CHRISTOPHER F. VILLALTA Ph.D.
SUMMARY OF QUALIFICATIONS:
- Ph.D. in Microbiology with 11 years of Bioinformatics and Molecular Biology experience.
- Experienced in the data analysis of Illumina next generation sequencing (NGS) data, both RNASeq and DNASeq, in industry and academic settings.
- Involved in fabrication of microarrays for use in graduate research and Neurospora genome project.
- Experience in plasmid construction and filamentous fungi strain generation.
- Skilled at building phylogenetic and gene trees.
- Worked with Fungi (Neurospora and Histoplasma) and Bacteria (Escherichia coli). Trained to work in a BSL3 lab.
- Experienced in using Unix command line environment and working remotely by SSH.
- A Biologist comfortable with programming in python to create analysis pipelines.
- Emacs, pycharm, ipython
- Can program in R and Perl.
- Comfortable working with large datasets in python (Pandas).
- Querying Datomic and SQL databases with python.
- Biopython, SciPy, Numpy, pybedtools, pysam, Matplotlib, Seaborn.
- R Bioconductor packages.
- Familiar with using multiple hypothesis testing, the hypergeometric model, GLM, Mann-Whitney Wilcoxon test, and ANOVA in R for statistical significance testing.
- Graph and display data in Python and R.
- Use version control (GIT)
- Comfortable working with a LIMS system programmatically (e.g. accessing LIMS Datomic database with python or by web interface)
- Knowledge of bioinformatics tools available for sequence quality control, human sequence mapping, and variant calling.
- Link to Git repositories with scripts from graduate school and postdoc: https://github.com/cfvillalta
University of California, Berkeley, Ca
Ph.D. Microbiology, December 2011
San José State University, San Jose, Ca
B.S., Biology, May 2005
Concentration in Microbiology
Saint Ignatius College Preparatory, San Francisco, Ca
High School Diploma, June 2000
Assay Development (R&D), Invitae, San Francisco, Ca
Bioinformatics Scientist (04/2015-10/2016)
- Responsible for getting Illumina Sequencing data through analysis pipeline for all R&D runs.
- Involved in the analysis of Assay Development team data.
- Played a significant role in the preparation and validation of Illumina HS4000 machines for production use.
- Involved in the analysis (variant/ copy number concordance) and validation, including writing validation documents, of new assays before entering production.
- Role involved interacting with production bioinformatics, R&D, production pipeline engineering group, LIMS, QA group, and Assay Development project manager.
Laboratory of Anita Sil, University of California, San Francisco, San Francisco, Ca
Postdoctoral Fellow (01/2012-04/2015)
Research Project: Characterization of tyrosinases in Histoplasma and their role in mammalian infection.
Principal Investigator: Anita Sil, M.D., Ph.D.
- Histoplasma experiments were done in BSL3 and BSL2 laboratory settings.
Laboratory of John W. Taylor, University of California, Berkeley, Berkeley, Ca
Ph.D. Student (02/2006-12/2011)
Dissertation Research: Testing the phylogenetic species concept in Neurospora and understanding gene expression during early mycelia contact.
Principal Investigator: John W. Taylor, Ph.D.
- RNASeq analysis led to discovery of a previously undescribed BZIP transcription factor and putative glutaredoxin both important to fungal interactions.
- Discovery and description of three new phylogenetic species of Neurospora
Laboratory of Molecular Gerontology, National Institute of Aging, Baltimore, MD
Undergraduate Researcher (06/2005-08/2005)
Research Project: Role of Werner protein in the cellular response to DNA interstrand cross-links.
Principal Investigators: Vilhelm A. Bohr, M.D., Ph.D. and Wen-Hsing Cheng Ph.D.
Laboratory of Robert Fowler, San José State University, San José, Ca
Undergraduate Researcher (04/04-05/05)
Research Project: Studied the mechanisms of spontaneous mutagenesis in E. coli mutants, specifically frameshift mutagenesis.
OTHER RELEVANT EXPERIENCE
- Bilingual in English and Spanish
- Familiar working with Issue and project manager JIRA
Vongphachan P, Villalta CF, Songvilay P, Chittarhath, Sayapatha S, Walsh JL, Burgess LW. Neurospora contamination of cultures in Lao PDR – a sticky rice issue. 2013. Australian Plant Disease Notes. 8(1), 9-12.
Villalta CF, Jacobson DJ, Taylor JW. 2009. Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii. Mycologia. 101(6), 777-789.
Hardin A, Villalta CF, Doan M, Jabri M, Chockalingham V, White SJ, Fowler RG. 2007. A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli. DNA Repair. 6(2), 177-189.
Co-instructor, Biology 425: Emerging Infectious Diseases, San Francisco State University, Spring 2014
Teaching Assistant, QB3 Introduction to Python Bioinformatics Course, University of California, Berkeley, Summer 2011.
Graduate Student Instructor, PMB110: The Diversity of Fungi, University of California, Berkeley, Fall 2008.
Graduate Student Instructor, Biology 1B: Introduction to Biology, University of California, Berkeley, Fall 2006.
Comparison of Neurospora crassa transcription profiles before and after mycelia contact with fungi of increasing phylogenetic distance. Plant and Microbial Biology Graduate Student and Post Doctoral Fellow Seminar Series. Berkeley, Ca. April 2010.
Neurospora, Coccidiodes and Batrachochytrium: Models for Fungal Evolution and Genomics. Department of Plant and Microbial Biology Retreat. Asilomar, Ca. September 2008.
Neurospora as a model for evolutionary biology. Neurospora Meeting 2008. Asilomar, Ca. March 2008.
Comparison of Neurospora crassa transcription profiles before and after mycelia contact with fungi of increasing phylogenetic distance. The 26th Fungal Genetics Conference. Asilomar, Ca April 2011.
Comparison of Neurospora crassa transcription profiles before and after mycelia contact with fungi of increasing phylogenetic distance. Neurospora Meeting 2010. Asilomar, Ca. April 2010
Search for new phylogenetic species among wild Neurospora sitophila isolates. The 25th Fungal Genetics Conference. Asilomar, Ca. March 2009.
RFLP analysis reveals more isolates belonging to new Neurospora species. Neurospora Meeting 2008. Asilomar, Ca. March 2008.
Role of Werner Syndrome protein in the cellular response to DNA interstrand cross-links. National Institute of Aging Summer Program Poster Session. Baltimore, Maryland. August 2005.
Frameshift Reversion Analysis in Escherichia coli. Annual Biomedical Research Conference for Minority Students. Dallas, Texas. November 2004. West Coast Biological Undergraduate Research Conference. April 2005.
- IRACDA Scholar in Science (ISIS) NIH K12 Fellowship (01/12-01/16)
- UCSF/NIH MPHD T32 Training Grant (01/12-01/13)
- University of California, Berkeley International House Housing Fellowship (08/05-05/06).
- Minority Access to Research Careers (MARC) NIH Fellowship (03/04-08/05).
- Research Mentor for SPUR (Sponsored Projects for Undergraduate Research) researcher Michelle Nguyen. Summer and Fall 2008.
- Printing of Neurospora crassa microarrays at UCSF CAT for use in the Neurospora Genome Project and by Neurospora research community. 2007-2008.
- Meeting with San José State MARC undergraduates where I spoke about and answered questions about graduate school applications and my first year in graduate school. April 2006.