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, Masterfs 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 Masterfs 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 Deanfs and Chairfs 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

G Protein-Coupled Receptors: Structure, Signalling and Drug Discovery, Keystone, Colorado, Feb 21-25, 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 Reasoningh 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)