Challenges for Intelligent Systems in Biology. - Russ B. Altman; Alfonso Valencia; Satoru Miyano; Shoba Ranganathan (IEEE Intell. Syst., 2001)

MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. - Kunde Ramamoorthy Govindarajan; Pandjassarame Kangueane; Tin Wee Tan; Shoba Ranganathan (Bioinform., 2003)

XdomView: protein domain and exon position visualization. - Vivek Gopalan; Tin Wee Tan; Shoba Ranganathan (Bioinform., 2003)

MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences. - Bernett T. K. Lee; Tin Wee Tan; Shoba Ranganathan (Nucleic Acids Res., 2003)

Delineation of modular proteins: Domain boundary prediction from sequence information. - Lesheng Kong; Shoba Ranganathan (Briefings Bioinform., 2004)

DEDB: a database of Drosophila melanogaster exons in splicing graph form. - Bernett T. K. Lee; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2004)

Xpro: database of eukaryotic protein-encoding genes. - Vivek Gopalan; Tin Wee Tan; Bernett T. K. Lee; Shoba Ranganathan (Nucleic Acids Res., 2004)

SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. - Lesheng Kong; Bernett Teck Kwong Lee; Joo Chuan Tong; Tin Wee Tan; Shoba Ranganathan (Nucleic Acids Res., 2004)

MVC Architecture in Bioinformatics web applications and its Java implementation. - Durgaprasad Bollina; Bernett T. K. Lee; Shoba Ranganathan (iiWAS, 2005)

SPdb - a signal peptide database. - Khar Heng Choo; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2005)

Bioinformatics Education - Perspectives and Challenges. - Shoba Ranganathan (PLoS Comput. Biol., 2005)

Prediction of HLA-DQ3.2ß Ligands: evidence of multiple registers in class II binding peptides. - Joo Chuan Tong; Guanglan Zhang; Tin Wee Tan; J. Thomas August; Vladimir Brusic; Shoba Ranganathan (Bioinform., 2006)

Establishing bioinformatics research in the Asia Pacific. - Shoba Ranganathan; Martti Tammi; Michael Gribskov; Tin Wee Tan (BMC Bioinform., 2006)

Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris. - Joo Chuan Tong; Tin Wee Tan; Animesh A. Sinha; Shoba Ranganathan (BMC Bioinform., 2006)

SVM-based prediction of caspase substrate cleavage sites. - Lawrence J. K. Wee; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2006)

ASGS: an alternative splicing graph web service. - Durgaprasad Bollina; Bernett T. K. Lee; Tin Wee Tan; Shoba Ranganathan (Nucleic Acids Res., 2006)

OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. - Johann Lenffer; Frank W. Nicholas; Kao Castle; Arjun Rao; Stefan Gregory; Michael Poidinger; Matthew D. Mailman; Shoba Ranganathan (Nucleic Acids Res., 2006)

A hitchhiker's guide to expressed sequence tag (EST) analysis. - Shivashankar H. Nagaraj; Robin B. Gasser; Shoba Ranganathan (Briefings Bioinform., 2007)

Methods and protocols for prediction of immunogenic epitopes. - Joo Chuan Tong; Tin Wee Tan; Shoba Ranganathan (Briefings Bioinform., 2007)

In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. - Joo Chuan Tong; Tin Wee Tan; Shoba Ranganathan (Bioinform., 2007)

CASVM: web server for SVM-based prediction of caspase substrates cleavage sites. - Lawrence J. K. Wee; Tin Wee Tan; Shoba Ranganathan (Bioinform., 2007)

A Workflow for Mutation Extraction and Structure Annotation. - Kanagasabai Rajaraman; Khar Heng Choo; Shoba Ranganathan; Christopher J. O. Baker (J. Bioinform. Comput. Biol., 2007)

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. - Shivashankar H. Nagaraj; Nandan Deshpande; Robin B. Gasser; Shoba Ranganathan (Nucleic Acids Res., 2007)

Critical technologies for bioinformatics. - Vladimir Brusic; Shoba Ranganathan (Briefings Bioinform., 2008)

Flanking signal and mature peptide residues influence signal peptide cleavage. - Khar Heng Choo; Shoba Ranganathan (BMC Bioinform., 2008)

Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage. - Khar Heng Choo; Joo Chuan Tong; Shoba Ranganathan (BMC Bioinform., 2008)

CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge. - Jitendra Gaikwad; Varun Khanna; Subramanyam Vemulpad; Joanne Jamie; Jim Kohen; Shoba Ranganathan (BMC Bioinform., 2008)

Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. - Lesheng Kong; Shoba Ranganathan (BMC Bioinform., 2008)

In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches. - Shivashankar H. Nagaraj; Robin B. Gasser; Alasdair J. Nisbet; Shoba Ranganathan (BMC Bioinform., 2008)

Bioinformatics research in the Asia Pacific: a 2007 update. - Shoba Ranganathan; Michael Gribskov; Tin Wee Tan (BMC Bioinform., 2008)

Emerging strengths in Asia Pacific bioinformatics. - Shoba Ranganathan; Wen-Lian Hsu; Ueng-Cheng Yang; Tin Wee Tan (BMC Bioinform., 2008)

A comprehensive assessment of N-terminal signal peptides prediction methods. - Khar Heng Choo; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2009)

Physicochemical property space distribution among human metabolites, drugs and toxins. - Varun Khanna; Shoba Ranganathan (BMC Bioinform., 2009)

