Limviphuvadh V

AllerCatPro - Prediction of protein allergenicity potential from the protein sequence

Published date : 18 Jan 2019

MOTIVATION:
Due to the risk of inducing an immediate type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens.

type
Journal Paper
journal
Bioinformatics. 2019 Jan 18. doi: 10.1093/bioinformatics/btz029
Impact Factor
5.481

Exome sequencing and rare variant analysis reveals multiple filaggrin mutations in Bangladeshi atopic eczema families and additional risk genes

Published date : 30 May 2018

Atopic eczema (AE) is a heterogeneous chronic inflammatory skin condition that affects approximately 15–20% of children worldwide (Nutten, 2015). The prevalence varies widely among different countries, between rural and urban areas within a single country, and particular Asian skin types are more sensitive to urban environments (Ben-Gashir et al., 2004; Krutmann et al., 2014; Nutten, 2015; Odhiambo et al., 2009).

type
Journal Paper
journal
Journal of Investigative Dermatology, May 2018, doi: 10.1016/j.jid.2018.05.013
Impact Factor
6.448

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy

Published date : 11 May 2018

Background
Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy treatment outcome in Singaporean non-small cell lung cancer (NSCLC) patients.

type
Journal Paper
journal
BMC Cancer (2018), 18:555, doi: 10.1186/s12885-018-4471-x
Impact Factor
3.288

Genome-wide Analysis of Protein-Coding Variants in Leprosy

Published date : 22 Aug 2017

Although genome-wide association studies (GWAS) have greatly advanced our understanding on the contribution of common non-coding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in 7,048 leprosy patients and 14,398 healthy controls of Han Chinese.

type
Journal Paper
journal
Journal of Investigative Dermatology, 2017, Aug 22, doi: 10.1016/j.jid.2017.08.004
Impact Factor
6.287

Angiopoietin receptor TEK mutations underlie primary congenital glaucoma with variable expressivity

Published date : 06 Jun 2016

Primary congenital glaucoma (PCG) is a devastating eye disease and an important cause of childhood blindness worldwide. In PCG, defects in the anterior chamber aqueous humor outflow structures of the eye result in elevated intraocular pressure (IOP); however, the genes and molecular mechanisms involved in the etiology of these defects have not been fully characterized. Previously, we observed PCG-like phenotypes in transgenic mice that lack functional angiopoietin-TEK signaling.

type
Journal Paper
journal
The Journal of Clinical Investigation, 2016, doi:10.1172/JCI85830
Impact Factor
12.575

GGIP: structure and sequence-based GPCR-GPCR interaction pair predictor

Published date : 18 May 2016

G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases.

type
Journal Paper
journal
Proteins 2016 May 18. doi: 10.1002/prot.25071
Impact Factor
2.499

HPMV : Human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes

Published date : 26 Oct 2015

Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g.

type
Journal Paper
journal
Journal of Bioinformatics and Computational Biology, Vol. 13, No. 5 (2015), doi: 10.1142/S0219720015500286
Impact Factor
0.783

Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients

Published date : 08 Dec 2014

Background: Non-small cell lung cancer (NSCLC) is a major cause of cancer-related death worldwide due to poor
patient prognosis and clinical outcome. Here, we studied the genetic variations underlying NSCLC pathogenesis
based on their association to patient outcome after gemcitabine therapy.

Results: Bioinformatics analysis was used to investigate possible effects of POLA2 G583R (POLA2+1747 GG/GA,
dbSNP ID: rs487989) in terms of protein function. Using biostatistics, POLA2+1747 GG/GA (rs487989, POLA2 G583R)

type
Journal Paper
journal
BMC Genomics 2014, 15(Suppl 9):S20, http://www.biomedcentral.com/1471-2164/15/S9/S20
Impact Factor
4.04

Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia

Published date : 02 May 2013

Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere.

type
Journal Paper
journal
The American Journal of Human Genetics, Vol. 92, issue 5, Pg 820-826, 2 May 2013, doi:10.1016/j.ajhg.2013.04.005

Whole exome sequencing identifies a mutation for a novel form of corneal intraepithelial dyskeratosis

Published date : 24 Jan 2013

BACKGROUND:

Corneal intraepithelial dyskeratosis is an extremely rare condition. The classical form, affecting Native American Haliwa-Saponi tribe members, is called hereditary benign intraepithelial dyskeratosis (HBID). Herein, we present a new form of corneal intraepithelial dyskeratosis for which we identified the causative gene by using deep sequencing technology.
METHODS AND RESULTS:

type
Journal Paper
journal
Journal of Medical Genetics, 24 Jan 2013, doi:10.1136/jmedgenet-2012-101325
Impact Factor
6.365