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List of works by Shoba Ranganathan

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

scientific article published on 22 December 2016

A Bioinformatics Approach to Mine the Microbial Proteomic Profile of COVID-19 Mass Spectrometry Data

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

scientific article

A bioinformatics potpourri.

scientific article published on 19 January 2018

A common site within factor H SCR 7 responsible for binding heparin, C-reactive protein and streptococcal M protein.

scientific article published in April 2003

A comparative structural bioinformatics analysis of inherited mutations in β-D-Mannosidase across multiple species reveals a genotype-phenotype correlation.

scientific article

A comprehensive assessment of N-terminal signal peptides prediction methods

scientific article

A computational analysis of the electrostatic potentials and relative bond strengths of hydrazine and some of its 1,1-dimethyl derivatives

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

scientific article

A male-specific (cysteine-rich) protein of Oesophagostomum dentatum (Strongylida) with structural characteristics of a serine protease inhibitor containing two trypsin inhibitor-like domains.

scientific article

A multi-factor model for caspase degradome prediction

scientific article

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation

scientific article

A novel drug combination strategy that redesigns the pharmacological management of oral cancer

A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes' stages A-D colorectal cancers.

scientific article published on 8 April 2015

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

scientific article published on 01 January 2007

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

scientific article

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

scientific article

A site for direct integrin αvβ6·uPAR interaction from structural modelling and docking.

scientific article published on 11 January 2014

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

scientific article

A two-stage computational approach to predict novel ligands for a chemosensory receptor

A workflow for mutation extraction and structure annotation.

scientific article

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

scientific article published on 18 April 2019

APBioNet-transforming bioinformatics in the Asia-Pacific region

scientific article (publication date: October 2013)

APBioNet: the Asia-Pacific regional consortium for bioinformatics.

scientific article published in January 2002

ASGS: an alternative splicing graph web service

scientific article

Ab initio study of the stepwise hydration of NO +

Accelerating the search for the missing proteins in the human proteome

scientific article published on 24 January 2017

Accurate prediction of scorpion toxin functional properties from primary structures

scientific article published on 01 September 2005

Adaptive Immune System

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

scientific article

Advances in translational bioinformatics and population genomics in the Asia-Pacific

scientific article published on 13 December 2012

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

scientific article

An ab initio study of the binding of N2 to Na+ and K+

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

scientific article

An ethnobotanical study of medicinal plants used by the Yaegl Aboriginal community in northern New South Wales, Australia

scientific article

An integrated transcriptomics and proteomics analysis of the secretome of the helminth pathogen Fasciola hepatica: proteins associated with invasion and infection of the mammalian host.

scientific article published on 14 May 2009

Antisense Suppression of a Cytokinin-binding Protein from Petunia Causes Excessive Branching and Reduces Adventitious Shoot Bud Induction in Vitro

Applications of machine learning in GPCR bioactive ligand discovery

scientific article published on 18 April 2019

Ascaris suum draft genome

scientific article

Author Correction: Enhancing protein backbone angle prediction by using simpler models of deep neural networks

B Cell-mediated Immune Response

BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling

scientific article published on 07 April 2021

Bacterial Antigens Reduced the Inhibition Effect of Capsaicin on Cal 27 Oral Cancer Cell Proliferation

scientific article published in 2021

Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans‐Proteomic Pipeline

Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform.

scientific article

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

scientific article

Bioinformatics approaches for improving seminal plasma proteome analysis

scientific article published on 31 May 2019

Bioinformatics education--perspectives and challenges ⬇️

scientific article published in November 2005

Bioinformatics meets parasitology.

scientific article published on May 2012

Bioinformatics research in the Asia Pacific: a 2007 update

scientific article

Biological Data Integration Using Network Models

Bond-order-bond-energy correlations

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

scientific article published on 28 June 2007

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

scientific article

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

scientific article

Characterization of the interaction between heterodimeric αvβ6 integrin and urokinase plasminogen activator receptor (uPAR) using functional proteomics

scientific article published on 29 October 2014

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

scientific article published in 2018

Cloning and molecular characterization of the first aquatic hyaluronidase, SFHYA1, from the venom of stonefish (Synanceja horrida).

