Bernie Pope

Academia

Orcid

My Orcid is 0000-0002-4840-1095.

Grants

Expanding diagnostic approaches for Lynch syndrome

  • Funding body: National Health and Medical Research Council (NHMRC, Australia)
  • Period: 2017 - 2019 (3 years)
  • Value: $1,269,355 AUD
  • Chief Investigators: Daniel Buchanan, Ingrid Winship, Amanda Spurdle, Aung Ko Win, Bernard Pope, Christophe Rosty, Finlay Macrae
  • My Role: Chief Investigator (E)

A functional assay to classify genetic variants in Lynch syndrome

  • Funding body: National Health and Medical Research Council (NHMRC, Australia)
  • Period: 2016 - 2018 (2 years)
  • Value: $368,194.80 AUD
  • Chief Investigators: Daniel Park, Daniel Buchanan, Bryony Thompson
  • My Role: Associate Investigator

High risk genes for childhood cancer: using massively parallel sequencing to identify cancer susceptibility

  • Funding body: Cancer Australia
  • Period: 2014 - 2016 (2 years)
  • Value: $200,000 AUD
  • Chief Investigators: John Heath, Melissa Southey, John Hopper, Andrew Lonie, Daniel Park, Tu Nguyen-Dumont, Gillian Dite, Bernard Pope.
  • My Role: Chief Investigator (H)

Mouse phenotype-driven breast cancer risk gene discovery

  • Funding body: Cancer Council Victoria
  • Period: 2014 - 2015
  • Value: $200,000 AUD
  • Chief Investigators: Daniel Park, David Goldgar, Bernard Pope, Tu Nguyen-Dumont, Andrew Lonie
  • My Role: Chief Investigator (C)

Massively parallel sequencing and PCR optimised for DNA-based diagnosis and discovery

  • Funding body: National Health and Medical Research Council (NHMRC, Australia)
  • Period: 2012 - 2014
  • Value: $196,544 AUD
  • Chief Investigators: Daniel Park and Bernard Pope.
  • My Role: Chief Investigator (B)

High Risk Genes for Lobular Breast Cancer

  • Funding body: Cancer Australia
  • Period: 2013 - 2015
  • Value: $300,000 AUD
  • Chief Investigators: Melissa Southey, David Goldgar, Daniel Park, Andrew Lonie, Ingrid Winship, Peter Simpson, Sunil Lakhani.
  • My Role: Associate Investigator

Identifying key players in the spread of antimicrobial resistance.

  • Funding body: National Health and Medical Research Council (NHMRC, Australia)
  • Preiod: 2013 - 2016
  • Value: $789,320 AUD
  • Chief Investigators: Kathryn Holt, Michael Inouye, Justin Zobel, Ruth Hall.
  • My Role: Associate Investigator

Internships

  • Microsoft Research Cambridge, UK. January – April 2007. Project: A breakpoint debugger for the Glasgow Haskell Compiler. Supervisor: Dr Simon Marlow.
  • Ludwig Institute for Cancer Research, Melbourne. Summer break 1995-96. Project: molecular dynamics simulation of trans-membrane signalling in the Aspartate receptor of E. Coli. Supervisor: Dr Herbert Treutlein.

Awards and Scholarships

  • South Pacific Championship Award (coach), 2009, ACM International Collegiate Programming Contest, World Finals, Stockholm, Sweden.
  • Excellence in Teaching Award, 2008, Department of Computer Science and Software Engineering, The University of Melbourne.
  • Australasian Distinguished Doctoral Dissertation Award, 2007. Best Computer Science PhD Thesis in Australia and New Zealand, awarded by the Computing Research and Education Association of Australasia (CORE).
  • Excellence in Tutoring Award, 2005, Department of Computer Science and Software Engineering, The University of Melbourne.
  • Gold Medal (coach), 2000, ACM International Collegiate Programming Contest, World Finals, Florida, USA.
  • Australian Government Department of Education, Science and Training - Australian Postgraduate Award, 2000-2003.
  • The Computer Science Department Certificate of Excellence, Artificial Intelligence, 1996, The University of Melbourne.
  • The Computer Science Department Certificate of Excellence, Operating Systems, 1996, The University of Melbourne.
  • Dean’s Prize, 1994, Faculty of Science, The University of Melbourne.
  • Australian Students Prize for Excellence, 1993. National recognition of outstanding achievement in secondary education.
  • The Sutherland Award, 1993, The Australian Institute of Physics. For outstanding achievement in the VCE.
  • The Victorian Premier’s Award, 1993, for outstanding achievement in the VCE.

Teaching

Elements of Bioinformatics

  • Institution: The University of Melbourne
  • Date: Semester 1, 2016
  • Year Level: Masters
  • Class Size: 30
  • Topics: Bioinformatics, High-Throughput DNA sequencing, Systems Biology, Pathogenomics, Bioinformatics Databases, RNA Sequencing, Natural Language Processing, Structure Modelling and Visualisation, Protein Prediction, Cancer Genomics, and Clinical Genomics.
  • My Role: Lecturer and Coordinator

Foundations of Computing

  • Institution: The University of Melbourne
  • Date: Semester 2, 2014
  • Year Level: First Year Undergraduate
  • Class Size: 230
  • Topics: Introduction to Programming in Python, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Lecturer and Coordinator

Foundations of Computing

  • Institution: The University of Melbourne
  • Date: Semester 2, 2013
  • Year Level: First Year Undergraduate
  • Class Size: 130
  • Topics: Introduction to Programming in Python, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Lecturer and Coordinator

Foundations of Computing

  • Institution: The University of Melbourne
  • Date: Semester 2, 2012
  • Year Level: First Year Undergraduate
  • Class Size: 70
  • Topics: Introduction to Programming in Python, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Lecturer and Coordinator

People Data and the Web

  • Institution: The University of Melbourne
  • Dates: 2008 - 2009
  • Year Level: First Year Undergraduate
  • Topics: Python Programming, Data Manipulation, Web Programming
  • My Role: Lecturer

Functional Programming

  • Institution: The University of Melbourne
  • Date: Semester 1 2008
  • Year Level: Honours and Masters
  • Class Size: 12
  • Topics: Functional Programming, Type Systems, Semantics
  • My Role: Lecturer

Algorithmic Problem Solving

  • Institution: The University of Melbourne
  • Dates: 2007 - 2009
  • Year Level: First Year Undergraduate
  • Class Size: 160
  • Topics: Introduction to Programming in C, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Lecturer

Software Engineering Principles and Tools

  • Institution: The University of Melbourne
  • Dates: 2007 - 2009
  • Year Level: Second Year Undergraduate
  • Class Size: 44 students
  • Topics: Software Development Tools, Revision Control, Shell Scripting
  • My Role: Lecturer

Melbourne University Program for High Achieving Students (MUPHAS)

  • Institution: The University of Melbourne
  • Date: Semesters 1 and 2, 2000
  • Year Level: First Year Undergraduate
  • Class Size: 15
  • Topics: MUPHAS provided high achieving high school students an opportunity to undertake a first year university subject sequence (Computing Fundamentals A/B). This was the first time the program was run in the department. The class size was fifteen students. For an evaluation of the course see: Anne Venables, A Taste of Computer Science: A University Experience for Gifted Secondary Students, Australasian Journal of Gifted Education, 10(2), 2001.
  • My Role: Lecturer

Computing Fundamentals B Advanced Stream

  • Institution: The University of Melbourne
  • Date: Semester 2, 1999
  • Year Level: First Year Undergraduate
  • Class Size: 20
  • Topics: Introduction to Programming in C, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Lecturer

Introduction to Programmming

  • Institution: The University of Melbourne
  • Dates: 2000 - 2006
  • Year Level: First Year Undergraduate
  • Topics: Introduction to Programming in C, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Tutor

Algorithmic Problem Solving (Advanced Stream)

