About

Hi! My name is Matthew Jacobson.

I am an experienced software developer and data scientist with a history of working in both a professional and research setting. I currently contract with the University of British Columbia to develop web-applications based on research in the field of bioinformatics. Leading up to this, I worked full-time as a senior software developer in the Pavlidis Bioinformatics Lab. My overarching job function at the Pavlidis Lab was to architect and implement research-oriented applications dealing in large-scale computations and/or data. Furthermore, I would both engage in neuroinformatics research and mentor staff in the benefits of applying sound development practices. Prior to the Pavlidis Lab I worked as an analyst and software developer in the financial sector at Pivotal Payments. My role there was to develop programmatic solutions to automate operations tasks while acting as a liaison between financial reporting and the development scrums.

The strengths I bring to my work are not particular to any specific discipline but to the field of scientific programming itself. I am remarked for my ability to apply my skill-sets while learning a novel field of study and distinguished for my ability to become a knowledgeable contributor in ways outside the scope of expectation.

Projects

Web Applications

RDMMN

The Rare Diseases: Models & Mechanisms Network has been established to catalyze connections between people discovering new genes in patients with rare diseases, and basic scientists who can analyze equivalent genes and pathways in model organisms. Catalyst Grants fund projects that will allow rapid confirmation of potentially disease-causing genes, and fuel pilot studies to improve understanding of how specific gene mutations cause disease. It is intended that collaborations across the Canadian biomedical community will expedite the understanding of disorders, enabling the design of new therapies to the ultimate benefit of those affected by rare diseases.

GOtrack

A web-based system and database that provides access to historical records and trends in the Gene Ontology and GO annotations (GOA). GOTrack gives users access to gene- and term-level information on annotations for nine model organisms (including human) as well as an interactive tool that measures the stability of enrichment results over time for user-provided “hit lists” of genes. Capable of performing and visualizing real-time statistical analyses on large datasets.

Gemma

Gemma is a set of tools for genomics data meta-analysis, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results.

aspireDB

ASPIREdb is a web-based software system for the analysis and visualization of genomic variants (CNVs, SNVs, and Indels) and phenotypes. Potential users include researchers who are trying to understand the relationships between discovered variants and phenotypes.

VariCarta

Web application and database providing a harmonized and comprehensive collection of of human DNA genetic variants found in individuals diagnosed with Autism Spectrum Disorder (ASD) and reported in peer-reviewed scientific literature.

MoRF

Web-based queuing system used by a computational cluster for finding fast and accurate predictions of molecular recognition features (MoRFs) in an amino acid query sequence.

IDRBind

IDRBind is a protein interface predictor for binding sites of intrinsically disordered protein regions (IDRs), ranging from short linear motifs (SLiMs) to molecular recognition features (MoRFs).

LIST

LIST predicts the deleteriousness of amino acid mutations in human proteomes. The current release, 0.9 includes precomputed predictions of ~20,000 SwissProt protein sequences identified by their UniProt accession number. Prediction scores in the range [0 .. 1], where lower scores indicate more benign and higher indicate deleteriousness effect.

LIST 2.0

LIST 2.0 predicts the deleteriousness of amino acid mutations in human protein sequences. First, it aligns (pair-wise alignment) the query sequence to all protein sequences in the UniProt Swiss-Prot/TrEMBL database and then it identifies the most relevant homologies based on their local identity to the query sequence around the position of the target mutation. And finally, it estimates the potential deleteriousness of mutations based on Taxonomy distance of species with variations to the query.

Resume

Education

McGill University 2009 - 2013
Bachelor of Science
Joint Honours Mathematics & Physics
Marianopolis College 2007 - 2009
Diploma of College Studies
Pure & Applied Science

Work Experience

MindGeek - Data Services 2019 - current
Senior Software Developer
  • Develop new features for existing projects handling hundreds of billions of events daily.
  • Assist junior members of the team when needed.
  • Participate in the full software development life cycle (design, implementation, integration, and interaction with quality assurance).
  • Write well designed, testable, efficient code.
  • Provide expert advice and assistance to other teams in the company.
Contract Software Developer 2018 - current
Software Developer
  • Develop web applications that implement research-driven computational solutions.
  • Deliver full-stack solutions from systems architecture to database design to backend and frontend layers.
Centre for High-Throughput Biology, UBC 2014 - 2018
Software Developer
  • Lead development of new applications.
  • Architect web-applications and infrastructure in the field of bioinformatics.
  • Design and assess computational methods, networks, databases and tools.
  • Manage multiple replicate database servers, CI servers, and web servers.
  • Engage in neuroinformatics research.
  • Mentor staff and students in the benefits of sound development practices.
Pivotal Payments 2008 - 2011
Analyst & Developer
  • Liaison between financial reporting and IT, developing programmatic solutions to streamline repeated operations tasks and automate financial reporting systems.
  • Improved pipelines for internal billing of U.S. merchants, merchant pricing in new acquisitions and HR benefits programs.

Skills

Expert
  • Object-oriented design
  • Version control
  • Database design, optimization
  • End-to-end web development
  • Data structures
  • Performance programming
  • CI and automation
Experienced
  • Algorithm design, implementation
  • Secure, maintainable infrastructure
  • Web server deployment
  • API design
  • Unit, integration testing
  • Statistical methods
  • Linux OS
Proficient
  • Machine learning techniques
  • Intuitive web design
  • Interactive visualization design

Papers

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i = 0;

while (!deck.isInOrder()) {
    print 'Iteration ' + i;
    deck.shuffle();
    i++;
}

print 'It took ' + i + ' iterations to sort the deck.';

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Item One Ante turpis integer aliquet porttitor. 29.99
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100.00

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