scientific article published on 11 November 2004

Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions

scientific article published on 29 April 2015

Comparative Genomic Analysis of Glycoylation Pathways in Yeast, Plants and Higher eukaryotes

article

Compliant fields for formic acid and formamide

Compliant fields for molecular interactions: Water dimer and formic acid dimer

Compliant fields for water, ammonia and methane

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

scientific article published on 7 July 2009

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses.

scientific article

Computer-aided vaccine design

Correlations between the solvent hydrogen bond acceptor parameter .beta. and the calculated molecular electrostatic potential

Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock

scientific article published on 27 May 2015

Critical technologies for bioinformatics

scientific article published on 22 May 2008

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

scientific article

Database design

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

scientific article

Deduction of functional peptide motifs in scorpion toxins

scientific article published on 01 June 2006

Deep insights into Dictyocaulus viviparus transcriptomes provides unique prospects for new drug targets and disease intervention

scientific article published on 22 December 2010

Delineation of modular proteins: domain boundary prediction from sequence information.

scientific article

Discrete structural features among interface residue-level classes.

scientific article published on 9 December 2015

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

scientific article published on 25 January 2017

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

scientific article published on 04 February 2019

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

scientific article published in June 2007

Ecological niche modeling of customary medicinal plant species used by Australian Aborigines to identify species-rich and culturally valuable areas for conservation

article

Editorial overview: Theory and simulation: demystifying GPCRs - structure, function and drug design

scientific article published on 01 April 2019

Editorial: Bioinformatics and the Translation of Data-Driven Discoveries

Emerging strengths in Asia Pacific bioinformatics

scientific article

Enhancing protein backbone angle prediction by using simpler models of deep neural networks

scientific article published on 10 November 2020

Establishing bioinformatics research in the Asia Pacific

article

Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes

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

scientific article published on 28 December 2017

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

scientific article

Extracting Biomarker Information Applying Natural Language Processing and Machine Learning

scholarly article by Md. Tawhidul Islam et al published June 2010 in International Conference on Bioinformatics and Biomedical Engineering : [proceedings]. International Conference on Bioinformatics and Biomedical Engineering

First transcriptomic analysis of the economically important parasitic nematode, Trichostrongylus colubriformis, using a next-generation sequencing approach

scientific article published on 6 August 2010

Flanking signal and mature peptide residues influence signal peptide cleavage

scientific article

Functional and structural implications of the complement factor H Y402H polymorphism associated with age-related macular degeneration

scientific article published on 8 February 2008

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

scientific article published on 11 January 2013

GIW and InCoB are advancing bioinformatics in the Asia-Pacific.

scientific article

GIW and InCoB, two premier bioinformatics conferences in Asia with a combined 40 years of history

scientific article

Gender-enriched transcripts in Haemonchus contortus--predicted functions and genetic interactions based on comparative analyses with Caenorhabditis elegans

scientific article published on 26 July 2007

Genome Databases and Browsers

Genome of the human hookworm Necator americanus

scientific article

Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases

scientific article

Genomic characterization of Tv-ant-1, a Caenorhabditis elegans tag-61 homologue from the parasitic nematode Trichostrongylus vitrinus

scientific article published on 30 March 2007

Graphs in Bioinformatics

Head and Neck Cancer Immunotherapy: Molecular Biological Aspects of Preclinical and Clinical Research

Helminth secretome database (HSD): a collection of helminth excretory/secretory proteins predicted from expressed sequence tags (ESTs).

scientific article

High-Throughput Functional Annotation and Data Mining of Fungal Genomes to Identify Therapeutic Targets

