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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

Automatic module selection from several microarray gene expression studies

Zollinger, Alix ; Zollinger, Alix ; Davison, Anthony C. ; Goldstein, Darlene R.

In: Biostatistics, 2018, vol. 19, no. 2, p. 153-168

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

NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis

Singer, Jochen ; Ruscheweyh, Hans-Joachim ; Hofmann, Ariane L. ; Thurnherr, Thomas ; Singer, Franziska ; Toussaint, Nora C. ; Ng, Charlotte K Y. ; Piscuoglio, Salvatore ; Beisel, Christian ; Christofori, Gerhard ; Dummer, Reinhard ; Hall, Michael N. ; Krek, Wilhelm ; Levesque, Mitchell P. ; Manz, Markus G. ; Moch, Holger ; Papassotiropoulos, Andreas ; Stekhoven, Daniel J. ; Wild, Peter ; Wüst, Thomas ; Rinn, Bernd ; Beerenwinkel, Niko ; Berger, Bonnie ; Berger, Bonnie

In: Bioinformatics, 2018, vol. 34, no. 1, p. 107-108

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

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...

Large-scale comparison of toxin and antitoxins in Listeria monocytogenes

Agüero, José Antonio ; Akarsu, Hatice ; Aguilar-Bultet, Lisandra ; Oevermann, Anna ; Falquet, Laurent

In: Toxins, 2020, vol. 12, no. 1, p. 29

Toxin–antitoxin systems (TASs) are widely distributed in prokaryotes and encode pairs of genes involved in many bacterial biological processes and mechanisms, including pathogenesis. The TASs have not been extensively studied in Listeria monocytogenes (Lm), a pathogenic bacterium of the Firmicutes phylum causing infections in animals and humans. Using our recently published TASmania...

Long non-coding RNAs as molecular signatures for canine B-Cell lymphoma characterization

Cascione, Luciano ; Giudice, Luca ; Ferraresso, Serena ; Marconato, Laura ; Giannuzzi, Diana ; Napoli, Sara ; Bertoni, Francesco ; Giugno, Rosalba ; Aresu, Luca

In: Non-coding RNA, 2019, vol. 5, no. 3, p. 47

Diffuse large B-cell lymphoma (DLBCL), marginal zone lymphoma (MZL) and follicular lymphoma (FL) are the most common B-cell lymphomas (BCL) in dogs. Recent investigations have demonstrated overlaps of these histotypes with the human counterparts, including clinical presentation, biologic behavior, tumor genetics, and treatment response. The molecular mechanisms that underlie canine BCL are...

TASmania: A bacterial Toxin-Antitoxin Systems database

Akarsu, Hatice ; Bordes, Patricia ; Mansour, Moise ; Bigot, Donna-Joe ; Genevaux, Pierre ; Falquet, Laurent

In: PLOS Computational Biology, 2019, vol. 15, no. 4, p. e1006946

Bacterial Toxin-Antitoxin systems (TAS) are involved in key biological functions including plasmid maintenance, defense against phages, persistence and virulence. They are found in nearly all phyla and classified into 6 different types based on the mode of inactivation of the toxin, with the type II TAS being the best characterized so far. We have herein developed a new in silico discovery...

Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage : CASP und CAMEO

Haas, Jürgen ; Schwede, Torsten

In: BIOspektrum, 2014, vol. 20, no. 2, p. 236-237