Skip to main content
Premium Trial:

Request an Annual Quote

Early to Bioinformatics, Early to Rise


With an undergraduate degree in astrophysics and a PhD in ocean engineering, KENNETH JACOBSEN doesn’t seem exactly cut out for his new job as vice president of independent software programs at SGI. But this is another case of the early bird getting the worm. Jacobsen, who hits the office most days by 6 am, initiated SGI’s entry into bioinformatics and operations research back in 1993 and worked his way up the ranks. He now has responsibility for all partner programs and technical support, and horizontal applications marketing. He still oversees SGI’s three-person bioinformatics team ¯ JULI NASH, HARUNA COFER, and DMITRI MIKHAILOV ¯ but says bioinformatics occupies only about 4 percent of his time now: there are some 100 other employees in the ISV group. Before joining SGI, Jacobsen, Nash, and another current SGI employee, Jeff Fear, all worked at MasPar, a hardware provider that made massively parallel machines with 16,000 processors and had The Institute for Genomic Research as a client. The MasPar boxes “were ideally suited for genomics,” because they used a SIMDI (single instruction multiple data) architecture where all the processors perform the same function with different data. This is good for doing matches on protein strings, for example, but the machines were difficult to program and hence “not commercially viable,” Jacobsen says. Later, when he and his MasPar colleagues joined SGI, they adapted that technology onto RISC (reduced instruction set computer) processors as a way to avoid SIMDI’s limitations.

— Matthew Dougherty

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.