Shoba Ranganathan

发表

Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors

Lesheng Kong, Shoba Ranganathan, S. Ranganathan, 2008, BMC Bioinformatics.

Prediction of interface residue based on the features of residue interaction network.

Shoba Ranganathan, Xiong Jiao, S. Ranganathan, 2017, Journal of theoretical biology.

Flanking signal and mature peptide residues influence signal peptide cleavage

Shoba Ranganathan, Khar Heng Choo, K. Choo, 2008, BMC Bioinformatics.

Rational Structure-Based Drug Design

Nikolai Petrovsky, Shoba Ranganathan, Varun Khanna, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Protocol for Protein Structure Modelling

Shoba Ranganathan, Amara Jabeen, Abidali Mohamedali, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris

Tin Wee Tan, Joo Chuan Tong, Shoba Ranganathan, 2006, BMC Bioinformatics.

MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules

Tin Wee Tan, Pandjassarame Kangueane, Shoba Ranganathan, 2003, Bioinform..

Biomarker information extraction tool (BIET) development using natural language processing and machine learning

Abhaya C. Nayak, Shoba Ranganathan, Md. Tawhidul Islam, 2010, ICWET.

XdomView: protein domain and exon position visualization

Tin Wee Tan, Vivek Gopalan, Shoba Ranganathan, 2003, Bioinform..

A hitchhiker's guide to expressed sequence tag (EST) analysis

Robin B. Gasser, Shoba Ranganathan, Shivashankar H. Nagaraj, 2006, Briefings Bioinform..

CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge

Varun Khanna, Shoba Ranganathan, Jitendra Gaikwad, 2008, BMC Bioinformatics.

Xpro: database of eukaryotic protein-encoding genes

Tin Wee Tan, Vivek Gopalan, Shoba Ranganathan, 2004, Nucleic Acids Res..

A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes.

Shoba Ranganathan, Abidali Mohamedali, Mohammad Tawhidul Islam, 2017, Methods in molecular biology.

Methods and protocols for prediction of immunogenic epitopes

Tin Wee Tan, Joo Chuan Tong, Shoba Ranganathan, 2006, Briefings Bioinform..

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform

Shoba Ranganathan, Shivashankar H. Nagaraj, Robin B Gasser, 2007, Nucleic Acids Res..

APBioNet: the Asia-Pacific regional consortium for bioinformatics.

Tin Wee Tan, Shoba Ranganathan, S Subbiah, 2002, Applied bioinformatics.

In silico grouping of peptide/HLA class I complexes using structural interaction characteristics

Tin Wee Tan, Joo Chuan Tong, Shoba Ranganathan, 2007, Bioinform..

Critical technologies for bioinformatics

Vladimir Brusic, Shoba Ranganathan, 2008, Briefings Bioinform..

Protein-protein interactions and prediction: a comprehensive overview.

Shoba Ranganathan, Gopichandran Sowmya, S. Ranganathan, 2013, Protein and peptide letters.

A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era

Tin Wee Tan, Shoba Ranganathan, Shen Jean Lim, 2009, BMC Genomics.

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics

Shoba Ranganathan, Christian Schönbach, Kenta Nakai, 2019 .

Adaptive immune system [encyclopaedia entry]

Shoba Ranganathan, S. Ranganathan, 2013 .

Graphs in bioinformatics

Shoba Ranganathan, Elsa Chacko, S. Ranganathan, 2010 .

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

Dana Pascovici, Mehdi Mirzaei, Vivek Gupta, 2018, International journal of molecular sciences.

OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI

Matthew D. Mailman, Shoba Ranganathan, Frank W. Nicholas, 2005, Nucleic Acids Res..

In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches

Robin B. Gasser, Shoba Ranganathan, Shivashankar H. Nagaraj, 2008, BMC Bioinformatics.

SPdb – a signal peptide database

Tin Wee Tan, Shoba Ranganathan, Khar Heng Choo, 2005, BMC Bioinformatics.

DEDB: a database of Drosophila melanogaster exons in splicing graph form

Tin Wee Tan, Shoba Ranganathan, Bernett T. K. Lee, 2004, BMC Bioinformatics.

MVC Architecture in Bioinformatics web applications and its Java implementation

Shoba Ranganathan, Bernett T. K. Lee, Durgaprasad Bollina, 2005, iiWAS.

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases

Fei Liu, Muhammad Yusuf, Ari Hardianto, 2017, BMC Bioinformatics.

Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage

Joo Chuan Tong, Shoba Ranganathan, Khar Heng Choo, 2008, BMC Bioinformatics.

MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences

Tin Wee Tan, Shoba Ranganathan, Bernett T. K. Lee, 2003, Nucleic Acids Res..

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA

Ari Hardianto, Shoba Ranganathan, Fei Liu, 2018, J. Chem. Inf. Model..

Emerging strengths in Asia Pacific bioinformatics

Tin Wee Tan, Wen-Lian Hsu, Shoba Ranganathan, 2008, BMC Bioinformatics.

In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance

Varun Khanna, Shoba Ranganathan, S. Ranganathan, 2011, BMC Bioinformatics.

iSwathX: an interactive web-based application for extension of DIA peptide reference libraries

Dana Pascovici, Shoba Ranganathan, Mark P. Molloy, 2018, Bioinform..

Physiochemical property space distribution among human metabolites, drugs and toxins

Varun Khanna, Shoba Ranganathan, S. Ranganathan, 2009, BMC Bioinformatics.

GIW and InCoB are advancing bioinformatics in the Asia-Pacific

Tin Wee Tan, Paul Horton, Siu-Ming Yiu, 2015, BMC Bioinformatics.

Towards a career in bioinformatics

Shoba Ranganathan, 2009, BMC Bioinformatics.

Challenges for Intelligent Systems in Biology

Satoru Miyano, Russ B. Altman, Alfonso Valencia, 2001, IEEE Intell. Syst..

SVM-based prediction of caspase substrate cleavage sites

Tin Wee Tan, Shoba Ranganathan, Lawrence J. K. Wee, 2006, BMC Bioinformatics.

Establishing bioinformatics research in the Asia Pacific

Tin Wee Tan, Michael Gribskov, Shoba Ranganathan, 2006, BMC Bioinformatics.

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs

Tin Wee Tan, Vladimir Brusic, Jonathan H. Chan, 2012, BMC Bioinformatics.

InCoB2014: bioinformatics to tackle the data to knowledge challenge

Tin Wee Tan, Shoba Ranganathan, Christian Schönbach, 2014, BMC Bioinformatics.

SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins

Tin Wee Tan, Joo Chuan Tong, Lesheng Kong, 2004, Nucleic Acids Res..

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region

Tin Wee Tan, Shoba Ranganathan, Asif M. Khan, 2013, PLoS Comput. Biol..

Bioinformatics research in the Asia Pacific: a 2007 update

Tin Wee Tan, Michael Gribskov, Shoba Ranganathan, 2008, BMC Bioinformatics.

Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference

Tin Wee Tan, Burkhard Rost, Janet Kelso, 2011, BMC Bioinformatics.

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε

Varun Khanna, Fei Liu, Ari Hardianto, 2019, BMC Bioinformatics.

TranSeqAnnotator: large-scale analysis of transcriptomic data

Robin B. Gasser, Shoba Ranganathan, Gagan Garg, 2012, BMC Bioinformatics.

InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010

Tin Wee Tan, Kenta Nakai, Shoba Ranganathan, 2010, BMC Bioinformatics.

InCoB2014: mining biological data from genomics for transforming industry and health

Tin Wee Tan, Shoba Ranganathan, Christian Schönbach, 2014, BMC Genomics.

De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data.

Shoba Ranganathan, Abidali Mohamedali, Mohammad Tawhidul Islam, 2017, Methods in molecular biology.

InCoB2013 introduces Systems Biology as a major conference theme

Tin Wee Tan, Bairong Shen, Shoba Ranganathan, 2013, BMC Systems Biology.

