Articles for Journal Club

Highest priority:

  • Majik & Payne (2020) Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/37/4/1165/5679780 - Anna/Andreas/Margaux/Hanna/Katrin/Bharat/suitable for a student presentation
  • Wacholder & Carvunis (2021) New genes from borrowed parts. Science - https://science.sciencemag.org/content/371/6531/779 - Carsten/Elias/Baki/suitable for a student presentation
  • Prabh & Tautz (preprint) Frequent lineage-specific substitution rate changes support an episodic model for protein evolution. bioRxiv - https://www.biorxiv.org/content/10.1101/2020.08.25.266486v2.full
  • Pinney et al. (2021) Parallel molecular mechanisms for enzyme temperature adaptation. Science - https://science.sciencemag.org/content/371/6533/eaay2784.full - Berndjan/Margaux
  • Husain and Murugan (2020) Physical constraints on epistasis. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/37/10/2865/5839750 - Bharat/Margaux/Berndjan
  • Mandelboum et al. (2019) Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias. PLoS Biology - doi: 10.1371/journal.pbio.3000481 - to be presented at group retreat
  • Hochberg et al. (2020) A hydrophobic ratchet entrenches molecular complexes. Nature - https://doi.org/10.1038/s41586-020-3021-2
  • Kaushik & Zhang (2020) A protein sequence fitness function for identifying natural and non-natural proteins. Proteins: Structure, Function and Bioinformatics - https://doi.org/10.1002/prot.25900
  • Gould & Lewontin (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme. Proc. R. Soc. Lond. B. 205581–598 - http://doi.org/10.1098/rspb.1979.0086 - to be done together with Nielsen 2009 (below)
  • Nielsen (2009) Adaptionism-30 years after Gould and Lewontin. Evolution 63:2487-90 - https://www.ncbi.nlm.nih.gov/pubmed/19744124 - to be done together with Gould & Lewontin (above)


High priority:

  • Xie et al. Contingency and chance erase necessity in the experimental evolution of ancestral proteins. eLife - https://elifesciences.org/articles/67336
  • Zhang et al. (2020) ASTRAL-Pro: Quartet-based species-tree inference despite paralogy. Molecular Biology and Evolution - https://doi.org/10.1093/molbev/msaa139 - Elias/Carsten/Virginia/suitable for a student presentation
  • Mérel et al. (2021) The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Molecular Biology and Evolutio n - https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab155/6281075 - Bertrand/Mark/Alice
  • Cheng and Kirkpatrick (2021) Molecular evolution and the decline of purifying selection with age. Nature Communications - https://doi.org/10.1038/s41467-021-22981-9
  • Theofanopoulou et al. (2021) Universal nomenclature for oxytocin-vasotocin ligand and receptor families. Nature - https://www.nature.com/articles/s41586-020-03040-7
  • Roddy et al. (2021) Mammals with small populations do not exhibit larger genomes. Molecular Biology and Evolution - https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab142/6270792 - to be presented at group retreat together with Hodgkinson & Eyre-Walker (2011) and the two Lynch papers below
  • Hodgkinson & Eyre-Walker (2011) Variation in the mutation rate across mammalian genomes. Nature Reviews Genetics - https://www.nature.com/articles/nrg3098 - to be presented at a group retreat together with Roddy et al. (2021) and the two Lynch papers below
  • Lynch & Conery (2003) The origins of genome complexity. Science – to be presented at group retreat together with Lynch (2010), Roddy et al. (2021) and Hodgkinson & Eyre-Walker (2011)
  • Lynch (2010) Evolution of the mutation rate. Trends in Genetics - https://doi.org/10.1016/j.tig.2010.05.003 - to be presented at group retreat together with Lynch & Conery (2003), Roddy et al. (2021) and Hodgkinson & Eyre-Walker (2011)
  • Peter et al. (2021) A novel, universally active C-terminal protein degradation signal generated by alternative splicing. Journal of Molecular Biology - https://doi.org/10.1016/j.jmb.2021.166890
  • Romero-Romero et al. (2021) Evolution, folding and design of TIM barrels and related proteins. Current Opinion in Structural Biology - https://doi.org/10.1016/j.sbi.2020.12.007 - suitable for a student talk
  • Besnard et al. (2020) A broad mutational target explains a fast rate of phenotypic evolution. eLife - https://elifesciences.org/articles/54928 - Anna
  • Cagiada et al. (2021) Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance. Molecular Biology and Evolution - Alice
  • Garriga et al. (2019) Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology - https://www.nature.com/articles/s41587-019-0333-6 - ASSIGNED (Carsten)
  • Kudella et al. (2021) Structured sequences emerge from random pool when replicated by templated ligation. PNAS - https://doi.org/10.1073/pnas.2018830118 - Margaux/Hanna
  • Ascencio et al. (2021) Expression attenuation as a mechanism or robustness against gene duplication. PNAS - https://doi.org/10.1073/pnas.2014345118 - Elias
  • Nedrud et al. (2021) A large-scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains. Proteins - https://doi.org/10.1002/prot.26067
  • Wang et al. (2021) Characterizing the function of domain linkers in regulating the dynamics of multi-domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence. Proteins - https://doi.org/10.1002/prot.26066
  • Almudi et al. (2020) Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications - https://doi.org/10.1038/s41467-020-16284-8 - Alina/Bertrand
  • Davidson et al. (2017) SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. Genome Biology - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1 - ASSIGNED (Mark)
  • Chen et al. (2021) Efficient assembly of nanopore reads via highly accurate and intact error correction. Nature Communications - https://doi.org/10.1038/s41467-020-20236-7
  • Bourke (2021) The role and rule of relatedness altruism. Nature - https://www.nature.com/articles/d41586-021-00210-z - suitable for a student presentation
  • Gao et al. High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonic. GigaScience - https://doi.org/10.1093/gigascience/giaa143 - Alina/Bertrand
  • Tong et al. Genome-wide, genic, and site-specific changes associated with the convergent evolution of sociality in spiders. bioRxiv - https://doi.org/10.1101/2021.01.27.428473 - ASSIGNED (Alina)
  • Otten et al. (2020) How directed evolution reshapes the energy landscape in an enzyme to boost catalysis. Science - https://science.sciencemag.org/content/370/6523/1442 - Brennen/Berndjan/Margaux
  • Yan & Wang (2020) Funneled energy landscape unifies principles of protein binding and evolution. PNAS - https://doi.org/10.1073/pnas.2013822117 - Margaux
  • Baraniuk et al. (2020) The science of deep learning. PNAS - https://doi.org/10.1073/pnas.2020596117 - if possible, combine this article presentation with a report on alpha-fold. - Brennen
  • Choi & Kim (2020) Reply to Li et al.: Organism tree of life: gene phylogeny vs whole-proteome phylogeny. PNAS - https://doi.org/10.1073/pnas.2015631117
  • Chen et al. (2020) Sequence-based prediction of metamorphic behavior in proteins. BioRxiv - https://doi.org/10.1101/2020.02.27.967935 - Andreas/Margaux
  • Singh (2020) Inducing phase separation using artificial disordered proteins. Nature Methods - https://www.nature.com/articles/s41592-020-00972-w
  • Emond et al. (2020) Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nature Communications
  • Long et al. (2018) Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology & Evolution - ASSIGNED
  • Dyson & Goodisman (2020) Gene duplication in the honeybee: patterns of DNA methylation, gene expression and genomic environment. Molecular Biology and Evolution - https://doi.org/10.1093/molbev/msaa088
  • Shafee et al. (2020) Evolution of sequence-diverse disordered regions in a protein family: order within the chaos. Molecular Biology and Evolution - https://doi.org/10.1093/molbev/msaa096
  • Campitelli et al. (2020) The role of conformational dynamics and allostery in modulating protein evolution. Annual Review of Biophysics - https://doi.org/10.1146/annurev-biophys-052118-115517
  • Lukačišinová et al. (2020) Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance. Nature Communications - https://www.nature.com/articles/s41467-020-16932-z - ASSIGNED
  • Nong et al. (2020) Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nature Communications - https://www.nature.com/articles/s41467-020-16801-9
