| Accepted Posters |
| Category 'F'- Evolution' |
| Poster F01 |
| Phylogenetic reconstruction by Automatic Likelihood Model Selector (PALM) : A Framework for Phylogenetic Analysis with the Best Substitution Model |
| Chung-Yen Lin- Academia Sinica |
| No additional authors |
| Short Abstract: To make the whole phylogenetic analysis smoothly and avoid tedious manipulations of various programs, we build an intuitive framework named as Phylogentic Reconstruction by Automatic Likelihood Model selector (PALM) with the most convinced, updated algorithms and models in a seamless way. |
| Long Abstract: Click Here |
| Poster F02 |
| Inference of huge polygenetic trees |
| Martin Simonsen- University of Aarhus |
| Thomas Mailund (Aarhus university, BIRC); Christian Pedersen (Aauhus university, BIRC); |
| Short Abstract: RapidDiskNJ is a heuristic for the canonical phylogenetic inference method, Neighbour-Joining, which utilise external memory to reduce the need for internal memory while also reducing the running time of the canonical Neighbour-Joining method. RapidDiskNJ makes it feasible to efficiently infer huge phylogenies with more than 40000 taxa. |
| Long Abstract: Click Here |
| Poster F03 |
| Gene duplication is a key driver of adaptation within a species |
| Ryan Ames- University of Manchester |
| Bharatkumar Rash (University of Manchester, Faculty of Life Sciences); David Robertson (University of Manchester, Faculty of Life Sciences); Daniela Delneri (University of Manchester, Faculty of Life Sciences); Simon Lovell (University of Manchester, Faculty of Life Sciences); |
| Short Abstract: Using genomic sequences from multiple strains of S. cerevisiae and S. paradoxus we identified and compared duplicates within populations of the same species. We show an abundance of duplication in both species and demonstrate that the duplicates have experienced selection. Differential duplicate retention also leads to predictable differences in phenotype. |
| Long Abstract: Click Here |
| Poster F04 |
| Three-Dimensional Structural Determinants of Amino Acid Conservation in Proteins |
| Sungsam Gong- Cambridge University |
| Tom Blundell (University of Cambridge, Department of Biochemistry); |
| Short Abstract: In this poster, we try to answer the question “what determines amino acid substitutions in the three-dimensional structures of proteins”. We show that solvent accessibility is the most important determinant, followed by the existence of hydrogen-bonds from the side-chain to main-chain functions and the nature of the element of secondary structure |
| Long Abstract: Click Here |
| Poster F05 |
| Adaptability contra biodiversity – comparative modeling of closed trophic webs using “Evolutionary Constructor” program |
| Sergey Lashin- THE INSTITUTE OF CYTOLOGY AND GENETICS |
| Valentin Suslov (THE INSTITUTE OF CYTOLOGY AND GENETICS, Laboratory of Theoretical Genetics); |
| Short Abstract: Coevolution of the two trophic rings of haploid organism populations which exchanged of metabolites and consumed of the common substrat was in silico modeled. The trophic ring with Rubel’s factors replaceability was more competitive according to total growth of biomass and adaptability, ring with Liebig’s trophism - in biodiversity and potentially evolvability. |
| Long Abstract: Click Here |
| Poster F06 |
| The computational analysis of GTF2I gene family evolution |
| Irina Medvedeva- Institute of Cytology and Genetics SB RAS |
| Vladimir Ivanisenko (Institute of Cytology and Genetics SB RAS, Laboratory of theoretical genetics); Konstantin Gunbin (Institute of Cytology and Genetics SB RAS, Laboratory of theoretical genetics); Anatoly Ruvinsky (University of New England, Institute for Genetics and Bioinformatics); |
| Short Abstract: The GTF2I gene family consist of the genes of transcriptional factors that contain the different number of GTF2I repeats. We analyzed the exon-intron structure of genes, their phylogenetic relationships and tertiary structure. These techniques could be used for the developing software tools for genome-level analysis of the exon-intron structures evolution. |
| Long Abstract: Click Here |
| Poster F07 |
| The Evolution of Beta Amyloid Cleaving Enzyme (BACE1): an Alzheimer’s disease Drug Target |
| Christopher Southan- ChrisDS Consulting |
| John Hancock (MRC Harwell, Bioinformatics); |
| Short Abstract: We have used new genome data to examine the evolution of this important drug target. A tree of 30 BACE-like sequences showed a single membrane-anchored Eumetazoan ancestor. After duplication in fish the paralogue BACE2 evolved more rapidly suggesting BACE1 has maintained its ancestral neuronal function. |
| Long Abstract: Click Here |
| Poster F08 |
| A Single beta-beta Hairpin is the Ancestor of Bacterial Outer Membrane beta-barrels |
| Michael Remmert- Gene Center, LMU |
| Andreas Biegert (Gene Center, LMU, Computational Biology); Dirk Linke (Max-Planck-Institute for Developmental Biology, Protein Evolution); Andrei N. Lupas (Max-Planck-Institute for Developmental Biology, Protein Evolution); Johannes Soeding (Gene Center, LMU, Computational Biology); |
| Short Abstract: We show that bacterial outer membrane beta-barrels (OMBBs) arose by duplication of an ancestral beta-beta hairpin: We link all known families of single-chain OMBBs by transitive profile searches, detect a clear repeat pattern in most OMBB families, and demonstrate that the observed sequence similarity cannot be explained by structural convergence. |
| Long Abstract: Click Here |
| Poster F09 |
| Animal proteins acquire new domains through gene duplications and joining of adjacent genes’ exons |
| Marija Buljan- Wellcome Trust Sanger Institute |
| Adam Frankish (Wellcome Trust Sanger Institute, Sanger Institute); Alex Bateman (Wellcome Trust Sanger Institute, Sanger Institute); |
| Short Abstract: The relative contributions of different molecular mechanisms that underlie domain gains in animals are as yet unclear. Here we show that the major mechanism for domain gains in metazoa is gene duplication and joining of adjacent genes' exons, possibly mediated by non-allelic homologous recombination. |
| Long Abstract: Click Here |
| Poster F10 |
| Darwin Rocks! |
| Daniel Huson- Tuebingen University |
| Johannes Faber (Tuebingen University, Biology); Nico Michiels (Tuebingen University, Biology); |
| Short Abstract: In this poster we present Darwin Rocks!, a program for demonstrating principles of evolution using "tuneomes", which are like genomes, except that they encode pieces of music rather than organisms. The Darwin Rocks! program is freely available from www.darwinrocks.de. |
| Long Abstract: Click Here |
| Poster F11 |
| Signature genes as a phylogenomic tool |
| Bas Dutilh- Radboud University Nijmegen Medical Centre |
| Berend Snel (Utrecht University, Department Biology and Academic Biomedical Centre); Thijs J.G. Ettema (Uppsala Universitet, Department of Molecular Evolution); Ying He (Ghent University, VIB Department of Plant Systems Biology); Maarten L. Hekkelman (Radboud University Nijmegen Medical Centre, CMBI); Martijn A. Huynen (Radboud University Nijmegen Medical Centre, CMBI); |
| Short Abstract: Signature genes are unique to a taxonomic clade andare present in all daughter lineages. They can be usedfor the phylogenetic characterisation of sequencesamples, including incomplete genomes and metagenomicsamples. We have tested the reliability of signaturegenes as a phylogenomic tool, and implementedthe method in a web server. |
| Long Abstract: Click Here |
| Poster F12 |
| Assessing the impact of protein structure on sequence evolution |
| Claudia Kleinman- Université de Montréal |
| Nicolas Rodrigue (University of Ottawa, Biology); Nicolas Lartillot (Universite de Montreal, Biochemistry); Hervé Philippe (Universite de Montreal, Biochemistry); |
| Short Abstract: Despite the undeniable role that protein structure plays in the evolution of protein sequences, tools for considering it explicitly in models of sequence evolution remain primitive. We present a statistical potential (a scoring system for sequence-structure compatibility) specifically designed for the recently developed structurally constrained evolutionary models. |
| Long Abstract: Click Here |
| Poster F13 |
| Insertion Sequences Distribution And Evolution In Prokaryotic Genomes Using Network Approach. |
| Nicola Vitulo- CRIBI Biotecnology Centre, University of Padova |
