Bio Saga Blog - A Chronicle of Life Sciences & Informatics

Established in 2011, Bionivid Technology, located in the happening start-up hub of Bangalore, is a genomics and informatics start-up, jointly cofounded by Mr Madavan Vasudevan, Mr Rohit Nandan Shukla and Mr Hitesh Goswami. Mr Madavan is a qualified microbiologist-turned-bioinformatician; His partner Mr Rohit is also a qualified bioinformatician and a certified programmer; and Mr Hitesh is a neurobiologist with a fine business acumen. All three of them make a perfect ingredient for raising a hot bioinformatics start-up. - See more at: http://www.biospectrumindia.com/biospecindia/features/221910/hot-start-ups-believe-leap-faith#.dpuf

The Department of Energy's Joint Genome Institute has chosen 41 research projects out of 152 applicants to use its sequencing services under its 2012 Community Sequencing Program, JGI said Thursday. Researchers for this year's CSP program, which provides the scientific community with access to JGI's high-throughput sequencing technologies, proposed projects to study plant-microbe interactions, how microbes are involved in carbon capture and greenhouse gas emission, and metagenomics. “These selections truly take advantage of the DOE JGI’s massive-scale sequencing and data analysis capabilities,” DOE JGI Director Eddy Rubin said in a statement.  “The projects span the globe and the unexplored branches of the tree of life, and promise to yield a better understanding of the interplay between climate, ecosystem, and organism.  Still other projects are targeting improvements in biofuel feedstock production, focusing on the potential of microorganisms to improve feedstock growth a...

Lectures presented by Dr George Grills, Director of Operations of Core Facilities in the Life Sciences, Cornell University.   http://www.mgrc.com.my/ess_Dr_George.shtml Share |

Life Technologies announced after the close of the market Tuesday that it will acquire sequencing technologies startup Ion Torrent Systems for $375 million in cash and stock. The total value of the deal could rise by another $350 million if certain technical and time-based milestones are met through 2012. Ion Torrent has developed the Personal Genome Machine, a benchtop instrument that is currently being used by early-access customers and will be launched later this year at an entry cost of less than $100,000. The system will be "optimal for mid-scale sequencing projects, such as targeted and microbial sequencing. The transaction is expected to be dilutive by $.02 for Life Tech's earnings per share in 2010, and neutral to earnings in 2011. It is expected to be accretive in 2012 and beyond. Life Tech said that its EPS guidance for FY 2010 remains unchanged at $3.35 to $3.50. The firms expect to close the transaction in the fourth quarter of this year. in early Wednesday trade ...

Courtesy Bioclues The growing bioinformatics unit in the Cancer Research Center in Sheba medical center (Tel Hashomer) is looking for a PhD student and a bioinformatician (see attachments). The Cancer Research Center is equipped with state of the art technologies for high throughput data analysis, including Solexa sequencing machine. We also have the benefits of close access to clinical and diagnostics data. All making it a gold mine for bioinformaticans. The bioinformatics unit in the Sheba cancer research cancer is seeking for a bioinformatican. The projects involve programming and usage of advanced bioinformatics tools and include analysis of deep sequencing data. Contact:   eran.eyal@sheba.health.gov.il ,  972- 03-5308148 Share |

The tables turn, it's 23andMe's turn to send a letter to FDA... Continuing the story  Reading Between Lines   slapped with cease and desist  letters . Direct-to-consumer genomics firm 23andMe has sent a letter to the heads of the US Food and Drug Administration and National Institutes of Health asking for a collaborative effort to develop guidelines for genetic testing. The firm  posted the letter  that it sent to FDA Commissioner Margaret Hamburg and NIH Director Francis Collins on its blog, The Spittoon, last night. 23andMe is one of several companies to be targeted recently by FDA, which  sent letters to several firms  saying that it believes the firms are selling unapproved diagnostic devices. The other firms that received letters were Knome, 23andMe, Decode Genetics, Navigenics, and Illumina, the last of which was cited for providing the tools that are used to provide genetic information to certain of the DTC genomics' customers. In the letter...

In a paper appearing in the early, online edition of the Proceedings of the National Academy of Sciences yesterday, an international research team reported that they have sequenced the genome of the human body louse , Pediculus humanus humanus . In the process, the researchers also generated sequence that helped them piece together the genome of a bacterial symbiont residing in the louse. Together, the two genomes are providing clues about louse adaptations to obligate parasitism on the human body. In addition, those involved say the work may ultimately provide insights needed to pave the way for more targeted control measures. "Understanding the genome should ultimately open up doors to better understanding how to deal with louse populations," co-senior author Barry Pittendrigh, an entomologist at the University of Illinois at Urbana-Champaign, told GenomeWeb Daily News .

