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Corrections & Kudos, Complaints & Congrats

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Error corrected, suspect eliminated

On page 26 of the article about Lee Hood (“Lee Hood’s $200 Million New Thing,” September 2000), it is stated incorrectly that “Hood chairs Stowers’ scientific advisory board.” Lee Hood resigned from the Scientific Advisory Board of the Stowers Institute for Medical Research in March 2000. The chair is Douglas A. Melton, PhD, Thomas Dudley Cabot Professor in the Natural Sciences and Chair of the Department of Molecular and Cellular Biology at Harvard University.

Neither the Stowers Institute nor the Institute’s founders, James and Virginia Stowers, are the source of seed funds at the Institute for Systems Biology.

William B. Neaves, PhD
President and CEO
Stowers Institute for Medical Research

Praise of the Highest order: We Kick Butt

Congrats on the new magazine! I really like it. You are covering an angle that nobody else has tried!

Martin Gollery
Bioinformatics
TimeLogic Corporation

Dr. Cantor asked me to tell you he thought the article in Genome Technology (“Lee Hood’s $200 Million New Thing,” September 2000) was very good. And good luck with your new magazine!

Ann Butler
Assistant to Dr. Charles Cantor
Chief Scientific Officer
Sequenom

Congratulations on your new magazine. I''ve enjoyed reading each issue. I know you''ve worked hard for this. Your success is well deserved. Keep up the good work.

Eric Blossom,
Senior Software Designer
Neomorphic

Just got the October issue of Genome Technology ... excellent! You guys are seriously kicking butt on relevant and interesting issues. I think you are a new wave of journals.

Gabriella Armin,
Product Manager, Bio-Rad

It looks these days like you really have your finger on the pulse of the industry. Congratulations.

Christian C. Oste, PhD
VP Business Development & Director of European Operations
CyGene

I missed your first issue but was fortunate enough to see the second. I really enjoyed the content.

Kevin B. Sweeney
Director of Industry Relations
Keck Graduate Institute of Applied Life Sciences

DoubleTwist Differs

Nat Goodman performs an analysis of four commercial bioinformatics Web sites (“Private Portals: Where’s the Payback?” September 2000) and makes several insightful comments regarding Web-based genomic discovery. However, we were concerned with a number of statements made about our product, DoubleTwist.com, and have subsequently investigated the author’s claims.

We wish to address some of the statements made in the article about DoubleTwist.com that were incorrect due to an apparent misinterpretation of our data. We acknowledge that usability issues, many of which were addressed with our July product release, may have contributed to this misinterpretation.

Prior to our analysis, we contacted Dr. Goodman, and he was kind enough to provide us with his test sequence and his account information. The first statement we investigated was that DoubleTwist.com “gave the wrong answer on a simple test case.” We performed an identical analysis using Dr. Goodman’s test sequence and the Double-Twist.com Retrieve Assembled ESTs Research Agent. This agent, which queries against our proprietary human gene index, identified six consensus sequences with high identity to Dr. Goodman’s test sequence. Inspection of the agent report revealed that the cluster that contained these consensus sequences did in fact list full-length cDNAs corresponding to the multiple isoforms of the caspase-1 gene. However, we do acknowledge that the cDNA was listed under the name interleukin 1 beta convertase (the original name for this gene) rather than caspase-1, reflecting the fact that GenBank typically does not update the description of its sequences.

We then investigated Dr. Goodman’s own research report where we found that the Retrieve Assembled ESTs Research Agent had identified the identical cluster of mRNAs and ESTs containing the full-length cDNAs corresponding to caspase-1 isoforms. Based on customer feedback, we improved the navigation of these reports during our July product release in order to make these results more obvious.

In order to make the underlying science and technology transparent to the end user, we provide details describing the databases and tools used to create the databases throughout the site, both within our support area and in the online help. [For example, on the Retrieved Assembled ESTs report page, select the “about this page” link and then select the “DoubleTwist Gene Indices” link.] This includes literature citations of peer-reviewed articles that document and validate the clustering methods relevant to Dr. Goodman’s analysis. Nevertheless, we agree that the technical details Dr. Goodman sought should be more obvious to the user.

We sincerely regret that we were not invited to work with the author in the writing of the article to avoid misunderstandings and inaccurate conclusions.

Leah Jaffe-Greenwood, PhD, Science Editor
Yannick Pouliot, PhD, Director of Bioinformatics Knowledge Engineering
Michael B. Gonzales, PhD, Product Scientist
DoubleTwist

 

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