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Molecular Connections, Georgetown University Medical Center, Institute for Systems Biology, New York University

Molecular Connections Attains ISO Certification
Molecular Connections, a life science informatics company based in Bangalore, India, said on Friday that it has obtained ISO/IEC 27001:2005 certification.
ISO/IEC 27001:2005 is an information security standard developed by the International Organization for Standardization and the International Electrotechnical Commission. It defines requirements for “establishing, implementing, operating, monitoring, reviewing, maintaining and improving a documented information security management system within the context of the organization's overall business risks,” according to the ISO website.
Molecular Connections said it is the first Indian life science and informatics company to be certified under ISO/IEC 27001:2005.

Genomic, Proteomic Tools May Yield 'Simplistic' or 'Misleading' Conclusions
Data generated by genomic and proteomic technologies are overly complex, causing some cancer researchers to arrive at “simplistic” or “misleading” conclusions, according to a review article in the January issue of Nature Reviews Cancer.
The study, led by researchers at Georgetown University Medical Center, concluded that scientists “don’t appreciate how complex the data is that is being generated.”
High-throughput genomic and proteomic tools “have allowed us to see that nature is more complex than we thought, and while we don’t yet know what the overarching biological rules are — such as the interrelationship between multiple signaling pathways that can lead to cancer development — we are trying to play the game like we do,” lead author Robert Clarke, professor of oncology and physiology and biophysics at GUMC’s Lombardi Comprehensive Cancer Center, said in a statement released yesterday.
“The answers to our questions are probably there in the data, but the issue is whether we can get them using these complex tools and, also, how we will know they are right when we see them,” he added.
Clarke, who is also interim director of GUMC’s Biomedical Graduate Research Organization and co-director of the school’s Breast Cancer Program, led the analysis with six other scientists from Georgetown and from Virginia Polytechnic Institute.
In the statement, GUMC said researchers like Clarke are currently studying ways to “understand the theory and properties of the data” generated by genomic and proteomic tools and “how they may affect data analysis and interpretation.”
At the core of the challenge is that in the clinical evaluation of cancer, the “thousands of active molecules” that exist in a single excised tumor sample produce “very high-dimensional data spaces.” As a result, researchers face “10,000 or so dimensions, if you consider a molecule working along a pathway as a dimension.”
Clarke uses the analogy of a box, which has a height, a width, and a length. But if you add color and fiber you add two dimensions, he said. “There are countless things going on in a cell that could describe it; this is the essence of multi-dimensionality and these tools tell you all of that.”
Not all of these data will be relevant to the research that yielded them. “Some cells in a tumor are dying, some are not. Some are growing, others are not. Some are trying to spread and the rest aren’t,” Clarke said. “Everything is going on in a tumor at once, and all of these activities require coordination of different genes. So it may not be accurate to analyze these molecules as if they are all focused on performing a single function.
“We need to discover what specific genes perform which function,” he said. “If we knew the rules” — which genes participate in which process, for instance — “we should be able to understand some of the questions we have, but we are not there yet.”

ISB, NYU Team Use Genomic, Proteomic Tools to Create Model for Improving Genetic Engineering
Scientists at the Institute for Systems Biology and New York University have developed a model that can characterize and predict how a free-living cell responds on the molecular level to genetic and environmental changes.
Called EGRIN, for Environmental and Gene Regulatory Influence, the mode uses data from genome-wide binding-location analyses for eight transcription factors; mass spectrometry-based proteomic analysis; protein-structure predictions; computational analysis of genome structure; and protein evolution.
The results of their study may enable researchers to perform “more complex” genetic engineering with “fewer unintended consequences,” the scientists said in a statement.
Writing in the online edition of the current issue of the journal Cell, the researchers showed that EGRIN was able to link biological processes with previously unknown molecular relationships. They also showed that it could predict new regulatory powers of know biological processes as well as how more than 1,900 genes respond to “novel” genetic and environmental experiments.
To arrive at their results, the researchers studied the “poorly characterized” archaeon Halobacterium salinarum NRC-1. They perturbed the organism by altering 10 environmental factors and 32 genes, characterizing the resulting growth and/or survival phenotype, and quantitatively measuring steady state and dynamic changes in mRNA.
There next step will be to apply EGRIN to more complex organisms or networks and to "actually reengineer organisms based on knowledge obtained" through the model.

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The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.