Title: 'Evolution of new genes in primates'
Title: "Evolution-Inspired Protein Engineering and Design: Learning from the Evolutionary History of Enzymes on the example of Haloalkane Dehalogenases"
Title: "Molecular evolution of ionontropic receptors in Blattodea"
Title: "The genomics of nestmate recognitions of slavemaker ants and their hosts - Initial results for Temnothorax longispinosus and Cardiocondyla obscurior"
Kalyaanamoorthy et. al. (2017) ModelFinder: fast model selection for accurate phylogenetic estimates Nature methods - https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4285.html
Title: "Molecular evolution of Ionotropic Receptors in Blattodea"
Zhou & Zhang (2017) Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution. Mol. Biol. Evol. msx109 - https://academic.oup.com/mbe/article/doi/10.1093/molbev/msx109/3098657/Gene-Tree-Discordance-Does-Not-Explain-Away-the
Title: Understanding the mechanisms of de novo gene evolution using transcriptomics and ribosome profiling data
Title: "Expression and purification of possible mouse de novo genes"
Title: "Translational readthrough in Saccaromyces cerivisiae"
Chakrabortee et al. (2016) Intrinsically disordered proteins drive emergence and inheritance of biological traits. Cell 167:369-381.e12 - http://www.cell.com/cell/abstract/S0092-8674(16)31250-8
Onno et al. (2017) Widespread Genetic Incompatibilities between First-Step Mutations during Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment. PLoS Biology 15:e1002591 - http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002591
Blevins et al. (2017) Hybrid incompatibility caused by an epiallele. PNAS - http://www.pnas.org/content/early/2017/03/06/1700368114.abstract
Topic: Osiris gene cluster
Prieto-Godino et al. (2016) Olfactory receptor pseudo-pseudogenes. Nature 539:93–97 - https://www.ncbi.nlm.nih.gov/pubmed/27776356
Title: Dynamics of Gene Families Implicated in the Evolution of Termite Eusociality
Hurley & Dunlap (2013) A fable of too much too fast. Nature 495
Morata et al. (2013) The relationship between gene isoform multiplicity, number of exons and protein divergence. PLoS One 8 *
Title: "A program for detection and location determination of conserved eucaryotic domains - a pilot study"
Title: "De Novo genes in the Drosophila clades"
New & Lehner (2015) Systems biology: Network evolution hinges on history. Nature 523:297-298 - http://www.ncbi.nlm.nih.gov/pubmed/26153857 *
Gumulya & Gillam (2017) Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering. Biochem J. 474, 1-19 - http://www.biochemj.org/content/474/1/1.long
Title: "The genomics of nestmate recognition in slaves and slavemaker ants"
Steinberg & Ostermeier (2016) Shifting Fitness and Epistatic Landscapes Reflect Trade-offs along an Evolutionary Pathway. J Mol Biol 428:2730-2743 - https://www.ncbi.nlm.nih.gov/pubmed/27173379
Paper: "Sardar et al. (2014) The Evolution of Human Cells in Terms of Protein Innovation. Mol Biol Evol 31: 1364-1374 - https://academic.oup.com/mbe/article/31/6/1364/2925650/The-Evolution-of-Human-Cells-in-Terms-of-Protein"
Title: "Insect genes & DomainWorld"
Brandis & Hughes (2016) The selective advantage of synonymous codon usage bias in Salmonella . PLoS Genetics - http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1005926
Buhr et al. (2016) Synonymous codons direct cotranslational folding toward different protein conformations . Molecular Cell 61 61: 341–351 - http://dx.doi.org/10.1016/j.molcel.2016.01.008
Title: "Hexamery hypothesis: Evolution of the echinoderm Bauplan in the light of paleontological and developmental evidence."
