Bio Saga Blog - A Chronicle of Life Sciences & Informatics

A new paper written by researchers from the Institute for Systems Biology describes a computational approach for studying regulatory activities in cells that relies on integrated networks of transcriptional and metabolic data. The study, published in PLOS Computational Biology earlier this month, describes software called the Gene Expression and Metabolism Integrated for Network Inference (GEMINI) which uses an integrated model of network and metabolic data to explore growth phenotypes in Saccharomyces cerevisiae . GEMINI builds on work from the same researchers published in 2010 in the Proceedings of the National Academy of Sciences . That paper describes the Probabilistic Regulation of Metabolism (PROM), which provides a mechanism for integrating transcriptional regulatory networks and metabolic networks in a single in silico model and using it to make predictions about phenotypes such as flux and growth rate. While based on PROM, GEMINI is designed to tackle a slightly dif...

January 10-12, 2014  Birla Institute of Scientific Research, Statue Circle, Jaipur, India  [link]   Bioinformatics Centre at Birla Institute of Scientific Research, Jaipur is organizing a three-day Bioinformatics workshop on "Structural Bioinformatics". BISR is known for providing a high quality training in advance area of Biotechnology and Bioinformatics.  This workshop will enable participants to learn tools & techniques that are being used to analyze biological structures i.e. proteins and DNA along with application in drug design. The workshop will feature morning lectures, demonstrations with evening hands-on session in Bioinformatics lab.  The no. of participants is limited to 40 only. The participants of the course may be the UG/PG students, research scholars, faculty member and industry personnel with background in Biological Sciences and/or Information Technology. The workshop is self-contained and does not assume any special knowledge of the subjec...

Accelrys has bought Qumas, a provider of cloud-based and on-premise enterprise compliance software for regulatory and quality operations in regulated industries including the life sciences, for $50 million. Accelrys said that the added intellectual property extends its informatics portfolio by providing document and process management compliance solutions that improve its ability to help customers reduce regulatory risks and quality costs, improve compliance, and increase operational efficiency across their product development lifecyles. Operating from offices in Cork, Ireland and New Jersey, Qumas provides an electronic document management application with related research and development submission and QA documentation packages based on customer and industry requirements and best practices. Its business process management applications include corrective action/preventive action, audit, change control, deviation, complaint, and more. For the last two decades, the company has been ...

Here are some bioinformatics courses, These are geared towards: - Scientists, so they can think like a programmer and solve bottlenecks in data-based Biology - Computer programmers, so they know how to solve bioinformatics problems for scientists - Bioinformaticians, so they can advance their skills in newer application areas Some of these courses include scripting and database management with Linux, Perl, R, Matlab and MySql, while others include learning to use software for analyzing data from Microarray, NGS, Metabolomics and Proteomics platforms. A course on High Performance Computing and Primer Design is also offered. A detailed roster of scheduled courses is available at: http://www.bioinformatics.org/edu/calendar/view.php?view=upcoming Additionally, through Bioinformatics.org, an instructor-led program in practical bioinformatics is being offered. The goal here is to provide attendees a broad overview of the bioinformatics landscape, while giving them hands-on experienc...

GATTACA has always been one of my favorites; every now and then I have used it as a reference in many of my posts, this one being the recent! Genome From Birth - Dawn of the GATTACA era! This is what Senator Rand Paul (R-Ky.) says in his latest public address; Speaking at a Liberty University event in Virginia, Senator Rand Paul (R-Ky.) warned that genetic testing could lead to eugenics à la the 1997 movie Gattaca , reports the Associated Press . "In your lifetime, much of your potential — or lack thereof — can be known simply by swabbing the inside of your cheek," Paul said. "Are we prepared to select out the imperfect among us?" He was campaigning in Virginia for gubernatorial candidate Ken Cuccinelli. Other aspects of Paul's speech referring to the dystopian movie, though, resembled the Wikipedia entry on the movie, Rachel Maddow pointed out on her show on Monday. USA Today notes that Paul has not responded to those accusations. Paul added tha...

Illumina today announced it signed a definitive agreement to acquire clinical software firm NextBio. NextBio, based in Santa Clara, Calif., provides platforms to aggregate and analyze large amounts of phenotypic and genomic data for research and clinical applications. It currently has customers at more than 50 commercial entities and academic institutions. By acquiring the firm, Illumina "will be able to offer customers enterprise-level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare," according to a company statement. NextBio's platform allows customers to compare experimental data against existing data sets using a correlation engine, enabling them to discover new associations. It uses "highly scalable" software-as-a-service enterprise technology and is capable of analyzing petabytes of data. Illumina plans ...

