Computational Analysis of Genome Complexity

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.

METHODS:

type
Journal Paper
journal
BMC Genomics. 2017; 18(Suppl 6): 692, doi: 10.1186/s12864-017-4027-5
Impact Factor
11.922

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

Published date : 29 Aug 2017

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type
Book/Book Chapter
journal
Biological Networks and Pathway Analysis, Methods in Molecular Biology, Vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

Published date : 29 Aug 2017

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed.

type
Book/Book Chapter
journal
Biological Networks and Pathway Analysis, Methods in Molecular Biology, vol. 1613, Pg 193-276, doi: 10.1007/978-1-4939-7027-8_9

EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis

Published date : 21 Aug 2017

Epithelial carcinomas are well known to activate a prolonged wound-healing program that promotes malignant transformation. Wound closure requires the activation of keratinocyte migration via a dual-state molecular switch. This switch involves production of either the anti-migratory microRNA miR-198 or the pro-migratory follistatin-like 1 (FSTL1) protein from a single transcript; miR-198 expression in healthy skin is down-regulated in favor of FSTL1 upon wounding, which enhances keratinocyte migration and promotes re-epithelialization.

type
Journal Paper
journal
The Journal of Experimental Medicine, 2017,doi: 10.1084/jem.20170354
Impact Factor
11.991

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Published date : 26 May 2017

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes.

type
Journal Paper
journal
Journal of Extracellular Vesicles 2017, Vol. 6, 2017, Issue 1, doi: 10.1080/20013078.2017.1321455
Impact Factor
4.259

Transposon insertional mutagenesis in mice identifies human breast cancer susceptibility genes and signatures for stratification

Published date : 01 Mar 2017

Robust prognostic gene signatures and therapeutic targets are difficult to derive from expression profiling because of the significant heterogeneity within breast cancer (BC) subtypes. Here, we performed forward genetic screening in mice using Sleeping Beauty transposon mutagenesis to identify candidate BC driver genes in an unbiased manner, using a stabilized N-terminal truncated β-catenin gene as a sensitizer. We identified 134 mouse susceptibility genes from 129 common insertion sites within 34 mammary tumors.

type
Journal Paper
journal
Proceedings of the National Academy of Sciences of the Unites States of America, PNAS, Vol. 114, No. 11, E2215–E2224, doi: 10.1073/pnas.1701512114
Impact Factor
9.661

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

Big genomics and clinical data analytics strategies for precision cancer prognosis

Published date : 07 Nov 2016

The field of personalized and precise medicine in the era of big data analytics is growing rapidly. Previously, we proposed our model of patient classification termed Prognostic Signature Vector Matching (PSVM) and identified a 37 variable signature comprising 36 let-7b associated prognostic significant mRNAs and the age risk factor that stratified large high-grade serous ovarian cancer patient cohorts into three survival-significant risk groups.

type
Journal Paper
journal
Scientific Reports 6, 2016, Article no. 36493 (2016), doi:10.1038/srep36493