A multi-factor model for caspase degradome prediction (2009)
Wee, Lawrence JK, Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Abstract Background Caspases belong to a class of cysteine proteases which function as critical effectors in cellular processes such as apoptosis and inflammation by cleaving substrates immediately...
Tan, Tin, Lim, Shen, Khan, Asif M, Ranganathan, Shoba
Abstract Background The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular...
Khan, Javed, Ranganathan, Shoba
Abstract Background Lysosomal α-mannosidase is an enzyme that acts to degrade N-linked oligosaccharides and hence plays an important role in mannose metabolism in humans and other mammalian species,...
Chacko, Elsa, Ranganathan, Shoba
Abstract Background Alternative splicing (AS) is a primary mechanism of functional regulation in the human genome, with 60% to 80% of human genes being alternatively spliced. As part of the bovine...
Extending Asia Pacific bioinformatics into new realms in the "-omics" era (2009)
Ranganathan, Shoba, Eisenhaber, Frank, Tong, Joo, Tan, Tin
Abstract The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8 th International...
A comprehensive assessment of N-terminal signal peptides prediction methods (2009)
Choo, Khar, Tan, Tin, Ranganathan, Shoba
Abstract Background Amino-terminal signal peptides (SPs) are short regions that guide the targeting of secretory proteins to the correct subcellular compartments in the cell. They are cleaved off...
Physicochemical property space distribution among human metabolites, drugs and toxins (2009)
Khanna, Varun, Ranganathan, Shoba
Abstract Background The current approach to screen for drug-like molecules is to sieve for molecules with biochemical properties suitable for desirable pharmacokinetics and reduced toxicity, using...
Towards a career in bioinformatics (2009)
Abstract The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8 th International Conference on...
Secretome: clues into pathogen infection and clinical applications (2009)
Ranganathan, Shoba, Garg, Gagan
Abstract The secretome encompasses the complete set of gene products secreted by a cell. Recent studies on secretome analysis reveal that secretory proteins play an important role in pathogen...
Emerging strengths in Asia Pacific bioinformatics (2009)
Bmc Bioinformatics, Shoba Ranganathan, Wen-lian Hsu, Ueng-cheng Yang, Wee Tan
Chacko, Elsa, Ranganathan, Shoba
Abstract Background Alternative transcript diversity manifests itself as a prime cause of complexity in higher eukaryotes. Recently, transcript diversity studies have suggested that 60–80% of human...
patterns in chicken, compared to human (2009)
Bmc Genomics, Elsa Chacko, Shoba Ranganathan
Comprehensive splicing graph analysis of alternative splicing
Bmc Bioinformatics, Khar Heng Choo, Shoba Ranganathan, Shoba Ranganathan
Proceedings A comprehensive assessment of N-terminal signal peptides prediction methods
Gaikwad, Jitendra, Khanna, Varun, Vemulpad, Subramanyam, Jamie, Joanne, Kohen, Jim, Ranganathan, Shoba
Abstract Background The customary medicinal plant knowledge possessed by the Australian Aboriginal people is a significant resource. Published information on it is scattered throughout the...
Flanking signal and mature peptide residues influence signal peptide cleavage (2008)
Choo, Khar, Ranganathan, Shoba
Abstract Background Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient...
Emerging strengths in Asia Pacific bioinformatics (2008)
Ranganathan, Shoba, Hsu, Wen-Lian, Yang, Ueng-Cheng, Tan, Tin Wee
Abstract The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7 th International Conference...
Shivashankar H. Nagaraj, Shoba Ranganathan
an expressed sequence tag (EST) assembly and annotation platform.
Phd Student In Bioinformatics, Shivashankar H. Nagaraj, Robin B. Gasser, Alasdair J. Nisbet, Shivashankar H. Nagaraj, Shivashankar H. Nagaraj, ...
To use my skills in biology and bioinformatics in innovative research.
Department Of Biochemistry, Shoba Ranganathan
structural bioinformatics analysis of small disulphickbonded proteins. He has received several ISCB travel awards to present his work at international bioinformatics conferences in Australia,...
Kong, Lesheng, Ranganathan, Shoba
Abstract Background The Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the...
Choo, Khar, Tong, Joo, Ranganathan, Shoba
Abstract Background Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across...
Nagaraj, Shivashankar H, Gasser, Robin B, Nisbet, Alasdair J, Ranganathan, Shoba
Abstract Background The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods...
