Simon Eng

Curriculum Vitae

Simon W. M. Eng

Contact and Links

Shortwhale
@simoneng
Twitter
@simoneng
LinkedIn
@simoneng
GitHub
@simonwmeng
ORCID
0000-0001-5495-0157

Education

2011–2018
PhD in Immunology and Combined Graduate Program in Genome Biology and Bioinformatics
University of Toronto, Toronto, Ontario, Canada
Co-supervisors: Dr. Rae Yeung and Dr. Quaid Morris
2005–2010
BSc Combined Honours in Computer Science and Microbiology & Immunology (Co-op)
University of British Columbia, Vancouver, British Columbia, Canada
Supervisor: Dr. Steven Hallam
2004–2005
International Baccalaureate Diploma
Richmond Secondary School, Richmond, British Columbia, Canada
2000–2005
British Columbia Provincial Dogwood Diploma
Richmond Secondary School, Richmond, British Columbia, Canada

Experience

2019–current
Bioinformatician
Understanding Childhood Arthritis Network Initiative at The Hospital for Sick Children (SickKids), Toronto, Ontario, Canada
  • Provided computational expertise to an existing project within the Division of Rheumatology comparing several childhood and adult arthritis classifications, resulting in a paper in progress.
  • Provided guidance to two biostatisticians and a data analyst in understanding data produced in prior clinical studies and an ongoing clinical study, enabling them to align fields between these studies.
2018–2019
Lab Research Project Coordinator
Understanding Childhood Arthritis Network Initiative at The Hospital for Sick Children (SickKids), Toronto, Ontario, Canada
  • Published an analysis of patterns of joint presentation in childhood arthritis in a major journal, PLOS Medicine, resulting in exposure through Twitter and press releases from University of Toronto, Donnelly Centre for Cellular and Biomedical Research, and SickKids.
  • Produced and compiled text and figures for a patent application stemming from my PhD work, which is currently under review.
  • Assisted in designing the UCAN CAN-DU and UCAN CURE study websites, which now serve as important resources for patients, parents, and clinicians.
  • Leveraged experience in website design and print production to produce professional visual materials and take event photographs at the Childhood Arthritis & Beyond conference.
2011–2018
PhD (Immunology and Combined Graduate Program in Genome Biology and Bioinformatics)
University of Toronto, Toronto, Ontario, Canada
  • Explored and advised on applying machine learning to classify and reclassify rare autoimmune diseases from multi-omic data, producing foundations for classifications for these diseases that link clinical and biological features.
  • Provided guidance in analyzing multi-omic data to a graduate student supervised by a collaborating computational biologist, resulting in the identification of a single nucleotide polymorphism that formed the basis of a PhD project in Dr. Rae Yeung’s laboratory.
  • Mentored two medical school students and one undergraduate student on applying machine learning their areas of expertise, enabling them to provide valuable scientific contributions with one paper in submission.
  • Summarized complex computational concepts to non-expert and lay audiences at conferences, resulting in four awards, including an award for the One-Minute Thesis Competition at the Canadian Society for Immunology 2016 Scientific Meeting.
  • Collaborated with computational biologists, clinicians from the United States and Europe, and two Canada-wide consortia of paediatric rheumatologists and study coordinators to analyze complex data sets, resulting in one published paper and two in progress.
2014–2015
Co-President
Immunology Graduate Students Association at University of Toronto, Toronto, Ontario, Canada
  • Partnered with the Immunology Students’ Association to provide mentorship opportunities through a co-hosted event providing mentorship to prospective graduate applicants.
  • Organized overnight accommodations, travel, and logistics for 110 students and faculty at the 9th Department of Immunology Annual Retreat, an annual research retreat, with 97% of feedback survey respondents expressing interest in returning the following year.
  • Overhauled IGSA’s outdated constitution, ratified unanimously after public consultation, to reflect IGSA’s current operations and adhere to University of Toronto Graduate Student Union guidelines.
2012–2014
Social Representative
Immunology Graduate Students Association at University of Toronto, Toronto, Ontario, Canada
  • Organized community-building social gatherings for graduate students and faculty in the Department of Immunology.
2009–2010
BSc Honours (Computer Science and Microbiology and Immunology)/Research Assistant (Co-op)
Dr. Steven Hallam's Laboratory at University of British Columbia, Vancouver, British Columbia, Canada
  • Spearheaded an application of a computational analysis, providing a foundation for future research projects including two derivative thesis projects.
2009
Software Test Tools Developer (Co-op)
BlackBerry, Waterloo, Ontario, Canada
  • Helped to develop a Python-based platform for testing devices according to telecommunications provider requirements.
2008–2010
Lab Information Management System Developer (Co-op/Part-Time)
Moerman Laboratory Gene Knockout Facility at University of British Columbia, Vancouver, British Columbia, Canada
  • Overhauled a laboratory information management system using PHP and MySQL, resulting in a more responsive system.
2007
Undergraduate Teaching Assistant, CPSC 211, Introduction to Software Development
University of British Columbia, Vancouver, British Columbia, Canada
2007
Undergraduate Teaching Assistant, CPSC 111, Introduction to Computation
University of British Columbia, Vancouver, British Columbia, Canada
2006
Undergraduate Teaching Assistant, CPSC 101/WMST 201, Connecting with Computer Science
University of British Columbia, Vancouver, British Columbia, Canada

