# YAML (http://www.yaml.org/)
-
 cat: Title
 anchor: ~
 title: John T. Prince
 subtitle: Curriculum vitae
-
  cat: Education
  info:
  -
    events: 
    -
      name: HHMI Research Specialist (Post-doctoral)
      date: May 2008 - present
      location: Department of Chemistry and Biochemistry, University of Colorado (CU-Boulder), Boulder, Colorado
      description:
      - Mass spectrometric identification of transient protein complexes
      - 'Advisor: Natalie Ahn'
      resume duplicate: 
        location: University of Colorado (CU), Boulder, Colorado
    -
      name: PhD in Cell and Molecular Biology
      date: Aug 2001 - May 2008
      location: Institute for Cellular and Molecular Biology (ICMB), Center for Systems and Synthetic Biology, University of Texas (UT), Austin, Texas
      description:
      - 'Thesis Title: Integration and Validation of Mass Spectrometry Proteomics Data Sets'
      - 'Advisor: Edward Marcotte'
      - Bioinformatics and Computational Biology Track
      - GPA 4.00/4.00
      resume duplicate:
        name: PhD, Cell and Molecular Biology (Bioinformatics and Computational Biology)
        location: University of Texas (UT), Center for Systems and Synthetic Biology, Austin, Texas
        description: 
        - GPA 4.00/4.00
    -
      name: Bachelor of Science in Microbiology
      date: Dec. 2000
      location: Department of Biology and Agriculture, Brigham Young University (BYU), Provo, Utah
      description:
      - Minor in Chemistry
      - Graduated Magna Cum Laude (3.89/4.00) 
      resume duplicate:
        name: B.S., National Merit Scholar, Microbiology (Chemistry Minor)
        location: Brigham Young University (BYU), Provo, Utah
        description: 
        - Graduated Magna Cum Laude (3.89/4.00) 

-
  cat: Honors & Awards
  anchor: Awards
  info:
  -
    events:
    -
      name: Department of Energy Scholarship (Proteomics and Applications)
      date: 2003
      location: Keystone Symposium, Keystone, Colorado
    -
      name: ICMB Research Assistantship
      date: 2001
      location: Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas
    -
      name: ICMB Graduate Fellowship Award (Supplementary)
      date: 2001 - 2005
      location: Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas
    -
      name: Cancer Research Center Summer Fellowship
      date: 1999
      location: Brigham Young University, Provo, Utah
    -
      name: Office of Research and Creative Activities Scholarship.
      date: 1999
      location: Brigham Young University, Provo, Utah
    -
      name: Trustees Scholarship (Full Tuition)
      date: 1994
      location: Brigham Young University, Provo, Utah
    -
      name: National Merit Scholarship
      date: 1994
      location: Manor High School, Manor, Texas
    -
      name: Robert Byrd Scholarship
      date: 1994
      location: Manor High School, Manor, Texas
    -
      name: Applied Materials Scholarship
      date: 1994
      location: Manor High School, Manor, Texas
    -
      name: 1st in High School Class
      date: 1994
      location: Manor High School, Manor, Texas
    -
      name: Eagle Scout Award
      date: 1993
      location: Boy Scouts of America, Baton Rouge, Louisiana
-
  cat: Scientific Experience
  anchor: Experience
  info:
  - 
    events:
    -
      name: Signal Transduction
      date: May 2008 - present
      location: Dr. Natalie Ahn Lab, University of Colorado, Boulder, Colorado.
      description:
      - '<i>in vivo</i> cross-linking and mass spectrometry analysis of transient protein-protein interactions'
      resume duplicate:
        location: Dr. Natalie Ahn Lab, CU
    -
      name: Proteomics & Bioinformatics
      date: Jan. 2002 - May 2008
      location: Dr. Edward Marcotte Lab, University of Texas, Austin, Texas.
      description:
      - Computational analysis of mass spectrometry proteomics data
      - Maintenance and operation of 2D-LC nanoelectrospray LTQ-Orbitrap and Ion Trap mass spectrometers
      - Creator and curator of the Open Proteomics Database (OPD)
      resume duplicate:
        location: Dr. Edward Marcotte Lab, UT
    -
      name: 'Proteomics: Sequence, Structure, Function; High Throughput Technologies and Methods of Analysis (workshop)'
      date: Mar. 2004
      location: Institute for Pure and Applied Mathematics, University of California, Los Angeles, California
    -
      name: Laboratory Instructor of Cell and Molecular Biology Lab (Bio205L)
      date: 2003
      location: School of Biological Sciences, University of Texas, Austin, Texas
      description:
      - Instruction and assistance in microscopy, gels, westerns, etc.
    -
      name: Computational Phylogenetics
      date: Mar. - May 2002
      location: Dr. David Hillis Lab, University of Texas, Austin, Texas
      description:
      - Investigation of site-likelihood parameters of Maximum Likelihood models
      - Wrote programs and performed computer simulations
      resume duplicate:
        location: Dr. David Hillis Lab, UT
    -
      name: Antibody Engineering
      date: Oct. 2001 - Jan. 2002
      location: Dr. George Georgiou Lab , University of Texas, Austin, Texas
      description:
      - Directed evolution of heat stable antibodies by Phage Display
      resume duplicate:
        location: Dr. George Georgiou Lab, UT
    -
      name: Organic Synthesis
      date: Jun. 1999 - Aug. 2001
      location: Dr. Merritt Andrus Lab, Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
      description:
      - Synthesis of Multi-Drug Resistance reversal agents (cancer research)
      - Worked out a mass spectrometry screening assay
      - Performed NMR, column and radial chromatography, TLC
      resume duplicate:
        location: Dr. Merritt Andrus Lab, BYU
    -
      name: Molecular Biology
      date: Fall 2000
      location: Dr. Michael Leavitt Lab, Department of Microbiology, Brigham Young University, Provo, Utah
      description:
      - Isolated large, high adherence plasmid in E. coli for design of bacterial interference agents in poultry
      - Performed gel electrophoresis, plasmid preps, electroporation, high adherence assay, fluorescence microscopy
      resume duplicate:
        location: Dr. Michael Leavitt Lab, BYU
-
  cat: Computational Experience
  anchor: ~
  info:
  -
    tables:
    -
      Operating Systems:
      - [Linux/Unix, extensive]
      - [Windows, extensive]
      - [Macintosh, basic]
    -
      Software:
      - [Perl, extensive]
      - [Perl Data Language, extensive]
      - [Ruby, extensive ]
      - [Ruby on Rails, basic]
      - [C/C++, substantial]
      - [Mass Spec Analysis software, substantial]
      - [Matlab, substantial]
      - [HTML/CSS, substantial]
      - [Php, basic]
      - [Apache, basic]
      - [MySQL, substantial]
      - [AVS, basic]
      - [Java, basic]
      - [Rational Rose, basic]
      - ['Office (Word, Excel, PPt)', substantial]
  -
    events:
    -
      name: Certifications
      date: 1999
      location: Utah Department of Workforce Services, Provo, Utah
      description:
      - 'Typing: 54 WPM (Net)'
      - 'Ten-Key: 112 SPM (100% accuracy)'
      - WordPerfect 6.0
      - Spelling
-
  cat: Work Experience
  anchor: ~
  info:
  -
    events:
    - 
      name: Youth Technician
      date: Summer 1999
      location: Youth Detention Center, Strawberry Work Camp, Provo, Utah
      description:
      - Organized and directed labor forces
      - Led activities and discussion
      - Mediated conflict resolution
    -
      name: Head Teacher
      date: Summer 1998
      location: "The Children's Courtyard, Austin, Texas"
      description:
      - Created and carried out teaching plans
      - Designed original activities
      - Organized science projects and explorations
    -
      name: Sales Counselor
      date: Nov 1997 - Jan 1998
      location: Circuit City Express, Austin, Texas
      description:
      - Courteously served customers
      - Helped train new sales counselors
      - Organized store sections and worked cash register
    -
      name: Usher
      date: Summer 1995
      location: General Cinema
    -
      name: Shelving
      date: Summer 1995
      location: Opening Used Book Store, Austin, Texas
    -
      name: Waiter
      date: Summer 1994
      location: Pizza Hut, Austin, Texas
    -
      name: Apartment Mover
      date: Summer 1992
      location: Apartment Movers, Baton Rouge, Louisiana
    -
      name: Lawn Maintenance
      date: Summer 1991 & 1992
      location: Properties Unlimited, Baton Rouge, Louisiana
-
  cat: Volunteer Experience
  anchor: ~
  info:
  -
    events:
    -
      name: Scoutmaster
      date: 2002 - 2007
      location: Troop 100, Boy Scouts of America, Austin, Texas
      description:
      - Planned scouting tours, camps, and meetings.
