James Collier

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Visiting my dear friend, Marie Wolffhugel, in Lyon, France. 2014.


About Me

I hail from a small town in country Victoria called Beechworth. I completed my undergraduate degree in Science (majoring in mathematics and computer science) at Monash University in 2010, followed by an honours degree in Computer Science in 2011. I've recently completed a PhD at Monash University under the supervision of Arun Konagurthu and Maria Garcia de la Banda. My PhD research involved the investigation of methods for formally describing the comparison of protein structures such that alignments of these structures can be rigorously ranked and searched for. This culminated in an alignment tool that is demonstrated to produce statistically rigorous and biologically meaningful alignments.

Research Summary

Structural molecular biology relies heavily on computational techniques that compare protein three-dimensional structures and generate structural alignments. Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. My research is a radical departure from traditional techniques, and presents new alignment methods using principles of Bayesian and information-theoretic inference. These methods have been demonstrated to produce statistically rigorous and biologically meaningful alignments. My work provides direct payoffs to research in the important fields of protein science, crystallography, and bioinformatics.


E-mail: james.collier412(a)gmail.com
Phone: +31 06 541 690 16

Breukrand 407
5403LJ Nederland

Gitlab: bimmie

Curriculum Vitae


Public PGP Key

For email address: james.collier412(a)gmail.com

SHA256 checksum of above file: febb30b2290c9af13d754bdb3d50cf21aecbfd3cce9ef0ecef24297176690586

Laboratory of Computational Biology (LCB)

I am part of the Laboratory of Computational Biology in the department of computer science at Monash University.

External Collaborators


Refereed Journal Publications

  • James H. Collier, Lloyd Allison, Arthur M. Lesk, Peter J. Stuckey, Maria G. de la Banda, Arun S. Konagurthu, Statistical Inference of Protein Structural Alignments. Bioinformatics (accepted) 19-Nov-2016 Web: MMLigner.
  • James H. Collier, Lloyd Allison, Arthur M. Lesk, Maria G. de la Banda, Arun S. Konagurthu, A new statistical framework to assess structural alignment quality using information compression. Bioinformatics 30(17): i512-i518. September, 2014.
  • Arun S. Konagurthu, Parthan Kasarapu, Lloyd Allison, James H. Collier, Arthur M. Lesk, On sufficient statistics of least-squares superposition of vector sets. In the Eighteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2014, Apr 2-5 2014 Pittsburgh (PA), USA) LNCS/LNBI 8394: 144-159
  • James H. Collier, Arthur M. Lesk, Maria Garcia de la Banda, Arun S. Konagurthu, Super: A web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank. Nucleic Acids Research 40(W1): W334-W339. July 2012.

Refereed Conference Proceedings

  • James H. Collier, Arun S. Konagurthu, An information measure for comparing top k lists, Proceedings 2014 IEEE 10th International Conference on eScience (eScience 2014), pp. 127-134.


  • FIT3139: Computational Science (2011 s2, 2012 s2, 2013 s2, 2014 s2, 2015 s2)
  • FIT2004: Algorithms and Data Structures (2014 s1)

Software I've written

  • MMLigner: Pairwise protein structural alignment program
  • I-value: Protein structural alignment quality measure
  • Super: Very fast whole database protein structural fragment search
  • liblcb: General purpose C++ library for structural computational biology (not yet published)
  • MADclient: Direct Connect client

Software I have an interest in



  • Free Software [1]
  • Long-distance running
  • Sudoku
  • Powerful and elegant programming languages (I like scheme)
  • Reading




  • V for Vendetta
  • Thank You for Smoking
  • Good Morning Vietnam
  • Mr Pip
  • Sophie Scholl: The Final Days

Things I never remember when I need them

  • Show APT resolver output: `apt-get -o Debug::pkgProblemResolver=yes dist-upgrade`
  • Free filesystem cached memory: [2]
  • List installed packages by size: dpkg-query -W --showformat='${Installed-Size} ${Package}\n' | sort -n
  • Prevent a particular package from upgrading: apt-mark hold [pakage name]
  • List held packages: apt-mark showhold
  • Debian Cleanup Tips:
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