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

Grape RNA-Seq analysis pipeline environment

(2013) D. G. Knowles et al.   BIOINFORMATICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Biotinylation of lysine 16 in histone H4 contributes toward nucleosome condensation

(2012) Mahendra P. Singh et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse

(2012) Benjamin D. Pope et al.   HUMAN MOLECULAR GENETICS

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Infections and immunodeficiency in Down syndrome

(2011) G. Ram et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Identification of the translocation breakpoints in the Ts65Dn and Ts1Cje mouse lines: relevance for modeling down syndrome

(2011) Arnaud Duchon et al.   MAMMALIAN GENOME

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21

(2011) Valerio Costa et al.   PLoS One

Transcriptional regulation by HMGN proteins

(2010) Nan Zhu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes

(2010) Rachit Bakshi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes

(2010) Valerie Pestinger et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Regulation of chromatin structure and function By HMGN proteins

(2009) Yuri Postnikov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

DYRK1A-Dosage Imbalance Perturbs NRSF/REST Levels, Deregulating Pluripotency and Embryonic Stem Cell Fate in Down Syndrome

(2008) Claudia Canzonetta et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Monozygotic twins discordant for trisomy 21 and maternal 21q inheritance: A complex series of events

(2008) Sophie Dahoun et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Genotype–phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21

(2008) Robert Lyle et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Identification of dysregulated genes in lymphocytes from children with Down syndrome

(2008) Cesar A. Sommer et al.   GENOME

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Aneuploidy Affects Proliferation and Spontaneous Immortalization in Mammalian Cells

(2008) B. R. Williams et al.   SCIENCE

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY