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Bioinformatics 101 – Running BLAST – Video

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Signal Genetics to Buy ChipDx, Gaining Cancer Test Pipeline, Bioinformatics Resources

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In Print: January's Bioinformatics Papers of note

Life Technologies this week named Alan Sachs as head of global research and development and Ronnie Andrews as president of medical sciences.

Sachs was previously the vice president of exploratory and translational sciences for Merck Research Laboratories, where he spent 10 years in various leadership roles, Life Tech said. Prior to that Sachs served an associate professor of biochemistry and molecular biology at the University of California, Berkeley, and as a Whitehead fellow at the Whitehead Institute for Biomedical Research.

Andrews joins Life Tech from GE Molecular Diagnostics, where he served as a segment leader following GE's 2010 acquisition of Clarient, where Andrews was CEO. Andrews has also held executive positions with Abbott Diagnostics, Roche Diagnostics, and Immucor.

Stephen O'Brien has left the National Cancer Institute's Laboratory of Genomic Diversity after 25 years to help launch a genome bioinformatics program at St. Petersburg University in Russia. O'Brien received a $5 million grant from the Russian Ministry of Education and Science last year under a program that aims to lure big-name researchers to Russia. Over the coming three years, O'Brien will spend at least four months per year in Russia working at the center, which is scheduled to open in May.

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.

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Bioinformatics Startup Scale Genomics Touts Flexibility as Key Differentiator of Cloud Platform

Ewan Birney, who will become an associate director at the European Molecular Biology Laboratory's European Bioinformatics Institute in April, tells Nature that his love of science “has helped me to get through some difficult times, when I've pushed myself and others perhaps too hard.” Birney, whose career trajectory the journal profiles this week, says that for his new managerial post, “hiring excellent people, setting up situations for them to succeed in and coaching and mentoring them will be key parts.”

Over at his blog, Birney expands on Nature's coverage, discussing how became interested in bioinformatics — which he says is no longer a stand-alone field. “I would argue that bioinformatics has already become an everyday part of modern biology, and that it has begun to filter through the entire system,” Birney says. Of his upcoming job change, Birney adds that “one thing I'll regret as I take on the new co-Associate Director job is working on the kind of big scientific consortia I've been so involved with over the past decade — human, mouse, chicken and above all ENCODE. That work has been a huge part of my career and I'm sure I will miss being so deeply involved in that kind of research.”

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On to Management

Ewan Birney, who will become an associate director at the European Molecular Biology Laboratory's European Bioinformatics Institute in April, tells Nature that his love of science “has helped me to get through some difficult times, when I've pushed myself and others perhaps too hard.” Birney, whose career trajectory the journal profiles this week, says that for his new managerial post, “hiring excellent people, setting up situations for them to succeed in and coaching and mentoring them will be key parts.”

Over at his blog, Birney expands on Nature's coverage, discussing how became interested in bioinformatics — which he says is no longer a stand-alone field. “I would argue that bioinformatics has already become an everyday part of modern biology, and that it has begun to filter through the entire system,” Birney says. Of his upcoming job change, Birney adds that “one thing I'll regret as I take on the new co-Associate Director job is working on the kind of big scientific consortia I've been so involved with over the past decade — human, mouse, chicken and above all ENCODE. That work has been a huge part of my career and I'm sure I will miss being so deeply involved in that kind of research.”

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CAREERS: On to Management

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UCSF leaders explore bioinformatics in research, patient care and education

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Bioinformatics @ SFU: Dr. Cenk Sahinalp – Video

CRAIGAVON, Northern Ireland–(BUSINESS WIRE)– Almac’s Diagnostics business unit today announced launch of its advanced Next Generation Sequencing (NGS) data Analysis services.

These latest enhancements to Almac’s service portfolio include a comprehensive range of NGS solutions from professional study design to sample processing and expert data analysis for DNA and RNA samples. Uniquely, the services are highly customizable and are available on a standalone basis or in combination with Almac’s established bioinformatics offerings in the areas of biological analysis, biomarker and drug discovery and development and diagnostic product development. Almac will utilize the latest sequencing technologies and most sophisticated modern computational analysis techniques to ensure optimal results from customer data.

The solutions are delivered through a large and experienced bioinformatics team from a wide range of disciplines including biology, medicine, mathematics and biostatistics. In addition to the team's expertise in bioinformatics and biostatistics they also have substantial experience in molecular and cell biology, drug discovery and development, and diagnostic product development.

Michael Sloan, Vice President of Business Development for Almac said:

“NGS is a rapidly maturing technology that continues to demonstrate significant benefits over traditional methods as well as making substantial steps toward routine use in the clinical setting. By expanding our services to include this range of DNA and RNA-Seq analysis we are empowering our customers with the most cutting edge technologies, opening new avenues within their research and boosting the potential for advancement of human health in a variety of disease settings”.

Almac’s NGS services build upon long standing expertise in the application of cutting edge technology to the improvement of human health.

Notes to Editors

The Almac Group provides a broad range of services from R&D, biomarker discovery and development, API manufacture, formulation development, clinical trial supply and IXRS® technology (IVRS/IWRS), to commercial-scale manufacture. Almac provides services to more than 600 companies, including all the world leaders in the pharmaceutical and biotech sectors.

The company employs over 3,300 individuals and is headquartered in Craigavon, Northern Ireland. US operations are based in Pennsylvania, North Carolina and California.

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Almac Announce Launch of Next Generation Sequencing (NGS) Data Analysis Services

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Free Webinar on RCSB Protein Data Bank

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UCSF School of Medicine Leaders Explore Bioinformatics

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.

Helicos Biosciences has elected Bruce Ginsberg to its board of directors to review certain financing matters. Ginsberg is president and CEO of MooBella, a food service provider, and a member of the board of directors of Mac-Gray.

Life Technologies VP of Research and Development Manohar Furtado has been appointed to serve as an advisor on the National Biodefense Science Board, a federal advisory committee for the Department of Health and Human Services. The board provides advice on bioterrorism and other public health emergencies. Furtado was appointed to serve a four-year term on the board. Kevin Jarrell, CEO of Modular Genetics, also will continue to serve on the board.

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Almac Expands Bioinformatics Offering to Include Sequence Data Analysis Services

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Seminars scheduled to spread awareness about bioinformatics

January 31, 2012

Genetic mutations that boost an individual’s adaptability have greater chances of getting through to X chromosomes – at least in chimpanzees, according to new Danish research.

One of the most important questions for evolution researchers is how a species develops and adapts during the course of time. An analysis of the genes of twelve chimpanzees has now demonstrated that the chimpanzee X chromosome plays a very special role in the animal’s development. The analysis was carried out by researchers at the Bioinformatics Research Center, Aarhus University, the Section of Bioinformatics, University of Copenhagen, the Copenhagen Zoo and the sequencing center at the Beijing Genomics Institute (BGI), China. The results have just been published online in the esteemed journal PNAS.

The background for evolution is found in our genome – in DNA. Evolution is driven by mutations that create changes in the genome on an ongoing basis. These mutations are most often deleterious, but they are sometimes beneficial for bearers in the environment in which they live. Their survivability can be improved, which in turn increases the likelihood of having more offspring. These beneficial variants then increase in number until all the individuals in a species have the new variant. This process is called natural selection.

One X is enough

By sequencing all the genes in twelve chimpanzees from Central Africa, the researchers demonstrated that beneficial variants are accumulated on the X chromosome in particular.
Why does this chromosome behave in such a special way? The gender of the individual is determined by the X chromosome along with the Y chromosome. Males have one X chromosome and one Y chromosome, while females have two X chromosomes.
A new beneficial variant on one X chromosome in the female can ‘hide itself’ if it is not expressed as strongly as the old variant sitting on the other copy of the X chromosome. In this case, the new variant is called recessive, i.e. it is suppressed by the other more dominant gene. This means that a new beneficial recessive variant does not immediately provide a benefit for the females. On the other hand, the males only have one X chromosome and it is expressed immediately, thus enabling natural selection to ‘catch sight’ of it. This does not apply to the remaining twenty-two chromosomes in the genome, because both males and females have two copies of each of these.

One third are good changes

The researchers found that about a third of all the changes that have taken place on the X chromosome since humans and chimpanzees diverged approximately four to six million years ago have been beneficial for the chimpanzee. This is far from the case for the chimpanzee’s remaining twenty-two chromosomes. The researchers therefore conclude that most of the new beneficial mutations must be recessive. This was already known regarding deleterious mutations on the X chromosome, e.g. color blindness as a recessive trait and therefore only occurring in men. However, the new results show that this must also be the case for the more interesting beneficial mutations, i.e. those that develop a species over a period of time.

Disease leads to development

The new results make it probable that corresponding activity takes place in the human X chromosome. They also provide an explanation of previous studies in which it was observed that the X chromosome behaved strangely during the speciation process of humans and chimpanzees, in that it was considerably less variable than the remaining chromosomes. This lack of variation can be explained by the fact that natural selection, which actually eliminates variation, works stronger on the X chromosome than on the remaining chromosomes.

By closely studying all the chimpanzee genes, the researchers found examples of natural selection in the remaining chimpanzee chromosomes all being associated with genes that are important for the immune system, including a gene that gives partial resistance to HIV in humans. This indicates that diseases are one of the most important factors in the evolutionary development and adaptability of the chimpanzee.

Aarhus University researchers who took part are: Yu Qian; Thomas Mailund; Asger Hobolth; Kasper Munch; Thomas Bataillon; and Mikkel H. Schierup

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Source: Peter F. Gammelby, Aarhus University

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X Factor Determined Chimpanzee Development

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Chimp 'X factor': Extensive adaptive evolution specifically targeting the X chromosome of chimpanzees

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Genetic mutations that boost individual's adaptability have greater chances of getting through to X chromosomes

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Bioinformatic Tutorial: how to find human gene orthologs in early metazoans organisms – Video

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Looking to Build Life Science Business, Appistry Hires New VP, Inks Deal with UM Bioinformatics Arm

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Diagnostic Partnering Agreements Discussed in New In-demand Report Published at MarketPublishers.com

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