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2020 Open Access Award Finalists Named



By Bio-IT World Staff 

February 17, 2020 | Bioinformatics.org today announced the finalists in the 2020 Benjamin Franklin Award for Open Access in the Life Sciences. Voting is open to Bioinformatics.org members on http://www.bioinformatics.org/franklin/, and will be open until Friday, February 28. The winner will be announced at the 2020 Bio-IT World Conference & Expo. 

The 13 finalists include:

  • Amos Bairoch, University of Geneva and Swiss Institute of Bioinformatics
  • Keith A. Crandall, George Washington University
  • Chris Dagdigian, BioTeam
  • Xiaole Shirley Liu, Dana-Farber Cancer Institute
  • Maria Nattestad, Google Health
  • Christine Orengo, University College London
  • B.F. Francis Ouellette, Bioinformatics.ca
  • Aviv Regev, Broad Institute
  • Knut Reinert, Freie Universität Berlin
  • Mark Robinson, University of Zurich and Swiss Institute of Bioinformatics
  • Susanna Sansone, University of Oxford
  • John D., Westbrook, RCSB Protein Data Bank
  • Nadine Ziemert, Universität Tübingen

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by Bioinformatics.org to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. 

This year, the organizers of Bioinformatics.org expressed a renewed commitment to recognizing the achievements of the diverse bioinformatics community, including the important contributions of women and minorities to the field of bioinformatics and the open resources that drive it. For the first time, the organization accepted nominations from non-members. As in previous years, any person who received more than one nomination has been added to the finalist roster. The group also announced plans to convene a steering committee to improve the awards process for the future.

The 2020 final winner will be chosen by votes from the Bioinformatics.org membership. Membership is free; anyone wishing to cast a vote for the 2020 laureate can join online immediately.  


2020 Franklin Award Finalists

Amos Bairoch, University of Geneva and Swiss Institute of Bioinformatics

Amos Bairoch has played an instrumental role in the development of world-renowned open access databases and software tools in the field of protein sequence analysis.  He helped to develop Swiss-Prot, which was operational in 1986. Other tools include PROSITE, ExPASy, and neXtProt. They have been broadly accessed and used by a very large number of researchers in proteomics. This can be illustrated, for example, by over 74,000 citations to Amos's publications.

 

Keith A. Crandall, George Washington University

Keith Crandall has worked in developing open access methods and generating publicly available data in the life sciences focused in evolutionary biology and now in microbiome characterization.  From evolutionary model selection with ModelTest to network approaches to estimating gene genealogies and collaborative team projects like OpenTreeofLife and the Earth Biogenome Project, Keith has been involved with a variety of open access projects and software development. Importantly, projects like OpenTree and EBP advocate for open access to software and data and in the case of OpenTree, treating phylogenetic estimates as data for future research. Keith has served as an Academic Editor at PLoSOne and a founding Section Editor in Bioinformatics and Genomics at PeerJ.

 

Chris Dagdigian, BioTeam

Chris was one of the founders of the Open Bioinformatics Foundation, home of BioPython, BioJava, and other open source tools for bioinformatics. He currently specializes in research computing and infrastructure technology issues in the life sciences. A long time supporter of free software and open standards for life science research, Chris was a founding member of the BioPerl Project. He also single-handedly kept the open source version of Sun Grid Engine (SGE) alive, open and free.

 

Xiaole Shirley Liu, Dana-Farber Cancer Institute

Shirley Liu is a leader in developing open source algorithms and software for the integration of high-throughput genomics data to better understand gene regulation. Published in 2008, her most widely-used software is MACS, a peak-finding algorithm that has been cited more than 6,000 times. MACS has been essential to the interpretation of ChIP-seq data and was an integral component of both research in individual labs worldwide, but also large-scale projects such as ENCODE. To date, she has published more than 30 scientific software packages and has more recently developed important new tools for CRISPR/Cas9 study design and for understanding tumor development, drug response and resistance. Her research has helped to popularize the creation of open source software for genomics research and has had a tremendous impact on our understanding of gene regulation.

