Q&A: U of Maryland's Steven Salzberg on Assembling Genomes with Short-Read Sequence Data

July 06, 2010

Salzberg, who has developed a suite of open-source, freely available tools for genome assembly, alignment, and analysis, spoke with In Sequence recently on the challenges of developing informatics tools for next-generation sequencing technology.

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In this issue of In Sequence

Video Spotlight

A Conversation with the American Museum of Natural History's George Amato

The American Museum of Natural History's George Amato, director of the museum's Sackler Institute for Comparative Genomics, discusses conservation and "landscape" genetics, his PLoS One paper on the use of DNA barcoding to detect illegal bushmeat in New York-area airports, and more.

May 22, 2012

Shashikant Kulkarni at ACMG

BioArray News editor Justin Petrone sat down with Shashikant Kulkarni, an associate professor at Washington University School of Medicine at St. Louis, to discuss chromosomal microarrary analysis in the clinic, SNP arrays versus CGH platforms for post-natal testing, and more.

May 16, 2012

Miragen Therapeutics' Eva van Rooij

Miragen Therapeutics' Eva van Rooij discusses microRNA-based therapeutics, the challenges associated with chronic microRNA knockdown, therapeutic microRNA antagonists, and more.

May 08, 2012

A Conversation with CeGaT's Saskia Biskup

In this video, Julia Karow, Editor of Clinical Sequencing News, interviews Saskia Biskup, CEO of the Center for Genomics and Transcriptomics, or CeGaT, at the company's headquarters in Tübingen, Germany.

May 02, 2012
Young Investigator Profile

Erin Carlson

Assistant Professor
Indiana University

Bacterial Pathogenesis

The Carlson lab researches the development and application of advanced chemical biology and systems biology technologies to both define the mechanisms of bacterial pathogenesis and identify potential therapeutic agents. They are pursuing the development of technologies for natural product discovery including innovative methods for compound isolation, screening, and diversification. In addition, they are also utilizing state of the art metabolomic and proteomic methods to map the biochemical pathways associated with bacterial pathogenesis and antibiotic resistance.
Blog

HPC & Cryo-Electron Microscopy Data

Researchers at the Texas Advanced Computing Center are using every piece of HPC hardware they can get their hands on to ramp up drug design.

May 24, 2012

DARPA's Synthetic Army

DARPA's getting into the genetic engineering business, with the help of the J. Craig Venter Institute and others.

May 24, 2012

Watch and Learn

A science journal presents researchers' work in video form.

May 24, 2012

Peaks and Valleys in the Private Sector

While funding has tightened, returns on investments made in the life-science sector have risen, Nature Biotechnology reports.

May 24, 2012
Papers of Note

Connection Between Epigenome, Selective Mutability, Evolution, and Human Disease
Li, Harris et al., PLoS Genetics
Researchers at the Baylor College of Medicine and elsewhere propose a "connection between the epigenome, selective mutability, evolution, and human disease" based on the findings of their study on associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination mediated by low-copy repeats. "Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability," the Baylor-led team writes.

Genetic Data for Modern Genetic Breeds 'Have Yet to Shed Light on Dog Origins'
Larson, Karlsson et al., PNAS
A team led by researchers at the University of Durham investigate the value of modern genetic data to elucidate the origins of dog domestication by analyzing 49,024 autosomal SNPs in 19 wolves and 1,375 dogs, representing 35 breeds. The team reports having uncovered conflicting evidence when correlating the earliest archeological dogs with the geographic locations of 14 breeds thought to be ancient. "These genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins," the authors write.
People on the Move

IntegenX has appointed David Smith to serve as its new COO. Smith most recently served as CFO of Thoratec, and previous to that was CFO at Chiron. He currently is chair of the audit committee and a director of OncoGenex Pharmaceuticals and previously was chair of the audit committee and a director of Perlegen Sciences.

Vermillion said this week that President and CEO Gail Page will be leaving the company by September and the firm has begun the process to find her successor. Page also has resigned her seat on the board of directors, and effective immediately Vermillion amended its bylaws to eliminate the vacant seat, reducing its board from seven to six members.

Genomic Health has appointed Richard Tompane as president of its new subsidiary InVitae, which will focus on developing next-generation-based sequencing diagnostics for genetic diseases. Tompane was previously president and CEO of Gemfire and has also served as an independent consultant.
Upcoming Events

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May 16-17 / Boston
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May 19-22 / Heidelberg, Germany
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TIDES: Oligonucleotides and Peptide Technology & Product Development
Applications of Nucleic Acids Technologies in Molecular Diagnostics, Oligonucleotide Therapeutics Discovery, and Peptide Discovery and Development
May 20-23 / Las Vegas
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Microtubules: Structure, Regulation and Functions
May 23-26 / Heidelberg, Germany
EMBL

Evidence for Clinical Utility of Molecular Diagnostics in Oncology: A Workshop
May 24 / Washington, DC
Institute of Medicine

Abstract & Registration Deadlines

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Science
A pair of studies, one published in Nature and one published in Nature Genetics, detail the efforts of researchers who used exome sequencing to look into the mutational profiles and pathways that can contribute to prostate cancer. The first group found nine genes with recurrent somatic mutations, six of which had previously been implicated in the disease. The second group demonstrated that recurrent mutations in the ubiquitin ligase-coding gene called SPOP define a non-ETS gene fusion containing prostate cancer subtype.
Business
Based on expectations of mid-single digit organic revenue growth annually, Thermo Fisher Scientific's revenues for 2016 could fall between $14.5 billion and $15.5 billion, the firm said in a presentation at its analyst meeting. The firm also said that it plans to ramp up its presence in Asia-Pacific and the emerging markets. Last year, about 19 percent of its business came from the APAC and emerging markets. By 2016, it has a goal of increasing that figure to 25 percent with a strategy that seeks to replicate a "successful China/India formula."
Funding
The UK's Biotechnology and Biological Sciences Research Council will invest £19 million ($29.8 million) in the Genome Analysis Center at the Norwich Research Park in the UK as part of a broader, five-year £250 million ($392 million) investment in the biosciences. As part of the larger investment, the Roslin Institute in Scotland will receive £23 million to further its livestock animal genomics research, the Babraham Institute in Cambridge will get £37 million, and the John Innes Centre will receive £42 million.
Genome Technology Magazine
More than a decade ago, fluorescent reporter studies highlighted the stochastic nature of gene expression, and biologists then began to examine the phenotypic heterogeneity they saw in clonal cell populations, through they chalked up what they saw to noisiness in gene expression. Still, researchers wondered about the cause of the randomness they had observed. Now, biophysicists and systems biologists are looking into that question and aim to figure out how and why single cells and molecules behave the way they do, and the consequences of that behavior.

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Q&A: U of Maryland's Steven Salzberg on Assembling Genomes with Short-Read Sequence Data

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