Sanguthevar Rajasekaran

Summary

Affiliation: University of Connecticut
Country: USA

Publications

  1. ncbi request reprint High-performance exact algorithms for motif search
    Sanguthevar Rajasekaran
    Department of CSE, University of Connecticut, Storrs, CT 06269, USA
    J Clin Monit Comput 19:319-28. 2005
  2. ncbi request reprint Minimotif Miner: a tool for investigating protein function
    Sudha Balla
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
    Nat Methods 3:175-7. 2006
  3. pmc Reducing false-positive prediction of minimotifs with a genetic interaction filter
    Jerlin C Merlin
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 7:e32630. 2012
  4. pmc PMS: a panoptic motif search tool
    Hieu Dinh
    Computer Science and Engineering Department, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 8:e80660. 2013
  5. pmc Achieving high accuracy prediction of minimotifs
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    PLoS ONE 7:e45589. 2012
  6. pmc Efficient algorithms for biological stems search
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    BMC Bioinformatics 14:161. 2013
  7. pmc A proposed syntax for Minimotif Semantics, version 1
    Jay Vyas
    Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030 3305 USA
    BMC Genomics 10:360. 2009
  8. pmc MimoSA: a system for minimotif annotation
    Jay Vyas
    Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave Farmington, CT 06030 3305, USA
    BMC Bioinformatics 11:328. 2010
  9. pmc A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions
    Sanguthevar Rajasekaran
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269 2155, USA
    Proteins 79:153-64. 2011
  10. doi request reprint Improved algorithms for parsing ESLTAGs: a grammatical model suitable for RNA pseudoknots
    Sanguthevar Rajasekaran
    Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Rd, Unit 2155, Storrs, CT 06269 2155, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:619-27. 2010

Research Grants

  1. Efficient Algorithms for Motif Search
    Sanguthevar Rajasekaran; Fiscal Year: 2010

Collaborators

Detail Information

Publications34

  1. ncbi request reprint High-performance exact algorithms for motif search
    Sanguthevar Rajasekaran
    Department of CSE, University of Connecticut, Storrs, CT 06269, USA
    J Clin Monit Comput 19:319-28. 2005
    ..In this paper we study the problem of identifying meaningful patterns (i.e., motifs) from biological data, the motif search problem...
  2. ncbi request reprint Minimotif Miner: a tool for investigating protein function
    Sudha Balla
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
    Nat Methods 3:175-7. 2006
    ..Functional motifs predicted by MnM can be ranked by several approaches, and we validated these scores by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifs in EFF-1...
  3. pmc Reducing false-positive prediction of minimotifs with a genetic interaction filter
    Jerlin C Merlin
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 7:e32630. 2012
    ..Any new approach that reduces false-positives will be of great help to biologists...
  4. pmc PMS: a panoptic motif search tool
    Hieu Dinh
    Computer Science and Engineering Department, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 8:e80660. 2013
    ..Identification of DNA/Protein motifs is a crucial problem for biologists. Computational techniques could be of great help in this identification. In this direction, many computational models for motifs have been proposed in the literature...
  5. pmc Achieving high accuracy prediction of minimotifs
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    PLoS ONE 7:e45589. 2012
    ..The minimotif multi-filter with its excellent accuracy represents the state-of-the-art in minimotif prediction and is expected to be very useful to biologists investigating protein function and how missense mutations cause disease...
  6. pmc Efficient algorithms for biological stems search
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    BMC Bioinformatics 14:161. 2013
    ..Kuksa and Pavlovic have presented an efficient algorithm to find motif stems for inputs from large alphabets. Ideally, the number of stems output should be as small as possible since the stems form a superset of the motifs...
  7. pmc A proposed syntax for Minimotif Semantics, version 1
    Jay Vyas
    Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, CT 06030 3305 USA
    BMC Genomics 10:360. 2009
    ..With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation...
  8. pmc MimoSA: a system for minimotif annotation
    Jay Vyas
    Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Ave Farmington, CT 06030 3305, USA
    BMC Bioinformatics 11:328. 2010
    ..Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature...
  9. pmc A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions
    Sanguthevar Rajasekaran
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut 06269 2155, USA
    Proteins 79:153-64. 2011
    ..This tool also can be used to reduce false-positive predictions in the discovery of novel minimotifs. The statistical significance of these algorithms is demonstrated by an ROC analysis (P = 0.001)...
  10. doi request reprint Improved algorithms for parsing ESLTAGs: a grammatical model suitable for RNA pseudoknots
    Sanguthevar Rajasekaran
    Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Rd, Unit 2155, Storrs, CT 06269 2155, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:619-27. 2010
    ..Our algorithm for ESLTAGs parsing takes O(min{m,n⁴}) time and O(min{m,n⁴}) space. We show that these algorithms perform better, in practice, than the algorithms of Uemura et al...
  11. pmc A speedup technique for (l, d)-motif finding algorithms
    Sanguthevar Rajasekaran
    Department of CSE, University of Connecticut, Storrs, CT 06269, USA
    BMC Res Notes 4:54. 2011
    ..abstract:..
  12. ncbi request reprint Computational techniques for motif search
    Sanguthevar Rajasekaran
    Dept of CSE, University of Connecticut, Storrs, CT 06269 2155, USA
    Front Biosci (Landmark Ed) 14:5052-65. 2009
    ..Thus it is vital to develop efficient techniques to identify motifs. In this paper we survey some of the techniques that have been proposed in the literature for motifs identification...
  13. pmc Minimotif miner 2nd release: a database and web system for motif search
    Sanguthevar Rajasekaran
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06029 2155, USA
    Nucleic Acids Res 37:D185-90. 2009
    ..A sample analysis of prion shows how MnM 2 can be used. Weblink: http://mnm.engr.uconn.edu, weblink for version 1 is http://sms.engr.uconn.edu...
  14. pmc Partitioning of minimotifs based on function with improved prediction accuracy
    Sanguthevar Rajasekaran
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 5:e12276. 2010
    ..As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions...
  15. ncbi request reprint Randomized and parallel algorithms for distance matrix calculations in multiple sequence alignment
    Sanguthevar Rajasekaran
    School of Computer Science and Engineering, Harvard University, Boston, MA, USA
    J Clin Monit Comput 19:351-9. 2005
    ..We show that our algorithms are amenable to parallelism in Section. In Section we back up our claim of speedup and accuracy with empirical data and examples. In Section we provide some concluding remarks...
  16. ncbi request reprint Exact algorithms for planted motif problems
    S Rajasekaran
    Department of CSE, University of Connecticut, Storrs, CT 06269, USA
    J Comput Biol 12:1117-28. 2005
    ..Our algorithms are very simple and are based on some ideas that are fundamentally different from the ones employed in the literature. We believe that the techniques we introduce in this paper will find independent applications...
  17. ncbi request reprint Fast and practical algorithms for planted (l, d) motif search
    Jaime Davila
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 3155, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:544-52. 2007
    ..In particular, one of the proposed algorithms, PMSprune, is able to solve the challenging instances, such as (17, 6) and (19, 7), which were not previously reported as solved in the literature...
  18. ncbi request reprint Parallel pattern identification in biological sequences on clusters
