Joseph O'Neill

Bioinformatician at Vineland Research and Innovation Centre
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Contact Information
us****@****om
(386) 825-5501
Location
CA
Languages
  • English Native or bilingual proficiency
  • French Professional working proficiency
Skills

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Bio

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Credentials

  • Machine Learning
    Stanford Online
    Jun, 2020
    - Nov, 2024

Experience

  • Vineland Research and Innovation Centre
    • Canada
    • Research
    • 1 - 100 Employee
    • Bioinformatician
      • Mar 2015 - Present

      NGS processing, NLP to decode the meaning of biological sequences, pipeline development, variant mining, genetic mapping, GWAS, genome browsers (JBrowse), protein structure prediction, protein design, machine learning, computer vision for robotics, docker, genome assembly, statistical genetics, GATK, phylogenetic trees, genomic selection, data visualization, RNA-Seq, plant breeding etc. NGS processing, NLP to decode the meaning of biological sequences, pipeline development, variant mining, genetic mapping, GWAS, genome browsers (JBrowse), protein structure prediction, protein design, machine learning, computer vision for robotics, docker, genome assembly, statistical genetics, GATK, phylogenetic trees, genomic selection, data visualization, RNA-Seq, plant breeding etc.

  • Genesys Design Technologies
    • Software Developer
      • Oct 2014 - Feb 2015

      Responsible for image filter algorithm design, accommodation to the customer, abstraction, and structured thinking. The software presents the user with several filtered versions of a loaded image then asks the user to select ones they like. Based on the selections, additional filtered images are presented and the process iterates, editing the image step by step. I created the software with Java. (Supervisor: Mr. Robert Loucks) Responsible for image filter algorithm design, accommodation to the customer, abstraction, and structured thinking. The software presents the user with several filtered versions of a loaded image then asks the user to select ones they like. Based on the selections, additional filtered images are presented and the process iterates, editing the image step by step. I created the software with Java. (Supervisor: Mr. Robert Loucks)

  • Department of Plant Agriculture, University of Guelph
    • Guelph, ON
    • Research Assistant
      • Sep 2014 - Feb 2015

      Responsible for NGS RNA-Seq analysis, iPLant platform utilization, pipeline execution (“the tuxedo protocol”), differentially expressed gene/gene ontology identification, and report writing. Responsible for statistical method development/testing applicable to genome-assisted selection for traits important for crop improvement. Generated synthetic maize populations with Perl scripts. (Supervisor: Dr. Lewis Lukens) Responsible for NGS RNA-Seq analysis, iPLant platform utilization, pipeline execution (“the tuxedo protocol”), differentially expressed gene/gene ontology identification, and report writing. Responsible for statistical method development/testing applicable to genome-assisted selection for traits important for crop improvement. Generated synthetic maize populations with Perl scripts. (Supervisor: Dr. Lewis Lukens)

  • Department of Mathematics and Statistics, University of Guelph
    • Guelph, ON
    • Research Assistant
      • Sep 2014 - Feb 2015

      Responsible for algorithm design, software development, performance analysis, public presentation and report writing in developing evolutionary computation methods for industrial applications and for statistical genetics. Programmed new and existing procedures in R/C++. (Supervisor: Dr. Daniel Ashlock) Responsible for algorithm design, software development, performance analysis, public presentation and report writing in developing evolutionary computation methods for industrial applications and for statistical genetics. Programmed new and existing procedures in R/C++. (Supervisor: Dr. Daniel Ashlock)

  • Math Department
    • The University of Guelph, Guelph, ON
    • An artificial bacterial colony project
      • May 2014 - Nov 2014

      Working with Ph.D. candidate Stephen Rush, we have built a simulated population of bacteria objects that grows and mutates according to specified functions. The end purpose is to test the accuracy of phylogenetic tree reconstruction methods under different parameters. The population grows according to the Velhurst-Pearl equation, the DNA mutates probabilistically, deletions and insertions happen probabilistically, and there must be a certain level of complimentarity between certain areas of the DNA string.

  • POLYCON
    • Guelph, ON
    • Assistant Production
      • 2013 - 2014

      Responsible for work protocol design and labour for several manufacturing contracts. (Supervisor: Andrea Zak) Responsible for work protocol design and labour for several manufacturing contracts. (Supervisor: Andrea Zak)

  • U of G Economics and Finance Association
    • Guelph,ON
    • Programmer, Senior Analyst
      • Sep 2011 - Sep 2013

      I held the position of ‘Senior Analyst’ in the Economics and Finance Association. Aside from helping organize club activities and events like trading floor simulations, this position entailed coding and developing experimental trading strategies for the FOREX markets and stock markets. Furthermore, risk modeling was undertaken to provide analytics with an emphasis on mortgage modelling, which consists of 46%+ of the Canadian commercial bank loan portfolio. Forecasting corrections in the market was the goal. In these endeavours I evolved populations of neural networks that would output a trading decision or an imminent correction forecast.

  • Precision Builders
    • Mallorytown, ON
    • Carpenter's Assistant
      • May 2006 - Jan 2011

      Responsible for general labour, design assistance, engineering calculations, and logistics for numerous residential contracts exceeding $100,000.(Supervisor: Mr. Steve Miller) Responsible for general labour, design assistance, engineering calculations, and logistics for numerous residential contracts exceeding $100,000.(Supervisor: Mr. Steve Miller)

  • Providence Care St. Mary's of the Lake
    • Kingston, ON
    • Lifeguard
      • Jan 2007 - Apr 2007

      • Supervised the swimming sessions of elderly or handicapped patients and ensured there were zero accidents on my watch. • Cleared the pool decisively upon the detection of a hazard preventing possible injuries. • Trained in CPR and lifesaving techniques to possess the skills to respond quickly and correctly in case of emergency. • Supervised the swimming sessions of elderly or handicapped patients and ensured there were zero accidents on my watch. • Cleared the pool decisively upon the detection of a hazard preventing possible injuries. • Trained in CPR and lifesaving techniques to possess the skills to respond quickly and correctly in case of emergency.

Education

  • University of Guelph
    Master of Bioinformatics
    2013 - 2014
  • University of Detroit Mercy School of Dentistry
    DDS Candidate, Dentistry
    2012 - 2013
  • University of Guelph
    Bachelor of Science (BS), Biological and Biomedical Sciences
    2008 - 2011

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