EZ
Zdobnov, Evgeny
| Title | Published in | Access level | OA Policy | Year | Views | Downloads | |
|---|---|---|---|---|---|---|---|
| Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research | Cell host & microbe |  | 2025 | 35 | 27 | ||
| Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno | The ISME journal | | 2023 | 100 | 106 | ||
| OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity | Nucleic acids research | | 2023 | 112 | 957 | ||
| Identification of a miRNA multi-targeting therapeutic strategy in glioblastoma | Cell death and disease | | 2023 | 326 | 186 | ||
| Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart | PLoS computational biology | | 2022 | 220 | 79 | ||
| Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop | MBio | | 2022 | 118 | 152 | ||
| A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand | Nucleic acids research | | 2022 | 81 | 27 | ||
| Enterovirus D: a small but versatile species | Microorganisms | | 2021 | 193 | 163 | ||
| BUSCO Update : Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes | Molecular biology and evolution | | 2021 | 210 | 423 | ||
| Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera | Genome Biology and Evolution | | 2020 | 374 | 328 | ||
| LEMMI: a continuous benchmarking platform for metagenomics classifiers | Genome Research | | 2020 | 384 | 196 | ||
| Phigaro: high-throughput prophage sequence annotation | Bioinformatics |  | 2020 | 367 | 0 | ||
| ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data | BMC Bioinformatics | | 2020 | 326 | 720 | ||
| Enhanced genome assembly and a new official gene set for Tribolium castaneum | BMC Genomics | | 2020 | 329 | 261 | ||
| Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest | BMC Genomics | | 2020 | 326 | 192 | ||
| Gene content evolution in the arthropods | Genome Biology | | 2020 | 340 | 167 | ||
| The genome of the blind soil-dwelling and ancestrally wingless dipluran campodea augens: a key reference hexapod for studying the emergence of insect innovations | Genome Biology and Evolution | | 2020 | 269 | 262 | ||
| Comparative genomics groups phages of negativicutes and classical firmicutes despite different gram-staining properties | Environmental Microbiology | | 2019 | 407 | 0 | ||
| OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs | Nucleic Acids Research | | 2019 | 490 | 530 | ||
| Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease | Frontiers in Pediatrics | | 2019 | 343 | 177 | ||
| Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease | Genes | | 2019 | 464 | 147 | ||
| BUSCO: assessing genome assembly and annotation completeness | Methods in Molecular Biology | | 2019 | 752 | 9,942 | ||
| Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome | Genome Biology | | 2019 | 379 | 64 | ||
| Using BUSCO to Assess Insect Genomic Resources | Methods in Molecular Biology | | 2019 | 473 | 3 | ||
| ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages | Environmental Microbiology | | 2018 | 347 | 0 | ||
| In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence | Frontiers in Genetics | | 2018 | 458 | 228 | ||
| Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank | Vox Sanguinis | | 2018 | 546 | 431 | ||
| Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation | Clinical Microbiology and Infection | | 2018 | 1,399 | 631 | ||
| OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs | Nucleic acids research | | 2017 | 1,021 | 349 | ||
| Metagenomics analysis of red blood cell and fresh-frozen plasma units | Transfusion | | 2017 | 552 | 2 | ||
| [Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes] | Biomeditsinskaya Khimiya | 2017 | 385 | 0 | |||
| Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites | Frontiers in Microbiology | | 2017 | 375 | 240 | ||
| BUSCO applications from quality assessments to gene prediction and phylogenomics | Molecular Biology and Evolution | | 2017 | 525 | 0 | ||
| Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders | Genome biology and evolution | | 2017 | 568 | 391 | ||
| Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures | Journal of Allergy and Clinical Immunology | | 2017 | 653 | 3 | ||
| Understanding key features of bacterial restriction-modification systems through quantitative modeling | BMC systems biology | | 2017 | 401 | 283 | ||
| Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution | Genome biology and evolution | | 2016 | 527 | 607 | ||
| CEGA - a catalog of conserved elements from genomic alignments | Nucleic acids research | | 2016 | 576 | 240 | ||
| The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases | Nucleic acids research | | 2016 | 631 | 731 | ||
| Genomic insights into the Ixodes scapularis tick vector of Lyme disease | Nature communications | | 2016 | 571 | 288 | ||
| Unique features of a global human ectoparasite identified through sequencing of the bed bug genome | Nature communications | | 2016 | 548 | 465 | ||
| Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection | Emerging infectious diseases | | 2016 | 680 | 339 | ||
| Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface | GenomeBiology.com | | 2016 | 535 | 307 | ||
| Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology | Emerging microbes & infections | | 2016 | 555 | 276 | ||
| Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses | Clinical microbiology and infection | | 2015 | 756 | 277 | ||
| A depauperate immune repertoire precedes evolution of sociality in bees | GenomeBiology.com | | 2015 | 619 | 463 | ||
| Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report | Lancet. Infectious diseases | | 2015 | 715 | 1 | ||
| OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software | Nucleic acids research | | 2015 | 715 | 534 | ||
| Social evolution. Genomic signatures of evolutionary transitions from solitary to group living | Science | | 2015 | 489 | 1 | ||
| The genomes of two key bumblebee species with primitive eusocial organization | GenomeBiology.com | | 2015 | 554 | 550 | ||
| Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions | Nature communications | | 2015 | 591 | 217 | ||
| E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient | The Journal of infectious diseases | 2015 | 766 | 0 | |||
| BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | | 2015 | 758 | 0 | ||
| A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor | Current biology | | 2015 | 499 | 1 | ||
| Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study | Journal of clinical microbiology | | 2014 | 786 | 325 | ||
| Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans | American journal of human genetics | | 2014 | 668 | 1 | ||
| Finding the missing honey bee genes: lessons learned from a genome upgrade | BMC genomics | | 2014 | 614 | 252 | ||
| Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response | International journal of cancer | | 2014 | 757 | 496 | ||
| Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support | Nucleic acids research | | 2014 | 925 | 73 | ||
| The common marmoset genome provides insight into primate biology and evolution | Nature genetics | | 2014 | 563 | 321 | ||
| Big data and other challenges in the quest for orthologs | Bioinformatics | | 2014 | 589 | 493 | ||
| The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment | Journal of heredity | | 2013 | 558 | 0 | ||
| Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality | Genome research | | 2013 | 685 | 1 | ||
| miRmap web: Comprehensive microRNA target prediction online | Nucleic acids research | | 2013 | 827 | 1 | ||
| OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs | Nucleic acids research | | 2013 | 785 | 0 | ||
| Dampening of arginase 2 expression by microRNA-155 is critical for dendritic cell function | Immunology | | 2012 | 482 | 4 | ||
| Toward community standards in the quest for orthologs | Bioinformatics | | 2012 | 542 | 0 | ||
| Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection | PLOS pathogens | | 2012 | 845 | 437 | ||
| MiRmap: comprehensive prediction of microRNA target repression strength | Nucleic acids research | | 2012 | 705 | 0 | ||
| Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections | AIDS | | 2012 | 745 | 463 | ||
| The ecoresponsive genome of Daphnia pulex | Science | | 2011 | 1,037 | 1 | ||
| OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 | Nucleic acids research | | 2011 | 688 | 0 | ||
| A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits | BMC evolutionary biology | | 2011 | 695 | 384 | ||
| Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice | Molecular & cellular proteomics | | 2011 | 728 | 0 | ||
| Rhinovirus genome variation during chronic upper and lower respiratory tract infections | PloS one | | 2011 | 631 | 606 | ||
| Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi | Genome biology and evolution | | 2011 | 685 | 0 | ||
| Rhinovirus genome evolution during experimental human infection | PloS one | | 2010 | 799 | 574 | ||
| Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics | Science | | 2010 | 720 | 1 | ||
| The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell | Bioinformatics | | 2010 | 688 | 0 | ||
| Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle | Proceedings of the National Academy of Sciences of the United States of America | | 2010 | 587 | 1 | ||
| A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes | PloS one | | 2010 | 762 | 306 | ||
| Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances | PLoS computational biology | | 2010 | 648 | 372 | ||
| Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens | Science | | 2010 | 611 | 0 | ||
| Functional and evolutionary insights from the genomes of three parasitoid Nasonia species | Science | | 2010 | 655 | 2 | ||
| Sociality is linked to rates of protein evolution in a highly social insect | Molecular biology and evolution | | 2010 | 575 | 0 | ||
| Impact of newly HIV diagnosed individuals on the transmission of drug resistance | Antiviral therapy | 2009 | 452 | 0 | |||
| Sertoli cell Dicer is essential for spermatogenesis in mice | Developmental biology | | 2009 | 751 | 0 | ||
| Comparative Genome Analysis | Bioinformatics: A Swiss Perspective | 2009 | 1,046 | 0 | |||
| Integration of microRNA miR-122 in hepatic circadian gene expression | Genes & development | | 2009 | 723 | 0 | ||
| Comparative Genomics of Insect Immunity | Insect Infection and Immunity: Evolution, Ecology, and Mechanisms | 2009 | 671 | 0 | |||
| The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection | AIDS | | 2009 | 579 | 0 | ||
| New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses | Emerging infectious diseases | | 2009 | 612 | 0 | ||
| The genome sequence of taurine cattle: a window to ruminant biology and evolution | Science | | 2009 | 739 | 5 | ||
| Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates | BMC genomics | | 2009 | 731 | 491 | ||
| The bovine lactation genome: insights into the evolution of mammalian milk | GenomeBiology.com | | 2009 | 672 | 370 | ||
| miROrtho: computational survey of microRNA genes | Nucleic acids research | | 2009 | 709 | 325 | ||
| Mapping of small RNAs in the human ENCODE regions | American journal of human genetics | | 2008 | 624 | 0 | ||
| The genome of the model beetle and pest Tribolium castaneum | Nature | | 2008 | 894 | 2 | ||
| The cis-acting replication elements define human enterovirus and rhinovirus species | RNA | | 2008 | 766 | 2 | ||
| The Aedes aegypti genome: a comparative perspective | Insect molecular biology | | 2008 | 569 | 1 | ||
| Drug resistance in newly HIV diagnosed individuals: transmission rate, clusters and persistence | Antiviral therapy | 2008 | 368 | 0 | |||
| OrthoDB: the hierarchical catalog of eukaryotic orthologs | Nucleic acids research | | 2008 | 673 | 562 | ||
| Quantification of ortholog losses in insects and vertebrates | GenomeBiology.com | | 2007 | 619 | 777 | ||
| Genome sequence of Aedes aegypti, a major arbovirus vector | Science | | 2007 | 685 | 2 | ||
| New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features | BMC genomics | | 2007 | 659 | 1,126 | ||
| Quantification of insect genome divergence | Trends in genetics | | 2007 | 579 | 0 | ||
| VectorBase: a home for invertebrate vectors of human pathogens | Nucleic acids research | | 2007 | 646 | 0 | ||
| Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes | Science | | 2007 | 816 | 496 | ||
| Computational and transcriptional evidence for microRNAs in the honey bee genome | GenomeBiology.com | | 2007 | 721 | 798 | ||
| Evolution of genes and genomes on the Drosophila phylogeny | Nature | | 2007 | 732 | 0 | ||
| Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster | Proceedings of the National Academy of Sciences of the United States of America | | 2007 | 619 | 0 | ||
| Overgrowth caused by misexpression of a microRNA with dispensable wild-type function | Developmental biology | | 2006 | 629 | 0 | ||
| AnoEST: toward A. gambiae functional genomics | Genome research | | 2005 | 684 | 429 | ||
| Consistency of genome-based methods in measuring Metazoan evolution | FEBS letters | | 2005 | 536 | 0 | ||
| Protein coding potential of retroviruses and other transposable elements in vertebrate genomes | Nucleic acids research | | 2005 | 633 | 0 | ||
| Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages | Genome research | | 2005 | 651 | 0 | ||
| Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution | Nature | | 2004 | 578 | 3 | ||
| Genome sequence of the Brown Norway rat yields insights into mammalian evolution | Nature | | 2004 | 494 | 2 | ||
| Have fun, Be useful | The Scientist | | 2003 | 466 | 89 | ||
| The InterPro Database, 2003 brings increased coverage and new features | Nucleic acids research | | 2003 | 708 | 521 | ||
| A genome-wide survey of human pseudogenes | Genome research | | 2003 | 626 | 0 | ||
| Genome evolution reveals biochemical networks and functional modules | Proceedings of the National Academy of Sciences of the United States of America | | 2003 | 578 | 0 | ||
| Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae | Proceedings of the National Academy of Sciences of the United States of America | | 2002 | 519 | 0 | ||
| The EBI SRS server - new features | Bioinformatics | | 2002 | 621 | 0 | ||
| The genome sequence of the malaria mosquito Anopheles gambiae | Science | | 2002 | 676 | 2 | ||
| Initial sequencing and comparative analysis of the mouse genome | Nature | | 2002 | 809 | 6 | ||
| Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster | Science | | 2002 | 668 | 0 | ||
| Interactive InterPro-based comparisons of proteins in whole genomes | Bioinformatics | | 2002 | 647 | 0 | ||
| The EBI SRS server - recent developments | Bioinformatics | | 2002 | 631 | 0 | ||
| Immunity-related genes and gene families in Anopheles gambiae | Science | | 2002 | 884 | 0 | ||
| CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins | Nucleic acids research | | 2001 | 695 | 0 | ||
| Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes | Nucleic acids research | | 2001 | 573 | 0 | ||
| Bioinformatics: using the molecular biology data | Essentials of Genomics and Bioinformatics | 2001 | 506 | 0 | |||
| The InterPro database, an integrated documentation resource for protein families, domains and functional sites | Nucleic acids research | | 2001 | 689 | 565 | ||
| InterProScan--an integration platform for the signature-recognition methods in InterPro | Bioinformatics | | 2001 | 689 | 0 | ||
| InterPro--an integrated documentation resource for protein families, domains and functional sites | Bioinformatics | | 2000 | 718 | 463 | ||
| A pseudoknot-compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center | FEBS letters | | 1999 | 626 | 0 | ||
| Three-dimensional model for slipped loop RNA | Journal of biomolecular structure & dynamics | | 1997 | 657 | 530 | ||
| Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain | Journal of biomolecular structure & dynamics | 1995 | 563 | 0 |
