Papers in refereed journals

N.Grigg, A.Schoenrock, K.Dick, J.R.Green, A.Golshani, A.Wong, F.Dehne, E.C.Tsai, K.K.Biggar, “Insights into the suitability of utilizing brown rats (Rattus norvegicus) as a model for healing spinal cord injury with epidermal growth factor and fibroblast growth factor-II by predicting protein-protein interactions”, Computers In Biology And Medicine, Vol. 104, pp.220-226, 2019. [pdf]

D.Burnside, A.Schoenrock, H.Moteshareie, M.Hooshyar, P.Basra, M.Hajikarimlou, K.Dick, B.Barnes, T.Kazmirchuk, M.Jessulat, S.Pitre, B.Samanfar, M.Babu, J.R.Green, A.Wong, F.Dehne, K.K.Biggar, A.Golshani, “In silico engineering of synthetic binding proteins from random amino acid sequences”, iScience, Vol. 11, pp.375-387, 2018. [pdf]

J.F. de Alencar Vasconcellos, E.N.Cáceres, H.Mongelli, S.W.Song, F.Dehne, J.L.Szwarcfiter, “New BSP/CGM algorithms for spanning trees”, The International Journal of High Performance Computing Applications, 1-18, 2018. [pdf]

K.Omidi, M.Jessulat, M.Hooshyar, D.Burnside, A.Schoenrock, T.Kazmirchuk, M.Hajikarimlou, M.Daniel, H.Moteshareie, U.Bhojoo, M.Sanders, D.Ramotar, F.Dehne, B.Samanfar, M.Babu, A.Golshani, “Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae”, Gene, Vol. 639, pp.128-136, 2018. [pdf]

F.Dehne, D.E.Robillard, A.Rau-Chaplin, N.Burke, “VOLAP: A scalable distributed real-time OLAP system for high velocity data”, IEEE Transactions on Parallel and Distributed Systems, Vol. 29 (1), pp.226-239, 2018. [pdf]

K.Omidi, M.Jessulat, M.Hooshyar, D.Burnside, A.Schoenrock, T.Kazmirchuk, M.Hajikarimlou, M.Daniel, H.Moteshareie, U.Bhojoo, M.Sanders, D.Ramotar, F.Dehne, B.Samanfar, M.Babu, A.Golshani, “Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae”, Gene, Vol. 639, pp.128-136, 2018. [pdf]

T.Kazmirchuk, K.Dick, D.J.Burnside, B.Barnes, H.Moteshareie, M.Hajikarimlou, K.Omidi, D.Ahmed, A.Low, C.Lettl, M.Hooshyar, A.Schoenrock, S.Pitre, M.Babu, E.Cassol, B.Samanfar, A.Wong, F.Dehne, J.R.Green, A.Golshani, “Designing anti-Zika virus peptides derived from predicted human-Zika virus protein-protein interactions”, Computational Biology and Chemistry, Vol. 71, pp. 180-187, 2017 . [pdf]

A. Schoenrock, D. Burnside, H. Moteshareie, S. Pitre, M. Hooshyar, J.R. Green, A. Golshani, F. Dehne, A. Wong, “Evolution of protein-protein interaction networks in yeast”, PLoS ONE Vol.12, No.3, e0171920, 2017. [pdf]

B. Samanfar, S.J. Molnar, M. Charette, A. Schoenrock, F. Dehne, A. Golshani, F. Belzile, E.R. Cober, “Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean”, Theoretical and Applied Genetics, 130:377, 2016. [pdf]

D.E. Robillard, P.T. Mpangase, S. Hazelhurst, F. Dehne, “SpeeDB: Fast structural protein searches”, Bioinformatics, Vol. 31, No. 18, pp. 3027-3034, 2015. [pdf]

F. Dehne, Q. Kong, A. Rau-Chaplin, H. Zaboli, R. Zhou, “Scalable real-time OLAP on cloud architectures”, Journal of Parallel and Distributed Computing (JPDC), Vol. 79-80, pp. 31-41, 2015. [pdf]

F.Dehne and H.Zaboli, “Parallel real-time OLAP on multi-core processors”, Int. J. Data Warehousing and Mining (IJDWM), Vol. 11, No.1, pp. 22-44, 2015. [pdf]

