KUZNETSOV Vladimir

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

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type: 
Journal Paper
journal: 
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
pubmed: 
28724991
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28724991
Impact Factor: 
4.259
Date of acceptance: 
2017-06-07

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

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

Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers

Background: The lack of consensus among reported gene signature subsets (GSSs) in multi-gene biomarker
discovery studies is often a concern for researchers and clinicians. Subsequently, it discourages larger scale prospective studies, prevents the translation of such knowledge into a practical clinical setting and ultimately hinders the progress of the field of biomarker-based disease classification, prognosis and prediction.

type: 
Journal Paper
journal: 
BMC Genomics 2015, 16(Suppl 7):S2 doi:10.1186/1471-2164-16-S7-S2
Url: 
http://www.biomedcentral.com/1471-2164/16/S7/S2
Impact Factor: 
3.99

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
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