    Chun Hsi Huang
    Department of Computer Science and Engineering, U 155, University of Connecticut, Storrs, CT 06269, USA
    IEEE Trans Nanobioscience 2:29-34. 2003
    ..The low communication overhead of the algorithm is essential in achieving reasonable speedups on clusters, where the inter-processor communication latency is usually higher...
  19. pmc qPMS7: a fast algorithm for finding (ℓ, d)-motifs in DNA and protein sequences
    Hieu Dinh
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 7:e41425. 2012
    ..engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com...
  20. pmc PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem
    Hieu Dinh
    Department of CSE, University of Connecticut, Storrs, CT 06269, USA
    BMC Bioinformatics 12:410. 2011
    ..They are helpful in finding transcriptional regulatory elements, transcription factor binding sites, and so on. As a result, the problem of identifying motifs is very crucial in biology...
  21. ncbi request reprint Efficient sequential and parallel algorithms for planted motif search
    Marius Nicolae
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    BMC Bioinformatics 15:34. 2014
    ..Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances...
  22. pmc Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 2155, USA
    Nucleic Acids Res 40:D252-60. 2012
    ..This online database can be used to predict new functions in proteins and causes of disease...
  23. doi request reprint Optimized bzip2 compression for reducing diffraction effects in protein-based computing: a study of feasibility
    Dragoş Trincă
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:2783-6. 2009
    ..In this paper, we propose an algorithm for coping with diffraction effects, thus providing a solution to a long-standing problem...
  24. ncbi request reprint Efficient sequential and parallel algorithms for record linkage
    Abdullah Al Mamun
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA
    J Am Med Inform Assoc 21:252-62. 2014
    ..In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms...
  25. pmc A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly
    Hieu Dinh
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
    Bioinformatics 27:1901-7. 2011
    ..In this article, we propose a novel data structure using which the overlap graph can be compactly stored. This data structure requires only linear time to construct and and linear memory to store...
  26. pmc Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
    Vamsi K Kundeti
    Department of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way, U 2155, Storrs, CT 06269, USA
    BMC Bioinformatics 11:560. 2010
    ..Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ) messages (Σ being the size of the alphabet)...
  27. ncbi request reprint A greedy algorithm for gene selection based on SVM and correlation
    Mingjun Song
    Department of Computer Science and Engineering, University of Connecticut, Storrs 06269, CT, USA
    Int J Bioinform Res Appl 6:296-307. 2010
    ..Experiments show that the new algorithm, called GCI-SVM, obtains a higher classification accuracy using a smaller number of selected genes than the well-known algorithms in the literature...
  28. ncbi request reprint An efficient algorithm for minimum degeneracy primer selection
    Sudha Balla
    Computer Science and Engineering Department, University of Connecticut, Storrs, CT 06269 2155, USA
    IEEE Trans Nanobioscience 6:12-7. 2007
    ..Our algorithm combines methodologies in motif discovery and an iterative technique to design the primer...
  29. pmc Efficient algorithms for fast integration on large data sets from multiple sources
    Tian Mi
    Department of Computer Science and Engineering, University of Connecticut Storrs, Connecticut, USA
    BMC Med Inform Decis Mak 12:59. 2012
    ..Several algorithms have been proposed in the literatures that are adept in integrating records from two different datasets. Our algorithms are aimed at integrating multiple (in particular more than two) datasets efficiently...
  30. ncbi request reprint HealthGrid--bridging life science and information technology
    Chun Hsi Huang
    Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
    J Clin Monit Comput 19:259-62. 2005
  31. ncbi request reprint Border length minimization problem on a square array
    Vamsi Kundeti
    Computer Science and Engineering Department, University of Connecticut, Storrs, CT
    J Comput Biol 21:446-55. 2014
    ..We also present a hierarchical refinement algorithm that can refine any heuristic solution for the BLMP and prove that the TSP+1-threading heuristic is an O(N)-approximation. ..
  32. ncbi request reprint Identifying offline muscle strength profiles sufficient for short-duration FES-LCE exercise: a PAC learning model approach
    Randy D Trumbower
    Sensory Motor Performance Program, Rehabilitation Institute of Chicago and Northwestern University, Storrs, CT, USA
    J Clin Monit Comput 20:209-20. 2006
    ..However, there exists no systematic approach to predict whether an individual has sufficient thigh muscle strength necessary for FES-LCE exercise...
  33. pmc Efficient techniques for genotype-phenotype correlational analysis
    Subrata Saha
    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA
    BMC Med Inform Decis Mak 13:41. 2013
    ..In this paper, we propose efficient, scalable, and reliable algorithms to select a small subset of SNPs from a large set of SNPs which can together be employed to perform phenotypic classification...
  34. pmc Photochemical and thermal stability of green and blue proteorhodopsins: implications for protein-based bioelectronic devices
    Matthew J Ranaghan
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269, USA
    J Phys Chem B 114:14064-70. 2010
    ..The biological relevance of our results is also discussed. The lower cyclicity of BPR is found to be adequate for the long-term biological function of the host organism at ocean depths of 50 m or more...

Research Grants1

  1. Efficient Algorithms for Motif Search
    Sanguthevar Rajasekaran; Fiscal Year: 2010
    ..Open source versions of all the algorithms and data developed will be made available to users. In addition, the web system will support online processing of queries that involve the solution of PMS and EMS. ..