  • Miao et al. (2020) Putative cell type discovery from single-cell expression data. Nature Methods (preferably presented in the same session as Heaton et al. below)
  • Heaton et al. (2020) Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genomes. Nature Methods (preferably presented in the same session as Miao et al. above)
  • Lai et al. (2020) Evolutionary model of protein secondary structure capable of revealing new biological relationships. Proteins: Structure, Function and Bioinformatics - https://doi.org/10.1002/prot.25898
  • Agarwal & Shendure (2020) Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks. Cell Reports https://doi.org/10.1016/j.celrep.2020.107663 - ASSIGNED (Christopher)
  • Mehlhoff et al. (preprint) Collateral fitness effects of mutations. BioRxiv - https://www.biorxiv.org/content/biorxiv/early/2019/10/29/820068.full.pdf
  • Arendsee et al. (2019) fagin: synteny-based phylostratigraphy and finer classification of young genes. BMC Bioinformatics - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3023-y
  • Durand et al. (2019) Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. Genome Res. 29:932-943.
  • Van Nyatten et al. (2019) To see or not to see: molecular evolution of the rhodopsin visual pigment in neotropical electric fishes. Proc Biol Sci 286: 20191182 - http://dx.doi.org/10.1098/rspb.2019.1182
  • Alvarez-Ponce et al. (2019) Molecular chaperones accelerate the evolution of their protein clients in yeast. Genome Biol Evol (Epub ahead of print) https://www.biorxiv.org/content/biorxiv/early/2019/02/15/552349.full.pdf
  • Pagnani et al. (2019) The intrinsic dimension of protein sequence evolution. PLoS Comput Biol. 15: e1006767 - https://doi.org/10.1371/journal.pcbi.1006767
  • Zarin et al. (2019) Proteome-wide signatures of function in highly diverged intrinsically disordered regions. bioRxiv - https://www.biorxiv.org/content/biorxiv/early/2019/03/16/578716.full.pdf
  • 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
  • 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
  • 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
  • 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
  • Park & Lehner (2013) Epigenetic epistatic interactions constrain the evolution of gene expression. Mol Syst Biol - https://www.ncbi.nlm.nih.gov/pubmed/23423319
  • 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 - suitable for student presentation
  • 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
  • Crabtree (2013) Our fragile intellect. Part I. Trends in Genetics - https://www.sciencedirect.com/science/article/pii/S0168952512001588 (also suitable for group retreat)
  • Crabtree (2013) Our fragile intellect. Part II. Trends in Genetics - https://www.sciencedirect.com/science/article/pii/S016895251200159X (also suitable for group retreat)


Lower Priority:

  • 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
  • Andersen et al. (2017) A heterochromatin-dependent transcription machinery drives piRNA expression. Nature - https://www.nature.com/nature/journal/vaop/ncurrent/full/nature23482.html
  • 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
  • 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
  • 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
  • Stress et al. (2019) Eine DNA‐kodierte Molekülbibliothek mit Elementen natürlicher Makrocyclen. Angew. Chem. - https://onlinelibrary.wiley.com/doi/full/10.1002/ange.201902513
  • Chen et al. (2019) Molecular evolution in large steps - codon subsitutions under positive selection. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/36/9/1862/5488198
  • Marchi et al. (2019) Size and structure of the sequence space of repeat proteins. PLOS Comp Bio - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007282
  • Dzuricky et al. (2020) De novo engineering of intracellular condensates using artificial disordered proteins. Nature Chemistry
  • Mudge et al. (2020) Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research
  • Selberg et al. (2021) Ancestral sequence reconstruction: from chemical paleogenetics to maximum likelihood algorithms and beyond. PLoS Comp Bio - https://link.springer.com/article/10.1007/s00239-021-09993-1 - suitable for student presentation
