High-throughput sequencing for biology and medicine

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Non-invasive prenatal measurement of the fetal genome

(2012) H. Christina Fan et al.   NATURE

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Erratum: Corrigendum: Performance comparison of whole-genome sequencing platforms

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

(2012) Akihiro Fujimoto et al.   NATURE GENETICS

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

A public resource facilitating clinical use of genomes

(2012) Madeleine P. Ball et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Cell-to-Cell Variability--A New Era in Molecular Biology

(2012) L. Pelkmans   SCIENCE

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Human Genome Sequencing in Health and Disease

(2011) Claudia Gonzaga-Jauregui et al.   Annual Review of Medicine

Efficient capture of circulating tumor cells with a novel immunocytochemical microfluidic device

(2011) Mary Nora Dickson et al.   Biomicrofluidics

Identification of genomic indels and structural variations using split reads

(2011) Zhengdong D Zhang et al.   BMC GENOMICS

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Genetic Testing for Potentially Lethal, Highly Treatable Inherited Cardiomyopathies/Channelopathies in Clinical Practice

(2011) David J. Tester et al.   CIRCULATION

Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

(2011) L. Wang et al.   GENOME RESEARCH

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

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Development of a low-cost magnetic microfluidic chip for circulating tumour cell capture

(2011) J. Xia et al.   IET Nanobiotechnology

Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene

(2011) John S. Welch   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

Circulating tumour cells, their role in metastasis and their clinical utility in lung cancer

(2011) John D. O’Flaherty et al.   LUNG CANCER

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

When catastrophe strikes a cell

(2011) Jose M. C. Tubio et al.   NATURE

Single-cell analysis: The deepest differences

(2011) Charlotte Schubert   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

More to Hi-C than meets the eye

(2011) Myong-Hee Sung et al.   NATURE GENETICS

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

(2011) Adam J Bass et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

(2011) Natalie A. Twine et al.   PLoS One

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

(2011) Juliane Hannemann et al.   PLoS One

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

(2011) A. Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-Genome Sequencing for Optimized Patient Management

(2011) M. N. Bainbridge et al.   Science Translational Medicine

ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma

(2011) Julia Salzman et al.   PLOS BIOLOGY

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

(2011) Wigard P Kloosterman et al.   GENOME BIOLOGY

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

(2011) Henrik Edgren et al.   GENOME BIOLOGY

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Personal genome sequencing: current approaches and challenges

(2010) M. Snyder et al.   GENES & DEVELOPMENT

Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

Integrative analysis of the melanoma transcriptome

(2010) M. F. Berger et al.   GENOME RESEARCH

Rapid isolation and detection of cancer cells by utilizing integrated microfluidic systems

(2010) Kang-Yi Lien et al.   LAB ON A CHIP

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Defining transcribed regions using RNA-seq

(2010) Brian T Wilhelm et al.   Nature Protocols

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

(2010) Brian B. Tuch et al.   PLoS One

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Single cell analysis: the new frontier in ‘omics’

(2010) Daojing Wang et al.   TRENDS IN BIOTECHNOLOGY

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Global and unbiased detection of splice junctions from RNA-seq data

(2010) Adam Ameur et al.   GENOME BIOLOGY

Tumor heterogeneity: Causes and consequences

(2009) Andriy Marusyk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis

(2009) Rafael de Cid et al.   NATURE GENETICS

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Mapping accessible chromatin regions using Sono-Seq

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

Mapping Human Genetic Diversity in Asia

(2009) et al.   SCIENCE

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

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

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Where shall we meet? A role for genome organisation and nuclear sub-compartments in mediating interchromosomal interactions

(2008) Cameron S. Osborne et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

(2008) Steven A McCarroll et al.   NATURE GENETICS

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Isolation of endothelial cells from fresh tissues

(2008) Judy R van Beijnum et al.   Nature Protocols

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells

(2008) Christine Fuhrmann et al.   NUCLEIC ACIDS RESEARCH

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

(2008) H. C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germline Allele-Specific Expression of TGFBR1 Confers an Increased Risk of Colorectal Cancer

(2008) L. Valle et al.   SCIENCE

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE