List of works - Jean-Fred Fontaine

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

scientific article published on 17 March 2016

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

scientific article

Alkemio: association of chemicals with biomedical topics by text and data mining

scientific article

Annotation and Analysis of 3902 Odorant Receptor Protein Sequences from 21 Insect Species Provide Insights into the Evolution of Odorant Receptor Gene Families in Solitary and Social Insects

scientific article published on 20 May 2022

Aversion to nicotine is regulated by the balanced activity of β4 and α5 nicotinic receptor subunits in the medial habenula.

scientific article published on May 2011

Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality

scientific article published in 2022

CELDA -- an ontology for the comprehensive representation of cells in complex systems

scientific article

CXCL5 limits macrophage foam cell formation in atherosclerosis

scientific article

CellFinder: a cell data repository

scientific article (publication date: 2014)

DNA microarray and miRNA analyses reinforce the classification of follicular thyroid tumors.

scientific article published on 08 April 2013

Death-associated protein 3 is overexpressed in human thyroid oncocytic tumours

scientific article

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate.

scientific article published on August 2017

Development and application of a DNA microarray-based yeast two-hybrid system

scientific article

Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors

scientific article

Evaluation of in vivo and in vitro models of toxicity by comparison of toxicogenomics data with the literature

scientific article published on 14 July 2017

Génie: literature-based gene prioritization at multi genomic scale

scientific article

HIPPIE: Integrating protein interaction networks with experiment based quality scores.

scientific article

LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships ⬇️

scientific article (publication date: February 2010)

Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets

scientific article published in PLoS ONE

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

scientific article published on 29 October 2007

Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.

scientific article published on September 2013

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

scientific article

QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards.

scientific article

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay

scientific article published on 22 July 2019

The ERPIN server: an interface to profile-based RNA motif identification

scientific article

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.

scientific article published on 28 July 2011

Using cited references to improve the retrieval of related biomedical documents

scientific article (publication date: 27 March 2013)

seqQscorer: automated quality control of next-generation sequencing data using machine learning

scientific article published on 05 March 2021

List of works by Jean-Fred Fontaine

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

Alkemio: association of chemicals with biomedical topics by text and data mining

Annotation and Analysis of 3902 Odorant Receptor Protein Sequences from 21 Insect Species Provide Insights into the Evolution of Odorant Receptor Gene Families in Solitary and Social Insects

Aversion to nicotine is regulated by the balanced activity of β4 and α5 nicotinic receptor subunits in the medial habenula.

Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality

CELDA -- an ontology for the comprehensive representation of cells in complex systems

CXCL5 limits macrophage foam cell formation in atherosclerosis

CellFinder: a cell data repository

DNA microarray and miRNA analyses reinforce the classification of follicular thyroid tumors.

Death-associated protein 3 is overexpressed in human thyroid oncocytic tumours

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate.

Development and application of a DNA microarray-based yeast two-hybrid system

Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors

Evaluation of in vivo and in vitro models of toxicity by comparison of toxicogenomics data with the literature

Génie: literature-based gene prioritization at multi genomic scale

HIPPIE: Integrating protein interaction networks with experiment based quality scores.

LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships ⬇️

Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets

Microarray analysis refines classification of non-medullary thyroid tumours of uncertain malignancy

Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards.

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay

The ERPIN server: an interface to profile-based RNA motif identification

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.

Using cited references to improve the retrieval of related biomedical documents

seqQscorer: automated quality control of next-generation sequencing data using machine learning