Bioinformatics position

Courtesy Bioclues

Are you a skilled bioinformatician? Do you have experience with analysis and integration 

of large data sets? Would you like to work with leading experts and constantly improve 

your skills? Then you may be Intomics’ next bioinformatician.

We are expanding our bioinformatics team and are seeking a skilled bioinformatician to 

help the team provide innovative solutions for our clients in the pharmaceutical industry. 

You will play an important role in implementing data mining strategies for projects in 

areas such as target identification, biomarker identification, disease systems biology, and 

translation research.

Our preferred candidate has the following profile:

• Bioinformatics or computational biology background
• Experience with large-scale data mining
• Strong experience with programming (e.g.  Perl,  Python,  Java),  databases (e.g. MySQL, PostgreSQL), and Unix
• Excellent communication skills and the ability to work in a team
• Strong reporting and documentation skills
• A PhD in bioinformatics or systems biology is an advantage, but not a requirement
• A solid understanding of basic molecular biology
• Experience with several large scale data types is further an advantage

We are offering an  exciting and challenging job, where you get the opportunity to 

develop your skills and qualifications. You will get to work with interesting projects  in 

close collaboration with our clients.  Intomics A/S offers  a competitive salary  and  a 

friendly working environment. Some traveling must be expected.

Applications should be submitted electronically before 31st of January 2011 by email to 

applications@intomics.com marked with “application-1182” in the subject header.

Enquiries about the position can be made to CEO Thomas S. Jensen, tel: +45 88807979 

or  skot@intomics.com. All interested candidates irrespective of age, gender, race, or 

religion are encouraged to apply.

EMBO Courses, Workshops & Conference Series

Practical Course - European Molecular Biology Organization

Bioinformatics & Comparative Genome Analyses

27 June - 09 July, 2011 |Institute Pasteur | Paris | France

About the Practical Course

In the context of large-scale genome comparisons, the main objectives of this general purpose practical course are to strengthen capacities of students in Bioinformatics and data analyses skills by introducing reviews on advanced fundamental algorithms used in Bioinformatics and their applications in genome studies. 

Theoretical presentations will be followed by practical sessions, so that the same speaker will ensure links between theory and practice.

Reviews on each suggested topic will include their corresponding research perspectives, aiming at helping young scientists to gain insights into ongoing research in this domain. 

The course topics will include theoretical and practical aspects in: large-scale genome comparisons, evolutionary analyses, sequence and genome alignments, orthologs prediction and classification, Genome data visualization and statistical methods needed in Genome Wide Association Studies. 

Lectures related to recent hot topics in Bioinformatics and Genome studies will be programmed. 

Practical sessions in a Linux environment will involve Unix shell and Perl scripting. Students are expected to be familiar with this environment. 

Similar previous course programmes can be found here: 

Who can attend the course:
The course is aimed at motivated Phd students and young researchers in academic Institutions with background in Mathematics, Statistics, computing or Biology and who are involved in Bioinformatics and Genome Analyses. The course is intense and active participation of the students is expected.

Do you wish to know more?

Next generation sequencing establishes genetic link between two rare diseases

This one is not so recent article, nevertheless very interesting and path breaking,

Scientists have successfully used "next generation sequencing" to identify mutations that may cause a rare and mysterious genetic disorder. The research, published by Cell Press on July 29th in the American Journal of Human Genetics, demonstrates that sequencing an affected individual's entire "exome"; that is, all of the genes that carry instructions for producing proteins, can reveal critical genes that when mutant, cause inherited disorders.

Perrault syndrome is a recessive disorder that is associated with hearing loss in both boys and girls, and failure of ovarian function in girls. Some individuals with Perrault syndrome also have neurological symptoms. Prior to the current study, no genes for Perrault syndrome had been identified.

A research group led by Mary-Claire King, PhD, from the University of Washington in Seattle studied the genetics of Perrault syndrome in a small family, originally of Irish and Italian ancestry, that included two sisters with well-characterized Perrault syndrome.

"Because the family is small and not consanguineous (both parents descended from a common ancestor), standard genetic mapping techniques would not have been informative in identifying the responsible gene," explains Dr. King. "Instead, we attempted to identify the gene responsible for Perrault syndrome in this family through the use of whole exome sequencing." The exome can be thought of as a kind of genetic blueprint for the synthesis of proteins.

After sequencing the entire exome of one of the sisters, the researchers identified a single gene (HSD17B4) that exhibited two rare functional variants. This gene encodes D-bifunctional protein (DBP), a multifunctional enzyme involved in lipid metabolism. Underscoring the genetic diversity of the disease, the researchers went on to show that six other families with Perrault syndrome had normal HSD17B4.

"Other mutations in HSD17B4 are known to cause a very severe congenital syndrome called DBP deficiency that is generally fatal within the first two years of life," says Dr. King. "No girls with DBP deficiency have been reported to survive past puberty, so ovarian abnormalities have not previously been known to be associated with this illness. The few reported long term survivors of DBP deficiency exhibit hearing loss and neurological dysfunction."

Taken together, the findings indicate that Perrault syndrome and DBP deficiency share some clinical symptoms and that very mild cases of DBP deficiency may be under-diagnosed. "Our research also demonstrates that whole exome sequencing can reveal critical genes in small nonconsanguinous families," concludes Dr. King.

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

This something really interesting to PPI, Systems biology  and molecular networks people, I just recently came across,

Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities.

Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways. 

Results: We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes.

Finally, these extended pathways and processes are used to analyse their enrichment in pancreatic mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes. 

Conclusions: The proposed method for extending cellular pathways helps to explain the functions of cancer mutated genes by exploiting the synergies of canonical knowledge and large-scale interaction data.

Author: Enrico GlaabAnais BaudotNatalio KrasnogorAlfonso Valencia

Credits/Source: BMC Bioinformatics 2010, 11:597

Largest Network Of Alzheimer’s Disease Protein Interactions

Through a complex analysis of protein interactions, researchers from IRB Barcelona and the Joint Programme IRB-BSC have discovered new molecular mechanisms that may be involved in the development of Alzheimer’s disease. The study, a collaboration between bioinformaticians and cell biologists, was led by IRB Barcelona group leader and ICREA researcher Patrick Aloy and appears today in the Genome Research, a reference journal in the field of genomics.

Alzheimer’s disease is an age-related neurodegenerative disease. Despite the considerable efforts made in recent years to understand the mechanisms that trigger this disease, an effective treatment is not yet available. This study reveals new molecular and functional data that could help researchers gain a better understanding of the disease and potentially to develop new therapies.

From the computer to the lab

Proteins are the molecular instruments that cells use to carry out their functions. Proteins don’t normally act alone, but interact with other proteins to form cellular networks. In this study, rather than looking at individual proteins as been done in many previous studies, the scientists analyzed the biology behind Alzheimer’s disease using a global approach. “We have combined computational and experimental methods to study the connections between proteins and put them in the context of their environment”, says Aloy.


To do so, the researchers used genetic methods to study the thousands of possible interactions between proteins known or thought likely to be involved in the disease, including proteins derived from the genes located on the chromosomes related to the Alzheimer’s disease. They obtained a total of 200 new interactions. This information, added to what is already known, brings the total number of Alzheimer’s-related interactions to 6000, and involves 1700 proteins, resulting in the largest network of interactions between proteins related to Alzheimer’s disease.

The computational analysis of these interactions, performed by the MareNostrum Supercomputer of the Barcelona Supercomputing Center (BSC), revealed that many of the groups of proteins are highly interconnected and have similar functions in cells. Some of these functions suggest new molecular mechanisms that could be linked to Alzheimer’s. A clear example is a protein called ECSIT, that relates oxidative stress to inflammation and changes in the mitochondria, indicating that these processes may play a role in the development of the disease.

The 94 terabyte MareNostrum is housed in the deconsecrated Chapel Torre Girona at the Polytechnic University of Catalonia, Barcelona, Spain:

Increased life expectancy and improvements in health care and diagnostics have led to the increased prevalence of the Alzheimer’s disease, which is a serious problem in both developed and developing countries. This study opens the door to new research aimed at finding a cure for the disease.

Sources: Institute for Research in Biomedicine-IRB, AlphaGalileo Foundation.

Reckitt Benckiser Buys India’s Paras Pharmaceuticals Ltd

Reckitt Benckiser emerged successful in race to buy Pars in spite of 4 global drugmakers submit bids for India's Paras Pharma buy. 

Reckitt Benckiser Group plc (RB) today announces that it has agreed to buy Paras Pharmaceuticals Limited (Paras) forINR 32.6 billion (Indian Rupees) (approximately GBP 460 million) from the current shareholders, including the Patel family and Actis, the emerging markets private equity investor. RB will finance the transaction from existing facilities. 
 
Paras is a privately-owned Indian company with a portfolio of leading Indian over the counter Health and Personal Care brands including: 
 
Moov, the No 2 topical analgesic pain ointment,
D’Cold, the No 2 cold & flu remedy,
Dermicool, the No 2 for prickly heat,
Krack, the No 1 medicated skin treatment for cracked heels and
Itch Guard and Ring Guard anti fungal creams.

In addition, Paras has a personal care business led by Set Wet, a leading hair gel and deodorant brand. In the fiscal year ending March 2010, Paras generated net sales of INR 4,014 million, representing a mid-teens average growth rate over the last four years, and operating EBITDA for the same year of INR 1,083 million (approximately GBP 56 million and GBP 15 million respectively). The company has a brand new state of the art and GMP compliant manufacturing plant located at Baddi in Northern India, which employs around 700 people.

Commenting on the acquisition, Reckitt Benckiser CEO, Bart Becht, says, “The acquisition of Paras is another step forward in RB’s growth strategy in consumer health care. It creates a material health care business in India, one of the most promising health care markets in the world with the addition of a number of strong and leading brands.”

“We believe the Paras business has not only extremely good growth potential, when supported by RB’s investment and innovation strength, we also expect to realize material synergies as a result of the integration of Paras into Reckitt Benckiser.”

“The growth potential of the business, the creation of a material health care business in India’s large and growing health care market and the global synergies available make Paras an exciting addition to our portfolio and attractive opportunity for our shareholders.”

RB was advised by JPMorgan. Actis and the other Paras shareholders were advised by Morgan Stanley.

New programming language will drive DNA

This is no Sci-Fi but reel to real! Yes we can in deed program the DNA for real Now! 

Bioinformatics scientists have built two logic gates for what they hope will become a new programming language for drug design as well as chemical and agricultural product engineering. The accomplishment seems hardly noteworthy except that these logic gates are made of E. coli. The two computational switches are based on two strains of the common bacterium. Researchers are now working to assemble them to perform computations.

This genetic programming software would resemble any other programming language, says Kevin Clancy, senior staff scientist for bioinformatics at Life Technologies Corp. The Carlsbad, CA, company is funding the work, which is being done by researchers at the UC San Francisco School of Pharmacy. Life Tech plans to commercialize the technology.

The software would convert instructions into a DNA sequence to be inserted into a bacterial, yeast or mammal cell. "It allows you to access and rewire biological systems on a scale that hasn't been possible in genetic engineering to date," says Christopher Voigt, UCSF associate professor.

Do you wish to know more?

ECCB 2010 Next-gen sequencing Tutorial

Check out this SlideShare Presentation:

ECCB 2010 Next-gen sequencing Tutorial

View more presentations from Thomas Keane.

