Andrey Alekseenko

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; Rantapää-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; Böttger 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.

Franzén 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; Pontén V; Mattsson JSM; Djureinovic D; Persson J; Brunnström H; Isaksson J; Brandén 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.

Franzén 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. 2018;46(W1):W163-W170

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A; Alekseenko Z; Petrov I; 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; Näsman A; Franzén 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; Stål O; Alexeyenko A; Jansson A

Article: NATURE PLANTS. 2017;3:17061

Spatially resolved transcriptome profiling in model plant species.

Giacomello S; Salmén F; Terebieniec BK; Vickovic S; Navarro JF; Alexeyenko A; Reimegård J; McKee LS; Mannapperuma C; Bulone V; Ståhl PL; Sundström 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; Guvén 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 & 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; Lehtiö 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 D; 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; Dworzyński 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; Lovrečić L; Palandačić 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; González-Lamuño 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; Hällman J; Keech O; Klasson L; Koriabine M; Kucukoglu M; Käller M; Luthman J; Lysholm F; Niittylä T; Olson A; Rilakovic N; Ritland C; Rosselló JA; Sena J; Svensson T; Talavera-López C; Theißen G; Tuominen H; Vanneste K; Wu Z-Q; Zhang B; Zerbe P; Arvestad L; Bhalerao R; Bohlmann J; Bousquet J; Garcia Gil R; 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; Lehtiö J; Pawitan Y

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; Hällman J; Lundberg E; Uhlén 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.

Szatmári T; Mundt F; Heidari-Hamedani G; Zong F; Ferolla E; Alexeyenko A; Hjerpe A; Dobra K

Article: NUCLEIC ACIDS RESEARCH. 2012;40(Database issue):D821-D828

Comparative interactomics with Funcoup 2.0.

Alexeyenko A; Schmitt T; Tjärnberg A; Guala D; Frings O; Sonnhammer ELL

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: JOURNAL OF ALZHEIMERS 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; Grönberg 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

Visa fler

Artiklar

Alla övriga publikationer

Anställningar

Examina och utbildning

Nyheter från KI

Kalenderhändelser från KI