20042020

Research output per year

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Research Output

Conference Paper

An information measure for comparing top k lists

Collier, J. & Konagurthu, A. S., 2014, Proceedings 2014 IEEE 10th International Conference on eScience (eScience 2014). Medeiros, C. B. (ed.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 127 - 134 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

Design of an efficient out-of-core read alignment algorithm

Konagurthu, A. S., Allison, L., Conway, T., Beresford-Smith, B. & Zobel, J., 2010, Proceedings of the 10th International Workshop on Algorithms in Bioinformatics. Moulton, V. & Singh, M. (eds.). Berlin Germany: Springer-Verlag London Ltd., Vol. 6293. p. 189 - 201 13 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2 Citations (Scopus)

On sufficient statistics of least-squares superposition of vector sets

Konagurthu, A. S., Kasarapu, P., Allison, L., Collier, J. H. & Lesk, A. M., 2014, Research in Computational Molecular Biology: 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings. Sharan, R. (ed.). Cham [Switzerland]: Springer, p. 144 - 159 16 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperOtherpeer-review

5 Citations (Scopus)

Statistical Compression of Protein Folding Patterns for Inference of Recurrent Substructural Themes

Subramanian, R., Allison, L., Stuckey, P. J., de la Banda, M. G., Abramson, D., Lesk, A. M. & Konagurthu, A. S., 8 May 2017, Proceedings - DCC 2017, 2017 Data Compression Conference: 4 - 7 April 2017, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Piscataway, NJ: IEEE, Institute of Electrical and Electronics Engineers, p. 340-349 10 p. 7923707. (Data Compression Conference. Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

3 Citations (Scopus)

Statistical inference of protein 'LEGO bricks'

Konagurthu, A. S., Allison, L., Abramson, D. A., Stuckey, P. J. & Lesk, A. M., 2013, Proceedings, IEEE 13th International Conference on Data Mining. Xiong, H., Karypis, G., Thuraisingham, B., Cook, D. & Wu, X. (eds.). Los Alamitos CA USA: IEEE, Institute of Electrical and Electronics Engineers, p. 1091 - 1096 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

1 Citation (Scopus)

The bits between proteins

Sumanaweera, D., Allison, L. & Konagurthu, A. S., 27 Mar 2018, Proceedings: DCC 2018 - 2018 Data Compression Conference. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 177-186 10 p. (Data Compression Conference Proceedings; vol. 2018-March).

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

1 Citation (Scopus)
Chapter (Book)

Canonical network motifs

Konagurthu, A. S. & Lesk, A. M., 2013, Encyclopedia of Systems Biology. Dubitzky, W., Wolkenhauer, O., Cho, K-H. & Yokota, H. (eds.). Berlin Germany: Springer, p. 167 - 170 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Other

Information-theoretic inference of an optimal dictionary of protein supersecondary structures

Konagurthu, A. S., Subramanian, R., Allison, L., Abramson, D., de la Banda, M. G., Stuckey, P. J. & Lesk, A. M., 2019, Protein Supersecondary Structures: Methods and Protocols. E. Kister, A. (ed.). 2nd ed. New York NY USA: Springer, p. 123-131 9 p. (Methods in molecular biology (Clifton, N.J.); vol. 1958).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

1 Citation (Scopus)

Structure description and identification using the tableau representation of protein folding patterns

Konagurthu, A. S. & Lesk, A. M., 2013, Protein Supersecondary Structures. Kister, A. E. (ed.). New York NY USA: Humana Press, p. 51 - 59 9 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

2 Citations (Scopus)
Article

A fast indexing approach for protein structure comparison

Zhang, L., Bailey, J., Konagurthu, A. S. & Ramamohanarao, K., 2010, In : BMC Bioinformatics. 11, S1, p. 1 - 9 9 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

A new statistical framework to assess structural alignment quality using information compression

Collier, J., Allison, L., Lesk, A. M., Garcia De La Banda, M. J. & Konagurthu, A. S., 2014, In : Bioinformatics. 30, 17, p. 512 - 518 7 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Cataloging topologies of protein folding patterns

Konagurthu, A. S. & Lesk, A. M., 2010, In : Journal of Molecular Recognition. 23, 2, p. 253 - 257 5 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

Mahmood, K., Webb, G. I., Song, J., Whisstock, J. C. & Konagurthu, A. S., 2012, In : Nucleic Acids Research. 40, 6 (Art. ID: e44), p. 1 - 11 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
17 Citations (Scopus)

EGM: Encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

Mahmood, K., Konagurthu, A. S., Song, J., Buckle, A. M., Webb, G. I. & Whisstock, J. C., 2010, In : Bioinformatics. 26, 17, p. 2076 - 2084 9 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

How precise are reported protein coordinate data?

