Curriculum vitae

Simon W.M. Eng
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Experiences

2021–current

Senior Data Scientist

BioSymetrics

Toronto, Ontario, Canada

  • Advanced BioSymetrics' computer vision platform to identify target compounds for various conditions by implementing a pipeline analyzing zebrafish motion data with a diverse team of data scientists, resulting in several candidate compounds pursued for in vivo validation.
  • Applied novel signal processing techniques to zebrafish motion analyses, reducing outlier noise.
  • Analyzed genomic, transcriptomic, and proteomic datasets for various programs and client projects, resulting in one publication in Nature Communications and enabling downstream drug discovery efforts.
  • Trained a chemical foundation transformer model on 550 million compounds, producing a valuable asset for BioSymetrics that is being integrated into new projects ranging from drug discovery to biodefence applications.
  • Professionalized the design language of BioSymetrics' internal web applications, enabling polished external presentations and client pitches.
  • Co-authored BioSymetrics' developer guidelines and best practices now adopted by BioSymetrics' data scientists.
  • Introduced reproducible analyses via Snakemake to BioSymetrics, enabling client projects to include reproducibility and implicit documentation as key considerations.
  • Introduced modern tooling such as uv and Pixi to BioSymetrics, substantially reducing the time needed to iterate over adjustments to internal software dependencies.
  • Introduced AI tooling, including OpenAI Codex, to BioSymetrics, substantially reducing the iteration time for data science explorations and feature implementations.
  • Led a client project during a critical period (colleague's paternity leave) upon starting at BioSymetrics, delivering it to client specifications and on schedule.
  • Grew BioSymetrics' social media presence on LinkedIn, maintaining the frequency of posts on the company's LinkedIn page, producing a blog series highlighting individual team members, and increasing its number of LinkedIn followers by over 350 (10%) over the past year.
  • Participated in the rebranding of BioSymetrics' post-merger parent company to Lunai Bioworks, assisting in generating new visual assets, collaborating with an external marketing and design agency on Lunai Bioworks' website through Webflow, launching this new website on schedule.
  • Collaborated with the same marketing agency to expand the site to include details about Lunai Bioworks' offerings in time for the 2026 JP Morgan Healthcare Conference, enabling interested collaborators and investors to learn more about the offerings post-conference.
  • Assembled Lunai Bioworks' social media presence on LinkedIn, X, Bluesky, Threads, and Instagram, increasing the number of platforms covered by BioSymetrics and/or Lunai Bioworks' reach by three and increasing the visibility of both companies, with Lunai Bioworks gaining over 120 LinkedIn followers in its first quarter of existence.

2021–current

Consulting Bioinformatician

The Hospital for Sick Children (SickKids)

Toronto, Ontario, Canada

  • Defined hiring criteria for bioinformatician and biostatistician positions in Dr. Rae Yeung's laboratory as part of my transition to BioSymetrics, enabling the successful recruitment of three candidates to fulfill my previous full-time responsibilities.
  • Developed a PyTorch-based method to translate assay measurements between 96-analyte NanoString gene expression panels, achieving higher accuracy compared to vendor-recommended approaches.
  • Co-developed an analytical plan with an incoming staff physician for developing an index for a group of inflammatory disorders, resulting in a successful grant application.

2018–2021

Bioinformatician/Lab Research Project Coordinator

The Hospital for Sick Children (SickKids)

Toronto, Ontario, Canada

  • Refined biomarker panels from my Ph.D. work, identifying smaller, more robust sets of biomarkers that increased the defensibility of the patent.
  • Identified, screened, and interviewed prospective biostatistician candidates, resulting in the recruitment of a biostatistician to UCAN.
  • Led a team of two biostatisticians and a data analyst, enabling UCAN to iterate over analyses more quickly and deliver results to stakeholders in a more timely fashion.
  • Identified improvements to UCAN’s electronic health record (EHR) system to align with clinician expectations and led an initiative to implement downstream automated validation checks, increasing trust in the results of data analyses.
  • Guided a biostatistician and data analyst in understanding data produced in prior clinical studies and an ongoing clinical study, helping them align fields between studies and enlarging the pool of potential studies to consider for analyses.
  • Co-developed and conducted an analysis to compare several childhood and adult arthritis classifications, showing major differences in the assignments of patients between these classifications, published in Arthritis Rheumatology.
  • Co-designed the UCAN CAN-DU and UCAN CURE study websites, engaging patients, families, and clinicians with accessible resources on clinical studies and research.
  • Designed and produced professional visual materials, including the program booklet and photographs, for the Childhood Arthritis & Beyond conference organized by UCAN, reaching 176 attendees including patients, families, and clinicians, and facilitating knowledge-sharing around arthritis research.

2017–current

Soundboard Operator/Livestream Audio Mixer/Worship Team Instrumentalist

Grace Toronto Church

Toronto, Ontario, Canada

  • Mixed audio for worship teams and vocal contributors in weekly Sunday services, enabling congregants to participate fully in Sunday worship.
  • Mixed audio for livestreamed Sunday services during and after the COVID-19 pandemic, enabling congregants to access weekly and archived worship services.
  • Led an initiative to standardize compression and equalization parameters for vocal contributors across in-house and livestream fields, improving consistency and intelligibility.
  • Authored guidelines for livestream mixing, increasing consistency in volume of the livestream mixes.
  • Learned bass guitar and performed on worship teams, filling a critical shortage of bass guitarists and bridging audio/visual and worship team ministries.

2012–2015

Co-President/Social Coordinator

Immunology Graduate Students Association (IGSA)

Toronto, Ontario, Canada

  • Co-organized a mentorship event with the Immunology Students’ Association, connecting prospective graduate applicants with current students and faculty.
  • Organized overnight accommodations, travel, and logistics for 110 students and faculty at the 9th Department of Immunology Annual Retreat, an annual research retreat, with 35 of 36 feedback survey respondents expressing interest in returning the following year.
  • Led an overhaul of IGSA’s outdated constitution, ratified unanimously after public consultation, to reflect IGSA’s current operations and comply with University of Toronto Graduate Student Union guidelines.

2011–2018

Ph.D.

Dr. Rae Yeung and Dr. Quaid Morris' labs, University of Toronto

Toronto, Ontario, Canada

  • Designed and conducted an unsupervised machine learning analysis, using principal component analysis and Gaussian mixture models, identifying five novel juvenile idiopathic arthritis subtypes linking clinical presentations with distinct molecular features, published in Arthritis Rheumatology.
  • Designed and conducted an analysis using non-negative matrix factorization to identify seven interpretable patterns of joint involvement, enabling future clinical risk stratification, published in PLOS Medicine with press coverage from University of Toronto, Donnelly Centre, and SickKids.
  • Designed an analytical pipeline to identify signature genes and proteins for juvenile idiopathic arthritis from microarray data and multi-bead protein assays, producing a set of biomarkers currently being validated for a patent.
  • Mentored a graduate student in applying similarity network fusion to multi-omic data, enabling the discovery of a single nucleotide polymorphism that became the foundation for an incoming student's Ph.D. project in Dr. Rae Yeung’s laboratory.
  • Mentored two medical school students and one undergraduate student on applying machine learning on clinical and bioassay data in their areas of expertise, enabling them to provide valuable scientific contributions with two published papers in ACR Open Rheumatology.
  • Communicated complex computational concepts to non-expert audiences, winning four presentation awards including the Canadian Society for Immunology 2016 Scientific Meeting 1-Minute Thesis Competition.

2008–2010

Honours/Undergraduate Research Associate

Dr. Steven Hallam's lab, University of British Columbia

Vancouver, British Columbia, Canada

  • Designed and conducted a metabolic pathway analysis of ocean water column samples using Pathway Tools, catalyzing future research projects including two derivative thesis projects.

Skills

Education

2011–2018

Ph.D., Immunology and Combined Program in Genome Biology and Bioinformatics

University of Toronto

Toronto, Ontario, Canada

2005–2010

B.Sc., Combined Honours Computer Science and Microbiology & Immunology with Co-op

University of British Columbia

Vancouver, British Columbia, Canada

Awards and Distinctions

2019

Donnelly Centre Thesis Award winner

University of Toronto

Toronto, Ontario, Canada

2016

Podium presentation, 1st place winner

University of Toronto Department of Paediatrics Research Day

Toronto, Ontario, Canada

2016

1-Minute Thesis Competition winner

Canadian Society for Immunology Scientific Meeting

Ottawa, Ontario, Canada

2014

Poster presentation, 2nd place winner

SickKids Ogryzlo Day

Toronto, Ontario, Canada

2013

Poster presentation, 1st place winner

University of Toronto Department of Paediatrics Research Day

Toronto, Ontario, Canada

2013

The Arthritis Society/Canadian Arthritis Network Graduate Ph.D. Award

2012-2013

Toronto Musculoskeletal Centre for Bone and Mineral Group Studentship

2011

Dick and Peggy Sharpe Graduate Student Award

2011

University of Toronto Open Fellowship

2006-2007, 2010

University of British Columbia Dean’s Honour List

2005

University of British Columbia President’s Entrance Book Award

Publications

2025

Large-scale serum protein biomarkers discovery associated with function and clinical milestones in Duchenne muscular dystrophy

Ikelaar NA, Barnard AM, Eng SWM, Hosseini Vajargah S, Ha KCH, Kan HE, Vandenborne K, Niks EH, Walter GA, Spitali P

Nat Commun (2025)

2022

Gene expression profiles of treatment response and non-response in children with juvenile dermatomyositis

Stingl C, Dvergsten JA, Eng SWM, Yeung RSM, Fritzler MJ, Mason T, Crowson C, Voora D, Reed AM

ACR Open Rheumatol (2022)

2022

A comparison of International League of Associations for Rheumatology and Pediatric Rheumatology International Trials Organization Classification systems for juvenile idiopathic arthritis among children in a Canadian arthritis cohort

Lee JJY, Eng SWM, Guzman J, Duffy CM, Tucker LB, Oen K, Yeung RSM, Feldman BM on behalf of the ReACCh-Out Investigators

Arthritis Rheumatol (2022)

2020

The promise of machine learning to inform the management of juvenile idiopathic arthritis

Eng SWM, Yeung RSM, Morris Q

Exp Rev Clin Immunol (2020)

2020

Associations 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 AL, Dancey P, Duffy C, 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 for the BBOP Study Group

ACR Open Rheumatol (2020)

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

ACR Open Rheumatol (2020)

2020

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

PLOS Med (2020)

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

Mol Cell (2018)

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

Arthritis Res Ther (2017)

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

Arthritis Rheumatol (2014)

Talks

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

University of Toronto Department of Paediatrics Research Day

Toronto, Ontario, Canada

2013

Using machine learning to find clinically and biologically homogeneous patient subgroups of children with arthritis

Eng SWM, Yeung RSM, Morris Q

Genome Biology & Bioinformatics Annual Retreat

Toronto, Ontario, Canada

2012

Computational learning to identify and characterize clinically and biologically homogeneous subgroups of patients with juvenile idiopathic arthritis

Eng SWM, Yeung RSM, Morris Q

Toronto Musculoskeletal Centre Second Annual Research Day

Toronto, Ontario, Canada

2010

Introduction to the Pathway Tools Software

Walsh DA, Eng SWM

bigDATA at the University of British Columbia

Vancouver, British Columbia, Canada

Posters

2023

Protein biomarkers predicting clinical milestones in Duchenne muscular dystrophy

Ikelaar NA, Barnard AM, Meijer-Krom YD, van der Holst M, Hosseini Vajargah S, Eng SWM, Ha KCH, Vandenborne K, Niks EH, Walter GA, Spitali P

2023

A tiered strategy for variant selection in patients with epilepsy

Fonzi A, Scalzini L, Eng SWM, Ha KCH, Geread RS, Ottalevi R, Luciano M, Baldini I, Paone R, Ianniciello G, Caceres J

European Human Genetics Conference

Glasgow, Scotland, United Kingdom

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

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 Scientific Meeting

Ottawa, Ontario, Canada

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

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

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

2015

Data-driven gene expression indicators towards a comprehensive disease classification for childhood arthritis

Eng SWM, Rosenberg AM, Morris QD, Yeung RSM on behalf of the BBOP Consortium

Arthritis Alliance of Canada Annual Meeting

Kananaskis, Alberta, Canada

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

2014

Patterns of joint involvement in childhood arthritis

van Veenendaal M, Eng SWM, Morris Q, Yeung RSM

SickKids Ogryzlo Day

Toronto, Ontario, Canada

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 Ogryzlo Day

Toronto, Ontario, Canada

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

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

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

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

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

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

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

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 Department of Immunology Annual Retreat

Orillia, Ontario, Canada

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

SickKids Ogryzlo Day

Toronto, Ontario, Canada

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

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

2009

Assessing the role of a 182 kb plasmid containing the xplAB genes in degradation of RDX by Gordonia sp. KTR9

Indest K, Crocker F, Jung C, Chen H-P, Florizone C, Eng SWM, Hallam SJ, Eltis LD

Strategic Environmental Research and Development Program