General

Claussnitzer, Melina, Judy H. Cho, Rory Collins, Nancy J. Cox, Emmanouil T. Dermitzakis, Matthew E. Hurles, Sekar Kathiresan, et al. “A Brief History of Human Disease Genetics.” Nature 577, no. 7789 (January 2020): 179–89. https://doi.org/10.1038/s41586-019-1879-7. - Timeline and milestones in genomics development focusing on disease genetics.

Cordaux, Richard, and Mark A. Batzer. “The Impact of Retrotransposons on Human Genome Evolution.” Nature Reviews Genetics 10, no. 10 (October 2009): 691–703. https://doi.org/10.1038/nrg2640.

Goodwin, Sara, John D. McPherson, and W. Richard McCombie. “Coming of Age: Ten Years of Next-Generation Sequencing Technologies.” Nature Reviews Genetics 17, no. 6 (2016): 333–51. https://doi.org/10.1038/nrg.2016.49. - From microarrays to long read sequencing, single-cell sequencing. Technology review. Table with all technologies and costs. Figures.

Green, Eric D., Mark S. Guyer, Teri A. Manolio, and Jane L. Peterson. “Charting a Course for Genomic Medicine from Base Pairs to Bedside.” Nature 470, no. 7333 (February 10, 2011): 204–13. https://doi.org/10.1038/nature09764. - Perspective on genomics development, technologies. Figure 1 - pictorial roadmap.

Hagen, J. B. “The Origins of Bioinformatics.” Nature Reviews Genetics 1, no. 3 (2000): 231–36. https://doi.org/10.1038/35042090.

Heather, James M., and Benjamin Chain. “The Sequence of Sequencers: The History of Sequencing DNA.” Genomics 107, no. 1 (January 2016): 1–8. https://doi.org/10.1016/j.ygeno.2015.11.003. - Review of sequencing technologies, from pre-Sanger to current PacBio, Oxford Nanopore, Ion Torrent.

Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, et al. “Initial Sequencing and Analysis of the Human Genome.” Nature 409, no. 6822 (February 15, 2001): 860–921. https://doi.org/10.1038/35057062. - Genome sequencing landmark paper.

Mardis, Elaine R. “Next-Generation DNA Sequencing Methods.” Annual Review of Genomics and Human Genetics 9 (2008): 387–402. https://doi.org/10.1146/annurev.genom.9.081307.164359. - Sequencing technologies review. DNA-/RNA-/ChIP-seq. Figures.

Mardis, Elaine R. “DNA Sequencing Technologies: 2006-2016.” Nature Protocols 12, no. 2 (February 2017): 213–18. https://doi.org/10.1038/nprot.2016.182. - DNA sequencing technologies introduction, references.

Rothberg, Jonathan M., and John H. Leamon. “The Development and Impact of 454 Sequencing.” Nature Biotechnology 26, no. 10 (October 2008): 1117–24. https://doi.org/10.1038/nbt1485. - 454 sequencing, history of sequencing development, pyrosequencing. Other technologies - Box 1, Table 2.

Genomics Resources

Biostar Handbook: Bioinformatics Survival Guide. “A Practical Overview for the Data Analysis Methods of Bioinformatics.” https://www.biostarhandbook.com/index.html. GitHub repository: https://github.com/ialbert/biostar-handbook-web.

Biotools. “A Massive Collection of References on the Topics of Bioinformatics, Sequencing Technologies, Programming, Machine Learning, and More.” GitHub repository. https://github.com/jdidion/biotools.

Akalin, Altuna. Computational Genomics with R. https://compgenomr.github.io/book/. GitHub repository: https://github.com/compgenomr/book.

Getting Started with Genomics Tools and Resources. “Links and References to Many Resources.” GitHub repository. https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources.

SequencEnG. “An Interactive Learning Resource for Next-Generation Sequencing (NGS) Techniques. Each Technology Had the Corresponding Reference and Infographics.” http://education.knoweng.org/sequenceng/index.html. - An interactive learning resource for next-generation sequencing (NGS) techniques. Each technology had the corresponding reference and infographics.