List of works - Yvan Saeys

A Murine Intestinal Intraepithelial NKp46-Negative Innate Lymphoid Cell Population Characterized by Group 1 Properties.

scientific article published on May 2017

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

scientific article published on 08 October 2015

A cell atlas of human thymic development defines T cell repertoire formation

scientific article published on 01 February 2020

A comparison of single-cell trajectory inference methods

scientific article published on 01 April 2019

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

scientific article

A review of estimation of distribution algorithms in bioinformatics

scientific article published on 11 September 2008

An integrated network of Arabidopsis growth regulators and its use for gene prioritization

scientific article published on December 2015

An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

scientific article published on 07 February 2020

An overview of state-of-the-art image restoration in electron microscopy

scientific article published on 08 June 2018

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

scientific article published on 27 January 2016

Building genomic profiles for uncovering segmental homology in the twilight zone

scientific article

CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies

scientific article

Challenges in translational machine learning

scientific article published on 04 March 2022

Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing

scientific article published on 11 May 2015

Classification of Human White Blood Cells Using Machine Learning for Stain-Free Imaging Flow Cytometry

scientific article published on 05 November 2019

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

scientific article published on 16 February 2022

Computational analysis of multimorbidity between asthma, eczema and rhinitis

scientific article

Discriminative and informative features for biomolecular text mining with ensemble feature selection

scientific article

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

scientific article

Fibrotic enzymes modulate wound-induced skin tumorigenesis

scientific article published on 29 March 2021

FloReMi: Flow density survival regression using minimal feature redundancy

scientific article

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

scientific article

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.

scientific article

GATA1-Deficient Dendritic Cells Display Impaired CCL21-Dependent Migration toward Lymph Nodes Due to Reduced Levels of Polysialic Acid.

scientific article published on 4 November 2016

Generic eukaryotic core promoter prediction using structural features of DNA.

scientific article

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

scientific article

GenomeView: a next-generation genome browser

scientific article

HIGH-PRECISION BIO-MOLECULAR EVENT EXTRACTION FROM TEXT USING PARALLEL BINARY CLASSIFIERS

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

scientific article

Large-scale structural analysis of the core promoter in mammalian and plant genomes

scientific article

Macrophages are metabolically heterogeneous within the tumor microenvironment

scientific article published in 2021

Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis

scientific article published in Nature Communications

Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes

scientific article

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms

scientific article

Netter: re-ranking gene network inference predictions using structural network properties

scientific article published on 9 February 2016

NicheNet: modeling intercellular communication by linking ligands to target genes

scientific article published on 09 December 2019

Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures

scientific article published in 2022

PeacoQC: Peak-based selection of high quality cytometry data

Phenotyping asthma, rhinitis and eczema in MeDALL population-based birth cohorts: an allergic comorbidity cluster

scientific article published on 20 May 2015

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

scientific article

Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry

scientific article

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

scientific article published on 25 November 2009

Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors ⬇️

journal article from 'bioRxiv' published in 2020

SpliceMachine: predicting splice sites from high-dimensional local context representations

scientific article

Stabilization of human whole blood samples for multi-center and retrospective immunophenotyping studies

scientific article published on 18 October 2020

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery ⬇️

scientific article published on April 25, 2012

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

scientific article published on 24 September 2019

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks

scientific article published on 31 March 2014

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

scientific article published on November 2002

The checkpoint for agonist selection precedes conventional selection in human thymus.

scientific article published on February 2017

The function of Fcγ receptors in dendritic cells and macrophages

scientific article published on 21 January 2014

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α+ dendritic cells.

scientific article published on 19 January 2014

Toward a gold standard for promoter prediction evaluation

scientific article published on June 2009

Trajectory-based differential expression analysis for single-cell sequencing data

scientific article published on 05 March 2020

Translation initiation site prediction on a genomic scale: beauty in simplicity

scientific article published in July 2007

Validating module network learning algorithms using simulated data

scientific article

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions

scientific article

List of works by Yvan Saeys

A Murine Intestinal Intraepithelial NKp46-Negative Innate Lymphoid Cell Population Characterized by Group 1 Properties.

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

A cell atlas of human thymic development defines T cell repertoire formation

A comparison of single-cell trajectory inference methods

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

A review of estimation of distribution algorithms in bioinformatics

An integrated network of Arabidopsis growth regulators and its use for gene prioritization

An interactive ImageJ plugin for semi-automated image denoising in electron microscopy

An overview of state-of-the-art image restoration in electron microscopy

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

Building genomic profiles for uncovering segmental homology in the twilight zone

CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies

Challenges in translational machine learning

Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing

Classification of Human White Blood Cells Using Machine Learning for Stain-Free Imaging Flow Cytometry

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Computational analysis of multimorbidity between asthma, eczema and rhinitis

Discriminative and informative features for biomolecular text mining with ensemble feature selection

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Fibrotic enzymes modulate wound-induced skin tumorigenesis

FloReMi: Flow density survival regression using minimal feature redundancy

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.

GATA1-Deficient Dendritic Cells Display Impaired CCL21-Dependent Migration toward Lymph Nodes Due to Reduced Levels of Polysialic Acid.

Generic eukaryotic core promoter prediction using structural features of DNA.

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

GenomeView: a next-generation genome browser

HIGH-PRECISION BIO-MOLECULAR EVENT EXTRACTION FROM TEXT USING PARALLEL BINARY CLASSIFIERS

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Large-scale structural analysis of the core promoter in mammalian and plant genomes

Macrophages are metabolically heterogeneous within the tumor microenvironment

Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis

Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms

Netter: re-ranking gene network inference predictions using structural network properties

NicheNet: modeling intercellular communication by linking ligands to target genes

Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures

PeacoQC: Peak-based selection of high quality cytometry data

Phenotyping asthma, rhinitis and eczema in MeDALL population-based birth cohorts: an allergic comorbidity cluster

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Radiation-induced alternative transcription and splicing events and their applicability to practical biodosimetry

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors ⬇️

SpliceMachine: predicting splice sites from high-dimensional local context representations

Stabilization of human whole blood samples for multi-center and retrospective immunophenotyping studies

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery ⬇️

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

Systematic structural characterization of metabolites in Arabidopsis via candidate substrate-product pair networks

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

The checkpoint for agonist selection precedes conventional selection in human thymus.

The function of Fcγ receptors in dendritic cells and macrophages

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α+ dendritic cells.

Toward a gold standard for promoter prediction evaluation

Trajectory-based differential expression analysis for single-cell sequencing data

Translation initiation site prediction on a genomic scale: beauty in simplicity

Validating module network learning algorithms using simulated data

Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions