2009
Genome Analyzer
Targeted re-sequencing by array-capture
"Detection of genomic variation by selection of a 9 Mb DNA region and high throughput sequencing"
Sergey I. Nikolaev, Christian Iseli, Andrew J. Sharp, Daniel Robyr, Jacques Rougemont, Corinne Gehrig, Laurent Farinelli and Stylianos E. Antonarakis.
Collaboration between the University of Geneva Medical School, Ludwig Institute for Cancer Research (LICR), Swiss Institute of Bioinformatics (SIB), Ecole Polytechnique Fédérale de Lausanne (EPFL) and Fasteris.
PLoS One (2009) 4: e6659
Metagenomics
"Metagenomic study of the oral microbiota by Illumina high-throughput sequencing"
Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P
Collaboration between the Genomic Research Laboratory, Geneva University Hospitals, Switzerland and Fasteris.
J. Microbiol. Methods (2009) 79: 266-71
2008
Genome Analyzer
ROLEXA software published
"Probabilistic base calling of Solexa sequencing data"
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios and Felix Naef
Collaboration between Fasteris, Ecole Polytechnique Fédérale de Lausanne (EPFL), Ludwig Institute for Cancer Research (LICR) and Swiss Institute of Bioinformatics (SIB).
BMC Bioinformatics (2008) 9: 431-43.
De novo assembly EDENA software published in Genome Research
"De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer"
Written by David Hernandez as part of a collaboration between Fasteris and the group of Prof. Jacques Schrenzel at the Geneva University Hospitals.
Genome Research (2008) 18: 802-809.
Poster at USGEB 2008 on accuracy of Solexa Sequencing
In collaboration with the group of Prof. Schrenzel at the Geneva University Hospitals, we studied the accuracy of Genome Analyzer data using Staphylococcus aureus MW2 as a model, with a combination of re-sequencing and de novo sequencing.
Published by our clients
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2010
Genome Analyzer
"Targeted Next-Generation Sequencing Appoints C16orf57 as Clericuzio-Type Poikiloderma with Neutropenia Gene"
Volpi et al. Universita` degli Studi di Milano, Italy
Am. J. Human Genet. (2010), doi:10.1016/j.ajhg.2009.11.014
16S
"HspR Mutations Are Naturally Selected in Bifidobacterium longum When Successive Heat Shock Treatments Are Applied"
Berger et al. Nestlé Research Center, Lausanne, Switzerland
J. Bact. (2010) 192: 256-63
2009
Genome Analyzer
"Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions"
Corradi et al. Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC, Canada; Universität Basel, Zoologisches Institut, Basel, Switzerland; Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
Genome Biol. (2009) 10: R106.
"miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression"
Wang et al. National Chiao Tung University, Hsin-Chu, Taiwan; Academia Sinica, Nankang, Taiwan; National Cheng Kung University, Tainan, Taiwan
BMC Bioinformatics (2009) 10: 328-340.
"A single-base substitution within an intronic repetitive element causes dominant retinitis pigmentosa with reduced penetrance"
Rio Frio et al. University of Lausanne, Switzerland; Harvard Medical School, Boston, Ma, USA; Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Lausanne, Switzerland; Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
Hum. Mutat. (2009) 30: 1-8.
"Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses"
Kreuze et al. International Potato Center (CIP), Lima, Peru
Virology (2009) 388: 1-7.
"Elimination of antiviral defense by viral RNase III"
Cuellar et al. University of Helsinki, Finland; International Potato Center (CIP), Lima, Peru; Swedish University of Agricultural Sciences, Uppsala, Sweden
PNAS (2009) 106: 10354-10358.
"Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing"
Willenbrock et al. Exiqon A/S; University of Copenhagen, Denmark
RNA (2009) 15: e1699809.
"The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function"
Guillon et al. Institut Curie, Paris, France
PLoS ONE. (2009) 4: e4932.
"Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower"
Kaufmann et al. Plant Research International, Wageningen, The Netherlands
PLoS Biology (2009) 7: e1000090.
Capillary sequencing
"The ectoparasitic mite Tropilaelaps mercedesae (Acari, Laelapidae) as a vector of honeybee viruses"
Dainat et al. Agroscope Liebefeld-Posieux Research Station (ALP), Bern, Switzerland
Insect. Soc. (2009) 56: 40-43.
16S
"Characterization of Cronobacter recovered from dried milk and related products"
El-Sharoud et al. Food Safety and Microbial Physiology Laboratory, Mansoura University, Mansoura, Egypt
BMC Microbiol. (2009) 9: 24-32.
"Improving the enrichment procedure for Enterobacteriaceae detection "
Weber et al. Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland
Food Microbiol. (2009) : .
"Physiological and biochemical characterization of the two -L-rhamnosidases of Lactobacillus plantarum NCC245"
Ávila et al. Nestlé Research Center, Switzerland
Microbiology (2009) 155: 2739-2749.
Plasmids
"Respiratory syncytial virus subunit vaccine based on a recombinant fusion protein expressed transiently in mammalian cells"
Nallet et al. École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Pevion Biotech Ltd., Bern, Switzerland; Zürcher Hochschule für Angewandte Wissenschaften, Wädenswil, Switzerland
Vaccine (2009) 27: 6415-19.
2008
Capillary sequencing
"In Vitro Budding of Intralumenal Vesicles into Late Endosomes Is Regulated by Alix and Tsg101"
Falguières et al. Biochemistry Department, University of Geneva, Switzerland
Mol. Biol. Cell (2008) 19: 4942-4955.
"Distinct sets of aß TCRs confer similar recognition of tumor antigen NY-ESO-1157-165 by interacting with its central Met/Trp residues"
Derré et al. Ludwig Institute for Cancer Research, Switzerland
PNAS (2008) 105: 15010-15.
"Lysobisphosphatidic Acid Controls Endosomal Cholesterol Levels"
Chevallier et al. University of Geneva, Switzerland
J. Biol. Chem. (2008) 283: 27871-880.
"Yeast Est2p Affects Telomere Length by Influencing Association of Rap1p with Telomeric Chromatin"
Ji et al. Vanderbilt University, USA
Mol. and Cell. Biol. (2008) 28: 2380-90.
"Intraspecific and within-isolate sequence variation in the ITS rRNA gene region of Pythium mercuriale sp. nov. (Pythiaceae)"
Belbahri et al. University of Applied Sciences of Western Switzerland
FEMS Microbiol. Letters (2008) 284: 17-27.
"Emergence of Secretion-Defective Sublines of Pseudomonas aeruginosa PAO1 Resulting from Spontaneous Mutations in the vfr Global Regulatory Gene"
Fox et al. Centre National de la Recherche Scientifique, Marseille, France
Appl. Environ. Microbiol. (2008) 74: 1902-08.
16S
"Development of a Novel Screening Method for the Isolation of Cronobacter spp. (Enterobacter sakazakii)"
Iversen et al. University of Zürich, Switzerland
Appl. Environ. Microbiol. (2008) 74: 2550-53.
2007
Capillary sequencing
"Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli"
Zuber et al. Nestlé Research Center, Switzerland
J. Bact. (2007) 189: 8206-14.
"Life in Darwin’s dust: intercontinental transport and survival of microbes in the nineteenth century"
Gorbushina et al. University of Oldenburg, Germany
Env. Microbiol. (2007) 9: 2911-22.
"Variable-Number Tandem Repeats as Molecular Markers for Biotypes of Pasteuria ramosa in Daphnia spp."
Mouton et al. University of basel, Switzerland and University of Florida, USA
Appl. Environ. Microbiol. (2007) 73: 3715-18.
"Closely related dermatophyte species produce different patterns of secreted proteins"
Giddey et al. Centre Hospitalier Universitaire Vaudois, Switzerland
FEMS Microbiol. Letters (2007) 267: 95-101.
"In Vivo Persistence of Codominant Human CD8+ T Cell Clonotypes Is Not Limited by Replicative Senescence or Functional Alteration"
Derré et al. Ludwig Institute for Cancer Research, Switzerland
J. Immunol. (2007) 179: 2368-79.
"Direct-PCR Detection and Epidemiology of Ramularia collo-cygni Associated with Barley Necrotic Leaf Spots"
Frei et al. Agroscope Changins-Wädenswil Research Station ACW, Switzerland
J. Phytopathol (2007) 155: 281-88.
"Pivotal Involvement of Fcy Receptor IIA in the Neutralization of Lipopolysaccharide Signaling via a Potent Novel Anti-TLR4 Monoclonal Antibody 15C1"
Dunn-Siegrist et al. Novimmune SA, Switzerland
J. Biol. Chem. (2007) 282: 34817-27.
"Single Gene-Mediated Shift in Pollinator Attraction in Petunia"
Hoballah et al. University of Bern, Switzerland
Plant Cell (2007) 19: 779-90.
"Telomerase repeat addition processivity is increased at critically short telomeres in a Tel1-dependent manner in Saccharomyces cerevisiae"
Chang et al. Swiss Institute for Experimental Cancer Research (ISREC), Switzerland
Genes Dev. (2007) 21: 2485-94.
16S
"Similarity and Differences in the Lactobacillus acidophilus Group Identified by Polyphasic Analysis and Comparative Genomics"
Berger et al. Nestlé Research Center, Switzerland
J. Bacteriol. (2007) 189: 1311-21.
"The taxonomy of Enterobacter sakazakii: proposal of a new genus Cronobacter gen. nov. and descriptions of
Cronobacter sakazakii comb. nov. Cronobacter sakazakii
subsp. sakazakii, comb. nov., Cronobacter sakazakii
subsp. malonaticus subsp. nov., Cronobacter turicensis
sp. nov., Cronobacter muytjensii sp. nov., Cronobacter
dublinensis sp. nov. and Cronobacter genomospecies"
Iversen et al. Nestlé Research Center, Switzerland
BMC Evol. Biol (2007) 7: 64-75.
2006
Capillary sequencing
"Evidence for Distinct Mechanisms of Starch Granule Breakdown in Plants"
Delatte et al. ETH Zurich, Switzerland
J. Biol. Chem. (2006) :281 12050-59.
"A Novel Approach to Characterize Clonality and Differentiation of Human Melanoma-Specific T Cell Responses: Spontaneous Priming and Efficient Boosting by Vaccination"
Speiser et al. Ludwig Institute for Cancer Research, Switzerland
J. Immunol. (2006) 177: 1338-48.
"Rapid identification of potato virus Y strains by one-step triplex RT-PCR"
Rigotti et al. Agroscope Changins-Wädenswil Research Station ACW, Switzerland
J. Virol. Meth. (2006) 140: 90-94.
2005
Capillary sequencing
"State transitions and light adaptation require chloroplast thylakoid protein kinase STN7"
Bellafiore et al. University of Geneva, Switzerland
Nature (2007) 433: 892-96, and suppl.
