Selected papers:

  • Durairaj et al (2023) Uncovering new families and folds in the natural protein universe – Nature – https://pubmed.ncbi.nlm.nih.gov/37704037/ – Lars
  • uz-Zaman et al. (2024). Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli. PLoS Biology – https://doi.org/10.1371/journal.pbio.3002418 – Andreas
  • Morales et al. (2024) Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs. MBE. https://doi.org/10.1093/molbev/msae165 – Sarah R

Highest priority:

High priority:

  • Chisholm et al. (2024). Ancestral Reconstruction and the Evolution of Protein Energy Landscapes. Annual Rev. Biophysics. https://doi.org/10.1146/annurev-biophys-030722-125440
  • Moss et al. (2024). The Effects of Codon Usage on Protein Structure and Folding. Annual Rev. Biophysics. https://doi.org/10.1146/annurev-biophys-030722-020555
  • Holstad et al. (2024) Evolvability predicts macroevolution under fluctuating selection. Science – https://doi.org/10.1126/science.adi8722
  • Xia et al (2023) On the Genetic basis of tail evolution in humans and apes – Nature – https://www.nature.com/articles/s41586-024-07095-8
  • Rhie et al (2023) The complete sequence of a human Y chromosome – Nature -https://pubmed.ncbi.nlm.nih.gov/37612512/
  • Hallst et al (2023) Assembly of 43 human Y chromosomes reveals extensive complexity and variation – Nature – https://pubmed.ncbi.nlm.nih.gov/37612510/
  • Greenbury et al. (2022) The structure of genotype-phenotype maps makes fitness landscapes navigable. Nature Ecology and Evolution – https://www.nature.com/articles/s41559-022-01867-z – Bharat
  • 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)
  • Besnard et al. (2020) A broad mutational target explains a fast rate of phenotypic evolution. eLife – https://elifesciences.org/articles/54928
  • Kudella et al. (2021) Structured sequences emerge from random pool when replicated by templated ligation. PNAS – https://doi.org/10.1073/pnas.2018830118 – Margaux
  • 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
  • Yan & Wang (2020) Funneled energy landscape unifies principles of protein binding and evolution. PNAS – https://doi.org/10.1073/pnas.2013822117 – Margaux
  • Chen et al. (2020) Sequence-based prediction of metamorphic behavior in proteins. BioRxiv – https://doi.org/10.1101/2020.02.27.967935 – Andreas/Margaux
  • Emond et al. (2020) Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nature Communications
  • 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
  • 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)
  • 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.
  • 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
  • Shafer et al. (2022) Gene family evolution underlies cell-type diversification in the hypothalamus of teleosts. Nature Ecology and Evolution – https://www.nature.com/articles/s41559-021-01580-3

Lower Priority:

  • Samer I. Al-Saffar and Matthew W. (2022) HahnEvaluating methods for estimating the proportion of adaptive amino acid substitutions. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.08.15.504017v1 – Alina/Carsten
  • Shen et al. (2022) On the fitness effects and disease relevance of synonymous mutations. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.08.22.504687v1
  • Liu H, Zhang. (2022) Is the mutation rate lower in genomic regions of stronger selective constraints?. MBE – https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msac169/6652438?login=false
  • Kucera et al. (2022) Conditional generative modeling for de novo protein design with hierarchical functions. Bioinformatics – https://academic.oup.com/bioinformatics/article/38/13/3454/6593486

Done:

* = suitable for BSc presentation.

