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IT Guy Tells It Like It Is

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I appreciate Nat Goodman’s articles addressing important current genomics research issues.

I’m referring first to his article (“Microarray Mining Made Easy … Almost,” Nov. ’00) questioning why microarray users didn’t feel the need to replicate. How did they determine if a gene was up- or down-regulated to a significant level as opposed to the null hypothesis that it didn’t change in expression? How was the notorious “x-fold” level determined?”

Then I read his article about annotation of the human genome sequence (“The Wicked Truth about Annotated Data,” Feb. ’01). I understand the researchers working on the Arabidopsis genome have requested additional funding to re-annotate that genome, because they aren’t satisfied with how it was done the first time. The annotation science and software are still in an experimental stage. The media paints the picture that “sequenced” genomes are more finished than they really are.

I also am still concerned that the whole point (I thought) of whole-genome sequencing projects was to associate sequence with function on an organism level. What I’ve seen is work at the mRNA and protein level plus approaches to knock out gene function in hopes that an associated phenotype will become evident. What we need is integrated information on all these levels.

Dr. Kim Lewers, USDA-ARS-PSI-SARL

Mutated copy

In the January issue, Stephen Heller was incorrectly identified in “Who Let the Dogs Out?” (p. 34) as working at the USDA. Dr. Heller retired from the USDA last August and is now a guest researcher at NIST/SRD.

In the same article, the name of Alexis Rockman, the artist who painted “The Farm,” was misspelled. We apologize for the errors.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.