Search Results - "Dylus, David"

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web by Robinson, Oscar, Dylus, David, Dessimoz, Christophe

“…Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple…”
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FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis by Czarkwiani, Anna, Dylus, David V, Carballo, Luisana, Oliveri, Paola

“…Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and…”
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The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces by Altenhoff, Adrian M, Glover, Natasha M, Train, Clément-Marie, Kaleb, Klara, Warwick Vesztrocy, Alex, Dylus, David, de Farias, Tarcisio M, Zile, Karina, Stevenson, Charles, Long, Jiao, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe

“…Abstract The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent…”
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OMA standalone: orthology inference among public and custom genomes and transcriptomes by Altenhoff, Adrian M, Levy, Jeremy, Zarowiecki, Magdalena, Tomiczek, Bartłomiej, Warwick Vesztrocy, Alex, Dalquen, Daniel A, Müller, Steven, Telford, Maximilian J, Glover, Natasha M, Dylus, David, Dessimoz, Christophe

“…Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many…”
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Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution by Dylus, David V, Czarkwiani, Anna, Blowes, Liisa M, Elphick, Maurice R, Oliveri, Paola

“…Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative…”
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Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis by Czarkwiani, Anna, Dylus, David V., Oliveri, Paola

“…•Analysis of brittle star regenerating arms using differentiation markers.•Identification of the early segregation of skeletal and muscle progenitor…”
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How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved] by Dylus, David, Nevers, Yannis, Altenhoff, Adrian M., Gürtler, Antoine, Dessimoz, Christophe, Glover, Natasha M.

“…Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species…”
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NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test by Dylus, David, Pillonel, Trestan, Opota, Onya, Wüthrich, Daniel, Seth-Smith, Helena M B, Egli, Adrian, Leo, Stefano, Lazarevic, Vladimir, Schrenzel, Jacques, Laurent, Sacha, Bertelli, Claire, Blanc, Dominique S, Neuenschwander, Stefan, Ramette, Alban, Falquet, Laurent, Imkamp, Frank, Keller, Peter M, Kahles, Andre, Oberhaensli, Simone, Barbié, Valérie, Dessimoz, Christophe, Greub, Gilbert, Lebrand, Aitana

“…Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical…”
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New genome assembly of the barn owl (Tyto alba alba) by Ducrest, Anne‐Lyse, Neuenschwander, Samuel, Schmid‐Siegert, Emanuel, Pagni, Marco, Train, Clément, Dylus, David, Nevers, Yannis, Warwick Vesztrocy, Alex, San‐Jose, Luis M., Dupasquier, Mélanie, Dessimoz, Christophe, Xenarios, Ioannis, Roulin, Alexandre, Goudet, Jérôme

“…New genomic tools open doors to study ecology, evolution, and population genomics of wild animals. For the Barn owl species complex, a cosmopolitan nocturnal…”
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Antibacterial inhibitors targeting the lipoprotein transport pathway by Vercruysse, Maarten, Dylus, David

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Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks by Dylus, David Viktor, Czarkwiani, Anna, Stångberg, Josefine, Ortega-Martinez, Olga, Dupont, Sam, Oliveri, Paola

“…The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related…”
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Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree by Dylus, David, Altenhoff, Adrian, Majidian, Sina, Sedlazeck, Fritz J., Dessimoz, Christophe

“…Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints…”
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The phylogenetic range of bacterial and viral pathogens of vertebrates by Shaw, Liam P., Wang, Alethea D., Dylus, David, Meier, Magda, Pogacnik, Grega, Dessimoz, Christophe, Balloux, François

“…Many major human pathogens are multihost pathogens, able to infect other vertebrate species. Describing the general patterns of host–pathogen associations…”
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A novel antibiotic class targeting the lipopolysaccharide transporter by Zampaloni, Claudia, Mattei, Patrizio, Bleicher, Konrad, Winther, Lotte, Thäte, Claudia, Bucher, Christian, Adam, Jean-Michel, Alanine, Alexander, Amrein, Kurt E., Baidin, Vadim, Bieniossek, Christoph, Bissantz, Caterina, Boess, Franziska, Cantrill, Carina, Clairfeuille, Thomas, Dey, Fabian, Di Giorgio, Patrick, du Castel, Pauline, Dylus, David, Dzygiel, Pawel, Felici, Antonio, García-Alcalde, Fernando, Haldimann, Andreas, Leipner, Matthew, Leyn, Semen, Louvel, Séverine, Misson, Pauline, Osterman, Andrei, Pahil, Karanbir, Rigo, Sébastien, Schäublin, Adrian, Scharf, Sebastian, Schmitz, Petra, Stoll, Theodor, Trauner, Andrej, Zoffmann, Sannah, Kahne, Daniel, Young, John A. T., Lobritz, Michael A., Bradley, Kenneth A.

“…Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a major global pathogen with limited treatment options 1 . No new antibiotic chemical class…”
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Skeletal regeneration in the brittle star Amphiura filiformis by Czarkwiani, Anna, Ferrario, Cinzia, Dylus, David Viktor, Sugni, Michela, Oliveri, Paola

“…BACKGROUND: Brittle stars regenerate their whole arms post-amputation. Amphiura filiformis can now be used for molecular characterization of arm regeneration…”
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Author Correction: A novel antibiotic class targeting the lipopolysaccharide transporter by Zampaloni, Claudia, Mattei, Patrizio, Bleicher, Konrad, Winther, Lotte, Thäte, Claudia, Bucher, Christian, Adam, Jean-Michel, Alanine, Alexander, Amrein, Kurt E., Baidin, Vadim, Bieniossek, Christoph, Bissantz, Caterina, Boess, Franziska, Cantrill, Carina, Clairfeuille, Thomas, Dey, Fabian, Di Giorgio, Patrick, du Castel, Pauline, Dylus, David, Dzygiel, Pawel, Felici, Antonio, García-Alcalde, Fernando, Haldimann, Andreas, Leipner, Matthew, Leyn, Semen, Louvel, Séverine, Misson, Pauline, Osterman, Andrei, Pahil, Karanbir, Rigo, Sébastien, Schäublin, Adrian, Scharf, Sebastian, Schmitz, Petra, Stoll, Theodor, Trauner, Andrej, Zoffmann, Sannah, Kahne, Daniel, Young, John A. T., Lobritz, Michael A., Bradley, Kenneth A.

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Extracellular matrix gene expression during arm regeneration in Amphiura filiformis by Ferrario, Cinzia, Czarkwiani, Anna, Dylus, David Viktor, Piovani, Laura, Candia Carnevali, Maria Daniela, Sugni, Michela, Oliveri, Paola

“…Extracellular matrix (ECM) plays a dynamic role during tissue development and re-growth. Body part regeneration efficiency relies also on effective ECM…”
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Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes by Altenhoff, Adrian M., Levy, Jeremy, Zarowiecki, Magdalena, Tomiczek, Bartłomiej, Vesztrocy, Alex Warwick, Dalquen, Daniel A., Müller, Steven, Telford, Maximilian J., Glover, Natasha M., Dylus, David, Dessimoz, Christophe

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Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop by Greub, Gilbert, Palagi, Patricia M., Dylus, David, Egli, Adrian, Pillonel, Trestan, Rossen, John W.A., Seth-Smith, Helena M.B., Lebrand, Aitana

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RecPhyloXML: a format for reconciled gene trees by Duchemin, Wandrille, Gence, Guillaume, Arigon Chifolleau, Anne-Muriel, Arvestad, Lars, Bansal, Mukul S, Berry, Vincent, Boussau, Bastien, Chevenet, François, Comte, Nicolas, Davín, Adrián A, Dessimoz, Christophe, Dylus, David, Hasic, Damir, Mallo, Diego, Planel, Rémi, Posada, David, Scornavacca, Celine, Szöllősi, Gergely, Zhang, Louxin, Tannier, Éric, Daubin, Vincent

“…Abstract Motivation A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer,…”
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