Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors

Human iPSC-derived Down syndrome astrocytes display genome-wide perturbations in gene expression, an altered adhesion profile, and increased cellular dynamics

(2020) Blandine Ponroy Bally et al.   HUMAN MOLECULAR GENETICS

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

The Nuclear Lamina as an Organizer of Chromosome Architecture

(2019) Yuri Y. Shevelyov et al.   Cells

Senolytic therapy alleviates Aβ-associated oligodendrocyte progenitor cell senescence and cognitive deficits in an Alzheimer’s disease model

(2019) Peisu Zhang et al.   NATURE NEUROSCIENCE

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D

(2019) Michael I. Robson et al.   MOLECULAR CELL

Transcriptome signature of cellular senescence

(2019) Gabriel Casella et al.   NUCLEIC ACIDS RESEARCH

Induced Chromosomal Aneuploidy Results in Global and Consistent Deregulation of the Transcriptome of Cancer Cells

(2019) Darawalee Wangsa et al.   NEOPLASIA

Senolytics decrease senescent cells in humans: Preliminary report from a clinical trial of Dasatinib plus Quercetin in individuals with diabetic kidney disease

(2019) LaTonya J. Hickson et al.   EBioMedicine

DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency

(2019) Katy McLaughlin et al.   Cell Reports

Neurogenesis impairment: An early developmental defect in Down syndrome

(2018) Fiorenza Stagni et al.   FREE RADICAL BIOLOGY AND MEDICINE

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

(2018) Anne Zirkel et al.   MOLECULAR CELL

APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer’s Disease Phenotypes in Human iPSC-Derived Brain Cell Types

(2018) Yuan-Ta Lin et al.   NEURON

Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21

(2018) Patrick K. Gonzales et al.   PLoS One

NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence

(2018) Aled J. Parry et al.   Nature Communications

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Modeling Down Syndrome with Patient iPSCs Reveals Cellular and Migration Deficits of GABAergic Neurons

(2018) Hai-Qin Huo et al.   Stem Cell Reports

SOX10 Single Transcription Factor-Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells

(2018) Juan Antonio García-León et al.   Stem Cell Reports

A Library of Phosphoproteomic and Chromatin Signatures for Characterizing Cellular Responses to Drug Perturbations

(2018) Lev Litichevskiy et al.   Cell Systems

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Chemical screen identifies a geroprotective role of quercetin in premature aging

(2018) Lingling Geng et al.   Protein & Cell

Massive reshaping of genome–nuclear lamina interactions during oncogene-induced senescence

(2017) Christelle Lenain et al.   GENOME RESEARCH

The Clinical Potential of Senolytic Drugs

(2017) James L. Kirkland et al.   JOURNAL OF THE AMERICAN GERIATRICS SOCIETY

An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells

(2017) Julia TCW et al.   Stem Cell Reports

Widespread cerebellar transcriptome changes in Ts65Dn Down syndrome mouse model after lifelong running

(2016) Marius Walus et al.   BEHAVIOURAL BRAIN RESEARCH

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Down Syndrome Developmental Brain Transcriptome Reveals Defective Oligodendrocyte Differentiation and Myelination

(2016) Jose Luis Olmos-Serrano et al.   NEURON

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Placental transcriptomes in the common aneuploidies reveal critical regions on the trisomic chromosomes and genome-wide effects

(2016) Katherine Bianco et al.   PRENATAL DIAGNOSIS

Changes in the Transcriptome of Human Astrocytes Accompanying Oxidative Stress-Induced Senescence

(2016) Elizabeth P. Crowe et al.   Frontiers in Aging Neuroscience

Reorganization of chromosome architecture in replicative cellular senescence

(2016) Steven W. Criscione et al.   Science Advances

Self-Organizing 3D Human Neural Tissue Derived from Induced Pluripotent Stem Cells Recapitulate Alzheimer’s Disease Phenotypes

(2016) Waseem K. Raja et al.   PLoS One

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

(2016) Brian Egan et al.   PLoS One

Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line

(2016) Mireia Borràs-Fresneda et al.   Scientific Reports

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

(2015) Li Lu et al.   Epigenetics

Building the Connectivity Map of epigenetics: Chromatin profiling by quantitative targeted mass spectrometry

(2015) Amanda L. Creech et al.   METHODS

mTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype

(2015) Nicolás Herranz et al.   NATURE CELL BIOLOGY

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Unique features of the transcriptional response to model aneuploidy in human cells

(2014) Milena Dürrbaum et al.   BMC GENOMICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Down-regulation of Sp1 suppresses cell proliferation, clonogenicity and the expressions of stem cell markers in nasopharyngeal carcinoma

(2014) Jing-Ping Zhang et al.   Journal of Translational Medicine

Domains of genome-wide gene expression dysregulation in Down’s syndrome

(2014) Audrey Letourneau et al.   NATURE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation

(2014) Andrew A Lane et al.   NATURE GENETICS

Long-Term Quiescent Fibroblast Cells Transit into Senescence

(2014) Shiva Marthandan et al.   PLoS One

p38MAPK Plays a Crucial Role in Stromal-Mediated Tumorigenesis

(2014) E. Alspach et al.   Cancer Discovery

Multiplex Genetic Fate Mapping Reveals a Novel Route of Neocortical Neurogenesis, Which Is Altered in the Ts65Dn Mouse Model of Down Syndrome

(2013) W. A. Tyler et al.   JOURNAL OF NEUROSCIENCE

Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia

(2013) Jacob D Jaffe et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Deficits in human trisomy 21 iPSCs and neurons

(2013) J. P. Weick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcriptional consequences of aneuploidy

(2012) J. M. Sheltzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Altered hematopoiesis in trisomy 21 as revealed through in vitro differentiation of isogenic human pluripotent cells

(2012) G. A. MacLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific inhibition of NF-Y subunits triggers different cell proliferation defects

(2011) Paolo Benatti et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Widespread Proliferation Impairment and Hypocellularity in the Cerebellum of Fetuses with Down Syndrome

(2010) Sandra Guidi et al.   BRAIN PATHOLOGY

p21Waf1is required for cellular senescence but not for cell cycle arrest induced by the HDAC inhibitor sodium butyrate

(2010) Vasily S. Romanov et al.   CELL CYCLE

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Clinical practice

(2010) Michel E. Weijerman et al.   EUROPEAN JOURNAL OF PEDIATRICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Proliferation deficits and gene expression dysregulation in Down's syndrome (Ts1Cje) neural progenitor cells cultured from neurospheres

(2009) Randal X. Moldrich et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling

(2009) Stuart M Chambers et al.   NATURE BIOTECHNOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Cell Cycle Elongation Impairs Proliferation of Cerebellar Granule Cell Precursors in the Ts65Dn Mouse, an Animal Model for Down Syndrome

(2008) Andrea Contestabile et al.   BRAIN PATHOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY