Computational Analysis of Genome Complexity

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

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
Url: 
http://jem.rupress.org/content/early/2017/08/18/jem.20170354
Impact Factor: 
11.991
Date of acceptance: 
2017-07-12

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

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
Url: 
http://www.tandfonline.com/doi/abs/10.1080/20013078.2017.1321455
Impact Factor: 
4.259

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

Big genomics and clinical data analytics strategies for precision cancer prognosis

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
pubmed: 
27819294
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27819294
Date of acceptance: 
2016-10-12

Big data and computational biology strategy for personalized prognosis

The era of big data and precision medicine has led to accumulation of massive datasets of gene expression data and clinical information of patients.

type: 
Journal Paper
journal: 
Oncotarget, 28 Jun 2016, Vol. 7, No. 26, Pg 40200-40220, doi: 10.18632/oncotarget.9571
pubmed: 
27229533
Url: 
http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path[]=9571&pubmed-linkout=1
Impact Factor: 
5.008
Date of acceptance: 
2016-05-01

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Background: The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation
also increases with increasing genome complexity. Though the number of genes appear to be equal between human
and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (miRBase Release 19).
It appears that most of the miRNAs in zebrafish are yet to be discovered.

Results: We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut

type: 
Journal Paper
journal: 
BMC Genomics (2015) 16:950, doi:10.1186/s12864-015-2135-7
Url: 
http://www.biomedcentral.com/1471-2164/16/950
Impact Factor: 
3.99
Date of acceptance: 
2015-10-23

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

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
pubmed: 
26517092
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/?term=26517092
Impact Factor: 
6.359
Date of acceptance: 
2015-09-30

Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development

Invasive ductal carcinoma (IDC) is a major histo-morphologic type of breast cancer. Histological grading (HG) of IDC is widely adopted by oncologists as a prognostic factor. However, HG evaluation is highly subjective with only 50%–85% inter-observer agreements. Specifically, the subjectivity in the assignment of the intermediate grade (histologic grade 2, HG2) breast cancers (comprising ~50% of IDC cases) results in uncertain disease outcome prediction and sub-optimal systemic therapy.

type: 
Journal Paper
journal: 
Oncotarget 2015, DOI: 10.18632/oncotarget.5543
Url: 
http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5b%5d=5543
Impact Factor: 
6.359
Date of acceptance: 
2015-09-25

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

Expression and clinical role of chemoresponse-associated genes in ovarian serous carcinoma

Objective
To validate our earlier observation that 11 chemoresistance-associated mRNAs are molecular markers of poor overall survival in ovarian serous carcinoma.

Methods

type: 
Journal Paper
journal: 
Gynecologic Oncology, Oct 2105, Vol 139, Issue 1, Pg 30-39, doi:10.1016/j.ygyno.2015.07.107
Url: 
http://www.gynecologiconcology-online.net/article/S0090-8258(15)30091-3/abstract
Impact Factor: 
3.774
Date of acceptance: 
2015-07-27
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