WONGSURAWAT Thidathip

"Towards Predictive R-loop Computational Biology: Genome-Scale Prediction of R-loops Reveals Their association with Complex Promoter Structures, G-Quadruplexes and Transcriptionally Active Enhancers"

Published date : 26 Jun 2018

R-loops are three-stranded RNA:DNA hybrid structures essential for many normal and pathobiological processes. Previously, we generated a quantitative R-loop forming sequence (RLFS) model, quantitative model of R-loop-forming sequences (QmRLFS) and predicted ∼660 000 RLFSs; most of them located in genes and gene-flanking regions, G-rich regions and disease-associated genomic loci in the human genome. Here, we conducted a comprehensive comparative analysis of these RLFSs using experimental data and demonstrated the high performance of QmRLFS predictions on the nucleotide and genome scales.

type
Journal Paper
journal
Nuclei Acids Research, 2018 Jun 26. doi: 10.1093/nar/gky554
Impact Factor
11.561

Gene expression profile analysis of aortic vascular smooth muscle cells reveals upregulation of cadherin genes in myocardial infarction patients

Published date : 18 May 2018

Myocardial infarction (MI) induced by acute coronary arterial occlusion is usually secondary to atherosclerotic plaque rupture. Dysregulated response of vascular smooth muscle cells (VSMCs) in atherosclerotic plaques may promote plaque rupture. Cadherins (CDHs) form adherens junctions and are known stabilizers of atherosclerotic plaques. To date, the expression patterns of cadherin have not been well investigated in MI aortic VSMCs. We aimed to investigate the expression of cadherin genes in the aortic wall of patients with and without MI.

type
Journal Paper
journal
Physiological Genomics, 18 May 2018, doi: 10.1152/physiolgenomics.00042.2017
Impact Factor
2.782

Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients

Published date : 06 Feb 2018

This article contains further data and information from our published manuscript [1]. We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Microarray gene analysis was applied to evaluate VSMCs of MI and non-MI patients. Prediction Analysis of Microarray (PAM) identified genes that significantly discriminated the two groups of samples. Incorporation of gene ontology (GO) identified a VSMCs-associated classifier that discriminated between the two groups of samples.

type
Journal Paper
journal
Data in Brief, Vol. 17, April 2018, Pg 1112-1135, doi: 10.1016/j.dib.2018.01.108
Impact Factor
0.287

Distinctive molecular signature and activated signaling pathways in aortic smooth muscle cells of patients with myocardial infarction

Published date : 31 Jan 2018

BACKGROUND AND AIMS:
We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Providing a robust transcriptomic signature, we aim to highlight the most likely aberrant pathway(s) in MI VSMCs.

type
Journal Paper
journal
Atherosclerosis, April 2018, Vol. 271, Pg 237-244, doi: 10.1016/j.atherosclerosis.2018.01.024
Impact Factor
4.467

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

Published date : 16 Apr 2015

The possible formation of three-stranded RNA and DNA hybrid structures (R-loops) in thousands of functionally important guanine-rich genic and inter-genic regions could suggest their involvement in transcriptional regulation and even development of diseases. Here, we introduce the first freely available R-loop prediction program called Quantitative Model of R-loop Forming Sequence (RLFS) finder (QmRLFS-finder), which predicts RLFSs in nucleic acid sequences based on experimentally supported structural models of RLFSs. QmRLFS-finder operates via a web server or a stand-alone command line tool.

type
Journal Paper
journal
Nucleic Acids Research, 2015, 1, doi: 10.1093/nar/gkv344

R-loops in proliferating cells but not in the brain: implications for AOA2 and other autosomal recessive ataxias

Published date : 17 Mar 2014

Disruption of the Setx gene, defective in ataxia oculomotor apraxia type 2 (AOA2) leads to the accumulation of DNA/RNA hybrids (R-loops), failure of meiotic recombination and infertility in mice. We report here the presence of R-loops in the testes from other autosomal recessive ataxia mouse models, which correlate with fertility in these disorders. R-loops were coincident in cells showing high basal levels of DNA double strand breaks and in those cells undergoing apoptosis.

type
Journal Paper
journal
PLOS One, March 2014, Vol. 9, Issue 3, doi: 10.1371/journal.pone.0090219
Impact Factor
3.73

Quantitative model of R-loop forming structures reveals a novel level of RNA–DNA interactome complexity

Published date : 25 Nov 2011

R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66 803 sequences defined by UCSC as ‘known’ genes.

type
Journal Paper
journal
Nucleic Acids Research 2012 January; 40(2): e16, doi: 10.1093/nar/gkr1075
Impact Factor
8.026