My research focuses on computational analysis of DNA, proteins and small molecules. In particular, I am interested in:

• Protein and DNA remote homology detection
• Computational protein structure determination
• Computational analysis of small molecule similarities

Prior to joining UNI, I was a Senior Scientist at Eidogen-Sertanty, Inc., a San-Diego based biotech company. My research at Eidogen focused on computational protein structure determination.

Recent publications:

• 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 (with M. Fienup) (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).

• UNI-FOLD: Increasing the accuracy of protein sequence alignments generated by profile-profile methods, provisional patent application (with M. Fienup) (2008).

• Poleksic A, Danzer JF, Protein side-chain modeling using a combination of knowledge and energy based approaches, Proceedings of the 2007 International Conference on Bioinformatics & Computational Biology, Las Vegas, Nevada, USA (2007).

• 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)

• Method for determining sequence alignment significance, US patent No. 6,988,039, International patent No. WO2004074990 (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)

• Aleksandar Poleksic, Joseph F. Danzer, Kevin Hambly, Derek A. Debe, Convergent Island Statistics: a fast method for determining local alignment score significance. Bioinformatics, 21, 2827-2831 (2005)