JENJAROENPUN Piroon

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

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
Url: 
https://academic.oup.com/nar/article/45/D1/D119/2605726/R-loopDB-a-database-for-R-loop-forming-sequences
Impact Factor: 
9.202
Date of acceptance: 
2016-10-20

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

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
Url: 
http://cancerres.aacrjournals.org/content/75/15_Supplement/1990

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response.

type: 
Journal Paper
journal: 
Scientific Reports 5,Article no: 9737, 2015, doi: 10.1038/srep09737
Url: 
http://www.nature.com/srep/2015/150527/srep09737/full/srep09737.html
Date of acceptance: 
2015-02-04

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

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
pubmed: 
25958397
Url: 
http://nar.oxfordjournals.org/content/43/11/5630.long
Impact Factor: 
9.112
Date of acceptance: 
2016-01-06

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

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
pubmed: 
25883153
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/25883153
Date of acceptance: 
2015-04-06

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

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
pubmed: 
25324314
Url: 
http://nar.oxfordjournals.org/content/early/2014/10/16/nar.gku970.full?keytype=ref&ijkey=mAOj0VL101EhMQN
Date of acceptance: 
2014-10-02

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

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
pubmed: 
24637776
Url: 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090219
Impact Factor: 
3.73
Date of acceptance: 
2014-01-27

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing

Exosomes are nanosized (30-100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics.

type: 
Journal Paper
journal: 
PeerJ. 2013 Nov 5, http://dx.doi.org/10.7717/peerj.201
pubmed: 
24255815
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/?term=24255815
Date of acceptance: 
2013-10-13

Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells

Background

type: 
Journal Paper
journal: 
BMC Systems Biology 2013, 7(Suppl 3):S11, doi:10.1186/1752-0509-7-S3-S11
Url: 
http://www.biomedcentral.com/1752-0509/7/S3/S11
Impact Factor: 
2.98

How to discriminate between potentially novel and considered biomarkers within molecular signature?

The lack of consensus among reported molecular (gene, protein, regulatory marker) signatures (MSs) in the literature is often an initial concern for researchers and subsequently it discourages larger scale prospective studies,prevent the translation of such knowledge into a practical clinical setting and ultimately hindering the progress of the field of

type: 
Conference Paper/Poster
journal: 
2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2013), April 15-19, Singapore
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