  • Institution: The University of Melbourne
  • Dates: 2000 - 2006
  • Year Level: First Year Undergraduate
  • Topics: Introduction to Programming in Haskell, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Tutor

Languages and Machines

  • Institution: The University of Melbourne
  • Dates: 1996 - 2000
  • Year Level: Second Year Undergraduate
  • Topics: Formal Languages, State Machines
  • My Role: Tutor, Senior Tutor

Computing Fundamentals B

  • Institution: The University of Melbourne
  • Dates: 1996 - 2000
  • Year Level: First Year Undergraduate
  • Topics: Introduction to Programming in C, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Laboratory Demonstrator, Tutor, Senior Tutor

Computing Fundamentals A

  • Institution: The University of Melbourne
  • Dates: 1996 - 2000
  • Year Level: First Year Undergraduate
  • Topics: Introduction to Programming in Miranda/Haskell, Algorithms, Problem Solving, Introduction to Complexity
  • My Role: Laboratory Demonstrator, Tutor, Senior Tutor, Senior Tutor

Computer Graphics

  • Institution: The University of Melbourne
  • Dates: 1997 - 2000
  • Year Level: Third Year Undergraduate
  • Topics: Computer Graphics, Image Processing
  • My Role: Head Tutor, Senior Tutor

Artificial Intelligence

  • Institution: The University of Melbourne
  • Dates: 1997 - 2000
  • Year Level: Third Year Undergraduate
  • Topics: Artificial Intelligence, Search Algorithms, Logic Programming, Deduction
  • My Role: Senior Tutor

Professional Issues in Computing

  • Institution: The University of Melbourne
  • Date: 1998
  • Year Level: Third Year Undergraduate
  • Topics: Morals, Ethics, Professionalism, Society
  • My Role: Tutor

Logic and Computation

  • Institution: The University of Melbourne
  • Dates: 1998 - 2000
  • Year Level: Second Year Undergraduate
  • Topics: Predicate Logic, Propositional Logic, Proof, Logic Programming
  • My Role: Head Tutor

Student Supervision

VLSCI interns

  • Sori Kang, 2012-2013.
  • Adrian Hecker, 2013-2014.
  • Luke Shillabeer, 2013-2014.
  • Luke Zappia, 2014-2015.
  • Edmund Lau, 2016.

UROP students

  • Roger Li, 2014.
  • Edmund Lau, 2015.

Masters of Bioinformatics

  • With Kat Holt I co-supervised David Edwards, 2012, 2013.

Service

Conference committees

  • Haskell Symposium, Canada, 2008.
  • eResearch Australasia, 2012-2016.

Reviews

Recent peer reviews:

  • BMC Genomics 2016.
  • National Health and Medical Research Council (NHMRC Australia) 2016.
  • BMC Bioinformatics 2016
  • MIT Press 2016.
  • GigaScience 2016.
  • BMC Bioinformatics 2015.
  • PLOS ONE 2015.
  • PeerJ 2014.
  • Science of Computer Programming 2014.
  • Bioinformatics 2014.
  • FLOPS: International Symposium on Functional and Logic Programming 2014.
  • Haskell Symposium 2012.
  • 21st European Symposium on Programming (ESOP) 2012.
  • Advances in Engineering Software (Journal) 2011.
  • ACM SIGPLAN Workshop on Partial Evaluation and Program Manipulation 2010.
  • Principles and Practice of Declarative Programming (PPDP) 2009.
  • The 16th International Static Analysis Symposium (SAS) 2009.
  • Principles and Practice of Declarative Programming (PPDP) 2008.
  • Practical Aspects of Declarative Languages (PADL) 2007.
  • International Conference on Logic Programming (ICLP) 2006.
  • Programming Languages and Systems, 4th Asian Symposium (APLAS) 2006.
  • Practical Aspects of Declarative Langauges (PADL) 2005.
  • 13th European Symposium on Programming (ESOP) 2004.
  • Foundations of Software Technology and Theoretical Computer Science 2000.

PhD examination

I have examined one PhD thesis on the topic of programming language implementation.