GC bias in Illumina

Domainoid: domain-oriented orthology inference - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3137-2

 -- Cancelled

Title: "ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models"

Title: "Molecular function limits divergent protein evolution on planetary timescales"

Title: "Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals"

Title: "Pervasive pairwise intragenic epistasis among sequential mutations in TEM-1 beta-lactamase"

Title: "Gene co-expression network reveals both signs of ageing and an upregulation of compensatory mechanisms in old ant queens"

Title: "Discovering novel protein functions"

Title: "De novo emergence of peptides that confer antibiotic resistance"

Cancelled

Vernon et al. (2018) PiPi contacts are an overlooked protein feature relevant to phase separation. eLife - https://doi.org/10.7554/eLife.31486

Zheng et al. (2019) Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks.

https://doi.org/10.1126/science.aax1837

Title - DESTINI: A deep-learning approach to contact-driven protein structure prediction

https://www.nature.com/articles/s41598-019-40314-1

Title: "De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences"

Title: Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba

Title: "MK test between D. melanogaster populations and Drosophila species to study genes under positive selection"

Title: "Repeat annotation in the socially parasitized ant Temnothorax longispinosus"

Schmiedel & Lehner (2019) Determining protein structures using deep mutagenesis. Nature 51: 1177-1186 - ttps://www.nature.com/articles/s41588-019-0431-x

Rollins et al. (2019) Inferring protein 3D structure from deep mutation scans. Nature 51: 1170-1176 - https://www.nature.com/articles/s41588-019-0432-9

Seung Hwan Hong et al. (2019) ConDo: protein domain boundary prediction using coevolutionary information. Bioinformatics bty973 - https://doi.org/10.1093/bioinformatics/bty973

Title: "Annotation & Analysis of Ionotropic Receptors in Blattodea"

Title: "Crystallisation of insect esterases B2 of Anopheles gambiae and E3-H4 of Lucilia cuprina associated with insecticide resistance"

Figuet et al. (2016) Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Molecular Biology and Evolution 33: 1517–1527 - https://doi.org/10.1093/molbev/msw033

Sieber et al. (2018) The Definition of Open Reading Frame Revisited. Trends in Genetics 34: 167-170 - https://doi.org/10.1016/j.tig.2017.12.009

Title: "Annotation & Analysis of Ionotropic Receptors in Blattodea"

Title: "Ageing in a long lived ant queen"

Title: "What makes us human? - Investigating de novo gene evolution in the human lineage"

Title: "De novo gene emergence in Drosophila"

Title: "Investigation how chaperones might influence the folding pattern of de novo proteins from D.melanogaster"

Title: "Influence of Sociality and Selection on Blattodean Genomes"

Title: "Purification and characterisation of Acp36DE and other de novo genes of D. melanogaster"

Title: "Reading frame in C-terminal and N-terminal extensions in Drosophila as possible cause for the emergence of De novo genes"

Title: "What makes us human? - Investigating de novo gene evolution in the human lineage"

Title: "Improvement of Protein Annotations by Enhancing HMM Domain Detection with Context Analyses"

Title: "Analysis of Multidomain Protein Families"

Title: "Historical Enzyme Evolution - Emergence of Sulfatases in the Metallo-β-Lactamase Superfamily""

Andreatta et al. (2015) The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol - doi:10.1093/gbe/evv098

Yu et al. (2018) Grammar of protein domain architectures. PNAS 116:3636-3645 - https://www.pnas.org/content/116/9/3636

Linkeviciute et al. (2015) Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie 119: 269–277 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679076/

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

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

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

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

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

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

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

Carroll et al. (2019) MultiDomainBenchmark: a multi-domain query and subject database suite. BMC Bioinformatics - https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2660-5

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

Title: "Laboratory Evolution of Sulfatases: Testing the Exaptive Subfunctionalization Model"

Lagator et al. (2017) Regulatory network structure determines patterns of intermolecular epistasis. Elife - https://elifesciences.org/articles/28921

Title: "Evolution of novel ORFs in primates"

Steindel et al. (2017) Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases. Protein Science 25:1319-31 - https://www.ncbi.nlm.nih.gov/pubmed/26889885

Boucher et al. (2014) An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Elife doi: 10.7554/eLife.02304 - https://www.ncbi.nlm.nih.gov/pubmed/24966208

Title: "DomainWorld webserver"

Alberto et al. (2018) Convergent genomic signatures of domestication in sheep and goats. Nature communications - https://www.nature.com/articles/s41467-018-03206-y

Saudemont et al. (2017) The fitness cost of mis-splicing is the main determinant of alternative splicing patterns. Genome Biol. - https://www.ncbi.nlm.nih.gov/pubmed/29084568

Title: “Comparative and functional genomic analysis of E. coli Nissle 1917 in deliberately colonized premature infants”

