Publications by Mallika Veeramalai

1. Mallika Veeramalai and David Gilbert. "Functional analysis of TIM Barrel proteins using TOPS+ Comparison method" (Manuscript in preparation)

2. Mallika Veeramalai David Gilbert and Gabriel Valiente. "An Optimized TOPS+ Comparison Method for Enhanced TOPS models"(Submitted)

3. Mallika Veeramalai and David Gilbert. "A Novel Method for Comparing Topological Models of Protein Structures Enhanced with Ligand Information" Bioinformatics, (2008), 24(23):2698-2705; doi:10.1093/bioinformatics/btn518 [Paper] [TOPS+ Server]

4. Mallika Veeramalai, Yuzhen Ye and Adam Godzik. "TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model" BMC Bioinformatics , 9:358, 2008. [PubMed] [TOPS++FATCAT Server]
5. David Gilbert, Francesc Rosselló, Gabriel Valiente, Mallika Veeramalai. Alignment-Free Comparison of TOPS Strings. In J. Daykin, M. Mohamed, K. Steinhöfel (Ed.), London Algorithmics and Stringology, volume 8 of Texts in Algorithmics, College Publications (2007), ch. 11, pp. 177-197.

6. Mallika Veeramalai, "A Novel Method for Comparing Topological Models of Protein Structures Enhanced with Ligand Information", (2005) PhD Thesis in Computing Science, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, UK.

7. Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert, "MSAT : a Multiple Sequence Alignment tool based on TOPS", Appl Bioinformatics 2004;3(2-3):149-158. [PubMed].

8. Lubna Nasir, Elizabeth Gault, Sarah Campbell, Mallika Veeramalai, David Gilbert, Robert McFarlane, Alison Munro and David J Argyle. "Isolation and expression of the reverse transcriptase component of the canis familiaris telomerase ribonucleoprotein (canTERT)", Gene. 2004 Jul 7;336(1):105-13. [PubMed].

9. Te Ren, Mallika Veeramalai, Aik Choon Tan and David Gilbert, "MSAT : a Multiple Sequence Alignment tool based on TOPS", In the Proceedings of the Biological Language Conference (BLC 2003) J. Klein-Seetharaman, R. Rosenfeld and R. Reddy (editors), BLC., 2003 Nov,p:286-301. [PDF] [MSAT webserver]

10. Mallika Veeramalai and David Gilbert.,"Bioinformatics tools for Protein Structure". Bioinformatics World, Scientific Computing World, May/June 2002 Issue 64:12-15. [online-version].

11. Mallika V, Anirban Bhaduri and Sowdhamini R., "PASS2: Semi-Automated database of Protein Alignments Organized as Structural Superfamilies". Nucleic Acids Res., 2002, Jan 1;30(1):284-8. [PubMed]. [PASS2 Database]

12. Bhaduri A, Mallika V and Sowdhamini R., "Genome analysis of pass2 a semi-automated database of protein alignments organised as structural superfamilies". TheScientificWorldJournal. 2002 Jan 2;2(1 Suppl 2):9-10. [online]|[PubMed].

13. Chakrabarti S, Bhavana S, Mallika V and Sowdhamini R., (2002) "Protein structural similarities and prediction of protein function", in a book 'Trends in Chemistry' (ed. Srivastava, M.M.)., India.

Posters

1. Mallika Veeramalai, Yuzhen Ye and Adam Godzik, "TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model" in 16th International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, Poster Q:46.[Abstract].

2. Mallika Veeramalai and David Gilbert., "The TOPStrings Protein Structure Comparison Method - A Novel Approach". In Algorithmic Biology 2006, November 30, held in conjunction with RECOMB Satellite Workshops on Systems Biology and Computational proteomics, Center for Algorithmic and Systems Biology, California Institute for Telecommunications and Information Technology, University of California, San Diego, USA. [Abstract].

3. Mallika Veeramalai, David Gilbert and David Westhead., "Incorporating Sequence and Biochemical Information in TOPS models - for Biologically Significant Pattern Matching and Pattern Discovery in Protein Structures". In the Proccedings of the Proceedings of the European Conference on Computational Biology (ECCB 2003) in conjunction with JOBIM 2003, Paris, France, September 27 - 30, 2003. C. Christophe, H.-P. Lenhof and M.-F. Sagot (editors), PS-5:p.167-168. ISBN: 2-7261-1257. [Abstract].

4. Mallika Veeramalai, David Gilbert and David Westhead., "Incorporating Sequence and Biochemical Information in TOPS models - For Biologically Significant Pattern Matching and Pattern Discovery in Protein". In the Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB 2003), Brisbane, Australia, June 29 - July 3, 2003, J-11:p.134. [Abstract].

5. Mallika Veeramalai, David Gilbert and David Westhead., "Incorporating Sequence and Biochemical Information in Topological Models of Protein Structure Towards the Structural and Functional Genomics". In the Proceedings of the European Conference on Computational Biology (ECCB 2002) in conjunction with GCB 2002, Saarbrucken, Germany, October 6 - 9, 2002. T. Lengauer, H.-P. Lenhof, R. Christmann (editors), P-169:p.249. [Abstract]

6. Mallika Veeramalai, David Gilbert and David Westhead., "Incorporating Sequence and Biochemical Information in Topological Models of Protein Structure Towards the Structural and Functional Genomics". In the Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology (ISMB 2002), Edmonton, Canada, August 3-7, 2002, 102-A:p.71. [Abstract], [Poster].

7. Bhaduri A, Mallika V and Sowdhamini R., "Genome Analysis of PASS2 A Semi Automated Database of Protein Alignments Organized as Structural Superfamiles". In the 'TheScientificWorld' supplement of the Genome and Beyond Genomics and Structural Biology for Medicine, (Miami Nature Symposium 2002), Radisson Deauville Resort Hotel, Miami Beach, Florida, February 2-6, 2002. [Abstract].

8. Mallika Vand Sowdhamini R., "PASS2: Semi-Automated database of Protein Alignments Organized as Structural Superfamilies". In the Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001), Denmark, July 21-25, 2001, 257-A. [Abstract].