Nuclear topology modulates the mutational landscapes of cancer genomes

Nucleotide excision repair is impaired by binding of transcription factors to DNA

(2016) Radhakrishnan Sabarinathan et al.   NATURE

Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes

(2016) Dilmi Perera et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types

(2016) Vera B. Kaiser et al.   PLoS Genetics

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

Chromatin at the nuclear periphery and the regulation of genome functions

(2015) Charlene Lemaître et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Differential DNA mismatch repair underlies mutation rate variation across the human genome

(2015) Fran Supek et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types

(2015) K. S. Smith et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions

(2015) Marat D. Kazanov et al.   Cell Reports

Mutational signatures: the patterns of somatic mutations hidden in cancer genomes

(2014) Ludmil B Alexandrov et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Activation-induced cytidine deaminase (AID) is localized to subnuclear domains enriched in splicing factors

(2014) Yi Hu et al.   EXPERIMENTAL CELL RESEARCH

Nuclear position dictates DNA repair pathway choice

(2014) Charlène Lemaître et al.   GENES & DEVELOPMENT

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

(2014) Kai Wang et al.   NATURE GENETICS

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing

(2013) R. D. Morin et al.   BLOOD

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes

(2013) B. S. Pedersen et al.   NUCLEIC ACIDS RESEARCH

Regulation of Nucleotide Excision Repair by Nuclear Lamin B1

(2013) Veronika Butin-Israeli et al.   PLoS One

DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes

(2013) Lin Liu et al.   Nature Communications

Dynamic Association of NUP98 with the Human Genome

(2013) Yun Liang et al.   PLoS Genetics

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

(2012) Yong H Woo et al.   Nature Communications

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Damage site chromatin: open or closed?

(2011) Alexander R Ball et al.   CURRENT OPINION IN CELL BIOLOGY

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes

(2011) Subhajyoti De et al.   NATURE BIOTECHNOLOGY

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

DNA secondary structures and epigenetic determinants of cancer genome evolution

(2011) Subhajyoti De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A genome-wide view of mutation rate co-variation using multivariate analyses

(2011) Guruprasad Ananda et al.   GENOME BIOLOGY

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

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

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Lamin B1 controls oxidative stress responses via Oct-1

(2009) Ashraf N. Malhas et al.   JOURNAL OF CELL BIOLOGY

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

The emerging role of nuclear architecture in DNA repair and genome maintenance

(2009) Tom Misteli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Conditional Variable Importance for Random Forests

(2008) Carolin Strobl et al.   BMC BIOINFORMATICS

Spatial organization of nucleotide excision repair proteins after UV-induced DNA damage in the human cell nucleus

(2008) L. Solimando et al.   JOURNAL OF CELL SCIENCE

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

(2008) Lars Guelen et al.   NATURE

Functional Targeting of DNA Damage to a Nuclear Pore-Associated SUMO-Dependent Ubiquitin Ligase

(2008) S. Nagai et al.   SCIENCE