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List of works by Evgeny M. Zdobnov

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

scientific article published on 06 November 2020

A depauperate immune repertoire precedes evolution of sociality in bees

scientific article published on 24 April 2015

A genome-wide survey of human pseudogenes

scientific article

A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor.

scientific article published on 5 February 2015

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

scientific article

A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes

scientific article

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

scientific article published on 01 June 2018

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

scientific article published on 22 June 2020

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

scholarly article by Jelena Guzina et al published 2018 in Frontiers in Genetics

AnoEST: toward A. gambiae functional genomics

scientific article

Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection

scientific article published on May 2016

Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology

scientific article published on 7 September 2016

Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology

scientific article published on 6 July 2016

BUSCO applications from quality assessments to gene prediction and phylogenomics

scientific article

BUSCO: Assessing Genome Assembly and Annotation Completeness

scientific article published on 01 January 2019

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

scientific article

Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

scientific article published on 21 June 2022

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

scientific article published on 14 March 2020

CEGA--a catalog of conserved elements from genomic alignments

scientific article

Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report

scientific article

Comparative Genome Analysis

article

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

scientific article

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

scientific article

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

scientific article published on 31 July 2019

Comparative genomics of insect immunity

scholarly article published 25 June 2009

Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study

scientific article

Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response

scientific article published on 8 May 2014

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart

scientific article published on 08 March 2022

Computational and transcriptional evidence for microRNAs in the honey bee genome

scientific article published on January 2007

Consistency of genome-based methods in measuring Metazoan evolution

scientific article

Correction to: Genome-enabled insights into the biology of thrips as crop pests

scientific article published on 16 November 2020

Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi

scientific article

E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient

scientific article

Enhanced genome assembly and a new official gene set for Tribolium castaneum

scientific article published on 14 January 2020

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes

scientific article

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates

scientific article (publication date: 12 January 2009)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

scientific article

Finding the missing honey bee genes: lessons learned from a genome upgrade

scientific article

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

scientific article

Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances

scientific article

Gene age predicts the strength of purifying selection acting on gene expression variation in humans

scientific article

Gene content evolution in the arthropods

scientific article published on 23 January 2020

Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution

scientific article

Genome evolution reveals biochemical networks and functional modules

scientific article

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface ⬇️

scientific article (publication date: 11 November 2016)

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

scientific article

Genome-enabled insights into the biology of thrips as crop pests

scientific article published on 19 October 2020

Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders

scientific article

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

scientific article published on 9 February 2016

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

scientific article published on 19 December 2019

Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection

scientific article

Immunity-related genes and gene families in Anopheles gambiae

scientific article published in October 2002

Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections

scientific article published in October 2012

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integration of microRNA miR-122 in hepatic circadian gene expression

scientific article

LEMMI: A continuous benchmarking platform for metagenomics classifiers

scientific article published on 02 July 2020

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

scholarly article

Loss of Dicer in Sertoli cells has a major impact on the testicular proteome of mice

scientific article

Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions.

scientific article published on 25 June 2015

Mapping of small RNAs in the human ENCODE regions

scientific article published on April 2008

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

scientific article published on 11 May 2017

Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank

article

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

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

scientific article published on 02 April 2019

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features

scientific article

New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses

scientific article published on May 2009

OrthoDB in 2020: evolutionary and functional annotations of orthologs

scientific article published on 16 November 2020

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

article

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

scientific article

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

scientific article

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

scientific article

OrthoDB: the hierarchical catalog of eukaryotic orthologs

scientific article

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

scientific article

Overgrowth caused by misexpression of a microRNA with dispensable wild-type function

scientific article

Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens

scientific article

Phigaro: high throughput prophage sequence annotation

scientific article published on 20 April 2020

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

scientific article published on 07 August 2017

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes

scientific article

Quantification of insect genome divergence

scholarly article by Evgeny M. Zdobnov & Peer Bork published January 2007 in Trends in Genetics

Quantification of ortholog losses in insects and vertebrates.

scientific article

Repression of arginase-2 expression in dendritic cells by microRNA-155 is critical for promoting T cell proliferation.

scientific article published on 9 July 2014

Rhinovirus genome evolution during experimental human infection

scientific article

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

scientific article

Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera ⬇️

scientific article published on 22 May 2020

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

scientific article published on 22 November 2017

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

scientific article

Sertoli cell Dicer is essential for spermatogenesis in mice

scientific article

Silencing of c-Fos expression by microRNA-155 is critical for dendritic cell maturation and function.

scientific article published on 8 March 2011

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

scientific article

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

scientific article published on May 2013

Sociality is linked to rates of protein evolution in a highly social insect

scientific article published on 28 January 2010

The EBI SRS server-new features

scientific article

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

scientific article

The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

scientific article published on 01 January 2020

The Genomic Basis of Arthropod Diversity

article published in 2018

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

scientific article

The SIB Swiss Institute of Bioinformatics Semantic Web of data

scientific article published on 25 October 2023

The bovine lactation genome: insights into the evolution of mammalian milk

scientific article

The cis-acting replication elements define human enterovirus and rhinovirus species.

scientific article published on 9 June 2008

The ecoresponsive genome of Daphnia pulex

scientific article

The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

article

The genome of the model beetle and pest Tribolium castaneum

scientific article

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

scientific article published on 10 March 2021

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The genomes of two key bumblebee species with primitive eusocial organization ⬇️

scientific article

The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection

scientific article

Three-Dimensional Model for Slipped Loop RNA ⬇️

scientific article published on 01 August 1997

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

scientific article

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome ⬇️

scientific article published on 2 February 2016

Using BUSCO to Assess Insect Genomic Resources

article

Using BUSCO to Assess Insect Genomic Resources

article by Robert M. Waterhouse et al published 10 November 2018 in Methods in Molecular Biology

VectorBase: a home for invertebrate vectors of human pathogens

scientific article

Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease

scientific article published on 19 August 2019

miROrtho: computational survey of microRNA genes.

scientific article published on 15 October 2008

miRmap web: Comprehensive microRNA target prediction online

scientific article

miRmap: Comprehensive prediction of microRNA target repression strength ⬇️

scientific article published on October 2, 2012

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