      - Instructed in a variety of disciplines
      - Trained youth leaders
    -
      name: Tutor, Organic Chemistry
      date: Winter 1998
      location: Brigham Young University, Provo, Utah
      description:
      - Taught principles of organic chemistry one-on-one
    -
      name: Missionary
      date: Nov. 1995 - Nov. 1997
      location: The Church of Jesus Christ of Latter Day Saints, Scotland Edinburgh Mission, Scotland, United Kingdom
      description:
      - Full-time teaching responsibility
      - Supervised and trained missionaries
-
  cat: Leadership, Clubs, & Societies
  anchor: Societies
  info:
  -
    events:
    - 
      name: Member, American Society for Mass Spectrometry
      date: 2005 - 2006
    -
      name: Founder, Cell and Molecular Biology Graduate Student Association
      date: 2004
      location: University of Texas, Austin, Texas
      description:
      - Initiated and formed committee of involved students
      - Led the drafting of a constitution
      - Administered the first elections
    -
      name: Member, Society for Computational Biology
      date: 2002 - 2005
      location: University of Texas, Austin, Texas
    -
      name: Member, Golden Key National Honor Society
      date: 2000 - Present
      location: National Organization
    -
      name: Vice President, Health Occupations Students of America
      date: 1999 - 2000
      location: Brigham Young University Chapter, Provo, Utah
-
  cat: Publications, Presentations, & Posters
  anchor: Publications
  info:
  -
    bibliographies:
    - 
      bib_type: article_submitted
      title: Sample bias validation to examine the accuracy of large scale mass spectrometry proteomics peptide identification error estimates
      authors: Prince JT and Marcotte EM
      journal: Analytical Chemistry
      year: 2008
      resume duplicate: {} 
    -
      bib_type: article_submitted
      title: 'mspire: Mass spectrometry proteomics in Ruby'
      authors: Prince JT and Marcotte EM
      journal: Bioinformatics
      year: 2008
      resume duplicate: {}
    -
      bib_type: article
      title: Chromatographic alignment of ESI-LC-MS proteomics datasets by bijective interpolated dynamic time warping
      authors: Prince JT and Marcotte EM
      journal: Analytical Chemistry
      year: 2006
      vol: 78(17)
      pages: 6140-52
      resume duplicate: {}
    -
      bib_type: article_to_be_submitted
      title: 'Boosting protein identification in shotgun proteomics experiments'
      authors: Ramakrishnan SR, Vogel C, Wang R, Prince JT, Li Z, Myers M, Marcotte EM, Miranker DP
      journal: Bioinformatics
    -
      bib_type: article
      title: 'Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias'
      journal: Genome Research
      authors: Wang R, Prince JT, Graham DE, Marcotte EM
      year: 2005 
      vol: 15(8)
      pages: 1118-26
      resume duplicate: {}
    -
      bib_type: article
      title: The need for a public proteomics repository
      journal: Nature Biotechnology
      authors: Prince JT, Carlson MW, Wang R, Lu P, Marcotte EM
      year: 2004
      vol: 22(4)
      pages: 471-2
      resume duplicate: {}
    -
      bib_type: article_to_be_submitted
      title: 'MSFound2: A web based protein identification system for MS/MS mass spectrometry using metric space database indexing'
      authors: SR Ramakrishnan, Prince JT, Marcotte EM, Miranker DP
      journal: To Be Determined
    -
      bib_type: article_to_be_submitted
      title: 'Proteomics by comparative mass spectrometry using the peptide signature method: a complementary approach to MS2 spectra identification'
      authors: Nakorchevskiy AA, Adai AT, Prince JT, Marcotte EM
      journal: Analytical Chemistry
    -
      bib_type: article
      title: A fast course filtering method for peptide identification by mass spectrometry
      journal: Bioinformatics
