My name is Matt Shirley and I work as an Investigator in Oncology Bioinformatics at Novartis Institutes for BioMedical Research.

You can find my publications on ORCID and Scholar. View the impact of my research products on ImpactStory. Send me a pull request on GitHub. Ask me about bioinformatics on BioStars.org or ask me a general question on Quora. Network with me on LinkedIn or Twitter. Read my blog too if you like.

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Matthew Shirley, Ph.D.

Rare disease and cancer genomics researcher, developer of software for genomics data. 250 Massachussetts Ave
3C-470-03
Cambridge MA 02139
mdshw5@gmail.com
(443) 637-2459

Education

2013Ph.D. Biochemistry, Cellular, and Molecular Biology,  Johns Hopkins School of Medicine, Baltimore, MD
2008B.S. Biochemistry, University of Missouri, Columbia, MO

Research & Professional Experience

May 2015 - currentInvestigator II, Novartis Institutes for BioMedical Research, Cambridge MA
Mar 2013 - May 2015Postdoctoral Fellow, Department of Oncology, Johns Hopkins School of Medicine
  • Developing statistical framework for integrative whole-genome genetic and epigentic analysis.
  • Mining genomic data for epigenetic prostate cancer biomarkers.
  • Collaboratively developing and deploying new software tools in the genomics community.
  • Mentoring graduate and undergraduate students in computational methods.
  • Teaching classes and workshops for computational biology and programming.
Aug 2008 - Mar 2013Ph.D. Candidate, Department of Neuroscience, Johns Hopkins School of Medicine
Jun 2006 - May 2008 Research Assistant, Department of Biochemistry, University of Missouri-Columbia
  • Studied genetics of heavy metal bioremediation in bacterium Desulfovibrio vulgaris Hildenborough.
  • Sequenced transposon insertion mutagenesis library in DvH.
  • Characterized metabolites of DvH anaerobic growth using gas chromatography.

Skills

  • Sequencing Analysis
  • Molecular Biology
  • Applied Statistics
  • Python
  • R
  • Bash
  • Code Version Control
  • SQL
  • Continuous Integration Testing
  • Unix
  • Cloud Computing
  • Software Development

Publications

Shirley MD, Ma Z, Pederson B, Wheelan S. Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints. 2015.
Shirley MD, Tang H, Gallione CJ, Baugher JD, Frelin LP, Cohen B, North PE, Marchuk DA, Comi AM, Pevsner J. Sturge–Weber Syndrome and Port-Wine Stains Caused by Somatic Mutation in GNAQ. New England Journal of Medicine. 2013.
Baugher JD, Baugher BD, Shirley MD, Pevsner J. Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method. BMC Genomics. 2013.
R.H. Newman, J. Hu, H. Rho, Z. Xie, C. Woodard, J. Neiswinger, C. Cooper, M. Shirley et al. Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 2013.
Stevens EL, Baugher JD, Shirley MD, Frelin LP, Pevsner J.  Unexpected Relationships and Inbreeding in HapMap Phase III Populations. PLoS ONE. 2012.
Shirley MD, Baugher JD, Stevens EL, Tang Z, Gerry N, Beiswanger CM, Berlin DS, Pevsner J.  Chromosomal variation in lymphoblastoid cell lines. Human Mutation. 2012.

Software

pyfaidx: efficient & pythonic random access to fasta subsequences
simplesam: Simple pure Python SAM parser and objects for working with SAM records
fastqp: Python FASTQ and SAM read quality assessment and plotting
sra-tools-galaxy: NCBI SRA toolkit Galaxy package and tool wrappers
hamstring: Python module for Hamming7,4 error-correcting DNA barcodes
tripod: web interface for the triPOD mosaicism analysis

Grants

2013Amazon Web Services in Education Grant, supporting Introduction to Python

Teaching Experience

2013Center for Computational Genomics, Johns Hopkins School of Medicine, Baltimore MD
2013Bioinformatics & Computational Biology Department, Foundation for Advanced Education in the Sciences, Bethesda MD

Lectures

Titles of talks link to slides.

Invited Talks

Abstracts and Posters

Awards

2007 Undergraduate Research Ambassador
2007 Chancellor’s Award for Excellence in Research
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