Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content

The molecular hallmarks of epigenetic control

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

Do short, frequent DNA sequence motifs mould the epigenome?

(2016) Timo Quante et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Quantitative visualization of alternative exon expression from RNA-seq data

(2015) Yarden Katz et al.   BIOINFORMATICS

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

(2015) Sigal Shachar et al.   CELL

Nuclear lamins are not required for lamina-associated domain organization in mouse embryonic stem cells

(2015) M. Amendola et al.   EMBO REPORTS

H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation

(2015) Yoshihiro Matsumura et al.   MOLECULAR CELL

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

A novel mechanism of post-translational modulation of HMGA functions by the histone chaperone nucleophosmin

(2015) Laura Arnoldo et al.   Scientific Reports

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

HMGA2 Is a Driver of Tumor Metastasis

(2013) A. Morishita et al.   CANCER RESEARCH

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis

(2013) M. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Genome-wide analysis of HMGA2 transcription factor binding sites by ChIP on chip in gastric carcinoma cells

(2012) Lang Zha et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Crystal Structure of a Complex of DNA with One AT-Hook of HMGA1

(2012) Elsa Fonfría-Subirós et al.   PLoS One

Tandemly repeated DNA families in the mouse genome

(2011) Aleksey S Komissarov et al.   BMC GENOMICS

Core promoter-selective function of HMGA1 and Mediator in Initiator-dependent transcription

(2011) M. Xu et al.   GENES & DEVELOPMENT

Conformational Role for the C-Terminal Tail of the Intrinsically Disordered High Mobility Group A (HMGA) Chromatin Factors

(2011) Elisa Maurizio et al.   JOURNAL OF PROTEOME RESEARCH

Cross-linking of DNA through HMGA1 suggests a DNA scaffold

(2011) Benjamin Vogel et al.   NUCLEIC ACIDS RESEARCH

Chromatin Immunoprecipitation to Analyze DNA Binding Sites of HMGA2

(2011) Nina Winter et al.   PLoS One

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

(2011) Florian Lienert et al.   PLoS Genetics

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Identification of target genes for wild type and truncated HMGA2 in mesenchymal stem-like cells

(2010) Jørn Henriksen et al.   BMC CANCER

Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions

(2010) S. Cuddapah et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Detection of splice junctions from paired-end RNA-seq data by SpliceMap

(2010) K. F. Au et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HMGA molecular network: From transcriptional regulation to chromatin remodeling

(2009) Riccardo Sgarra et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Nuclear functions of the HMG proteins

(2009) Raymond Reeves   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

High mobility group proteins and their post-translational modifications

(2008) Qingchun Zhang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY