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UC Davis’ Jonathan Eisen Wins 2011 Benjamin Franklin Award

By Bio-IT World staff 

 March 15, 2011 | Jonathan Eisen, an evolutionary geneticist and professor in the Genome Center at University of California, Davis, is the winner of the Benjamin Franklin Award for 2011. 

Eisen told Bio-IT World he is extremely excited to win this year’s award, bestowed by the Bioinformatics Organization, particularly after he was short-listed in 2009. “I actually kind of supported the winning candidate [in 2009], Phil Bourne, who at the time I think deserved it much more than me,” commented Eisen. But Eisen felt his chances for recognition had grown in the intervening two years given his work towards “Open Science.” 

Eisen joins a distinguished list of previous winners, including his brother Michael, who won the first Franklin Award in 2002. He is the academic editor-in-chief of the pioneering open-access journal PLoS Biology, and uses his high visibility in social media, notably his popular “Tree of Life” blog, to advocate for open access in science publishing and data release. Eisen has been involved with numerous freely available software packages, including AMPHORA and PhyloOTU. He also helped release a new open data sharing tool for scientists called BioTorrents, to encourage scientists to share data and results. 

The Eisen lab at the UC Davis Genome Center focuses on understanding the genomic basis for the origin of novelty in microorganisms, which is an exploding area of research thanks to the emergence of next-generation sequencing technologies.  

Eisen was one of six open-source, open-access evangelists short-listed for the 2011 Frankllin Award. The other finalists were: 

Gary Bader (The Donnelly Centre, University of Toronto)  

Computational biologist Gary Bader developed the Biomolecular Interaction Network Database (BIND), one of the first of dozens of molecular interaction databases.  He also plays an active role in the development of open-source biological pathway and network data exchange formats such as PSI-MI, BioPAX, Pathway Commons and Cytoscape visualization and analysis software. 

Eugene Koonin (NCBI)  

Koonin, the leader of the evolutionary genomics research group at NCBI, is a co-founder of Biology Direct, which champions signed peer review. His organization of the Clusters of Orthologous Groups (COG) project opened up the field of comparative genomics, providing a new avenue of access to large repositories of sequence data, as well as allowing investigators to make sense of their research in the light of evolution.   

John Quackenbush (Harvard School of Public Health/Dana Farber Cancer Institute)  

Quackenbush has promoted open-source and publicly available software tools in computational biology, particularly in the field of gene expression tools, for more than a decade. Since joining the Dana Farber, Quackenbush has focused on cancer treatment and translational medicine.  

Steven Salzberg (University of Maryland) 

Salzberg had made many contributions to the field of bioinformatics, including the development of some widely used computational tools for genome assembly, gene prediction, and genome comparison, including Glimmer, Bowtie, TopHat, MUMmer, the AMOS assembler, and JIGSAW. He is an advocate for open access in bioinformatics, and has actively campaigned against software and gene patents. 

Alex Zhavoronkov (Johns Hopkins University)  

Zhavoronkov helped establish the International Aging Research Portfolio (IARP), an independent non-profit initiative serving the aging research community worldwide. Without public funding, the volunteer efforts of experts from the fields of biology, mathematics, computer science, engineering, psychology and economics provides different views on age-related projects in order to find trends, monitor progress across disciplines, and build new classification taxonomies. (See 

Eisen will be presented with the award in an open-access ceremony at Bio-IT World Expo on April 13 in Boston, and discuss his views on unrestricted access to data. 

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