With background in biology and Ph.D. degree in plant genetics, Andrey Alexeyenko has focused his research interests on understanding normal physiology and pathology with gene network and systems biology approaches. It implies development of computational infrastructure, i.e. tools that integrate diverse high-throughput data across technological platforms and species. The set of tools and methods includes FunCoup: a computational framework for reconstructing gene networks via systematic integration of heterogeneous datasets http://funcoup2.sbc.su.se/and EviNet: a web suit for network enrichment analysis https://www.evinet.org.
Network enrichment analysis; pathway enrichment; global interaction networks; network science
NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.
BMC Bioinformatics 2017 Mar;18(Suppl 5):118
RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Proc. Natl. Acad. Sci. U.S.A. 2017 02;114(8):E1413-E1421
Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.
J. Exp. Clin. Cancer Res. 2015 Jun;34():62
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
BMC Bioinformatics 2014 Sep;15():308
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.
BMC Bioinformatics 2012 Sep;13():226
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.
PLoS ONE 2010 May;5(5):e10465
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
Bioinformatics 2006 Jul;22(14):e9-15
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
GENOME BIOLOGY 2014;15(3):R53-
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis
BMC bioinformatics 2014;15():308-
Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent
Proceedings of the National Academy of Sciences of the United States of America 2014;111(48):17188-93
MGclus: network clustering employing shared neighbors
Molecular bioSystems 2013;9(7):1670-5
Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks
PLOS ONE 2013;8(1):e54945-
The Norway spruce genome sequence and conifer genome evolution
Comparative interactomics with Funcoup 2.0
NUCLEIC ACIDS RESEARCH 2012;40(D1):D821-8
Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines
GENOME MEDICINE 2012;:86-
Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression
SCIENTIFIC WORLD JOURNAL 2012;:130491-
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
BMC bioinformatics 2012;13():226-
Genetic association of sequence variants near AGER/NOTCH4 and dementia
Journal of Alzheimer's disease : JAD 2011;24(3):475-84
Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk
HUMAN MOLECULAR GENETICS 2010;19(10):2068-78
Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity
PLOS ONE 2010;5(5):e10465-
Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease
JOURNAL OF HUMAN GENETICS 2010;55(10):707-9
Global networks of functional coupling in eukaryotes from comprehensive data integration
GENOME RESEARCH 2009;19(6):1107-16
Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD
BEHAVIORAL AND BRAIN FUNCTIONS 2007;:33-
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans
PLOS BIOLOGY 2007;5(9):e237-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis
TRENDS IN GENETICS 2006;22(11):589-93
Overview and comparison of ortholog databases
Drug discovery today. Technologies 2006;3(2):137-43