Experience

Affini-T Therapeutics(Watertown, MA)

Associate Director, Computational Biology December, 2021—Present

Takeda Oncology (Cambridge, MA)

Principal Scientist, Computational Biologist October 2017—November 2021 Translational Sciences; Computational Oncology

  • Computational oncology support of multiple cell therapy discovery projects
  • Lead pilot study of spatial transcriptomic platform/technology evaluations
  • Manage 3 direct reports (RA, SRA, Scientist II)
  • Lead cell therapy project to optimize combination of armoring, target, platform, and patient populations
  • Lead effort to identify and evaluate cell therapy targets, with an eye toward clinical and competitive landscape
  • Key member of hiring team for a new group leader and 3 new members
  • Assisted onboarding of new members into computational environments and workflows across multiple Takeda organizations and drug discovery units
  • Integrated multiple data sources and types (dna, rna, protein) from public and private sources to identify tumor associated antigens uniquely over expressed in lung cancer
  • Developed and applied scRNA-Seq pipelines to both public and Takeda-generated data from multiple platforms
  • Organized a working group of scientists interested in scRNA-Seq technology, publications, and applications
  • Collaborated with Cell Therapy teams and programs to develop preclinical translational experiments and analysis
  • Helped revitalize the TBOS Scientific Computing environments, including transition to cloud-based and dynamically scalable infrastructures
  • Management of NGS outsourcing for multiple project teams and departments.
  • One direct report (Scientist level)
  • Core Member of IT program to pilot the use of Apple Macbooks as main laptops in Discovery
  • Supported GI-DDU scientists in the analysis of RNA-Seq/scRNA-Seq datasets, as well as novel design of external therapeutic platforms

Ohana Biosciences/VL34 Inc

A Flagship Pioneering-backed startup focused on human and animal reproductive health. Closed in early 2021.

Senior Scientist, Computational Biology October 2016 — October 2017

  • Designed and implemented a collaborative computing environment using Amazon Web Services (AWS)
  • Created robust and distributed computing pipelines for transcript reconstruction and whole chromosome haplotype phasing
  • Analyzed and interpreted whole genome, exome, and single cell sequencing data from multiple species including human, bull, mouse, and non-human primates
  • Assembled tissue- and cell-type-specific transcriptomes using public sequencing data
  • Integrated RNA-Seq data from >15 distinct bovine tissues to create a comprehensive set of gene and transcript annotations
  • Exome sequenced genomically-interesting commercial dairy bulls to find novel tissue-specific protein isoforms
  • Identified and developed relationships with forward-thinking diary farmers in the field of cattle genetics
  • Integrated public phenotypic data from cattle breeding associations with in-house generated genotype data
  • Created candidate evaluation portals which integrated DNA, RNA, and protein level information for the purposes of efficient candidate selection

Takeda Oncology (Cambridge, MA)

Scientist 2, Computational Biologist October 2014 — October 2016 Discovery Molecular and Cellular Oncology; Genomics Subgroup

  • Advance oncology small molecule drug development via public and in-house generated HTS data
  • Comprehensive bioinformatic assessment of potential oncology targets including: general expression, indication identification, mutational status and/or other ’omic features
  • Early translation strategy identification using tool molecule response metrics in hundreds of cell lines
  • Identify translationally appropriate in vitro and in vivo model systems for early target validation experiments
  • Genome-wide and systematic identification of antibody drug conjugate targets
  • Analysis of treatment-induced differential gene expression in cell lines and in vivo tumor models
  • Advance department-wide computational biology approaches and abilities including command-line operated analytic environments and cloud computing

Voyager Therapeutics (Cambridge, MA)

Consultant, Computational Biology June 2014 – October 2014 Vector Design Group

  • Created Amazon cloud-based computational biology HTS analysis environment
  • Directed AAV vector design using public small RNA-Seq data
  • Analyzed and interpreted company-generated HTS data

Graduate School (Worcester, MA)

Graduate Student September 2007 — June 2014 See Education

Genzyme (Framingham, MA)

Research Associate April 2003 – September 2007 Bioanalytical Development Group

  • GLP/GMP biochemical assay development in support of recombinant protein clinical trials
  • HPLC assay development to quantify recombinant protein glycosylation
  • QPCR assay development to test for viral contamination of recombinant protein-producing cell lines

Research Intern Summer 2003 Bioanalytical Development Group

  • IEF assays and ELISAs in support of preclinical and clinical research

Achillion Pharmaceuticals (New Haven, CT)

Research Internship Summer 2002 Preclinical Candidate Selection

  • ELISAs and cell culture in support of small molecule screening

Education

University of Massachusetts Medical School (Worcester, MA)

Doctor of Philosophy, Biochemistry and Molecular Pharmacology Advisors: Melissa J. Moore & Phillip D. Zamore September 2007 – May 2014 Graduate School of Biomedical Sciences RNA Therapeutics Institute and Howard Hughes Medical Institute

  • Developed novel ligation-based assay to profile long (1,000—10,000 nt) RNAs (eLife 2015)
  • Defined and characterized piRNA-producing lncRNAs via multiple high-throughput sequencing (HTS) data types (Molecular Cell 2013)

Worcester Polytechnic Institute (Worcester,MA)

Bachelor of Science with High Distinction September 2000 – May 2004 Major: Biology & Biotechnology, Minor: Management

Skills

  • General
    • Experienced bench and computational experimentalist
    • Clear communicator and presenter
    • Highly motivated and self-driven scientist
    • Manuscript and figure generation (Illustrator, work, LaTeX)
  • Computational
    • UNIX/Linux/GNU; bash; PERL; R; SQL; SGE; LSF; ZFS; some Python
    • scRNA-Seq processing and analysis
    • Windows and OSx
    • Amazon Cloud Services
    • HTS data analysis and maintenance (command line tools and Omicsoft ArrayStudio)
    • Data visualization and communication (knitr; Shiny; Spotfire)
    • Analysis and mining of public data (SRA, dbGaP, Ensembl, UCSC, etc.)
  • Bench
    • Standard Molecular Biology and Biochemical laboratory techniques
    • Gel electrophoresis (agarose, PAGE, IEF)
    • HTS library construction
    • Nucleic acid radioactive manipulation
    • Cell culture
    • Spectrophotometry
    • High Performance Liquid Chromatography (HPLC)

Patent and Publications

Widespread haploid-biased gene expression enables sperm-level natural selection Science (March 2021) Kunal Bhutani, Katherine Stansifer, Simina Ticau, Lazar Bojic, Chloe Villani, Joanna Slisz, Claudia Cremers, Christian Roy, Jerry Donovan, Brian Fiske, Robin Friedman

Subsets of mononuclear phagocytes are enriched in the inflamed colons of patients with IBD BMC Immunology (November 2019) Hong Liu, Suryasarathi Dasgupta, Yu Fu, Brandi Bailey, Christian Roy, Eric Lightcap & Benjamin Faustin

Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation eLife (April 2015) Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ.

Deducing Exon Connectivity by RNA-Templated DNA Ligation/Sequencing Patent US8975019 B2 (March 2015) Zamore PD, Moore MJ, Roy CK

Putting the Pieces Together: Exons and piRNAs UMMS Dissertation (May 2014) Roy CK

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes Molecular Cell (April 2013) Li XZ•, Roy CK• (•Equal contribution), Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD

Defining piRNA primary transcripts Cell Cycle (May 2013) Li XZ, Roy CK, Moore MJ, Zamore PD.

UPF1 Is Crucial for the Infectivity of Human Immunodeficiency Virus Type 1 Progeny Virions Journal of Virology (August 2013) Serquiña AKP, Suman RD, Popova E, Ojelabi OA, Roy CK, and Göttlinger HG

Presentations

Conference / Event (Date) Work Presented
Gordon Conference: The Biology Of Post-Transcriptional Gene Regulation, Newport RI (2014) Short Talk Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation
17th Annual Meeting of the RNA Society, Ann Arbor, MI (2012) Poster “SeqZip—A versatile methodology for analyzing long RNAs” Winner - Nature Reviews Molecular Cell Biology Poster Prize for Innovation and Interdisciplinary Research
Gordon Conference: The Biology Of Post-Transcriptional Gene Regulation, Newport RI (2010) Poster “A novel technique to discover connectivity between distant alternatively spliced exons”
Umass Medical School RNA Club, Worcester MA, (2009) Presentation “Uncovering connectivity between distant alternatively spliced exons”