      authors: Ramakrishnan SR, Rui M, Nakorchevskiy AA, Prince JT, Willard WS, Xu W, Marcotte EM, Miranker DP
      year: 2006
      pages: 1524-31
      vol: 22(12)
      resume duplicate: {}
    -
      bib_type: poster 
      title: Chromatographic Alignment of Multi-Dimensional Mass Spectra using Interpolated Dynamic Time Warping
      event: 53rd American Society of Mass Spectrometry Conference
      authors: Prince JT, Marcotte EM
      year: 2005
      month: Jun
    -
      bib_type: poster
      title: 'Bias in Large Scale Mass Spectrometry Proteomics Protein/Peptide Identification Error Estimates'
      event: Keystone Symposium (Cell Signaling and Proteomics)
      authors: Prince JT, Marcotte EM
      year: 2007
      month: Mar
    -
      bib_type: presentation
      title: The Open Proteomics Database (OPD) and publishing mass spectrometry based protein identifications
      event: The Paris Committee for Guidelines for Proteomic Data Publication
      authors: Prince JT, Marcotte EM
      year: 2005
      month: May
    -
      bib_type: article
      title: Revised Draft Guidelines for Proteomic Data Publication
      journal: Molecular and Cellular Proteomics
      authors: The Paris Committee for Guidelines for Proteomic Data Publication
      year: 2005
      vol: 4
      pages: 1223-5
    -
      bib_type: poster
      title: Analysis and Identification of Proteins in Human Placental Mitochondria
      event: Keystone Symposium (Proteomics and Applications)
      authors: Prince JT, Fuqua B, Johnson J, Marcotte EM
      year: 2003 
      month: Mar
- 
  cat: Contact
  info:
  -
    contact: 
      address1: 5517 War Admiral Dr.
      address2: Del Valle, TX 78617 
      home: (512) 247-7541
      work: (512) 232-3919
      email: [see .html or .pdf]
      resume:
        email: [see .html or .pdf]
-
  cat: References
  info:
  -
    references:
    - 
      name: Edward M. Marcotte, Professor, Ph.D.
      address:
      - The University of Texas at Austin
      - Cellular & Molecular Biology
      - 1 University Station, A4800
      - Austin, TX 78712
      location: MBB 3.210AA
      office: 512-471-5435
      email: [see .html or .pdf]
    -
      name: Vishwanath R. Iyer, Assoc Professor, Ph.D.
      address:
      - The University of Texas at Austin
      - Cellular & Molecular Biology
      - 1 University Station, A4800
      - Austin, TX 78712
      location: MBB 3.212A
      office: 512-232-7833
      email: [see .html or .pdf]
    -
      name: Daniel P. Miranker, Professor, Ph.D.
      address:
      - The University of Texas at Austin
      - Computer Science Dept.
      - 1 University Station, C0500
      - Austin, TX 78712
      location: TAY 3.140B
      office: 512-471-9541
      email: [see .html or .pdf]
    -
      name: Maria, Person, Asst Professor, Director Analytical Instr Facility Core
      address:
      - The University of Texas at Austin
      - PHAR-PHARMACOLOGY
      - 1 University Station
      - Austin, TX 78712
      location: PHR 1.110, MBB 1.420
      office: 512-232-4340, 512-475-9329
      email: [see .html or .pdf]
#    -
#      name: Delia Brownson, Research Engineer, Ph.D.
#      address:
#      - The University of Texas at Austin
#      - School of Biological Sciences
#      - 1 University Station, A6500
#      - Austin, TX 78712
#      location: PAI 1.22
#      office: 512-232-9281
#      email: [see .html or .pdf]
    -
      name: Michael T. Smith, Coordinator, M.A.
      address:
      - University of Texas at Austin
      - International Office, A700
      - PO Box A
      - Austin, Texas 78713
      location: SHC 339
      office: 512-471-2482
      email: [see .html or .pdf]
    -
      name: Merritt B. Andrus, Professor, Ph.D.
      address:
      - Brigham Young University
      - Department of Chemistry and Biochemistry
      - Provo, UT 84602
      location: C410 BNSN
      office: 801-422-8171
      email: [see .html or .pdf]

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