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De novo transcriptome assembly with RNA-seq data: Using Trinity to examine Caribbean Millepora

Despite the abundance of the hydrocoral genus Millepora, which consists of 19 species distributed in warm waters around the globe, the milleporids have received limited attention in coral reef studies. However, Millepora act as an important component of the reef framework and thus are geologically important. We recently hosted a …

Written by carol

The Global Alliance for Genomics and Health – Meeting Notes

On March 4th, over 200 experts in genomics, healthcare, biomedical research, bioinformatics, ethics, and patient advocacy converged on London. Their destination: The Wellcome Trust at 215 Euston Rd, host of the first meetup of the Global Alliance for Genomics and Health. As a partner of the alliance, we were thrilled …

Written by deniz

Lior Pachter, biological networks, and the future of science

The scientific community is assessing manners, I think, because so many of us are in a better position to comment on those than on the science. There’s more drama in bioinformatics this past month, as Lior Pachter, with his student Nicolas Bray, published a series of blog posts eviscerating, among …

Written by Nate

Algorithms for Bioinformaticians

One opportunity that comes from working in an infant discipline is that of being able to examine and influence its basic tools. You are more likely to fundamentally improve alignment or assembly than you are to improve the foundations of thermodynamics. And given the state of bioinformatics software, it is …

Written by Nate

Ion Proton RNA-Seq: in search of the best alignment method

Each sequencing technology comes with a unique and unavoidable error profile due to the chemistry, biology, and hardware involved [1,2,3]. If we want avoid analysis artifacts and arrive safely at the biological reality underlying the data, we must to account for these errors during informatic analysis. Recently, researchers have begun tackling …

Written by Kate Blair

World Economic Forum: Technology Pioneers are Boston Strong

With less than a week until Super Bowl XLVIII in New Jersey, we’re taking a look at a different meeting of elites. We’re not talking about Peyton Manning, and we’re certainly not talking about Russell Wilson. Instead, we’re focusing our attention on the World Economic Forum’s Annual Meeting, which took …

Written by carol

Seven Bridges talks genomics with MongoDB and AstraZeneca

  Our CEO, Deniz Kural, recently joined Jason Tetrault, Architect at AstraZeneca Pharmaceuticals, for a panel discussion of topics in genomics and pharmaceuticals in an event hosted by MongoDB. Before the panel, Jason gave what he described as a “fairly inaccurate overview of genetics processing” from the sequencer to the …

Written by carol

Microsoft Research CABI 2013

This Monday we went to Microsoft’s beautiful NERD building for Microsoft Research’s 2013 conference in Computational Aspects of Biological Information (CABI). The pastries were good and the presentations were even better. Jim Collins spoke about implementing flip-flops in bacteria, and about the prospects of biocomputation more generally; Pardis Sabeti discussed …

Written by Nate

The GTEx methods debate

This week, a dialogue erupted around the Genotype-Tissue Expression (GTEx) Consortium and its methods for analyzing RNA-Seq data. Tracking the debate will take you through Twitter threads, into blog posts, down comments sections, past PubMed entries, and over Nature‘s login wall.

Written by Kate Blair

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