Arun S. konagurthu

अरुण सिद्धार्थ कोनगुर्तुhttp://en.wikipedia.org/wiki/Devanagari
అరుణ్ సిద్ధార్థ కొనగుర్తు http://en.wikipedia.org/wiki/Telugu_alphabet
 


Invited Book Chapters


  1. ✦ A. S. Konagurthu, A. M. Lesk, Canonical Network Motifs: Formal Definitions and Enumeration Algorithms. Encyclopedia of Systems Biology (Springer) 2013 [Book link]


  1. ✦ A. S. Konagurthu, A. M. Lesk, Structure description and identification using the tableau representation of protein folding patterns. Protein Supersecondary Structures (Springer Protocols) 2013 [Book link]


Refereed Journal publications


  1. ✦ A. S. Konagurthu, , R. Subramanian, L. Allison, D. Abramson, P. J. Stuckey, M. Garcia de la Banda, and A. M. Lesk. Universal architectural concepts underlying protein folding patterns. Frontiers in Molecular Biosciences 7:612920 (2021). [BioRXiv preprint] [open acess article]


  1. ✦ A. M. Lesk, and A. S. Konagurthu, Paths Through the Yeast Regulatory Network in Different Physiological States. Journal of Molecular Biology (Elsevier) 433 (21), 1671818 (2021). [PDF]


  1. ✦ A. M. Lesk, and A. S. Konagurthu, Neighbourhoods in the Yeast Regulatory Network in Different Physiological States. Bioinformatics (Oxford Univeristy Press) 37 (4), 551-558 (2021). [PDF]


  1. ✦ A. M. Lesk, A. S. Konagurthu, L. Allison, M. Garcia de la Banda, P. Stuckey, and D. Abramson, Computer modelling of a potential agent against SARS-Cov-2 (COVID-19) protease. Proteins 88(12):1557-1558 (Brief communication)


  1. ✦ D. Sumanaweera, L. Allison, and A. S. Konagurthu, Statistical Compression of Protein Sequences and Inference of Marginal Probability Landscapes over Competing Alignments using Finite State Models and Dirichlet Priors. Bioinformatics (Oxford University Press) 35 (14): i360-i369 (2019) -- ISMB/ECCB 2019 issue. [PDF] [Abstract] [software page]
    News: Dinithi won the ISCB's 2019 Ian Lawson Van Toch Memorial Award for Outstanding Student Paper [photo]


  1. ✦ J. H. Collier, L. Allison, A. M. Lesk, P. J. Stuckey, M. Garcia de la Banda, A. S. Konagurthu, Statistical inference of protein structural alignments using information and compression. Bioinformatics (Oxford University Press) 33(7): 1005-10013 (2017) [PDF] [Abstract] [BioRxiv preprint] [MMLigner software page]


  1. ✦  A. S. Konagurthu, P. Kasarapu, L. Allison, J. H. Collier, A. M. Lesk, On sufficient statistics of least-squares superposition of vector sets. Journal of Computational Biology 20(6): 487-497 (2015) (selected RECOMB 2014 papers special issue. This reviewed journal version supersedes the version published in the proceedings of the conference) [PDF] [Superpose3D software]


  1. ✦  P. Kasarapu, M. Garcia de la Banda, A. S. Konagurthu, On representing protein folding patterns using non-linear parametric curves, IEEE/ACM Transactions on Computational Biology and Bioinformatics 11(6):1218-1228 (2014)


  1. ✦ J. H. Collier, L. Allison, A. M. Lesk, M. Garcia de la Banda, A. S. Konagurthu, A new statistical framework to assess structural alignment quality using information compression. Bioinformatics (Oxford University Press) 30(17): i512-i518 (2014) [PDF] [Abstract]


  1. ✦ A. S. Konagurthu, L. Allison, D. Abramson, P. J. Stuckey, A. M. Lesk, How precise are reported protein coordinate data? Acta Crystallographica Section D: Biological Crystallography (International Union of Crystallography (IUCr)) (Short Communication)  D70, 904-906  (2014)


  1. ✦ A. S. Konagurthu,  A. M. Lesk,  L. Allison, Minimum Message Length inference of secondary structure from protein coordinate data. Bioinformatics (Oxford University Press) 28(12):i97-105 (2012) [PDF] [Abstract]


  1. ✦ J. H. Collier, A. M. Lesk, M. Garcia de la Banda, A. S. Konagurthu, Super: A web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank. Nucleic Acids Research (Oxford University Press) 40(W1): 334-339 (2012) [PDF] [Open access link]


  1. ✦ K. Mahmood, G. Webb, J. Song, J. C. Whisstock, A. S. Konagurthu, Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs.  Nucleic Acids Research (Oxford University Press) 40(6):e44 (2012) [PDF]