Towards a career in bioinformatics. - Shoba Ranganathan (BMC Bioinform., 2009)

Biomarker information extraction tool (BIET) development using natural language processing and machine learning. - Md. Tawhidul Islam; M. Shaikh; Abhaya C. Nayak; Shoba Ranganathan (ICWET, 2010)

Network analysis of human protein location. - Gaurav Kumar; Shoba Ranganathan (BMC Bioinform., 2010)

InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. - Christian Schönbach; Kenta Nakai; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2010)

Towards BioDBcore: a community-defined information specification for biological databases. - Pascale Gaudet; Amos Bairoch; Dawn Field; Susanna-Assunta Sansone; Chris F. Taylor; Teresa K. Attwood; Alex Bateman; Judith A. Blake; Carol J. Bult; J. Michael Cherry; Rex L. Chisholm; Guy Cochrane; et al. (Database J. Biol. Databases Curation, 2011)

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures. - Javed Mohammed Khan; Harish Reddy Cheruku; Joo Chuan Tong; Shoba Ranganathan (Bioinform., 2011)

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. - Varun Khanna; Shoba Ranganathan (BMC Bioinform., 2011)

Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. - Shoba Ranganathan; Christian Schönbach; Janet Kelso; Burkhard Rost; Sheila Nathan; Tin Wee Tan (BMC Bioinform., 2011)

Structural diversity of biologically interesting datasets: a scaffold analysis approach. - Varun Khanna; Shoba Ranganathan (J. Cheminformatics, 2011)

TranSeqAnnotator: large-scale analysis of transcriptomic data. - Ranjeeta Menon; Gagan Garg; Robin B. Gasser; Shoba Ranganathan (BMC Bioinform., 2012)

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs. - Christian Schönbach; Sissades Tongsima; Jonathan H. Chan; Vladimir Brusic; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2012)

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. - Gaurav Kumar; Edmond J. Breen; Shoba Ranganathan (BMC Syst. Biol., 2013)

InCoB2013 introduces Systems Biology as a major conference theme. - Christian Schönbach; Bairong Shen; Tin Wee Tan; Shoba Ranganathan (BMC Syst. Biol., 2013)

APBioNet - Transforming Bioinformatics in the Asia-Pacific Region. - Asif M. Khan; Tin Wee Tan; Christian Schönbach; Shoba Ranganathan (PLoS Comput. Biol., 2013)

InCoB2014: bioinformatics to tackle the data to knowledge challenge. - Shoba Ranganathan; Tin Wee Tan; Christian Schönbach (BMC Bioinform., 2014)

InCoB2014: Systems Biology update from the Asia-Pacific. - Shoba Ranganathan; Tin Wee Tan; Christian Schönbach (BMC Syst. Biol., 2014)

Introduction to selected papers from GIW/InCoB 2015. - Paul Horton; Christian Schönbach; Shoba Ranganathan; Siu-Ming Yiu (J. Bioinform. Comput. Biol., 2015)

GIW and InCoB are advancing bioinformatics in the Asia-Pacific. - Christian Schönbach; Paul Horton; Siu-Ming Yiu; Tin Wee Tan; Shoba Ranganathan (BMC Bioinform., 2015)

Discrete structural features among interface residue-level classes. - Gopichandran Sowmya; Shoba Ranganathan (BMC Bioinform., 2015)

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016). - Christian Schönbach; Chandra Verma; Peter J. Bond; Shoba Ranganathan (BMC Bioinform., 2016)

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. - Ari Hardianto; Muhammad Yusuf; Fei Liu 036; Shoba Ranganathan (BMC Bioinform., 2017)

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses. - Xinrui Zhou; Jie Zheng 002; Fransiskus Xaverius Ivan; Rui Yin 002; Shoba Ranganathan; Vincent T. K. Chow; Chee-Keong Kwoh 001 (BMC Genom., 2018)

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA. - Ari Hardianto; Fei Liu 036; Shoba Ranganathan (J. Chem. Inf. Model., 2018)

iSwathX: an interactive web-based application for extension of DIA peptide reference libraries. - Zainab Noor; Jemma X. Wu; Dana Pascovici; Abidali Mohamedali; Mark P. Molloy; Mark S. Baker; Shoba Ranganathan (Bioinform., 2019)

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε. - Ari Hardianto; Varun Khanna; Fei Liu 036; Shoba Ranganathan (BMC Bioinform., 2019)

Structure-Based Drug Design Workflow. - Ari Hardianto; Muhammad Yusuf; Fei Liu 036; Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Protocol for Protein Structure Modelling. - Amara Jabeen; Abidali Mohamedali; Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Rational Structure-Based Drug Design. - Varun Khanna; Shoba Ranganathan; Nikolai Petrovsky (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Quantification of Proteins From Proteomic Analysis. - Zainab Noor; Subash Adhikari; Shoba Ranganathan; Abidali Mohamedali (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Identification of Proteins From Proteomic Analysis. - Zainab Noor; Abidali Mohamedali; Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Preface. - Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Genome Databases and Browsers. - Dean Southwood; Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Host-Pathogen Interactions. - Dean Southwood; Shoba Ranganathan (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Mass spectrometry-based protein identification in proteomics - a review. - Zainab Noor; Seong Beom Ahn; Mark S. Baker; Shoba Ranganathan; Abidali Mohamedali (Briefings Bioinform., 2021)