JENJAROENPUN Piroon

"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

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

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

Published date : 13 Oct 2017

The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications.

type
Journal Paper
journal
Genome Research 2017, 27, Pg 1783-1794, doi: 10.1101/gr.223313.117
Impact Factor
11.922

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

Published date : 28 Nov 2016

R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes.

type
Journal Paper
journal
Nucleic Acids Research, 2016, 1, doi: 10.1093/nar/gkw1054
Impact Factor
9.202

Sense-antisense gene-pairs in breast cancer and associated pathological pathways

Published date : 28 Oct 2015

More than 30% of human protein-coding genes form hereditary complex genome architectures composed of sense-antisense (SA) gene pairs (SAGPs) transcribing their RNAs from both strands of a given locus. Such architectures represent important novel components of genome complexity contributing to gene expression deregulation in cancer cells. Therefore, the architectures might be involved in cancer pathways and, in turn, be used for novel drug targets discovery. However, the global roles of SAGPs in cancer pathways has not been studied.

type
Journal Paper
journal
Oncotarget. 2015 Dec 8;6(39):42197-221. doi: 10.18632/oncotarget.6255
Impact Factor
6.359

Abstract 1990: The key role of MECOM complex locus and its products in high-grade ovarian carcinoma pathogenesis and clinical outcomes

Published date : 01 Aug 2015

The ecotropic virus integration site 1(Evi1) transcription factor, encoded in the MECOM complex locus, is implicated in several cancers, including ovarian cancer(OC). High-grade serous OC(HG-SOC) represents its most common and aggressive form. The pathobiological and clinical roles of MECOM and its products in HG-SOC are poorly understood.

type
Journal Paper
journal
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA: Cancer Research Aug 1, 2015 75,1990, doi: 10.1158/1538-7445.AM2015-1990

Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study

Published date : 09 May 2015

Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters.

type
Journal Paper
journal
Nuclei Acids Research 2015, Vol. 43, No. 11, Pg 5630-5646, doi: 10.1093/nar/gkv355
Impact Factor
9.112

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

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

Published date : 16 Oct 2014

A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases.

type
Journal Paper
journal
Nucleic Acids Research, 2014, doi: 10.1093/nar/gku970

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