Host-Pathogen Interactions

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

scientific article

Hybrid Quantum and Molecular Mechanical (QM/MM) Studies on the Pyruvate tol-Lactate Interconversion inl-Lactate Dehydrogenase

scientific article published in July 1997

Identification of Proteins From Proteomic Analysis

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

scientific article

Imaginative Order from Reasonable Chaos: Conformation-Driven Activity and Reactivity in Exploring Protein–Ligand Interactions

Improved insights into the transcriptomes of the human hookworm Necator americanus--fundamental and biotechnological implications

scientific article published on 18 October 2008

In Silico Methods for the Analysis of Metabolites and Drug Molecules

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 7 November 2006

In silico secretome analysis approach for next generation sequencing transcriptomic data.

scientific article

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

scientific article

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

scientific article

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs

scientific article published on 13 December 2012

InCoB2013 introduces Systems Biology as a major conference theme

scientific article published on 4 November 2013

InCoB2014: Systems Biology update from the Asia-Pacific. Introduction

scientific article published on 8 December 2014

InCoB2014: bioinformatics to tackle the data to knowledge challenge. Introduction

scientific article published on 8 December 2014

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

scientific article published on 8 December 2014

Infectious disease informatics

scholarly article published 2013

Intelligent Agent System for Bio-medical Literature Mining

Introduction to selected papers from GIW/InCoB 2015

Leveraging homologies for cross-species plasma proteomics in ungulates using data-independent acquisition

Linking structural features of protein complexes and biological function.

scientific article

Looking for Missing Proteins

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

scientific article

ML218 HCl Is More Efficient Than Capsaicin in Inhibiting Bacterial Antigen-Induced Cal 27 Oral Cancer Cell Proliferation

scientific article published in 2021

MPID-T

scientific article published on 01 January 2006

MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures

scientific article

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

scientific article published on 01 January 2003

Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors

scientific article published in 2021

Major colour patterns of reef-building corals are due to a family of GFP-like proteins

Mass spectrometry-based protein identification in proteomics-a review

scientific article published on 11 February 2020

Massively parallel sequencing and analysis of the Necator americanus transcriptome

scientific article published on 11 May 2010

Mechanistic aspects of biological redox reactions involving NADH. Part 5.—AM1 transition-state studies for the pyruvate–L-lactate interconversion inL-lactate dehydrogenase

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

scientific article (publication date: 25 December 2010)

Metaproteomic Analysis of an Oral Squamous Cell Carcinoma Dataset Suggests Diagnostic Potential of the Mycobiome

scientific article published in 2023

Methods and protocols for prediction of immunogenic epitopes

scientific article published on 31 October 2006

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

scientific article

Modeling the bound conformation of Pemphigus vulgaris-associated peptides to MHC Class II DR and DQ alleles

scientific article

Modeling the structure of bound peptide ligands to major histocompatibility complex

scientific article published on September 2004

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

scientific article published on 17 January 2018

Molecular similarity and diversity approaches in chemoinformatics

Needles in the EST haystack: large-scale identification and analysis of excretory-secretory (ES) proteins in parasitic nematodes using expressed sequence tags (ESTs)

scientific article

Network analysis of human protein location.

scientific article

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

scientific article

Oesophagostomum dentatum: potential as a model for genomic studies of strongylid nematodes, with biotechnological prospects

scientific article published on 7 February 2007

PMHC Epitope

PMHC Imprint

PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids

scientific article published in Scientific Reports

Physiochemical property space distribution among human metabolites, drugs and toxins

scientific article

Pinpointing the putative heparin/sialic acid-binding residues in the 'sushi' domain 7 of factor H: a molecular modeling study

scientific article published on 01 January 2000

Predicted structure of the extracellular region of ligand-gated ion-channel receptors shows SH2-like and SH3-like domains forming the ligand-binding site

scientific article

Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides

scientific article published in March 2006

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

scientific article published on 18 December 2006

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

scientific article published on 14 August 2017

Prediction of novel mouse TLR9 agonists using a random forest approach

scientific article published on 20 December 2019

Preface

Proliferation and Apoptosis Pathways and Factors in Oral Squamous Cell Carcinoma

scientific article published in 2022

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

scientific article published on 13 December 2013

Protein-protein interactions and prediction: a comprehensive overview

scientific article published on January 2014

Protocol for Protein Structure Modelling

Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly

Quantification of Proteins From Proteomic Analysis

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

scientific article published on 15 June 2015

Radial behavior of the average local ionization energies of atoms

Rational Structure-Based Drug Design

Role of solvent accessibility for aggregation-prone patches in protein folding

scientific article published in Scientific Reports

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

scientific article published on 30 January 2006

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

scientific article published on July 2004

SPdb--a signal peptide database.

