Andrey Alekseenko

Publikationer
CV
Populärvetenskap och samverkan

Artiklar

Article: SCIENCE ADVANCES. 2020;6(38):eaba8196
A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
Dias JM; Alekseenko Z; Jeggari A; Boareto M; Vollmer J; Kozhevnikova M; Wang H; Matise MP; Alexeyenko A; Iber D; Ericson J
Article: ARTHRITIS RESEARCH & THERAPY. 2019;21(1):288
Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis
Brink M; Lundquist A; Alexeyenko A; Lejon K; Rantapaa-Dahlqvist S
Article: SCIENTIFIC REPORTS. 2019;9(1):2379
Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data
Franco M; Jeggari A; Peuget S; Bottger F; Selivanova G; Alexeyenko A
Article: MOLECULAR ONCOLOGY. 2019;13(2):376-391
Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer
Franzen B; Alexeyenko A; Kamali-Moghaddam M; Hatschek T; Kanter L; Ramqvist T; Kierkegaard J; Masucci G; Auer G; Landegren U; Lewensohn R
Article: INTERNATIONAL JOURNAL OF CANCER. 2018;143(7):1741-1752
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; Ponten V; Mattsson JSM; Djureinovic D; Persson J; Brunnstrom H; Isaksson J; Branden E; Koyi H; Micke P; Karlsson MCI; Botling J
Article: MOLECULAR ONCOLOGY. 2018;12(9):1415-1428
A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions
Franzen B; Kamali-Moghaddam M; Alexeyenko A; Hatschek T; Becker S; Wik L; Kierkegaard J; Eriksson A; Muppani NR; Auer G; Landegren U; Lewensohn R
Article: NUCLEIC ACIDS RESEARCH (NAR). 2018;46(W1):W163-W170
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets
Jeggari A; Alekseenko Z; Petrov L; Dias JM; Ericson J; Alexeyenko A
Article: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2018;19(4):E978-978
Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome
Ramqvist T; Nasman A; Franzen B; Bersani C; Alexeyenko A; Becker S; Haeggblom L; Kolev A; Dalianis T; Munck-Wikland E
Article: ONCOTARGET. 2017;8(37):62183-62194
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; Stal O; Alexeyenko A; Jansson A
Article: NATURE PLANTS. 2017;3(6):17061
Spatially resolved transcriptome profiling in model plant species
Giacomello S; Salmen F; Terebieniec BK; Vickovic S; Navarro JF; Alexeyenko A; Reimegard J; McKee LS; Mannapperuma C; Bulone V; Stahl PL; Sundstrom JF; Street NR; Lundeberg J
Article: BMC BIOINFORMATICS. 2017;18(Suppl 5):118
NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis
Jeggari A; Alexeyenko A
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2017;114(8):E1413-E1421
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; Turunen SP; Lehti K; Kashuba V; Madapura HS; Bozoky B; Lundberg E; Balland M; Guven H; Klein G; Gad AKB; Pavlova T
Article: ONCOTARGET. 2016;7(2):1895-1911
Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis
Bersani C; Huss M; Giacomello S; Xu L-D; Bianchi J; Eriksson S; Jerhammar F; Alexeyenko A; Vilborg A; Lundeberg J; Lui W-O; Wiman KG
Article: JOURNAL OF EXPERIMENTAL AND CLINICAL CANCER RESEARCH. 2015;34(1):62
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; Wiklund P; Egevad L; Csermely P; Korcsmaros T; Guven H; Klein G
Article: DISEASE MARKERS. 2015;2015:241301-13
Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis
Dmitriev AA; Rosenberg EE; Krasnov GS; Gerashchenko GV; Gordiyuk VV; Pavlova TV; Kudryavtseva AV; Beniaminov AD; Belova AA; Bondarenko YN; Danilets RO; Glukhov AI; Kondratov AG; Alexeyenko A; Alekseev BY; Klein G; Senchenko VN; Kashuba VI
Article: BIOMED RESEARCH INTERNATIONAL. 2015;2015:462549-13
Identifying and Assessing Interesting Subgroups in a Heterogeneous Population
Lee W; Alexeyenko A; Pernemalm M; Guegan J; Dessen P; Lazar V; Lehtio J; Pawitan Y
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2014;111(48):17188-17193
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; Szekely L; Klein G; Guven H
Article: BMC BIOINFORMATICS. 2014;15(1):308
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis
Merid SK; Goranskaya D; Alexeyenko A
Article: BMC GENOMICS. 2014;15(1):439
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 R; Knudsen B; Simonsen M; Turner B; de Jong P; Wu C-C; Lundeberg J
Article: GENOME BIOLOGY. 2014;15(3):R53
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; DeChene ET; Towne MC; Savage SK; Price EN; Holm IA; Luquette LJ; Lyon E; Majzoub J; Neupert P; McCallie DJ; Szolovits P; Willard HF; Mendelsohn NJ; Temme R; Finkel RS; Yum SW; Medne L; Sunyaev SR; Adzhubey I; Cassa CA; de Bakker PIW; Duzkale H; Dworzynski P; Fairbrother W; Francioli L; Funke BH; Giovanni MA; Handsaker RE; Lage K; Lebo MS; Lek M; Leshchiner I; MacArthur DG; McLaughlin HM; Murray MF; Pers TH; Polak PP; Raychaudhuri S; Rehm HL; Soemedi R; Stitziel NO; Vestecka S; Supper J; Gugenmus C; Klocke B; Hahn A; Schubach M; Menzel M; Biskup S; Freisinger P; Deng M; Braun M; Perner S; Smith RJH; Andorf JL; Huang J; Ryckman K; Sheffield VC; Stone EM; Bair T; Black-Ziegelbein EA; Braun TA; Darbro B; DeLuca AP; Kolbe DL; Scheetz TE; Shearer AE; Sompallae R; Wang K; Bassuk AG; Edens E; Mathews K; Moore SA; Shchelochkov OA; Trapane P; Bossler A; Campbell CA; Heusel JW; Kwitek A; Maga T; Panzer K; Wassink T; Van Daele D; Azaiez H; Booth K; Meyer N; Segal MM; Williams MS; Tromp G; White P; Corsmeier D; Fitzgerald-Butt S; Herman G; Lamb-Thrush D; McBride KL; Newsom D; Pierson CR; Rakowsky AT; Maver A; Lovrecic L; Palandacic A; Peterlin B; Torkamani A; Wedell A; Huss M; Alexeyenko A; Lindvall JM; Magnusson M; Nilsson D; Stranneheim H; Taylan F; Gilissen C; Hoischen A; van Bon B; Yntema H; Nelen M; Zhang W; Sager J; Zhang L; Blair K; Kural D; Cariaso M; Lennon GG; Javed A; Agrawal S; Ng PC; Sandhu KS; Krishna S; Veeramachaneni V; Isakov O; Halperin E; Friedman E; Shomron N; Glusman G; Roach JC; Caballero J; Cox HC; Mauldin D; Ament SA; Rowen L; Richards DR; San Lucas FA; Gonzalez-Garay ML; Caskey CT; Bai Y; Huang Y; Fang F; Zhang Y; Wang Z; Barrera J; Garcia-Lobo JM; Gonzalez-Lamuno D; Llorca J; Rodriguez MC; Varela I; Reese MG; De la Vega FM; Kiruluta E; Cargill M; Hart RK; Sorenson JM; Lyon GJ; Stevenson DA; Bray BE; Moore BM; Eilbeck K; Yandell M; Zhao H; Hou L; Chen X; Yan X; Chen M; Li C; Yang C; Gunel M; Li P; Kong Y; Alexander AC; Albertyn ZI; Boycott KM; Bulman DE; Gordon PMK; Innes AM; Knoppers BM; Majewski J; Marshall CR; Parboosingh JS; Sawyer SL; Samuels ME; Schwartzentruber J; Kohane IS; Margulies DM
Article: MOLECULAR BIOSYSTEMS. 2013;9(7):1670-1675
MGclus: network clustering employing shared neighbors
Frings O; Alexeyenko A; Sonnhammer ELL
Article: NATURE. 2013;497(7451):579-584
The Norway spruce genome sequence and conifer genome evolution
Nystedt B; Street NR; Wetterbom A; Zuccolo A; Lin Y-C; Scofield DG; Vezzi F; Delhomme N; Giacomello S; Alexeyenko A; Vicedomini R; Sahlin K; Sherwood E; Elfstrand M; Gramzow L; Holmberg K; Hallman J; Keech O; Klasson L; Koriabine M; Kucukoglu M; Kaller M; Luthman J; Lysholm F; Niittyla T; Olson A; Rilakovic N; Ritland C; Rossello JA; Sena J; Svensson T; Talavera-Lopez C; Theissen G; Tuominen H; Vanneste K; Wu Z-Q; Zhang B; Zerbe P; Arvestad L; Bhalerao R; Bohlmann J; Bousquet J; Gil RG; Hvidsten TR; de Jong P; MacKay J; Morgante M; Ritland K; Sundberg B; Thompson SL; Van de Peer Y; Andersson B; Nilsson O; Ingvarsson PK; Lundeberg J; Jansson S
Article: PLOS ONE. 2013;8(1):e54945
Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks
McCormack T; Frings O; Alexeyenko A; Sonnhammer ELL
Article: BMC BIOINFORMATICS. 2012;13:226
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
Alexeyenko A; Lee W; Pernemalm M; Guegan J; Dessen P; Lazar V; Lehtio J; Pawitan Y
Article: THE SCIENTIFIC WORLD JOURNAL. 2012;2012:130491-10
Network Analysis of Functional Genomics Data: Application to Avian Sex-Biased Gene Expression
Frings O; Mank JE; Alexeyenko A; Sonnhammer ELL
Article: GENOME MEDICINE. 2012;4(11):86
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; Hallman J; Lundberg E; Uhlen M; Lundeberg J
Article: PLOS ONE. 2012;7(10):e48091
Novel Genes and Pathways Modulated by Syndecan-1: Implications for the Proliferation and Cell-Cycle Regulation of Malignant Mesothelioma Cells
Szatmari T; Mundt F; Heidari-Hamedani G; Zong F; Ferolla E; Alexeyenko A; Hjerpe A; Dobra K
Article: NUCLEIC ACIDS RESEARCH (NAR). 2012;40(D1):D821-D828
Comparative interactomics with Funcoup 2.0
Alexeyenko A; Schmitt T; Tjarnberg A; Guala D; Frings O; Sonnhammer ELL
Article: JOURNAL OF ALZHEIMER'S DISEASE. 2011;24(3):475-484
Genetic Association of Sequence Variants Near AGER/NOTCH4 and Dementia
Bennet AM; Reynolds CA; Eriksson UK; Hong M-G; Blennow K; Gatz M; Alexeyenko A; Pedersen NL; Prince JA
Article: JOURNAL OF HUMAN GENETICS. 2010;55(10):707-709
Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease
Hong M-G; Alexeyenko A; Lambert J-C; Amouyel P; Prince JA
Article: HUMAN MOLECULAR GENETICS. 2010;19(10):2068-2078
Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk
Reynolds CA; Hong M-G; Eriksson UK; Blennow K; Wiklund F; Johansson B; Malmberg B; Berg S; Alexeyenko A; Gronberg H; Gatz M; Pedersen NL; Prince JA
Article: PLOS ONE. 2010;5(5):e10465
Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity
Alexeyenko A; Wassenberg DM; Lobenhofer EK; Yen J; Linney E; Sonnhammer ELL; Meyer JN
Article: GENOME RESEARCH. 2009;19(6):1107-1116
Global networks of functional coupling in eukaryotes from comprehensive data integration
Alexeyenko A; Sonnhammer ELL
Article: PLOS BIOLOGY. 2007;5(9):e237-1997
High-throughput in vivo analysis of gene expression in Caenorhabditis elegans
Hunt-Newbury R; Viveiros R; Johnsen R; Mah A; Anastas D; Fang L; Halfnight E; Lee D; Lin J; Lorch A; McKay S; Okada HM; Pan J; Schulz AK; Tu D; Wong K; Zhao Z; Alexeyenko A; Burglin T; Sonnhammer E; Schnabel R; Jones SJ; Marra MA; Baillie DL; Moerman DG
Article: BEHAVIORAL AND BRAIN FUNCTIONS. 2007;3:33
Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD
Heijtz RD; Alexeyenko A; Castellanos FX
Article: TRENDS IN GENETICS. 2006;22(11):589-593
Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis
Alexeyenko A; Millar AH; Whelan J; Sonnhammer ELL
Article: DRUG DISCOVERY TODAY: TECHNOLOGIES. 2006;3(2):137-143
Overview and comparison of ortholog databases.
Alexeyenko A; Lindberg J; Pérez-Bercoff A; Sonnhammer ELL
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Published conference paper: BIOINFORMATICS. 2006;22(14):e9-15
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
Alexeyenko A; Tamas I; Liu G; Sonnhammer ELL

Anställningar

Anknuten till Forskning, Cell- och molekylärbiologi, Karolinska Institutet, 2023-2025
Anknuten till Forskning, Cell- och molekylärbiologi, Karolinska Institutet, 2023-2024

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Docent, bioinformatik, Karolinska Institutet, 2016

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Kalenderhändelser från KI