre in addition to its current laboratories and offices at its headquarters in the MaRS Centre. The announcement was made today by Dr. Tom Hudson, President and Scientific Director.
Today's announcement means continued support for the Institute in fulfilling the ambitious goals set out in its second Strategic Plan for 2010-2015, which focuses on the adoption of more personalized approaches to cancer diagnosis and treatment. OICR's current research activities in genomics and bioinformatics will be expanded in the new space in Phase II, allowing the Institute to increase its capacity to make new discoveries and move them out of the laboratory into the clinic for the benefit of patients. The funding will also enable the Ontario Health Study to complete its recruitment plans for the Study which will lead to better prevention of cancer and other chronic diseases.

Read more: Ontario Institute for Cancer Research Receives $420 Million Over Five Years for Important Cancer Research in Ontario - FierceBiotech