Andrey Alexeyenko

Andrey Alexeyenko

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Andrey Alexeyenko

Andrey Alexeyenko

Publications by authors named "Andrey Alexeyenko"

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36Publications

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Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.

Sci Rep 2019 Feb 20;9(1):2379. Epub 2019 Feb 20.

Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41598-019-39019-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382934PMC
February 2019

A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions.

Mol Oncol 2018 09 9;12(9):1415-1428. Epub 2018 Aug 9.

Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.

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http://dx.doi.org/10.1002/1878-0261.12350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120227PMC
September 2018

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

Nucleic Acids Res 2018 07;46(W1):W163-W170

Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gky485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030852PMC
July 2018

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

Int J Cancer 2018 Apr 18. Epub 2018 Apr 18.

Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Department of Pathology, Uppsala University Hospital, Uppsala, Sweden.

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http://dx.doi.org/10.1002/ijc.31545DOI Listing
April 2018

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.

Int J Mol Sci 2018 Mar 25;19(4). Epub 2018 Mar 25.

Department of Clinical Science and Technology (CLINTEC), Karolinska Institutet, Karolinska University Hospital, 171 76 Stockholm, Sweden.

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http://dx.doi.org/10.3390/ijms19040978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979357PMC
March 2018

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.

Oncotarget 2017 Sep 10;8(37):62183-62194. Epub 2017 Jul 10.

Department of Clinical and Experimental Medicine and Department of Oncology, Faculty of Health Sciences, Linköping University, Linköping, Sweden.

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http://www.oncotarget.com/fulltext/19136
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http://dx.doi.org/10.18632/oncotarget.19136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617496PMC
September 2017

Spatially resolved transcriptome profiling in model plant species.

Nat Plants 2017 May 8;3:17061. Epub 2017 May 8.

Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology, Science for Life Laboratory, 17165 Solna, Sweden.

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http://dx.doi.org/10.1038/nplants.2017.61DOI Listing
May 2017

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

BMC Bioinformatics 2017 Mar 23;18(Suppl 5):118. Epub 2017 Mar 23.

National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm, Sweden.

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http://dx.doi.org/10.1186/s12859-017-1534-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374688PMC
March 2017

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.

Dis Markers 2015 28;2015:241301. Epub 2015 Sep 28.

Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev 03680, Ukraine ; Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden.

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http://dx.doi.org/10.1155/2015/241301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602334PMC
July 2016

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

Biomed Res Int 2015 3;2015:462549. Epub 2015 Aug 3.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17177 Stockholm, Sweden.

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http://dx.doi.org/10.1155/2015/462549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539210PMC
May 2016

Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.

Proc Natl Acad Sci U S A 2014 Dec 17;111(48):17188-93. Epub 2014 Nov 17.

Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden;

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http://dx.doi.org/10.1073/pnas.1419554111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260581PMC
December 2014

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

BMC Bioinformatics 2014 Sep 19;15:308. Epub 2014 Sep 19.

Department of Microbiology, Tumour and Cell biology, Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institutet, 17177 Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-15-308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262241PMC
September 2014

Overview and comparison of ortholog databases.

Drug Discov Today Technol 2006 ;3(2):137-43

Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-106 91, Stockholm, Sweden. Electronic

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http://linkinghub.elsevier.com/retrieve/pii/S174067490600026
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http://dx.doi.org/10.1016/j.ddtec.2006.06.002DOI Listing
July 2014

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.

Genome Med 2012 18;4(11):86. Epub 2012 Nov 18.

KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, SE-171 65 Solna, Sweden.

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http://dx.doi.org/10.1186/gm387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580420PMC
May 2014

