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"The rapid improvement in DNA sequencing has sparked a big data revolution in genomic sciences, which has in turn led to a proliferation of bioinformatics tools. To date, these tools have encountered little adversarial pressure. This paper evaluates the robustness of such tools if (or when ) adversarial attacks manifest. We demonstrate, for the first time, the synthesis of DNA which - when sequenced and processed - gives an at- tacker arbitrary remote code execution. To study the feasibility of creating and synthesizing a DNA-based exploit, we performed our attack on a modified down- stream sequencing utility with a deliberately introduced vulnerability. "

"uBiome is a citizen science project that allows the public access to cutting edge sequencing technology to understand their health through the microbiome. How does the microbiome affect my health? We are all covered in trillions of microbes -- in fact, they outnumber human cells 10:1. The trillions of bacteria live on and in us are collectively called the microbiome. Like the rainforest, the healthy human microbiome is a balanced ecosystem. The correct balance of microbes keeps potential pathogens in check and regulates our immune system. Microbes also perform essential functions such as digesting food and synthesizing vitamins. Studies have also linked the microbiome to human mood and behavior, as well as many gut disorders, eczema, and chronic sinusitis."

UCSC Genome Bioinformatics Genocoding Project Genomic Text Indexing: Scanning papers for genomic identifiers and mapping them to the human genome. We currently recognize DNA and protein sequences, SNPs, bands and gene symbols.

Come work with us Interested in working with researchers from different disciplines within the Harvard, MIT and Broad community and an unique opportunity to participate in world-class research to make an impact on human health? Come work with us! We are looking for a computational biologists to handle data from a wide variety of experimental methods, focusing on next-gen sequencing technologies. Keep Reading...  SCDE is live The Stem Cell Discovery Engine (SCDE) is an integrated platform that allows users to consistently describe, share and compare cancer and tissue stem cell data. It is made up of an online database of curated experiments coupled to a customized instance of the Galaxy analysis engine with tools for gene list manipulation and molecular profile comparisons. The SCDE currently contains more than 50 stem cell-related experiments. Each has been manually curated and encoded using the ISA-Tab standard to ensure the quality of the data and its annotation. Keep Reading...  The Center for Health Bioinformatics at the Harvard School of Public Health provides consults to researchers for the management, integration and contextual analysis of biological high-throughput data. We are a member of the Center for Stem Cell Bioinformatics, the Environmental Statistics and Bioinformatics Core at the Harvard NIEHS Center for Environmental Health and the Genetics & Bioinformatics Consulting group for Harvard Catalyst and work closely with our colleagues in the Department of Biostatistics and the Program in Quantitative Genomics to act as a single point of contact for computational biology,

"Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake."

"The aim of the project is to get acquainted with usually inaccessible laboratory procedures - extraction of various organic substances and study them further, growing bacteria on agar plates, DNA extraction and sequencing, explant cultures, various behavioral studies (see BrmRat ) and even heredity experiments. A lot of this may be simple stuff you do not need a well-equipped lab for - once we understand the principles, we can make our way forward. Goals The goal of this project is mainly to enable access to experimental biology for everyone interested in it"

ScienceDaily (June 2, 2010) - Using high-throughput sequencing to map the locations of a common type of jumping gene within a person's entire genome, researchers at the University of Pennsylvania School of Medicine found extensive variation in these locations among the individuals they studied, further underscoring the role of these errant genes in maintaining genetic diversity.

A massive analysis of almost every bacterial genome sequenced to date suggests a new shape for the tree of life. digg_url

Telomeres, the repetitive sequences of DNA at the ends of linear chromosomes, have an important function: They protect vulnerable chromosome ends from molecular attack. Researchers at Rockefeller University now show that telomeres have their own weakness. They resemble unstable parts of the genome called fragile sites where DNA replication can stall and go awry. But what keeps our fragile telomeres from falling apart is a protein that ensures the smooth progression of DNA replication to the end of a chromosome.

A new strain of MRSA has been identified in cows' milk and in people, but don't stop drinking milk - the bug is killed off in pasteurisation. However, the strain evades detection by standard tests used by some hospitals to screen for MRSA (methicillin-resistant Staphylococcus aureus), potentially putting people at risk. Laura Garcia Alvarez, then at the University of Cambridge, and colleagues were studying infections in British cows when they discovered antibiotic-resistant bacteria that they thought were MRSA. However, tests failed to identify the samples as any known strains of the superbug. Sequencing the mystery bacteria's genomes revealed a previously unknown strain of MRSA with a different version of a gene called MecA. The new strain was also identified in samples of human MRSA, and is now known to account for about 1 per cent of human MRSA cases.

In 1967, Simon Kochen and Ernst Specker proved mathematically that even for a single quantum object, where entanglement is not possible, the values that you obtain when you measure its properties depend on the context. So the value of property A, say, depends on whether you chose to measure it with property B, or with property C. In other words, there is no reality independent of the choice of measurement. It wasn't until 2008, however, that Alexander Klyachko of Bilkent University in Ankara, Turkey, and colleagues devised a feasible test for this prediction. They calculated that if you repeatedly measured five different pairs of properties of a quantum particle that was in a superposition of three states, the results would differ for the quantum system compared with a classical system with hidden variables. That's because quantum properties are not fixed, but vary depending on the choice of measurements, which skews the statistics. "This was a very clever idea," says Anton Zeilinger of the Institute for Quantum Optics, Quantum Nanophysics and Quantum Information in Vienna, Austria. "The question was how to realise this in an experiment." Now he, Radek Lapkiewicz and colleagues have realised the idea experimentally. They used photons, each in a superposition in which they simultaneously took three paths. Then they repeated a sequence of five pairs of measurements on various properties of the photons, such as their polarisations, tens of thousands of times. A beautiful experiment They found that the resulting statistics could only be explained if the combination of properties that was tested was affecting the value of the property being measured. "There is no sense in assuming that what we do not measure about a system has [an independent] reality," Zeilinger concludes.

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