  1. ✦ A. S. Konagurthu, L. Allison, P. J. Stuckey, A. M. Lesk, Piecewise Linear Approximation of Protein Structures using the Principle of Minimum Message Length. Bioinformatics (Oxford University Press) 27(13): i43-i51 (2011) [PDF]


  1. ✦ K. Mahmood, A. S. Konagurthu, J. Song, A. Buckle, G. Webb, J. C.  Whisstock, EGM: Encapsulated Gene-by-Gene Matching to Identify Gene Orthologs and Homologous Segments in Genomes. Bioinformatics (Oxford University Press) 26(17): 2076-2084 (2010)  [PDF] [Abstract]


  1. ✦ A. S. Konagurthu, C. F. Reboul, J. W. Schmidberger, J. Irving, A. M. Lesk, P. J. Stuckey, J. C. Whisstock, MUSTANG-MR Structural sieving server: Applications in Protein Structural Analysis and Crystallography. PLoS One (Public Library of Science) 5(4):e10048 (2010). [PDF]  [Open access link]


  1. ✦ A. S. Konagurthu, A. M. Lesk, Cataloging topologies of protein folding patterns,  Journal of Molecular Recognition (John Wiley publishers) 23(2):253-257 (2010). [PDF] [Abstract]


  1. ✦ L. Zhang, J. Bailey, A. S. Konagurthu, R. Kotagiri, A fast indexing approach for protein structure comparison.  BMC Bioinformatics (BioMed Central)  11(S1):46 (2010). (Selected article from APBC 2010) [PDF] [Open access link]


  1. ✦ A. S. Konagurthu, A. M. Lesk, On the origin of distribution patterns of motifs in Biological networks. BMC Systems Biology (BioMed Central) 2:73 (2008). [PDF] [Open access link]


  1. ✦ A. S. Konagurthu, A. M. Lesk, Single and multiple input modules in regulatory networks. Proteins (John Wiley publishers) 73(2): 320-324 (2008). [PDF] [Abstract]


  1. ✦ A. S. Konagurthu, P. J. Stuckey, A. M. Lesk, Structural search and retrieval using tableau representation of protein folding patterns. Bioinformatics (Oxford University Press) 24:645-661 (2008). [PDF]


  1. ✦ A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk, MUSTANG: A multiple structural alignment algorithm. Proteins (John Wiley publishers) 64(3): 559-574 (2006). [PDF] [Abstract]


  1. ✦ A. S. Konagurthu, P. J. Stuckey, Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo-and-Lipman bounds. Journal of Computational Biology (May Ann Liebert publishers) 13(3): 668-685 (2006).  [PDF] [Abstract]


  1. ✦ A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, Progressive multiple alignment using sequence triplet optimizations and three-residue exchange costs. Journal of Bioinformatics and Computational Biology (Imperial College Press), 2(4):719-745 (2004). [PDF]



Refereed Conferences


  1. ✦ D. Sumanaweera, L. Allison, A. S. Konagurthu, Bridging the Gaps in Statistical Models of Protein Alignment, Thirtieth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2022 July 10-14 Madison, USA) (Acceptance rate: 19.7%; Acceptance data: 6/4/22)


  1. ✦ S. Rajapaksa, D. Sumanaweera, A. M. Lesk, L. Allison, P. Stuckey, M. Garcia de la Banda, P. Stuckey, D. Abramson, A. S. Konagurthu, On the reliability and limits of protein sequence alignments. Thirtieth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2022 July 10-14 Madison, USA) (Acceptance rate: 19.8%; Acceptance date: 6/4/22) Thirtieth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2022 July 10-14 Madison, USA) (Acceptance rate: 19.8%; Acceptance date: 6/4/22)


  1. ✦ L. Allison, D.Schidt, A. S. Konagurthu, On Universal Codes for Integers: Wallace Tree, Elias Omega and Beyond. In Proceedings of the Thirty-First IEEE Data Compression Conference (DCC2021 March 23-26, 2021, held online due to COVID-19) [PDF]


  1. ✦ S. Rajapaksa, D. Sumanaweera, M. Garcia de la Banda, P. Stuckey, D. Abramson, L. Allison, A.M. Lesk, A. S. Konagurthu, On identifying statistical redundancy at the level of amino acid subsequences. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2021) pages 64-71 (2021), doi:10.1109/BIBM52615.2021.9669282, BIBM 2021 Dec 9-12, held online due to COVID-19) (Acceptance rate: 19.6%)


  1. ✦ D. Sumanaweera, L. Allison, A. S. Konagurthu, Statistical Compression of Protein Sequences and Inference of Marginal Probability Landscapes over Competing Alignments using Finite State Models and Dirichlet Priors. Twenty Seventh Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2019 July 21-26 Basel, Switzerland) (Acceptance rate: 19%) [PDF]


  1. ✦ D. Sumanaweera, L. Allison, A. S. Konagurthu, The bits between proteins. In the Proceedings of the Twenty-eighth IEEE Data Compression Conference (DCC2018 March 27-30, 2018, Salt Lake City (UT), USA) [PDF]


