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| = Soon Heng TAN (Chris) = == Profile == Chris possesses a B.Sc (Honours, 2nd Upper) in Molecular Biology and M.Sc in Computer Science from National University of Singapore (NUS). His research interest is in bioinformatics and computational biology, in particular, designing algorithms and computational approaches for knowledge discovery in biology. He is currently pursuing a Ph.D at the Department of Molecular Genetics and Microbiology in University of Toronto under the supervision of [http://pawsonlab.mshri.on.ca: Tony Pawson] and [:GaryBader:Gary Bader]. == Contact == '''Email''': chris.tan[at]utoronto.ca [http://www.google.com/calendar/embed?src=h2hoq53lpig6gh8etg7ai1r558%40group.calendar.google.com&pvttk=c3e8bc89cf0a72313f0b5e5ee97c30f3 My Schedule] == Research Experience == ---- === Algorithm design for automated sequence motif discovery from protein interaction data === * '''A correlated motif approach for finding short linear motifs from protein interaction networks''' . '''S.H. Tan''', W. Hugo, W.K. Sung and S.K. Ng . BMC Bioinformatics, 7:502 (2006) * '''Discovering novel interacting motif pairs from large protein-protein interaction datasets''' . '''S.H. Tan''', W.K. Sung and S.K. Ng . BIBE 2004, Taichung, Taiwan, May 19-21, pp568-575. * '''Automated linear motif discovery from protein interaction network''' . M.Sc Dissertation in Computer Science (2005) ---- === Elucidating the underlying domain structures and co-evolution between interacting proteins for interaction prediction/validation === * '''Protein interaction prediction using inferred domain interactions and biologically-significant negative dataset''' . X.L. Li, '''S.H. Tan''' and S.K. Ng . Lectures Notes in Computer Science, 3482: pp318 (2005) * '''ADVICE: automated detection and validation of interaction by co-evolution''' . '''S.H. Tan''', Z. Zhang and S.K. Ng . Nucleic Acids Research, Vol. 32: W69-W72 (2004) * '''Integrative approach for computationally inferring protein domain interactions''' . S.K. Ng, Z. Zhang and '''S.H. Tan''' . Bioinformatics 8: 923-929 (2003) * '''InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes''' . S.K. Ng, Z. Zhang and '''S.H. Tan''', K. Lin . Nucleic Acids Research 31: 251-254 (2003) ---- === Understanding the cell’s functional organization through network analysis and graph mining of protein interaction network === * '''Interaction graph mining for protein complexes using local clique merging''' . X.L. Li, '''S.H. Tan''', C.S. Foo and S.K. Ng . GIW2005, in Genome Informatics 16(2): 260-269 ---- === Extraction of protein-protein interaction data from free text === * '''Challenges in biological literature mining for online discovery of molecular interaction pathways''' . S.K. Ng and '''S.H. Tan''' . International Journal of Computer Applications in Technology (IJCAT), Special Issue on "Data Mining Applications" (2007) * '''Recognition of protein and gene names from text using an ensemble of classifiers and effective abbreviation resolution''' . G. Zhou, D. Shen, J. Zhang, J. Su, '''S.H. Tan''' and C.L. Tan . BMC Bioinformatics, 6 (Suppl 1):S7 (2005) ---- === Functional study of genes from expression data === * '''On combining multiple microarray studies for improved functional classification by whole-dataset feature selection''' . S.K Ng, S.H. Tan and V.S. Sundararajan . GIW2003'', in Genome Informatics 14: 44-53 |
