Papers

  • Biomedical Informatics

    Biomedical Informatics

    Dr. Gerry Higgins, PhD

    3rd generation sequencing may provide investigators with a tool to better resolve genomic structural variants than previous microarray and NGS technologies.

  • Personalized Medicine and Pharmacogenomics: Part Two – Pharma

    Personalized Medicine and Pharmacogenomics: Part Two – Pharma

    Dr. Gerry Higgins, PhD

    Pharmacogenomics has grown from an experimental strategy to the basis of drug discovery and development, with the support of the FDA and NCATS.

  • Personalized Medicine and Pharmacogenomics: Part One – The Clinic

    Personalized Medicine and Pharmacogenomics: Part One – The Clinic

    Dr. Gerry Higgins, PhD

    Genomic Clinical Decision Support systems will enable personally tailored drug therapies that improve patient safety, increase drug effectiveness, and provide better economic efficiency for the healthcare system.

  • Next Generation Pathology

    Next Generation Pathology: Integration of Histology and Genomic Data

    Dr. Gerry Higgins, PhD

    Advanced biomedical informatics analysis, based on integration of data from a “clinical grade” database of histopathology and genomics, will become the gold standard in molecular pathology.

  • WGA in Oncology

    Whole Genome Analysis in Oncology

    Dr. Gerry Higgins, PhD

    The rapid fall in the cost of whole genome sequencing and analysis presents an opportunity to evaluate whole genome diagnostics in the clinical setting.

Publications

  • Mutation discovery in mice by whole exome sequencing

    Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey Jeddeloh, Jay Shendure and Laura G Reinholdt Genome Biology 2011, 12:R86

  • Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses.

    Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A.Arch Virol. 2011 Mar;156(3):397-403.

  • GASSST: global alignment short sequence search tool.

    Rizk G, Lavenier D.Bioinformatics. 2010 Oct 15;26(20):2534-40.

  • Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus.

    Al Rwahnih M, Daubert S, Golino D, Rowhani A. Virology. 2009 May 10;387(2):395-401.

  • A comparative study of patent sequence databases

    Piet Jan Andree, Mark F. Harper, Stéphane Nauche, Robert A. Poolman, Jo Shaw, Joop C. Swinkels, Sally Wycherley World Patent Information 30 (2008) 300–308.

  • Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference.

    Bastien O, Lespinats S, Roy S, Métayer K, Fertil B, Codani JJ, Maréchal E. Gene. 2004 Jul 21;336(2):163-73.

  • High similarity sequence comparison in clustering large sequence databases.

    Dudoignon L, Glemet E, Heus HC, Raffinot M. Proc IEEE Comput Soc Bioinform Conf. 2002;1:228-36.

  • Patent searches for genetic sequences: how to retrieve relevant records from patented sequence databases.

    Dufresne G, Takács L, Heus HC, Codani JJ, Duval M. Nat Biotechnol. 2002 Dec;20(12):1269-71. No abstract available.

  • Significance of Z-value statistics of Smith-Waterman scores for protein alignments.

    Comet JP, Aude JC, Glémet E, Risler JL, Hénaut A, Slonimski PP, Codani JJ. Comput Chem. 1999 Jun 15;23(3-4):317-31.

  • Applications of the pyramidal clustering method to biological objects.

    Aude JC, Diaz-Lazcoz Y, Codani JJ, Risler JL. Comput Chem. 1999 Jun 15;23(3-4):303-15.

  • Removing redundancy in SWISS-PROT and TrEMBL.

    O’Donovan C, Martin MJ, Glemet E, Codani JJ, Apweiler R. Bioinformatics. 1999 Mar;15(3):258-9.

  • The complete genome sequence of the gram-positive bacterium Bacillus subtilis.

    Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, et al. Nature. 1997 Nov 20;390(6657):249-56.

  • Using video-oriented instructions to speed up sequence comparison.

    Wozniak A. Comput Appl Biosci. 1997 Apr;13(2):145-50.

  • LASSAP, a LArge Scale Sequence compArison Package.

    Glémet E, Codani JJ. Comput Appl Biosci. 1997 Apr;13(2):137-43.