9:18 PM

Researcher Dr. Sohrab Shah Awarded Two CIHR/Genome Canada Bioinformatics Grants

April 25, 2013


1. Measuring and modeling tumour evolution from next generation sequencing data: enabling clinical study of clonal diversity in cancer patients
2. Computational interpretation of cancer genomes: defining mutational landscapes for translational genomics (Project Leaders: Dr. Sohrab Shah and Dr. Paul Boutros (OICR), in collaboration with Dr. Ryan Morin (SFU))
From GenomeBC.ca:
Vancouver, BC – Local researchers have successfully punched above their weight in securing $2.7 million out of $6.2 million available in a recent national funding competition for bioinformatics related research.
Massive amounts of data are being generated by genomics research across all life science sectors. The lack of efficient tools and methodologies available to effectively rapidly access, mine and efficiently analyze vast quantities of genomic information and integrate it with other data sets is a major challenge for the research community. To help meet these needs, Genome Canada, in partnership with the Canadian Institutes of Health Research (CIHR) hosted a national funding competition to fuel the infrastructure required for computational biology.
Of 17 successful projects across Canada, seven will be led here in British Columbia by Genome BC-funded researchers and further illustrates that our province is a leader in this field. “BC is clearly at the forefront of providing some very significant technological tools to address unmet research needs,” said Dr. Alan Winter, President and CEO of Genome BC. “Our province has the ability to apply these funds and leverage the outcomes across life sciences that ultimately will benefit Canadians.”
BC-led projects include noteworthy technologies to research microbial public health genomics, computational interpretation for cancer genomics, improved examination and processing times for cancer samples and applied tools for exploratory genomics. The researchers funded hail from the BC Cancer Agency, University of British Columbia (UBC), Simon Fraser University and the UBC Centre for Molecular Medicine & Therapeutics.
The research projects will be conducted over a three-year period starting this June. Expected outcomes of the work include improved analytical approaches to the detection of variations and mutations in DNA and RNA related to cancer diagnosis and care, easy-to-use bioinformatics and genomic analytical tools to allow health care workers to better manage communicable diseases and provide quicker responses to infectious disease outbreaks.
For more information on the projects please click here for a background document.
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3:26 PM
Aberystwyth University

Bioinformatician / Analyst - Plant Bioinformatics


Aberystwyth University -Institute of Biological Environmental and Rural Sciences


Fixed term for 3 years
Grade 7: £31,331 - £36,298
The Institute of Biological, Environmental and Rural Sciences (IBERS) is a world class research, enterprise and education centre at Aberystwyth University.  It is an internationally recognised centre of excellence and students' choice for the study of biological, environmental and rural sciences.
This position within the BBSRC-funded Institute Strategic Programmes at IBERS will focus on developing bioinformatics approaches to exploit the potential of new sequencing technologies in the overall context of developing a sustainable bio-based economy for food and fuel security. Working in close collaboration with the IBERS bioinformatics research leaders and team, the focus will be on processing and assembling de novo genome and transcriptome next generation sequencing (NGS) data for ryegrasses, forage legumes, oats and the bioenergy grass, Miscanthus. With the ability to work independently within the overall programme, the post-holder will take the lead in establishing tailored and automated pipelines and developing integrated platforms to access, analyse and visualize sequence, annotation and other datasets. Through having excellent communication skills the post-holder will be able to deliver appropriate training to staff and students in the analysis of NGS data. By establishing and maintaining links with other bioinformaticians and computer scientists within and outside of the University, the post-holder will facilitate the execution of existing and future collaborative work programmes. This post represents an excellent opportunity to join a productive bioinformatics program in a translationally focused innovative research environment.
For an informal discussion regarding the post, you may contact:-
Narcis Fernandez-Fuentes (naf4@aber.ac.uk)
Ian Armstead (ipa@aber.ac.uk) +44(0)1970 823108
Iain Donnison (isd@aber.ac.uk); +44(0)1970 823092
Ref: IBERS.13.21
Closing Date: 27 May 2013
For information and application forms please go to www.aber.ac.uk/en/hr/jobs/vacancies-external/
Completed Applications Forms should be signed and returned to the Human Resources Recruitment Team by e-mail, fax or post. Email address: vacancies@aber.ac.uk / Tel:  01970 628555 / Fax:  01970 622975
NOTE: Please put the post reference on the front of your envelope and on your application form.
We are a Bilingual Institution which operates a Welsh Language scheme and is committed to Equal Opportunities.
Appointments are normally made within 4-8 weeks of the closing date.  If we have not been in touch within this timescale you may assume that your application is not being further considered and no other communication will be sent.

