Lab PI

Treangen Lab PI (Dr. Todd J. Treangen)

CV (updated September 2024)

Full Name Todd J. Treangen
Languages English, Galician, Spanish

Education

  • 2008
    Ph.D. in Computer Science
    Polytechnic University of Catalonia, Barcelona, Spain
    • Focus on bioinformatics and computational biology.
    • Research involved the development of algorithms for genome analysis.
    • Dissertation
      • {"Title"=>"Novel Computational Methods for Large Scale Genome Comparison"}
      • {"Advisor"=>"Dr. Xavier Messeguer"}
  • 2004
    MS in Computer Science
    Polytechnic University of Catalonia, Barcelona, Spain
    • Specialized in algorithm development for large-scale genomic data.
    • Completed a thesis on "Efficient Methods for Genome Alignment."

Experience

  • 2023 - present
    Associate Professor, Computer Science
    Rice University, Houston, Texas, USA
    • Affiliate faculty in Department of Bioengineering
    • Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.
    • Developed tools for microbial detection and outbreak tracking.
    • Research
      • Focus on AI-driven approaches for genomic data analysis.
      • Developed algorithms for rapid pathogen detection.
  • 2018 - 2023
    Assistant Professor, Computer Science
    Rice University, Houston, Texas, USA
    • Leads the Treangen Lab, focusing on bioinformatics, genomics, and metagenomics.
    • Developed tools for microbial detection and outbreak tracking.
    • Research
      • Focus on AI-driven approaches for genomic data analysis.
      • Developed algorithms for rapid pathogen detection.
  • 2016 - 2018
    Research Assistant Professor, UMIACS
    University of Maryland, College Park, Maryland, USA
    • Conducted research on genome assembly and metagenomics.
    • Collaborated on the development of scalable bioinformatics tools.
  • 2012 - 2016
    PI and Bioinformatics Scientist
    National Biodefense Analysis and Countermeasures Center (NBACC)
    • Focused on pathogen detection and large scale genome comparison of microbes
  • 2011 - 2012
    Postdoctoral Scientist, School of Public Health
    Johns Hopkins University (Salzberg lab)
    • Focused on genome assembly
  • 2010 - 2011
    Postdoctoral Scientist, CBCB
    University of Maryland College Park (Pop and Salzberg labs)
    • Focused on genome and metagenome assembly
  • 2008 - 2010
    Postdoctoral Scientist
    Institut Pasteur, Paris, France (Rocha lab)
    • Focused on evolutionary microbial genomics (GEM)

Open Source Projects

  • 2010-2015
    MetAMOS
    • An open-source metagenomic assembly and analysis pipeline.
  • 2010-2015
    ParSNP
    • An open-source microbial core genome alignment tool.
  • 2013-2018
    Mash
    • Fast genome and metagenome distance estimation using MinHash.
  • 2018-2024
    Treangen lab software
    • Variety of open-source tools for microbial genomics and metagenomics

Honors and Awards

  • 2008
    • Europeus Doctor
  • 2023
    • NSF CAREER Award
  • 2024
    • Rice School of Engineering (SoE) University Research and Teaching Award

Academic Interests

  • Microbial genomics
    • Development of algorithms for microbial genome assembly, alignment analysis.
    • Comparative genomics of bacterial pathogens.
  • Metagenomics
    • Computational methods for studying microbial communities.
    • Metagenomics and the study of microbial diversity.