Anjali Silva

Researcher @ University of Toronto, Canada
Pronouns: she/her
Email: a.silva@utoronto.ca

EDUCATION

2014-2018 Ph.D., Bioinformatics
Department of Mathematics and Statistics
University of Guelph, Canada

2012-2013 M.Binf., Bioinformatics
University of Guelph, Canada

2008-2012 Hon. B.Sc., Genetics Specialist
University of Toronto, Canada

2004-2008
Martingrove Collegiate Institute, Canada

PAST APPOINTMENTS

2018 Professor
School of Biological Sciences and Applied Chemistry
Graduate Bioinformatics Program, Seneca@York, Canada

2018-2021 Postdoctoral Research Fellow
Department of Medical Oncology & Hematology
Princess Margaret Cancer Centre - UHN, Canada
Department of Medicine, University of Toronto, Canada

2016 Visiting PhD Research Student
Department of Mathematics and Statistics
State University of New York at Binghamton, USA

2015-2016 (summers only) Research Assistant
Informatics Research Unit
Centre for Biodiversity Genomics, Canada

2014-2017 Graduate Teaching Assistant
Department of Mathematics and Statistics
Department of Molecular and Cellular Biology
University of Guelph, Canada

2013 Research Assistant
McGill University and Génome Québec Innovation Centre, Canada

ACADEMIC AWARDS

2019 National Postdoctoral HealthFellowship
Canadian Institutes of Health Research, Canada

2019 PostgraduateAffiliate
Vector Institute for Artificial Intelligence, Canada

2019 Distinguished DissertationAward
Classification Society, International

2017 Food from Thought Research Assistantship
Arrell Food Institute, Canada

2016 Queen Elizabeth II Graduate Scholarship in
Science & Technology
Ontario Provincial Award, Canada

2016 Arthur Richmond Memorial Scholarship
University of Guelph, Canada

2015 Ontario Graduate Fellowship
Ontario Provincial Award, Canada

2014-2017 Dean's Scholarship
College of Engineering & Physical Sciences
University of Guelph, Canada

TRAVEL AWARDS

2023 TREnD Award
For TREnD2023 Conference, Toronto, Canada

2018 University Health Network ORTAward, Canada
For ASH Conference, San Diego, USA

2017 Canadian Statistical Sciences Institute Award
For Workshop in Modeling Longitudinal Data, Calgary, Canada

2016 UGuelph Registrar’s Travel Award, Canada
For Program in Quantitative Genomics, Boston, USA

2016 Graduate Students' Association Award, Canada
For International Conference of ERCIM Working Group, Seville, Spain

2016 Statistical Society of Canada Award, Canada
For Statistical Society of Canada Meeting, Brock, Canada

2015-2017 Women in Machine Learning Award, USA
For Women in Machine Learning Workshops, Canada and USA

2015 Consortium for the Barcode of Life International, USA
For International Barcode of Life Conference, Guelph, Canada

OTHER AWARDS

Spark the Spirits (Volunteering)
William Osler Health System, Canada

Leafs Dreams Arts Scholarship
Ontario Arts Foundation, Canada

Ontario Scholar
Toronto District School Board, Canada

Cross Country West Regional Championship
Toronto District Secondary Schools Athletic Association, Canada

SERVICE

2023 Reviewer
Journal of Classification

2022 Instructor
The Carpentries

2018 Registration Assistant
Ontario Advanced Research Computing Congress

2015-2018 Student Representative
Bioinformatics Graduate Program
University of Guelph, Canada

2015-2018 Member
Statistical Society of Canada

2012-2018 Member
Canadian Society for Molecular Biosciences

TRAININGS

2023 Rethinking & Redesigning Assignments in the Wake of Generative AI
Centre for Teaching Support & Innovation
University of Toronto, Canada

2019-2023 Teaching in Arts & Science
Digital by Design: Practical Strategies for Teaching
University of Toronto, Canada

2022 Unconscious Bias
University of Toronto, Canada

2022 Software Carpentry
The Carpentries

2021 Suicide Alertness Training
LivingWorks Education Organization &
University of Toronto, Canada

2018-2019 Cancer Trainee Professional
Enrichment Program, Cancer Campus
Princess Margaret Cancer Centre, Canada

2017 Compute Ontario Summer School on High Performance Computing
SciNet and Centre for Advanced Computing, Canada

2014 Accessibility for Ontarians with Disabilities Act
Ontario, Canada

2013 Graduate Research and Project Management
Office of Research, University of Guelph, Canada

ABOUT

My research interests are in the development of statistical clustering and classification methods for data analysis via mixture models with applications in trend analysis. I am involved in teaching, multi-omics data analysis projects, expanding of web-based bioinformatics tools, and development of R packages, Shiny apps and Tableau dashboards.

APPOINTMENTS

Analyst
Collection Development Department
University of Toronto Libraries, Canada

Lecturer
Bioinformatics and Computational Biology Program
Department of Cell & Systems Biology

Data Science Certificate Program
Summer Undergraduate Data Science Research Program
Data Sciences Institute
University of Toronto, Canada

PUBLICATIONS

Visit: Google Scholar

Visit: ORCID

SOFTWARE/TOOLS

Code: GitHub

R packages with Shiny apps for Clustering:
MPLNClust
mixMVPLN
mixMPLNFA
mixGaussian

Other R packages with Shiny apps:
gateCounts

eFP Browser:
Solanum tuberosum
Arabidopsis thaliana Root;Tissue Specific
Arabidopsis thaliana Abiotic Stress;Biotic Stress

PRESENTATIONS

Silva, A. et al. (2023) Exploring expression dynamics of RNA-sequencing data defined by a three-way structure, Toronto RNA Enthusiasts’ Day (TREnD), August 1-2, Peter Gilgan Centre for Research and Learning, Toronto, Canada (poster).

Silva, A. and S. Subedi. (2022) A software for clustering three-way count data using mixtures of matrix variate distributions, CANSSI Ontario Statistical Software Conference, November 10, Faculty of Information, University of Toronto, Toronto, Canada (oral).

Silva, A. et al. (2022) Uncovering biological heterogeneity via clustering to identify gene expression networks and patient similarity networks, Section on Statistical Learning and Data Science, 2022 Joint Statistical Meetings, August 09, Walter E. Washington Convention Center, Washington, USA (oral).Invited.

Silva, A. (2020) Integration of multiple data dimensions to understand molecular heterogeneity of cancer, Bioinformatics Seminar Series, November 13, University of Guelph, Guelph, Canada (oral).Invited.

Silva, A., et al. (2020) Deciphering molecular heterogeneity of follicular lymphoma via DNA methylation, Lymphoma Research Meeting, May 12, Princess Margaret Cancer Centre, Toronto, Canada (oral).

Silva, A., et al. (2020) Delineation of the molecular heterogeneity in follicular lymphoma via unsupervised clustering, Cancer Artificial Intelligence & Big Data, February 20-21, Courtyard Marriott Hotel, Toronto, Canada (poster).

Silva, A. (2019) Clustering of multivariate biological data in the multi-omics era, Conference on Data Science, November 14, The Fields Institute for Research in Mathematical Sciences, University of Toronto, Toronto, Canada (oral).Invited.

Silva, A. (2019) Bayesian clustering approaches for discrete data. Distinguished Dissertation Award Lecture, The Classification Society, June 20, MacEwan University, Edmonton, Canada (oral).Invited.

Silva, A. (2019) Mixtures of multivariate Poisson-log normal distributions and extensions for clustering. Computational Statistics and Data Science Seminar, June 5, Department of Mathematics and Statistics, McMaster University, Hamilton, Canada (oral). Invited.

Silva, A. (2019) Unsupervised learning of biological heterogeneity underlying follicular lymphoma. Vector Institute Postgraduate Affiliate Welcome Event, May 1, Vector Institute for Artificial Intelligence, Toronto, Canada (oral).

Silva, A. (2019) Bayesian model-based clustering approaches for discrete-valued gene expression data. SciNet User Group Meeting, April 10, SciNet Supercomputing Centre of University of Toronto, Toronto, Canada (oral).Invited.

Silva, A. and R. Kridel. (2019) 23-Gene expression-Based score and FOXP1 for outcome prediction in patients diagnosed with follicular lymphoma. Lymphoma Research Meeting, January 8, Princess Margaret Cancer Centre, Toronto, Canada (oral).

Silva, A., et al. (2018) Prognostic biomarkers converge on a germinal centre dark zone phenotype as a determinant of adverse outcome in follicular lymphoma patients treated with rituximab and chemotherapy. Terry Fox Research Institute Ontario Node Symposium Day, December 10, MaRS Discovery District, Toronto, Canada (poster).

Silva, A., et al. (2018) Prognostic biomarkers converge on a germinal centre dark zone phenotype as a determinant of adverse outcome in follicular lymphoma patients treated with rituximab and chemotherapy. American Society of Hematology Annual Meeting, December 3, San Diego, USA (poster).

Silva, A. (2018) Bayesian clustering and other approaches for gene expression data analysis. Pugh Lab Research Visit Seminar, February 16, Princess Margaret Cancer Research Tower, Toronto, Canada (oral).

Silva, A. (2018) Methods for handling high-dimensional gene expression data. Kridel Lab Research Visit Seminar, January 9, Princess Margaret Cancer Research Tower, Toronto, Canada (oral).

Silva, A. (2017) Mixtures of factor analyzers for unsupervised clustering of RNA sequencing data. The Women in Machine Learning Workshop , December 4, Long Beach Convention and Entertainment Center, Long Beach, USA (poster).

Silva, A. (2017) Mixture models for cluster detection in transcriptome sequencing data. Toronto RNA Society Seminars, April 21, The Hospital for Sick Children, Toronto, Canada (oral).

Silva, A., et al. (2016) Mixture-model based clustering of high-throughput sequencing data. 9th International Conference of the European Research Consortium for Informatics and Mathematics Working Group, December 9-11, University of Seville, Seville, Spain (oral).

Silva, A., et al. (2016) Model-driven analysis of transcriptome data via mixtures of multivariate Poisson-log normal distribution. The Women in Machine Learning Workshop , December 5, Centre de Convencions Internacional Barcelona, Barcelona, Spain (poster).

Silva, A., Rothstein, S., and Subedi, S. (2016) Identification of heterogeneity in sequencing data via Poisson mixture models reveals gene co-expression networks and their pathways. 10th Annual Conference of Program in Quantitative Genomics, November 3-4, Harvard Medical School, Boston, USA (poster).

Silva, A., et al. (2016) Mixture model selection for cluster analysis of RNA sequencing data. Annual Meeting of Statistical Society of Canada, May 29-June 1, Brock University, St. Catharines, Canada (oral).

Silva, A., et al. (2015) Comparative analysis of clustering techniques for RNA-seq data. Annual Meeting of Statistical Society of Canada, June 2, Dalhousie University, Halifax, Canada (poster).

Silva, A. (2013) Modelling the structure of Starch Branching Enzyme IIb. Bourque Bioinformatic Lab Research Visit Seminar, June 07, McGill University and Génome Québec Innovation Centre, Montreal, Canada (oral).

Silva, A., et al. (2012) Electronic fluorescent pictographs for visualizing gene expression data of Arabidopsis, maize and potato. Undergraduate Student Research Seminar, April 18, University of Toronto, Toronto, Canada (oral).