My name is Matt Shirley and I work as a Data Scientist in Oncology Bioinformatics at Novartis Institutes for BioMedical Research, and I advise the Sturge-Weber Foundation's patient-focused research as CSO.

You can find my publications on ORCID and Scholar , and read my reviews on Publons . Send me a pull request on GitHub . Ask me about bioinformatics on BioStars.org. Network with me on LinkedIn or Twitter . Find my things on Thingiverse. Schedule a meeting with me.

GITHUB REPOSITORIES
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Matthew Shirley, Ph.D.
Computational biologist working in rare disease and cancer genomic; developer of software for genomics data. 250 Massachussetts Ave
Cambridge MA 02139
[email protected]
[email protected]
(443) 637-2459
(617) 871-5544
mattshirley.com

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 2021 - currentChief Scientific Officer, The Sturge-Weber Foundation, Aurora CO
  • Funding innovative translational research proposals through the Lisa's Fellowship program with the goal of advancing therapeutics for Sturge-Weber Syndrome towards the clinic.
  • Organizing multidisciplinary international research conferences and discussions under the three core SWS research domains: neurology, dermatology, and opthamology.
  • Hosted the 2022 & 2023 Sturge Weber International Research Network Conferences in Grapevine TX and Charlotte NC, bringing together top researchers and labs from the Sturge-Weber research community. Applied for and recieved funding through NIH R13 to support conference activities. Managed a collaborative goal-setting process to build consensus around long-term research strategy.
  • Established public/private collaborations utilizing the SWS patient registry data, seeking to accelerate discovery for rare epillepsies through the C-Path Rare Disease Cures Accelerator Program.
May 2015 - currentAssociate Director and Senior Principle Data Scientist, Novartis BioMedical Research, Cambridge MA
  • Developed alignment-free RNA-seq pipeline for processing thousands of internal and external experiments across Novartis R&D portfolio.
  • Managed resourcing and stakeholder relationships for the Novartis Oncology Data Science drug discovery portfolio to ensure continued support of research programs.
  • Identified and validated novel pharmacodynamic markers to support multiple oncology drug discovery and development programs.
  • Interfaced wet lab biologists and sequencing facilities to guide experimental design, execution and perform data analysis of multiple NGS assays.
  • Designed new tools for validation of CRISPR/Cas9 sgRNA efficiency.
  • Mined internal and public genomics data to identify and validate new drug targets.
  • Organized 2019-2023 yearly global computational research symposia spanning six geographical sites.
  • Chaired a global employee resource group for Novartis computational biology, bioinformatics and data science staff.
Mar 2013 - May 2015Postdoctoral Fellow, Department of Oncology, Johns Hopkins School of Medicine
  • Developed statistical framework for integrative whole-genome genetic and bisulfite sequence analysis.
  • Mined genomic data for epigenetic prostate cancer biomarkers.
  • Collaboratively developed and deployed new software tools in the genomics community.
  • Mentored graduate and undergraduate students in computational methods.
  • Taught 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

  • Next Generation Sequencing Analysis
  • Molecular Biology
  • Applied Statistics
  • Python
  • R
  • Team and Project Management
  • Code Version Control
  • SQL
  • Continuous Integration Testing
  • Unix
  • Cloud Computing
  • Software Development

