Software tools for Biological discovery.
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Lyon KF, Cai X, Young RJ, Mamun AA, Rajasekaran S, Schiller MR. (2017). Minimotif Miner 4: a million peptide minimotifs and counting. Nucleic Acids Res., Epub ahead of print, PMID: 29140456
Schiller MR. (2016). The Minimotif Synthesis Hypothesis for the Origin of Life. J. of Translational Sci., 2, 289-296. PMID: 28083146 PDF
Sharma S, Toledo O, Hedden M, Lyon KF, Brooks S, David RP, Limtong J, Newsome J, Rajasekaran S, Thapar V, Williams S, and Schiller MR . (2016). The Human C-terminome. PLOS One, 11, e0152731. PMID: 27050421 PDF
Lyon K, Strong CL, Schooler S, Young R, Roy N, Ozar B, Bachmeier M, Rajasekaran S, Schiller M,. (2015). Natural variability of minimotifs in 1,092 people indicates that minimotifs are targets of evolution. Nucleic Acids Res., pii, gkv580. PMID: 26068475 PDF
Pathak S, Kundeti VK, Schiller MR, and Rajasekaran S. (2013). A Structure Based Algorithm for Improving Motifs Prediction. Pattern Recognition in Bioinformatics, 7986, 242-252. PDF
Merlin JC, Rajasekaran S, Mi T, and Schiller MR. (2012). Reducing false-positive prediction of minimotifs with a genetic interaction filter. PLoS One, 7, e32630. PMID: 22403687 PDF
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. (2012). Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.. Nucleic Acids Res., 40 (Database issue), D252-60. PMID: 22146221 PDF
Li L, Tibiche C., Fu C, Kaneko T, Moran MF, Schiller MR, Li SS, Wang E. (2012). The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer.. Genome Res., 22, 1222-30. PMID: 22194470 PDF
Mi T, Rajasekaran S, Merlin JC, Gryk M, Schiller MR.. (2012). Achieving High Accuracy Prediction of Minimotifs.. PLoS One. , 7, e45589. PMID: 23029121 PDF
Sargeant DP, Gryk MR, Maciejewski MW, Thapar V, Kundeti V, Rajasekaran S, Romero P, Dunker K, Li S-C, Kaneka T, and Schiller MR. (2012). Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions. PLoS One, 7, e49957. PMID: 23236358 PDF
Jay Vyas, Ronald J.Nowling, Thomas Meusberger, David Sargeant, Krishna Kadaveru. Michael R. Gryk, Vamsi Kundeti Sanguthevar Rajasekaran and Martin R. Schiller. (2010). MimoSA: a system for minimotif annotation. BMC Bioinformatics, 11, 328. PMID: 19656955 PDF
Rajasekaran S, Mi T, Camilus J, Vyas J, Schiller MR. (2010). Partitioning of Minimotifs Based on Function with Improved Prediction Accuracy. Plos One, 19, pii: e12276. 20808856 PDF
Kundeti V, Rajasekaran S, and Schiller MR. (2010). Algorithms for local structural alignment and structural motif identification. Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, Wiley Series in Bioinformatics, Summary PDF
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. (2010). A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. Proteins, 79, 153-164. PMID: 20938975 PDF
Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR. (2009). Minimotif Miner 2nd release: a database and web system for motif search. Nucleic. Acids Res., 37, D185-190. PMID: 18978024 PDF
Vyas J, Nowling RJ, Maciejewski MW, Rajasekaran S, Gryk MR, and Schiller MR. (2009). A Proposed Syntax for Minimotif Semantics, Version 1. BMC Genomics., 10, 360. PMID: 19656396 PDF
Krishna Kadaveru K, Vyas J, and Schiller MR. (2008). Viral infection and human disease - insights from minimotifs. Front. Biosci., 6455-6471. PMID: 18508672 PDF
Schiller MR*. (2007). Minimotif Miner, a computational tool to investigate protein function, disease, and genetic diversity. Current Protocols in Protein Science, Eds. Coligan JE, Dunn BM, Speicher DW, Winkler H., Unit 2.12.1 - 2.12.14. PMID: 18429315 PDF
Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang C-H, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, and Schiller MR. (2006). Minimotif Miner, a tool for investigating protein function.. Nat. Methods, 3, 175-177. PMID: 16489333 PDF
Rajasekaran S, Balla S, Huang C, Thapar C, Gryk M, Maciejewski M, and Schiller M.. (2005). High Performance Algorithms for Motif Search. J. Clin. Mon. Comp., 19, 319-328. PMID: 16328946 PDF