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12:01 PM

 

Can we bring back the Tasmanian tiger? Photo by the author.

De-extinction: the wooly mammoth is the biophysicist’s cancer

On my first day teaching bioinformatics, I brought Michael Crichton’s book Jurassic Park to class. I showed the students a DNA sequence from the book  – a long string of A, T, C, and G that was supposed to form part of one dinosaur gene. As a class exercise, I asked students to convert that string into a protein sequence (it seems more bioinformatics teachers had the same idea).
The students were instantly intrigued. I attribute that class’ success to Jurassic Park. Both book and movie are embedded in our collective imagination. Who isn’t enthralled by the possibility of engineering dinosaur DNA and bringing the lumbering giants back to life?
Can we bring back the Tasmanian tiger? Mike Archer at TEDx. Photo by the author.
I was able to attend the TEDx DeExtinction event in DC, thanks to an awesome boss and crew, who came along. There, molecular biologists and conservationists discussed the possibility of resurrecting extinct animals, while fans vouched for their favorite species (hello, dire wolf). The lecturers presented the technology, while ethicists and ecologists watched in horror.
The passenger pigeon is another candidate for de-extinction. Photo by the author.
The passenger pigeon is another candidate for de-extinction. Ben Novak at TEDx. Photo by the author.
There was talk of bringing back the wooly mammoth, passenger pigeon, bucardo, Tasmanian tiger and others. But like speaker and “molecular paleontologist” Beth Shapiro points out, we are still very far from step one. No surprise here. I went to this event not expecting to see a herd of mammoths any time soon. I went there to marvel at technology  and its applications. Or, like my colleague described it, “the moon race for biologists”.
Beth Shapiro is cautiously optimistic. Photo by the author.
Beth Shapiro is cautiously optimistic. Photo by the author.
Conservation efforts can benefit from de-extinction technologies. Lack of genetic diversity among captive breed populations is a serious problem. Breeding programs and SSPs (species survival plan) keep a studbook: a record of the genetic make up of all individuals of that species. Pairings are carefully calculated in order to increase genetic diversity. TEDx host Stewart Brand (check out his Reddit AMA) believes de-extinction can help with that: “de-extinction technology… can be applied immediately to help diagnose and treat genetic issues with endangered populations of living species. Viable cryopreserved DNA … can be used to reintroduce genetic variability in ‘genetic bottleneck’ situations for animals now rare and facing inbreeding problems.” And that’s not all. Cloning or iPCS (induced pluripotent stem cells) are technologies with immense potential, with applications that range from tissue engineering to livestock breeding, and perhaps even to support reproduction.
DSC00970
Stewart Brand at TEDx. Photo by the author.
Funding dictates what research projects will go on and which ones will die.  And that is why I’m ok if a woolly mammoth or Jurassic Park-based creature functions as research ambassadors. Scientists depend heavily on policymakers and public support to guarantee funds for their work. It is increasingly difficult to obtain funds for basic research or anything that doesn’t have the word “cancer” or “heart disease” attached to it. Throughout my PhD I happened to work with both most of the time (design of protein inhibitors for breast cancer, and angiogenesis molecules for cardiovascular disease). I mean most of the time: when an application is not so direct or obvious (e.g., of studying the folding of a protein) we always highlight its future, potential, exciting, indirect and perhaps one day possible outcome (e.g., better understand Alzheimer’s). The woolly mammoth is the biophysicist’s cancer, and the passenger pigeon is his heart disease. I believe de-extinctioners were trying this PR approach.
Biotechnology for de-extinction. Photo by the author.
George Church explains the biotechnology behind de-extinction. Photo by the author.
But did it backfire? I saw many ecologists and ethicists disapproving of the entire thing. Are they spreading the fear? Is fear of science creeping out and reaching our scientific and (scientific-supporting) community? As Brand pointed out in his AMA, “fear has been institutionalized, not only by government but by (…) environmental groups broadcasting irrational fear of GMOs and radiation (to the detriment of genuine green goals like more wild lands and damping of climate change)”.
Very much alive (i.e. non extinct) blue hyacinth Margaret was present at the event. Photo by the author.
Very much alive (i.e. non extinct) blue hyacinth macaw Margaret was present at the event. Photo by the author.
George Mallory was a mountain climber and one of the English pioneers to Mount Everest expeditions on the 20′s. Why take on such endeavor? It was risky, challenging, and with no direct application. So, “why climb the Everest?”, he was asked.
“Because it is there.”
Sometimes it is all the motivation we need.

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11:37 AM
The global bioinformatics market, valued at nearly $3.2 billion in 2012, is forecast to grow to nearly $7.5 billion by 2017, according to Wellesley, Mass.-based BCC Research.
The market attracts considerable funding from central governments and is driven by applications across a variety of sectors, including biotechnology, pharmaceutical research and development, agriculture, food safety, chemicals, manufacturing, and more recently, clinical genomics, according to the research.
Growth in the market has been driven by the industries' need to adopt more cost-effective and productive methods for commercializing proprietary information, researchers found. Companies are looking for suppliers that can offer total integration of data infrastructure, which includes data sharing, data security, customization, data searching and analysis.
The United States holds the largest segment of the bioinformatics market, accounting for 52.8 percent of global sales, followed by Europe and the Asia-Pacific region. The majority of revenues are generated from analysis software and analytical services, which account for nearly 47.6 percent of revenues, although data-analysis software and analytical services comprise the strongest growing segment with a 2012-2017 compound annual growth rate of 20.3 percent.
The research also found the following:
  • Bioinformatics tools and services have important roles to play in all aspects of drug discovery and development as they help to design drugs, predict drug metabolism and toxicity, and model drug-gene or drug-protein interactions.
  • In the post-genomic era, gathering biological information is no longer a bottleneck for scientific researchers. The major hurdle remains in the efficient organization, analysis, and interpretation of the data. The establishment, maintenance and open access of large datasets has been important in driving this field forward, as they have allowed researchers throughout the world to find new ways to analyze and interpret information into new knowledge.
  • Raw data is meaningless without context. The ultimate goal of bioinformatics is to extract knowledge from large-scale data. There are currently hundreds of software tools available online, many of which were developed by leading academic institutions and are freely available, enabling researchers to undertake sequencing, alignment, structure, and function analysis for a range of biological data.
  • More data is being collected than can be physically stored; the storage gap is widening, and selecting which data to archive has become a major issue. During the last 30 years, IT infrastructure has become more integrated, and it has rapidly evolved from a computer cluster model to a cloud computing platform that allows computational capacity to be purchased as a service from a cloud computing provider.
 
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11:21 AM
 

OTTAWA, Ontario, April 30 — New Canadian bioinformatics and computational biology research projects will help manage, analyze and interpret vast amounts of genomics data to accelerate advances in personalized medicine, public health and other areas of importance to Canadians and the economy.

"Our government is investing in the technological solutions needed to advance genomics to its full potential for the benefit of Canadians and their families," said the Honourable Gary Goodyear, Minister of State (Science and Technology). "These leading-edge research projects will put Canada at the forefront of innovation globally in the specialized fields of bioinformatics and computational biology."

Through Genome Canada’s 2012 Bioinformatics and Computational Biology Competition, a partnership with the Canadian Institutes of Health Research (CIHR), 17 projects across the country will receive funding.

The mix of large-scale applied and small-scale innovative projects will produce new tools and methodologies to enhance genomics data management and analysis, contributing to improving cancer treatments, quicker responses to infectious disease outbreaks, improved food production, and more. Bioinformatics expands the use of genomics data through the research, development or application of computational tools and approaches. It enables better ways to acquire, store, organize, archive, analyze and visualize data. Computational biology helps make sense of genomics data through computational analysis, modelling, and prediction.

"Managing and analyzing the huge amounts of data generated by genomics technologies is a major challenge. These new projects will offer much-needed innovations that will address this dilemma so that the data can translate into useful genomics applications such as disease treatments, breeding strategies for agriculture, forestry management, bioenergy and aquaculture," said Pierre Meulien, President and CEO of Genome Canada.