Nick Loman at Pathogens: Genes and Genomes says that the key players emerging third-generation sequencing market are comparable to the Intel x86 family and its famed competitor, reduced instruction set computing — or RISC — chips in the early 1990s. "Despite the seeming obvious killer advantages … RISC chips resoundingly failed in the desktop PC market, never challenging Intel’s dominance," Loman recalls. He writes that labs considering which third-gen sequencing instruments to invest in is "very similar to the common nerd dilemma: buy a new laptop now, or wait for the next model?" Loman wonders whether the theory behind Moore's law will hold true for the transition from second- to third-generation sequencing technologies. "I propose that Illumina are Intel, and the Genetic Analyzer family — GA1, GA II, GAIIx, HiSeq 2000 — are x86. Life Tech is AMD, producing similar technology with much reduced market share," Loman writes, adding that "the thir...

Senior Bioinformatics Analyst Requirements: - PhD or equivalent experience in life science / biology. - 4+ years demonstrated success in working in the life sciences, preferably in an industry research settings. -In-depth understanding, analysis and processing of data from various post genomic technologies and their applications. - In-depth knowledge in gene expression (genotyping, chromosomal copy number, SNPs, gene signatures) and sequencing -Wide understanding of commercially available bioinformatics/clinical genomics tools and databases -Ability to handle complex / multi projects in rapidly changing environment. - Good knowledge on Perl, C / java and any relational databases. Responsibilities: - Analyzing and documenting project requirements. -Developing biocomputing algorithms for tools development and data analysis. -Performing biological analysis on data from various domains like gene expression, sequencing , molecular lab. -Co-ordination with sales team on projects to understan...

Computercraft seeks a highly motivated Molecular Biologist to join the Gene Expression Omnibus (GEO) curation team onsite at the National Institutes of Health (NIH) in Bethesda, MD. GEO is the largest fully public repository for functional genomic data, primarily microarray and next-generation sequence datasets. More information on GEO can be found on the web site http://www.ncbi.nlm.nih.gov/geo . RESPONSIBILITIES: We are currently looking for someone with a background in molecular biology , genomics, or biomedicine that is capable of working with large datasets. This person will be a member of the GEO curation team, helping to review and process incoming data submissions. The successful candidate will work at NIH's National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM). The successful candidate will perform the following tasks: - Review and evaluate data submissions for structural integrity and content. - Communicate extensively with rese...

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News . As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009 . The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database. The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant ...

The National Institutes of Health has awarded more than 12,000 grants totaling around $5 billion so far under the economic recovery and stimulus package, the White House said today. President Barack Obama commuted to Bethesda this morning to announce the funding as a milestone, to unveil a $175 million grant for cancer genomics, and to tour the NIH campus. In late-morning speeches before a crowd of NIH staff, President Obama, Health and Human Services Secretary Kathleen Sebelius, and NIH Director Francis Collins loosely outlined how the $5 billion in grants over two years — nearly half of NIH’s total $10 billion appropriation under the American Recovery and Reinvestment Act — will stimulate research and create jobs. A number of genomics-focused programs will be funded under the stimulus package, including $175 million over two years for The Cancer Genome Atlas, a joint effort between the National Human Genome Research Institute and the National Cancer Institute, according to a fact...

VisiGen Biotechnologies , a University of Houston gene-sequencing outfit acquired by Invitrogen in October for $20 million, represents the university’s biggest return on a spinout to date, and could eventually become one of its biggest overall tech-transfer wins, the school said last week. As a result of VisiGen’s acquisition, UH, which held an undisclosed equity stake in the startup, will receive nearly $500,000 from the initial installment of the deal. Plans for follow-on installments were not disclosed. An indirect benefit comes from the fact that approximately half of VisiGen’s current employees are UH graduates, the school said. Several of the scientists that founded the company will now continue to research second-generation sequencing techniques in their UH laboratories. Whether this research eventually sparks additional collaborations between VisiGen and the university is now up to Life Technologies, the biotech tool giant that resulted from Invitrogen’s multi-billion-dolla...

In Heidelberg, Germany, today researchers from eight countries and the European Commission announced the formation of a new research enterprise, the International Human Microbiome Consortium (IHMC), which will sequence the genomes of tens of thousands of microorganisms that live in and on the human body and that influence human health. Initial funding of more than US$200 million is being provided by the U.S. National Human Genome Research Institute (NHGRI) and the European Commission (EC). Jane Peterson, associate director of extramural research at the NHGRI, said international collaboration is very important in advancing science, and that “the sum is more than the parts.” Participants in the IHMC have agreed in principle to the free and open release of data and resources, and the coordination of research plans, as well as to sharing innovative developments, she reported. Data from microbiome research already being conducted by the NIH Human Microbiome Project and the EC Metagenomics ...

Previously blogging on GINA Dawn of the GATTACA era! now Industry Survey Shows: The surveyors found that only five percent of consumers said that they were “very likely” to take a disease-specific genetic test in the next few years, and 15 percent said they would be “likely” to take one. A total of 35 percent said that they would not submit to genetic tests, with 14 percent citing concerns about privacy, 5 percent saying they would not want to know about the results of their tests, and 16 percent saying both reasons would compel them to avoid genetic tests. Although more than 50 percent of those who responded said that they are concerned about getting cancer or heart disease, only 4 percent of those said they had taken a genetic test for a particular disease. Two-thirds of those who did have a genetic test were advised to do so by a doctor. The respondents had about the same comfort level of sharing genetic information with their spouses or partners as with their doctors, 72...

At JGI, we use whole-genome shotgun sequencing. This is a technique for determining the DNA sequence of a genome by randomly shearing the DNA, sequencing multiple fragments whose sequences overlap, and inferring the original sequence by reassembling the fragments. Three sizes of fragments are sequenced, 2-4 kb (kilobase, or 1000 bases), 8-10 kb, and 40 kb. This explanation follows the procedure for 2-4-kb fragments. Animation of the JGI production sequencing process Do you want to know more?

The United States Department of Agriculture has released the complete genetic sequences of 150 different avian influenza viruses and will make the information available through the National Institutes of Health’s GenBank. The USDA said on Friday that the sequencing data is part of the federal government’s Initiative on Avian Influenza, and that this information will be combined with studies that compare the viruses’ ability to infect poultry such as chickens, turkeys, and domestic ducks. This virus research that generated this data was conducted by the USDA’s Agricultural Research Service’s Southeast Poultry Research Laboratory (SEPRL), by the University of Georgia, the Ohio State University, the University of Delaware, and the University of Alaska-Fairbanks. "The project's ultimate goal is to sequence 900 avian influenza viruses from the SEPRL repository," David Suarez, a researcher with SEPRL, said in a statement. "These include avian influenza viruses col...

While nonribosomal peptides (NRPs) are of tremendous pharmacological importance, there is currently no technology capable of high-throughput sequencing of NRPs. Difficulties in sequencing NRPs slow down the progress in elucidating the non-ribosomal genetic code and negatively affect various screening programs aimed at the discovery of natural compounds of medical importance. We propose to employ multi-stage mass-spectrometry (MS n ) for the data acquisition, followed by alignment-based heuristic algorithms for data analysis. Since mass spectrometry based analysis of NRPs is fast and inexpensive, this approach opens the possibility of high-throughput sequencing of many unknown NRPs accumulated in large screening programs. Do you want to know more?

An “ecosystem” of partners who will use programmable hardware to create a standardized approach for analyzing data from second-generation sequencing instruments. Intel Seeks Partners to Develop FPGA-Based Solution for Next-Gen Sequencing Analysis . “Primary data analysis seems to be where Intel can play the most useful role” in the field, considering the initial analytical steps in sequencing: image processing, base calling, and alignment and assembly. One downside to this scenario, however, is that these codes would need to be written for FPGA-based systems – a very specialized programming skill that many bioinformatics developers don’t have. This challenge could present an opportunity for companies that develop FPGA-based algorithms and software-development toolkits. While the task of harvesting data from second-generation sequencing instruments has only just begun, both large and small labs are already facing some big choices over how to store the terabytes of data that these tools...

It's the technology. Watson's genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn't a $1000 genome , but it's a step in that direction. The real value of Watson's genome sequence is a proof of principle. This project was completed at a low cost (relative to the previous methods of sequencing genome), but with high quality. They were able to identify not only sequence variation between Watson and the reference genomes, but also structural variation. To truly realize the potentials of personal genomics, we need many more of these genomes, with the phenotypic data on the individuals. Along with the article, Nature has published a News and Views piece on the Watson genome paper . The article takes many steps to point out that, while we are at the cusp of an era of personal genomics, there are many limitations as to what we can do with these data. Given our current knowledge, w...