  • Lamoureux et al. (2020) The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Research - https://doi.org/10.1093/nar/gkaa774 - suitable for a student presentation
  • Chak et al. (2020) Eusociality shapes convergent patterns of molecular evolution across mitochondrial genomes of snapping shrimps. Mol Biol Evol - suitable for a student presentation
  • Broom et al. (2020) Evolution of an enzyme conformational ensemble guides design of an efficient biocatalyst. bioRxiv
  • Tretyachenko et al. (2020) CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics - https://doi.org/10.1093/bioinformatics/btaa804
  • To et al. (2020) Non-refoldability is pervasive across the E. coli proteome. bioRxiv preprint - https://www.biorxiv.org/content/10.1101/2020.08.28.273110v1.full.pdf
  • Frenkel-Pinter et al. (2020) Mutually stabilized interactions between proto-peptides and RNA. Nature Communications - https://www.nature.com/articles/s41467-020-16891-5
  • Zhong et al. (2020) Automated continuous evolution of proteins in vivo. ACS Synth Biol - https://doi.org/10.1021/acssynbio.0c00135
  • Freedman et al. (preprint) Error, noise and bias in de novo transcriptome assemblies. bioRxiv - https://doi.org/10.1101/585745
  • Fellber et al. (2015) Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. BMC Evol Biol - doi: 10.1186/s12862-015-0558-z
  • Blanco-Melo et al. (2016) Origins and Evolution of tetherin, an Orphan Antiviral Gene. Cell Host Microbe - doi: 10.1016/j.chom.2016.06.007
  • Mahalak & Chamberlin (2015) Orphan Genes Find a Home: Interspecific Competition and Gene Network Evolution. PLoS Genet - doi: 10.1371/journal.pgen.1005254
  • Warsi et al. (2020) Evolution of a new function by fusion between phage DNA and a bacterial gene. Molecular Biology and Evolution - https://doi.org/10.1093/molbev/msaa007
  • Clyde (2019) piRNAs make sense of retroviral invaders Nature Reviews Genetics - doi:10.1038/s41576-019-0187-2
  • Assis (2019) Out of the testis, into the ovary: biased outcome of gene duplication and deletion in Drosophila. Evolution - https://doi.org/10.1111/evo.13820
  • Katsnelson et al. (2019) On the feasibility of saltational evolution. PNAS - https://doi.org/10.1073/pnas.1909031116
  • Li et al. (2019) Systematic analysis reveals the prevalence and principles of bypassable gene essentiality Nature Communications - https://doi.org/10.1038/s41467-019-08928-1
  • Vernon et al. (2018) PiPi contacts are an overlooked protein feature relevant to phase separation. eLife - https://doi.org/10.7554/eLife.31486
  • Vernon & Forman-Kay (2019) First-generation predictors of biological protein phase separation. Current Opinion in Structural Biology - https://doi.org/10.1016/j.sbi.2019.05.016
  • Navarro et al. (2019) TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLOS Comp Bio - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007293
  • Barido-Sottani et al. (2019) Measuring similarity between gene interaction profiles. BMC Bioinformatics - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3024-x
  • Kristensen et al. (2019) The biogenesis, biology and characterization of circular RNAs. Nature - https://www.nature.com/articles/s41576-019-0158-7
  • Razban (2019) Protein melting temperature cannot fully assess whether protein folding free energy underlies the universal abundance-evolutionary rate correlation seen in proteins. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/36/9/1955/5489915
  • Ishikawa et al. (2019) A fast likelihood method to reconstruct and visualize ancestral scenarios. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/36/9/2069/5498561
  • Perron et al. (2019) Modeling structural constraints on protein evolution via side-chain conformational states. Molecular Biology and Evolution - https://academic.oup.com/mbe/article/36/9/2086/5494692
  • 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
  • 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
  • Hguyen et al. (2017) Innovation and constraint leading to complex multicellularity in the Ascomycota. Nature Communications - https://www.nature.com/articles/ncomms14444
  • 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
  • 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.