"Technological advances in genomics and in high-resolution imaging promise to drastically improve the precision and efficacy of Canadian health care. However, the development of strategies to handle the enormous amounts of data generated from these technologies is essential for us to achieve their full potential. We are proud to be working together with our partners at Genome Canada and the regional Genome Centres in this new initiative in bioinformatics and computational biology that will facilitate research in this critical area," said Paul Lasko, Scientific Director for CIHR’s Institute of Genetics.

The Harper Government's investment in these projects is approximately $6.4 million ($5 million from Genome Canada and another $1.4 million from CIHR). The balance of funding is secured by regional Genome Centres from provincial governments, the private sector and other partners, bringing the total value of these projects to almost $11 million.

To build on Genome Canada’s achievements to date, Economic Action Plan 2013 proposes to provide $165 million in 2014–15 to support Genome Canada’s multi-year strategic plan.

Since 2006, the Harper Government has provided more than $9 billion in new funding for initiatives to support science, technology and the growth of innovative firms, helping to foster a world-class research and innovation system. Economic Action Plan 2013 builds on this strong foundation, helping to position Canada for sustainable, long-term economic prosperity and a higher quality of life for Canadians.

Genome Canada is a not-for-profit organization that invests in genomics research to generate economic and social benefits for Canadians. Genome Canada builds bridges between government, academia and industry to forge a genomics-based public-private innovation enterprise focused on key life science sectors. It develops these partnerships to invest in and manage large-scale research and translate discoveries into commercial opportunities, new technologies, applications and solutions.

Canadian Institutes of Health Research (CIHR) is the Government of Canada’s health research investment agency. CIHR’s mission is to create new scientific knowledge and to enable its translation into improved health, more effective health services and products, and a strengthened Canadian health care system. Composed of 13 Institutes, CIHR provides leadership and support to more than 14,100 health researchers and trainees across Canada. 

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11:05 AM
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Something we feel strongly about at Nextgenediting is the use of computational biology to support and contextualise the main experimental findings of a biological paper. There is a wealth of primary research that can be performed before you even get started doing your experiments in the lab, and the best papers know how to make the best use of it. These data can be particularly useful for grant applications, too. We sometimes send recommendations back to our biomedical authors saying ‘go to GEO and analyse this dataset - you have all the information available to you tell you exactly what the expression of your gene of interest is in thousands of breast cancers…or colon cancers…or cardiovascular patients….or whatever your disease of interest is’. When you take this approach you often find the experiment you were planning (in vitro or in vivo) has already been performed, or there is supporting mouse data, or often clinical data. They can be used to generate the first figure(s) of the paper, put the experimental data in clinical context, and save a huge amount of time and effort performing costly -omics experiments. If you don’t know how to use these resources or need more information, please contact us.

What we hadn’t realised until very recently was that the same can be done for epidemiological data. We are currently planning our Nextgenediting Global Initiative (for more information click here), and while researching health and income statistics of third-world countries we found the World Bank World Databank. This is a free, online database of Development Indicators, Gender Statistics, and other useful data, which you can mine and interrogate at will for hundreds of different countries - both developed and otherwise. Most exciting for us however, is the Health, Nutrition, and Population Statistics Database which allows you to mine health and disease-related data. You just choose your country or countries of interest, the data series you want, and the range of years you are comparing (from 1961 to present) and the results are presented as tables, graphs, or on a map. You can even download the raw data and work with it yourself to present your own graphs or figures. Truly amazing.

We remember feeling like this when we first realised we could get our hands on raw gene expression data. What a powerful tool to contextualise your own work.

So if, for instance, if you are doing a study on HIV, and you need to know what the AIDS death rates are in various African countries, it would take two minutes to get this chart:

Pasted Graphic

which you can then fully customise. So much better than some outdated and over-cited WHO data, don’t you think? You can then get a first-hand grip on the numbers, trends, and associations relevant to your own research.

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12:40 PM

 

NEW YORK, April 29, 2013 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:

STUDY GOALS AND OBJECTIVES

BCC Research's goal for this study is to provide a comprehensive analysis of the bioinformatic market by reviewing the recent advances in high-throughput 'omic technologies and computer-enabled technologies that have driven the field forward. It examines the market trends and analysis regarding industry service providers, software solution developers, and IT and bioinformatics service providers that support the pharma industry.

