2020

Scientific Articles

unige:139347	ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data	Kieser, Silas; Brown, Joseph; Zdobnov, Evgeny; Trajkovski, Mirko; McCue, Lee Ann
unige:139350	Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest	Sparks, Michael E; Ioannidis, Panagiotis; Zdobnov, Evgeny; Gundersen-Rindal, Dawn E;
unige:139365	Enhanced genome assembly and a new official gene set for Tribolium castaneum	Herndon, Nicolae; Ioannidis, Panagiotis; Zdobnov, Evgeny; Bucher, Gregor;
unige:139364	Gene content evolution in the arthropods	Thomas, Gregg W C; Ioannidis, Panagiotis; Zdobnov, Evgeny; Richards, Stephen;
unige:139248	LEMMI: a continuous benchmarking platform for metagenomics classifiers	Seppey, Mathieu; Manni, Mose; Zdobnov, Evgeny;
unige:139349	Phigaro: high-throughput prophage sequence annotation	Starikova, Elizaveta V; Tikhonova, Polina O; Prianichnikov, Nikita A; Rands, Christopher; ... Govorun, Vadim M
unige:139348	Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera	Oeyen, Jan Philip; Zdobnov, Evgeny; Niehuis, Oliver;
unige:139369	The genome of the blind soil-dwelling and ancestrally wingless dipluran campodea augens: a key reference hexapod for studying the emergence of insect innovations	Manni, Mose; Simao Neto, Felipe; Robertson, Hugh M; Gabaglio, Marco Aurelio; ... Zdobnov, Evgeny

Thesis supervisions

unige:143927	Benchmarking in (meta-) genomics: LEMMI & BUSCO	Seppey, Mathieu;
unige:144344	Metagenomic Characterization of the Virome of Clinical Samples	Brito, Francisco;

2019

Scientific Articles

unige:123167	BUSCO: assessing genome assembly and annotation completeness	Seppey, Mathieu; Manni, Mose; Zdobnov, Evgeny;
unige:123152	Comparative genomics groups phages of negativicutes and classical firmicutes despite different gram-staining properties	Rands, Christopher; Brüssow, Harald; Zdobnov, Evgeny;
unige:139372	Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease	L'Huillier, Arnaud; Brito, Francisco; Wagner, Noémie; Cordey, Samuel; ... Kaiser, Laurent
unige:123160	Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome	Panfilio, Kristen A; Vargas Jentzsch, Iris M; Benoit, Joshua B; Erezyilmaz, Deniz; ... Richards, Stephen
unige:115368	OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs	Kriventseva, Evgenia; Kouznetsov, Dimitri; Tegenfeldt, Fredrik; Manni, Mose; ... Zdobnov, Evgeny
unige:115501	Using BUSCO to Assess Insect Genomic Resources	Waterhouse, Robert M; Seppey, Mathieu; Simao Neto, Felipe; Zdobnov, Evgeny;
unige:123149	Viral sequences detection by high-throughput sequencing in cerebrospinal fluid of individuals with and without central nervous system disease	Schibler, Manuel; Brito, Francisco; Zanella, Marie-Céline; Zdobnov, Evgeny; ... Kaiser, Laurent

2018

Scientific Articles

unige:126289	ACI-1 beta-lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages	Rands, Christopher; Starikova, Elizaveta V; Brüssow, Harald; Kriventseva, Evgenia; ... Zdobnov, Evgeny
unige:111768	Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation	Vu Cantero, Diem-Lan; Cordey, Samuel; Simonetta, Federico; Brito, Francisco; ... Kaiser, Laurent
unige:115849	In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence	Guzina, Jelena; Chen, Wei-Hua; Stankovic, Tamara; Djordjevic, Magdalena; ... Djordjevic, Marko
unige:109659	Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank	Brito, Francisco; Cordey, Samuel; Delwart, Eric; Deng, Xutao; ... Preynat-Seauve, Olivier

Thesis supervisions

unige:109542

De novo genomics of non-model arthropods

Simao Neto, Felipe;

