KUROCHKIN Igor

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

Genome-wide analysis of mRNAs associated with mouse peroxisomes

Background: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.

type: 
Journal Paper
journal: 
BMC Genomics 2016, 17 (Supp 13), 1028, doi: 10.1186/s12864-016-3330-x
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259856/
Impact Factor: 
3.869

Towards allosterically increased catalytic activity of insulin degrading enzyme (IDE) against amyloid peptides

Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate.

type: 
Journal Paper
journal: 
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783
Url: 
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00783
Impact Factor: 
2.87

Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding

Aminoacyl-tRNA synthetases (ARSs) play an essential role in the protein synthesis by catalyzing an attachment of their cognate amino acids to tRNAs. Unlike their prokaryotic counterparts, ARSs in higher eukaryotes form a multiaminoacyl-tRNA synthetase complex (MARS), consisting of the subset of ARS polypeptides and three auxiliary proteins. The intriguing feature of MARS complex is the presence of only nine out of twenty ARSs, specific for Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met, and Pro, regardless of the organism, cell, or tissue types.

type: 
Journal Paper
journal: 
Protein Science 24 (2015) Pg. 1475-1485, doi: 10.1002/pro.2735
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/pro.2735/abstract;jsessionid=7DDC2FC94E81512F0A4D3C835352EBDA.f01t04
Date of acceptance: 
2015-06-24

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

Long noncoding RNAs: a potential novel class of cancer biomarkers

Long noncoding RNAs (lncRNAs) are a novel class of RNA molecules defined as transcripts longer than 200 nucleotides that lack protein coding potential. They constitute a major, but still poorly characterized part of human transcriptome, however, evidence is growing that they are important regulatory molecules involved in various cellular processes. It is becoming increasingly clear that many lncRNAs are deregulated in cancer and some of them can be important drivers of malignant transformation.

type: 
Journal Paper
journal: 
Frontiers in Genetics, April 2015, Vol. 6, Article 145, doi:10.3389/fgene.2015.00145
Url: 
http://journal.frontiersin.org/article/10.3389/fgene.2015.00145/abstract
Date of acceptance: 
2015-03-27

Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles

Secreted membrane-enclosed vesicles, collectively called extracellular vesicles (EVs), which include exosomes, ectosomes, microvesicles, microparticles, apoptotic bodies and other EV subsets, encompass a very rapidly growing scientific field in biology and medicine. Importantly, it is currently technically challenging to obtain a totally pure EV fraction free from non-vesicular components for functional studies, and therefore there is a need to establish guidelines for analyses of these vesicles and reporting of scientific studies on EV biology.

type: 
Journal Paper
journal: 
Journal of Extracellular Vesicles 2014, 3: 26913 - http://dx.doi.org/10.3402/jev.v3.26913
Url: 
http://www.journalofextracellularvesicles.net/index.php/jev/article/view/26913

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

Background
Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies.

Results

type: 
Journal Paper
journal: 
BMC Genomics 2014, 15(Suppl 9):S7 doi:10.1186/1471-2164-15-S9-S7
Url: 
http://www.biomedcentral.com/1471-2164/15/S9/S7
Impact Factor: 
4.04

Understanding the Functions of Peroxisomal Proteins: The Peroxisomal Proteome, Peroxisomal Import, Proteases and Other Protein Families and Their Network Organization: What Has Computational Biology Contributed?

Computational studies based on high-throughput experimental datasets, some of which were even not generated in the context of peroxisome research, have considerably shaped the understanding of the peroxisomal proteome. Most importantly, this research revealed to a considerable extent how the total peroxisomal proteome is composed and what is its network and pathway structure. Computational prediction tools have been instrumental for finding proteins that are imported into peroxisomes via canonical import mechanisms.

type: 
Book/Book Chapter
journal: 
Molecular Machines Involved in Peroxisome Biogenesis and Maintenance, 2014, PG 187-232, doi: 10.1007/978-3-7091-1788-0_9
Url: 
http://link.springer.com/chapter/10.1007%2F978-3-7091-1788-0_9

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
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