Aleksandar Poleksić
Ph.D. Florida State University

Poleksic A. Numerical Optimization in Hyperbolic Space - Applications to Drug-Target Interaction Prediction, LNCS Springer Nature, in press (2024)

Poleksic, A. "Fast Dual-Regularized Autoencoder for Sparse Biological Data." arXiv preprint arXiv:2401.16664 (2024).

Poleksic A. Hyperbolic matrix factorization improves prediction of drug-target associations, Nature Scientific Reports, 13(1), 959 (2023)

Poleksic A. Overcoming sparseness of biomedical networks to identify drug repositioning candidates. IEEE/ACM Trans Comput Biol Bioinform 19, 2377-2384 (2022)

Poleksic A. Hyperbolic Matrix Factorization Methods and Systems, US Patent Application 18/067,245 (2022)

Lee B, Zhang S, Poleksic A, Xie L. Heterogeneous multi-layered network model for omics data integration and analysis. Frontiers in Genetics
, 10 (2020): 1381 (2020).

Poleksic A, Xie L. Database of adverse events associated with drugs and drug combinations. Scientific Reports, 9:20025 (2019).
Drug Repurposing for Chronic Pancreatitis- abstract and poster on the results of research study performed by MissionCure, Cincinnati Children’s Hospital Medical Centre, Pistoia Alliance, University of Northern Iowa, Ariel Precision Medicine, and Entellect Elsevier. Presented by Finlay MacLean at PancreasFest 2019, Pittsburgh, PA – July 24-26, 2019.

Poleksic A, Xie L. Predicting serious rare adverse reactions of novel chemicals. Bioinformatics
, 1, 8 (2018)

Lim H, Poleksic A, Xie L. Exploring Landscape of Drug-Target-Pathway-Side Effect Associations. AMIA 2018 Informatics Summit (San Francisco, CA, March 12-15, 2018)

Poleksic A
, Turner C, Dalal R, Gray P, Xie L. Mining FDA resources to compute population-specific frequencies of adverse drug reactions. IEEE International Conference on Bioinformatics and Biomedicine, Kansas City, MO, USA, November 13-16, 2017.

Lim H, Gray P, Xie L, Poleksic A, Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem. Scientific Reports, 6:38860 (2016)

Lim H, Poleksic A, Tong H, He D, Zhuang L, Meng P, Xie L, Large-scale Off-target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing, PLOS Comput Biol, 12(10) e1005135 (2016)

Poleksic A. A polynomial time algorithm for computing the area under a GDT curve, Algorithms for Molecular Biology, 10:27 (2015).

Poleksic A. Detecting non-trivial protein structure relationships, Current Bioinformatics, 11(2):234-242 (2016)

Poleksic A. Towards a better measure of protein 3D model quality. IEEE Xplore® (Best Paper Award at IEEE eit 2015, Naperville, Illinois, May 21-23, 2015).

Poleksic A, Gray P. Utilizing twilight zone sequence similarities to increase the accuracy of protein 3D structure comparison, Proceedings of the Fifth ACM Conference on Bioinformatics, Computational Biology and Health Informatics – ACM BCB 2014 (Newport Beach, CA, September 20 – September 23, 2014).

Poleksic A. Gaussian Network Models for Protein Binding Site Comparison, Proceedings of the International Conference on Numerical Computations: Theory and Algorithms - NUMTA2013, Falerna, Italy (2013).

Arriagada M, Poleksic A. On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem, BioMed Research International, 2013:459248 (2013)

Poleksic A. Improved algorithms for matching r-separated sets with applications to protein structure alignment, IEEE/ACM Trans Comput Biol Bioinform, 10, 226-229 (2013)

Kattnig H, Poleksic A. StructAlignViewer: A software package for visualizing protein structural superpositions and alignments, Proceedings of 16th International Conference on Information Visualization, (IV 2012) p573-577, Montpelier, France (2012)

Arriagada M, Poleksic A. Protein structure alignment: Is there room for improvement?, Proceedings of the 6th International Conference on Complex, Intelligent and Software Intensive Systems- CISIS p597-602, Palermo, Italy, July 4-6, 2012

Poleksic A. On complexity of protein structure alignment problem under distance constraint, IEEE/ACM Trans Comput Biol Bioinform, 9, 511-516 (2012)

Poleksic A. Optimal pairwise alignment of fixed protein structures in sub-quadratic time, Journal of Bioinformatics and Computational Biology, 9, 367-382 (2011)

Poleksic A. Optimizing a widely used protein structure alignment measure in expected polynomial time, IEEE/ACM Trans Comput Biol Bioinform, 8, 1716-20 (2011)

Arriagada M, Poleksic A. On the Accuracy of Protein Tertiary Structure Comparison, 9th annual ISCB Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, Colorado (abstract) December 8-10, 2011.

Poleksic A. Optimal protein structure alignment in sub-quadratic time, Proceedings of BIONETICS'10, Springer Verlag (2010)

Poleksic A. Algorithms for optimal protein structure alignment, Bioinformatics, 25, 2751-2756 (2009)

Poleksic A. Island method for estimating the statistical significance of profile-profile alignment scores, BMC Bioinformatics, 10(1):112 (2009)

Method and system for generating protein sequence alignments, US patent application PCT/US09/49749 (2009)

Poleksic A, Fienup M. Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms, Bioinformatics, 24, 1145-53 (2008)

Poleksic et al. A different look at the quality of modeled three-dimensional protein structures, Journal of Bioinformatics and Computational Biology, 6, 335-45 (2008)

Poleksic A, Analytical approaches to comparative modeling of protein structures, Prot. Res. Journal, 1, 55-68 (2008)

Poleksic A, Danzer JF. Protein side-chain modeling using a combination of knowledge and energy based approaches, Proceedings of the International Conference on Bioinformatics & Computational Biology – BIOCOMP 2007, 378-382

Poleksic A. Method for determining sequence alignment significance, US patent No. 6,988,039 (2006)

Poleksic A, Danzer JF, Olafson BD, Debe DA. SPINFAST: Utilizing Structure Alignment Profiles to Enhance the Accuracy and Assess the Reliability of Protein Sidechain Modeling, Proteins, 65, 953-958 (2006)

Debe DA, Danzer JF, Goddard WA, Poleksic A. STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring, Proteins, 64, 960-967 (2006)

Poleksic A et al. A probabilistic approach to remote homology detection and 3D protein structure modeling -- abstract, Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Pacific Grove, CA, November 26-30, 2006.

Poleksic A, Danzer JF, Hambly K, Debe DA. Convergent Island Statistics: a fast method for determining local alignment score significance. Bioinformatics, 21, 2827-2831 (2005)

Neuwald AF, Kannan N, Poleksic A, Hata N and Liu JS. Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases. Genome Research, 13, 673-92 (2003)

Lipovac MN, Holland T, Poleksic A, Killian C, Lajtha A. The possible role of glutamate uptake in metaphit-induced seizures. Neurochemical Research, 28, 723-731 (2003)

Neuwald AF, Poleksic A. PSI-BLAST searches using hidden Markov models of structural repeats: prediction of an unusual sliding DNA clamp and of β-propellers in UV-damaged DNA-binding protein, Nucleic Acid Research, 28, 3570-358 (2000)

Poleksic, A. Groups acting on quasiconvex spaces and translation numbers, Proceedings of the American Mathematical Society, 128, 3177-3183 (2000)

Poleksic, A. Translation numbers in negatively curved groups, Topology and its applications, 102, 203-205 (2000)

Poleksic, A. The boundary of a quasi-convex space, Topology and its applications, 102, 195-202 (2000)