2017

Scientific Articles

unige:94544	Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders	Ioannidis, Panagiotis; Simao Neto, Felipe; Waterhouse, Robert; Manni, Mose; ... Zdobnov, Evgeny
unige:94543	Metagenomics analysis of red blood cell and fresh-frozen plasma units	Lau, Pierre; Cordey, Samuel; Brito, Francisco; Tirefort, Diderik; ... Preynat-Seauve, Olivier
unige:92739	OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs	Zdobnov, Evgeny; Tegenfeldt, Fredrik; Kuznetsov, D; Waterhouse, Robert; ... Kriventseva, Evgenia
unige:98726	Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures	Essaidi, Manel; Brito, Francisco; Benaoudia, Sacha; Royston, Lena; ... Tapparel, Caroline
unige:94545	Understanding key features of bacterial restriction-modification systems through quantitative modeling	Rodic, Andjela; Blagojevic, Bojana; Zdobnov, Evgeny; Djordjevic, Magdalena; Djordjevic, Marko
unige:112638	[Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes]	Starikova, E V; Prianichnikov, N A; Zdobnov, Evgeny; Govorun, V M;

Professional Articles

unige:111030	BUSCO applications from quality assessments to gene prediction and phylogenomics	Waterhouse, Robert; Seppey, Mathieu; Simao Neto, Felipe; Manni, Mose; ... Zdobnov, Evgeny
unige:112636	Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites	Djordjevic, Marko; Djordjevic, Magdalena; Zdobnov, Evgeny;

2016

Scientific Articles

unige:85369	Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection	Cordey, Samuel; Vu Cantero, Diem-Lan; Schibler, Manuel; L'Huillier, Arnaud; ... Kaiser, Laurent
unige:94499	Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology	Cordey, Samuel; Brito, Francisco; Vu Cantero, Diem-Lan; Turin, Lara; ... Kaiser, Laurent
unige:92747	CEGA - a catalog of conserved elements from genomic alignments	Dousse, Aline; Junier, Thomas; Zdobnov, Evgeny;
unige:94546	Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface	McKenna, Duane D; Scully, Erin D; Pauchet, Yannick; Hoover, Kelli; ... Zdobnov, Evgeny
unige:92752	Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution	Hoy, Marjorie A; Waterhouse, Robert; Wu, Ke; Estep, Alden S; ... Richards, Stephen
unige:92749	Genomic insights into the Ixodes scapularis tick vector of Lyme disease	Gulia-Nuss, Monika; Nuss, Andrew B; Meyer, Jason M; Waterhouse, Robert; Zdobnov, Evgeny
unige:92755	The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases	Zdobnov, Evgeny;
unige:92748	Unique features of a global human ectoparasite identified through sequencing of the bed bug genome	Benoit, Joshua B; Ioannidis, Panagiotis; Waterhouse, Robert; Zdobnov, Evgeny; ... Richards, Stephen

Thesis supervisions

unige:82294

Computational identification and analysis of conserved non-coding vertebrate elements

Dousse, Aline;

2015

Scientific Articles

unige:78148	A depauperate immune repertoire precedes evolution of sociality in bees	Barribeau, Seth M; Sadd, Ben M; du Plessis, Louis; Brown, Mark JF; ... Schmid-Hempel, Paul
unige:78552	A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor	Zhao, Chaoyang; Waterhouse, Robert; Ioannidis, Panagiotis; Zdobnov, Evgeny;
unige:78678	BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs	Simao Neto, Felipe; Waterhouse, Robert; Ioannidis, Panagiotis; Kriventseva, Evgenia; Zdobnov, Evgeny
unige:76379	Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report	Schibler, Manuel; Vetter, Pauline; Cherpillod, Pascal; Petty, Tom J; ... Kaiser, Laurent
unige:75570	E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient	L'Huillier, Arnaud; Abed, Yacine; Petty, Tom; Cordey, Samuel; ... Kaiser, Laurent
unige:78971	Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions	Anstead, Clare A.; Korhonen, Pasi K.; Young, Neil D.; Hall, Ross S.; ... Gasser, Robin B.
unige:78551	OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software	Kriventseva, Evgenia; Tegenfeldt, Fredrik; Petty, Tom; Waterhouse, Robert; ... Zdobnov, Evgeny
unige:78681	Social evolution. Genomic signatures of evolutionary transitions from solitary to group living	Kapheim, K. M.; Waterhouse, Robert; Zdobnov, Evgeny;
unige:78550	The genomes of two key bumblebee species with primitive eusocial organization	Sadd, Ben M; Zdobnov, Evgeny;
unige:74556	Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses	Cordey, Samuel; Bel, Michael; Petty Ii, Thomas John; Docquier, Mylene; ... Kaiser, Laurent

2014

Scientific Articles

unige:78451

Big data and other challenges in the quest for orthologs

Sonnhammer, E. L. L.; Gabaldon, T.; Sousa da Silva, A. W.; Martin, M.; ... Zdobnov, Evgeny