Resolving the variable genome and epigenome in human disease

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

New methods for next generation sequencing based microRNA expression profiling

(2011) Henk PJ Buermans et al.   BMC GENOMICS

Sickle Hemoglobin Confers Tolerance to Plasmodium Infection

(2011) Ana Ferreira et al.   CELL

Genomics Reaches the Clinic: From Basic Discoveries to Clinical Impact

(2011) Teri A. Manolio et al.   CELL

Recent Insights Into the Genetics of Inflammatory Bowel Disease

(2011) Judy H. Cho et al.   GASTROENTEROLOGY

Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort

(2011) B Namjou et al.   GENES AND IMMUNITY

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex

(2011) C. Vandiedonck et al.   GENOME RESEARCH

Current status of genome-wide association studies in cancer

(2011) Charles C. Chung et al.   HUMAN GENETICS

Revisiting Mendelian disorders through exome sequencing

(2011) Chee-Seng Ku et al.   HUMAN GENETICS

Genetic risk prediction in complex disease

(2011) Luke Jostins et al.   HUMAN MOLECULAR GENETICS

Differential microRNA regulation of HLA-C expression and its association with HIV control

(2011) Smita Kulkarni et al.   NATURE

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy

(2011) Furen Zhang et al.   NATURE GENETICS

Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2

(2011) Fred A Wright et al.   NATURE GENETICS

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

(2011) Robert E Handsaker et al.   NATURE GENETICS

Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes

(2011) Kerrin S Small et al.   NATURE GENETICS

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

(2011) Manuel A Rivas et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Understanding type 1 diabetes through genetics: advances and prospects

(2011) Constantin Polychronakos et al.   NATURE REVIEWS GENETICS

Quantifying the Underestimation of Relative Risks from Genome-Wide Association Studies

(2011) Chris Spencer et al.   PLoS Genetics

A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci

(2011) Jonathan P. Bradfield et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Allelic Skewing of DNA Methylation Is Widespread across the Genome

(2010) Leonard C. Schalkwyk et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic imprinting and human disease

(2010) Ryutaro Hirasawa et al.   Essays in Biochemistry

A sequence variant on 17q21 is associated with age at onset and severity of asthma

(2010) Eva Halapi et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

(2010) S. V. Ramagopalan et al.   GENOME RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

(2010) Maxim Barenboim et al.   HUMAN MUTATION

Functionally defective germline variants of sialic acid acetylesterase in autoimmunity

(2010) Ira Surolia et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Multiple common variants for celiac disease influencing immune gene expression

(2010) Patrick C A Dubois et al.   NATURE GENETICS

Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency

(2010) Tobias B Haack et al.   NATURE GENETICS

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome

(2010) Peter M Krawitz et al.   NATURE GENETICS

De novo mutations of SETBP1 cause Schinzel-Giedion syndrome

(2010) Alexander Hoischen et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia

(2010) Christopher T Johansen et al.   NATURE GENETICS

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

(2010) Elizabeth K Speliotes et al.   NATURE GENETICS

Genome-wide association analysis identifies three psoriasis susceptibility loci

(2010) Philip E Stuart et al.   NATURE GENETICS

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome

(2010) Sarah B Ng et al.   NATURE GENETICS

A de novo paradigm for mental retardation

(2010) Lisenka E L M Vissers et al.   NATURE GENETICS

Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis

(2010) Benjamin F Voight et al.   NATURE GENETICS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Missing heritability and strategies for finding the underlying causes of complex disease

(2010) Evan E. Eichler et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

Exome Sequencing,ANGPTL3Mutations, and Familial Combined Hypolipidemia

(2010) Kiran Musunuru et al.   NEW ENGLAND JOURNAL OF MEDICINE

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

Inherited genetic markers discovered to date are able to identify a significant number of men at considerably elevated risk for prostate cancer

(2010) Jielin Sun et al.   PROSTATE

Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes

(2010) Shiwei Duan et al.   RNA Biology

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

(2010) Alexandra C. Nica et al.   PLoS Genetics

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

(2010) Nara L. M. Sobreira et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

(2009) Dominique J. Verlaan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

A SNP discovery method to assess variant allele probability from next-generation resequencing data

(2009) Y. Shen et al.   GENOME RESEARCH

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Parental origin of sequence variants associated with complex diseases

(2009) Augustine Kong et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C

(2009) Rasmi Thomas et al.   NATURE GENETICS

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

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

(2009) Kun Zhang et al.   NATURE METHODS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Genomewide Association Study of Leprosy

(2009) Fu-Ren Zhang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Primary Biliary Cirrhosis Associated withHLA, IL12A,andIL12RB2Variants

(2009) Gideon M. Hirschfield et al.   NEW ENGLAND JOURNAL OF MEDICINE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi 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

Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes

(2009) S. Nejentsev et al.   SCIENCE

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

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

Tissue Effect on Genetic Control of Transcript Isoform Variation

(2009) Tony Kwan et al.   PLoS Genetics

Expression of the Multiple Sclerosis-Associated MHC Class II Allele HLA-DRB1*1501 Is Regulated by Vitamin D

(2009) Sreeram V. Ramagopalan et al.   PLoS Genetics

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Genome-wide survey of allele-specific splicing in humans

(2008) Victoria Nembaware et al.   BMC GENOMICS

Long-range regulation of ?? globin gene expression during erythropoiesis

(2008) Douglas R Higgs et al.   CURRENT OPINION IN HEMATOLOGY

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

(2008) Roger Horton et al.   IMMUNOGENETICS

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

(2008) Jeffrey C Barrett et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genetic complexity in sickle cell disease

(2008) D. R. Higgs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

MicroRNA target site polymorphisms and human disease

(2008) Praveen Sethupathy et al.   TRENDS IN GENETICS

Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression

(2008) David Serre et al.   PLoS Genetics

New links to the pathogenesis of Crohn disease provided by genome-wide association scans

(2007) Christopher G. Mathew   NATURE REVIEWS GENETICS