Genome and Gene Expression Data Analysis

"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

Plasma Ceramides as Prognostic Biomarkers and Their Arterial and Myocardial Tissue Correlates in Acute Myocardial Infarction

Published date : 30 May 2018

We identified a plasma signature of 11 C14 to C26 ceramides and 1 C16 dihydroceramide predictive of major adverse cardiovascular events in patients with acute myocardial infarction (AMI). Among patients undergoing coronary artery bypass surgery, those with recent AMI, compared with those without recent AMI, showed a significant increase in 5 of the signature’s 12 ceramides in plasma but not simultaneously-biopsied aortic tissue.

type
Journal Paper
journal
JACC: Basic to Translational Science, Vol. 3, Issue 2, April 2018, pg 163-175, doi: 10.1016/j.jacbts.2017.12.005
Impact Factor
0.844

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

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

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

Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition

Published date : 08 Jan 2018

In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs.

type
Journal Paper
journal
Development, 8 Jan 2018, Vol 145, Issue 1, doi: 10.1242/dev.159566
Impact Factor
5.843

Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma

Published date : 12 Dec 2017

Currently, molecular markers are not used when determining the prognosis and treatment strategy for patients with hepatocellular carcinoma (HCC). In the present study, we proposed that the identification of common pro-oncogenic pathways in primary tumors (PT) and adjacent non-malignant tissues (AT) typically used to predict HCC patient risks may result in HCC biomarker discovery. We examined the genome-wide mRNA expression profiles of paired PT and AT samples from 321 HCC patients.

type
Journal Paper
journal
Molecular Oncology, 8 Nov 2017, doi: 10.1002/1878-0261.12153
Impact Factor
5.314

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

Identification of common oncogenic and early developmental pathways in the ovarian carcinomas controlling by distinct prognostically significant microRNA subsets

Published date : 03 Oct 2017

Background
High-grade serous ovarian carcinoma (HG-SOC) is the dominant tumor histologic type in epithelial ovarian cancers, exhibiting highly aberrant microRNA expression profiles and diverse pathways that collectively determine the disease aggressiveness and clinical outcomes. However, the functional relationships between microRNAs, the common pathways controlled by the microRNAs and their prognostic and therapeutic significance remain poorly understood.

type
Journal Paper
journal
BMC Genomics. 2017; 18(Suppl 6): 692, doi: 10.1186/s12864-017-4027-5
Impact Factor
3.729