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Short Reads: Oct 1, 2001 (rev. 1)


In January, open-source bioinformaticists will participate in the first international "bio hackathon" — a programming event coordinated with the O’Reilly Bioinformatics Technology Conference in Tucson, Ariz., and co-produced by Electric Genetics in Cape Town, South Africa. The hackathon will take place in two parts over eight weeks and is intended to encourage collaboration and new ideas among various open-source bioinformatics groups.


PamGene, Plant Research International, and Whatman joined forces to develop rapid assays for agrobiotechnology applications. PamGene contributes its microarray platform and Whatman lends its technology for nucleic acid isolation, and the research will be performed at Plant Research International in the Netherlands.


For everyone who happily ignored Bush’s decision on stem cells, it may not be that easy to get away from the topic. Genomics companies may have an interest in stem-cell research after all: Gene Logic’s spinoff MetriGenix recently announced an alliance with stem-cell company Neuralstem, and Celera Genomics has a partnership with Geron capitalizing on Geron’s stem-cell work.


CombiMatrix will license and supply its microarrays to NASA’s Ames Research Center for functional analysis of genomes on earth and in space.

Qiagen’s getting busy. The Netherlands-based company announced microarray agreements with Bayer and Genicon Sciences.


As if artificial intelligence weren’t enough, now we’re faced with Artificial Life. The New York-based builder of software robot technology announced that it would begin targeting its products toward the genomics market. Don’t say we didn’t warn you.


News from the SNP Consortium: Celera and ABI will work with the consortium on a genome-wide SNP-based linkage map, to be analyzed by the Laboratory of Computational Genetics at Rutgers University. Meanwhile, the consortium has collaborated with Motorola to do genotyping for the linkage map.

Genomics Collaborative teamed up with ActivX Bioscience to identify and validate targets associated with colon cancer. The effort will rely on ActivX’s proteomics technology and use tissue samples from GCI’s database.


Celera and SomaLogic announced a proteomics collaboration. SomaLogic plays on its aptamer expertise, providing Celera with early access to aptamers and aptamer arrays, which should help link proteins with certain diseases. For its part, Celera gives SomaLogic access to its sequencing and proteins.


Bacteria vote for open source! The 5.67 million-base sequence of Agrobacterium, completed by researchers at the University of Washington School of Medicine, DuPont, and the University of Campinas in Brazil, was made freely available to the public at its own website (


Focusing on their strengths in drug and small-molecule discovery, Pharmacopeia and Eos Biotechnology will merge in a $197 million stock-for-stock deal.


Partnership pays off: BioBridge Computing finished developing its protein identification software (Protein Identification Using Mass Spectrometry, or PIUMS) and handed over the first unit to AstraZeneca, which partnered with the Swedish company in July. The software is expected to be launched in November with a $10,000 price tag.


Bio-Quant, a San Diego company typically dealing with diagnostics, looks to GPCRs as its next endeavor. The company created a new business division designed to offer screening technology for cell motility and GPCR activitation.


Ponce de Léon would be proud: Sydney-based Proteome Systems is working with California’s Buck Institute for Age Research to study the proteomics of aging. The first aim will be degenerative neurological disease. As soon as they find the fountain of youth, we’ll let you know.


The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.