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: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
unige:74559	Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study	Petty Ii, Thomas John; Cordey, Samuel; Padioleau, Ismael; Docquier, Mylene; ... Kaiser, Laurent
unige:43800	Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response	Cosset, Erika; Petty Ii, Thomas John; Dutoit Vallotton, Valérie; Cordey, Samuel; ... Preynat-Seauve, Olivier
unige:36888	Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support	Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos Marc; ... Appel, Ron David
unige:78454	Finding the missing honey bee genes: lessons learned from a genome upgrade	Elsik, Christine G; Worley, Kim C; Waterhouse, Robert; Zdobnov, Evgeny;
unige:44366	Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans	Popadin, Konstantin; Gutierrez Arcelus, Maria; Lappalainen, Tuuli Emilia; Buil Demur, Alfonso Alberto; ... Antonarakis, Stylianos
unige:78452	The common marmoset genome provides insight into primate biology and evolution	Worley, Kim C; Gerlach, Daniel; Kriventseva, Evgenia; Zdobnov, Evgeny;

2013

Scientific Articles

unige:30574	miRmap web: Comprehensive microRNA target prediction online	Vejnar, Charles; Blum, Matthias; Zdobnov, Evgeny;
unige:30577	OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs	Waterhouse, Robert; Tegenfeldt, Fredrik; Li, Jia; Zdobnov, Evgeny; Kriventseva, Evgenia
unige:30571	Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality	Simola, Daniel F; Wissler, Lothar; Donahue, Greg; Waterhouse, Robert; ... Zdobnov, Evgeny
unige:78421	The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment	Zdobnov, Evgeny;

Thesis supervisions

unige:30428

Analysis of evolutionary constraints on gene arrangements in animal genomes

Li, Jia;