  • Escobedo et al. (2024). Genetics, energetics and allostery during a billion years of hydrophobic protein core evolution. bioRxiv – https://doi.org/10.1101/2024.05.11.593672 (long paper, ideal for retreat) – Sarah L
  • Andjus et al. (2024) Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast. RNA https://doi.org/10.1261/rna.079903.123 – Marie
  • Bénitière, Necsulea & Duret (2024) Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife – https://doi.org/10.7554/eLife.93629.3 – Sarah
  • Mehlholff et al (2020) Collateral fitness effects of mutations – PNAS – https://www.pnas.org/doi/epdf/10.1073/pnas.1918680117 – Alun
  • Zarin et al. (2019) Proteome-wide signatures of function in highly diverged intrinsically disordered regions. eLife – https://elifesciences.org/articles/46883 – Nils
  • Frumkin an Taub (2023) Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways – Nature Ecology and Evolution – https://pubmed.ncbi.nlm.nih.gov/37945946/ – Andreas
  • Camellato et al. (2024) Synthetic reversed sequences reveal default genomic states. Nature – https://doi.org/10.1038/s41586-024-07128-2 – Bharat
  • Enright et al. (2023) Low Complexity Regions in Proteins and DNA are Poorly Correlated. Molecular Biology and Evolution – https://academic.oup.com/mbe/article/40/4/msad084/7111731 – Marie
  • Pinto et al (2023) Decay of Skin-Specific Gene Modules in Pangolins. Journal of Molecular Evolution – https://link.springer.com/article/10.1007/s00239-023-10118-z – Alina
  • 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 – Alina M.
  • Muffato et al (2023) Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom – NEE – https://www.nature.com/articles/s41559-022-01956-z – Sarah
  • 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 – Carsten
  • Xie et al. Contingency and chance erase necessity in the experimental evolution of ancestral proteins. eLife – https://elifesciences.org/articles/67336 – Margaux
  • 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 – Andreas
  • Jiang et al. (2023) On the Decoupling of Evolutionary Changes in mRNA and Protein Levels. MBE – https://pubmed.ncbi.nlm.nih.gov/37498582/ – Alun
  • Sachin Kaushik – Effect of beneficial sweeps and background selection on genetic diversity in changing environments. Journal of Theoretical Biology https://www.sciencedirect.com/science/article/abs/pii/S0022519323000279 – Anna G
  • Haghani, Amin, et al. (2023) – DNA methylation networks underlying mammalian traits. Science – Mark
  • 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 – Elias
  • Nevers et al. (2023) Protein length distribution is remarkably uniform across the tree of life. Genome Biology – https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02973-2 – Carsten
  • Andreas Wagner (2023) Evolvability-enhancing mutations in the fitness landscapes of an RNA and a protein. Nature Communications. https://doi.org/10.1038/s41467-023-39321-8 : Bharat
  • Zhou et al (2023) Eighty million years of rapid evolution of the primate Y chromosome – Nature Ecology and Evolution – https://pubmed.ncbi.nlm.nih.gov/37268856/ – Margaux
  • Tsuboyama et al – Mega-scale experimental analysis of protein folding stability in biology and design. Nature – Lasse
  • Gabzi et al. (2022) Fitness Landscape Analysis of a tRNA Gene Reveals that the Wild Type Allele is Sub-optimal, Yet Mutationally Robust. MBE – https://academic.oup.com/mbe/article/39/9/msac178/6670756 – Bharat
  • 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 – Elias
  • Biba et al. (2021) Pairs of mutually compensatory frameshifting mutations contribute to protein evolution in vertebrates and insects. bioarxiv – https://www.biorxiv.org/content/10.1101/2020.12.25.424394v2 -Anna
  • Yang et al. (2022) Characterization of sequence determinants of enhancer function using natural genetic variation. eLife – https://elifesciences.org/articles/76500 – Alun
  • 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 – Lasse
  • Peng et al. (2023) The origin and structural evolution of de novo genes in Drosophila. biorxiv – https://doi.org/10.1101/2023.03.13.532420 – Lars
  • 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 – Carsten
  • 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 – Alina J.
  • 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
  • Kovacs et al. (2017) Frozen in Time: The History of Proteins. MBE – https://doi.org/10.1093/molbev/msx086
  • 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
  • Johri et al. (2022) A population-genetic lens into the process of gene loss following whole-genome duplication. MBE – https://pubmed.ncbi.nlm.nih.gov/35639978/
  • Rives et al. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. PNAS – https://www.pnas.org/doi/10.1073/pnas.2016239118
  • Zheng and Zhao. (2022) Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. elife – https://elifesciences.org/articles/78772
  • 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 – Carsten
