ADNAN SLJOKA
Kwansei Gakuin
University, Sanda, Japan
Department of
Informatics, School of Science and Technology
CREST, Japan
Science and Technology Agency, Japan
webpage: http://www.math.yorku.ca/~adnanslj
NATIONALITY: Canadian
RESEARCH INTERESTS: Rigidity theory, computational
biology, graph theory, protein function, algorithms, mathematical modeling,
mechanical engineering and robotics, interdisciplinary research.
EDUCATION:
• Doctor of Philosophy (2012)
Applied
Mathematics, York University: (Toronto)
Dissertation title: Algorithms in
rigidity theory with applications to protein flexibility and
mechanical linkages, Advisor: Walter Whiteley
• Master of Science (2006)
Applied and Industrial
Mathematics, York
University: (Toronto)
Thesis title: Counting for Rigidity,
Flexibility and Extensions via the Pebble Game
Algorithm, Supervisor: Walter Whiteley,
Awards: York University Thesis prize
• Canadian
Certificate in Bioinformatics
(2005)
Canadian Genetic Disease Network
• Bachelor of
Education (2004)
University of Windsor: (Windsor)
Division: Intermediate/Senior,
Teachable: Mathematics and Geography
Awards: Most Valuable Student Award
• Bachelor of
Science With Honours (2002)
Applied Mathematics
Specialized Honours, York
University: (Toronto)
WORK EXPERIENCE:
• Postdoctoral Research Fellow (2015 -
present)
Kwansei Gakuin
University, Sanda, Japan
CREST, Japan
Science and Technology Agency, Japan
http://www.alg.cei.uec.ac.jp/itohiro/crest/eng/algorithm.html
• Postdoctoral Research Fellow (2015)
Kyoto University,
Kyoto, Japan
CREST, Japan
Science and Technology Agency, Japan
http://www.alg.cei.uec.ac.jp/itohiro/crest/eng/algorithm.html
• Postdoctoral Fellow (2013 – 2014)
Department of
Psychology and Neuroscience , University of Colorado Boulder (Denver, Colorado)
and Department of Physics, Ryerson University (Toronto, Canada)
http://www.ryerson.ca/science/newsevents/news/cordes.html
• Research Visit (July-August, 2015,
March 2016)
Department of
Chemical and Physical Sciences, University of Toronto, Prof.
Scott Prosser
• Research Visit (January, 2015)
Faculty of
Engineering, Tel-Aviv University, Israel, Prof. Offer
Shai
• Research Visit (July 2013, April 2014)
Graduate
School of Engineering, Kyoto University, Kyoto, Japan
• Research Visit (September 2012) Institut de
Robòtica i Informàtica Industrial
Universitat Politècnica de Catalunya, Barcelona, Spain
• Teaching and Research Assistant (2004 –
2012)
Department of Mathematics and
Statistics, York University: (Toronto)
-Held tutorial sessions and
tutored students in Calculus of single and multi-variables, Linear Algebra,
Discrete Mathematics, Mathematical Education, Financial Mathematics, Technical
and Business Mathematics.
- Conducted research on applied
mathematics and its applications to biomedicine
- Part of NIH (USA) and
NSERC (Canada) funded grant
Scientific
Publications:
[14] Higashikawa Y., Katoh N.,
Kobayashi Y. and Sljoka A., k-Edge-Rigid
Body-Hinge Graphs, to appear
in Information Processing Letters, 2015.
[13] Zhu S., Shala A., Bezginov
A., Sljoka A., Audette G. and Wilson D., Hyperphosphorylation of Intrinsically Disordered Tau Protein
Induces an Amyloidogenic Shift in Its Conformational
Ensemble, PLoS ONE, 10(3), 2015.
[12] Nixon A., Schulze B., Sljoka A., Whiteley W., Symmetry Adapted Assur Decompositions, Symmetry,
6(3), 516-550, 2014.
[11] Porta J.M., Ros L, Schulze B., Sljoka
A. and Whiteley W., On the Symmetric Molecular
Conjectures, in Computational Kinematics, Vol 15 of Mechanisms and Machine
Science, pp. 175-184, Springer, 2014.
[10] Schulze B., Sljoka A. and Whiteley
W., How does symmetry impact the flexibility of proteins?,
Philosophical Transactions of Royal Society A 372, 20120041, 2014.
[9] Sljoka A. and Wilson D., Probing Protein Ensemble Rigidity and
predictions of Hydrogen-Deuterium exchange, Physical Biology, 10
056013, 2013.
[8] Shai O., Sljoka A. and Whiteley
W., Directed Graphs, decompositions and Spatial Decompositions, Discrete Applied Mathematics, 161
3028–3047, 2013.
[7] Sljoka A., Shai O. and Whiteley W., Checking Mobility and Decomposition of Linkages
via Pebble Game Algorithm, Proceedings of the ASME 2011 International
Design Engineering Technical Conferences and Computers and Information in
Engineering Conference, IDETC/CIE 2011, August 29-31, 2011, Washington, DC,
USA., 2011.
[6] Sljoka A. and Bezginov A., Predicting hinge motions
and allostery using rigidity theory, Advances in Mathematical and Computational Methods:
Addressing Modern Challenges of Science, Technology, and Society, The International Conference on Applied
Mathematics, Modeling and Computational Science, Volume 1368, pp. 167- 170, Waterloo, Canada, 2011.
[5] Schulze B., Sljoka A. and Whiteley W., Protein
flexibility of dimers: Do symmetric motions play role in allosteric
interactions, Advances in Mathematical
and Computational Methods: Addressing Modern Challenges of Science, Technology,
and Society, The
International Conference on Applied Mathematics, Modeling and Computational
Science, Volume 1368, pp. 135-138 , Waterloo, Canada, 2011.
[4] Sljoka A., Counting for Rigidity, Flexibility and Extensions via the Pebble
Game Algorithm – Hinge Predictions and other Biological Applications (2nd
prize) , Third Canadian Student Conference on
Biomedical Computing, 2008.
In preparation/submitted:
[3] Kim T., Mehrabi P., Sljoka A., Ing
C., Bezginov A., Pomes R., Prosser S. and Pai E., The Role of Dimer Asymmetry and Subunit Dynamics in
Enzyme Catalysis, 2016
Thesis:
[2] Sljoka A., Algorithms in rigidity
theory with applications to protein flexibility and mechanical linkages, PhD
dissertation, York University, Toronto, 2012.
[1] Sljoka A., Counting for Rigidity, Flexibility and Extensions via the Pebble
Game Algorithm, Masterfs Thesis, York University, Toronto, 2006. This
thesis won Best Thesis Prize.
SELECTION OF INVITED TALKS:
• Applications of rigidity theory to predicting protein flexibility and
allosteric interactions, The Hospital for Sick Children, Toronto, March 17,
2016.
• Towards a general mechanism of allosteric communication, CREST meeting
on Big Data Algorithms, Tokyo, Japan, Dec, 19, 2015.
• Probing GPCR allostery communication via transmissions of rigidity, GPCR
Workshop, Hawaii, December 1-5, 2015
• Probing rigidity and flexibility of proteins via rigidity theory,
University of Toronto, July 27, 2015
• Body-hinge Assur graphs: Inductive Construction Techniques, Advances in Combinatorial and Geometric Rigidity Theory, Banff
International Research Station (BIRS), Banff, Canada, July12, 2015.
• Allostery with rigidity theory – insights
into GPCRs, CREST meeting on Big Data Algorithms, Sapporo, Japan, July, 13,
2015.
•Counting for rigidity and flexibility - applications to protein flexibility, CREST meeting on Big Data Algorithms, Ikaho, Japan, March, 20, 2015.
• Rigidity Theory
and applications to protein flexibility, Japan Advanced Institute of
Technology, Nomi, Japan, March, 16, 2015
• Rigidity-based allostery in GPCRs, The 28th Annual Symposium of The Protein Society, San
Diego, California, July 27-31, 2014.
• A new
rigidity-based model for allosteric communication in G-Protein coupled
receptors, G Protein-Coupled Receptors: Structural Dynamics and Functional
Implications, Snowbird, Utah, March 30th – April 4th,
2014.
• Algorithms in
rigidity theory – allostery and hinge detections, Department of Biophysics, Graduate School
of Science, Kyoto University, Kyoto, Japan, July 25, 2013.
• Counting for rigidity and flexibility - algorithms
and applications to protein flexibility and linkage decompositions, Seminar
at Institut de Robòtica i Informàtica Industrial,
Barcelona, Spain, (Sept 21, 2012).
• Rigidity-based
Allosteric communication (poster), Allosteric Regulation of Cell Signalling,
Spanish National Cancer Research Centre, Madrid, Spain, (September 17-19,
2012).
•
Predicting Rigidity and Flexibility of proteins using rigidity theory, Recomb 2011, 15th Annual International Conference on
Research in Computational Molecular Biology, Vancouver, BC, (March 28, 29,
2011).
• Decomposition
of Mechanisms: Assur Graphs and Algorithms, Geometry day at York, York
University, Toronto, Canada, (January, 26, 2011).
• Predicting flexibility and motions of
proteins using rigidity theory, MITACS
/ CORS 2010 Annual Conference, Edmonton, Canada, (May 25, 2010)
• Pebble Game Algorithm, Hinge predictions
and allostery, Molecular Simulations: Algorithms,
Analysis, and Applications, Institute of Mathematics and its Applications
(IMA), University of Minnesota, Minneapolis, MN, USA (May 18, 2009)
•
Pebble Game Extensions: Relevant Regions, Hinge Motions and Allostery.
Recent Progress in Rigidity Theory, Banff International Research Station
(BIRS), Banff, Canada (July 11, 2008)
• Third Canadian Student Conference on Biomedical Computing,
Institute of Biomaterials and Biomedical
Engineering, Toronto (March 13, 2008)
• Algorithms in Rigidity Theory: The Pebble
Game Algorithm, York University (January 2007)
AWARDS,
SCHOLARSHIPS AND ACHIEVEMENTS:
· Young
Investigator/ Finn World Presentation Award, Annual Symposium of Protein
Society, 2013 and 2014.
· Postdoctoral
Fellowship, University of Boulder and
Ryerson University, National Institute of Health (USA) 2013
· Postdoctoral
Fellowship, York University, 2012
· Research Assistantship Scholarship, York
University (2004 – 2011)
· Teaching Assistantship Scholarship, York
University (2004 – 2011)
· Support from
National Institute of Health (US) and University of Illinois at
Urbana-Champaign to attend a Hands on Workshop on Computational Biophysics,
Beckman Institute, University of Illinois, Urbana-Champaign, Illinois, November
1-5, 201.
· Support from
London Mathematical Society (UK) to attend London Mathematical Society
Workshop: Rigidity of Frameworks and Applications, Lancaster University,
Lancaster, UK, July
12-15, 2010
· Support from
National Science Foundation (US) and MITACS (Canada) to attend DIMACS/MBI
US-African Advanced Study Institute and workshop on Mathematical Economic
Epidemiology in Kampala, Uganda, July 17 - August 5, 2009
· Performed
simulation of the motion of the key mutant and nonmutant
protein of Cystic Fibrosis which appeared on the film for Television of Ontario
(TVO) series and Knowledge Network, Donald Coxeter:
The Man Who Saved Geometry. http://www.imdb.com/title/tt1541130/combined
· Support from University of Georgia (US) to attend Summer School on
Multivariate Splines and Applications, Athens, GA, May 11-22, 2009
· Poster prize, second place. Third Canadian
Conference on Biomedical Computing, Toronto (May 2008)
· Best Masterfs Thesis Award, Faculty of Graduate Studies, York University
(2006)
· Burroughs Wellcome Fund, International Competition, (To attend
Genomics Workshop organized by Canadian Genetics Disease Network at University
of Calgary) (May 2005)
· Canadian Institute of
Health Research (CIHR) Institute of Genetics Short Term Research Visit
Competition (2005) to attend the Bioinformatics, Genomics and Proteomics
Workshops at University of British Columbia, University of Calgary, Université de Montréal
· MITACS Mobility Fund Award (To attend MITACS-METHEON
workshop "Complex Networks in the Life Sciences" and "Minisymposium on Mathematics in the Life Sciences" in
Berlin, Germany, March 29-April 04, 2007).
· Support from
Pacific Institute of Mathematical Sciences (PIMS) to attend "The eighth
PIMS graduate industrial math modelling camp", University of
Lethbridge,
Lethbridge, Canada (May 7 – 11, 2005).
· Support from
Pacific Institute of Mathematical Sciences (PIMS) to attend "The ninth
PIMS industrial problem solving workshop", University of
Calgary, Calgary,
Canada (May 15 – 19, 2005).
· Most Valuable
Student Award, Faculty of Education, University of Windsor (2004)
· Member of
Deanfs and Chairfs Honour Roll, York University (2000-2002)
Selection of Workshops/Conferences attended
and research visits:
• Research visit, with Andrew Wooley and Scott Prosser group, University of Toronto, Canada,
July-August, 2016
• GPCR Workshop Hawaii, Kona, Hawaii, Dec 1-5, 2015
• Research visit, with Scott Prosser group, Department of Chemical and Physical
Sciences, University of Toronto, Canada, July-August, 2015
• Advances in Combinatorial and Geometric Rigidity Theory, Banff
International Research Station (BIRS), Banff, Canada, July12-17, 2015.
•The 9th Hungarian-Japanese Symposium on Discrete
Mathematics and Its Applications, Fukuoka, Japan, June2-5, 2015.
• Research visit with Offer Shai, Faculty of Engineering, Tel-Aviv University, Israel,
January, 2015
•The 28th Annual
Symposium of The Protein Society, San Diego, California, July 27-31, 2014.
