Genomes and Genomics

Cordero, O.X., and M.F. Polz. 2014. Explaining microbial genomic diversity in light of evolutionary ecology. Nat. Rev. Microbiol. 4:263–273.

Fitch, W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19:99–114. The paper that introduced the concept of orthologs and paralogs.

Giallourakis, C., C. Henson, M. Reich, X. Xie, and V.K. Mootha. 2005. Disease gene discovery through integrative genomics. Annu. Rev. Genomics Hum. Genet. 6:381–406. A good summary of how these important searches are done.

Koonin, E.V. 2005. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39:309–338.

Mardis, E.R. 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9:387–402.

Marques-Bonet, T., O.A. Ryder, and E.E. Eichler. 2009. Sequencing primate genomes: What have we learned? Annu. Rev. Genomics Hum. Genet. 10:355–386.

Prüfer, K., K. Munch, I. Hellmann, K. Akagi, J.R. Miller, B. Walenz, S. Koren, G. Sutton, C. Kodira, R. Winer, et al. 2012. The bonobo genome compared with the chimpanzee and human genomes. Nature 486:527–531.

Rasmussen, M., Y. Li, S. Lindgreen, J.S. Pedersen, A. Albrechtsen, I. Moltke, M. Metspalu, E. Metspalu, T. Kivisild, R. Gupta, et al. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo Nature 463:757–762.

Rusch, D.B., A.L. Halpern, G. Sutton, K.B. Heidelberg, S. Williamson, S. Yooseph, D. Wu, J.A. Eisen, J.M. Hoffman, K. Remington, et al. 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5:e77. Every molecular biologist would enjoy this kind of work.

Sikela, J.M. 2006. The jewels of our genome: The search for the genomic changes underlying the evolutionarily unique capacities of the human brain. PLoS Genet. 2:e80. A favorite subject for every human.

Transcriptomes and Proteomes

Altelaar, A.F.M., J. Munoz, and A.J.R. Heck. 2013. Next-generation proteomics: Towards an integrative view of protein dynamics. Nat. Rev. Genet. 14:35–48.

Bensimon, A., A.J.R. Heck, and R. Aebersold. 2012. Mass spectrometry–based proteomics and network biology. Annu. Rev. Biochem. 81:379–405.

Ly, T., Y. Ahmad, A. Shlien, D. Soroka, A. Mills, M.J. Emanuele, M.R. Stratton, and A.I. Lamond. 2014. A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells. eLife 3:e01630.

Martin, J.A., and Z. Wang. 2011. Next-generation transcriptome assembly. Nat. Rev. Genet. 12:671–682.

Nie, L., G. Wu, D.E. Culley, J.C. Scholten, and W. Zhang. 2007. Integrative analysis of transcriptomic and proteomic data: Challenges, solutions and applications. Crit. Rev. Biotechnol. 27:63–75.

Wang, Z., M. Gerstein, and M. Snyder. 2009. RNA Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57–63.

Our Genetic History

Acevedo-Rocha, C.G., G. Fang, M. Schmidt, D.W. Ussery, and A. Danchin. 2013. From essential to persistent genes: A functional approach to constructing synthetic life. Trends Genet. 29:273–279.

Cavalli-Sforza, L.L. 2007. Human evolution and its relevance for genetic epidemiology. Annu. Rev. Genomics Hum. Genet. 8:1–15.

Ciccarelli, F.D., T. Doerks, C. von Mering, C.J. Creevey, B. Snel, and P. Bork. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287. Building an evolutionary tree based on sequences of 36 genes in 191 species, with methods that eliminate the effects of horizontal gene transfer.

Forster, A.C., and G.M. Church. 2006. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2:45. An update on efforts to synthesize a living system from chemical components.

Galperin, M.Y. 2006. The minimal genome keeps growing. Environ. Microbiol. 8:569–573. A description of a project to define the minimum number of genes required for independent life.

Hellenthal, G., G.B.J. Busby, G. Band, J.F. Wilson, C. Capelli, D. Falush, and S. Myers. 2014. A genetic atlas of human admixture history. Science 343:747–751.

Li, R., Y. Li, H. Zheng, R. Luo, H. Zhu, Q. Li, W. Qian, Y. Ren, G. Tian, J. Li, et al. 2010. Building the sequence map of the human pan-genome. Nat. Biotechnol. 28:57–63.

Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, et al. 2012. The complete genome sequence of a Neanderthal from the Altai mountains. Nature 505:43–49.

Rannala, B., and Z. Yang. 2008. Phylogenetic inference using whole genomes. Annu. Rev. Genomics Hum. Genet. 9:217–231.

Wade, C.H., B.A. Tarini, and B.S. Wilfond. 2013. Growing up in the genomic era: Implications of whole-genome sequencing for children, families, and pediatric practice. Annu. Rev. Genomics Hum. Genet. 14:535–555.