Selected papers:

  • Mehlholff et al (2020) Collateral fitness effects of mutations – PNAS – https://www.pnas.org/doi/epdf/10.1073/pnas.1918680117 – Alun
  • 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
  • Durairaj et al (2023) Uncovering new families and folds in the natural protein universe – Nature – https://pubmed.ncbi.nlm.nih.gov/37704037/ – Lars
  • 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

Highest priority:

  • 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 reserved

High priority:

  • 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
  • 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.
  • 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)
  • 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 – Berndjan
  • Besnard et al. (2020) A broad mutational target explains a fast rate of phenotypic evolution. eLife – https://elifesciences.org/articles/54928 – Anna
  • 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.
  • 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
  • Garcia-Seisdedos et al. (2017) Proteins evolve on the edge of supramolecular self-assembly. Nature – https://www.nature.com/articles/nature23320
  • 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
  • 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)
  • 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
  • Zarin et al. (2019) Proteome-wide signatures of function in highly diverged intrinsically disordered regions. eLife – https://elifesciences.org/articles/46883

Lower Priority:

  • 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
  • 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
  • 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
  • Singh NP and Krumlauf R. (2022) Diversification and functional evolution of HOX proteins. Front Cell Dev Biol – https://pubmed.ncbi.nlm.nih.gov/35646905/
  • Theofanopoulou et al. (2021) Universal nomenclature for oxytocin-vasotocin ligand and receptor families. Nature – https://www.nature.com/articles/s41586-020-03040-7
  • 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
  • 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
  • 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
  • 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
  • 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

Done:

  • 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)
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* = suitable for BSc presentation.