The report's main focus is on identifying the challenges and opportunities that exist in the bioinformatic market following the adoption of high- throughput technologies and the generation of big data. It aims to identify innovative companies and institutes that are extending the boundaries of science and technology to develop innovative solutions and enable knowledge to be extracted from burgeoning data so that it may be put to use for the greater good.

REASONS FOR DOING THE STUDY

Since the Human Genome Project was completed in April 2003, genome-wide association studies (GWAS) have contributed toward a greater understanding of the genetic basis of complex diseases and advances in high-throughput technologies. This has enabled researchers to rapidly map the genome of vertebrates, invertebrates and pathogens through cost-effective methods.

More recently, improvements in cloud computing capabilities and advances in data-analysis software services have helped to expand the evaluation of available datasets, allowing researchers to build systems biology models of various diseases. Still, the challenge to translate this wealth of information into tangible clinical benefits, to support the development of new therapeutic interventions and to reduce the current prohibitively high cost of drug development remains.

SCOPE OF REPORT

The scope of the study encompasses the global bioinformatic market based on geography, category and application. It provides a detailed analysis of recent advances in 'omic technologies and examines their impact on the bioinformatics market. It discusses the ways in which bioinformatics have been utilized by the pharma and biotech industries to streamline the research and development (R&D) process and improve efficiencies. It provides a detailed analysis of leading countries, companies and technologies that will drive the field forward.

INTENDED AUDIENCE

The study provides a detailed analysis of the economic, technological and potential application of bioinformatics; it also examines the market factors and identifies the market potential through the year 2017. The study is aimed at the pharmaceutical industry, biotechnology firms, research laboratories and individuals interested in exploiting the commercial opportunities offered in this field.

METHODOLOGY AND INFORMATION SOURCES

Both primary and secondary sources were used in preparing this study. This analysis of bioinformatics breaks down the market by geography, category and application, and also analyzes current and potential opportunities for bioinformatic business. It includes market sizes from 2011 and forecasts market revenues through 2017.

Primary research involved e-mail correspondence and telephone interviews for each market, category, segment and sub-segment across geographies. BCC Research extends its thanks those who took part in interviews for this report, especially the following, who gave so generously of their time:
• Paul Clemons , PhD, Director of Computational Chemical Biology Research Broad Institute, U.S.
• Rolf Apweiler, PhD, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, U.K.
• John Atack , PhD, Translational Drug Discovery Group, School of Life Science, University of Sussex, U.K.
• Tom Schwei , Vice President, CFO and General Manager DNASTAR Inc., U.S.
• Simon M. Lin , MD, Editor-in-Chief at the Journal of Computer Science and System Biology, BIRC, U.S.

Secondary research was performed on internal and external sources to acquire qualitative and quantitative information for this report. These sources include:
• Company websites, annual reports, financial reports and investor presentations.
• Industry trade journals, scientific journals and other technical literature.
• Relevant patent and regulatory databases.
• National government documents, statistical databases and market reports.
• News articles, press releases and webcasts specific to the companies.

ANALYST CREDENTIALS

Dr. C.L. Barton has more than 10 years' practical pharmaceutical research experience with a leading pharmaceutical company and has served as a Pan-European Pharmaceutical analyst with a European bank. Dr. C. L. Barton Ltd. aims to provide independent, tailor-made, pharmaceutical thematic research to investment houses. Research reports combine independent scientific analysis with patients- and prescription-based models to forecast the potential sales growth of key developmental drugs and to isolate the key drivers within the pharmaceutical sector.

REPORT HIGHLIGHTS

The report provides:
• An overview of the global market for bioinformatics.
• Analyses of global market trends, with data from 2011 and 2012, and projections of compound annual growth rates (CAGRs) through 2017.
• Technological descriptions and patenting trends in bioinformatics.
• Examination of the economic environment affecting the deployment of bioinformatics.
• Discussion of other influential factors, such as R&D spending in the pharmaceutical sector, the growth of agrobiotechnology, and the expanded use of microbial genomics.

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