  • Holden et al. (2022) Aqueous microdroplets enable abiotic synthesis and chain extension of unique peptide isomers from free amino acids. PNAS – https://www.pnas.org/doi/10.1073/pnas.2212642119 – Berndjan
  • Oman et al. (2022) How Sequence Context-Dependent Mutability Drives Mutation Rate Variation in the Genome. genomebiology – https://academic.oup.com/gbe/article/14/3/evac032/6537538?login=false – Sarah
  • Marsch-Martinez et al. (2022) Twisting development, the birth of a potential new gene. iScience – https://www.sciencedirect.com/science/article/pii/S2589004222018995 – Denovo person
  • Bergman et al. (2022) Worldwide late-Quaternary population declines in extant megafauna are due to Homo sapiens rather than climate. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.08.13.503826v1 – Bertrand
  • Yan et al.(2022) Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.08.21.504711v1 – Alun
  • Ocaña-Pallarès et al (2022) Divergent genomic trajectories predate the origin of animals and fungi. Nature – https://www.nature.com/articles/s41586-022-05110-4 – Alina M.
  • Seal et al. (2022) Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains. JACS – https://pubs.acs.org/doi/pdf/10.1021/jacs.2c03819 – Lars
  • Ascencio et al. (2021) Expression attenuation as a mechanism or robustness against gene duplication. PNAS – https://doi.org/10.1073/pnas.2014345118 – Elias
  • Dzuricky et al. (2020) De novo engineering of intracellular condensates using artificial disordered proteins. Nature Chemistry – Kai
  • Singh (2020) Inducing phase separation using artificial disordered proteins. Nature Methods – https://www.nature.com/articles/s41592-020-00972-w -Kai
  • Zhang et al. (2020) ASTRAL-Pro: Quartet-based species-tree inference despite paralogy. Molecular Biology and Evolution – https://doi.org/10.1093/molbev/msaa139 – Carsten
  • Rosenberg et al. (2022) Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. Nature Communications – https://www.nature.com/articles/s41467-022-30390-9 – Lars
  • Harris et al. (2022) Ancestral sequence reconstruction of a cytochrome P450 family involved in chemical defence reveals the functional evolution of a promiscuous, xenobiotic-metabolizing enzyme in vertebrates . MBE – https://academic.oup.com/mbe/article/39/6/msac116/6593376 – Baki
  • Weisman et al. (2022) Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes. Current Biology https://www.cell.com/current-biology/fulltext/S0960-9822(22)00721-7 – Elias
  • Stupp et al (2021) Co-evolution based machine-learning for predicting functional interactions between human genes – https://www.nature.com/articles/s41467-021-26792-w – Margaux
  • 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 (Mark)
  • 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 – Alina M
  • 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 – Alina M.
  • Del Marmol et al. (2021) The structural basis of odorant recognition in insect olfactory receptors. Nature – https://pubmed.ncbi.nlm.nih.gov/34349260/ – Alice
  • 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 Alun
  • Kato et al (2022) How do protein domains of low sequence complexity work?. RNA – https://pubmed.ncbi.nlm.nih.gov/34670847/ – Lars
  • Park & Lehner (2013) Epigenetic epistatic interactions constrain the evolution of gene expression. Mol Syst Biol – https://www.ncbi.nlm.nih.gov/pubmed/23423319 – Kai
  • 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
  • Wu et al (2021) Expression level is a major modifier of the fitness landscape of a protein coding gene. Nature ecology and evolution – https://www.nature.com/articles/s41559-021-01578-x – Bernjan
  • 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
  • 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
  • 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
  • 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
  • Agarwal and Shendure (2020) Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks – https://www.sciencedirect.com/science/article/pii/S2211124720306161
  • Cardoso-Moreira et al (2019) Gene expression across mammalian organ development. Nature – https://www.nature.com/articles/s41586-019-1338-5
  • Blevins et al (2021) Uncovering de novo gene birth in yeast using deep transcriptomics. Nature communication – https://www.nature.com/articles/s41467-021-20911-3
  • Hochberg et al (2020) A hydrophobic ratchet entrenches molecular complexes. Nature – https://www.nature.com/articles/s41586-020-3021-2
  • 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
  • Long et al. (2018) Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology & Evolution -https://www.nature.com/articles/s41559-017-0425-y
  • Jumper, J., Evans, R., Pritzel, A. et al.(2021) Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 – https://doi.org/10.1038/s41586-021-03819-2 – Lars
  • Natalia de Souza Araujo & Maria Cristina Arias. (2021) Gene expression and epigenetics reveal species‑specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. Scientific reports – https://www.nature.com/articles/s41598-020-75432-8
  • Minh et al. (2020) IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. MBE – https://academic.oup.com/mbe/article/37/5/1530/5721363
