Mallika Veeramalai's profile
What I do
Bioinformatics, structural bioinformatics, protein structure and function analysis and prediction, comparison and
classification, protein sequence-structural-functional relationships, protein-ligand classification, pattern discovery,
pattern matching approaches, fold-recognition.
Affiliations
Current affiliations
-
- Position
- Postdoctoral Research Associate
- Company
- Burnham Institute for Medical Research
- Duration
- 2006 - Present
- Further information
Past affiliations
-
- Position
- Postdoctoral researcher
- Company
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, UK
- Duration
- 2005 - 2006
- Further information
-
- Position
- PhD Research Student
- Company
- Bioinformatics Research Centre Department of Computing Science at University of Glasgow Scotland, UK
- Duration
- 2001 - 2005
- Further information
Location
- City:
- San Diego, California, United States
- Hub:
- San Diego
Interests
Bioinformatics, structural bioinformatics, protein structure and function analysis and prediction, comparison and
classification, protein sequence-structural-functional relationships, protein-ligand classification, pattern discovery,
pattern matching approaches, fold-recognition, machine learning/ artificial intelligence approaches, systems
biology, biochemical pathways modelling and analysis.
Projects
Research Projects
Protein molecular evolution analysis based on fold space.
Protein molecular modeling and evaluation analysis.
Recently we have developed a Method –
“TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model”.
Previous Reseach Projects
My PhD reseach work from the Bioinformatics
Research Centre
Department of Computing
Science at University
of Glasgow Scotland lead by Prof.David Gilbert.
Which was development of “A Novel Method for Comparing Topological
Models of Protein Structures Enhanced with ligand Interaction Information”.
TOPS+ server is available here.
Wellcome Trust Biocentre,
University of Dundee was on “Development of a
Splicing Factor Database”.
at NCBS Bangalore, India and we have
developed PASS2: a Semi-Automated database of Protein Alignments organised as
Structural Superfamilies.
Servers and Database Links – Related to My Project
Publications
-
Mallika Veeramalai, Yuzhen Ye and Adam Godzik. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model BMC Bioinformatics , 358 (2008)
-
David Gilbert, Francesc Rosselló, Gabriel Valiente, Mallika Veeramalai. Alignment-Free Comparison of TOPS Strings London Algorithmics and Stringology , 177-197 (2007)
-
Mallika Veeramalai. A Novel Method for Comparing Topological Models of Protein Structures Enhanced with Ligand Information PhD Thesis in Computing Science, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow, UK. (2005)
-
Ren T, Veeramalai M, Tan A, Gilbert D. MSAT: a multiple sequence alignment tool based on TOPS. Applied bioinformatics (2-3) , 149-58 (2004) PubMed ID:(15693740)
-
Mallika V, Bhaduri A, Sowdhamini R. PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Nucleic acids research (1) , 284-8 (2002) PubMed ID:(11752316)
Contact
- email:
- kaaviyam [ at ] gmail.com
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