Publications

2020
A Clinically and Biologically Based Subclassification of the Idiopathic Inflammatory Myopathies Using Machine Learning
Eng SWM, Olazagasti JM, Goldenberg A, Crowson CS, Oddis CV, Niewold TB, Yeung RSM, Reed AM
Journal: ACR Open Rheumatology
DOI: 10.1002/acr2.11115
2019
Association of clinical and inflammatory biomarker clusters with juvenile idiopathic arthritis categories
Rezaei E, Hogan D, Trost B, Kusalik AJ, Boire G, Cabral DA, Campillo S, Chédeville G, Chetaille A-L, Dancey P, Duffy C, Watanabe Duffy KW, Eng SWM, Gordon J, Guzman J, Houghton K, Huber AM, Jurencak R, Lang B, Laxer RM, Morishita K, Oen KG, Petty RE, Ramsey SE, Scherer SW, Scuccimarri R, Spiegel L, Stringer E, Taylor-Gjevre RM, Tse SML, Tucker LB, Turvey SE, Tupper S, Wintle RF, Yeung RSM, Rosenberg AM
Journal: Rheumatology (Oxford)
DOI: 10.1093/rheumatology/kez382
2019
Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization
Eng SWM, Aeschlimann FA, van Veenendaal M, Berard RA, Rosenberg AM, Morris Q, Yeung RSM on behalf of the ReACCh-Out Research Consortium
Journal: PLOS Medicine
DOI: 10.1371/journal.pmed.1002750
2018
High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies
Youn J-Y, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, Bagci H, Rathod B, MacLeod G, Eng SWM, Angers S, Morris Q, Fabian M, Côté J-F, Gingras A-C
Journal: Molecular Cell
DOI: 10.1016/j.molcel.2017.12.020
2017
Childhood Takayasu arteritis: disease course and response to therapy
Aeschlimann FA, Eng SWM, Sheikh S, Laxer RM, Hebert D, Noone D, Twilt M, Pagnoux C, Benseler SM, Yeung RSM
Journal: Arthritis Research & Therapy
DOI: 10.1186/s13075-017-1452-4
2014
The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis
Eng SWM, Duong TT, Rosenberg AM, Morris Q, Yeung RSM on behalf of the ReACCh-OUT and BBOP Research Consortia
Journal: Arthritis & Rheumatology
DOI: 10.1002/art.38875

Awards and Distinctions

2019
Donnelly Centre Thesis Award
University of Toronto, Toronto, Ontario, Canada
Amount: $3,000.00
2016
First-place podium presentation winner
University of Toronto Department of Paediatrics Research Day, Toronto, Ontario, Canada
Amount: $500.00
2016
One-minute thesis competition winner
Canadian Society for Immunology Annual Scientific Meeting, Ottawa, Ontario, Canada
2014
Second-place poster presentation winner
University of Toronto Division of Rheumatology Ogryzlo Research Day, Toronto, Ontario, Canada
Amount: $200.00
2013
First-place poster presentation winner
University of Toronto Department of Paediatrics Research Day, Toronto, Ontario, Canada
2013
The Arthritis Society/Canadian Arthritis Network Graduate Ph.D. Award
Amount: $31,500.00
2013
Toronto Musculoskeletal Centre for Bone and Mineral Group Studentship
Amount: $14,500.00
2012
Toronto Musculoskeletal Centre for Bone and Mineral Group Studentship
Amount: $12,500.00
2011
Dick and Peggy Sharpe Graduate Student Award
University of Toronto, Toronto, Ontario, Canada
Amount: $5,000.00
2011
University of Toronto Open Fellowship Award
University of Toronto, Toronto, Ontario, Canada
Amount: $4,020.68