Title: "Positive selection within proteins related to chemoperception in termites or
Searching for the needle in the haystack"
Title: "Genome-wide gene expression analyses in Trypanosoma congolense throughout its four major life cycle stages"
Ahrens et al. (2016) The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution. Mol Biol Evol 33:2248-2256 - http://mbe.oxfordjournals.org/content/33/9/2248.abstract
Title: "Beewolf genome assembly using long-read technology"
Title: "Analysis of Gene Expression Dynamics during Murine Retinal Angiogenesis"
Gould & Lewontin (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205:581-98 - https://www.ncbi.nlm.nih.gov/pubmed/42062
Lees et al. (2016) Functional innovation from changes in protein domains and their combinations. Current Opinion in Structural Biology 38:44–52 - http://www.sciencedirect.com/science/article/pii/S0959440X16300513
Drummond et al. (2006) A single determinant dominates the rate of yeast protein evolution. Molecular Biology and Evolution 23 - http://mbe.oxfordjournals.org/content/23/2/327
Title: "Protein multifunctionality: Analysis of transcription factor binding"
Title: "Evolution of Enzyme Specificity in the Alkaline Phosphatase Superfamily"
Topic: "Neutral networks"
Title: "Dehalogenase Evolution"
Title: "Enabling Comparative Genomics within Blattodea"
Lien et al. (2016) The Atlantic salmon genome provides insights into rediploidization. Nature 533:200–205 - http://www.nature.com/nature/journal/v533/n7602/full/nature17164.html
Title: "De Novo Gene Evolution: Methodological Challenges and Open Questions"
Title: "Curious case of Blattella gene count inflation - symptoms and remedies"
Title "Automated Improving of DomainANnotation (AIDAN)"
"Analysis and improvement of partial/split domains"
"Evolution of enzyme specificity in the alkaline phosphatase superfamily"
Title: "DomRates - a DomainWorld program"
"Evolutionary analyses of long non-coding RNAs in insects"
"Analysis and improvement of partial/split domains: Overview"
The fitness landscape of a tRNA gene - Li et al. 2016 Science - http://www.ncbi.nlm.nih.gov/pubmed/27080104
Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes - Park et al. 2011, Mol. Ecol. Biol - http://mbe.oxfordjournals.org/content/28/12/3345.full.pdf
Title: "Properties of putative bacterial <i>de novo</i> proteins"
Title: "The effect of selection pressure on secondary activities"
"Title: "Population genomics of coevolving Bacillus thuringiensis (BT) and Bacillus thuringiensis tenebrionis (BTT)"
The industrial melanism mutation in British peppered moths is a transposable element - van’t Hof et al. 2016 Nature - http://www.nature.com/nature/journal/v534/n7605/full/nature17951.html
Title: "Domain world"
Title: "Comparative Genomics to Investigate Longevity in Social Insects"
Alternative splicing and subfunctionalization generates fuctional diversity in fungal proteomes -
Marshall et al. 2013 PLoS genetics - http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003376
Title: "Cryptic phenotypic mutations"
"A Complex Cell Division Machinery Was Present in the Last Common Ancestor of Eukaryotes", by Laura Eme, et al.
"Origin and Spread of de Novo Genes in Drosophila melanogaster Populations", by Li Zhao , et al.
Kapheim et al. 2015: Genomic signatures of evolutionary transitions from solitary to group living
Determinants of the rate of protein evolution Nature Reviews Genetics 2015 Jianzhi Zhang & Jian-Rong Yang
"Environmental changes bridge evolutionary valleys" (by Steinberg and Ostermeier, /Science Advances/ from January 2016
Meini et al. (2015) Quantitative Description of a Protein Fitness Landscape Based on Molecular Features. Mol. Biol. Evol.
PLoS Genet. 2015 The Evolutionary Potential of Phenotypic Mutations.
“Out of Pollen” Hypothesis for Origin of New Genes in Flowering Plants: Study from Arabidopsis thaliana
Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module
Origin of the Yeast Whole-Genome Duplication Kenneth H. Wolfe
The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol. 2015
Galtier et al., 2009. GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends in Genetics 25 (1):1-5
Barve & Wagner (2013) A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature 500(7461), 203-206
Queitsch et al., 2002. HSP90 as a capacitor of phenotypic variation, Nature 417.
Barzel and Barabasi, 2013. Network link prediction by global silencing of indirect correlations. Nature Biotechnology.
N.B. This talk will be on Wednesday!
This talk will now take place in the lecture hall.