Delineation of modular proteins: Domain boundary prediction from sequence information

Lesheng Kong, Shoba Ranganathan, S. Ranganathan, 2004, Briefings Bioinform..

Structural diversity of biologically interesting datasets: a scaffold analysis approach

Varun Khanna, Shoba Ranganathan, S. Ranganathan, 2011, J. Cheminformatics.

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

Edmond J. Breen, Gaurav Kumar, Shoba Ranganathan, 2013, BMC Systems Biology.

Bioinformatics Education—Perspectives and Challenges

Shoba Ranganathan, S. Ranganathan, 2005, PLoS Comput. Biol..

CASVM: web server for SVM-based prediction of caspase substrates cleavage sites

Tin Wee Tan, Shoba Ranganathan, Lawrence J. K. Wee, 2007, Bioinform..

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016)

Shoba Ranganathan, Christian Schönbach, Chandra Verma, 2016, BMC Bioinformatics.

A comprehensive assessment of N-terminal signal peptides prediction methods

Tin Wee Tan, Shoba Ranganathan, Khar Heng Choo, 2009, BMC Bioinformatics.

Network analysis of human protein location

Gaurav Kumar, Shoba Ranganathan, S. Ranganathan, 2010, BMC Bioinformatics.

InCoB2014: Systems Biology update from the Asia-Pacific

Tin Wee Tan, Shoba Ranganathan, Christian Schönbach, 2014, BMC Systems Biology.

A Workflow for Mutation Extraction and Structure Annotation

Kanagasabai Rajaraman, Christopher J. O. Baker, Shoba Ranganathan, 2007, J. Bioinform. Comput. Biol..

Applications of machine learning in GPCR bioactive ligand discovery.

Shoba Ranganathan, Amara Jabeen, S. Ranganathan, 2019, Current opinion in structural biology.

Structural bioinformatics Prediction of HLA-DQ 3 . 2 b Ligands : evidence of multiple registers in class II binding peptides

Tin Wee Tan, Joo Chuan Tong, Vladimir Brusic, 2006 .

Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi)

Tin Wee Tan, Joo Chuan Tong, Shoba Ranganathan, 2010, BMC Genomics.

ASGS: an alternative splicing graph web service

Tin Wee Tan, Shoba Ranganathan, Bernett T. K. Lee, 2006, Nucleic Acids Res..

Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

Tin Wee Tan, Kenta Nakai, Shoba Ranganathan, 2010, BMC Genomics.

Accurate prediction of scorpion toxin functional properties from primary structures.

Tin Wee Tan, Vladimir Brusic, Shoba Ranganathan, 2005, Journal of molecular graphics & modelling.

An Integrated Transcriptomics and Proteomics Analysis of the Secretome of the Helminth Pathogen Fasciola hepatica

Shoba Ranganathan, Ranjeeta Menon, S. Ranganathan, 2009, Molecular & Cellular Proteomics.

A practical guide to structure-based prediction of MHC-binding peptides.

Joo Chuan Tong, Shoba Ranganathan, J. Tong, 2007, Methods in molecular biology.

Extending Asia Pacific bioinformatics into new realms in the "-omics" era

Tin Wee Tan, Joo Chuan Tong, Frank Eisenhaber, 2009, BMC Genomics.

2016 update on APBioNet’s annual international conference on bioinformatics (InCoB)

Shoba Ranganathan, Christian Schönbach, Chandra Verma, 2016, BMC Genomics.

Human Prestin: A Candidate PE1 Protein Lacking Stringent Mass Spectrometric Evidence?

Shoba Ranganathan, Abidali Mohamedali, Seong Beom Ahn, 2017, Journal of proteome research.

A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus

Shoba Ranganathan, Robin B Gasser, Shivashankar H Nagaraj, 2007, BMC Genomics.

MPID-T

Tin Wee Tan, Joo Chuan Tong, Lesheng Kong, 2006 .

Functional annotation of the human chromosome 7 "missing" proteins: a bioinformatics approach.

Shoba Ranganathan, Mark S Baker, S. Ranganathan, 2013, Journal of proteome research.

