Integrative detection and analysis of structural variation in cancer genomes

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

(2018) Claire Marchal et al.   Nature Protocols

Nucleome Analysis Reveals Structure–Function Relationships for Colon Cancer

(2017) Laura Seaman et al.   MOLECULAR CANCER RESEARCH

RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells

(2016) A. Rasim Barutcu et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A computational strategy to adjust for copy number in tumor Hi-C data

(2016) Hua-Jun Wu et al.   BIOINFORMATICS

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal 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

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

(2015) Vishnu Dileep et al.   GENOME RESEARCH

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

(2015) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

Integrative Analysis Reveals the Transcriptional Collaboration between EZH2 and E2F1 in the Regulation of Cancer-Related Gene Expression

(2015) H. Xu et al.   MOLECULAR CANCER RESEARCH

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

(2015) Martin Peifer et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

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

(2014) Suhas S.P. Rao et al.   CELL

Complex correlations: replication timing and mutational landscapes during cancer and genome evolution

(2014) Jiao Sima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

A comprehensive transcriptional portrait of human cancer cell lines

(2014) Christiaan Klijn et al.   NATURE BIOTECHNOLOGY

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Cancer Cytogenetics: Methodology Revisited

(2014) Thomas S. K. Wan   Annals of Laboratory Medicine

Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis

(2014) Milena Rondón-Lagos et al.   Molecular Cytogenetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types

(2013) Zheng Wang et al.   PLoS One

Massively Parallel Sequencing Reveals the Complex Structure of an Irradiated Human Chromosome on a Mouse Background in the Tc1 Model of Down Syndrome

(2013) Susan M. Gribble et al.   PLoS One

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

DNA Replication Timing

(2013) N. Rhind et al.   Cold Spring Harbor Perspectives in Biology

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

(2012) Matteo Benelli et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

(2012) T. Ryba et al.   GENOME RESEARCH

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

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease

(2012) Jesse M. Engreitz et al.   PLoS One

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

(2011) A. M. Hillmer et al.   GENOME RESEARCH

Transcriptional consequences of genomic structural aberrations in breast cancer

(2011) K. Inaki et al.   GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines

(2011) Oliver A. Hampton et al.   Cancer Genetics

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

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

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

Genomic instability and histone H3 phosphorylation induction by the Ras-mitogen activated protein kinase pathway in pancreatic cancer cells

(2008) Paula S. Espino et al.   INTERNATIONAL JOURNAL OF CANCER

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS