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Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
TLDR
It is demonstrated how the GSEA method yields insights into several cancer-related data sets, including leukemia and lung cancer, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer.
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MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.
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Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.
TLDR
A generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case and suggests a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.
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Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results
TLDR
Specific standards designed to maintain rigor while also promoting communication are proposed for the interpretation of linkage results in genetic studies under way for many complex traits.
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Integrative Genomics Viewer
TLDR
The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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A global reference for human genetic variation
  • Adam Gonçalo R. David M. Richard M. Gonçalo R. David R. Auton Abecasis Altshuler Durbin Abecasis Bentley C, A. Auton, Shane A. McCarthy
  • Biology
    Nature
  • 30 September 2015
TLDR
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
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PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
TLDR
An analytical strategy is introduced, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes, which identifies a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle.
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Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
TLDR
A set of analytical methods that modify and extend the classical theory for mapping quantitative trait loci (QTLs) and allow a substantial reduction in the number of progeny that need to be scored with the DNA markers.
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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
TLDR
Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
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