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Markers/Short Reads: Jan 1, 2005


Former Lynx Therapeutics CEO Norrie Russell joined Invitrogen as VP and general manager of the functional genomics business unit. Most recently, Russell served as president and CEO of Aviva Biosciences.

Zyomyx auctioned off some $50 million worth of equipment and whittled its staff to six employees, the company reported in late October. By early December, Zyomyx signed a product development deal with Invitrogen, which licensed more than 30 of Zyomyx’s protein-chip patents. Meantime, Peter Wagner was promoted to CEO of Zyomyx, replacing Robert Monaghan.

Optical mapping company OpGen appointed Joseph Shaw as its CEO. Shaw was formerly president of Bank on a Cure, which developed a myeloma-specific cancer patient DNA database.

John Bergeron, president of HUPO and director of the Montreal Proteomics Network, received the McLaughlin Medal from the Royal Society of Canada.

The University of North Carolina received a $1 million grant from NCRR to develop a genome fingerprint scanning program. The goal of the program is to match mass spec data to raw sequence data to identify proteins and novel genes, according to grant givers at the NIH.

Isidore Edelman, who helped found the Columbia Genome Center at Columbia University, died last November of gastrointestinal cancer at the age of 84.

Sun Microsystems launched two new off-the-shelf bioinformatics bundles late last year, and expected two more to follow suit before year end. The packages incorporate various genomic programs, such as Geospiza’s Finch Sequencing Center or Incogen’s VIBE software, running on Sun hardware.

Dennis Gilbert was bumped up to the CSO post at Applied Biosystems. He also serves as VP of research for the company and is a VP of Applera as well.

HapMap data is now freely available to the public, thanks to the end of the consortium’s computer-based click-wrap license restrictions. Previously, researchers interested in viewing the data had to agree that they would not do anything to it, such as obtain a patent on it, that would restrict others’ access to that data.

The NIH has proposed best practices for licensing government-funded genomic inventions, including antisense molecules, siRNAs, cDNAs, ESTs, haplotypes, genes, and more. The agency’s intramural tech transfer group and funding recipients will provide feedback on the proposal, which offers guidance on when to patent an invention, for example.

The Translational Genomics Research Institute and the International Genomics Consortium received seed capital worth $1.35 million in order to build a joint, for-profit reference laboratory. Money for what will be the Molecular Profiling Institute was provided by Scottsdale Healthcare, the Flinn Foundation, AmeriPath, and VC firm EA Management. IGC’s Bob Penny is the lab’s CEO.

Jeff Schneider, who co-founded artificial intelligence company Schenley Park Research, is the new chief informatics officer at PsychoGenics, where he will oversee a bioinformatics team.

Researchers at the Children’s Hospital of Boston will use microarrays to study RNA from white blood cells as part of an effort to find the genetic and biochemical causes of autism. For that part of the study, expected to include up to 150 children, scientists will try to find patterns among thousands of genes. In parallel research, Ingrid Holm and Louis Kunkel will perform association and linkage studies on DNA samples.

The National Institute of Dental and Craniofacial Research launched a three-year study to catalog the genes found in oral biofilms. The research is expected to yield tens of thousands of genes, and scientists hope to find gene expression patterns that could help predict or enable early detection of periodontal diseases.

Yale University and Enzo Biochem were granted an extended discovery phase in their patent infringement lawsuit against Applera and Tropix. Yale and Enzo charge that Applera has infringed seven patents, at least four of which relate to DNA sequencing. In other Applera news, the European Patent Office revoked one of the company’s patents on real-time PCR thermal cycling. The company plans to appeal the decision.

The University of St. Andrews in Scotland opened a new $11.5 million proteomics facility aimed at seeking treatments for “superbugs.”

Affymetrix and Roche Diagnostics filed for FDA approval to use their CYP 450 AmpliChip microarray as a de novo in vitro diagnostic.

After less than two years of operation, the Charles River Proteomic Services unit of Charles River Laboratories will close. The operation was a joint venture with Proteome Systems and failed to meet “its strategic goals,” according to Charles River Labs.

About 60 percent of the protein-coding genes in the chicken genome have counterparts in the human genome, according to a paper published late last year in Nature. The International Chicken Genome Sequencing Consortium comprised more than 170 researchers from nearly 50 different institutions.

Two proteomics research consortia based at the University of Michigan and the Fred Hutchinson Cancer Research Center were awarded $13.4 million in NCI grants to develop tools and resources for protein biomarker discovery using mouse models of human cancer. Research teams are led by UM’s Sam Hanash, and Martin McIntosh and Amanda Paulovich at the Hutch.

Orion Genomics and a research team at the North Carolina State University will share $1.59 million from the USDA to sequence the genome of the parasitic root knot nematode, a major vegetable pathogen.

Nicolas Roelofs was due to resign as COO of Stratagene by the end of last year. Roelofs, who wished to be closer to his family, will be temporarily replaced by Joseph Sorge.

Illumina is slated to save $3.3 million in various legal costs after a judge determined that punitive damages awarded in the wrongful termination suit of former CSO Anthony Czarnik were “grossly excessive.” Illumina will still have to pay the remainder of the punitive damages, which now come to $2.2 million.

Invitrogen intends to acquire Chinese reagent supplier Bio Asia for up to $8 million in cash. The company also said it would invest more than $20 million in China over the next five years.

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.