Fungus expert celebrates rare 10,000th citation

This week, a scientific publication by a team of UC Berkeley researchers from the laboratory of John Taylor, professor of plant and microbial biology, hit a rare benchmark when it was cited for the 10,000th time, according to Google Scholar. The publication, a chapter called “Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics,” appeared in the 1990 book “PCR Protocols: A Guide to Methods and Applications.”

Most scientific papers are cited just a few times, but seldom 100 times, and rarely a few thousand. The papers that earned Nobel prizes for UC Berkeley physicists Saul Perlmutter and George Smoot, for example, have been cited 8,882 and 2,260 times, respectively, according to Google Scholar. Taylor provided the NewsCenter with some perspective on this impressive milestone.

The four co-authors of the paper.

The four co-authors of the 1990 paper, left to right, Thomas D. Bruns, Thomas J. White, Steven B. Lee and John W. Taylor. Photo credit: James Block.

Q:  What did you report in the 1990 article?

A: We described how to quickly and easily sequence a region of DNA from fungi that identifies the fungus and places the fungus in the Tree of Life. This simple tool revolutionized two fields: fungal ecology and fungal phylogenetics, the process that builds the Tree of Life. The global effort to “barcode” all of life, that is, to catalog every organism using a DNA signature, has adopted our protocol for fungi, and efforts are afoot to do the same for plants.

Q:  Did the number of citations surprise you?

A: Surprise doesn’t fully describe our reaction; shock might be closer. Even more shocking is that the rate of citation is accelerating. Part of the shock is that our publication was just one of many in an edited book and not the short article in a highly visible journal – Nature, Science, PNAS or PLoS, for example – that you expect to be highly cited.

Q:   Why do you think this publication has been cited so often?

A: The most highly cited publications describe methods that are new, truly useful and not quickly superseded by a better method. Ours is no exception. It was the first publication to describe how to quickly and cheaply determine the sequence of a part of the genome that is ideally suited to putting organisms in the Tree of Life and also for identifying organisms through the sequence of their DNA, the ribosomal DNA (rDNA) region. Both of these tasks have been very useful and are now standard in fungal evolution and ecology laboratories. No better, single region has yet been found. However, when it becomes routine to sequence entire genomes – as routine as it now is to use our single region – then our method will be superseded.

Q:   Why are citations important, and what do they tell you about the underlying research?

A: When a scientist writes a paper about his or her research, he or she cites the previous publications that formed the foundation for that research. Those publications that help provide the foundation for the greatest number of additional research studies are the ones that are the most cited. Ergo, one objective measure of the impact of a particular publication is the number of times that it has been cited.  Ten thousand is a large number of citations. We are unable to find any other publication from the Berkeley campus over the past 25 years that has 10,000 citations.

Q:   How and why was industry involved in this work?

A: Our method uses the polymerase chain reaction (PCR) to facilitate sequencing the rDNA regions that are used to build the Tree of Life and to identify fungi. The lead author, Tom White, was head of the research group at CETUS Corporation in Emeryville that developed PCR, the discovery that warranted a Nobel Prize for then CETUS employee, Kary Mullis. Tom had earned his Ph.D. in molecular evolution from then UC Berkeley professor Allan Wilson and, as a CETUS scientist, had collaborated on a study of fungal evolution with me in the 1980s. When CETUS had difficulty recognizing the commercial worth of PCR, Tom asked for a sabbatical in my lab at Berkeley. I was in Australia at the time and Tom Bruns, then a postdoc and now a professor at Berkeley, and Steve Lee, then a student and now a professor at San Jose State University, welcomed Tom White into the lab. When I got back, Tom White suggested that we publish our method in the book on PCR applications to energize the field of fungal evolution and, as 10,000 citations show, he was right. His sabbatical was a short one because in 1990, Roche bought CETUS for $300 million and hired Tom White to lead the new campus that they were building to develop medical applications for PCR in Alameda, California.

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