Author details

Full Name

Andrey Alexeyenko

Affiliation

Karolinska Institutet

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

Emma Lundberg (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36533851	Protein Profiling in Presymptomatic Individuals Separates Myeloperoxidase-Antineutrophil Cytoplasmic Antibody and Proteinase 3-Antineutrophil Cytoplasmic Antibody Vasculitides.	Arthritis Rheumatol	2023
36386450	Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients.	Transl Lung Cancer Res	2022
35650213	Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.	Nat Commun	2022
35662462	EviCor: Interactive Web Platform for Exploration of Molecular Features and Response to Anti-cancer Drugs.	J Mol Biol	2022
35593700	Individualized discovery of rare cancer drivers in global network context.	Elife	2022
32938678	A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.	Sci Adv	2020
30451357	Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.	Mol Oncol	2019
31842970	Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.	Arthritis Res Ther	2019
30787419	Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.	Sci Rep	2019
29667169	Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.	Int J Cancer	2018
30019538	A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions.	Mol Oncol	2018
29893885	EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.	Nucleic Acids Res	2018
29587383	Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.	Int J Mol Sci	2018
28977936	The regulation of hydroxysteroid 17Î²-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.	Oncotarget	2017
28361684	NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.	BMC Bioinformatics	2017
28481330	Spatially resolved transcriptome profiling in model plant species.	Nat Plants	2017
28174275	RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.	Proc Natl Acad Sci U S A	2017
26672765	Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.	Oncotarget	2016
26081588	Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.	J Exp Clin Cancer Res	2015
26491211	Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.	Dis Markers	2015
26339613	Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.	Biomed Res Int	2015
24667040	An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.	Genome Biol	2014
25236784	Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.	BMC Bioinformatics	2014
25404301	Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.	Proc Natl Acad Sci U S A	2014
24906298	Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.	BMC Genomics	2014
23372799	Statistical assessment of crosstalk enrichment between gene groups in biological networks.	PLoS One	2013
23698360	The Norway spruce genome sequence and conifer genome evolution.	Nature	2013
23396516	MGclus: network clustering employing shared neighbors.	Mol Biosyst	2013
22110034	Comparative interactomics with Funcoup 2.0.	Nucleic Acids Res	2012
23319882	Network analysis of functional genomics data: application to avian sex-biased gene expression.	ScientificWorldJournal	2012
22966941	Network enrichment analysis: extension of gene-set enrichment analysis to gene networks.	BMC Bioinformatics	2012
23144729	Novel genes and pathways modulated by syndecan-1: implications for the proliferation and cell-cycle regulation of malignant mesothelioma cells.	PLoS One	2012
23158748	Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.	Genome Med	2012
21297263	Genetic association of sequence variants near AGER/NOTCH4 and dementia.	J Alzheimers Dis	2011
20167577	Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.	Hum Mol Genet	2010
20463971	Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.	PLoS One	2010
20668461	Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease.	J Hum Genet	2010
19246318	Global networks of functional coupling in eukaryotes from comprehensive data integration.	Genome Res	2009
17850180	High-throughput in vivo analysis of gene expression in Caenorhabditis elegans.	PLoS Biol	2007
17623072	Calcyon mRNA expression in the frontal-striatal circuitry and its relationship to vesicular processes and ADHD.	Behav Brain Funct	2007
16979780	Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis.	Trends Genet	2006
16873526	Automatic clustering of orthologs and inparalogs shared by multiple proteomes.	Bioinformatics	2006
24980400	Overview and comparison of ortholog databases.	Drug Discov Today Technol	2006

1 - 43 of 43

Ludwig Geistlinger

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 2008

Number of shared co-authors 0

Atanas Kamburov

Broad Institute of Harvard and MIT

Career Start Year 2007

Number of shared co-authors 3

Hai Fang

University of Bristol

Career Start Year 2006

Number of shared co-authors 0

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 0

Avi Ma'ayan

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 3

Bin Zhang

Graduate School of Medicine, The University of Tokyo

Career Start Year 2004

Number of shared co-authors 3

Xianghong Jasmine Zhou

David Geffen School of Medicine, University of California at Los Angeles

Career Start Year 2004

Number of shared co-authors 0

Jake Y. Chen (CM4AI)

University of Alabama at Birmingham

Career Start Year 2003

Number of shared co-authors 0

Tanusya M Murali

Yong Loo Lin School of Medicine, National University of Singapore

Career Start Year 2003

Number of shared co-authors 0

F??tima Al-Shahrour

Spanish National Cancer Research Centre (CNIO)

Career Start Year 2003

Number of shared co-authors 0

Andrey Sivachenko

Cystic Fibrosis Foundation

Career Start Year 2003

Number of shared co-authors 4

Ruth Isserlin

University of Toronto

Career Start Year 2002

Number of shared co-authors 0

Max Kotlyar

Schroeder Arthritis Institute

Career Start Year 2002

Number of shared co-authors 0

Haiyuan Yu

Weill Institute for Cell and Molecular Biology, Cornell University

Career Start Year 2001

Number of shared co-authors 2

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 2

Joshua M Stuart

University of California at Santa Cruz

Career Start Year 2000

Number of shared co-authors 3

Hedi Peterson

Institute of Computer Science, University of Tartu

Career Start Year 2000

Number of shared co-authors 0

Gary D Bader

University of Toronto

Career Start Year 2000

Number of shared co-authors 4

Marcio Luis Acencio

Norwegian University of Science and Technology

Career Start Year 2000

Number of shared co-authors 0

Igor Jurisica

Schroeder Arthritis Institute

Career Start Year 1998

Number of shared co-authors 0

Ralf Herwig

Max Planck Institute for Molecular Genetics

Career Start Year 1998

Number of shared co-authors 1

Benedikt Brors

German Cancer Research Center (DKFZ)

Career Start Year 1997

Number of shared co-authors 2

Mauro A A Castro

Federal University of Parana

Career Start Year 1997

Number of shared co-authors 1

Trey Ideker (CM4AI)

University of California San Diego

Career Start Year 1996

Number of shared co-authors 3

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 1

Andrea Califano

Columbia University

Career Start Year 1993

Number of shared co-authors 4

Jill P Mesirov

University of California San Diego

Career Start Year 1992

Number of shared co-authors 2

Robert Gentleman

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 1991

Number of shared co-authors 3

Andreas Beyer

University of Cologne

Career Start Year 1991

Number of shared co-authors 0

John Quackenbush

Harvard T. H. Chan School of Public Health

Career Start Year 1989

Number of shared co-authors 2

row(s) 1 - 30 of 30

Erik L L Sonnhammer

Stockholm University

Co-authored papers 10

Joakim Lundeberg

KTH Royal Institute of Technology

Co-authored papers 5

Mun-Gwan Hong

KTH Royal Institute of Technology

Co-authored papers 3

Nancy L Pedersen

Co-authored papers 2

Emma Lundberg (CM4AI)

Stanford University

Co-authored papers 2

Yudi Pawitan

Karolinska Institute

Co-authored papers 2

Janne Lehti??

Karolinska Institutet

Co-authored papers 2

Jimmie H??llman

KTH Royal Institute of Technology

Co-authored papers 2

Mikael Huss

Stockholm University

Co-authored papers 2

Ignaty Leshchiner

Broad Institute of Massachusetts Institute of Technology and Harvard

Co-authored papers 1

Max K??ller

KTH Royal Institute of Technology

Co-authored papers 1

David M Margulies

Renaissance School of Medicine, Stony Brook University

Co-authored papers 1

Francisco M De La Vega

Stanford University School of Medicine

Co-authored papers 1

Catherine A Brownstein

Harvard Medical School.

Co-authored papers 1

Christopher R Pierson

Co-authored papers 1

Michael F Murray

Yale School of Medicine

Co-authored papers 1

Anne E Kwitek

Medical College of Wisconsin

Co-authored papers 1

Gustavo Glusman

Institute for Systems Biology

Co-authored papers 1

Barry Moore

Utah Center for Genetic Discovery, University of Utah

Co-authored papers 1

Isaac S Kohane

Harvard Medical School

Co-authored papers 1

Matthew S Lebo

Harvard Medical School, Brigham and Women's Hospital

Co-authored papers 1

Peter Freisinger

Hospital Reutlingen

Co-authored papers 1

Filip Mundt

Co-authored papers 1

Val C Sheffield

Carver College of Medicine, University of Iowa

Co-authored papers 1

Pelin Akan

KTH Royal Institute of Technology

Co-authored papers 1

Bruce E Bray

University of Utah School of Medicine

Co-authored papers 1

Shamil R Sunyaev

Harvard Medical School

Co-authored papers 1

Peter White

The Ohio State University

Co-authored papers 1

Michele Cargill

Stanford University School of Medicine

Co-authored papers 1

Karen Eilbeck

University of Utah

Co-authored papers 1

1 - 30

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