 

Maria Nattestad, Google Health

Maria Nattestad is a vocal advocate for open source software and a rising star in genomics. Her major works include Assemblytics, to detect and analyze structural variants from a genome assembly by comparing it to a reference genome, and Ribbon, a genome browser that shows long reads and complex variants better. She was also a contributing author to the widely used FALCON genome assembler and NGMLR/Sniffles packages for long read alignment and structural variant calling. In addition to these research projects, she has developed a widely viewed Youtube channel where she teaches basic bioinformatics analysis that is accessible to novice users. She has also led a Girls Who Code group and Hour of Code event to bring more women into careers in science and technology.

 

Christine Orengo, University College London

Christine Orengo has contributed hugely to the availability of open data in the life sciences in the area of structural biology. One of Christine's key contributions provided the CATH classification of protein structures which enables understanding of the function, structure and evolution of proteins. As the sequences of complete genomes became available, Christine and her team developed GENE3D to classify proteins from these genomes into protein families that were both comprehensive and accurate and enabled understanding of protein structure and function across the tree of life. These resources are built upon various software packages that Christine and her team have released allowing others to reproduce the results that built them.

 

B.F. Francis Ouellette, Bioinformatics.ca

Francis Ouellette has been a true champion of Bioinformatics education, open source learning and open access to scientific data. He has been responsible for delivering bioinformatics education in Canada through bioinformatics.ca. Currently, Francis is chair of the SAB for Elixir Europe, and H3ABionet, whose goal is to build a sustainable African Bioinformatics Network. He currently serves our community on editorial boards for several journals (PLOS Computational Biology Education Editor; and Associate Editor for DATABASE, an OUP Open Access journal). Francis has also worked at the NIH, where he was involved in coordinating the success of GenBank, which is the largest open DNA sequence database in the world.

 

Aviv Regev, Broad Institute

Aviv Regev is a pioneer in the use of single-cell genomics and other techniques to dissect molecular networks. Her lab has originated several of the earliest open source packages for single cell sequencing, including Rahul Satija's Seurat package and Itay Tirosh's InferCNV, and she now hosts the Trinity assembly package. In her current work she is the co-organizer for the Human Cell Atlas project. The HCA is an extremely important project to create comprehensive reference maps of all human cells as a basis for understanding human health and diagnosing, monitoring, and treating disease. Importantly, the HCA promotes an open release policy to encourage the release of data prepublication, as well as open-source software to ensure the free exchange of ideas and methods.

 

Knut Reinert, Freie Universität Berlin

Knut Reinert is the distinguished leader of an outstanding research group dedicated to the development of efficient data structures and algorithms for computational biology, and the highly optimized implementation of the same in modern, state-of-the-art, open-source C++ libraries (SeqAn). He has supervised the development of SeqAn for over decade. This library is used by numerous projects and researchers across the globe for sophisticated sequence analysis.

 

Mark Robinson, University of Zurich and Swiss Institute of Bioinformatics

Mark Robinson develops robust data analysis solutions, including new or improved methods, for the analysis of genome-scale data. He has championed the development of publicly available open-source software tools, generally through the Bioconductor project, such as the well-known EdgeR package. He is an open science delegate at the University of Zurich, striving to support the transformation to greater cooperation and bring about major changes in the academic system.

 

Susanna Sansone, University of Oxford

Susanna Sansone has done tremendous work in the area of FAIR data as evidenced by her Google Scholar profile and presence in the media. She has developed novel resources, e.g. BioSharing, FAIRsharing, and contributed substantially to the development and critical implementation of genomic and microarray metadata standards and biomedical ontologies.

 

John D. Westbrook, RCSB Protein Data Bank 

John Westbrook is an internationally-recognized leader in developing ontologies, tools, and infrastructure for data acquisition, validation, standardization, and mining in the structural biology and life science domains.  This work has established the PDBx/mmCIF data dictionary and format as the foundation of the modern Protein Data Bank archive. John also established the Chemical Component Dictionary to maintain and distribute small molecule chemical reference data in the PDB. John contributes to community data standards enabling interoperation and data integration within the biology and structural biology domains. He also champions the FAIR and FACT principles and CoreTrustSeal accreditation.

 

Nadine Ziemert, Universität Tübingen

Nadine Ziemert's group is currently developing bioinformatic tools for the discovery of natural products from microbial genomes, elucidating the evolutionary history of their biosynthetic gene clusters and tracing their distribution in the environment.  The tools include AutoMLST: Automated Multi Locus Species Tree, Antibiotic Resistant Target Seeker (ARTS), which are open source and available on BitBucket.

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