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Authors:
Catherine A Brownstein Alan H Beggs Nils Homer Barry Merriman Timothy W Yu Katherine C Flannery Elizabeth T DeChene Meghan C Towne Sarah K Savage Emily N Price Ingrid A Holm Lovelace J Luquette Elaine Lyon Joseph Majzoub Peter Neupert David McCallie Peter Szolovits Huntington F Willard Nancy J Mendelsohn Renee Temme Richard S Finkel Sabrina W Yum Livija Medne Shamil R Sunyaev Ivan Adzhubey Christopher A Cassa Paul I W de Bakker Hatice Duzkale Piotr Dworzyński William Fairbrother Laurent Francioli Birgit H Funke Monica A Giovanni Robert E Handsaker Kasper Lage Matthew S Lebo Monkol Lek Ignaty Leshchiner Daniel G MacArthur Heather M McLaughlin Michael F Murray Tune H Pers Paz P Polak Soumya Raychaudhuri Heidi L Rehm Rachel Soemedi Nathan O Stitziel Sara Vestecka Jochen Supper Claudia Gugenmus Bernward Klocke Alexander Hahn Max Schubach Mortiz Menzel Saskia Biskup Peter Freisinger Mario Deng Martin Braun Sven Perner Richard J H Smith Janeen L Andorf Jian Huang Kelli Ryckman Val C Sheffield Edwin M Stone Thomas Bair E Ann Black-Ziegelbein Terry A Braun Benjamin Darbro Adam P DeLuca Diana L Kolbe Todd E Scheetz Aiden E Shearer Rama Sompallae Kai Wang Alexander G Bassuk Erik Edens Katherine Mathews Steven A Moore Oleg A Shchelochkov Pamela Trapane Aaron Bossler Colleen A Campbell Jonathan W Heusel Anne Kwitek Tara Maga Karin Panzer Thomas Wassink Douglas Van Daele Hela Azaiez Kevin Booth Nic Meyer Michael M Segal Marc S Williams Gerard Tromp Peter White Donald Corsmeier Sara Fitzgerald-Butt Gail Herman Devon Lamb-Thrush Kim L McBride David Newsom Christopher R Pierson Alexander T Rakowsky Aleš Maver Luca Lovrečić Anja Palandačić Borut Peterlin Ali Torkamani Anna Wedell Mikael Huss Andrey Alexeyenko Jessica M Lindvall Måns Magnusson Daniel Nilsson Henrik Stranneheim Fulya Taylan Christian Gilissen Alexander Hoischen Bregje van Bon Helger Yntema Marcel Nelen Weidong Zhang Jason Sager Lu Zhang Kathryn Blair Deniz Kural Michael Cariaso Greg G Lennon Asif Javed Saloni Agrawal Pauline C Ng Komal S Sandhu Shuba Krishna Vamsi Veeramachaneni Ofer Isakov Eran Halperin Eitan Friedman Noam Shomron Gustavo Glusman Jared C Roach Juan Caballero Hannah C Cox Denise Mauldin Seth A Ament Lee Rowen Daniel R Richards F Anthony San Lucas Manuel L Gonzalez-Garay C Thomas Caskey Yu Bai Ying Huang Fang Fang Yan Zhang Zhengyuan Wang Jorge Barrera Juan M Garcia-Lobo Domingo González-Lamuño Javier Llorca Maria C Rodriguez Ignacio Varela Martin G Reese Francisco M De La Vega Edward Kiruluta Michele Cargill Reece K Hart Jon M Sorenson Gholson J Lyon David A Stevenson Bruce E Bray Barry M Moore Karen Eilbeck Mark Yandell Hongyu Zhao Lin Hou Xiaowei Chen Xiting Yan Mengjie Chen Cong Li Can Yang Murat Gunel Peining Li Yong Kong Austin C Alexander Zayed I Albertyn Kym M Boycott Dennis E Bulman Paul M K Gordon A Micheil Innes Bartha M Knoppers Jacek Majewski Christian R Marshall Jillian S Parboosingh Sarah L Sawyer Mark E Samuels Jeremy Schwartzentruber Isaac S Kohane David M Margulies

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

MGclus: network clustering employing shared neighbors.

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

Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1039/c3mb25473aDOI Listing
July 2013

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

ScientificWorldJournal 2012 23;2012:130491. Epub 2012 Dec 23.

Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden.

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http://dx.doi.org/10.1100/2012/130491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540752PMC
June 2013

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.

BMC Bioinformatics 2012 Sep 11;13:226. Epub 2012 Sep 11.

School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-13-226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505158PMC
September 2012

Comparative interactomics with Funcoup 2.0.

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

School of Biotechnology, Royal Institute of Technology, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.

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http://dx.doi.org/10.1093/nar/gkr1062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245127PMC
January 2012

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

J Alzheimers Dis 2011 ;24(3):475-84

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.3233/JAD-2011-101848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477600PMC
September 2011

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

J Hum Genet 2010 Oct 29;55(10):707-9. Epub 2010 Jul 29.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/jhg.2010.92DOI Listing
October 2010

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

Genome Res 2009 Jun 25;19(6):1107-16. Epub 2009 Feb 25.

Stockholm Bioinformatics Center, Albanova, Stockholm University, 10691 Stockholm, Sweden.

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http://dx.doi.org/10.1101/gr.087528.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694487PMC
June 2009

Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD.

Behav Brain Funct 2007 Jul 10;3:33. Epub 2007 Jul 10.

Department of Neuroscience, Karolinska Institutet, Retzius väg 8, Stockholm, 171 77, Sweden.

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http://dx.doi.org/10.1186/1744-9081-3-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949817PMC
July 2007

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

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

Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.tig.2006.09.002DOI Listing
November 2006

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

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

Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btl213DOI Listing
July 2006