High priority:

Watson & Warr (2019) Errors in long-read assemblies can critically affect protein prediction. Nature Biotechnology 37 - https://www.nature.com/articles/s41587-018-0004-z

Rojas Echenique et al. (2019) Modular epistasis and the compensatory evolution of gene deletion mutants. PLoS Genet. 15(2):e1007958 - https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007958

Huang et al. (2018) Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life. Nucleic Acids Research, gky1009 - https://doi.org/10.1093/nar/gky1009

Mayr C (2018) Proteins assemble as they are being made. Nature 561: 186-187 - https://www.nature.com/magazine-assets/d41586-018-05905-4/d41586-018-05905-4.pdf

Venkat A et al. (2018) Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol. 2:1280-1288 - https://www.nature.com/articles/s41559-018-0584-5

Sedlazeck FJ et al. (2018) Piercing the dark matter: bioinformatics of long-range sequencing and mapping. Nature Rev. Genet. 19:329-346 - https://www.ncbi.nlm.nih.gov/pubmed/29599501

Konrad et al. (2018) Mutational and transcriptional landscape of spontaneous gene duplications and deletions in Caenorhabditis elegans. Proc Natl Acad Sci USA 115(28):7386-7391 - https://www.ncbi.nlm.nih.gov/pubmed/29941601

Bolívar P et al. (2018) Biased inference of selection due to GC-biased gene conversion and the rate of protein evolution in flycatchers when accounting for it. Mol Biol Evol. - https://doi.org/10.1093/molbev/msy149

Sandve et al. (2018) Subfunctionalization versus neofunctionalization after whole-genome duplication. Nature genetics - https://www.nature.com/articles/s41588-018-0162-4

Natan et al. (2018) Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nature Structural & Molecular Biologyvolume - https://www.nature.com/articles/s41594-018-0029-5

Lehner & Fraser (2004) Protein domains enriched in mammalian tissue-specific or widely expressed genes. Trends Genet. - https://www.ncbi.nlm.nih.gov/pubmed/15363898

Garcia-Seisdedos et al. (2017) Proteins evolve on the edge of supramolecular self-assembly. Nature - https://www.nature.com/articles/nature23320

Yang et al. (2017) Genetic Interaction Network as an Important Determinant of Gene Order in Genome Evolution. Mol Biol Evol - https://www.ncbi.nlm.nih.gov/pubmed/29029158

Risso et al. (2017) De novo active sites for resurrected Precambrian enzymes. Nature communications - https://www.nature.com/articles/ncomms16113

Jayasena et al. (2017) Stepwise Evolution of a Buried Inhibitor Peptide over 45 My. Mol Biol Evol - https://www.ncbi.nlm.nih.gov/pubmed/?term=Fisher+Panero

Park & Lehner (2013) Epigenetic epistatic interactions constrain the evolution of gene expression. Mol Syst Biol - https://www.ncbi.nlm.nih.gov/pubmed/23423319

Nelson & Masel (2017) Intercellular competition and multicellular aging the inevitability of of multicellular aging. PNAS - http://www.pnas.org/content/early/2017/10/25/1618854114.full

Andersen et al. (2017) A heterochromatin-dependent transcription machinery drives piRNA expression. Nature - https://www.nature.com/nature/journal/vaop/ncurrent/full/nature23482.html

Siddiq et al. (2017) Evolution of protein specificity: insights from ancestral protein reconstruction. Curr Opin Struct Biol - https://www.ncbi.nlm.nih.gov/pubmed/28841430

Levy (2017) On protein assembly and building blocks: Beyond the limits of the LEGO bricks metaphor. Biochemistry - https://www.ncbi.nlm.nih.gov/pubmed/28809494

Lees et al. (2016) Functional innovation from changes in protein domains and their combinations. Curr. Opin. Struct. Biol.https://www.ncbi.nlm.nih.gov/pubmed/27309309

Karam et al. (2017) Co-chaperone Hsp70/Hsp90 organizing protein (Hop) is Required for Transposon Silencing and piRNA Biogenesis. J. Biol. Chem. - http://www.jbc.org/content/early/2017/02/13/jbc.C117.777730.abstract

Sharma et al. (2017) Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22. Science 356:642-645 - http://science.sciencemag.org/content/356/6338/642

Krull et al. (2007) Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Research 17:1139-1145 - http://genome.cshlp.org/content/17/8/1139.long

Krull et al. (2005) Alu-SINE exonization: en route to protein-coding function. Molecular Biology and Evolution 22:1702-1711 - http://mbe.oxfordjournals.org/content/22/8/1702.long

McDonald et al. (2016) Sex speeds adaptation by altering the dynamics of molecular evolution . Nature 531:233–236 - http://www.nature.com/nature/journal/v531/n7593/full/nature17143.html

Figuet et al. (2016) Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Mol Biol Evol 33:1517-1527 - http://mbe.oxfordjournals.org/content/33/6/1517.long

Nielsen (2009) Adaptionism-30 years after Gould and Lewontin. Evolution 63:2487-90 - https://www.ncbi.nlm.nih.gov/pubmed/19744124

Chikina et al. (2016) Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. Mol Biol Evol 33:2182-2192 - http://mbe.oxfordjournals.org/content/33/9/2182.abstract

Newton et al. (2017) Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes. PNAS - http://www.pnas.org/content/early/2017/04/12/1618552114.full

Lower priority:

Saavedra et al. (2018) Dynamic allostery can drive cold adaptation in enzymes. Nature ; 558(7709):324-328 - https://www.nature.com/articles/s41586-018-0183-2

Ponnikas et al. (2018) Why do sex chromosomes stop recombining? Trends Genet. - https://www.ncbi.nlm.nih.gov/pubmed/29716744

Nocedal et al. (2017) Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator. eLife - https://elifesciences.org/articles/23250

Sieber et al. (2018) The Definition of Open Reading Frame Revisited. Trends Genet. - https://www.ncbi.nlm.nih.gov/pubmed/29366605

Hughes et al. (2018) The birth and death of olfactory receptor gene families in mammalian niche adaptation. Mol Biol Evol - https://academic.oup.com/mbe/article/35/6/1390/4943998

Dey et al. (2018) PDB-wide identification of biological assemblies from conserved quaternary structure geometry Nature Methods - https://www.nature.com/articles/nmeth.4510

Schimmel (2018) The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol. - https://www.ncbi.nlm.nih.gov/pubmed/28875994

Ho et al. (2017) Testing the neutral hypothesis of phenotypic evolution. PNAS - http://www.pnas.org/content/114/46/12219

Hguyen et al. (2017) Innovation and constraint leading to complex multicellularity in the Ascomycota. Nature Communications - https://www.nature.com/articles/ncomms14444

Chau & Goodisman (2017) Gene duplication and the evolution of phenotypic diversity in insect societies Evolution - https://onlinelibrary.wiley.com/doi/full/10.1111/evo.13356

Graur et al. (2013) On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE. Genome Biology and Evolution 5:578-590 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622293/

Bewick et al. (2016) Evolution of DNA methylation across insects. Mol Biol Evol 34, 654-665 - https://www.ncbi.nlm.nih.gov/pubmed/28025279

Xu & Zhang (2017) Insulin receptors and wing dimorphism in rice planthoppers. Phil. Trans. R. Soc. B 372, 20150489 - https://www.ncbi.nlm.nih.gov/pubmed/27994130 *

Cibele et al. (2017) Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 9: 161-177 - https://www.ncbi.nlm.nih.gov/pubmed/28158585

Partha & Raman (2014) Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces. PloS One 9, e112792 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229248/

Kovacs et al. (2017) Frozen in Time: The History of Proteins. Mol Biol Evol msx086 - https://www.ncbi.nlm.nih.gov/pubmed/28201543

Holinski et al. (2017) Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 85:312–321 - http://onlinelibrary.wiley.com/doi/10.1002/prot.25225/full

Laurino et al. (2016) An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol 14, e1002396. - http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002396

Yin et al. (2016) Old genes experience stronger translational selection than young genes. Gene 590:29-34 - https://www.ncbi.nlm.nih.gov/pubmed/27259662

Wang et al. (2016) microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes. Mol Biol Evol33:2232-2247 - http://mbe.oxfordjournals.org/content/33/9/2232.abstract

Dixon et al. (2016) Evolutionary Consequences of DNA Methylation in a Basal Metazoan. Mol Biol Evol 33: 2285-2293 - http://mbe.oxfordjournals.org/content/33/9/2285.abstract

Attwater & Holliger (2012) The cooperative gene. Nature 491 - https://web.natur.cuni.cz/filosof/markos/Evoluce/Attwater%20hypercycle.pdf

Amorós-Moya et al. (2010) Evolution in regulatory regions rapidly compensates the cost of non-optimal codon usage. Molecular Biology and Evolution 27: 2141-2151 - http://mbe.oxfordjournals.org/content/27/9/2141.long

Shum et al. (2016) The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay. Cell 165:382-395* April?

Michal Levin et al. The mid-developmental transition and the evolution of animal body plans. Nature

Burmann et al. (2012) An alpha-helix to Beta-barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell 150 *

Coyle (2013) Exploitation of latent allostery enables the evolution of new modes of MAP Kinase regulation. Cell 154

Fernandez & Lynch (2011) Non-adaptive origins of interactome complexity. Nature 474.

Goldstein et al. (2015) Non-adaptive amino acid convergence rates decrease over time. MBE

Hammerschmidt et al. (2014) Life cycles, fitness decoupling and the evolution of multicellularity. Nature

Mendonca et al. (2011) Loss of genetic redundancy in reductive genome evolution. PLoS Computational Biology 7

Piatigorsky (2003) Crystallin genes: specialization by changes in gene regulation may precede gene duplication. Journal of Structural and Functional Genomics 3

Salazar-Ciudad & Marin-Riera (2013) Adaptive dynamics under development-based genotype–phenotype maps. Nature

Sandler et al. (2013) Experimental analysis of co-evolution within protein complexes: The yeast exosome as a model. Proteins 1997

Williams et al. (2006) Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations. Evolutionary Bioinformatics online 2

Xu et al. (2009) Evolution of RNases in leaf monkeys: Being parallel gene duplications or parallel gene conversions is a problem of molecular phylogeny. Molecular Phylogenetics and Evolution 50

* = suitable for BSc presentation.