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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.

Forskningsbeskrivning

Keywords:

Network enrichment analysis; pathway enrichment; global interaction networks; network science

Main publications:

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.
Jeggari A, Alexeyenko A
BMC Bioinformatics 2017 Mar;18(Suppl 5):118
RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.
Alkasalias T, Alexeyenko A, Hennig K, Danielsson F, Lebbink R, Fielden M, et al
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.
Alexeyenko A, Alkasalias T, Pavlova T, Szekely L, Kashuba V, Rundqvist H, et al
J. Exp. Clin. Cancer Res. 2015 Jun;34():62
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
Merid S, Goranskaya D, Alexeyenko A
BMC Bioinformatics 2014 Sep;15():308
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.
Alexeyenko A, Lee W, Pernemalm M, Guegan J, Dessen P, Lazar V, et al
BMC Bioinformatics 2012 Sep;13():226
Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.
Alexeyenko A, Wassenberg D, Lobenhofer E, Yen J, Linney E, Sonnhammer E, et al
PLoS ONE 2010 May;5(5):e10465
Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
Alexeyenko A, Tamas I, Liu G, Sonnhammer E
Bioinformatics 2006 Jul;22(14):e9-15

 

Publikationer

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer
La Fleur L, Boura Vf, Alexeyenko A, Berglund A, Pontén V, Mattsson Jsm, et al
International journal of cancer 2018;():-

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome
Ramqvist T, Näsman A, Franzén B, Bersani C, Alexeyenko A, Becker S, et al
International journal of molecular sciences 2018;19(4):-

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis
Jeggari A, Alexeyenko A
BMC bioinformatics 2017;18(Suppl 5):118-

RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo
Alkasalias T, Alexeyenko A, Hennig K, Danielsson F, Lebbink Rj, Fielden M, et al
Proceedings of the National Academy of Sciences of the United States of America 2017;114(8):E1413-E1421

Spatially resolved transcriptome profiling in model plant species
Giacomello S, Salmén F, Terebieniec Bk, Vickovic S, Navarro Jf, Alexeyenko A, et al
Nature plants 2017;3():17061-

The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer
Hilborn E, Stål O, Alexeyenko A, Jansson A
Oncotarget 2017;8(37):62183-62194

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis
Bersani C, Huss M, Giacomello S, Xu Ld, Bianchi J, Eriksson S, et al
Oncotarget 2016;7(2):1895-911

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth
Alexeyenko A, Alkasalias T, Pavlova T, Szekely L, Kashuba V, Rundqvist H, et al
Journal of experimental & clinical cancer research : CR 2015;34():62-

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis
Dmitriev Aa, Rosenberg Ee, Krasnov Gs, Gerashchenko Gv, Gordiyuk Vv, Pavlova Tv, et al
Disease markers 2015;2015():241301-

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population
Lee W, Alexeyenko A, Pernemalm M, Guegan J, Dessen P, Lazar V, et al
BioMed research international 2015;2015():462549-

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Brownstein Ca, Beggs Ah, Homer N, Merriman B, Yu Tw, Flannery Kc, et al
GENOME BIOLOGY 2014;15(3):R53-

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis
Merid Sk, Goranskaya D, Alexeyenko A
BMC bioinformatics 2014;15():308-

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools
Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, Ye Rs, Knudsen B, et al
BMC GENOMICS 2014;:439-

Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent
Alkasalias T, Flaberg E, Kashuba V, Alexeyenko A, Pavlova T, Savchenko A, et al
Proceedings of the National Academy of Sciences of the United States of America 2014;111(48):17188-93

MGclus: network clustering employing shared neighbors
Frings O, Alexeyenko A, Sonnhammer El
Molecular bioSystems 2013;9(7):1670-5

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks
Mccormack T, Frings O, Alexeyenko A, Sonnhammer Ell
PLOS ONE 2013;8(1):e54945-

The Norway spruce genome sequence and conifer genome evolution
Nystedt B, Street Nr, Wetterbom A, Zuccolo A, Lin Yc, Scofield Dg, et al
Nature 2013;497(7451):579-84

Comparative interactomics with Funcoup 2.0
Alexeyenko A, Schmitt T, Tjarnberg A, Guala D, Frings O, Sonnhammer Ell
NUCLEIC ACIDS RESEARCH 2012;40(D1):D821-8

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines
Akan P, Alexeyenko A, Costea Pi, Hedberg L, Solnestam Bw, Lundin S, et al
GENOME MEDICINE 2012;:86-

Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression
Frings O, Mank Je, Alexeyenko A, Sonnhammer Ell
SCIENTIFIC WORLD JOURNAL 2012;:130491-

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
Alexeyenko A, Lee W, Pernemalm M, Guegan J, Dessen P, Lazar V, et al
BMC bioinformatics 2012;13():226-

Novel genes and pathways modulated by syndecan-1: implications for the proliferation and cell-cycle regulation of malignant mesothelioma cells
Szatmári T, Mundt F, Heidari-hamedani G, Zong F, Ferolla E, Alexeyenko A, et al
PloS one 2012;7(10):e48091-

Genetic association of sequence variants near AGER/NOTCH4 and dementia
Bennet Am, Reynolds Ca, Eriksson Uk, Hong Mg, Blennow K, Gatz M, et al
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
Reynolds Ca, Hong Mg, Eriksson Uk, Blennow K, Wiklund F, Johansson B, et al
HUMAN MOLECULAR GENETICS 2010;19(10):2068-78

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity
Alexeyenko A, Wassenberg Dm, Lobenhofer Ek, Yen J, Linney E, Sonnhammer Ell, et al
PLOS ONE 2010;5(5):e10465-

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease
Hong Mg, Alexeyenko A, Lambert Jc, Amouyel P, Prince Ja
JOURNAL OF HUMAN GENETICS 2010;55(10):707-9

Global networks of functional coupling in eukaryotes from comprehensive data integration
Alexeyenko A, Sonnhammer Ell
GENOME RESEARCH 2009;19(6):1107-16

Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD
Heijtz Rd, Alexeyenko A, Castellanos Fx
BEHAVIORAL AND BRAIN FUNCTIONS 2007;:33-

High-throughput in vivo analysis of gene expression in Caenorhabditis elegans
Hunt-newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, et al
PLOS BIOLOGY 2007;5(9):e237-

Automatic clustering of orthologs and inparalogs shared by multiple proteomes
Alexeyenko A, Tamas I, Liu G, Sonnhammer Ell
BIOINFORMATICS 2006;22(14):e9-15

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis
Alexeyenko A, Millar Ah, Whelan J, Sonnhammer Ell
TRENDS IN GENETICS 2006;22(11):589-93

Overview and comparison of ortholog databases
Alexeyenko A, Lindberg J, Pérez-bercoff A, Sonnhammer El
Drug discovery today. Technologies 2006;3(2):137-43

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