Publications by authors named "Evgeny Zdobnov"

110 Publications

OrthoDB in 2020: evolutionary and functional annotations of orthologs.

Nucleic Acids Res 2021 01;49(D1):D389-D393

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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January 2021

A Novel Anphevirus in Mosquitoes Is Distributed Worldwide and Interacts with the Host RNA Interference Pathway.

Viruses 2020 11 6;12(11). Epub 2020 Nov 6.

Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1206 Geneva, Switzerland.

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November 2020

LEMMI: a continuous benchmarking platform for metagenomics classifiers.

Genome Res 2020 Aug 2;30(8):1208-1216. Epub 2020 Jul 2.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland.

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August 2020

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.

BMC Bioinformatics 2020 Jun 22;21(1):257. Epub 2020 Jun 22.

Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.

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June 2020

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera.

Genome Biol Evol 2020 07;12(7):1099-1188

Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany.

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July 2020

Phigaro: high-throughput prophage sequence annotation.

Bioinformatics 2020 06;36(12):3882-3884

Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia.

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June 2020

Gene content evolution in the arthropods.

Genome Biol 2020 01 23;21(1):15. Epub 2020 Jan 23.

Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.

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January 2020

Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease.

Front Pediatr 2019 19;7:524. Epub 2019 Dec 19.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland.

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December 2019

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties.

Environ Microbiol 2019 11 31;21(11):3989-4001. Epub 2019 Jul 31.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.

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November 2019

BUSCO: Assessing Genome Assembly and Annotation Completeness.

Methods Mol Biol 2019 ;1962:227-245

Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Geneva, Switzerland.

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August 2019

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

Genome Biol 2019 04 2;20(1):64. Epub 2019 Apr 2.

Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.

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April 2019

Using BUSCO to Assess Insect Genomic Resources.

Methods Mol Biol 2019 ;1858:59-74

University of Geneva and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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July 2019

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.

Nucleic Acids Res 2019 01;47(D1):D807-D811

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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January 2019

Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence.

Front Genet 2018 17;9:474. Epub 2018 Oct 17.

Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Belgrade, Serbia.

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October 2018

ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages.

Environ Microbiol 2018 06 7;20(6):2288-2300. Epub 2018 Aug 7.

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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June 2018

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Mol Biol Evol 2018 Mar;35(3):543-548

Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, Geneva, Switzerland.

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March 2018

Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites.

Front Microbiol 2017 22;8:2314. Epub 2017 Nov 22.

Swiss Institute of Bioinformatics and Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.

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November 2017

Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures.

J Allergy Clin Immunol 2018 06 8;141(6):2074-2084. Epub 2017 Aug 8.

Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland; Division of Medical Specialties and Laboratory of Virology, University Hospital of Geneva, Geneva, Switzerland. Electronic address:

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June 2018

Metagenomics analysis of red blood cell and fresh-frozen plasma units.

Transfusion 2017 07 11;57(7):1787-1800. Epub 2017 May 11.

Department of Medical Specialties, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva.

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July 2017

Understanding key features of bacterial restriction-modification systems through quantitative modeling.

BMC Syst Biol 2017 02 24;11(Suppl 1):377. Epub 2017 Feb 24.

Institute of Physiology and Biochemistry, Faculty of Biology, University of Belgrade, Studentski trg 16, 11000, Belgrade, Serbia.

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February 2017

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs.

Nucleic Acids Res 2017 01 28;45(D1):D744-D749. Epub 2016 Nov 28.

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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January 2017