Konagurthu, A. S., Allison, L., Abramson, D. A., Stuckey, P. J. & Lesk, A. M., 2014, In : Acta Crystallographica Section D: Biological Crystallography. 70, 3, p. 904 - 906 3 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Minimum message length inference of secondary structure from protein coordinate data

Konagurthu, A. S., Lesk, A. M. & Allison, L., 2012, In : Bioinformatics. 28, 12, p. i97 - i105 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
19 Citations (Scopus)

MUSTANG: a multiple structural alignment algorithm

Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J. & Lesk, A. M., 2006, In : Proteins: Structure, Function, and Bioinformatics. 64, 3, p. 559 - 574 16 p.

Research output: Contribution to journalArticleResearchpeer-review

476 Citations (Scopus)

MUSTANG-MR structural sieving server: Applications in protein structural analysis and crystallography

Konagurthu, A. S., Reboul, C. F., Schmidberger, J. W., Irving, J. A., Lesk, A. M., Stuckey, P. J., Whisstock, J. C. & Buckle, A. M., 2010, In : PLoS ONE. 5, 4 (e10048), p. 1 - 7 7 p.

Research output: Contribution to journalArticleResearchpeer-review

37 Citations (Scopus)

On representing protein folding patterns using non-linear parametric curves

Kasarapu, P., Garcia De La Banda, M. J. & Konagurthu, A. S., 2014, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11, 6, p. 1218 - 1228 11 p.

Research output: Contribution to journalArticleResearchpeer-review

On sufficient statistics of least-squares superposition of vector sets

Konagurthu, A. S., Kasarapu, P., Allison, L., Collier, J. H. & Lesk, A. M., 2015, In : Journal of Computational Biology. 22, 6, p. 487-497 11 p.

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

On the origin of distribution patterns of motifs in biological networks

Konagurthu, A. S. & Lesk, A. M., 2008, In : BMC Systems Biology. 2, p. 1 - 8 8 p.

Research output: Contribution to journalArticleResearchpeer-review

24 Citations (Scopus)

Optimal sum-of-pairs multiple sequence alignment using incremental Carrillo and Lipman bounds

Konagurthu, A. S. & Stuckey, P. J., 2006, In : Journal of Computational Biology. 13, 3, p. 668 - 685 18 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Piecewise linear approximation of protein structures using the principle of minimum message length

Konagurthu, A., Allison, L., Stuckey, P. & Lesk, A., 2011, In : Bioinformatics. 27, 13, p. i43 - i51 9 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Progressive multiple alignment using sequence triplet optimizations and three-residue exchange costs

Konagurthu, A., Whisstock, J. & Stuckey, P., 2004, In : Journal of Bioinformatics and Computational Biology. 2, 4, p. 719 - 745 27 p.

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)

Single and multiple input modules in regulatory networks

Konagurthu, A. S. & Lesk, A. M., 2008, In : Proteins: Structure, Function, and Bioinformatics. 73, 2, p. 320 - 324 5 p.

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors

Sumanaweera, D., Allison, L. & Konagurthu, A., 5 Jul 2019, In : Bioinformatics. 35, 14, p. i360-i369 10 p., btz368.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Statistical inference of protein structural alignments using information and compression

Collier, J. H., Allison, L., Lesk, A. M., Stuckey, P. J., Garcia De La Banda, M. & Konagurthu, A. S., 1 Apr 2017, In : Bioinformatics. 33, 7, p. 1005-1013 9 p.

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Structural search and retrieval using a tableau representation of protein folding patterns

Konagurthu, A. S., Stuckey, P. J. & Lesk, A., 2008, In : Bioinformatics. 24, 5, p. 645 - 651 7 p.

Research output: Contribution to journalArticleResearchpeer-review

26 Citations (Scopus)

Super: A web server to rapidly screen superposable oligopeptide fragments from the protein data bank

Collier, J., Lesk, A. M., Garcia De La Banda, M. J. & Konagurthu, A. S., 2012, In : Nucleic Acids Research. 40, p. 1 - 6 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
4 Citations (Scopus)