List of works - Jaak Vilo

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments

scientific article published on 03 May 2007

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

scientific article

ArrayExpress--a public repository for microarray gene expression data at the EBI

scientific article (publication date: 2003)

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

scientific article

g:Profiler--a web server for functional interpretation of gene lists (2011 update).

scientific article

A first-generation linkage disequilibrium map of human chromosome 22

scientific article published in Nature

Robust rank aggregation for gene list integration and meta-analysis

scientific article

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

scientific article

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

scientific article published on 01 July 2019

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

scientific article

Meta-analysis of microRNA expression in lung cancer

scientific article published on 27 December 2012

Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer

scientific article

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods

scientific article published on 4 December 2009

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

scientific article

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

MicroRNA expression profiles of human blood monocyte-derived dendritic cells and macrophages reveal miR-511 as putative positive regulator of Toll-like receptor 4.

scientific article published on 6 June 2011

A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response

scientific article published on March 2016

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells

scientific article published on 21 May 2010

Expression Profiler: next generation--an online platform for analysis of microarray data

scientific article (publication date: July 2004)

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance

scientific article published on 06 May 2008

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

scientific article

Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes

scientific article published on 19 August 2015

Gene expression profiles of non-small cell lung cancer: survival prediction and new biomarkers

scientific article

Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks

scientific article

ArrayExpress: a public database of gene expression data at EBI.

scientific article

Mechanisms of IFN-γ-induced apoptosis of human skin keratinocytes in patients with atopic dermatitis

scientific article

Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells: identification of novel regulators of pluripotency

scientific article published on April 2009

Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta

scientific article

The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation

scientific article

A new way to protect privacy in large-scale genome-wide association studies

scientific article published on 14 February 2013

MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data

scientific article published on 21 December 2017

From genomes to vaccines: Leishmania as a model

scientific article

Relicensing of transcriptionally inactivated replication origins in budding yeast

scientific article published on 20 October 2010

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

scientific article

Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells

scientific article

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data

scientific article

Comprehensive Meta-analysis of MicroRNA Expression Using a Robust Rank Aggregation Approach

article

Autoimmune regulator is acetylated by transcription coactivator CBP/p300.

scientific article

KEGGanim: pathway animations for high-throughput data

scientific article

Gene expression data analysis#1Abridged version of article in FEBS Lett. 480 (2000) 17–24; with permission from Elsevier Science. PII of original article: S0014-5793(00)01772-5

scientific article published on 01 August 2001

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development

scientific article

Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives

scientific article

Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells

scientific article

Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions

scientific article published on 16 October 2018

Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populations

scientific article

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data

scientific article

Ranking genes by their co-expression to subsets of pathway members

scientific article published in March 2009

Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins

scientific article published on 16 August 2017

DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase

scientific article

List of works by Jaak Vilo

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

ArrayExpress--a public repository for microarray gene expression data at the EBI

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

g:Profiler--a web server for functional interpretation of gene lists (2011 update).

A first-generation linkage disequilibrium map of human chromosome 22

Robust rank aggregation for gene list integration and meta-analysis

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Protein interaction verification and functional annotation by integrated analysis of genome-scale data.

Meta-analysis of microRNA expression in lung cancer

Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

ASTD: The Alternative Splicing and Transcript Diversity database

MicroRNA expression profiles of human blood monocyte-derived dendritic cells and macrophages reveal miR-511 as putative positive regulator of Toll-like receptor 4.

A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response

A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells

Expression Profiler: next generation--an online platform for analysis of microarray data

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets

Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes

Gene expression profiles of non-small cell lung cancer: survival prediction and new biomarkers

Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks

ArrayExpress: a public database of gene expression data at EBI.

Mechanisms of IFN-γ-induced apoptosis of human skin keratinocytes in patients with atopic dermatitis

Characterization of the phosphoinositide 3-kinase-dependent transcriptome in murine embryonic stem cells: identification of novel regulators of pluripotency

Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta

The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation

A new way to protect privacy in large-scale genome-wide association studies

MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data

From genomes to vaccines: Leishmania as a model

Relicensing of transcriptionally inactivated replication origins in budding yeast

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data

Comprehensive Meta-analysis of MicroRNA Expression Using a Robust Rank Aggregation Approach

Autoimmune regulator is acetylated by transcription coactivator CBP/p300.

KEGGanim: pathway animations for high-throughput data

Gene expression data analysis#1Abridged version of article in FEBS Lett. 480 (2000) 17–24; with permission from Elsevier Science. PII of original article: S0014-5793(00)01772-5

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development

Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives

Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells

Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions

Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populations

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data

Ranking genes by their co-expression to subsets of pathway members

Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins

DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase