Convergent Island Statistics: a fast method for determining local alignment score significance. - Aleksandar Poleksic; Joseph F. Danzer; Kevin Hambly; Derek A. Debe (Bioinform., 2005)

Protein side-chain modeling using a combination of knowledge and energy based approaches. - Aleksandar Poleksic; Joseph F. Danzer (BIOCOMP, 2007)

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms. - Aleksandar Poleksic; Mark A. Fienup (Bioinform., 2008)

A Different Look at the Quality of Modeled Three-Dimensional protein Structures. - Aleksandar Poleksic; Mark A. Fienup; Joseph F. Danzer; Derek A. Debe (J. Bioinform. Comput. Biol., 2008)

Algorithms for optimal protein structure alignment. - Aleksandar Poleksic (Bioinform., 2009)

Island method for estimating the statistical significance of profile-profile alignment scores. - Aleksandar Poleksic (BMC Bioinform., 2009)

Protein Structure Alignment in Subquadratic Time. - Aleksandar Poleksic (BIONETICS, 2010)

Optimal Pairwise Alignment of Fixed protein Structures in Subquadratic Time. - Aleksandar Poleksic (J. Bioinform. Comput. Biol., 2011)

Optimizing a Widely Used Protein Structure Alignment Measure in Expected Polynomial Time. - Aleksandar Poleksic (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Protein Structure Alignment: Is There Room for Improvement? - Mauricio Arriagada; Aleksandar Poleksic (CISIS, 2012)

Visualizing Protein Structural Superpositions and Alignments with StructAlignViewer. - Harald Kattnig; Aleksandar Poleksic (IV, 2012)

On Complexity of Protein Structure Alignment Problem under Distance Constraint. - Aleksandar Poleksic (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Improved Algorithms for Matching r-Separated Sets with Applications to Protein Structure Alignment. - Aleksandar Poleksic (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Utilizing twilight zone sequence similarities to increase the accuracy of protein 3D structure comparison. - Aleksandar Poleksic; Paul Gray (BCB, 2014)

Towards a better measure of protein 3D model quality. - Aleksandar Poleksic (EIT, 2015)

A polynomial time algorithm for computing the area under a GDT curve. - Aleksandar Poleksic (Algorithms Mol. Biol., 2015)

Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. - Hansaim Lim; Aleksandar Poleksic; Yuan Yao 001; Hanghang Tong; Di He 003; Luke Zhuang; Patrick Meng; Lei Xie 006 (PLoS Comput. Biol., 2016)

Mining FDA resources to compute population-specific frequencies of adverse drug reactions. - Aleksandar Poleksic; Carson Turner; Rishabh Dalal; Paul Gray; Lei Xie (BIBM, 2017)

Predicting serious rare adverse reactions of novel chemicals. - Aleksandar Poleksic; Lei Xie (Bioinform., 2018)

Overcoming Sparseness of Biomedical Networks to Identify Drug Repositioning Candidates. - Aleksandar Poleksic (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Optimization in Hyperbolic Space - Applications to Drug-Target Interaction Prediction. - Aleksandar Poleksic (NUMTA (1), 2023)

Utilizing Comprehensive Biological Network to Improve Accuracy of Computational Drug Repurposing. - Aleksandar Poleksic (BIBM, 2024)

Fast Dual-Regularized Autoencoder for Sparse Biological Data. - Aleksandar Poleksic (CoRR, 2024)