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David Ussery

Key Words

Comparative Genomics; Pan- and Core-genomes; Bacterial Genomics; E. coli, Salmonella, Vibrio, Pseudomonas, Campylobacter, Burkholderia and Mycobacterium

Description of Research

Dr David Ussery is the Comparative Genomics group leader in the Bioscience Division of Oak Ridge National Laboratory (ORNL). Prior to joining ORNL in 2013, Dr Ussery was at the Center for Biological Sequence Analysis at the Technical University of Denmark. Dr Ussery is leading the Data Management activities for the BESC and PMI projects at ORNL. David Ussery was group leader of the Comparative Microbial Genomics group in the Center for Biological Sequence Analysis (CBS), at the Department of Systems Biology-DTU. Here he was working with bioinformatic analysis of bacterial genomes since the first sequence was published in 1995. His group published more than 100 papers since 2000, including the most highly cited paper in the field of industrial biotechnology in 2008. His popular DTU course on Comparative Microbial Genomics ran for 10 years; one-week workshops based on this course were held in North and South America, Europe, Asia, and Africa. David Ussery has collaborative projects with groups in the UK, Norway, Germany, Belgium, The Netherlands, France, and Spain as well as in the US.

Selected Publications

HB Nielsen, et al., “Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes”, Nature biotechnology 32 (8), 822-828 (2014).

Mette V Larsen, Salvatore Cosentino, Oksana Lukjancenko, Dhany Saputra, Simon Rasmussen, Henrik Hasman, Thomas Sicheritz-Pontén, Frank M Aarestrup, David W Ussery, Ole Lund, “Benchmarking of Methods for Genomic Taxonomy”, Journal of Clinical Microbiology, 52:1529-1539, (2014).

Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW. Veillonella, Firmicutes: Microbes disguised as Gram negatives. Stand Genomic Sci. 2013 Dec 15;9(2):431-48.

Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW. Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes.PLoS One. 2013 Jul 26;8(7):e69878.

AI Ozen, T Vesth, DW Ussery, “From Genome Sequence to Taxonomy: A Skeptics View”, "The Prokaryotes" (Springer Berlin Heidelberg, pages 209-227), 2013.

Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK. Non-O1 Vibrio cholerae unlinked to cholera in Haiti. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):E3206; author reply E3207. doi: 10.1073/pnas.1212443109.

Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium Proc Natl Acad Sci USA. 2012, May 15;109(20):E1277-86.

Rodriguez-Valera F, Ussery DW. Is the pan-genome also a pan-selectome? F1000Res. 2012 Sep 21;1:16.

Pimlapas Leekitcharoenphon, Oksana Lukjancenko, Carsten Friis, Frank M Aarestrup and David W Ussery, “Genomic variation in Salmonella enterica core genes for epidemiological typing”, BMC Genomics, 13:88 (2012).

Oksana Lukjancenko, David W. Ussery and Trudy M. Wassenaar, “Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera”, Microbial Ecology, 63:651-673, (2012).

Jon Bohlin, Mark WJ van Passel, Lars Snipen, Anja B Kristoffersen, David Ussery and Simon P Hardy, “Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands”, BMC Genomics, 13:66, (2012).

Asli I. Ozen and David W. Ussery, “Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?”, Microbial Ecology, 63:239-248 (2012).

Mette V. Larsen, Salvatore Cosentino, Simon Rasmussen, Carsten Friis, Henrik Hasman, Rasmus Lykke Marvig, Lars Jelsbak, Thomas Sicheritz Pontén, David W. Ussery, Frank M. Aarestrup, Ole Lund, “Multilocus Sequence Typing of Total Genome Sequenced Bacteria”, J. Clin Microbiol., 50:1355-1361 (2012).

Contact Information

David Ussery
Computational Biology & Bioinformatics

David Ussery
Oak Ridge National Lab
PO Box 2008 MS-6420
Oak Ridge, TN 37831-6420

Email: usserydw@ornl.gov

Degrees

MSc Biophysical Chemistry, University of New Mexico, Albuquerque, NM (1986)

PhD, Molecular Biology, University of Cincinnati, College of Medicine, Cinncinnati, Ohio (1993)