Bioinformatics research in the Asia Pacific: a 2007 update (2008)
Ranganathan, Shoba, Gribskov, Michael, Tan, Tin
Abstract We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998....
Genome Informatics 14: 474--475 (2003) MGAlign, a Reduced Search Space Approach to the (2008)
Alignment Of Mrna, Shoba Ranganathan, Bernett T. K. Lee, Tin Wee Tan
Introduction Alternative splicing is a cellular process that accounts for protein diversity in higher eukaryotes. As much as 60% of the human genome (Kan et al., 2001) and 41% of the mouse genome...
Choo, Khar Heng, Tong, Joo Chuan, Ranganathan, Shoba
Background: Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across biological...
Kong, Lesheng, Ranganathan, Shoba
Background: The Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the evolution...
Flanking signal and mature peptide residues influence signal peptide cleavage (2008)
Choo, Khar Heng, Ranganathan, Shoba
Background: Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is...
Bmc Bioinformatics, Lesheng Kong, Shoba Ranganathan
Proceedings Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors
Bmc Bioinformatics, Khar Heng Choo, Shoba Ranganathan
Flanking signal and mature peptide residues influence signal peptide cleavage
BMC Bioinformatics BioMed Central (2008)
Khar Heng Choo, Joo Chuan Tong, Shoba Ranganathan
Proceedings Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
CMKb: a web-based prototype for integrating Australian Aboriginal (2008)
Bmc Bioinformatics, Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen, ...
customary medicinal plant knowledge
BMC Bioinformatics BioMed Central (2008)
Shivashankar H Nagaraj, Robin B Gasser, Alasdair J Nisbet, Shoba Ranganathan
Proceedings In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches
A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus (2007)
Ranganathan, Shoba, Nagaraj, Shivashankar H, Hu, Min, Strube, Christina, Schnieder, Thomas, Gasser, Robin B
Abstract Background Lungworms of the genus Dictyocaulus (family Dictyocaulidae) are parasitic nematodes of major economic importance. They cause pathological effects and clinical disease in various...
In silicocharacterization of immunogenic epitopes presented by HLA-Cw*0401 (2007)
Tong, Joo Chuan, Zhang, Zong Hong, August, J Thomas, Brusic, Vladimir, Tan, Tin Wee, Ranganathan, Shoba
Abstract Background HLA-C locus products are poorly understood in part due to their low expression at the cell surface. Recent data indicate that these molecules serve as major restriction elements...
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform (2007)
Nagaraj, Shivashankar H., Deshpande, Nandan, Gasser, Robin B., Ranganathan, Shoba
The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome of an organism, but requiring several computational methods for...
Methods and protocols for prediction of immunogenic epitopes (2007)
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
T-cell recognition of peptide/major histocompatibility complex (MHC) is a prerequisite for cellular immunity. Recently, there has been an influx of bioinformatics tools to facilitate the...
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Motivation: Classification of human leukocyte antigen (HLA) proteins into supertypes underpins the development of epitope-based vaccines with wide population coverage. Current methods for HLA...
In silico characterization of immunogenic epitopes presented by HLA-Cw*0401 (2007)
Tong, Joo Chuan, Zhang, Zong Hong, August, J. Thomas, Brusic, Vladimir, Tan, Tin Wee, Ranganathan, Shoba
Background: HLA-C locus products are poorly understood in part due to their low expression at the cell surface. Recent data indicate that these molecules serve as major restriction elements for human...
A Transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus (2007)
Ranganathan, Shoba, Nagaraj, Shivashankar H, Hu, Min, Strube, Christina, Schnieder, Thomas, Gasser, Robin B
Lungworms of the genus Dictyocaulus (family Dictyocaulidae) are parasitic nematodes of major economic importance. They cause pathological effects and clinical disease in various ruminant hosts,...
Intelligent agent system for bio-medical literature mining (2007)
Islam, Md. Tawhidul, Bollina, Durgaprasad, Nayak, Abhaya, Ranganathan, Shoba
With the advances of World Wide Web technology and advanced research in bioinformatics and systems biology domain has highlighted the increasing need for automatic information extraction [IE] system...
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites (2007)
Wee, Lawrence J.K., Tan, Tin Wee, Ranganathan, Shoba
Summary: Caspases belong to a unique class of cysteine proteases which function as critical effectors of apoptosis, inflammation and other important cellular processes. Caspases cleave substrates at...
A hitchhiker's guide to expressed sequence tag (EST) analysis (2007)
Nagaraj, Shivashankar H., Gasser, Robin B., Ranganathan, Shoba
Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive...
