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 | 24 | 16 | |||
| 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 | 95 | 88 | |||
| OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity | Nucleic acids research | 2023 | 107 | 776 | |||
| Identification of a miRNA multi-targeting therapeutic strategy in glioblastoma | Cell death and disease | 2023 | 323 | 140 | |||
| Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart | PLoS computational biology | 2022 | 217 | 77 | |||
| Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop | MBio | 2022 | 115 | 142 | |||
| A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand | Nucleic acids research | 2022 | 77 | 26 | |||
| Enterovirus D: a small but versatile species | Microorganisms | 2021 | 190 | 153 | |||
| 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 | 207 | 332 | |||
| Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera | Genome Biology and Evolution | 2020 | 369 | 316 | |||
| LEMMI: a continuous benchmarking platform for metagenomics classifiers | Genome Research | 2020 | 378 | 187 | |||
| Phigaro: high-throughput prophage sequence annotation | Bioinformatics | 2020 | 364 | 0 | |||
| ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data | BMC Bioinformatics | 2020 | 321 | 643 | |||
| Enhanced genome assembly and a new official gene set for Tribolium castaneum | BMC Genomics | 2020 | 326 | 243 | |||
| 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 | 319 | 185 | |||
| Gene content evolution in the arthropods | Genome Biology | 2020 | 337 | 164 | |||
| 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 | 264 | 232 | |||
| Comparative genomics groups phages of negativicutes and classical firmicutes despite different gram-staining properties | Environmental Microbiology | 2019 | 404 | 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 | 487 | 412 | |||
| Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease | Frontiers in Pediatrics | 2019 | 340 | 163 | |||
| Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease | Genes | 2019 | 461 | 118 | |||
| BUSCO: assessing genome assembly and annotation completeness | Methods in Molecular Biology | 2019 | 738 | 7,326 | |||
| Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome | Genome Biology | 2019 | 375 | 44 | |||
| Using BUSCO to Assess Insect Genomic Resources | Methods in Molecular Biology | 2019 | 471 | 3 | |||
| ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages | Environmental Microbiology | 2018 | 344 | 0 | |||
| In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence | Frontiers in Genetics | 2018 | 454 | 218 | |||
| Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank | Vox Sanguinis | 2018 | 539 | 415 | |||
| Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation | Clinical Microbiology and Infection | 2018 | 1,394 | 593 | |||
| OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs | Nucleic acids research | 2017 | 1,017 | 328 | |||
| Metagenomics analysis of red blood cell and fresh-frozen plasma units | Transfusion | 2017 | 549 | 2 | |||
| [Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes] | Biomeditsinskaya Khimiya | 2017 | 381 | 0 | |||
| Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites | Frontiers in Microbiology | 2017 | 367 | 229 | |||
| BUSCO applications from quality assessments to gene prediction and phylogenomics | Molecular Biology and Evolution | 2017 | 523 | 0 | |||
| Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders | Genome biology and evolution | 2017 | 565 | 340 | |||
| Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures | Journal of Allergy and Clinical Immunology | 2017 | 649 | 3 | |||
| Understanding key features of bacterial restriction-modification systems through quantitative modeling | BMC systems biology | 2017 | 397 | 265 | |||
| Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution | Genome biology and evolution | 2016 | 523 | 568 | |||
| CEGA - a catalog of conserved elements from genomic alignments | Nucleic acids research | 2016 | 571 | 237 | |||
| The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases | Nucleic acids research | 2016 | 624 | 681 | |||
| Genomic insights into the Ixodes scapularis tick vector of Lyme disease | Nature communications | 2016 | 567 | 259 | |||
| Unique features of a global human ectoparasite identified through sequencing of the bed bug genome | Nature communications | 2016 | 543 | 429 | |||
| Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection | Emerging infectious diseases | 2016 | 676 | 314 | |||
| 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 | 531 | 293 | |||
| 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 | 551 | 249 | |||
| 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 | 753 | 263 | |||
| A depauperate immune repertoire precedes evolution of sociality in bees | GenomeBiology.com | 2015 | 614 | 462 | |||
| Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report | Lancet. Infectious diseases | 2015 | 710 | 1 | |||
| OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software | Nucleic acids research | 2015 | 710 | 450 | |||
| Social evolution. Genomic signatures of evolutionary transitions from solitary to group living | Science | 2015 | 484 | 1 | |||
| The genomes of two key bumblebee species with primitive eusocial organization | GenomeBiology.com | 2015 | 548 | 547 | |||
| Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions | Nature communications | 2015 | 587 | 214 | |||
| 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 | 762 | 0 | |||
| BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | 2015 | 753 | 0 | |||
| A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor | Current biology | 2015 | 495 | 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 | 772 | 311 | |||
| Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans | American journal of human genetics | 2014 | 665 | 1 | |||
| Finding the missing honey bee genes: lessons learned from a genome upgrade | BMC genomics | 2014 | 610 | 247 | |||
| Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response | International journal of cancer | 2014 | 751 | 486 | |||
| Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support | Nucleic acids research | 2014 | 922 | 62 | |||
| The common marmoset genome provides insight into primate biology and evolution | Nature genetics | 2014 | 557 | 305 | |||
| Big data and other challenges in the quest for orthologs | Bioinformatics | 2014 | 585 | 473 | |||
| The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment | Journal of heredity | 2013 | 554 | 0 | |||
| Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality | Genome research | 2013 | 681 | 1 | |||
| miRmap web: Comprehensive microRNA target prediction online | Nucleic acids research | 2013 | 824 | 1 | |||
| OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs | Nucleic acids research | 2013 | 782 | 0 | |||
| Dampening of arginase 2 expression by microRNA-155 is critical for dendritic cell function | Immunology | 2012 | 478 | 4 | |||
| Toward community standards in the quest for orthologs | Bioinformatics | 2012 | 537 | 0 | |||
| Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection | PLOS pathogens | 2012 | 837 | 431 | |||
| MiRmap: comprehensive prediction of microRNA target repression strength | Nucleic acids research | 2012 | 702 | 0 | |||
| Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections | AIDS | 2012 | 742 | 448 | |||
| The ecoresponsive genome of Daphnia pulex | Science | 2011 | 1,033 | 1 | |||
| OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 | Nucleic acids research | 2011 | 685 | 0 | |||
| A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits | BMC evolutionary biology | 2011 | 690 | 379 | |||
| Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice | Molecular & cellular proteomics | 2011 | 725 | 0 | |||
| Rhinovirus genome variation during chronic upper and lower respiratory tract infections | PloS one | 2011 | 627 | 596 | |||
| Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi | Genome biology and evolution | 2011 | 682 | 0 | |||
| Rhinovirus genome evolution during experimental human infection | PloS one | 2010 | 795 | 559 | |||
| Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics | Science | 2010 | 717 | 1 | |||
| The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell | Bioinformatics | 2010 | 685 | 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 | 584 | 1 | |||
| A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes | PloS one | 2010 | 759 | 299 | |||
| Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances | PLoS computational biology | 2010 | 645 | 342 | |||
| Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens | Science | 2010 | 607 | 0 | |||
| Functional and evolutionary insights from the genomes of three parasitoid Nasonia species | Science | 2010 | 652 | 2 | |||
| Sociality is linked to rates of protein evolution in a highly social insect | Molecular biology and evolution | 2010 | 572 | 0 | |||
| Impact of newly HIV diagnosed individuals on the transmission of drug resistance | Antiviral therapy | 2009 | 448 | 0 | |||
| Sertoli cell Dicer is essential for spermatogenesis in mice | Developmental biology | 2009 | 746 | 0 | |||
| Comparative Genome Analysis | Bioinformatics: A Swiss Perspective | 2009 | 1,043 | 0 | |||
| Integration of microRNA miR-122 in hepatic circadian gene expression | Genes & development | 2009 | 719 | 0 | |||
| Comparative Genomics of Insect Immunity | Insect Infection and Immunity: Evolution, Ecology, and Mechanisms | 2009 | 666 | 0 | |||
| The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection | AIDS | 2009 | 576 | 0 | |||
| New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses | Emerging infectious diseases | 2009 | 608 | 0 | |||
| The genome sequence of taurine cattle: a window to ruminant biology and evolution | Science | 2009 | 735 | 5 | |||
| Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates | BMC genomics | 2009 | 728 | 464 | |||
| The bovine lactation genome: insights into the evolution of mammalian milk | GenomeBiology.com | 2009 | 669 | 367 | |||
| miROrtho: computational survey of microRNA genes | Nucleic acids research | 2009 | 695 | 318 | |||
| Mapping of small RNAs in the human ENCODE regions | American journal of human genetics | 2008 | 621 | 0 | |||
| The genome of the model beetle and pest Tribolium castaneum | Nature | 2008 | 891 | 2 | |||
| The cis-acting replication elements define human enterovirus and rhinovirus species | RNA | 2008 | 764 | 2 | |||
| The Aedes aegypti genome: a comparative perspective | Insect molecular biology | 2008 | 566 | 1 | |||
| Drug resistance in newly HIV diagnosed individuals: transmission rate, clusters and persistence | Antiviral therapy | 2008 | 365 | 0 | |||
| OrthoDB: the hierarchical catalog of eukaryotic orthologs | Nucleic acids research | 2008 | 669 | 530 | |||
| Quantification of ortholog losses in insects and vertebrates | GenomeBiology.com | 2007 | 616 | 754 | |||
| Genome sequence of Aedes aegypti, a major arbovirus vector | Science | 2007 | 681 | 2 | |||
| New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features | BMC genomics | 2007 | 656 | 1,105 | |||
| Quantification of insect genome divergence | Trends in genetics | 2007 | 574 | 0 | |||
| VectorBase: a home for invertebrate vectors of human pathogens | Nucleic acids research | 2007 | 639 | 0 | |||
| Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes | Science | 2007 | 812 | 469 | |||
| Computational and transcriptional evidence for microRNAs in the honey bee genome | GenomeBiology.com | 2007 | 718 | 792 | |||
| Evolution of genes and genomes on the Drosophila phylogeny | Nature | 2007 | 725 | 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 | 616 | 0 | |||
| Overgrowth caused by misexpression of a microRNA with dispensable wild-type function | Developmental biology | 2006 | 625 | 0 | |||
| AnoEST: toward A. gambiae functional genomics | Genome research | 2005 | 675 | 416 | |||
| Consistency of genome-based methods in measuring Metazoan evolution | FEBS letters | 2005 | 532 | 0 | |||
| Protein coding potential of retroviruses and other transposable elements in vertebrate genomes | Nucleic acids research | 2005 | 625 | 0 | |||
| Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages | Genome research | 2005 | 647 | 0 | |||
| Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution | Nature | 2004 | 575 | 3 | |||
| Genome sequence of the Brown Norway rat yields insights into mammalian evolution | Nature | 2004 | 491 | 2 | |||
| Have fun, Be useful | The Scientist | 2003 | 462 | 88 | |||
| The InterPro Database, 2003 brings increased coverage and new features | Nucleic acids research | 2003 | 705 | 502 | |||
| A genome-wide survey of human pseudogenes | Genome research | 2003 | 623 | 0 | |||
| Genome evolution reveals biochemical networks and functional modules | Proceedings of the National Academy of Sciences of the United States of America | 2003 | 570 | 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 | 514 | 0 | |||
| The EBI SRS server - new features | Bioinformatics | 2002 | 615 | 0 | |||
| The genome sequence of the malaria mosquito Anopheles gambiae | Science | 2002 | 673 | 2 | |||
| Initial sequencing and comparative analysis of the mouse genome | Nature | 2002 | 806 | 6 | |||
| Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster | Science | 2002 | 665 | 0 | |||
| Interactive InterPro-based comparisons of proteins in whole genomes | Bioinformatics | 2002 | 644 | 0 | |||
| The EBI SRS server - recent developments | Bioinformatics | 2002 | 626 | 0 | |||
| Immunity-related genes and gene families in Anopheles gambiae | Science | 2002 | 878 | 0 | |||
| CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins | Nucleic acids research | 2001 | 692 | 0 | |||
| Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes | Nucleic acids research | 2001 | 566 | 0 | |||
| Bioinformatics: using the molecular biology data | Essentials of Genomics and Bioinformatics | 2001 | 502 | 0 | |||
| The InterPro database, an integrated documentation resource for protein families, domains and functional sites | Nucleic acids research | 2001 | 686 | 306 | |||
| InterProScan--an integration platform for the signature-recognition methods in InterPro | Bioinformatics | 2001 | 683 | 0 | |||
| InterPro--an integrated documentation resource for protein families, domains and functional sites | Bioinformatics | 2000 | 712 | 445 | |||
| A pseudoknot-compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center | FEBS letters | 1999 | 623 | 0 | |||
| Three-dimensional model for slipped loop RNA | Journal of biomolecular structure & dynamics | 1997 | 653 | 494 | |||
| Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain | Journal of biomolecular structure & dynamics | 1995 | 560 | 0 |
