Interpreting noncoding genetic variation in complex traits and human disease

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

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PLINK: a tool set for whole-genome association and population-based linkage analyses.

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

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An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Wang, K., Li, M., & Hakonarson, H. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq603 · Cited by 14,380 · see citing works

A method and server for predicting damaging missense mutations.

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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829 · see citing works

Principal components analysis corrects for stratification in genome-wide association studies

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

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Finding the missing heritability of complex diseases

Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336 · see citing works

Construction of a genetic linkage map in man using restriction fragment length polymorphisms.

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

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A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works

Identification of the Cystic Fibrosis Gene: Cloning and Characterization of Complementary DNA

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Molecular signatures database (MSigDB) 3.0

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SIFT: predicting amino acid changes that affect protein function

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The International HapMap Project

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Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.

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Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results

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Evolution and Functions of Long Noncoding RNAs

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Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

The International Schizophrenia Consortium (2009) · Nature · doi:10.1038/nature08185 · Cited by 4,821 · see citing works

Mendelian randomization: Using genes as instruments for making causal inferences in epidemiology

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Common SNPs explain a large proportion of the heritability for human height

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XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance.

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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

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

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Evolutionary Rate at the Molecular Level

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works

The cancer genome

Stratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,458 · see citing works

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

Hamosh, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki033 · Cited by 3,443 · see citing works

Mapping and analysis of chromatin state dynamics in nine human cell types

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P. A., & Hirschhorn, J. N. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2344 · Cited by 2,891 · see citing works

Annotation of functional variation in personal genomes using RegulomeDB

Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722 · see citing works

A new multipoint method for genome-wide association studies by imputation of genotypes

Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609 · see citing works

Human non-synonymous SNPs: server and survey

Ramensky, V. E. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf493 · Cited by 2,267 · see citing works

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

Ward, L. D., & Kellis, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr917 · Cited by 2,229 · see citing works

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217 · see citing works

The Genetic Landscape of a Cell

Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., Koh, J. L. Y., Toufighi, K., Mostafavi, S., et al. (2010) · Science · doi:10.1126/science.1180823 · Cited by 2,162 · see citing works

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Lango Allen, H., Estrada, K., Lettre, G., Berndt, S. I., Weedon, M. N., Rivadeneira, F., Willer, C. J., Jackson, A. U., Vedantam, S., Raychaudhuri, S., et al. (2010) · Nature · doi:10.1038/nature09410 · Cited by 1,945 · see citing works

The NIH Roadmap Epigenomics Mapping Consortium

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Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872 · see citing works

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

Li, Y., Willer, C. J., Ding, J., Scheet, P., & Abecasis, G. R. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20533 · Cited by 1,843 · see citing works

Non-Darwinian Evolution

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Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., & Batzoglou, S. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001025 · Cited by 1,757 · see citing works

Sequencing and comparison of yeast species to identify genes and regulatory elements

Kellis, M., Patterson, N. J., Endrizzi, M. G., Birren, B. W., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,731 · see citing works

An oestrogen-receptor-α-bound human chromatin interactome

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Matrix eQTL: ultra fast eQTL analysis via large matrix operations

Shabalin, A. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts163 · Cited by 1,694 · see citing works

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

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A genomic regulatory network for development

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The mystery of missing heritability: Genetic interactions create phantom heritability

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A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy

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Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

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Architecture of the human regulatory network derived from ENCODE data

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High-Resolution Mapping and Characterization of Open Chromatin across the Genome

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Detecting gene–gene interactions that underlie human diseases

Cordell, H. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2579 · Cited by 1,350 · see citing works

Genetics of gene expression and its effect on disease

Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A. S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G. B., Gunnarsdottir, S., et al. (2008) · Nature · doi:10.1038/nature06758 · Cited by 1,296 · see citing works

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS

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Personal omics profiling reveals dynamic molecular and medical phenotypes

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Rare and common variants: twenty arguments

Gibson, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3118 · Cited by 1,278 · see citing works

Epigenome-wide association studies for common human diseases

Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3000 · Cited by 1,272 · see citing works

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

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Assessing computational tools for the discovery of transcription factor binding sites

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

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Pre-mRNA splicing and human diseasePreprint

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The evolution of gene expression levels in mammalian organs

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N. N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., et al. (2010) · Science · doi:10.1126/science.1198374 · Cited by 1,223 · see citing works

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

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Hirschsprung disease, associated syndromes and genetics: a review

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Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis

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A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,160 · see citing works

Positive Natural Selection in the Human Lineage

Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T. S., Altshuler, D., & Lander, E. S. (2006) · Science · doi:10.1126/science.1124309 · Cited by 1,157 · see citing works

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

Cirulli, E. T., & Goldstein, D. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2779 · Cited by 1,136 · see citing works

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature · doi:10.1038/nature10530 · Cited by 1,108 · see citing works

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

Wang, Z., & Burge, C. B. (2008) · RNA · doi:10.1261/rna.876308 · Cited by 1,076 · see citing works

Initial impact of the sequencing of the human genome

Lander, E. S. (2011) · Nature · doi:10.1038/nature09792 · Cited by 1,044 · see citing works

Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

Hill, W. G., Goddard, M. E., & Visscher, P. M. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000008 · Cited by 1,039 · see citing works

Discovery and characterization of chromatin states for systematic annotation of the human genome

Ernst, J., & Kellis, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1662 · Cited by 1,033 · see citing works

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

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Sequence Variants in <i>SLITRK1</i> Are Associated with Tourette's Syndrome

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Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor

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Deciphering the splicing code

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Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease

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Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

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Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 760 · see citing works

Analysing biological pathways in genome-wide association studies

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Donor splice-site mutations in WT1 are responsible for Frasier syndrome

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Epigenetics as a unifying principle in the aetiology of complex traits and diseases

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Linking disease associations with regulatory information in the human genomePreprint

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Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

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Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

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