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1.
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Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li SC, Kaneko T, Schiller MR. Secondary structure, a missing component of sequence-based minimotif definitions. PLoS One. 2012; 7(12):e49957.
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2.
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Mi T, Rajasekaran S, Merlin JC, Gryk M, Schiller MR. Achieving high accuracy prediction of minimotifs. PLoS One. 2012; 7(9):e45589.
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3.
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Dinh H, Rajasekaran S, Davila J. qPMS7: a fast algorithm for finding (l, d)-motifs in DNA and protein sequences. PLoS One. 2012; 7(7):e41425.
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4.
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Mi T, Rajasekaran S, Aseltine R. Efficient algorithms for fast integration on large data sets from multiple sources. BMC Med Inform Decis Mak. 2012; 12:59.
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5.
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Merlin JC, Rajasekaran S, Mi T, Schiller MR. Reducing false-positive prediction of minimotifs with a genetic interaction filter. PLoS One. 2012; 7(3):e32630.
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6.
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Mi T, Merlin JC, Deverasetty S, Gryk MR, Bill TJ, Brooks AW, Lee LY, Rathnayake V, Ross CA, Sargeant DP, Strong CL, Watts P, Rajasekaran S, Schiller MR. Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. Nucleic Acids Res. 2012 Jan; 40(Database issue):D252-60.
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7.
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Dinh H, Rajasekaran S, Kundeti VK. PMS5: an efficient exact algorithm for the (l, d)-motif finding problem. BMC Bioinformatics. 2011; 12:410.
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8.
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Borodovsky M, Przytycka TM, Rajasekaran S, Zelikovsky A. Guest editors' introduction to the special section on bioinformatics research and applications. IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug; 8(4):865-6.
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9.
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Dinh H, Rajasekaran S. A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly. Bioinformatics. 2011 Jul 15; 27(14):1901-7.
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10.
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Rajasekaran S, Dinh H. A speedup technique for (l, d)-motif finding algorithms. BMC Res Notes. 2011; 4:54.
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11.
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Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V. Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs. BMC Bioinformatics. 2010; 11:560.
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12.
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Ranaghan MJ, Shima S, Ramos L, Poulin DS, Whited G, Rajasekaran S, Stuart JA, Albert AD, Birge RR. Photochemical and thermal stability of green and blue proteorhodopsins: implications for protein-based bioelectronic devices. J Phys Chem B. 2010 Nov 11; 114(44):14064-70.
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13.
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Rajasekaran S, Merlin JC, Kundeti V, Mi T, Oommen A, Vyas J, Alaniz I, Chung K, Chowdhury F, Deverasatty S, Irvey TM, Lacambacal D, Lara D, Panchangam S, Rathnayake V, Watts P, Schiller MR. A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. Proteins. 2011 Jan; 79(1):153-64.
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14.
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Rajasekaran S, Al Seesi S, Ammar RA. Improved algorithms for parsing ESLTAGs: a grammatical model suitable for RNA pseudoknots. IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec; 7(4):619-27.
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15.
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Rajasekaran S, Mi T, Merlin JC, Oommen A, Gradie P, Schiller MR. Partitioning of minimotifs based on function with improved prediction accuracy. PLoS One. 2010; 5(8):e12276.
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16.
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Vyas J, Nowling RJ, Meusburger T, Sargeant D, Kadaveru K, Gryk MR, Kundeti V, Rajasekaran S, Schiller MR. MimoSA: a system for minimotif annotation. BMC Bioinformatics. 2010; 11:328.
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17.
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Song M, Rajasekaran S. A greedy algorithm for gene selection based on SVM and correlation. Int J Bioinform Res Appl. 2010; 6(3):296-307.
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18.
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Vyas J, Nowling RJ, Maciejewski MW, Rajasekaran S, Gryk MR, Schiller MR. A proposed syntax for Minimotif Semantics, version 1. BMC Genomics. 2009; 10:360.
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19.
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Rajasekaran S. Computational techniques for motif search. Front Biosci. 2009; 14:5052-65.
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20.
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Trinca D, Rajasekaran S. Optimized bzip2 compression for reducing diffraction effects in protein-based computing: a study of feasibility. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:2783-6.
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21.
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Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR. Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res. 2009 Jan; 37(Database issue):D185-90.
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22.
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Davila J, Balla S, Rajasekaran S. Fast and practical algorithms for planted (l, d) motif search. IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec; 4(4):544-52.
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23.
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Balla S, Rajasekaran S. An efficient algorithm for minimum degeneracy primer selection. IEEE Trans Nanobioscience. 2007 Mar; 6(1):12-7.
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24.
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Trumbower RD, Rajasekaran S, Faghri PD. Identifying offline muscle strength profiles sufficient for short-duration FES-LCE exercise: a PAC learning model approach. J Clin Monit Comput. 2006 Jun; 20(3):209-20.
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25.
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Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR. Minimotif Miner: a tool for investigating protein function. Nat Methods. 2006 Mar; 3(3):175-7.
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26.
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Rajasekaran S, Balla S, Huang CH. Exact algorithms for planted motif problems. J Comput Biol. 2005 Oct; 12(8):1117-28.
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27.
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Huang CH, Lanza V, Rajasekaran S, Dubitzky W. HealthGrid--bridging life science and information technology. J Clin Monit Comput. 2005 Oct; 19(4-5):259-62.
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28.
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Rajasekaran S, Balla S, Huang CH, Thapar V, Gryk M, Maciejewski M, Schiller M. High-performance exact algorithms for motif search. J Clin Monit Comput. 2005 Oct; 19(4-5):319-28.
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29.
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Rajasekaran S, Thapar V, Dave H, Huang CH. Randomized and parallel algorithms for distance matrix calculations in multiple sequence alignment. J Clin Monit Comput. 2005 Oct; 19(4-5):351-9.
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30.
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Huang CH, Rajasekaran S. Parallel pattern identification in biological sequences on clusters. IEEE Trans Nanobioscience. 2003 Mar; 2(1):29-34.
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