List of works - Andrey Alexeyenko

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells

scientific article published on 16 September 2020

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

scholarly article by Bo Franzén et al published September 2018 in Molecular Oncology

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

scientific article

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk

scientific article

Automatic clustering of orthologs and inparalogs shared by multiple proteomes

scientific article published in July 2006

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

scientific article

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

article

Comparative interactomics with Funcoup 2.0.

scientific article

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

scientific article published on 18 November 2012

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth

scientific article published on 18 June 2015

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

scientific article

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity

scientific article

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

scientific article

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

scientific article published in July 2018

Genetic association of sequence variants near AGER/NOTCH4 and dementia

scientific article

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

scientific article published on 29 July 2010

Global networks of functional coupling in eukaryotes from comprehensive data integration

scientific article

High-throughput in vivo analysis of gene expression in Caenorhabditis elegans

scientific article

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

scientific article

Individualized discovery of rare cancer drivers in global network context

scientific article published on 20 May 2022

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

scientific article

MGclus: network clustering employing shared neighbors

scientific article

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

scientific article

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

scientific article published on 23 December 2012

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

scientific article

Novel genes and pathways modulated by syndecan-1: implications for the proliferation and cell-cycle regulation of malignant mesothelioma cells

scientific article

Overview and comparison of ortholog databases

scientific article published on January 2006

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

scientific article published on 20 February 2019

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

scientific article

Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis

scientific article published on 16 December 2019

Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer

scientific article published on 07 January 2019

Robust and clinically relevant prediction of response to anti-cancer drugs via network integration of molecular profiles

Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery

scientific article published on 01 June 2022

Spatially resolved transcriptome profiling in model plant species

scientific article

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

scientific article

The Norway spruce genome sequence and conifer genome evolution

scientific article

List of works by Andrey Alexeyenko

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells

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

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

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk

Automatic clustering of orthologs and inparalogs shared by multiple proteomes

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

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

Comparative interactomics with Funcoup 2.0.

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

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth

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

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

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

Genetic association of sequence variants near AGER/NOTCH4 and dementia

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

Global networks of functional coupling in eukaryotes from comprehensive data integration

High-throughput in vivo analysis of gene expression in Caenorhabditis elegans

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

Individualized discovery of rare cancer drivers in global network context

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

MGclus: network clustering employing shared neighbors

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

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

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

Novel genes and pathways modulated by syndecan-1: implications for the proliferation and cell-cycle regulation of malignant mesothelioma cells

Overview and comparison of ortholog databases

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

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

Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis

Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer

Robust and clinically relevant prediction of response to anti-cancer drugs via network integration of molecular profiles

Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery

Spatially resolved transcriptome profiling in model plant species

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

The Norway spruce genome sequence and conifer genome evolution