  1. ✦ R. Subramanian, L. Allison, P. J. Stuckey, M. Garcia de la Banda, D. Abramson, A. M. Lesk, A. S. Konagurthu, Statistical compression of protein folding patterns and inference of recurrent substructural themes. In the Twenty-seventh IEEE Data Compression Conference (DCC2017 April 4-7, 2017, Salt Lake City (UT), USA) [PDF]


  1. ✦ J. H. Collier, L. Allison, A. M. Lesk, M. Garcia de la Banda, A. S. Konagurthu, A new statistical framework to assess structural alignment quality using information compression. In the Thirteenth Annual European Conference on Computational Biology (ECCB 2014 Sept 7-10, 2014, Strasbourg, France) (Acceptance rate: 15%) [PDF]


  1. ✦ A. S. Konagurthu, P. Kasarapu, L. Allison, J. H. Collier, A. M. Lesk, On sufficient statistics of least-squares superposition of vector sets. In the Eighteenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2014, Apr 2-5 2014 Pittsburgh (PA), USA) LNCS/LNBI 8394: 144-159  (Acceptance rate: 22%) [PDF]


  1. ✦ A. S. Konagurthu, A. M. Lesk, D. Abramson, P. J. Stuckey, L. Allison, Statistical Inference of protein “LEGO Bricks”. In the Thirteenth IEEE International Conference on Data Mining (ICDM 2013, Dec 7-10 2013 Dallas (TX), USA) (Acceptance rate: 19%) [PDF]


  1. ✦ A. S. Konagurthu, A. M. Lesk,  L. Allison, Minimum Message Length Inference of Secondary Structure from Protein Coordinate Data.  In the Twentieth Annual International Conference on Intelligent Systems for Molecular Biology, (ISMB 2012 July 15-17 2012 Long Beach (CA), USA). (Acceptance rate: 13%)  [PDF]


  1. ✦ A. S. Konagurthu, L. Allison, P. J. Stuckey, A. M. Lesk, Piecewise Linear Approximation of Protein Structures using the Principle of Minimum Message Length.  In the Nineteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2011 July 17-19 Vienna, Austria)  (Acceptance rate: 17%)  [PDF]


  1. ✦ A. S. Konagurthu, L. Allison, T. Conway, B. Beresford-Smith, J. Zobel, Design of an efficient out-of-core read alignment algorithm. In the Tenth international Workshop on Algorithms in Bioinformatics (WABI 2010, Sept 6-8 Liverpool, UK) LNCS/LNBI 6293: 189-201 [PDF]


  1. ✦ L. Zhang, J. Bailey, A. S. Konagurthu, R. Kotagiri, A fast indexing approach for protein structure comparison. In the Eighth Asia Pacific Bioinformatics Conference (APBC 2010, Jan 18-21 Bangalore, India)  [PDF]



ArXiv/BioRxiv Preprints


  1. ✦ D. Sumanaweera, L. Allison, and A. S. Konagurthu. Bridging the Gaps in Statistical Models of Protein Alignment, 2020 [ArXiv preprint]


  1. ✦ L. Allison, A. S. Konagurthu, D. Schmidt. On Universal Codes for Integers: Wallace Tree, Elias Omega and Variations, 2019 [ArXiv preprint]


  1. ✦ A. M. Lesk, R. Subramanian, L. Allison, D. Abramson, P. J. Stuckey, M. Garcia de la Banda, A. S. Konagurthu, Universal architectural concepts underlying protein folding patterns. 2018. [BioRxiv preprint page]


  1. ✦ J. H. Collier, L. Allison, A. M. Lesk, P. J. Stuckey, M. Garcia de la Banda, A. S. Konagurthu, Statistical inference of protein structural alignments using information and compression. 2016. (This preprint is superseded by a version accepted for publication in the OUP journal, Bioinformatics) [BioRxiv preprint page]


    1. ✦ A. S. Konagurthu, A. M. Lesk, D. Abramson, P. J. Stuckey, L. Allison, Statistical Inference of a canonical dictionary of protein substructural fragments. 2013. (This forms the expanded version of the short paper published in the proceedings of 13th  IEEE International Conference on Data Mining (ICDM 2013, Dec 7-10 2013, Dallas (Tx) USA)) [ArXiv preprint page]


    1. ✦ A. S. Konagurthu, J. Collier. An information measure for comparing top k lists. 2013. (This preprint is superseded by a version published in the proceedings of the 10th IEEE  International Conference on eScience (IEEE eScience 2014, Oct 20-14 2014 Sao paulo, Brazil)) [ArXiv preprint page]


    Thesis


    1. ✦ A. S. Konagurthu, Multiple sequence and structural alignment problems in biology, PhD Thesis (Computer Science) University of Melbourne, March 2006. (Thesis nominated for the Australasian Distinguished Doctoral Dissertation Award, 2007)