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| * [:/Statistical Test: Statistical Test] * [:/thesis: Thesis] '''HOLDING AREA''' - To be organized.... [http://developer.apple.com/internet/opensource/osdb.html Installing mySQL on Mac] [http://www.truerwords.net/3556 Installing Perl's DBD::mysql on Mac] SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions PIDD: database for Protein Inter-atomic Distance Distributions FireDB—a database of functionally important residues from proteins of known structure Phospho3D: a database of three-dimensional structures of protein phosphorylation sites PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways * Contain HMM MMDB: annotating protein sequences with Entrez's 3D-structure database The SUPERFAMILY database in 2007: families and functions * HMM based on structures PEDANT genome database: 10 years online DOMINO: a database of domain–peptide interactions PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease DisProt: the Database of Disordered Proteins TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure HHsenser: exhaustive transitive profile search using HMM–HMM comparison http://bcz102.ust.hk/index_projects.htm [http://www.google.com/calendar/embed?src=h2hoq53lpig6gh8etg7ai1r558%40group.calendar.google.com&pvttk=c3e8bc89cf0a72313f0b5e5ee97c30f3 My Schedule] |
Soon Heng TAN (Chris)
Profile
Chris possesses a B.Sc (Honours, 2nd Upper) in Molecular Biology and M.Sc in Computer Science from National University of Singapore (NUS). His research interest is in bioinformatics and computational biology, in particular, designing algorithms and computational approaches for knowledge discovery in biology. He is currently pursuing a Ph.D at the Department of Molecular Genetics and Microbiology in University of Toronto under the supervision of [http://pawsonlab.mshri.on.ca: Tony Pawson] and [:GaryBader:Gary Bader].
Contact
Email: chris.tan[at]utoronto.ca
Research Experience
Algorithm design for automated sequence motif discovery from protein interaction data
A correlated motif approach for finding short linear motifs from protein interaction networks
S.H. Tan, W. Hugo, W.K. Sung and S.K. Ng
- BMC Bioinformatics, 7:502 (2006)
Discovering novel interacting motif pairs from large protein-protein interaction datasets
S.H. Tan, W.K. Sung and S.K. Ng
- BIBE 2004, Taichung, Taiwan, May 19-21, pp568-575.
Automated linear motif discovery from protein interaction network
- M.Sc Dissertation in Computer Science (2005)
Elucidating the underlying domain structures and co-evolution between interacting proteins for interaction prediction/validation
Protein interaction prediction using inferred domain interactions and biologically-significant negative dataset
X.L. Li, S.H. Tan and S.K. Ng
- Lectures Notes in Computer Science, 3482: pp318 (2005)
ADVICE: automated detection and validation of interaction by co-evolution
S.H. Tan, Z. Zhang and S.K. Ng
- Nucleic Acids Research, Vol. 32: W69-W72 (2004)
Integrative approach for computationally inferring protein domain interactions
S.K. Ng, Z. Zhang and S.H. Tan
- Bioinformatics 8: 923-929 (2003)
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
S.K. Ng, Z. Zhang and S.H. Tan, K. Lin
- Nucleic Acids Research 31: 251-254 (2003)
Understanding the cell’s functional organization through network analysis and graph mining of protein interaction network
Interaction graph mining for protein complexes using local clique merging
X.L. Li, S.H. Tan, C.S. Foo and S.K. Ng
- GIW2005, in Genome Informatics 16(2): 260-269
Extraction of protein-protein interaction data from free text
Challenges in biological literature mining for online discovery of molecular interaction pathways
S.K. Ng and S.H. Tan
- International Journal of Computer Applications in Technology (IJCAT), Special Issue on "Data Mining Applications" (2007)
Recognition of protein and gene names from text using an ensemble of classifiers and effective abbreviation resolution
G. Zhou, D. Shen, J. Zhang, J. Su, S.H. Tan and C.L. Tan
- BMC Bioinformatics, 6 (Suppl 1):S7 (2005)
Functional study of genes from expression data
On combining multiple microarray studies for improved functional classification by whole-dataset feature selection
- S.K Ng, S.H. Tan and V.S. Sundararajan
GIW2003, in Genome Informatics 14: 44-53
Chris's Log Book
[:/ToDo:To Dos]
[:/LiteratureReview: Literature Review]