cv.yml

- title: CV (updated September 2024)
  type: map
  contents:
    - name: Full Name
      value: Todd J. Treangen
    - name: Languages
      value: English, Galician, Spanish

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

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

- title: Open Source Projects
  type: time_table
  contents:
    - title: <a href="https://github.com/marbl/metamos">MetAMOS</a>
      year: 2010-2015
      description: An open-source metagenomic assembly and analysis pipeline.
    - title: <a href="https://github.com/marbl/parsnp">ParSNP</a>
      year: 2010-2015
      description: An open-source microbial core genome alignment tool.
    - title: <a href="https://github.com/marbl/mash">Mash</a>
      year: 2013-2018
      description: Fast genome and metagenome distance estimation using MinHash.
    - title: <a href="https://github.com/treangenlab">Treangen lab software</a>
      year: 2018-2024
      description: Variety of open-source tools for microbial genomics and metagenomics

- title: Honors and Awards
  type: time_table
  contents:
    - year: 2008
      items:
        - Europeus Doctor 
    - year: 2023
      items:
        - NSF CAREER Award
    - year: 2024
      items:
        - Rice School of Engineering (SoE) University Research and Teaching Award

- title: Academic Interests
  type: nested_list
  contents:
    - title: Microbial genomics
      items:
        - Development of algorithms for microbial genome assembly, alignment analysis.
        - Comparative genomics of bacterial pathogens.

    - title: Metagenomics
      items:
        - Computational methods for studying microbial communities.
        - Metagenomics and the study of microbial diversity.