Search Results - "Dessimoz, Christophe"

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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Structural variant calling: the long and the short of it by Mahmoud, Medhat, Gobet, Nastassia, Cruz-Dávalos, Diana Ivette, Mounier, Ninon, Dessimoz, Christophe, Sedlazeck, Fritz J

“…Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases,…”
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Inferring horizontal gene transfer by Ravenhall, Matt, Škunca, Nives, Lassalle, Florent, Dessimoz, Christophe

“…Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical…”
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Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes by Anisimova, Maria, Gil, Manuel, Dufayard, Jean-François, Dessimoz, Christophe, Gascuel, Olivier

“…Phylogenetic inference and evaluating support for inferred relationships is at the core of many studies testing evolutionary hypotheses. Despite the popularity…”
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Towards practical, high-capacity, low-maintenance information storage in synthesized DNA by Goldman, Nick, Bertone, Paul, Chen, Siyuan, Dessimoz, Christophe, LeProust, Emily M., Sipos, Botond, Birney, Ewan

“…An efficient and scalable strategy with robust error correction is reported for encoding a record amount of information (including images, text and audio…”
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference by Tan, Ge, Muffato, Matthieu, Ledergerber, Christian, Herrero, Javier, Goldman, Nick, Gil, Manuel, Dessimoz, Christophe

“…Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree…”
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Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast by Jeffares, Daniel C., Jolly, Clemency, Hoti, Mimoza, Speed, Doug, Shaw, Liam, Rallis, Charalampos, Balloux, Francois, Dessimoz, Christophe, Bähler, Jürg, Sedlazeck, Fritz J.

“…Large structural variations (SVs) within genomes are more challenging to identify than smaller genetic variants but may substantially contribute to phenotypic…”
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Approximate Bayesian computation by Sunnåker, Mikael, Busetto, Alberto Giovanni, Numminen, Elina, Corander, Jukka, Foll, Matthieu, Dessimoz, Christophe

“…Approximate Bayesian computation (ABC) constitutes a class of computational methods rooted in Bayesian statistics. In all model-based statistical inference,…”
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Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life by Sojo, Victor, Dessimoz, Christophe, Pomiankowski, Andrew, Lane, Nick

“…Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically…”
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OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more by Altenhoff, Adrian M, Train, Clément-Marie, Gilbert, Kimberly J, Mediratta, Ishita, Mendes de Farias, Tarcisio, Moi, David, Nevers, Yannis, Radoykova, Hale-Seda, Rossier, Victor, Warwick Vesztrocy, Alex, Glover, Natasha M, Dessimoz, Christophe

“…Abstract OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA…”
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Phylogenetic and functional assessment of orthologs inference projects and methods by Altenhoff, Adrian M, Dessimoz, Christophe

“…Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification…”
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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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A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor by Benton, Richard, Dessimoz, Christophe, Moi, David

“…The insect chemosensory repertoires of Odorant Receptors (ORs) and Gustatory Receptors (GRs) together represent one of the largest families of ligand-gated ion…”
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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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Protein length distribution is remarkably uniform across the tree of life by Nevers, Yannis, Glover, Natasha M, Dessimoz, Christophe, Lecompte, Odile

“…In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of…”
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Quality of computationally inferred gene ontology annotations by Skunca, Nives, Altenhoff, Adrian, Dessimoz, Christophe

“…Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e…”
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy by Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M E, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel

“…A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide…”
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The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements by Altenhoff, Adrian M, Škunca, Nives, Glover, Natasha, Train, Clément-Marie, Sueki, Anna, Piližota, Ivana, Gori, Kevin, Tomiczek, Bartlomiej, Müller, Steven, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe

“…The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e…”
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Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes by Moi, David, Kilchoer, Laurent, Aguilar, Pablo S, Dessimoz, Christophe

“…Phylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be…”
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A generalized Robinson-Foulds distance for labeled trees by Briand, Samuel, Dessimoz, Christophe, El-Mabrouk, Nadia, Lafond, Manuel, Lobinska, Gabriela

“…The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages…”
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