A. Schoenrock*, B. Samanfar*, S. Pitre*, M. Hooshyar*, K. Jin, C. Phillips, H. Wang, S. Phanse, K. Omidi, Y. Gui, M. Alamgir, A. Wong, F. Barrenas, M. Babu, M. Benson, M. Langston, J. Green, F. Dehne*, A. Golshani*, “Efficient prediction of human protein-protein interactions at a global scale”, BMC Bioinformatics 15:383, 2014. [pdf]

O.Baltzer, F.Dehne, A.Rau-Chaplin, “OLAP for moving object data”, Int. J. Intelligent Information and Database Systems, Vol. 7, No. 1, pp. 79-111, 2013. [pdf]

F.Dehne and H.Zaboli, “Parallel construction of data cubes on multi-core multi-disk platforms”, Parallel Processing Letters, Vol. 23, No.1, pp. 1350002 (20 pages), 2013. [pdf]

S.Pitre, M.Hooshyar, A.Schoenrock, B.Samanfar, M.Jessulat, J.R.Green, F.Dehne, A.Golshani, “Short co-occurring polypeptide regions can predict global protein interaction maps”, Scientific Reports (, vol.2, art.239, 2012. [pdf]

F.Dehne and H.Zaboli, “Deterministic sample sort for GPUs”, Parallel Processing Letters, vol. 22, no.3, pp. 1250008, 2012. [pdf]

F.Dehne, M.T.Omran, J.-R.Sack, “Shortest paths in time-dependent FIFO networks”, Algorithmica, vol.62, no.1-2, pp.416-435, 2012. [pdf]

A.Amos-Binks*, C.Patulea*, S.Pitre, A.Schoenrock, Y.Gui, J.R.Green, A.Golshani, F.Dehne*, “Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences”, BMC Bioinformatics, 12:225, 2011 (Note: flagged by the publisher as ‘highly accessed’). [pdf]

M.Jessula, S.Pitre, Y.Gui, M.Hooshyar, K.Omidi, B.Samanfar , H.Tan , M.Alamgir, J.Green, F.Dehne, A.Golshani, “Recent advances in protein-protein interaction prediction: experimental and computational methods”, Expert Opin Drug Discov, vol.6, no.9, pp.921-935, 2011. [pdf]

X.Luo*, M.McKeague*, S.Pitre, M.Dumontier, J.Green, A.Golshani, M.C.DeRosa*, F.Dehne*, “Computational approaches towards the design of pools for the in vitro selection of complex aptamers”, RNA, vol.12, no.16, pp.2252-2262, 2010. [pdf]

F.Dehne, G.Hickey, A.Rau-Chaplin, and M.Byrne, “Parallel catastrophe modelling on a Cell B.E.”, Int. Journal of Parallel, Emergent and Distributed Systems (formerly Parallel Algorithms and Applications), vol.25, no.5, pp.401-410, 2010. [pdf]

C.E. R.Alves, E.N.Cáceres, F.Dehne, and S.W.Song, “Some communication issues on scalable parallel computing”, Refereed survey article, Handbook of Research on Scalable Computing Techniques, K.-C.Li, C.H.Hsu, L.T.Yang, J.Dongarra, H.Zima (Ed.), IGI Global, 2010. [pdf]

G.Clermont, C.Auffray, Y.Moreau, D.M.Rocke, D.Dalevi, D.Dubhashi, D.Marshall, P.Raasch, F.Dehne, P.Provero, J.Tegner, B.J.Aronow, M.A.Langston, and M.Benson, “Bridging the gap between systems biology and medicine”, Genome Medicine, vol.1, no.9, pp.88 ff., 2009. [pdf]

F.Dehne, T.Eavis, and A.Rau-Chaplin, “Rcube: Parallel multi-dimensional rolap indexing”, Refereed survey article, Strategic Advancements in Utilizing Data Mining and Warehousing Technologies: New Concepts and Developments, IGI Global, 2009. [pdf]

F.Dehne, M.Lawrence, and A.Rau-Chaplin, “Cooperative caching for grid-enabled OLAP”, Int. Journal of Grid and Utility Computing, vol.1, no.2, pp.169-181, 2009. [pdf]

S.Pitre*, C.North*, M.Alamgir, M.Jessulat, A.Chan, X.Luo, J.R. Green, M.Dumontier, F.Dehne*, and A.Golshani*, “Global investigation of protein–protein interactions in yeast saccharomyces cerevisiae using re-occurring short polypeptide sequences”, Nucleic Acids Research, vol.36, pp.4286-4294, 2008. [pdf]

B.Bhattacharyya and F.Dehne, “Using spine decompositions to efficiently solve the length-constrained heaviest path problem for trees”, Information Processing Letters, vol.108, pp.293-297, 2008. [pdf]

Y.Chen, F.Dehne, T.Eavis, and A.Rau-Chaplin, “PnP: Sequential, external memory, and parallel iceberg cube computation”, Distributed and Parallel Databases, vol.23, no.2, pp.99-126, 2008. [pdf]

A.Chan, F.Dehne, P.Bose, and M.Latzel, “Coarse grained parallel algorithms for graph matching”, Parallel Computing, vol.34, p.47–62, 2008. [pdf]

G.Hickey, F.Dehne, A.Rau-Chaplin, and C.Blouin, “SPR distance computation for unrooted trees”, Evolutionary Bioinformatics, vol.4, pp.17-27, 2008. [pdf]

S.Pitre, M.Alamgir, J.Green, M.Dumontier, F.Dehne, and A.Golshani, “Computational methods for predicting protein-protein interactions”, Refereed survey article, Advances in Biochemical Engineering/Biotechnology, H. Seitz (Ed.), Springer-Verlag, 2008. [pdf]

F.Dehne, T.Eavis, and A.Rau-Chaplin, “RCUBE: Parallel multi-dimensional rolap indexing”, Journal of Data Warehousing and Mining, vol.4, no.3, pp.1-14, 2008. [pdf]

F.Dehne, T.Eavis, and B.Liang, “Compressing data cubes in parallel OLAP systems”, Data Science Journal, vol.6, pp.S184-S197, 2007. [pdf]

S.Pitre*, F.Dehne*, A.Chan, J.Cheetham, A.Duong, A.Emili, M.Gebbia, J.Greenblatt, M.Jessulat, N.Krogan, X.Luo, and A.Golshani*, “PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs”, BMC Bioinformatics, vol.7, p.365 (15 pages), 2006, (Note: flagged by the publisher as ‘highly accessed’ and cited e.g. in Nature Chemical Biology 3:83-84, 2007). [pdf]

F.Dehne, M.Fellows, M.Langston, F.Rosamond, and K.Stevens, “An o(2^O(k) n^3 ) FPT algorithm for the undirected feedback vertex set problem”, Theory of Computing Systems, vol.41, no.3, pp.479 – 492, 2007. [pdf]

F.Dehne, T.Eavis, and A.Rau-Chaplin, “The cgmCUBE project: Optimizing parallel data cube generation for ROLAP”, Distributed and Parallel Databases, vol.19, no.1, pp.29-62, 2006. [pdf]

F.Dehne, “Guest editor’s introduction: Special issue on coarse grained parallel algorithms for scientific applications”, Algorithmica, vol.45, no.3, pp.263-267, 2006. [pdf]

F.Dehne, R.Klein, and R.Seidel, “Maximizing a Voronoi region: the convex case”, Int. Journal of Computational Geometry and Applications, vol.15, no.5, pp.463-475, 2005. [pdf]

Y.Chen, F.Dehne, T.Eavis, and A.Rau-Chaplin, “Improved data partitioning for building large ROLAP data cubes in parallel”, Journal of Data Warehousing and Mining, vol.2, no.1, pp.1-26, 2006. [pdf]

A.Chan, F.Dehne, and R.Taylor, “Implementing and testing cgm graph algorithms on pc clusters and shared memory machines”, Int. Journal of High Performance Computing Applications, vol.19, no.1, pp.81-97, 2005. [pdf]

Y.Chen, F.Dehne, T.Eavis, and A.Rau-Chaplin, “Parallel ROLAP data cube construction on shared-nothing multiprocessors”, Distributed and Parallel Databases, vol.15, pp.219-236, 2004. [pdf]

F.Dehne, W.Dittrich, and D.Hutchinson, “Efficient external memory algorithms by simulating coarse-grained parallel algorithms”, Algorithmica, vol.36, pp.97-122, 2003. [pdf]

J.Cheetham, F.Dehne, A.Rau-Chaplin, U.Stege, and P.Taillon, “Solving large FPT problems on coarse grained parallel machines”, Journal of Computer and System Sciences, vol.67, no.4, pp.691-706, 2003. [pdf]

F.Dehne, W.Dittrich, D.Hutchinson, and A.Maheshwari, “Bulk synchronous parallel algorithms for the external memory model”, Theory of Computing Systems, vol.35, no.6, pp.567-598, 2002. [pdf]

F.Dehne, T.Eavis, S.Hambrusch, and A.Rau-Chaplin, “Parallelizing the data cube”, Distributed and Parallel Databases, vol.11, no.2, pp.181-201, 2002. [pdf]

F.Dehne, A.Ferreira, E.Caceres, S.Song, and A.Roncato, “Efficient parallel graph algorithms for coarse grained multicomputers and BSP”, Algorithmica, vol.33, no.2, pp.183-200, 2002. [pdf]

A.Chan and F.Dehne, “A note on coarse grained parallel integer sorting”, Parallel Processing Letters, vol.9, no.4, pp.533-538, 1999. [pdf]

F.Dehne, “Guest editor’s introduction: Special issue on coarse grained parallel algorithms”, Algorithmica, vol.24, no.3/4, pp.173-176, 1999. [pdf]

A.Chan, F.Dehne, and A.Rau-Chaplin, “Coarse grained parallel geometric search”, Journal of Parallel and Distributed Computing, vol.57, no.2, pp.224-236, 1999. [pdf]

F.Dehne and S.Song, “Randomized parallel list ranking for distributed memory multiprocessors”, Int. Journal of Parallel Programming, vol.25, no.1, pp.1-16, 1997. [pdf]

F.Dehne and K.Guimaraes, “Exact and approximate computational geometry solutions of an unrestricted point set stereo matching problem”, Information Processing Letters, vol.64, pp.107-114, 1997. [pdf]

F.Dehne, X.Deng, P.Dymond, A.Fabri, and A.Kokhar, “A randomized parallel 3d convex hull algorithm for coarse grained multicomputers”, Theory of Computing Systems, vol.30, pp.547-558, 1997. [pdf]

F.Dehne and R.Klein, “The big sweep: On the power of the beach line approach for Voronoi diagrams”, Algorithmica, vol.17, pp.19-32, 1997. [pdf]

F.Dehne, A.Fabri, and A.Rau-Chaplin, “Scalable parallel computational geometry for coarse grained multicomputers”, Int. Journal of Computational Geometry and Applications, vol.6, no.3, pp.379-400, 1996. [pdf]

F.Dehne, B.Flach, J.-R. Sack, and N.Valiveti, “Analog parallel computational geometry”, Parallel Algorithms and Applications, vol.5, pp.1-14, 1995. [pdf]

F.Dehne, A.Ferreira, and A.Rau-Chaplin, “Hypercube algorithms for parallel processing of pointer-based quadtrees”, Computer Vision and Image Understanding, vol.62, no.1, pp.1-10, 1995. [pdf]

F.Dehne, A.Ferreira, and A.Rau-Chaplin, “A massively parallel knowledge-base server using a hypercube multiprocessor”, Parallel Computing, vol.20, pp.1369-1382, 1994. [pdf]

F.Dehne, A.Fabri, M.Nasser, and A.Rau-Chaplin, “Construction of d-dimensional hyperoctrees on a hypercube multiprocessor”, Journal of Parallel and Distributed Computing, vol.23, pp.256-261, 1994. [pdf]

M.Atallah, F.Dehne, R.Miller, A.Rau-Chaplin, and J.Tsay, “Multisearch techniques: Parallel data structures on mesh-connected computers”, Journal of Parallel and Distributed Computing, vol.20, pp.1-13, 1994. [pdf]