| Riccardo Rosselli (CRIBI Biotecnology Centre, University of Padova, Biology); Alessandro Vezzi (CRIBI Biotecnology Centre, University of Padova, Biology); Enrico Negrisolo (University of Padova, Public Health, Comparative Pathology and Veterinary Hygiene); Giorgio Valle (CRIBI Biotecnology Centre, University of Padova- Biology, Biology); |
| Short Abstract: Insertion Sequences (IS) are the simplest form of transposable elements and considered key elements for genome plasticity and variability. We studied ISs distribution among 765 fully sequenced bacteria. The results suggest the existence of a “core†of ISs phyla specific, transferred with a vertical mechanisms and with a phylogenetic signal. |
| Long Abstract: Click Here |
| Poster F14 |
| Automated comparative analysis of transcriptional factors expressed in stem cells |
| Achille Zappa- Bioinformatics, National Cancer Research Institute (IST), Genoa – Italy ; IEIIT, National Research Council (CNR), Genoa – Italy |
| Mariangela Miele (National Cancer Research Institute (IST), Genoa – Italy, Bioinformatics); Paolo Romano (National Cancer Research Institute (IST), Genoa – Italy, Bioinformatics); |
| Short Abstract: An automated workflow has been designed and implemented in order to investigate the similarity among transcriptional factors involved in the maintenance of totipotency in plant, planarian, drosophila and mammalian stem cells. Identifiers or sequences of selected proteins are used as input; alignments, with relative phylogenetic distance files constitute the output. |
| Long Abstract: Click Here |
| Poster F15 |
| Detection of horizontal gene transfer in prokaryotes using BLAST and 16S rRNA distances |
| Apuã Paquola- Universidade de São Paulo |
| Wanessa Lima (Instituto de Ciências Biomédicas/Universidade de São Paulo, Depto. de Microbiologia); Carlos Menk (Instituto de Ciências Biomédicas/Universidade de São Paulo, Depto. de Microbiologia); |
| Short Abstract: We have developed a new HGT detection method based on BLAST and 16S rRNA sequence distances. Application in 408 prokaryotic genomes shows that: (i) operational genes are more prone to HGT than informational genes; (ii) genes with few interaction partners participate more often in HGT than those with many partners. |
| Long Abstract: Click Here |
| Poster F16 |
| Virus Classification Using Phylogenetic Networks |
| Ingo Bulla- University of Goettingen |
| Anne-Kathrin Schultz (University of Goettingen, Bioinformatics); Fabian Schreiber (University of Goettingen, Bioinformatics); Ming Zhang (Los Alamos National Laboratory, Theoretical Division); Thomas Leitner (Los Alamos National Laboratory, Theoretical Division); Bette Korber (Los Alamos National Laboratory, Theoretical Division); Burkhard Morgenstern (University of Goettingen, Bioinformatics); Mario Stanke (University of Goettingen, Bioinformatics); |
| Short Abstract: We developed the program ARGUS that scores classifications of HIV sequences into subtypes and recombinant forms. It reconstructs Ancestral Recombination Graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov Chain Monte Carlo approach. |
| Long Abstract: Click Here |
| Poster F17 |
| Robust phylogenetic trees for annotation of evolutionary inferences |
| Paul Thomas- SRI International |
| Stan Dong (SRI International, Evolutionary Systems Biology); |
| Short Abstract: Evolutionary gene trees are a workhorse of comparative genomics, yet they remain underutilized, partly due to lack of robustness as data are added or corrected. We present a new algorithm for gene tree inference that dramatically improves robustness; the Gene Ontology Consortium is annotating functional evolution within these trees. |
| Long Abstract: Click Here |
| Poster F19 |
| Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1 |
| Konrad Scheffler- University of Stellenbosch |
| Wayne Delport (University of Cape Town, Institute of Infectious Disease and Molecular Medicine); Cathal Seoighe (University of Cape Town, Institute of Infectious Disease and Molecular Medicine); |
| Short Abstract: We develop a phylogenetic model of immune escape and reversion and provide evidence that it outperforms existing models for the detection of selective pressure associated with host immune responses. The model demonstrates that amino acid toggling is a pervasive process in HIV-1 evolution. |
| Long Abstract: Click Here |
| Accepted Posters |
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