Structural Immunoinformatics: Understanding MHC-Peptide-TR Binding

Joo Chuan Tong, Shoba Ranganathan, Javed Mohammed Khan, 2009 .

Linking structural features of protein complexes and biological function

Edmond J. Breen, Shoba Ranganathan, Gopichandran Sowmya, 2015, Protein science : a publication of the Protein Society.

The S‐star trial bioinformatics course: An on‐line learning success *

Tin Wee Tan, Shoba Ranganathan, Winston Hide, 2003 .

An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications

Shoba Ranganathan, Makedonka Mitreva, Robin B Gasser, 2012, BMC Genomics.

MGAlign, a Reduced Search Space Approach to the Alignment of mRNA Sequences to Genomic Sequences

Tin Wee Tan, Shoba Ranganathan, Bernett T. K. Lee, 2003 .

Bond-order-bond-energy correlations

Shoba Ranganathan, Peter Politzer, S. Ranganathan, 1986 .

Genome of the human hookworm Necator americanus

Paul W. Sternberg, Robin B. Gasser, Philip L. Felgner, 2014, Nature Genetics.

Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

William S Hancock, Shoba Ranganathan, Mark S Baker, 2014, Journal of proteome research.

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Juan Antonio Vizcaíno, Yassene Mohammed, Ekaterina Mostovenko, 2015, Journal of proteome research.

In silico characterization of immunogenic epitopes presented by HLA-Cw*0401

Tin Wee Tan, Joo Chuan Tong, Vladimir Brusic, 2007, Immunome research.

Advanced in silico analysis of expressed sequence tag (EST) data for parasitic nematodes of major socio-economic importance--fundamental insights toward biotechnological outcomes.

Shoba Ranganathan, Robin B Gasser, Ranjeeta Menon, 2009, Biotechnology advances.

Unlocking the puzzling biology of the black Périgord truffle Tuber melanosporum.

Shoba Ranganathan, Abidali Mohamedali, Javed Mohammed Khan, 2013, Journal of proteome research.

Discrete structural features among interface residue-level classes

Shoba Ranganathan, Gopichandran Sowmya, S. Ranganathan, 2015, BMC Bioinformatics.

Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement.

Ari Hardianto, Shoba Ranganathan, Fei Liu, 2017, Organic & biomolecular chemistry.

InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia

Tin Wee Tan, Janet Kelso, Shoba Ranganathan, 2011, BMC Genomics.

Adaptive immune system

Shoba Ranganathan, S. Ranganathan, 2013 .

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform

Robin B. Gasser, Shoba Ranganathan, Shivashankar H. Nagaraj, 2007, Environmental health perspectives.

Ascaris suum draft genome

Paul W. Sternberg, Xun Xu, Robin B. Gasser, 2011, Nature.

Needles in the EST Haystack: Large-Scale Identification and Analysis of Excretory-Secretory (ES) Proteins in Parasitic Nematodes Using Expressed Sequence Tags (ESTs)

Robin B. Gasser, Shoba Ranganathan, Shivashankar H. Nagaraj, 2008, PLoS neglected tropical diseases.

pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes

Shoba Ranganathan, Javed Mohammed Khan, S. Ranganathan, 2010, Immunome research.

Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse

Shoba Ranganathan, Elsa Chacko, S. Ranganathan, 2009, BMC Genomics.

SCORPION2: a database for structure-function analysis of scorpion toxins.

Vladimir Brusic, Anitha Veeramani, Shoba Ranganathan, 2006, Toxicon : official journal of the International Society on Toxinology.

kappa-Hefutoxin1, a novel toxin from the scorpion Heterometrus fulvipes with unique structure and function. Importance of the functional diad in potassium channel selectivity.

Shoba Ranganathan, Isabelle Huys, Jan Tytgat, 2002, The Journal of biological chemistry.

Modeling the structure of bound peptide ligands to major histocompatibility complex

Shoba Ranganathan, T. Tan, J. Tong, 2004, Protein science : a publication of the Protein Society.

Whole-genome sequence of Schistosoma haematobium

Jian Wang, Xun Xu, Adhemar Zerlotini, 2012, Nature Genetics.