Title: "Protective symbiosis as a driver of reductive evolution? Genomic footprints of alternative
defense mechanisms in the immunome of Philanthus triangulum "

Title : "Protective symbiosis as a driver of reductive evolution? Genomic footprints of alternative defense mechanisms in the immunome of Philanthus triangulum"

Title: "Domain based phylogeny reconstruction"

Baier et al. (2018) Cryptic genetic variation defines the adaptive evolutionary potential of enzymes. bioRxiv - https://www.biorxiv.org/content/early/2017/12/12/232793

Shiber et al. (2018) Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling. Nature - https://www.nature.com/articles/s41586-018-0462-y

Title: "Goddard and its big brother Saturn"

Meyer WK et al. (2018) Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals. Science 361:591-594 - http://science.sciencemag.org/content/361/6402/591

Title: "Ancestral reconstruction and experimental testing of long- and short term evolvability using the AP-superfamily as a model system: Library creation, protein sequence networks and the evolutionary advantage of not playing along"

Willis S & Masel J (2018) Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes Genetics 210:303-313 - https://www.ncbi.nlm.nih.gov/pubmed/30026186

Wolf et al. (2015) Expression noise facilitates the evolution of gene regulation. eLife - https://elifesciences.org/articles/05856

Title: Significance of RNA bistability on evolvability - The return

Title: "The remarkable success story of a household pet"

Rotem et al. (2018) Evolution on the biophysical fitness landscape of an RNA virus Molecular Biology and Evolution. msy131 - https://doi.org/10.1093/molbev/msy131

Cortez et al. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508:488–493 - http://www.nature.com/nature/journal/v508/n7497/abs/nature13151.html

Yona et al. (2018) Random sequences rapidly evolve into de novo promoters. Nature Comm. 9:1530. - https://www.ncbi.nlm.nih.gov/pubmed/29670097

Title: "Translational read-through in yeast"

Title: "Analyzing proteomes concerning partial protein domains"

Title: “Transcriptome-wide Identification of Proteins encoded by small ORFs in Vertebrates”

Title: "Analysis of splice sites in protein domains and the effects of alternative splicing"

Title: "Reading frame extensions as possible source for de novo domain emergence"

Bonetti et al. (2018) How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein? Biophys J. 114(8):1889-1894 - https://www.ncbi.nlm.nih.gov/pubmed/29694866

O'Toole et al. (2017) Faster Evolving Primate Genes Are More Likely to Duplicate. Mol. Biol. Evol. 35:107-118 - https://academic.oup.com/mbe/article/35/1/107/4554431

Dunn et al. (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. PNAS - http://www.pnas.org/content/pnas/early/2018/01/03/1707515115.full.pdf

Sharma et al. (2018) A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nature Communications 9:1255 - https://www.ncbi.nlm.nih.gov/pubmed/29572503

Albalat & Cañestro (2016) Evolution by Gene Loss. Nature Rev Genetics 17: 379-391 - https://www.ncbi.nlm.nih.gov/pubmed/27087500

Campbell et al. (2016) The role of protein dynamics in the evolution of new enzyme function. Nature Chemical Biology 12: 944-952 - https://www.ncbi.nlm.nih.gov/pubmed/27618189

Hultqvist et al. (2017) Emergence and evolution of an interaction between intrinsically disordered proteins. eLife 6:e16059 - https://elifesciences.org/articles/16059

Title: "Is it time for directional evolution models to be the new standard?"

Title: "Database management in Ruby on Rails"

Leuenberger et al. (2017) Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science 355:eaai7825 - http://science.sciencemag.org/content/355/6327/eaai7825.full

Trible et al. (2017) orco mutagenesis causes loss of antennal lobe glomeruli and impaired social behavior in ants. Cell 170:727-735 - https://www.ncbi.nlm.nih.gov/pubmed/28802042

Yan, Opachaloemphan, Mancini et al. (2017) Olfactory receptors are required for social behavior and neural plasticity in ants, as evidenced by CRISPR-mediated gene knockout - https://www.biorxiv.org/content/early/2017/05/25/142232

Title: "Insect receptor gene prediction with GeMoMa - Benchmarking a novel annotation tool"

Rodrigo & Fares (2017) Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach Elife 7:e29739 - https://doi.org/10.7554/eLife.29739

Tretyachenko et al. (2017) Random protein sequences can form defined secondary structures and are well-tolerated in vivo Scientific reports 7:15449 - https://www.nature.com/articles/s41598-017-15635-8

Steindel et al. (2017) Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases. Protein Science 25:1319-31 - https://www.ncbi.nlm.nih.gov/pubmed/26889885

Title: "The genomics of nestmate recognition in a slavemaker ant and its ant host"

Title: "Methylation in hemimetabolous insects: A comparison of different species"

Lan et al. (2016) Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science 352:1009-1013 - https://www.ncbi.nlm.nih.gov/pubmed/27199432

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.

Cancelled

“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.

nrnrn