Qiagen has acquired CLC Bio, a privately held bioinformatics software company headquartered in Aarhus, Denmark. The news was first reported on AllSeq's blog . This is the second bioinformatics company that Qiagen has purchased this year. In May, it bought Ingenuity Systems for $105 million in cash to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions ( BI 5/3/2013 ). Qiagen has been making some interesting moves lately, slowly building an end to end sequencing solution. They’ve already established themselves as the market leaders in sample prep, but then they started acquiring the missing pieces. First they bought Intelligent BioSystems in June 2012, giving them access to a sequencing platform built with the clinical market in mind (fairly standard SBS chemistry, relatively fast runs and multiple flow cells to obviate the need for sample multiplexing). Then they ...

Following Roche's disclosure last week that it will shut down 454 Life Sciences and stop supporting 454 sequencing instruments by 2016, customers are making plans to move their sequencing over to other platforms, if they have not done so already. While Illumina, Life Tech's Ion Torrent, and Pacific Biosciences are eager to step in to fill the void, some customers say aspects of 454's technology cannot be replaced by other platforms at this point. Also, those customers who have started to use 454 for routine clinical applications need to revalidate their assays on a new platform. Roche said last week that it will close down 454, which is based in Branford, Conn., and lay off about 100 employees over the next three years ( GWDN 10/15/2013 ). By mid-2016, it will stop supporting the 454 sequencing platforms, the GS FLX+ and the GS Junior. Roche's decision to pull the plug on 454 came to light less than a month after the company announced a deal with Pacific Bios...

Dawn of the GATTACA era! this was one of my old post. AND now this is what we hear from Robert Green The idea of sequencing someone's genome at birth has been "has been around for a long time in a pie-in-the-sky way," Robert Green from Brigham and Women’s Hospital tells Carl Zimmer at Slate . But it is becoming more of a reality, Zimmer adds. Green's BabySeq project recently received funding from the US National Institutes of Health to study how sequencing the genomes of some 240 healthy and ill infants affects their lives. They will be compared to a similar cohort of infants whose genomes will not be sequenced. As the study is small, Zimmer notes that rare, deleterious mutations may not crop up. The project will, though, make the discussion of ethics in genomic medicine more concrete, he says. “We’ll be grappling with them in real life, with real babies and real families and real clinicians and real laboratory results,” Green adds.

By considering sequence data for individuals assessed through the 1000 Genomes Project, a team led by researchers from Yale University and Wellcome Trust Sanger Institute came up with a computational method for prioritizing potential disease culprits — including those in non-protein-coding parts of the genome. As they reported online today in Science , the researchers sifted through SNP profiles in coding and non-coding sequences in 1,092 genomes, focusing on functionally annotated areas. With the help of information from the ENCODE project, mutation databases, and other data sources, they narrowed in on sequences that seem especially sensitive to change. The group tapped these mutation-sensitive sites to develop an approach called FunSeq, which proved useful for uncovering new apparent driver mutations using sequences from around 90 cancer genomes. These included almost 100 driver candidates in non-coding sequences, according to study authors, who noted that FunSeq is expected...

PerkinElmer Reduces Headcount by More than 400 in 2012 PerkinElmer reduced its workforce by 62 employees during the first quarter as part of a restructuring plan, PerkinElmer Lays off 265 in Second Quarter PerkinElmer laid off 265 employees during the second quarter, the company said in its Form 10-Q today. In the document filed with the US Securities and Exchange Commission, it said that the reduction in workforce was part of a restructuring plan to move some of its operations into a newly established shared service center and to realign operations, R&D resources, and production resources as a result of previous acquisitions. During the company's recent second quarter earnings conference call , PerkinElmer Chairman and CEO Robert Friel said that the firm had consolidated three North American facilities, "and efforts are underway to consolidate two additional legacy Caliper sites, further simplifying our operational footprint and improving our R&D effi...

The nonprofit ECRI Institute has released a BRCA testing information guide for patients interested in learning more about the genetic risk of hereditary breast and ovarian cancer. The guide comes in response to the growing concern and questions among women about the information their genes contain about the risk for cancer, after actress Angelina Jolie wrote an op-ed piece discussing her decision to get a double mastectomy as a result of carrying a BRCA1 mutation associated with heightened risk of hereditary breast and ovarian cancer. There are reports that Jolie's highly publicized and controversial decision has caused a spike among women asking their physicians for BRCA testing. "People can get caught up in the headlines, which can lead to quick, uninformed decisions," says Vivian Coates, VP of information services and health technology assessment at ECRI Institute, in a statement. "Many women may find that after talking to their physicians about their ris...

                      -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-                         BI231 NGS Data Analysis                             June 24-28, 2013                       Online at Bioinformatics.Org          http://www.bioinformatics.org/wiki/BI231_NGS_Data_Analysis                    http://www.bioinformatics.org/edu/AGGT -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics to be covered include the description of sequencing strategies and platforms, experiment types, data format...

Qiagen said this week that it acquired Ingenuity Systems for $105 million in cash in order to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions — from sample preparation to data interpretation. Under its new parent, Ingenuity will continue to operate out of its offices in Redwood City, Calif., and retain all 120 current employees, while CEO Jake Leschly takes on new responsibilities within Qiagen's life science business unit. Ingenuity will also continue to develop and offer products under its existing licensing scheme. Its portfolio includes a knowledgebase of curated genomic variants; Ingenuity Pathway Analysis, its web-based application for modeling and analyzing biological pathways; Ingenuity Variant Analysis, which selects clinically relevant genomic variants from NGS data ( BI 1/13/2012 ); and Ingenuity iReport, its software for reporting the results of gene ...

Thermo Fisher Scientific Inc. has offered to pay about $13.6 billion to buy genetic testing equipment maker Life Technologies in a cash deal that will create a giant company serving research and specialty diagnostics. The Waltham, Mass., company said Monday it has agreed to pay $76 in cash for each share of Life Technologies, which is based in Carlsbad, Calif. Do you wish to know more?

Dako today said that the US Food and Drug Administration has approved two assays for use as companion diagnostics for a Genentech drug targeting HER2-positive metastatic breast cancer. FDA simultaneously approved Dako's HercepTest and HER2 IQFISH pharmDx assays and Genentech's drug Kadcyla (ado-trastuzumab emtansine). Kadcyla is for patients with HER2-positive metastatic breast cancer who have been previously treated with Genentech's Herceptin (trastuzumab) and a taxane chemotherapy. Dako, an Agilent company, and Genentech, a Roche company, have been collaborating on the development of companion diagnostics for Genentech's drugs for a few years. In May 2012 the two firms inked a pact to collaborate on the FDA submission of Dako's assays for Kadcyla. A month later the HercepTest and HER2 FISH pharmDx were approved by FDA as companion diagnostics for Genentech's breast cancer drug Perjeta (pertuzumab). In late 2011, FDA gave the thumbs up to Dako's H...

Courtesy Genomeweb & Julia Karow   Studying for a dual degree in mathematics and molecular biology, Nick Tatonetti became interested in using computational models to study biology and make sense of its massive datasets. As a bioinformatics PhD student at Stanford, he developed new statistical models and computational approaches for analyzing drug effects and drug-drug interactions. At Columbia, Tatonetti is now focusing on molecular mechanisms of drugs. "We can actually think of each time a patient is being given a drug as an experiment," he says. "When the drug goes into the human system, it interacts molecularly, and then phenotypes come out of this system," which can be connected to molecular mechanisms in new ways. In particular, he is developing techniques that use clinical data to develop networks that highlight interactions between different systems in the human body, such as two organs. "And once we know that certain gene produc...

NextBio said this week that it is partnering with Emory University’s Winship Cancer Institute and the Aflac Cancer Center to work on identifying biomarkers that can predict brain cancer metastasis in children, which will help clinicians determine which patients should receive radiation therapy. The partners will use NextBio Clinical software to analyze and interpret molecular and genomic data collected from children with medulloblastoma, a childhood brain tumor that affects around 500 children in the US every year and accounts for 20 percent of all brain cancers in children below the age of 19. Specifically, “this study will look at clinical and genomic data from real patients, as well as data from mouse models and frozen human tissue samples, and then will correlate these data sets with other data from the public domain,” Alpana Verma-Alag, NextBio’s head of clinical development, explained in a statement. Tobey MacDonald, director of Aflac’s brain tumor prog...