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Homepage of Adnan Sljoka (last updated Feb 2015)

E:mail: adnanslj@gmail.com

 

 

 

 

 

 

 
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Research Interests

About me – CV and current projects

Publications

Talks and conferences

Other info and links

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Research Interests:

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        Rigidity Theory, Algorithms for modeling protein rigidity/flexibility and protein motions, Allosteric interactions in proteins, Linkage Motions and Decompositions in Mechanical engineering and robotics, Matroid Theory, Graph Theory, Computational Biology and Bioinformatics, Computational Geometry, Mathematical Biology, fMRI data analysis and Mathematics Education.

 

Rigidity-based allosteric communication in agonist-bound adenosine receptor, a GPCR.

 
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About me:

 

        • I received my PhD in Applied Mathematics in October 2012. I worked with Walter Whiteley on applications of rigidity theory, which is a mix of geometry, graph theory and applied combinatorics. You can find my PhD thesis here.

 

         • My research is focused on the development of theory and algorithms with applications to a range of problems from protein flexibility predictions, bioinformatics and mechanical linkages – more specifically protein allostery, protein ensemble flexibility prediction, antibody flexibility prediction, protein hinge motion predictions, computational predictions of HD-exchange and decompositions of linkages (Assur graphs). Since my work is highly interdisciplinary, a significant part of my work involves collaborations with other mathematicians, biochemists, computer scientists and mechanical engineers / researchers in robotics.

 

• Upon completion of PhD I was a postdoctoral fellow at York University. Subsequently I was working on fMRI brain activity data analysis http://www.ryerson.ca/science/newsevents/news/cordes.html as a postdoctoral fellow at Ryerson University/University of Colorado Boulder.

 

• I am currently co-organizing the conference “Workshop on Making Models: Simulating Research in Rigidity Theory and Spatial-Visual Reasoning” at the Fields Institute for Research in Mathematical Sciences, Toronto, Canada, http://www.fields.utoronto.ca/programs/scientific/14-15/making_models/index.html. If you are interested in attending or want to know more please get in touch with me.

 

• I am also interested in mathematics education and teaching and have formal teacher training.

 

         • I play competitive tennis and was part of the York University varsity tennis team for 4 years.

 

         • You can find my full CV here. (updated Feb, 2017)

 

Current and ongoing research interests and projects:

 

• I have developed the first rigidity-theoretical allosteric mechanism and algorithms for predicting and detecting Allosteric communication in proteins. More specifically, the algorithms are designed to predict transmission of rigidity and shape changes between a pair of distant (binding) sites in a protein and to identify the regions that are crucial for the coupled communication (i.e. allosteric pathways). The current focus is on applying these techniques and algorithms to G-protein coupled receptors (GPCRs). Finding an allosteric mechanism of GPCRs is crucial as GPCRs are responsible for the control of most information that passes into the cell from the external environment. GPCRs play a critical role in many diseases (i.e heart disease, hypertension, cancer, asthma, diabetes, inflammation and psychological disorders) and are the most commonly targeted receptor class for medicinal therapeutics (it is estimated GPCRs are targets to more than 50% of all modern medicinal drugs). The recent discoveries of GPCRs structures have led to a Nobel prize in Chemistry.

 

         • Immunoglobulin (antibody) flexibility predictions with Jeffrey Gray group at John Hopkins University.

 

• Characterizing structural ensembles via HD-exchange and flexibility of intrinsically disordered proteins focusing on Tau protein, a key protein in Alzheimers disease, with Derek Wilson group at York University.

 

        • Redundant rigidity of body-hinge graphs with Naoki Katoh group at Kyoto University.

 

         • Robotics-Mechanical Linkages and Molecular decompositions via Assur Graphs with Offer Shai, Tel-Aviv University.

 

         • Impact of symmetry on protein motions and symmetry adapted Assur graphs.

 

• Coarse grained Molecular Dynamics simulations.

 

 

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Publications:

 

[15] Zhu S., Shala A., Bezginov A., Sljoka A., Audette G. and Wilson D., Probing Function-Related Shifts in the Conformational Ensembles of Intrinsically Disordered Proteins Using Time-Resolved Hydrogen/Deuterium Exchange  Mass Spectrometry, to appear in PLoS ONE, 2015.

 

[14] Nixon A., Schulze B., Sljoka A., Whiteley W., Symmetry Adapted Assur Decompositions, Symmetry, 6(3), 516-550, 2014. Symmetry link.  PDF

 

[13] Higashikawa Y., Katoh N., Kobayashi Y. and Sljoka A., k-Edge-Rigid Body-Hinge Graphs, submitted, 2014.

 

 [12]  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. Springer link.  PDF

 

[11] Schulze B., Sljoka A. and Whiteley W., How does symmetry impact the flexibility of proteins?, Philosophical Transactions of Royal Society A 372, 20120041, 2014. Royal Society Link.  PDF

 

[10] Sljoka A. and Wilson D., Probing Protein Ensemble Rigidity and predictions of Hydrogen-Deuterium exchange, Physical Biology, 10 056013, 2013. Phys. Biol. Link.  PDF

 

[9] Shai O., Sljoka A. and Whiteley W., Directed Graphs, decompositions and Spatial Decompositions,  Discrete Applied Mathematics, 161 3028–3047, 2013. Discrete Applied Math Link.  PDF

 

[8] 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. ASME link.  PDF

 

[7] 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. AIP link.  PDF

 

[6] 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. AIP link.  PDF

 

[5] 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.

 

Thesis:

 

[4] Sljoka A., Algorithms in rigidity theory with applications to protein flexibility and mechanical linkages, PhD dissertation, York University, Toronto, 2012.  PDF

 

[3] Sljoka A., Counting for Rigidity, Flexibility and Extensions via the Pebble Game Algorithm, Master’s Thesis, York University, Toronto, 2006. Best University-wide Thesis Prize.  PDF

 

Preprints:

 

[2] Sljoka A. Rigidity-based allosteric communication applied to G-protein coupled receptors, preprint, 2014.

 

[1] Vaidya N., Sammadi M., Sljoka A. and Huaxiong H., Coarse graining molecular dynamics with rigidity of hemagglutinin fusion peptides, in preparation.

 

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Selected invited talks / conferences:

 

Rigidity-based allostery in GPCRs (poster), 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.

The 19th Annual Meeting of the Organization for Human Brain Mapping (OHBM), Seattle, Washington, USA, June 16-20, 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, Allosteric Regulation of Cell Signalling, Spanish National Cancer Research Centre, Madrid, Spain, (September 17 - 19, 2012).

 

• Workshop on Rigidity, Fields Institute for Research in Mathematical Sciences, Toronto, Canada, (Oct 11- 14, 2011).

 

• ASME 2011 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference, IDETC/CIE 2011, Washington, DC, USA, (August 29-31, 2011).

 

• Predicting hinge motions and allostery using rigidity theory, 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.

 

• Predicting Rigidity and Flexibility of proteins using rigidity theory (Poster), 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).

 

• 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).

 

• Predicting flexibility and motions of proteins using rigidity theory, MITACS / CORS 2010 Annual Conference, Edmonton, Canada, (May 25, 2010).

 

• Counting for rigidity and flexibility - hinge predictions and allostery (Poster), MITACS Annual Conference, University of New Brunswick, NB, Canada (May 31, 2009).

 

• Pebble Game Algorithm, Hinge predictions and allostery (Poster), 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).

 

• Rigidity, Flexibility, and Motion: Theory, Computation and Applications to Biomolecules, Banff International Research Station (BIRS), Banff, Canada (July 6 – 11, 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).

 

 

 

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Links and group conference photos: