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Resume

Tech Skills​

Languages: Java, Python, JavaScript, SQL (PostgreSQL), Bash, R
Libraries/Frameworks/Tools: Spring Boot, Hibernate, Gradle, NodeJS, React, Material UI, Express, D3.js, OpenAPI, Read the Docs
Concepts: REST API, CI/CD, Infrastructure as Code (CloudFormation), ETL
Platforms: AWS, Git/Github, Github Actions, Jira
Bioinformatics: Docker, Singularity, WDL, Nextflow

Work Experience​

Team Lead, Global Alliance for Genomics and Health
Toronto, ON, Canada  August 2021 - Present

  • Lead development of the GA4GH Starter Kit, a reference implementation suite for API-based authorization, data access, and analysis according to GA4GH standards
  • Deploy Starter Kit at multiple institutes, including the European Bioinformatics Institute (EBI), for novel genomics analyses
  • Lead development of testbed infrastructure, enabling international collaborators to compliance and performance test their APIs to GA4GH standards

Software Developer, Global Alliance for Genomics and Health
Toronto, ON, Canada  April 2019 - August 2021

  • Developed RESTful APIs for dynamic and flexible transfer of genomic alignments (BAM, CRAM), variants (VCF, BCF), and gene expression matrices (Loom) over the web
  • Co-developed the RNAget API specification, which enables researchers to stream slices of large expression matrices based on gene and tissue/cell panels of interest
  • Developed a service registry API to monitor a network of federated genomic services
  • Supervised junior developers in the development of genomic API clients within the Genome Analysis Toolkit (GATK), a widely-used bioinformatics software package
  • Presented project updates to large audiences at international conferences

Big Data Developer, Solsys Corporation
Toronto, ON, Canada  March 2018 - April 2019

  • Developed applications to detect and report real-time fraudulent transactions for bank client using Python and Splunk (big data analytics platform)
  • Developed dashboards to monitor the health of bank applications deployed in the cloud
  • Designed custom visualizations in D3.js to display server availability and response times
  • Communicated with application teams and implemented requirements into new searches, reports, and visualizations

Bioinformatician, Ontario Institute for Cancer Research
Toronto, ON, Canada  September 2015 - March 2018

  • Processed and analyzed large genomic datasets in a high-performance computing environment
  • Developed and executed cancer dataset pipelines for genome alignment, somatic variant discovery, and differential expression analysis on large cohorts
  • Developed visualization tools in Python and R for quality control of patient tumor genome samples
  • Reviewed scientific literature to implement new bioinformatics software into our pipeline
  • Presented research on new technologies with lab group to keep our pipeline updated and optimized

Teaching Assistant, University of Waterloo
Waterloo, ON, Canada  September 2013 - September 2015

  • Taught molecular biology and genetics concepts to undergraduate students in tutorial
  • Organized and supervised labs on nervous and cardiovascular system physiology
  • Worked closely with students to ensure comprehensive understanding of course material
  • Marked student lab reports, essays, and tests in a fair and unbiased manner
  • Supervised and maintained control of midterm tests and exams

Education​

Master of Science in Biology, University of Waterloo
Waterloo, ON, Canada  September 2013 - September 2015

  • Received NSERC Canada Graduate Scholarship (CGS-M) - $17 500
  • Received University of Waterloo President’s Graduate Scholarship (PGS) - $10 000
  • Designed and programmed a novel software analysis pipeline to detect likely instances of protein functional evolution using structural algorithms
  • Taught Python coding seminars on bioinformatics analysis to students
  • Co-authored paper on my thesis research

Ontario Graduate Certificate in Bioinformatics, Seneca College
Toronto, ON, Canada  September 2012 - June 2013

  • Graduated with high honours (GPA over 3.95)
  • Analyzed next-generation sequencing data to screen for genomic variants and somatic mutations using SAMtools
  • Created dynamic web pages and scripts for querying biological databases, and designed graphical-user interfaces using Perl, SQL, Java, and R in the UNIX/Linux environment
  • Designed and built a yeast strain database and querying tool for an academic lab

Honours Bachelor of Science in Cell and Systems Biology, University of Toronto
Toronto, ON, Canada  September 2008 - June 2012

  • Graduated with high distinction (GPA over 3.50)
  • Learned molecular biology, genetics, and biochemistry concepts, as well as how to interpret experimental data from primary research papers in these fields
  • Cloned and expressed a gene of interest using molecular techniques
  • Purified recombinant protein of interest by affinity chromatography
  • Performed quantitative reverse transcription-PCR to create differential expression data
  • Detected protein-protein interaction by yeast two-hybrid screen

Publications​

  • Borozan I, Zaidi SH, Harrison TA, Phipps AI, ..., Adams J, ..., Peters U. Molecular and Pathology Features of Colorectal Tumors and Patient Outcomes Are Associated with Fusobacterium nucleatum and Its Subspecies animalis. Cancer Epidemiol Biomarkers Prev. 2022 Jan;31(1):210-220. doi: 10.1158/1055-9965.EPI-21-0463. Epub 2021 Nov 4. PMID: 34737207

  • Rehm HL, Page AJH, Smith L, Adams JB, ..., Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. PMID: 35072136

  • Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM. Refget: standardised access to reference sequences. Bioinformatics. 2021 Jul 14;38(1):299-300. doi: 10.1093/bioinformatics/btab524. PMID: 34260694

  • Zaidi SH, Harrison TA, Phipps AI, Steinfelder R, ..., Adams JB, ..., Peters U. Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. Nat Commun. 2020 Jul 20;11(1):3644. doi: 10.1038/s41467-020-17386-z. PMID: 32686686

  • Adams J, Mansfield MJ, Richard DJ, Doxey AC. Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function. Bioinformatics. 2017 May 1;33(9):1338-1345. doi: 10.1093/bioinformatics/btw815. PMID: 28052926

  • Mansfield MJ, Adams JB, Doxey AC. Botulinum neurotoxin homologs in non-Clostridium species. FEBS Lett. 2015 Jan 30;589(3):342-8. doi: 10.1016/j.febslet.2014.12.018. Epub 2014 Dec 23. PMID: 25541486

Other Professional Development​

Certificate in Big Data Analytics, York University
Toronto, ON, Canada  January 2019 - March 2019

  • Solved analytical problems with machine learning and related them to business goals
  • Developed and tested machine learning models in Python and R, including regression, decision tree, random forest, k-means clustering, and hierarchical clustering

Informatics on High-throughput Sequencing Data, Canadian Bioinformatics Workshops
Toronto, ON, Canada  June 2015

  • Aligned raw read data to reference genome using Amazon Cloud Computing resources
  • Detected small variants and structural variants using command-line tools
  • Visualized genomic variants using the Integrated Genomic Viewer
  • Designed custom sequencing analysis workflows on a graphical interface using the Galaxy web server

Informatics for RNA-seq Analysis, Canadian Bioinformatics Workshops
Toronto, ON, Canada  June 2015

  • Assessed quality of Illumina raw read data using FastQC
  • Performed transcriptome analysis using the Tuxedo suite of tools
  • Quantified mature transcript levels and performed differential expression analysis between tissues using Cufflinks
  • Detected alternative splicing patterns and discovered potential isoforms using Cufflinks