List of works - Paul Bertone

A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1

scientific article (publication date: 2013)

Advances in functional protein microarray technology

scientific article published in November 2005

An integrated approach for finding overlooked genes in yeast

scientific article published in January 2002

Analysis of yeast protein kinases using protein chips.

scientific article

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery

scientific article

Assessment of transcript reconstruction methods for RNA-seq

scientific article

CREB binds to multiple loci on human chromosome 22.

scientific article published on May 2004

Citrullination regulates pluripotency and histone H1 binding to chromatin

scientific journal article

Comparative analysis of neutrophil and monocyte epigenomes

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

scientific article

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

scientific article

Computational Methods and Bioinformatic Tools

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research

Design optimization methods for genomic DNA tiling arrays

scientific article

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

scientific article published on 9 October 2012

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency

scientific article published on 15 August 2019

Distribution of NF-kappaB-binding sites across human chromosome 22

scientific article

Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators.

scientific article

EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells

scientific article published on 28 June 2016

Epigenetic resetting of human pluripotency.

scientific article

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

scientific article

ExpressYourself: A modular platform for processing and visualizing microarray data

scientific article

Fast optimal genome tiling with applications to microarray design and homology search

scientific article published in January 2004

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

scientific article published on 07 November 2018

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing ⬇️

scientific article published on October 2002

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila

scientific article

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors

scientific journal article

Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest

scientific article published on 21 October 2015

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

scientific article published on 14 April 2021

Global analysis of protein activities using proteome chips

scientific article (publication date: 14 September 2001)

Global changes in STAT target selection and transcription regulation upon interferon treatments

scientific article

Global identification of human transcribed sequences with genome tiling arrays

scientific article (publication date: 24 December 2004)

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.

scientific article

Identification of pseudogenes in the Drosophila melanogaster genome

scientific article

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.

scientific article published on 13 August 2013

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast

scientific article

Integrative data mining: the new direction in bioinformatics.

scientific article

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

scientific article published on August 2005

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

scientific article

Mapping organelle proteins and protein complexes in Drosophila melanogaster

scientific article

Mbd3 and deterministic reprogramming

Modeling of C/EBPα Mutant Acute Myeloid Leukemia Reveals a Common Expression Signature of Committed Myeloid Leukemia-Initiating Cells

article

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22

scientific article

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

scientific article

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause

scientific article published on February 2016

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

scientific article published on 27 February 2016

NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment

scientific article

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression

scientific article

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

scientific article published on 23 December 2015

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

scientific article

Prospects and challenges in proteomics.

scientific article

Resetting transcription factor control circuitry toward ground-state pluripotency in human

scientific article

SMIM1 underlies the Vel blood group and influences red blood cell traits

scientific article

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes

scientific article published on 01 May 2002

SPINE 2: a system for collaborative structural proteomics within a federated database framework

scientific article

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics

scientific article

Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex

scientific article

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

article

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

article

Structural genomics: a new era for pharmaceutical research

scientific article

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

scientific article

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article

Target hub proteins serve as master regulators of development in yeast

scientific article

The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.

scientific article published in July 2018

The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

scientific article (publication date: June 2014)

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

scientific article published on January 2013

The transcriptional activity of human Chromosome 22

scientific article

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

scientific article

Tracking the embryonic stem cell transition from ground state pluripotency

scientific article

Transcriptional diversity during lineage commitment of human blood progenitors

scientific article

Transcriptional regulatory networks in bacteria: from input signals to output responses.

scientific article published on 30 August 2006

Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner

scientific article published on March 2013

List of works by Paul Bertone

A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1

Advances in functional protein microarray technology

An integrated approach for finding overlooked genes in yeast

Analysis of yeast protein kinases using protein chips.

Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery

Assessment of transcript reconstruction methods for RNA-seq

CREB binds to multiple loci on human chromosome 22.

Citrullination regulates pluripotency and histone H1 binding to chromatin

Comparative analysis of neutrophil and monocyte epigenomes

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

Computational Methods and Bioinformatic Tools

Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research

Design optimization methods for genomic DNA tiling arrays

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency

Distribution of NF-kappaB-binding sites across human chromosome 22

Elevated FOXG1 and SOX2 in glioblastoma enforces neural stem cell identity through transcriptional control of cell cycle and epigenetic regulators.

EphrinB2 drives perivascular invasion and proliferation of glioblastoma stem-like cells

Epigenetic resetting of human pluripotency.

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

ExpressYourself: A modular platform for processing and visualizing microarray data

Fast optimal genome tiling with applications to microarray design and homology search

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing ⬇️

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors

Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

Global analysis of protein activities using proteome chips

Global changes in STAT target selection and transcription regulation upon interferon treatments

Global identification of human transcribed sequences with genome tiling arrays

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.

Identification of pseudogenes in the Drosophila melanogaster genome

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor.

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast

Integrative data mining: the new direction in bioinformatics.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

Mapping organelle proteins and protein complexes in Drosophila melanogaster

Mbd3 and deterministic reprogramming

Modeling of C/EBPα Mutant Acute Myeloid Leukemia Reveals a Common Expression Signature of Committed Myeloid Leukemia-Initiating Cells

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass

NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

Prospects and challenges in proteomics.

Resetting transcription factor control circuitry toward ground-state pluripotency in human

SMIM1 underlies the Vel blood group and influences red blood cell traits

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes

SPINE 2: a system for collaborative structural proteomics within a federated database framework

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics

Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

Structural genomics: a new era for pharmaceutical research

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

Systematic evaluation of spliced alignment programs for RNA-seq data

Target hub proteins serve as master regulators of development in yeast

The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.

The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

The transcriptional activity of human Chromosome 22

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Tracking the embryonic stem cell transition from ground state pluripotency

Transcriptional diversity during lineage commitment of human blood progenitors

Transcriptional regulatory networks in bacteria: from input signals to output responses.

Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner