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The neXtProt peptide uniqueness checker: a tool for the proteomics community

Schaeffer, Mathieu ; Gateau, Alain ; Teixeira, Daniel ; Michel, Pierre-André ; Zahn-Zabal, Monique ; Lane, Lydie ; Hancock, John ; Hancock, John

In: Bioinformatics, 2017, vol. 33, no. 21, p. 3471-3472

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Ambrosini, Giovanna ; Groux, Romain ; Bucher, Philipp ; Hancock, John ; Hancock, John

In: Bioinformatics, 2018, vol. 34, no. 14, p. 2483-2484

Comparison of generic and product-specific Life Cycle Assessment databases: application to construction materials used in building LCA studies

Lasvaux, Sébastien ; Habert, Guillaume ; Peuportier, Bruno ; Chevalier, Jacques

In: The International Journal of Life Cycle Assessment, 2015, vol. 20, no. 11, p. 1473-1490

Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes

Alocci, Davide ; Ghraichy, Marie ; Barletta, Elena ; Gastaldello, Alessandra ; Mariethoz, Julien ; Lisacek, Frederique

In: Glycobiology, 2018, vol. 28, no. 6, p. 349-362

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Poux, Sylvain ; Arighi, Cecilia N. ; Magrane, Michele ; Bateman, Alex ; Wei, Chih-Hsuan ; Lu, Zhiyong ; Boutet, Emmanuel ; Bye-A-Jee, Hema ; Famiglietti, Maria Livia ; Roechert, Bernd ; UniProt Consortium, The ; Kelso, Janet ; Kelso, Janet

In: Bioinformatics, 2017, vol. 33, no. 21, p. 3454-3460

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids

Dorier, Julien ; Goundaroulis, Dimos ; Benedetti, Fabrizio ; Stasiak, Andrzej ; Valencia, Alfonso ; Valencia, Alfonso

In: Bioinformatics, 2018, vol. 34, no. 19, p. 3402-3404

NGS-based S. aureus typing and outbreak analysis in clinical microbiology laboratories : Lessons learned from a Swiss-wide proficiency test

Dylus, David ; Pillonel, Trestan ; Opota, Onya ; Wüthrich, Daniel ; Seth-Smith, Helena M. B. ; Egli, Adrian ; Leo, Stefano ; Lazarevic, Vladimir ; Schrenzel, Jacques ; Laurent, Sacha ; Bertelli, Claire ; Blanc, Dominique S. ; Neuenschwander, Stefan ; Ramette, Alban ; Falquet, Laurent ; Imkamp, Frank ; Keller, Peter M. ; Kahles, Andre ; Oberhaensli, Simone ; Barbié, Valérie ; Dessimoz, Christophe ; Greub, Gilbert ; Lebrand, Aitana

In: Frontiers in Microbiology, 2020, vol. 11, p. 591093

Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to...

Estimating and accounting for genotyping errors in RAD-seq experiments

Bresadola, Luisa ; Link, Vivian ; Buerkle, C. Alex ; Lexer, Christian ; Wegmann, Daniel

In: Molecular Ecology Resources, 2020, vol. 20, no. 4, p. 856–870

In non-model organisms, evolutionary questions are frequently addressed using reduced representation sequencing techniques due to their low cost, ease of use, and because they do not require genomic resources such as a reference genome. However, evidence is accumulating that such techniques may be affected by specific biases, questioning the accuracy of obtained genotypes, and as a...

Role of ETS1 in the transcriptional network of diffuse large B cell lymphoma of the activated B cell-like type

Priebe, Valdemar ; Sartori, Giulio ; Napoli, Sara ; Chung, Elaine Yee Lin ; Cascione, Luciano ; Kwee, Ivo ; Arribas, Alberto Jesus ; Mensah, Afua Adjeiwaa ; Rinaldi, Andrea ; Ponzoni, Maurilio ; Zucca, Emanuele ; Rossi, Davide ; Efremov, Dimitar ; Lenz, Georg ; Thome, Margot ; Bertoni, Francesco

In: Cancers, 2020, vol. 12, no. 7, p. 17 p

Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease that has been distinguished into at least two major molecular entities, the germinal center-like B cell (GCB) DLBCL and activated-like B cell (ABC) DLBCL, based on transcriptome expression profiling. A recurrent ch11q24.3 gain is observed in roughly a fourth of DLBCL cases resulting in the overexpression of two ETS transcription...

Linking comparative genomics of nine potato-associated pseudomonas isolates with their differing biocontrol potential against late blight

Vrieze, Mout De ; Varadarajan, Adithi R. ; Schneeberger, Kerstin ; Bailly, Aurélien ; Rohr, Rudolf P. ; Ahrens, Christian H. ; Weisskopf, Laure

In: Frontiers in Microbiology, 2020, vol. 11, p. 857

For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively recruited by plants. To gain more insights into...