scientific article

SVM-based prediction of caspase substrate cleavage sites

scientific article published on 18 December 2006

Scientific publications and databases

Secretome: clues into pathogen infection and clinical applications

scientific article

Semiempirical molecular-orbital studies on the problem of nonclassical resonance in the homoallylic cation

Simple re-instantiation of small databases using cloud computing.

scientific article

Structural Immunoinformatics

Structural Immunoinformatics

Structural Immunoinformatics: Understanding MHC-Peptide-TR Binding

Structural bioinformatics analysis of variants on GPCR function

scientific article published on 01 April 2019

Structural diversity of biologically interesting datasets: a scaffold analysis approach

scientific article

Structure-Based Clustering of Major Histocompatibility Complex (MHC) Proteins for Broad-Based T-Cell Vaccine Design

scientific article published on 01 January 2014

Substituent effects on carbonyl bond orders

Systems Proteomics View of the Endogenous Human Claudin Protein Family

scientific article

T Cell Activation

T Cell Epitopes

T Cell Signaling

TR Germline Bias

article

TR Recognition of MHC-Peptide Complexes

article published in 2013

TRPA1: A Potential Prognostic Indicator for Oral Squamous Cell Carcinoma

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

scientific article

The Gene for a Novel Member of the Whey Acidic Protein Family Encodes Three Four-disulfide Core Domains and Is Asynchronously Expressed during Lactation

scientific article published in Journal of Biological Chemistry

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

scholarly article by Yun Ping Lim published in January 2003

The force field of carbon suboxide

The force field of carbon suboxide

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The gramicidin A channel: comparison of the energy profiles of Na+ , K+ and Cs+

scientific article published on 01 August 1984

The gramicidin A channel: theoretical energy profile computed for single occupancy by a divalent cation, Ca2+

The hand, foot and mouth disease virus capsid: sequence analysis and prediction of antigenic sites from homology modelling.

scientific article published in January 2002

The integrin alpha L beta 2 hybrid domain serves as a link for the propagation of activation signal from its stalk regions to the I-like domain

scientific article published on 27 September 2004

The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease

scientific article

The transcriptome of Echinostoma caproni adults: further characterization of the secretome and identification of new potential drug targets.

scientific article published on 21 June 2013

The use of CNDO/force and compliance constant methods in evaluating quadratic potential functions of carbonyl and formyl fluorides

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

Towards a career in bioinformatics

scientific article

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

scientific article

TranSeqAnnotator: large-scale analysis of transcriptomic data.

scientific article

Transcriptional changes in the hookworm, Ancylostoma caninum, during the transition from a free-living to a parasitic larva

scientific article published on 9 January 2008

Transcriptome analysis reveals pathogenicity and evolutionary history of the pathogenic oomycete Pythium insidiosum

scientific article published on 6 February 2014

Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one.

scientific article

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

scientific article published on 6 November 2013

Untangling Biological Networks Using Bioinformatics

Vaccine adjuvant informatics

Whole-genome sequence of Schistosoma haematobium

scientific article

XdomView: protein domain and exon position visualization.

scientific article

Xpro: database of eukaryotic protein-encoding genes.

scientific article

iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors

scientific article published in 2024

iSwathX 2.0 for Processing DDA Spectral Libraries for DIA Data Analysis

scientific article published on 01 June 2020

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

scientific article published on 01 February 2019

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

scientific article

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

scientific article published on 27 September 2010

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