A Practical guide to structure-based prediction of MHC Binding Peptides (2007)
Ranganathan, Shoba, Tong, Joo Chuan
The binding of bound peptide ligands to major histocompatibility complex (MHC) molecules plays a key role in the activation of normal immune responses and is an intricate theoretical problem that...
A Workflow for mutation extraction and structure annotation (2007)
Kanagasabai, Rajaraman, Choo, Khar Heng, Ranganathan, Shoba, Baker, Christopher J. O
Rich information on point mutation studies is scattered across heterogeneous data sources. This paper presents an automated workflow for mining mutation annotations from full-text biomedical...
A Hitchhiker's guide to expressed sequence tag (EST) analysis (2007)
Nagaraj, Shivashankar H, Gasser, Robin B, Ranganathan, Shoba
Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive...
Methods and protocols for prediction of immunogenic epitopes (2007)
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
T-cell recognition of peptide/major histocompatibility complex (MHC) is a prerequisite for cellular immunity. Recently, there has been an influx of bioinformatics tools to facilitate the...
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Motivation: Classification of human leukocyte antigen (HLA) proteins into supertypes underpins the development of epitope-based vaccines with wide population coverage. Current methods for HLA...
CASVM : web server for SVM-based prediction of caspase substrates cleavage sites (2007)
Wee, Lawrence J. K., Tan, Tin Wee, Ranganathan, Shoba
Caspases belong to a unique class of cysteine proteases which function as critical effectors of apoptosis, inflammation and other important cellular processes. Caspases cleave substrates at specific...
Gasser, Robin B, Cottee, Pauline, Nisbet, Alasdair J, Ruttkowski, Bärbel, Ranganathan, Shoba, Joachim, Anja
There are substantial gaps in the knowledge of the molecular processes of development and reproduction in parasitic nematodes, despite the fact that understanding such processes could lead to novel...
Hu, Min, Campbell, Bronwyn E, Pellegrino, Mark, Loukas, Alex, Beveridge, Ian, Ranganathan, Shoba, ...
A full-length cDNA (Tv-ant-1) encoding an adenine nucleotide translocator (ANT or ADP/ATP translocase) (Tv-ANT-1) was isolated from Trichostrongylus vitrinus (order Strongylida), an economically...
ESTExplorer : an expressed sequence tag (EST) assembly and annotation platform (2007)
Nagaraj, Shivashankar H, Deshpande, Nandan, Gasser, Robin B, Ranganathan, Shoba
The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome of an organism, but requiring several computational methods for...
SVM-based prediction of caspase substrate cleavage sites (2006)
Wee, Lawrence JK, Tan, Tin, Ranganathan, Shoba
Abstract Background Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites....
Tong, Joo, Tan, Tin, Sinha, Animesh A, Ranganathan, Shoba
Abstract Background Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503....
Establishing bioinformatics research in the Asia Pacific (2006)
Ranganathan, Shoba, Tammi, Martti, Gribskov, Michael, Tan, Tin Wee
Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002,...
Tong, Joo, Bramson, Jeff, Kanduc, Darja, Chow, Selwyn, Sinha, Animesh A, Ranganathan, Shoba
Abstract Background Pemphigus vulgaris (PV) is a severe autoimmune blistering disorder characterized by the presence of pathogenic autoantibodies directed against desmoglein-3 (Dsg3), involving...
Deduction of functional peptide motifs in scorpion toxins (2006)
Tan, Paul T. J, Ranganathan, Shoba, Brusic, Vladimir
Scorpion toxins are important physiological probes for characterizing ion channels. Molecular databases have limited functional annotation of scorpion toxins. Their function can be inferred by...
SCORPION2 : a database for structure-function analysis of scorpion toxins (2006)
Tan, Paul T. J, Veeramani, Anitha, Srinivasan, Kellathur N, Ranganathan, Shoba, Brusic, Vladimir
Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation...
Tong, Joo Chuan, Kong, Lesheng, Tan, Tin Wee, Ranganathan, Shoba
Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors...
Tong, Joo Chuan, Zhang, Guang Lan, Tan, Tin Wee, August, J. Thomas, Brusic, Vladimir, Ranganathan, Shoba
Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and...
Tong, Joo Chuan, Bramson, Jeff, Kanduc, Darja, Chow, Selwyn, Sinha, Animesh A, Ranganathan, Shoba
Background: Pemphigus vulgaris (PV) is a severe autoimmune blistering disorder characterized by the presence of pathogenic autoantibodies directed against desmoglein-3 (Dsg3), involving specific DR4...
Establishing bioinformatics research in the Asia Pacific (2006)
Ranganathan, Shoba, Tammi, Martti, Gribskov, Michael, Tan, Tin Wee
In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet...
Tong, Joo Chuan, Tan, Tin Wee, Sinha, Animesh A, Ranganathan, Shoba
Background: Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The...
SVM-based prediction of caspase substrate cleavage sites (2006)
Wee, Lawrence J.K, Tan, Tin Wee, Ranganathan, Shoba
Background: Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of...
Comparative genomic analysis of glycoylation pathways in yeast, plants and higher eukaryotes (2006)
Ranganathan, Shoba, Wongsai, Sangdao, Nevalainen, K. M. Helena
N-linked glycosylation is an essential modification of secretory and membrane proteins in all eukaryotic cells. Here, we review the current metabolic pathways of N-linked oligosaccharide biosynthesis...
Deduction of functional peptide motifs in scorpion toxins (2006)
Tan, Paul T. J, Ranganathan, Shoba, Brusic, Vladimir
Scorpion toxins are important physiological probes for characterizing ion channels. Molecular databases have limited functional annotation of scorpion toxins. Their function can be inferred by...
SCORPION2 : a database for structure-function analysis of scorpion toxins (2006)
Tan, Paul T. J, Veeramani, Anitha, Srinivasan, Kellathur N, Ranganathan, Shoba, Brusic, Vladimir
Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation...
Tong, Joo Chuan, Kong, Lesheng, Tan, Tin Wee, Ranganathan, Shoba
Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors...
Tong, Joo Chuan, Zhang, Guang Lan, Tan, Tin Wee, August, J. Thomas, Brusic, Vladimir, Ranganathan, Shoba
Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and...
Tong, Joo Chuan, Bramson, Jeff, Kanduc, Darja, Chow, Selwyn, Sinha, Animesh A, Ranganathan, Shoba
Background: Pemphigus vulgaris (PV) is a severe autoimmune blistering disorder characterized by the presence of pathogenic autoantibodies directed against desmoglein-3 (Dsg3), involving specific DR4...
Establishing bioinformatics research in the Asia Pacific (2006)
Ranganathan, Shoba, Tammi, Martti, Gribskov, Michael, Tan, Tin Wee
In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet...
Tong, Joo Chuan, Tan, Tin Wee, Sinha, Animesh A, Ranganathan, Shoba
Background: Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The...
SVM-based prediction of caspase substrate cleavage sites (2006)
Wee, Lawrence J.K, Tan, Tin Wee, Ranganathan, Shoba
Background: Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of...
Comparative genomic analysis of glycoylation pathways in yeast, plants and higher eukaryotes (2006)
Ranganathan, Shoba, Wongsai, Sangdao, Nevalainen, K. M. Helena
N-linked glycosylation is an essential modification of secretory and membrane proteins in all eukaryotic cells. Here, we review the current metabolic pathways of N-linked oligosaccharide biosynthesis...
Bmc Bioinformatics, Joo Chuan Tong, Tin Wee Tan, Animesh A Sinha, Shoba Ranganathan
Proceedings Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris
doi:10.1093/nar/gkl268 ASGS: an alternative splicing graph web service (2006)
Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan
Alternative transcript diversity manifests itself a prime cause of complexity in higher eukaryotes. The Alternative Splicing Graph Server (ASGS) is a web service facilitating the systematic study of...
ASGS: an alternative splicing graph web service (2006)
Bollina, Durgaprasad, Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Alternative transcript diversity manifests itself a prime cause of complexity in higher eukaryotes. The Alternative Splicing Graph Server (ASGS) is a web service facilitating the systematic study of...
Tong, Joo Chuan, Zhang, Guang Lan, Tan, Tin Wee, August, J. Thomas, Brusic, Vladimir, Ranganathan, Shoba
Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and...
Lenffer, Johann, Nicholas, Frank W., Castle, Kao, Rao, Arjun, Gregory, Stefan, Poidinger, Michael, ...
Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a...
Tong, Joo Chuan, Zhang, Guang Lan, Tan, Tin Wee, August, J. Thomas, Brusic, Vladimir, Ranganathan, Shoba
Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and...
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Motivation: Classification of human leukocyte antigen (HLA) proteins into supertypes underpins the development of epitope-based vaccines with wide population coverage. Current methods for HLA...
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006)
Nagaraj, Shivashankar H., Gasser, Robin B., Ranganathan, Shoba
Expressed sequence tag (EST) sequencing projects are underway for numerous organisms, generating millions of short, single-pass nucleotide sequence reads, accumulating in EST databases. Extensive...
Methods and protocols for prediction of immunogenic epitopes (2006)
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
T-cell recognition of peptide/major histocompatibility complex (MHC) is a prerequisite for cellular immunity. Recently, there has been an influx of bioinformatics tools to facilitate the...
Lenffer, Johann, Nicholas, Frank W, Castle, Kao, Rao, Arjun, Gregory, Stefan, Poidinger, Michael, ...
Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a...
ASGS : an alternative splicing graph web service (2006)
Bollina, Durgaprasad, Lee, Bernett T.K, Tan, Tin Wee, Ranganathan, Shoba
Alternative transcript diversity manifests itself a prime cause of complexity in higher eukaryotes. The Alternative Splicing Graph Server (ASGS) is a web service facilitating the systematic study of...
SPdb – a signal peptide database (2005)
Choo, Khar, Tan, Tin, Ranganathan, Shoba
Abstract Background The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence...
Bioinformatics education : perspectives and challenges (2005)
This article discusses the evolution of curriculum, instructional methodologies and initiatives supporting the dissemination of bioinformatics. Building on the early applications of informatics to...
Bioinformatics education : perspectives and challenges (2005)
This article discusses the evolution of curriculum, instructional methodologies and initiatives supporting the dissemination of bioinformatics. Building on the early applications of informatics to...
Bioinformatics education : perspectives and challenges (2005)
This article discusses the evolution of curriculum, instructional methodologies and initiatives supporting the dissemination of bioinformatics. Building on the early applications of informatics to...
DEDB: a database of Drosophila melanogasterexons in splicing graph form (2004)
Lee, Bernett TK, Tan, Tin, Ranganathan, Shoba
Abstract Background A wealth of quality genomic and mRNA/EST sequences in recent years has provided the data required for large-scale genome-wide analysis of alternative splicing. We have capitalized...
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins (2004)
Lesheng Kong, Bernett Teck, Kwong Lee, Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan
Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a...
Xpro: Database of eukaryotic protein-encoding genes (2004)
Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, Shoba Ranganathan
Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture. In...
Bernett Tk Lee, Tin Wee Tan, Shoba Ranganathan
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Modeling the structure of bound peptide ligands to major histocompatibility complex (2004)
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues...
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins (2004)
Kong, Lesheng, Lee, Bernett Teck Kwong, Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a...
Delineation of modular proteins: Domain boundary prediction from sequence information (2004)
Kong, Lesheng, Ranganathan, Shoba
The delineation of domain boundaries of a given sequence in the absence of known 3D structures or detectable sequence homology to known domains benefits many areas in protein science, such as protein...
Xpro: database of eukaryotic protein-encoding genes (2004)
Gopalan, Vivek, Tan, Tin Wee, Lee, Bernett T. K., Ranganathan, Shoba
Xpro is a relational database that contains all the eukaryotic protein‐encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture....
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences (2003)
Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan
Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the...
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences (2003)
Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the...
Govindarajan, Kunde Ramamoorthy, Kangueane, Pandjassarame, Tan, Tin Wee, Ranganathan, Shoba
Summary: Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the first step in T-cell mediated immune response. To understand the structural principles governing...
XdomView: protein domain and exon position visualization (2003)
Vivek, Gopalan, Tan, Tin Wee, Ranganathan, Shoba
Summary: The relationship between intron distribution in the eukaryotic gene and protein structural elements is essential for understanding the origin and evolution of genes. XdomView is a web-based...
Srinivasan, Kellathur N ; JFA; CORA, Sivaraja, Vaithiyalingam, Huys, Isabelle; U0031958 ;, Sasaki, Toru, Cheng, Betty, Kumar, Thallampuranam Krishnaswamy S, ...
An important and exciting challenge in the postgenomic era is to understand the functions of newly discovered proteins based on their structures. The main thrust is to find the common structural...
Murray, Jane S., Sukumar, Nagamani, Ranganathan, Shoba, Politzer, Peter
We have carried out a computational study of hydrazine and five of its 1,1-dimethyl derivatives, focusing on their electrostatic potentials and relative bond strengths. Our approach has involved the...
Jill E. Gready, Shoba Ranganathan, Ken Nishikawa
Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand-binding site
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences
Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the...