• G
Protein-Coupled Receptors: Structural Dynamics and Functional Implications,
Snowbird, Utah, March 30th – April 4th, 2014).
•
Research visit, with Naoki Katoh group, Department of Architecture and
Architectural Systems, Graduate School of Engineering, Kyoto University,
Kyoto, Japan, July, 2013
• The 19th Annual
Meeting of the Organization for Human Brain Mapping (OHBM),
Seattle, Washington, USA, June
16-20, 2013.
•
Research visit, Lluis Ros, Institut de Robòtica i Informàtica Industrial,
Barcelona, Spain, (Sept 21 - 26, 2012).
• Allosteric
Regulation of Cell Signalling, Spanish National Cancer Research Centre, Madrid,
Spain, (September 17 - 19, 2012).
• Rigidity
Theory: Progress, Applications and Key Open Problems - Banff International
Research Station (BIRS), Banff, Canada, (July 15 - 20, 2012)
• CMS Winter Meeting (Special Session on Discrete Geometry), Toronto, ON,
Canada, (December 10 - 12, 2011)
• Workshop
on Rigidity, Fields Institute for Research in Mathematical Sciences, Toronto,
Canada - Oct 11- 14, 2011
• ASME
2011International Design Engineering Technical Conferences and Computers and
Information in Engineering Conference, IDETC/CIE 2011, August 29-31, 2011,
Washington, DC, USA.
• AMMCS: Addressing Modern Challenges of
Science, Technology, and Society, The International Conference on Applied
Mathematics, Modeling and Computational Science, Volume 1368, pp. 167- 170, Waterloo, Canada,
2011.
• Recomb 2011, 15th Annual International Conference on Research in Computational
Molecular Biology, Vancouver, Canada, (March 28 - 31, 2011)
• Hands on Workshop on Computational
Biophysics, Beckman Institute, University of Illinois, Urbana-Champaign,
Illinois, November 1-5, 2010
• Rigidity of Frameworks and Applications,
Lancaster University, Lancaster, UK, July 12-15, 2010
• MITACS
/ CORS 2010 Annual Conference, Edmonton, Canada, (May 25, 2010)
• MITACS Annual Conference, University of
New Brunswick, Fredericton, NB
(May 31 - June 5, 2009)
• Molecular Simulations: Algorithms,
Analysis, and Applications, Institute of Mathematics and its Applications
(IMA), University of Minnesota, Minneapolis, MN, USA (May 18 - 22, 2009)
• Rigidity,
Flexibility, and Motion: Theory, Computation and Applications to Biomolecules,
Banff International Research Station (BIRS), Banff, Canada (July 6 – 11, 2008)
• Recent
Progress in Rigidity Theory, Banff International Research Station (BIRS),
Banff, Canada (July 11 – 13, 2008)
• Rigidity, Flexibility and Motion in
Biomolecules, Tempe, Arizona (May 14 – 18, 2006)
• Proteomics, Canadian Bioinformatics
Workshops, Université de Montréal, Montreal (June
2005)
• Genomics, Canadian Bioinformatics
Workshops, University of Calgary, Calgary (May 2005)
• Bioinformatics, Canadian Bioinformatics
Workshops, Vancouver (February 2005)
• Discrete and Computational Geometry
Workshop at Mathematical and Scientific Research Institute (MSRI), Berkeley,
California (August 20 – 29, 2003)
Service,
Community Involvement and Leadership:
• Co-organizer of Conference gWorkshop on
Making Models: Simulating Research in Rigidity Theory and Spatial-Visual
Reasoningh at Fields Institute for Research in Mathematical Sciences, Toronto,
Canada, August 5-9, 2014
http://www.fields.utoronto.ca/programs/scientific/14-15/making_models/index.html
• Supervised a senior undergrad student's
research project (York University, 2012)
• Taught special topics in mathematics and
biomedicine to enriched grade 12 classes at the Ontario Science Centre
(Toronto, 2009).
• Vincent Massey Secondary School -
coordinated various mathematical contests (eg. The
Fryer, Galois, Hypatia, Euclid Contests) (April 2004,
Windsor)
• Attended several monthly meetings at the
Fields Institute for Mathematical Research with Council of Ontario Universities
task force to rebuild geometry education and other revisions into the Ontario
Mathematics Curriculum (Toronto, 2007 - 2009)
• Centre for Support of Teaching,
University Teaching Practicum, 2011
• Developed and coached inner city kids
tennis program for Doug Philpott Inner-City Children's Fund (Toronto, Ontario) (Summer 1999-2006)