I'm indebted to the University of Toronto for an incredible academic career. Together with a few brilliant colleagues from UofT and beyond, I've founded a Toronto-based genomics company called DNAstack.

Academic Background

PhD (2011 - 2015)

I am a PhD graduate of Department of Computer Science at the University of Toronto under the supervision of Michael Brudno. My main area of work is in developing software for Big Data visualization in genomics. I am the lead developer of the MedSavant platform.

Master's (2009 - 2011)


I got my Master's degree in Computer Science at the University of Toronto under the supervision of Michael Brudno. I mainly developed the Savant Genome Browser, a software program for visualizing and analyzing next-generation sequencing (and related) datasets.

Undergraduate (2005 - 2009)

I got my BSc. degree in Bioinformatics and Computational Biology, offered jointly by the Departments of Biochemistry and Computer Science at the University of Toronto.

cGPA: 3.83

High School (2000 - 2005)

I went to St. Michael's College in Toronto for the first three years of high school. I then spent two years at Villanova College in King City, where I graduated.

Graduating average: 96%

Positions

DNAstack (Feb 2014 - current)

I'm CEO and co-founder of DNAstack, which develops technology for genetic analysis.

Canadian Bioinformatics Workshop (June 2010 - current)

I'm an instructor for the High Throughput Sequencing workshop that is part of the CBW series.

The Center for Applied Genomics (May 2010 - February 2012)

I worked with members of TCAG at the Hospital for Sick Children in Toronto.

CompBio Group (May 2008 - current)

I worked with Dr. Michael Brudno among others at the CompBio Group at UofT.

Research

Publications

  • Global Alliance for Genomics & Health. A federated ecosystem for sharing genomic, clinical data, Science, June 2016
  • Dyke S, Philippakis A, Rambla J, ... , Fiume M, Sherry S. Consent Codes: Upholding Standard Data Use Conditions, PLOS Genetics, January 2016
  • Similarity Network Fusion: a fast and effective method to aggregate multiple data types on a genome wide scale, Nature Methods, January 2014
  • Girdea M, Dumitriu S, Fiume M, Bowdin S, Boycott K, Chenier S, Chitayat D, Faghfoury H, Meyn S, Ray P, So J, Stavropoulos D, Brudno M. PhenoTips: patient phenotyping software for clinical and research use. Human Mutation, August 2013
  • Mezlini A, Smith E, Fiume M, Buske O, Savich G, Shah S, Aparicion S, Chiang D, Goldenberg A, Brudno M. iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Research, November 2012
  • Fiume M, Smith E, Brook A, Strbenac D, Turner B, Mezlini A, Robinson M, Wodak S, Brudno M. Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research, May 2012
  • Medvedev P, Fiume M, Dzamba M, Brudno M. Method to Detect CNV via Mated Short Reads. Genome Research, August 2010 (designed the journal cover featuring our work)
  • Fiume M, Williams W, Brook A, Brudno M. Savant: Genome Browser for High Throughput Sequencing Data. Bioinformatics, August 2010
  • Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M. SHRiMP: Accurate Mapping of Short Color-space Reads. PLoS Computational Biology, May 2009
  • Presentations

  • Beacon Project for Rare Diseases. ICHG 2016, Apr 6.
  • Beacon Project. GA4GH Global Engagement Session, ICHG 2016, Apr 3.
  • GA4GH Genomics APIs. ASHG 2015.
  • Genomics Data Sharing using Beacons. ASHG 2015.
  • Beacon Project. ASHG 2015, Oct 6.
  • GA4GH Beacon Project. GA4GH 3rd Plenary 2015, Jun 10.
  • System for interpretation of personal genomes. Doctoral Thesis Defence, Feb 13 2015.
  • MedSavant: Database and search engine for genetic mutations. University of Toronto Big Data for Health 2014, Jul 3-4.
  • MedSavant. GBB Research Seminar Series 2014, Jan 9.
  • Finding causal genetic variants using MedSavant. Genome Informatics 2013, Oct 30 - Nov 2.
  • MedSavant: Visual analytics for genetic variation datasets. BioVis 2012, Oct 14-15.
  • Next-Generation Genome Browsing. TorBUG 2012, Sep 26.
  • MedSavant: Accelerating the discovery of casual variants in disease sequencing studies. Genome Informatics 2011, Nov 2-5.
  • MedSavant: Accelerating the discovery of casual variants in disease sequencing studies. HiTSeq SIG, ISMB 2011, Jul 15-16.
  • Savant Genome Browser. McGill-Toronto Computational Molecular and Systems Biology Retreat 2011, May 13-14.
  • Savant Genome Browser. Genome Informatics 2010, Sep 15-19.
  • Savant Genome Browser. HiTSeq SIG, ISMB 2010, Jul 9-13.
  • Posters

  • M. Fiume, M. Brudno (2014) MedSavant: Visual analytics for genetic variation datasets. ICCG 2014, Jun 11-12.
  • M. Fiume, M. Brudno (2012) MedSavant: Visual analytics for genetic variation datasets. SickKids Research Institute Retreat 2012, Nov 8.
  • M. Fiume, M. Brudno (2012) MedSavant: Visual analytics for genetic variation datasets. BioVis 2012, Oct 14-15. Best Poster Winner
  • M. Fiume, M. Brudno (2012) Towards Better and Faster Diagnostics of Genetic Diseases. Research in Action, Toronto.
  • M. Fiume, A. Brook, N. Nursimulu, E. Smith, M. Manker, J. Foong, M. Brudno (2012) MedSavant: Accelerating the discovery of casual variants in disease sequencing studies. VIZBI, Mar 5-8.
  • M. Fiume, A. Brook, N. Nursimulu, E. Smith, M. Manker, J. Foong, M. Brudno (2011) MedSavant: Accelerating the discovery of casual variants in disease sequencing studies. Personalized Medicine in the Genomics Era, Oct 16-17.
  • M. Fiume, A. Brook, N. Nursimulu, E. Smith, M. Manker, J. Foong, M. Brudno (2011) MedSavant: Accelerating the discovery of casual variants in disease sequencing studies. ICHG, Oct 11-15.
  • M. Fiume, E. Smith, V. Williams, A. Brook, M. Brudno (2011) Savant Genome Browser. McGill-Toronto Computational Molecular and Systems Biology Retreat, May 13-14.
  • M. Fiume, E. Smith, V. Williams, A. Brook, M. Brudno (2011) Savant Genome Browser. VIZBI, Mar 16-19.
  • M. Fiume, M. Brudno (2011) The Genetics of Autism. Research in Action, Toronto.
  • M. Fiume, V. Williams, A. Brook, M. Brudno (2010) Savant Genome Browser. ISMB, Jul 9-13.
  • M. Fiume, V. Williams, M. Brudno (2010) Savant Genome Browser. Genomic Disorders, Mar 24-26.
  • M. Fiume, M. Brudno (2009) Genetic Variation Discovery. Research in Action, Toronto.
  • M. Fiume, M. Brudno (2009) DEBUT - Desktop Genome Browser from University of Toronto. Genome Informatics, Oct 26-30.
  • P. Medvedev, M. Brudno, M. Fiume, S. Lee, T. Smith, and A. Dalca (2009) Detecting Copy Number Variation With Ultra Short Reads. ISMB, Jul 27-Jun 2.
  • P. Medvedev, M. Fiume, T. Smith, A. Dalca, S. Lee and M. Brudno (2009) CNV Discovery Using High Coverage Reads. RECOMB, May 18-21.
  • S. M. Rumble, V. Yanovsky, M. Fiume, A. V. Dalca, P. Lacroute, A. Sidow, M. Brudno. (2008) SHRiMP: The Short Read Mapping Package. ISMB, Jul 19-23.
  • Conferences

  • 2016 BIO - San Francisco, United States
  • 2016 International Congress of Human Genetics - Kyoto, Japan
  • 2015 American Society of Human Genetics - Baltimore, United States
  • 2015 Data Working Group Workshop - New York, United States
  • 2015 GA4GH 3rd Plenary - Leiden, Netherlands
  • 2014 American Society of Human Genetics - San Diego, United States
  • 2014 GA4GH 2nd Plenary - San Diego, United States
  • 2014 University of Toronto Big Data for Health - Toronto, Canada
  • 2014 ICCG - Bethesda, United States
  • 2013 Genome Informatics - Cold Spring Harbor, United States (co-chaired the Data Mining and Visualization session)
  • 2013 Google Summer of Code Mentor Summit - Mountain View, United States
  • 2013 McGill-Toronto Computational Molecular and Systems Biology Retreat - Montreal, Canada
  • OCE Discovery 13 - Toronto, Canada
  • 2012 SickKids Research Retreat - Toronto, Canada
  • 2012 VisWeek - Seattle, United States
  • 2012 McGill-Toronto Computational Molecular and Systems Biology Retreat - Toronto, Canada
  • OCE Discovery 12 - Toronto, Canada (helped set a Guinness World Record)
  • 2012 VIZBI - Heidelberg, Germany
  • 2011 Genome Informatics - Cold Spring Harbor, United States
  • 2011 Google Summer of Code Mentor Summit - Mountain View, United States
  • 2011 Personalized Medicine in the Genomics Era: An International Symposium on Childhood Heart Disease - Toronto, Canada
  • 2011 International Congress of Human Genetics - Montreal, Canada
  • 2011 Intelligent Systems for Molecular Biology - Vienna, Austria
  • 2011 McGill-Toronto Computational Molecular and Systems Biology Retreat - Montreal, Canada
  • 2011 VIZBI - Boston, United States
  • 2010 Genome Informatics - Hinxton, United Kingdom
  • 2010 Intelligent Systems for Molecular Biology - Boston, United States
  • 2010 Canadian Genetic Epidemiology & Statistical Genetics - King City, Canada
  • 2010 Genomic Disorders - Hinxton, United Kingdom
  • 2009 Genome Informatics - Cold Spring Harbor, United States
  • 2009 Intelligent Systems for Molecular Biology - Stockholm, Sweden
  • 2008 Intelligent Systems for Molecular Biology - Toronto, Canada
  • Grants