Xpro: database of eukaryotic protein-encoding genes
Gopalan, Vivek, Tan, Tin Wee, Lee, Bernett T. K., Ranganathan, Shoba
Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture. In...
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
Kong, Lesheng, Lee, Bernett Teck Kwong, Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a...
Lenffer, Johann, Nicholas, Frank W., Castle, Kao, Rao, Arjun, Gregory, Stefan, Poidinger, Michael, ...
Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a...
ASGS: an alternative splicing graph web service
Bollina, Durgaprasad, Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Alternative transcript diversity manifests itself a prime cause of complexity in higher eukaryotes. The Alternative Splicing Graph Server (ASGS) is a web service facilitating the systematic study of...
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences
Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the...
Xpro: database of eukaryotic protein-encoding genes
Gopalan, Vivek, Tan, Tin Wee, Lee, Bernett T. K., Ranganathan, Shoba
Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences contained in GenBank with associated data required for the analysis of eukaryotic gene architecture. In...
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
Kong, Lesheng, Lee, Bernett Teck Kwong, Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Small disulfide-bonded proteins (SDPs) are rich sources for therapeutic drugs. Designing drugs from these proteins requires three-dimensional structural information, which is only available for a...
Lenffer, Johann, Nicholas, Frank W., Castle, Kao, Rao, Arjun, Gregory, Stefan, Poidinger, Michael, ...
Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a...
ASGS: an alternative splicing graph web service
Bollina, Durgaprasad, Lee, Bernett T. K., Tan, Tin Wee, Ranganathan, Shoba
Alternative transcript diversity manifests itself a prime cause of complexity in higher eukaryotes. The Alternative Splicing Graph Server (ASGS) is a web service facilitating the systematic study of...
Establishing bioinformatics research in the Asia Pacific
Ranganathan, Shoba, Tammi, Martti, Gribskov, Michael, Tan, Tin Wee
In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet...
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
Nagaraj, Shivashankar H., Deshpande, Nandan, Gasser, Robin B., Ranganathan, Shoba
The analysis of expressed sequence tag (EST) datasets offers a rapid and cost-effective approach to elucidate the transcriptome of an organism, but requiring several computational methods for...
In silico characterization of immunogenic epitopes presented by HLA-Cw*0401
Tong, Joo Chuan, Zhang, Zong Hong, August, J Thomas, Brusic, Vladimir, Tan, Tin Wee, Ranganathan, Shoba
A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus
Ranganathan, Shoba, Nagaraj, Shivashankar H, Hu, Min, Strube, Christina, Schnieder, Thomas, Gasser, Robin B
Datu, Bennett J. D., Gasser, Robin B., Nagaraj, Shivashankar H., Ong, Eng K., O'Donoghue, Peter, McInnes, Russell, ...
Hookworms are soil-transmitted nematodes that parasitize hundreds of millions of people in developing countries. Here we describe the genes expressed when hookworm larvae make the transition from a...
Bioinformatics research in the Asia Pacific: a 2007 update
Ranganathan, Shoba, Gribskov, Michael, Tan, Tin Wee
We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From...
Modeling the structure of bound peptide ligands to major histocompatibility complex
Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues...
Nagaraj, Shivashankar H., Gasser, Robin B., Ranganathan, Shoba
Excretory-secretory (ES) proteins are an important class of proteins in many organisms, spanning from bacteria to human beings, and are potential drug targets for several diseases. In this study, we...
Gaikwad, Jitendra, Khanna, Varun, Vemulpad, Subramanyam, Jamie, Joanne, Kohen, Jim, Ranganathan, Shoba
Emerging strengths in Asia Pacific bioinformatics
Ranganathan, Shoba, Hsu, Wen-Lian, Yang, Ueng-Cheng, Tan, Tin Wee
The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on...
Towards a career in bioinformatics
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation from 1998, was organized as the 8th International Conference on...
Extending Asia Pacific bioinformatics into new realms in the "-omics" era
Ranganathan, Shoba, Eisenhaber, Frank, Tong, Joo Chuan, Tan, Tin Wee
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on...
A multi-factor model for caspase degradome prediction
Wee, Lawrence JK, Tong, Joo Chuan, Tan, Tin Wee, Ranganathan, Shoba
Secretome: clues into pathogen infection and clinical applications
Ranganathan, Shoba, Garg, Gagan
The secretome encompasses the complete set of gene products secreted by a cell. Recent studies on secretome analysis reveal that secretory proteins play an important role in pathogen infection and...