| Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research | Cell host & microbe | | | 2025 | 43 | 40 |
|
| 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 | 102 | 113 |
|
| OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity | Nucleic acids research | | | 2023 | 114 | 1,226 |
|
| Identification of a miRNA multi-targeting therapeutic strategy in glioblastoma | Cell death and disease | | | 2023 | 328 | 234 |
|
| Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart | PLoS computational biology | | | 2022 | 222 | 79 |
|
| Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop | MBio | | | 2022 | 120 | 158 |
|
| A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand | Nucleic acids research | | | 2022 | 83 | 28 |
|
| Enterovirus D: a small but versatile species | Microorganisms | | | 2021 | 195 | 175 |
|
| 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 | 212 | 484 |
|
| Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera | Genome Biology and Evolution | | | 2020 | 376 | 363 |
|
| LEMMI: a continuous benchmarking platform for metagenomics classifiers | Genome Research | | | 2020 | 386 | 197 |
|
| Phigaro: high-throughput prophage sequence annotation | Bioinformatics | | | 2020 | 369 | 0 |
|
| ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data | BMC Bioinformatics | | | 2020 | 328 | 770 |
|
| Enhanced genome assembly and a new official gene set for Tribolium castaneum | BMC Genomics | | | 2020 | 331 | 263 |
|
| 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 | 328 | 197 |
|
| Gene content evolution in the arthropods | Genome Biology | | | 2020 | 342 | 169 |
|
| 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 | 271 | 269 |
|
| Comparative genomics groups phages of negativicutes and classical firmicutes despite different gram-staining properties | Environmental Microbiology | | | 2019 | 409 | 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 | 493 | 743 |
|
| Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease | Frontiers in Pediatrics | | | 2019 | 345 | 178 |
|
| Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease | Genes | | | 2019 | 466 | 157 |
|
| BUSCO: assessing genome assembly and annotation completeness | Methods in Molecular Biology | | | 2019 | 755 | 12,853 |
|
| Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome | Genome Biology | | | 2019 | 381 | 65 |
|
| Using BUSCO to Assess Insect Genomic Resources | Methods in Molecular Biology | | | 2019 | 475 | 3 |
|
| ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages | Environmental Microbiology | | | 2018 | 349 | 0 |
|
| In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence | Frontiers in Genetics | | | 2018 | 460 | 234 |
|
| Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank | Vox Sanguinis | | | 2018 | 548 | 455 |
|
| Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation | Clinical Microbiology and Infection | | | 2018 | 1,401 | 640 |
|
| OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs | Nucleic acids research | | | 2017 | 1,023 | 359 |
|
| Metagenomics analysis of red blood cell and fresh-frozen plasma units | Transfusion | | | 2017 | 554 | 2 |
|
| [Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes] | Biomeditsinskaya Khimiya | | | 2017 | 387 | 0 |
|
| Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites | Frontiers in Microbiology | | | 2017 | 377 | 252 |
|
| BUSCO applications from quality assessments to gene prediction and phylogenomics | Molecular Biology and Evolution | | | 2017 | 527 | 0 |
|
| Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders | Genome biology and evolution | | | 2017 | 570 | 410 |
|
| Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures | Journal of Allergy and Clinical Immunology | | | 2017 | 655 | 3 |
|
| Understanding key features of bacterial restriction-modification systems through quantitative modeling | BMC systems biology | | | 2017 | 403 | 289 |
|
| Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution | Genome biology and evolution | | | 2016 | 529 | 632 |
|
| CEGA - a catalog of conserved elements from genomic alignments | Nucleic acids research | | | 2016 | 578 | 242 |
|
| The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases | Nucleic acids research | | | 2016 | 633 | 781 |
|
| Genomic insights into the Ixodes scapularis tick vector of Lyme disease | Nature communications | | | 2016 | 573 | 308 |
|
| Unique features of a global human ectoparasite identified through sequencing of the bed bug genome | Nature communications | | | 2016 | 550 | 506 |
|
| Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection | Emerging infectious diseases | | | 2016 | 682 | 372 |
|
| 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 | 537 | 322 |
|
| 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 | 557 | 291 |
|
| 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 | 758 | 299 |
|
| A depauperate immune repertoire precedes evolution of sociality in bees | GenomeBiology.com | | | 2015 | 621 | 463 |
|
| Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report | Lancet. Infectious diseases | | | 2015 | 717 | 1 |
|
| OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software | Nucleic acids research | | | 2015 | 717 | 601 |
|
| Social evolution. Genomic signatures of evolutionary transitions from solitary to group living | Science | | | 2015 | 491 | 1 |
|
| The genomes of two key bumblebee species with primitive eusocial organization | GenomeBiology.com | | | 2015 | 556 | 551 |
|
| Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions | Nature communications | | | 2015 | 593 | 221 |
|
| 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 | 768 | 0 |
|
| BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | | | 2015 | 760 | 0 |
|
| A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor | Current biology | | | 2015 | 501 | 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 | 788 | 346 |
|
| Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans | American journal of human genetics | | | 2014 | 670 | 1 |
|
| Finding the missing honey bee genes: lessons learned from a genome upgrade | BMC genomics | | | 2014 | 616 | 253 |
|
| Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response | International journal of cancer | | | 2014 | 759 | 509 |
|
| Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support | Nucleic acids research | | | 2014 | 927 | 80 |
|
| The common marmoset genome provides insight into primate biology and evolution | Nature genetics | | | 2014 | 565 | 326 |
|
| Big data and other challenges in the quest for orthologs | Bioinformatics | | | 2014 | 591 | 514 |
|
| The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment | Journal of heredity | | | 2013 | 560 | 0 |
|
| Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality | Genome research | | | 2013 | 687 | 1 |
|
| miRmap web: Comprehensive microRNA target prediction online | Nucleic acids research | | | 2013 | 829 | 1 |
|
| OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs | Nucleic acids research | | | 2013 | 787 | 0 |
|
| Dampening of arginase 2 expression by microRNA-155 is critical for dendritic cell function | Immunology | | | 2012 | 484 | 4 |
|
| Toward community standards in the quest for orthologs | Bioinformatics | | | 2012 | 544 | 0 |
|
| Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection | PLOS pathogens | | | 2012 | 847 | 440 |
|
| MiRmap: comprehensive prediction of microRNA target repression strength | Nucleic acids research | | | 2012 | 707 | 0 |
|
| Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections | AIDS | | | 2012 | 747 | 473 |
|
| The ecoresponsive genome of Daphnia pulex | Science | | | 2011 | 1,039 | 1 |
|
| OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 | Nucleic acids research | | | 2011 | 690 | 0 |
|
| A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits | BMC evolutionary biology | | | 2011 | 697 | 386 |
|
| Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice | Molecular & cellular proteomics | | | 2011 | 730 | 0 |
|
| Rhinovirus genome variation during chronic upper and lower respiratory tract infections | PloS one | | | 2011 | 633 | 612 |
|
| Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi | Genome biology and evolution | | | 2011 | 687 | 0 |
|
| Rhinovirus genome evolution during experimental human infection | PloS one | | | 2010 | 801 | 583 |
|
| Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics | Science | | | 2010 | 723 | 1 |
|
| The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell | Bioinformatics | | | 2010 | 690 | 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 | 589 | 1 |
|
| A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes | PloS one | | | 2010 | 764 | 309 |
|
| Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances | PLoS computational biology | | | 2010 | 650 | 378 |
|
| Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens | Science | | | 2010 | 613 | 0 |
|
| Functional and evolutionary insights from the genomes of three parasitoid Nasonia species | Science | | | 2010 | 657 | 2 |
|
| Sociality is linked to rates of protein evolution in a highly social insect | Molecular biology and evolution | | | 2010 | 577 | 0 |
|
| Impact of newly HIV diagnosed individuals on the transmission of drug resistance | Antiviral therapy | | | 2009 | 454 | 0 |
|
| Sertoli cell Dicer is essential for spermatogenesis in mice | Developmental biology | | | 2009 | 753 | 0 |
|
| Comparative Genome Analysis | Bioinformatics: A Swiss Perspective | | | 2009 | 1,049 | 0 |
|
| Integration of microRNA miR-122 in hepatic circadian gene expression | Genes & development | | | 2009 | 725 | 0 |
|
| Comparative Genomics of Insect Immunity | Insect Infection and Immunity: Evolution, Ecology, and Mechanisms | | | 2009 | 673 | 0 |
|
| The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection | AIDS | | | 2009 | 581 | 0 |
|
| New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses | Emerging infectious diseases | | | 2009 | 616 | 0 |
|
| The genome sequence of taurine cattle: a window to ruminant biology and evolution | Science | | | 2009 | 741 | 5 |
|
| Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates | BMC genomics | | | 2009 | 733 | 498 |
|
| The bovine lactation genome: insights into the evolution of mammalian milk | GenomeBiology.com | | | 2009 | 674 | 370 |
|
| miROrtho: computational survey of microRNA genes | Nucleic acids research | | | 2009 | 714 | 330 |
|
| Mapping of small RNAs in the human ENCODE regions | American journal of human genetics | | | 2008 | 626 | 0 |
|
| The genome of the model beetle and pest Tribolium castaneum | Nature | | | 2008 | 896 | 2 |
|
| The cis-acting replication elements define human enterovirus and rhinovirus species | RNA | | | 2008 | 768 | 2 |
|
| The Aedes aegypti genome: a comparative perspective | Insect molecular biology | | | 2008 | 571 | 1 |
|
| Drug resistance in newly HIV diagnosed individuals: transmission rate, clusters and persistence | Antiviral therapy | | | 2008 | 370 | 0 |
|
| OrthoDB: the hierarchical catalog of eukaryotic orthologs | Nucleic acids research | | | 2008 | 675 | 577 |
|
| Quantification of ortholog losses in insects and vertebrates | GenomeBiology.com | | | 2007 | 621 | 867 |
|
| Genome sequence of Aedes aegypti, a major arbovirus vector | Science | | | 2007 | 687 | 2 |
|
| New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features | BMC genomics | | | 2007 | 661 | 1,155 |
|
| Quantification of insect genome divergence | Trends in genetics | | | 2007 | 581 | 0 |
|
| VectorBase: a home for invertebrate vectors of human pathogens | Nucleic acids research | | | 2007 | 648 | 0 |
|
| Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes | Science | | | 2007 | 818 | 506 |
|
| Computational and transcriptional evidence for microRNAs in the honey bee genome | GenomeBiology.com | | | 2007 | 723 | 801 |
|
| Evolution of genes and genomes on the Drosophila phylogeny | Nature | | | 2007 | 735 | 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 | 621 | 0 |
|
| Overgrowth caused by misexpression of a microRNA with dispensable wild-type function | Developmental biology | | | 2006 | 631 | 0 |
|
| AnoEST: toward A. gambiae functional genomics | Genome research | | | 2005 | 686 | 440 |
|
| Consistency of genome-based methods in measuring Metazoan evolution | FEBS letters | | | 2005 | 538 | 0 |
|
| Protein coding potential of retroviruses and other transposable elements in vertebrate genomes | Nucleic acids research | | | 2005 | 635 | 0 |
|
| Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages | Genome research | | | 2005 | 653 | 0 |
|
| Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution | Nature | | | 2004 | 580 | 3 |
|
| Genome sequence of the Brown Norway rat yields insights into mammalian evolution | Nature | | | 2004 | 496 | 2 |
|
| Have fun, Be useful | The Scientist | | | 2003 | 468 | 90 |
|
| The InterPro Database, 2003 brings increased coverage and new features | Nucleic acids research | | | 2003 | 710 | 539 |
|
| A genome-wide survey of human pseudogenes | Genome research | | | 2003 | 628 | 0 |
|
| Genome evolution reveals biochemical networks and functional modules | Proceedings of the National Academy of Sciences of the United States of America | | | 2003 | 580 | 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 | 521 | 0 |
|
| The EBI SRS server - new features | Bioinformatics | | | 2002 | 623 | 0 |
|
| The genome sequence of the malaria mosquito Anopheles gambiae | Science | | | 2002 | 678 | 2 |
|
| Initial sequencing and comparative analysis of the mouse genome | Nature | | | 2002 | 811 | 6 |
|
| Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster | Science | | | 2002 | 670 | 0 |
|
| Interactive InterPro-based comparisons of proteins in whole genomes | Bioinformatics | | | 2002 | 649 | 0 |
|
| The EBI SRS server - recent developments | Bioinformatics | | | 2002 | 633 | 0 |
|
| Immunity-related genes and gene families in Anopheles gambiae | Science | | | 2002 | 886 | 0 |
|
| CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins | Nucleic acids research | | | 2001 | 697 | 0 |
|
| Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes | Nucleic acids research | | | 2001 | 575 | 0 |
|
| Bioinformatics: using the molecular biology data | Essentials of Genomics and Bioinformatics | | | 2001 | 508 | 0 |
|
| The InterPro database, an integrated documentation resource for protein families, domains and functional sites | Nucleic acids research | | | 2001 | 691 | 826 |
|
| InterProScan--an integration platform for the signature-recognition methods in InterPro | Bioinformatics | | | 2001 | 701 | 0 |
|
| InterPro--an integrated documentation resource for protein families, domains and functional sites | Bioinformatics | | | 2000 | 720 | 476 |
|
| A pseudoknot-compatible universal site is located in the large ribosomal RNA in the peptidyltransferase center | FEBS letters | | | 1999 | 628 | 0 |
|
| Three-dimensional model for slipped loop RNA | Journal of biomolecular structure & dynamics | | | 1997 | 659 | 546 |
|
| Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain | Journal of biomolecular structure & dynamics | | | 1995 | 565 | 0 |
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