  • Michael Ross et al. (2013) Characterizing and measuring bias in sequence data. GBE – https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-5-r51
  • Monroe et al (2022) Mutation bias reflects natural selection in Arabidopsis thaliana. Nature – https://www.nature.com/articles/s41586-021-04269-6
  • Vance et al (2022) Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes. GBE – https://academic.oup.com/gbe/article/14/1/evac003/6501445
  • 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
  • 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) – retreat
  • 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) – retreat
  • 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
  • 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 – Lars/Coral
  • Chak et al. (2021) Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps. Mol. Biol. Evo. – Kevin
  • Price et al (2022) Detecting signatures of selection on gene expression. Natue ecology and evolution – https://www.nature.com/articles/s41559-022-01761-8 – Alun
  • Paps and Holland. (2018) Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. nature Communications – https://www.nature.com/articles/s41467-018-04136-5 – Alina M.
  • 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 – Bertrand
  • 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 – Sarah
  • 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 – Alina B.
  • Baalsrud et al. (2017) De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. MBE – https://academic.oup.com/mbe/article/35/3/593/4693805 – Ina
  • 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 – Ina
  • Warner et al. (2019) Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes. Nature Communications https://www.nature.com/articles/s41467-019-10546-w – Jakob Materna
  • Patraquim et al. (2022) Translation and natural selection of micropeptides from long non-canonical RNAs. Nature Communications – https://www.nature.com/articles/s41467-022-34094-y – Marie
  • Liu et al. (2022) The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. MBE – https://pubmed.ncbi.nlm.nih.gov/35642310/
  • Baraniuk et al. (2020) The science of deep learning. PNAS – https://doi.org/10.1073/pnas.2020596117
  • 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
  • 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
  • Pinney et al. (2021) Parallel molecular mechanisms for enzyme temperature adaptation. Science – https://science.sciencemag.org/content/371/6533/eaay2784.full – Margaux
  • Bertram el al. (2022) CAGEE: computational analysis of gene expression evolution. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.11.18.517074v1 – Mark
  • Favreau et al. Co-expression Gene Networks and Machine-learning Algorithms Unveil a Core Genetic Toolkit for Reproductive Division of Labour in Rudimentary Insect Societies. GBE – https://doi.org/10.1093/gbe/evac174 – Mark
  • Bergeron et al. Evolution of the germline mutation rate across vertebrates. Nature – https://www.nature.com/articles/s41586-023-05752-y – Alina M.
  • Giannakis et al. (2022) Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention. Cell systems – https://www.sciencedirect.com/science/article/pii/S2405471222003519 – Bharat
  • Peng et al. (2023) The origin and structural evolution of de novo genes in Drosophila. biorxiv – https://doi.org/10.1101/2023.03.13.532420 – Lars
  • Chakravarty et al. Identification of a covert evolutionary pathway between two protein folds. Nature Communications – https://www.nature.com/articles/s41467-023-38519-0 – Lars
  • Bhattacharya et al. (2022) NMR-guided directed evolution. Nature – https://www.nature.com/articles/s41586-022-05278-9 – Andreas
  • Wen et al. (2023) Genome-Wide Identification of Gene Loss Events Suggest Loss Relics as a Potential source of Functional LncRNAs in Humans – https://academic.oup.com/mbe/article/40/5/msad103/7151558 – Brenda
  • Balart-Garcia et al. (2023) Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nature Communications – https://www.nature.com/articles/s41467-023-39603-1#Sec6 – Sarah
  • Hilditch et al (2023) Assembling membraneless organelles from de novo designed proteins – Nature Chemistry – https://www.nature.com/articles/s41557-023-01321-y – Lars
  • Nomburg et al (2023) Birth of a new protein folds and functions in the virome – bioArxiv – https://www.biorxiv.org/content/10.1101/2024.01.22.576744v1 – Margaux
  • Busch et al (2023) RetracingtheRapidEvolutionofanHerbicide-DegradingEnzymebyProteinEngineering – Catalysis https://pubs.acs.org/doi/10.1021/acscatal.3c04010#:~:text=Using%20a%20combination%20of%20structure,enzyme%20with%20guanine%20deaminase%20activity.
  • Luthra et al. (2024) Regulatory activity is the default DNA state in eukaryotes. Nature Struct. Mol. Biol. https://doi.org/10.1038/s41594-024-01235-4 – Bharat
  • Oliver et al. (2022) Primate Social Organization Evolved from a Flexible Pair-Living Ancestor. bioarxiv – https://www.biorxiv.org/content/10.1101/2022.08.29.505776v1 – Carsten