推荐阅读¶

入门框架¶

Conesa et al. 2016. A survey of best practices for RNA-seq data analysis. Genome Biology.
Stark, Grzelak and Hadfield. 2019. RNA sequencing: the teenage years. Nature Reviews Genetics.
Luecken and Theis. 2019. Current best practices in single-cell RNA-seq analysis. Molecular Systems Biology.

Macosko et al. 2015. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell.
Zheng et al. 2017. Massively parallel digital transcriptional profiling of single cells. Nature Communications.
Stuart et al. 2019. Comprehensive integration of single-cell data. Cell.
Ståhl et al. 2016. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science.
Asp et al. 2020. Spatially resolved transcriptomes: new tools for tissue exploration. BioEssays.

Buenrostro et al. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling. Nature Methods.
Buenrostro et al. 2015. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature.
Bock et al. 2016. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nature Biotechnology.

Robins et al. 2009. Comprehensive assessment of T-cell receptor beta-chain diversity. Blood.
Georgiou et al. 2014. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nature Biotechnology.
Caporaso et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods.
Callahan et al. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods.
Quince et al. 2017. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology.

Visscher et al. 2017. 10 years of GWAS discovery: biology, function, and translation. American Journal of Human Genetics.
Manolio et al. 2009. Finding the missing heritability of complex diseases. Nature.
GTEx Consortium. 2020. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science.
Cano-Gamez and Trynka. 2020. From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases. Frontiers in Genetics.

Aebersold and Mann. 2016. Mass-spectrometric exploration of proteome structure and function. Nature.
Gillet et al. 2012. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition. Molecular & Cellular Proteomics.
Sumner et al. 2007. Proposed minimum reporting standards for chemical analysis. Metabolomics.
Hasin, Seldin and Lusis. 2017. Multi-omics approaches to disease. Genome Biology.