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Items: 36

1.

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.

Sci Rep. 2019 Feb 20;9(1):2379. doi: 10.1038/s41598-019-39019-2.

2.

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.

Mol Oncol. 2019 Feb;13(2):376-391. doi: 10.1002/1878-0261.12410. Epub 2019 Jan 7.

3.

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.

Mol Oncol. 2018 Sep;12(9):1415-1428. doi: 10.1002/1878-0261.12350. Epub 2018 Aug 9.

4.

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.

Nucleic Acids Res. 2018 Jul 2;46(W1):W163-W170. doi: 10.1093/nar/gky485.

5.

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.

Int J Cancer. 2018 Apr 18. doi: 10.1002/ijc.31545. [Epub ahead of print]

PMID:
29667169
6.

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.

Int J Mol Sci. 2018 Mar 25;19(4). pii: E978. doi: 10.3390/ijms19040978.

7.

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 Jul 10;8(37):62183-62194. doi: 10.18632/oncotarget.19136. eCollection 2017 Sep 22.

8.

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.

Nat Plants. 2017 May 8;3:17061. doi: 10.1038/nplants.2017.61.

PMID:
28481330
9.

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.

Jeggari A, Alexeyenko A.

BMC Bioinformatics. 2017 Mar 23;18(Suppl 5):118. doi: 10.1186/s12859-017-1534-y.

10.

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 AK, Pavlova T.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):E1413-E1421. doi: 10.1073/pnas.1621161114. Epub 2017 Feb 7.

11.

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.

Bersani C, Huss M, Giacomello S, Xu LD, Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui WO, Wiman KG.

Oncotarget. 2016 Jan 12;7(2):1895-911. doi: 10.18632/oncotarget.6557.

12.

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.

Dis Markers. 2015;2015:241301. doi: 10.1155/2015/241301. Epub 2015 Sep 28.

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.

Biomed Res Int. 2015;2015:462549. doi: 10.1155/2015/462549. Epub 2015 Aug 3.

14.

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.

J Exp Clin Cancer Res. 2015 Jun 18;34:62. doi: 10.1186/s13046-015-0178-x.

15.

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.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17188-93. doi: 10.1073/pnas.1419554111. Epub 2014 Nov 17.

16.

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A.

BMC Bioinformatics. 2014 Sep 19;15:308. doi: 10.1186/1471-2105-15-308.

17.

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 CC, Lundeberg J.

BMC Genomics. 2014 Jun 6;15:439. doi: 10.1186/1471-2164-15-439.

18.

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 Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, 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 RJ, 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 PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM.

Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53.

19.

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, 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 ZQ, 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.

Nature. 2013 May 30;497(7451):579-84. doi: 10.1038/nature12211. Epub 2013 May 22.

PMID:
23698360
20.

MGclus: network clustering employing shared neighbors.

Frings O, Alexeyenko A, Sonnhammer EL.

Mol Biosyst. 2013 Jul;9(7):1670-5. doi: 10.1039/c3mb25473a. Epub 2013 Feb 11.

PMID:
23396516
21.

Statistical assessment of crosstalk enrichment between gene groups in biological networks.

McCormack T, Frings O, Alexeyenko A, Sonnhammer EL.

PLoS One. 2013;8(1):e54945. doi: 10.1371/journal.pone.0054945. Epub 2013 Jan 23.

22.

Network analysis of functional genomics data: application to avian sex-biased gene expression.

Frings O, Mank JE, Alexeyenko A, Sonnhammer EL.

ScientificWorldJournal. 2012;2012:130491. doi: 10.1100/2012/130491. Epub 2012 Dec 23.

23.

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.

Genome Med. 2012 Nov 18;4(11):86. doi: 10.1186/gm387. eCollection 2012.

24.

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.

PLoS One. 2012;7(10):e48091. doi: 10.1371/journal.pone.0048091. Epub 2012 Oct 29.

25.

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.

BMC Bioinformatics. 2012 Sep 11;13:226. doi: 10.1186/1471-2105-13-226.

26.

Comparative interactomics with Funcoup 2.0.

Alexeyenko A, Schmitt T, Tjärnberg A, Guala D, Frings O, Sonnhammer EL.

Nucleic Acids Res. 2012 Jan;40(Database issue):D821-8. doi: 10.1093/nar/gkr1062. Epub 2011 Nov 21.

27.

Genetic association of sequence variants near AGER/NOTCH4 and dementia.

Bennet AM, Reynolds CA, Eriksson UK, Hong MG, Blennow K, Gatz M, Alexeyenko A, Pedersen NL, Prince JA.

J Alzheimers Dis. 2011;24(3):475-84. doi: 10.3233/JAD-2011-101848.

28.

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease.

Hong MG, Alexeyenko A, Lambert JC, Amouyel P, Prince JA.

J Hum Genet. 2010 Oct;55(10):707-9. doi: 10.1038/jhg.2010.92. Epub 2010 Jul 29.

PMID:
20668461
29.

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.

Alexeyenko A, Wassenberg DM, Lobenhofer EK, Yen J, Linney E, Sonnhammer EL, Meyer JN.

PLoS One. 2010 May 5;5(5):e10465. doi: 10.1371/journal.pone.0010465.

30.

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, Malmberg B, Berg S, Alexeyenko A, Grönberg H, Gatz M, Pedersen NL, Prince JA.

Hum Mol Genet. 2010 May 15;19(10):2068-78. doi: 10.1093/hmg/ddq079. Epub 2010 Feb 18.

31.

Global networks of functional coupling in eukaryotes from comprehensive data integration.

Alexeyenko A, Sonnhammer EL.

Genome Res. 2009 Jun;19(6):1107-16. doi: 10.1101/gr.087528.108. Epub 2009 Feb 25.

32.

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.

PLoS Biol. 2007 Sep;5(9):e237.

33.
34.

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis.

Alexeyenko A, Millar AH, Whelan J, Sonnhammer EL.

Trends Genet. 2006 Nov;22(11):589-93. Epub 2006 Sep 18.

PMID:
16979780
35.

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Alexeyenko A, Tamas I, Liu G, Sonnhammer EL.

Bioinformatics. 2006 Jul 15;22(14):e9-15.

PMID:
16873526
36.

Overview and comparison of ortholog databases.

Alexeyenko A, Lindberg J, Pérez-Bercoff A, Sonnhammer EL.

Drug Discov Today Technol. 2006 Summer;3(2):137-43. doi: 10.1016/j.ddtec.2006.06.002.

PMID:
24980400

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