I'm a graduate student in my fifth year of a Computational Biology PhD program at Baylor College of Medicine, where I use bioinformatic techniques and large scale data-integration to help understand the aetiology of cancer.

My core research interests include:

  • Structural changes in the human genome and their contributions to disease
  • Cancer - studying the evolutionary pressures driving tumorigenesis
  • Integrative analysis - combining disparate sources of genomic data to place aberrations into a functional context

Other interests include:

  • Open-source software for integrating, mining, and visualizing genomic data
  • Teaching biologists how to leverage computational resources
  • Utilizing online technologies to drive science communication and collaboration



Chris Miller

Education

  • PhD Candidate, Structural and Computational Biology and Molecular Biophysics program
    Mentor: Dr. Aleksandar Milosavljevic
    Baylor College of Medicine
    (August 2005 - present. Expected graduation late 2010)
  • BS degrees in Biology and Computer Science
    Truman State University
    (graduated May 2005)

Publications

  • Discovering functional modules by identifying patterns of recurrent and mutually exclusive mutations in cancer. Miller, CA and Milosavljevic, A. 2009. (In submission)
  • A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.
    Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic, A. Genome Res. Advance Online Publication, December 3, 2008. doi:10.1101/gr.080259.108
  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
    The Cancer Genome Atlas Research Network. Nature 455, 1061-1068 (23 October 2008) doi:10.1038/nature07385

Posters/Presentations

  • Discovering genes with functionally related roles in cancer progression by searching for significant mutational patterns
    Poster: CSHL Genome Informatics (2009) and BCM Graduate Student Symposium (2009)
  • Integrative analysis of multi-dimensional genomic data identifies key relationships between cancer pathways
    Poster: SCBMB Retreat (2008)
  • An Integration Pipeline for the Analysis of Genomic Data
    Poster: Keck Annual Research Conference (2007)
  • Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing
    Poster: Rice University Computational Biology Conference (2006)
  • An Image Analytic Approach to Characterizing Vasculogenic Networks
    Presentation: Truman State University Student Research Symposium (2005)

Contact Information

  • Email is generally the best way to reach me: chrisamiller@gmail.com
    camiller@bcm.edu
  • Postal Mail can be addressed to:
    Christopher A Miller
    Alkek Bldg. N1619.03
    Baylor College of Medicine
    One Baylor Plaza
    Houston, TX 77030

Skills

  • Designing genomic analysis pipelines using Ruby, R, Perl, Bash, and Linux
  • Synthesizing data from a wide variety of genomic techniques and technologies, including:
    • massively-parallel paired-end sequencing for structural mapping and detection of copy-number aberrations
    • array comparative genomic hybridization (aCGH)
    • expression and methylation arrays
    • SNP and indel detection from resequencing
  • Design of machine-learning tools for extracting patterns from genomic data
  • Utilizing high-performance linux clusters to expidite analyses
  • Facilitating interdisciplinary collaborations
  • Web, graphic, and multimedia design

Teaching

  • Computer Aided Discovery Methods (2007 and 2008)
    Contributed to the development of the course and taught computational labs on:
    • Studies of genome variation
    • Transcriptional regulatory pathways
  • Computational Mathematics for Biomedical Scientists (2008)
    • Teaching Assistant
  • Advanced Topics: Quantitative Biology (2005)
    • Teaching Assistant

Past Research

  • Genotypic and phenotypic analysis of ABC transporter knockouts in Dictyostelium discoideum.
    Mentor: Dr. Gad Shaulsky
    Rotation Project - Spring 2006
  • Classification and analysis of Alu SINEs in Human and Chimpanzee Chromosomes 3 and 12
    Mentor: Dr. Aleksandar Milosavljevic (BCM)
    Rotation project - Fall 2005
  • Identifying structural elements in cryoEM reconstructions of proteins and correlating them with predictions from protein sequence.
    Mentor: Dr. Steve Ludtke (BCM)
    Rotation project - Fall 2005
  • Development of an open-source image analysis toolset for describing the structure and dynamics of biological tissue.
    Mentors: Dr Jason Miller (Truman State University) and Dr Robert Baer (Kirksville College of Osteopathic Medicine)
    Summer 2004 – Spring 2005

Other

  • I write about science, technology, and culture at http://www.chrisamiller.com/blog/
  • BCM Graduate Student Council
       - Vice-president 2008
       - SCBMB representative 2007
  • Member of Phi Sigma Pi National Honor Fraternity
       - Chapter Service Key recipient (2004)
  • Eagle Scout