Talks

June 2016
The biological basis of clinical heterogeneity in childhood arthritis: a gene expression perspective
Eng SWM, Rosenberg AM, Morris Q, Yeung RSM on behalf of the BBOP Consortium
Department of Paediatrics Research Day
Toronto, Ontario, Canada
First-place winner ($500.00)
May 2013
Using machine learning to find clinically and biologically homogeneous patient subgroups of children with arthritis
Eng SWM, Yeung RSM, Morris Q
Genome Biology and Bioinformatics Annual Retreat
Toronto, Ontario, Canada
October 2012
Computational learning to identify and characterize clinically and biologically homogeneous subgroups of patients with juvenile idiopathic arthritis
Eng SWM, Morris Q, Yeung RSM
Toronto Musculoskeletal Centre Second Annual Research Day
Toronto, Ontario, Canada
May 2010
Introduction to the Pathway Tools software
Walsh DA, Eng SWM
bigDATA
Vancouver, British Columbia, Canada

Posters and Abstracts

October 2017
Computational modelling of chromosomal catastrophes in cancer evolution
Atwal G, Rubanova Y, Wintersinger J, Eng S, PCAWG-6 Working Group, Bader G, Morris Q
April 2016
The biological basis for clinical heterogeneity in juvenile idiopathic arthritis: a gene expression perspective
Eng SWM, Rosenberg AM, Morris Q, Yeung RSM on behalf of the BBOP Research Consortium
Canadian Society for Immunology Annual Scientific Meeting
Ottawa, Ontario, Canada
One-minute thesis competition winner
November 2015
Patterns of vascular involvement in childhood Takayasu arteritis
Aeschlimann FA, Eng S, Grosse-Wortmann L, Benseler SL, Laxer R, Hebert D, Yeung RSM
American College of Rheumatology Annual Meeting
San Francisco, California, United States
November 2015
Patterns of enthesitis and arthritis in juvenile idiopathic arthritis
Aeschlimann FA, van Veenendaal M, Eng S, Yeung RSM
American College of Rheumatology Annual Meeting
San Francisco, California, United States
October 2015
Biologically based disease classification for childhood arthritis
Eng SWM, Rosenberg AM, Yeung RSM, Morris QD on behalf of the BBOP Consortium
Cold Spring Harbor Genome Informatics Meeting
Cold Spring Harbor, New York, United States
October 2015
Data-driven gene expression indicators towards a comprehensive disease classification for childhood arthritis
Eng SWM, Rosenberg AM, Yeung RSM, Morris QD on behalf of the BBOP Consortium
Arthritis Alliance of Canada Annual Meeting
Kananaskis, Alberta, Canada
November 2014
Patterns of joint involvement in JIA
Eng SWM, van Veenendaal M, Rosenberg AM, Oen K, Morris Q, Yeung RSM
American College of Rheumatology Annual Meeting
Boston, Massachusetts, United States
June 2014
Patterns of joint involvement in childhood arthritis
van Veenendaal M, Eng SWM, Morris Q, Yeung RSM
Ogrzylo Research Day
Toronto, Ontario, Canada
June 2014
The biological basis of clinical heterogeneity in childhood arthritis
Eng SWM, Duong TT, Morris Q, Yeung RSM on behalf of the REACCH OUT and BBOP Consortia
Ogrzylo Research Day
Toronto, Ontario, Canada
Second-place winner ($200.00)
June 2014
The biological basis of clinical heterogeneity in childhood arthritis
Eng SWM, Duong TT, Morris Q, Yeung RSM on behalf of the REACCH OUT and BBOP Consortia
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
May 2014
The biological basis of clinical heterogeneity in childhood arthritis
Eng SWM, Duong TT, Morris Q, Yeung RSM on behalf of the REACCH OUT and BBOP Consortia
University of Toronto Department of Paediatrics Research Day
Toronto, Ontario, Canada
May 2014
The biological basis of clinical heterogeneity in childhood arthritis
Eng SWM, Duong TT, Morris Q, Yeung RSM on behalf of the REACCH OUT and BBOP Consortia
SickKids Cell Biology Retreat
Toronto, Ontario, Canada
November 2013
The biological basis of clinical heterogeneity in childhood arthritis
Eng SWM, Duong TT, Morris Q, Yeung RSM on behalf of the REACCH OUT and BBOP Consortia
Arthritis Alliance of Canada Inaugural Conference and Research Symposium
Ottawa, Ontario, Canada
June 2013
Using computational learning to distinguish clinically and biologically homogeneous patient subgroups in juvenile idiopathic arthritis
Eng SWM, Morris Q, Yeung RSM on behalf of the REACCH OUT Consortium
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
May 2013
Using computational learning to distinguish clinically and biologically homogeneous patient subgroups in juvenile idiopathic arthritis
Eng SWM, Morris Q, Yeung RSM on behalf of the REACCH OUT Consortium
University of Toronto Department of Paediatrics Research Day
Toronto, Ontario, Canada
First-place winner ($500.00)
August 2012
Computational learning to identify and characterize clinically and biologically homogeneous subgroups of children with juvenile idiopathic arthritis
Eng SWM, Rosenberg A, Yeung RSM, Morris QD on behalf of the REACCH OUT Consortium
The 13th International Conference of Systems Biology
Toronto, Ontario, Canada
June 2012
Using machine learning methods to identify and characterize clinically and biologically homogeneous subgroups of children with juvenile idiopathic arthritis
Eng SWM, Benseler SL, Oen K, Rosenberg A, Morris QD, Yeung RSM on behalf of the REACCH OUT Consortium
University of Toronto Division of Rheumatology Ogryzlo Research Day
Toronto, Ontario, Canada
November 2011
Using data-driven methods to identify and characterize clinically and biologically homogeneous subgroups of juvenile idiopathic arthritis patients
Eng SWM, Kainth R, Duong TT, Benseler SM, Oen K, Morris QD, Yeung RSM, REACCH OUT Consortium
SickKids Research Institute Retreat
Toronto, Ontario, Canada
October 2011
Using data-driven methods to identify and characterize clinically and biologically homogeneous subgroups of juvenile idiopathic arthritis patients
Eng SWM, Kainth R, Duong TT, Benseler SM, Oen K, Morris QD, Yeung RSM, REACCH OUT Consortium
Canadian Arthritis Network Annual Scientific Conference and Canadian Association of Paediatric Rheumatology Investigators Annual Meeting
Québec City, Québec, Canada