Walk in interview - Project posts tenable at NCCS, Pune

Advertisement No. Admn P22/2010 Walk in interview program for the following Project posts tenable at NCCS, Pune. Name of the Position & No. of Post Reser- vations Name of the Project Upper Age Limit Qualification and Experience Monthly Emoluments    Tenure Date, Time and Place of Interview Research Associate (One Post) SC "Prognostic evaluation of the E-box binding transcription factors snail and slug in ovarian, breast, prostate and head and neck cancers" 35 Years Ph.D / M.Tech / M.E / M.D / M.V.Sc (A.H) in Life Sciences / Bioinformatics / Biostatistics / Biotechnology / Microbiology / Biochemistry. Rs. 17250/- +15% HRA for 1st & 2nd year and Rs. 20830/- + 15% HRA for 3rd year. 2.5 Years Date: 30.12.10 Time: 9:30 am at NCCS Complex Tenure: The Initial appointment will be for the period of one year likely to be extended for further one year and five months however, the salary for the extended period will be only made available after receipt of funds from the funding agencies. Age: Age Relaxation of 5 years in case of SC/ST/Women/PH candidates will be given as per Government of India Rules. Candidates fulfilling the above requirements may attend the Walk in Interview on the above date, time and address. No TA will be paid for attending the interview. Candidates are required to report sharp at 9:30 am on the date of interview with the following documents: 1.       *Biodata form duly filled in. 2.       All relevant original documents with a set of attested copies thereof. Director * Download Biodata Form Do you wish to know more?

BioFocus Extends Contract with Amgen

Belgian biotech firm Galapagos today announced its BioFocus service division has extended a contract with Amgen through 2012 to include target discovery and validation work.

The extension will include the use of BioFocus' target discovery platform to deliver novel targets to support Amgen's therapeutic programs. Galapagos will receive €2 million ($2.6 million) in research fees in the first year, under the terms of the deal. It is also eligible for access fees and milestone payments.

Originally forged in 2002, the collaboration between BioFocus, which Galapagos acquired in 2005, and Amgen involves identifying new molecules against drug targets. The partnership was extended in 2006 and 2008.

BioFocus' discovery platform includes the use of in vitro and cell-based screening, structural biology, and chemogenomic and informatics tools.

Artificial neural networks-based approach to design ARIs using QSAR for diabetes mellitus

In this article, in the first part, we propose an artificial neural network-based intelligent technique to determine the quantitative structure-activity relationship (QSAR) among known aldose reductase inhibitors (ARIs) for diabetes mellitus using two molecular descriptors, i.e., the electronegativity and molar volume of functional groups present in the main ARI lead structure. We have shown that the multilayer perceptron-based model is capable of determining the QSAR quite satisfactorily, with high R-value. Usually, the design of potent ARIs requires the use of complex computer docking and quantum mechanical (QM) steps involving excessive time and human judgement. In the second part of this article, to reduce the design cycle of potent ARIs, we propose a novel ANN technique to eliminate the computer docking and QM steps, to predict the total score. The MLP-based QSAR models obtained in the first part are used to predict the potent ARIs, using the experimental data reported by Hu et al. (J Mol Graph Mod 2006, 24, 244). The proposed ANN-based model can predict the total score with an R-value of 0.88, which indicates that there exists a close match between the predicted and experimental total scores. Using the ANN model, we obtained 71 potent ARIs out of 6.25 million new ARI compounds created by substituting different functional groups at substituting sites of main lead structure of known ARI. Finally, using high bioactivity relationship and total score values, we determined four potential ARIs out of these 71 compounds. Interestingly, these four ARIs include the two potent ARIs reported by Hu et al. (J Mol Graph Mod 2006, 24, 244) who obtained these through the complex computer docking and QM steps. This fact indicates the effectiveness of our proposed ANN-based technique. We suggest these four compounds to be the most promising candidates for ARIs to prevent the diabetic complications and further recommend for wet bench experiments to find their potential against AR in vitro and in vivo. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 http://onlinelibrary.wiley.com/doi/10.1002/jcc.21240/abstract