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 TitleAuthors / EditorsDate
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OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs Kriventseva, Evgenia; Kouznetsov, Dimitri; Tegenfeldt, Fredrik; Manni, Mose; ... Zdobnov, Evgeny 2019
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Using BUSCO to Assess Insect Genomic Resources Waterhouse, Robert M; Seppey, Mathieu; Simao Neto, Felipe; Zdobnov, Evgeny 2019
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Comparative genomics groups phages of negativicutes and classical firmicutes despite different gram-staining properties Rands, Christopher; Brüssow, Harald; Zdobnov, Evgeny 2019
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Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome Panfilio, Kristen A; Vargas Jentzsch, Iris M; Benoit, Joshua B; Erezyilmaz, Deniz; ... Richards, Stephen 2019
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BUSCO: assessing genome assembly and annotation completeness Seppey, Mathieu; Manni, Mose; Zdobnov, Evgeny 2019
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Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease Schibler, Manuel; Brito, Francisco; Zanella, Marie-Céline; Zdobnov, Evgeny; ... Kaiser, Laurent 2019
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In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence Guzina, Jelena; Chen, Wei-Hua; Stankovic, Tamara; Djordjevic, Magdalena; ... Djordjevic, Marko 2018
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Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank Brito, Francisco; Cordey, Samuel; Delwart, Eric; Deng, Xutao; ... Preynat-Seauve, Olivier 2018
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Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation Vu Cantero, Diem-Lan; Cordey, Samuel; Simonetta, Federico; Brito, Francisco; ... Kaiser, Laurent 2018
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OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs Zdobnov, Evgeny; Tegenfeldt, Fredrik; Kuznetsov, D; Waterhouse, Robert; ... Kriventseva, Evgenia 2017
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Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders Ioannidis, Panagiotis; Simao Neto, Felipe; Waterhouse, Robert; Manni, Mose; ... Zdobnov, Evgeny 2017
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Understanding key features of bacterial restriction-modification systems through quantitative modeling Rodic, Andjela; Blagojevic, Bojana; Zdobnov, Evgeny; Djordjevic, Magdalena; Djordjevic, Marko 2017
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BUSCO applications from quality assessments to gene prediction and phylogenomics Waterhouse, Robert; Seppey, Mathieu; Simao Neto, Felipe; Manni, Mose; ... Zdobnov, Evgeny 2017
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Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites Djordjevic, Marko; Djordjevic, Magdalena; Zdobnov, Evgeny 2017
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[Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes] Starikova, E V; Prianichnikov, N A; Zdobnov, Evgeny; Govorun, V M 2017
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Metagenomics analysis of red blood cell and fresh-frozen plasma units Lau, Pierre; Cordey, Samuel; Brito, Francisco; Tirefort, Diderik; ... Preynat-Seauve, Olivier 2017
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Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures Essaidi, Manel; Brito, Francisco; Benaoudia, Sacha; Royston, Lena; ... Tapparel, Caroline 2017
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CEGA - a catalog of conserved elements from genomic alignments Dousse, Aline; Junier, Thomas; Zdobnov, Evgeny 2016
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Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution Hoy, Marjorie A; Waterhouse, Robert; Wu, Ke; Estep, Alden S; ... Richards, Stephen 2016
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The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases Zdobnov, Evgeny 2016
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Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface McKenna, Duane D; Scully, Erin D; Pauchet, Yannick; Hoover, Kelli; ... Zdobnov, Evgeny 2016
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Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology Cordey, Samuel; Brito, Francisco; Vu Cantero, Diem-Lan; Turin, Lara; ... Kaiser, Laurent 2016
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Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection Cordey, Samuel; Vu Cantero, Diem-Lan; Schibler, Manuel; L'Huillier, Arnaud; ... Kaiser, Laurent 2016
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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software Kriventseva, Evgenia; Tegenfeldt, Fredrik; Petty, Tom; Waterhouse, Robert; ... Zdobnov, Evgeny 2015
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A depauperate immune repertoire precedes evolution of sociality in bees Barribeau, Seth M; Sadd, Ben M; du Plessis, Louis; Brown, Mark JF; ... Schmid-Hempel, Paul 2015
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simao Neto, Felipe; Waterhouse, Robert; Ioannidis, Panagiotis; Kriventseva, Evgenia; Zdobnov, Evgeny 2015
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Social evolution. Genomic signatures of evolutionary transitions from solitary to group living Kapheim, K. M.; Waterhouse, Robert; Zdobnov, Evgeny 2015
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Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions Anstead, Clare A.; Korhonen, Pasi K.; Young, Neil D.; Hall, Ross S.; ... Gasser, Robin B. 2015
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Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses Cordey, Samuel; Bel, Michael; Petty Ii, Thomas John; Docquier, Mylene; ... Kaiser, Laurent 2015
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E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient L'Huillier, Arnaud; Abed, Yacine; Petty, Tom; Cordey, Samuel; ... Kaiser, Laurent 2015
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Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report Schibler, Manuel; Vetter, Pauline; Cherpillod, Pascal; Petty, Tom J; ... Kaiser, Laurent 2015
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Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans Popadin, Konstantin; Gutierrez Arcelus, Maria; Lappalainen, Tuuli Emilia; Buil Demur, Alfonso Alberto; ... Antonarakis, Stylianos 2014
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Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos Marc; ... Appel, Ron David 2014
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Finding the missing honey bee genes: lessons learned from a genome upgrade Elsik, Christine G; Worley, Kim C; Waterhouse, Robert; Zdobnov, Evgeny 2014
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Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response Cosset, Erika; Petty Ii, Thomas John; Dutoit Vallotton, Valérie; Cordey, Samuel; ... Preynat-Seauve, Olivier 2014
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Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study Petty Ii, Thomas John; Cordey, Samuel; Padioleau, Ismael; Docquier, Mylene; ... Kaiser, Laurent 2014
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miRmap web: Comprehensive microRNA target prediction online Vejnar, Charles; Blum, Matthias; Zdobnov, Evgeny 2013
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OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs Waterhouse, Robert; Tegenfeldt, Fredrik; Li, Jia; Zdobnov, Evgeny; Kriventseva, Evgenia 2013
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Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality Simola, Daniel F; Wissler, Lothar; Donahue, Greg; Waterhouse, Robert; ... Zdobnov, Evgeny 2013
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MiRmap: comprehensive prediction of microRNA target repression strength Vejnar, Charles; Zdobnov, Evgeny 2012
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Dampening of arginase 2 expression by microRNA-155 is critical for dendritic cell function Zdobnov, Evgeny; Dunand-Sauthier, Isabelle; Santiago-Raber, Marie-Laure; Carnesecchi, Stéphanie; ... Reith, Walter 2012
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Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections Ambrosioni Czyrko, Juan; Junier, Thomas; Delhumeau, Cécile; Calmy, Alexandra; ... Yerly Ferrillo, Sabine 2012
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Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection Cordey, Samuel; Petty Ii, Thomas John; Schibler, Manuel; Martinez, Yannick; ... Tapparel, Caroline 2012
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A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits Li, Jia; Waterhouse, Robert; Zdobnov, Evgeny 2011
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Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi Waterhouse, Robert; Zdobnov, Evgeny; Kriventseva, Evgenia 2011
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OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 Waterhouse, Robert; Zdobnov, Evgeny; Tegenfeldt, Fredrik; Li, Jia; Kriventseva, Evgenia 2011
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Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice Papaioannou, Marilena D; Lagarrigue, Mélanie; Vejnar, Charles; Rolland, Antoine D; ... Nef, Serge 2011
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Rhinovirus genome variation during chronic upper and lower respiratory tract infections Tapparel, Caroline; Cordey, Samuel; Junier, Thomas; Farinelli, Laurent Luca Denis; ... Kaiser, Laurent 2011
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Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances Kim, Jaebum; Cunningham, Ryan; James, Brian; Wyder, Stefan; ... Sinha, Saurabh 2010
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The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell Junier, Thomas; Zdobnov, Evgeny 2010
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