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."


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

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.

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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 http://www.fiercebiotech.com/press-releases/ontario-institute-cancer-research-receives-420-million-over-five-years-impo#ixzz1TnYjBOiS

Scientists welcome bioinformatics bonanza

AUSTRALIAN researchers now have free access to one of the world's most comprehensive database resources.

Launched last month, a mirror facility at the University of Queensland in Brisbane means scientists can use their computers to enter the most used data services of the British arm of the European Molecular Biology Laboratory's European Bioinformatics Institute.

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Roche´s xCELLigence RTCA HT System: Fully-automated Measurement of Therapeutic Targets` Cellular Activity

"Label-free technologies have entered the stage of cellular drug discovery and high-throughput screening (HTS). For the measurement of G protein-coupled receptor (GPCR) activation electrical impedance represents an excellent universal readout technology, since different signaling pathways can be measured in one assay format using recombinant as well as primary cells. The recently developed xCELLigence RTCA HT Instrument from Roche Applied Science now allows to perform fully-automated impedance screens for GPCRs and other targets in the 384-well high-throughput format.
In a recent case study, Urs Lüthi and John Gatfield from Actelion Pharmaceuticals Ltd., Allschwil, Switzerland, integrated 2 RTCA HT (real-time cell analyzer for high-throughput) Instruments on an automated high-throughput screening platform from Agilent Technologies (Santa Clara, US). 263 antagonist hits of the orexin type 1 (Ox1) GPCR that had been identified in a classical calcium flux (FLIPR) HTS were screened for Ox1 inhibition in fully-automated RTCA HT assays. The overall performance, the quality of E-Plates 384 and intra- and inter-assay reproducibility were evaluated. 65% of the 263 antagonist hits were confirmed to be Ox1 receptor antagonists after impedance measurements. According to the researchers, the RTCA HT Instrument could be readily integrated into automated workflows and delivered a highly reproducible data set, making the RTCA HT Instrument a powerful screening technology. 

Compared to standard readout technologies one of the major advantages of label-free technologies is that cellular processes are measured in real-time kinetics in a non-invasive manner. The xCELLigence System uses gold electrodes at the bottom surface of microplate wells as sensors to which an alternating current is applied. Cells that are grown as adherent monolayers on top of such electrodes influence the alternating current at the electrodes by changing the electrical resistance (impedance). The degree of this change is primarily determined by the number of cells, strength of the cell-cell interactions, interactions of the cells with the microelectrodes and by the overall morphology of the cells."

U of Minnesota Spends $3.6M NIH Grant on Supercomputer for Biological and Medical Research

The University of Minnesota Supercomputing Institute for Advanced Computational Research has installed a new high-performance computing system from SGI, christened Koronis, that it will use for multi-scale modeling, chemical dynamics, bioinformatics, computational biology, and biomedical imaging.

The university purchased the 1,152-core system with a $3.6 million grant from the National Institutes of Health's National Center for Research Resources. It will support NIH-funded research projects at the university.

Jeff McDonald, assistant director of high-performance computing operations at MSI, told BioInform that the latest purchase is the largest system at MSI and that it was selected because its shared memory capabilities best fit the researchers' needs.

In the grant abstract, the researchers wrote that the new system will help 33 research groups supported by 91 NIH grants "tackle ... the acquisition, analysis and visualization of petascale data from high-performance computing and high-throughput technologies."

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Global Market for Bioinformatics to touch $2.4 billion in 2011

"According to the new market research report from Industry Experts ‘Bioinformatics – A Global Market Overview’, global market for bioinformatics is estimated at about $2.4 billion in 2011 and further projected to reach $7.6 billion by 2017 registering a CAGR of 18.3% during the period 2007-2017.

At the beginning of the “genomic revolution”, Bioinformatics was applied in creating and maintaining a database that stored biological information, such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but also the development of complex interfaces, whereby researchers could access existing data, in addition to submitting new or revised data.

Market for Bioinformatics product categories analyzed in this study includes Bioinformatics Content, Bioinformatics Analysis Software & Services and Bioinformatics IT Infrastructure & Other Services. The report also includes the market analysis for end-use application analysis of Bioinformatics – Biopharma & Diagnostics, Genomics, Agriculture, Chemicals and Environmental & Other."

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Network-Based Pipeline for Analyzing MS Data: An Application toward Liver Cancer

Current limitations in proteome analysis by high-throughput mass spectrometry (MS) approaches have sometimes led to incomplete (or inconclusive) data sets being published or unpublished. In this work, we used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the molecular changes that occur during HCC progression in human tumorous tissue. The first involved functional cluster analysis by incorporating an expansion step on a cleaned integrated network. The second used an in-house developed pathway database where recovery of shared neighbors was followed by pathway enrichment analysis. In the original MS data set, over 500 proteins were detected from the tumors of 12 male patients, but in this paper we reported an additional 1000 proteins after application of our bioinformatics pipeline. Through an integrative effort of network cleaning, community finding methods, and network analysis, we also uncovered several biologically interesting clusters implicated in HCC. We established that HCC transition from a moderate to poor stage involved densely connected clusters that comprised of PCNA, XRCC5, XRCC6, PARP1, PRKDC, and WRN. From our pathway enrichment analyses, it appeared that the HCC moderate stage, unlike the poor stage, is enriched in proteins involved in immune responses, thus suggesting the acquisition of immuno-evasion. Our strategy illustrates how an original oncoproteome could be expanded to one of a larger dynamic range where current technology limitations prevent/limit comprehensive proteome characterization.

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Strong Investments to Boost Global Bioinformatics Market

According to our latest report entitled “Global Bioinformatics Market Outlook”, the global bioinformatics industry has been witnessing a remarkable growth rate pattern for the past few years. Factors, such as increasing R&D investments by companies and regulatory support boosted the market revenue to reach around US$ 2.6 Billion in 2009. As the bioinformatics market is at the nascent stage, its full potential is yet to be exploited. Moreover, there are significant advances in technologies that will boost the bioinformatics industry in future. It is expected that the market will grow at a CAGR of nearly 26% during 2011-2013 to reach US$ 6.2 Billion.

Our report has found that the escalating importance of personalized medicines has significantly augmented the growth level in proteomics market. Rising awareness of protein research and its study has opened the market for different proteomic-related equipments, technologies, and services. It is estimated that by 2013, the proteomics market will be worth around US$ 17 Billion and it will act as an important contributor in the growth of bioinformatics.

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