Conferences Attended

April 2019
Childhood Arthritis and Beyond
Lake Louise, Alberta, Canada
Photographer and organizing team member
June 2017
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
June 2016
University of Toronto Division of Rheumatology Ogryzlo Research Day
Toronto, Ontario, Canada
June 2016
University of Toronto Department of Immunology Annual Retreat
Toronto, Ontario, Canada
May 2016
University of Toronto Department of Paediatrics Research Day
Toronto, Ontario, Canada
April 2016
Canadian Society for Immunology Annual Scientific Meeting
Ottawa, Ontario, Canada
October 2015
Cold Spring Harbor Genome Informatics Meeting
Cold Spring Harbor, New York, Canada
October 2015
Arthritis Alliance of Canada Annual Meeting and The Arthritis Society Trainee Session
Kananaskis, Alberta, Canada
June 2015
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
Co-lead organizer
November 2014
American College of Rheumatology Annual Meeting
Boston, Massachusetts, United States
October 2014
Arthritis Alliance of Canada Annual Meeting and The Arthritis Society Trainee Session
Toronto, Ontario, Canada
June 2014
University of Toronto Division of Rheumatology Ogryzlo Research Day
Toronto, Ontario, Canada
June 2014
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
May 2014
SickKids Department of Cell Biology Retreat
Toronto, Ontario, Canada
November 2013
Arthritis Alliance of Canada Inaugural Conference and Research Symposium
Ottawa, Ontario, Canada
June 2013
University of Toronto Division of Rheumatology Ogryzlo Research Day
Toronto, Ontario, Canada
June 2013
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
May 2013
University of Toronto Department of Paediatrics Research Day
Toronto, Ontario, Canada
May 2013
University of Toronto Genome Biology and Bioinformatics Annual Retreat
Toronto, Ontario, Canada
August 2012
The 13th International Conference of Systems Biology
Toronto, Ontario, Canada
June 2012
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
June 2012
University of Toronto Division of Rheumatology Ogryzlo Research Day
Toronto, Ontario, Canada
November 2011
SickKids Research Institute Retreat
Toronto, Ontario, Canada
October 2011
Canadian Arthritis Network Annual Scientific Conference and Canadian Association of Paediatric Rheumatology Investigators Annual Meeting
Québec City, Québec, Canada
June 2011
University of Toronto Department of Immunology Annual Retreat
Orillia, Ontario, Canada
October 2010
Pathway Tools Workshop
Menlo Park, California, United States

Teaching Experience

Summer 2007
CPSC 211: Introduction to Software Development
University of British Columbia
Summer 2007
CPSC 111: Introduction to Computation
University of British Columbia
Fall 2006
CPSC 101/WMST 201: Connecting with Computer Science
University of British Columbia