CV

Academic Background

PhD (2011 - current)

I am a PhD student in Department of Computer Science at the University of Toronto. I am privileged to be supervised by Michael Brudno.

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

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 - current)

I am working with members of TCAG at the Hospital for Sick Children in Toronto, which is directed by Dr. Stephen Scherer.

CompBio Group (May 2008 - current)

I am working with Michael Brudno among others at the CompBio Group at UofT.

Research

Publications

  • Medvedev P, Fiume M, Dzamba M, Brudno M. Method to Detect CNV via Mated Short Reads. Genome Research, August 2010 pre-print
  • 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

  • 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, 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

  • 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 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

    • Reviewer

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

  • Bioinformatics

    • Teaching

    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.

    Awards

    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.

    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.

    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.