S.Hambrusch and F.Dehne, “Determining maximum k-width-connectivity on meshes”, Computational Geometry: Theory and Applications, vol.3, pp.91-105, 1993. [pdf]

F.Dehne, A.Ferreira, and A.Rau-Chaplin, “Parallel fractional cascading on hypercube multiprocessors”, Computational Geometry: Theory and Applications, vol.2, pp.141-167, 1992. [pdf]

F.Dehne, R.Miller, and A.Rau-Chaplin, “Optical clustering on a mesh-connected computer”, Int. Journal of Parallel Programming, vol.20, no.6, pp.475-486, 1991. [pdf]

F.Dehne and S.Hambrusch, “Parallel algorithms for determining k-width-connectivity in binary images”, Journal of Parallel and Distributed Computing, vol.12, no.1, pp.12-23, 1991. [pdf]

F.Dehne and L.Ficocelli, “An efficient computational geometry method for detecting dotted lines in noisy images”, The Computer Journal, vol.33, no.5, pp.424-428, 1990. [pdf]

F.Dehne and M.Gastaldo, “A note on the load balancing problem for coarse grained hypercube dictionary machines”, Parallel Computing, vol.16, pp.75-79, 1990. [pdf]

F.Dehne, Q.Pham, and I.Stojmenovic, “Optimal visibility algorithms for binary images on the hypercube”, Int. Journal of Parallel Programming, vol.19, no.3, pp.213-224, 1990. [pdf]

F.Dehne, A.Ferreira, and A.Rau-Chaplin, “Parallel branch and bound on fine grained hypercube multiprocessors”, Parallel Computing, vol.15, pp.201-209, 1990. [pdf]

F.Dehne and A.Rau-Chaplin, “Implementing data structures on a hypercube multiprocessor and applications in parallel computational geometry”, Journal of Parallel and Distributed Computing, vol.8, no.4, pp.367-375, 1990. [pdf]

F.Dehne, A.Hassenklover, J.Sack, and N.Santoro, “Computational geometry algorithms for the systolic screen”, Algorithmica, vol.6, no.5, pp.734-761, 1991. [pdf]

F.Dehne, “Guest editor’s introduction: Special issue on parallel algorithms for geometric problems on digitized pictures”, Algorithmica, vol.6, no.5, pp.621-623, 1991. [pdf]

F.Dehne, “Computing the largest empty rectangle on one- and two-dimensional processor arrays”, Journal of Parallel and Distributed Computing, vol.9, no.1, pp.63-68, 1990. [pdf]

S.Akl and F.Dehne, “Pipelined search in coarse grained networks”, Int. Journal of Parallel Programming, vol.18, no.5, pp.359-364, 1989. [pdf]

F.Dehne, A.Hassenklover, and J.Sack, “Computing the configuration space for a robot on a mesh-of-processors”, Parallel Computing, vol.12, pp.221-231, 1989. [pdf]

F.Dehne, “Solving visibility and separability problems on a mesh-of-processors”, The Visual Computer, vol.4, no.6, pp.356-370, 1988. [pdf]

F.Dehne and I.Stojmenovic, “A root(n) algorithm for the ECDF. searching problem for arbitrary dimensions on a mesh-of-processors”, Information Processing Letters, vol.28, no.2, pp.67-70, 1988. [pdf]

F.Dehne and J.Sack, “Translation separability of sets of polygons”, The Visual Computer, vol.3, no.4, pp.227-235, 1987. [pdf]

F.Dehne and H.Noltemeier, “Voronoi trees and clustering problems”, Information Systems, vol.12, no.2, pp.171-175, 1987. [pdf]

F.Dehne, “O(root(n)) algorithms for the maximal elements and ECDF searching problem on a mesh-connected parallel computer”, Information Processing Letters, vol.22, no.6, pp.303-306, 1986. [pdf]

F.Dehne and H.Noltemeier, “Clustering methods for geometric objects and applications to design problems”, The Visual Computer, vol.2, no.1, pp.31-38, 1986. [pdf]

F.Dehne, “Optical clustering”, The Visual Computer, vol.2, no.1, pp.39-43, 1986. [pdf]