Publications

Ahmed MO Elbatsh, Ali Amin-Mansour, Anne Haberkorn, Claudia Textor, Nicolas Ebel, Emilie Renard, Lisa M Koch, Femke C Groenveld, Michelle Piquet, Ulrike Naumann, David A Ruddy, Vincent Romanet, Julia M Martínez Gómez, Matthew D Shirley, Peter Wipfli, Christian Schnell, Markus Wartmann, Martin Rausch, Martine J Jager, Mitchell P Levesque, Sauveur-Michel Maira, Eusebio Manchado. INPP5A phosphatase is a synthetic lethal target in GNAQ and GNA11-mutant melanomas. Nature Cancer. 2024.
S. Piperno-Neumann, M. S. Carlino, V. Boni, D. Loirat, F. M. Speetjens, J. J. Park, E. Calvo, R. D. Carvajal, M. Nyakas, J. Gonzalez-Maffe, X. Zhu, M. D. Shirley, T. Ramkumar, A. Fessehatsion, H. E. Burks, P. Yerramilli-Rao & E. Kapiteijn. A phase I trial of LXS196, a protein kinase C (PKC) inhibitor, for metastatic uveal melanoma. British Journal of Cancer. 2023.
Matthew S. Crowe, Tatiana Zavorotinskaya, Charles F Voliva, Matthew D. Shirley, Yanqun Wang, David A. Ruddy, Daniel P Rakiec, Jeffrey A. Engelman, Darrin D. Stuart and Alyson K Freeman. RAF-mutant melanomas differentially depend on ERK2 over ERK1 to support aberrant MAPK pathway activation and cell proliferation. Molecular Cancer Research. 2021.
Hui Qin Wang, Iain J Mulford, Fiona Sharp, Jinsheng Liang, Sema Kurtulus, Gina Trabucco, David S Quinn, Tyler A Longmire, Nidhi Patel, Roshani Patil, Matthew D. Shirley, Yan Chen, Hao Wang, David A. Ruddy, Claire Fabre, Juliet A. Williams, Peter S. Hammerman, Jennifer Mataraza, Barbara Platzer and Ensar Halilovic. Inhibition of MDM2 promotes anti-tumor responses in p53 wild-type cancer cells through their interaction with the immune and stromal microenvironment. Cancer Research. 2021.
Matthew D Shirley, Viveksagar K Radhakrishna, Javad Golji, Joshua M Korn. (Preprint) PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets. bioRxiv. 2020.
Florencia Rago, GiNell Elliott, Ailing Li, Kathleen Sprouffske, Grainne Kerr, Aurore Desplat, Dorothee Abramowski, Julie T. Chen, Ali Farsidjani, Kay X. Xiang, Geoffrey Bushold, Yun Feng, Matthew D. Shirley, Anka Bric, Anthony Vattay, Henrik Möbitz, Katsumasa Nakajima, Christopher D. Adair, Simon Mathieu, Rukundo Ntaganda, Troy Smith, Julien P.N. Papillon, Audrey Kauffmann, David A. Ruddy, Hyo-eun C. Bhang, Deborah Castelletti and Zainab Jagani. The Discovery of SWI/SNF Chromatin Remodeling Activity as a Novel and Targetable Dependency in Uveal Melanoma. Molecular Cancer Therapeutics. 2020.
Huai-Xiang Hao, Hongyun Wang, Chen Liu, Steven Kovats, Roberto Velazquez, Hengyu Lu, Bhavesh Pant, Matthew Shirley, Matthew J Meyer, Minying Pu, Joanne Lim, Michael Fleming, LeighAnn Alexander, Ali Farsidjani, Matthew J. LaMarche, Susan Moody, Serena J Silver, Giordano Caponigro, Darrin D. Stuart, Tinya J Abrams, Peter S. Hammerman, Juliet Williams, Jeffrey A. Engelman, Silvia Goldoni and Morvarid Mohseni. Tumor intrinsic efficacy by SHP2 and RTK inhibitors in KRAS mutant cancers. Molecular Cancer Therapeutics. 2019.
Zainab Jagani, Gregg Chenail, Kay Xiang, Geoffrey Bushold, Hyo-Eun C. Bhang, Ailing Li, GiNell Elliott, Jiang Zhu, Anthony Vattay, Tamara Gilbert, Anka Bric, Rie Kikkawa, Valérie Dubost, Rémi Terranova, John Cantwell, Catherine Luu, Serena Silver, Matt Shirley, Francois Huet, Rob Maher, John Reece-Hoyes, David Ruddy, Daniel Rakiec, Joshua Korn, Carsten Russ, Vera Ruda, Julia Dooley, Emily Costa, Isabel Park, Henrik Moebitz, Katsumasa Nakajima, Christopher D. Adair, Simon Mathieu, Rukundo Ntaganda, Troy Smith, David Farley, Daniel King, Xiaoling Xie, Raviraj Kulathila, Tiancen Hu, Xuewen Pan, Qicheng Ma, Katarina Vulic, Florencia Rago, Scott Clarkson, Robin Ge, Frederic Sigoillot, Gwynn Pardee, Linda Bagdasarian, Margaret McLaughlin, Kristy Haas, Jan Weiler, Steve Kovats, Mariela Jaskelioff, Marie Apolline-Gerard, Johanna Beil, Ulrike Naumann, Pascal Fortin, Frank P. Stegmeier, Michael G. Acker, Juliet Williams, Matthew Meyer, James E. Bradner, Nicholas Keen, William R. Sellers, Francesco Hofmann, Jeffrey A. Engelman, Darrin Stuart, Julien P.N. Papillon. (Preprint) In-Depth Characterization and Validation in BRG1-Mutant Lung Cancers Define Novel Catalytic Inhibitors of SWI/SNF Chromatin Remodeling. BioRxiv. 2019.
Grace P Leung, Tianshu Feng, Frederic D Sigoillot, Felipe Correa Geyer, Matthew D Shirley, David A Ruddy, Daniel Rakiec, Alyson K Freeman, Jeffrey A Engelman, Mariela Jaskelioff, Darrin D Stuart. Hyperactivation of MAPK Signaling is Deleterious to RAS/RAF Mutant Melanoma. Molecular Cancer Research. 2018.
Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD, Golji J, Ruddy DA, Yu K, McAllister G, DeWeck A, Abramowski D, Wan J, Shirley MD, Neshat SY, Rakiec D, de Beaumont R, Weber O, Kauffmann A, McDonald ER, Keen N, Hofmann F, Sellers WR, Schmelzle T, Stegmeier F, Schlabach MR. CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discovery. 2016.
Matthew D Shirley, Laurence Frelin , José Soria López , Anne Jedlicka , Amanda Dziedzic , Michelle A. Frank-Crawford , Wayne Silverman , Louis Hagopian , Jonathan Pevsner. Copy Number Variants Associated with 14 Cases of Self-Injurious Behavior. PLOS ONE. 2016.
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

PISCES: a package for rapid quantitation and quality control of large scale mRNA-seq datasets
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

Patents

Jonathan Pevsner, Anne Comi, Douglas Marchuk, Matthew Shirley Diagnostic and prognostic test for Sturge-Weber syndrome, Klippel-Trenaunay-Weber syndrome, and port-wine stains (PWSS). USPTO. 2020.

Grants

20231R13NS134286-01 - Sturge Weber Syndrome: Moving Translational Science Forward into the Clinical Realm
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

Seminars

Abstracts and Posters

Lectures

Titles of talks link to slides.