    My work has been funded by these grants, among others:

    • CanSHARE Press
    • OCE SmartStart
    • Genome Canada/CIHR Bioinformatics & Computational Biology 2012 Press
    • OGI SPARK 2011 Press

    Mentorship

    I have had the honour of mentoring the following students:

    • Miro Cupak (Google Summer of Code, summer 2013)
    • Kristopher Kivutha (Google Summer of Code, summer 2013)
    • Steve Tsourounis (NSERC USRA, summer 2013)
    • Khushi Chachcha (Google Summer of Code, summer 2012)
    • Andrew Brook (Google Summer of Code, summer 2011)
    • Nirvana Nirsimulu (NSERC USRA, summer 2011)

    Reviewer

    I have served as a reviewer for the following scientific journals:

    • Genome Medicine
    • Bioinformatics

    Teaching

    International Cancer Genome Workshop (2013)

    I gave a seminar at the 2013 ICGC Workshop in Toronto.

    Center for Computational Medicine (2012)

    I gave a seminar at the annual CCM Workshop at SickKids.

    Advanced Sequencing Technologies & Applications (2011)

    I instructed at the Advanced Sequencing Technologies and Applications course at Cold Spring Harbor.

    Canadian Bioinformatics Workshops (July 2010 - current)

    I am helping to teach the High Throughput Sequencing CBW held in Toronto.

    Undergraduate Computer Science Courses (September 2009 - current)

    I serve as a TA for undergraduate courses offered by the Department of Computer Science at UofT.

    • CSC209 (Winter 2014)
    • CSC207 (Winter 2013)
    • CSC207 (Winter 2012)
    • CSC207 (Winter 2011)
    • CSC148 (Fall 2009)

    Awards

    OBI Entrepreneur Award (2014)

    The Ontario Brain Institute's innovative initiative funds and supports scientists (e.g., neurotechnology, science or engineering) in entrepreneurial/commercialization opportunities to help establish neuroscience-related companies in the NeuroTech Ontario cluster.

    SGS Conference Grant (2014)

    The SGS Conference Grant is intended to encourage eligible students to actively present their research at a regional, national or international conference or equivalent academic event early in their program.

    SGS Doctoral Completion Award (2014)

    The SGS Doctoral Completion Award supports full-time PhD students beyond the funded cohort.

    SGS Conference Grant (2013)

    The SGS Conference Grant is intended to encourage eligible students to actively present their research at a regional, national or international conference or equivalent academic event early in their program.

    NSERC Alexander Graham Bell Canada Graduate Scholarship, Doctoral level (2011)

    The CGS D provides three years of financial support to top-ranked scholars who are engaged in doctoral programs in the natural sciences or engineering.

    There were 7 Computer Science students across Canada to receive this award. A full list of recipients is shown here.

    NSERC Alexander Graham Bell Canada Graduate Scholarship, Master's level (2010)

    The CGS M provides one year of financial support to top-ranked scholars who are engaged in master's programs in the natural sciences or engineering.

    Ontario Graduate Scholarship (2010, 2011)

    Encourages excellence in graduate studies at the master's and doctoral levels, awarded based on academic merit and research potential. Declined in favour of CGS award.

    St. Michael's College Silver Medal Award (2009)

    Awarded to students with a high cumulative grade point average upon graduation.

    NSERC Undergraduate Student Research Award (2008, 2009)

    Awarded to students on the basis of academic merit and research aptitude.

    University of Toronto Dean's List (2006, 2007, 2008, 2009)

    Awarded to the university's best students based on GPA.

    University of St. Michael's College In-Course Scholarship (2006, 2007)

    Awarded to St. Michael's best returning students according to GPA.

    University of Toronto Scholars Award (2005, 2006)

    Awarded to the top 150 students entering first year at the University of Toronto. The award is extended into second year if the student maintains an 'A' average in their first year.

    University of St. Michael's College Foundation Admission Scholarship (2005)

    Awarded to St. Michael's best incoming student in all admission categories.

    Villanova College Academic Scholarship (2005)

    Awarded to the 3 graduating students with the highest overall averages.

    Steven Stuart Memorial Bursary (2005)

    Awarded to the player who has made an outstanding contribution to the Richmond Hill Stars Hockey Association and surrounding community throughout his or her career with the organization.

    Declined Admission Offers

    I was offered the following scholarships on the basis of academic merit. I declined them in favour of my acceptance of offers from the University of Toronto.

    • McMaster University Entrance Award
    • Queen's University Principal's Scholarship
    • University of Waterloo National Scholarship
    • University of Waterloo President's Scholarship
    • University of Western Ontario Continuing Admission Scholarship

    Volunteering

    ISMB 2008 (July 2008)

    I volunteered at ISMB (a large bioinformatics conference) held at the Metro Toronto Convention Centre. I helped organize things there and in the meantime I had the chance to sit in on many interesting talks.

    Yonge-Spruce Chiropractic Clinic (May 2006 - Sept 2007)

    I volunteered at a chiropractic clinic in Richmond Hill, where I assisted in the treatment of patients.