Bold = Eurofins Employee
2024
16S Microbome profiling:Vižlin, A.; Andersch Björkman, Y.; Kumar, Y.; Göthe, M.; Gillstedt, M.; Osmančević, A. No Evidence of Gut Microbiota Alteration in Psoriasis Patients Switching to Brodalumab after Loss of TNFα Inhibition Effect.>Int. J. Mol. Sci. 2024,25 7745. https://doi.org/10.3390/ijms25147745
Microbiome profiling: Vižlin, A.; Bajramović, A.; Björkman, Y.A.; Kumar, Y.; Göthe, M.; Gillstedt, M.; Osmančević, A. The Effects of Brodalumab on the Fungal Microbiome in Patients with Psoriasis. Int. J. Mol. Sci. 2024, 25, 10239. https://doi.org/10.3390/ijms251910239
Genome Sequencing: Turco, S.; Drais, M.I.; Rossini, L.; Di Sora, N.; Brugneti, F.; Speranza, S.; Contarini, M.; Mazzaglia, A. Genomic and Pathogenic Characterization of Akanthomyces muscarius Isolated from Living Mite Infesting Hazelnut Big Buds. Genes
Genome Sequencing (ONT): Maleckis M., Wibowo M., Gren T., Jarmusch S., Sterndorff E., Booth T., Henriksen N., Whitford C., Jiang X., Jørgensen T., Ding L., Weber T., Biosynthesis of the Azoxy Compound Azodyrecin from Streptomyces mirabilis P8-A2, ACS Chemical Biology
Genome Sequencing: Wurzbacher, C.E., Haufschild, T., Hammer, J. et al. Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany. Sci Rep
Amplicon Sequencing: Hiralal A, Geelhoed J. Hidalgo-Martinez S., Smets B., van Dijk J., Meysman P., Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads, Microbial Genomics
Genome Sequencing: Martinet, M.G.; Lohde, M.; Higazy, D.; Brandt, C.; Pletz, M.W.; Middelboe, M.; Makarewicz, O.; Ciofu, O. Diversification of Pseudomonas aeruginosa Biofilm Populations under Repeated Phage Exposures Decreases the Efficacy of the Treatment. Microorganisms
INVIEW Resequencing: Alexandra M Kortsinoglou, Martyn J Wood, Antonis I Myridakis, Marios Andrikopoulos, Andreas Roussis, Dan Eastwood, Tariq Butt, Vassili N Kouvelis, Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity, G3 Genes|Genomes|Genetics
Whole Plasmid Sequencing (ONT): Pozojevic, J., Sivaprasad, R., Laß, J. et al. LINE1-mediated epigenetic repression of androgen receptor transcription causes androgen insensitivity syndrome. Sci Rep
Genome Sequencing: Spruijtenburg, B., de Souza Lima, B.J.F., Tosar, S.T.G. et al. The yeast genus Tardiomyces gen. nov. with one new species and two new combinations. Infection
Whole Plasmid Sequencing (ONT): Zongo, P.D., Cabanel, N., Royer, G. et al. An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages. Nat Commun
INVIEW Resequencing: Ulrich L, Steiner LX, Giez C, Lachnit T. 2024. Optimizing bacteriophage treatment of resistant Pseudomonas. mSphere
Genome Sequencing: Garrido V, Arrieta-Gisasola A, Migura-García L, Laorden L, Grilló MJ. 2024. Multidrug resistance in Salmonella isolates of swine origin: mobile genetic elements and plasmids associated with cephalosporin resistance with potential transmission to humans. Appl Environ Microbiol
Genome Sequencing: Bultreys A., Gheysen I., High Diversity of Curtobacterium flaccumfaciens in Poinsettia and Detection of Three Pathogenicity Plasmids for Identification of C. flaccumfaciens pv. poinsettiae, Phytobiomes Journal
2023
Custom target sequencing: Herzog C., Jones A., Evans I., Reisel D., Olaitan A., Doufekas K., MacDonald N., Flöter Radestad A., Gemzell-Danielsson K., Zikan M., Cibula D., Dostalek L, Paprotka T., Leimbach A., Schmitt M., Ryan A., Gentry-Maharaj A., Apostolidou S., Rostenthal A., Menon U., Widschwendter M., Plasma cell-free DNA methylation analysis for ovarian cancer detection: Analysis of samples from a case-control study and and ovarian cancer screening trial. International journal of Cancer
Metagenome sequencing: Mandl K., Suljic J., Bader C., Hofstetter I,, Faber F.. Bestimmung der Endophyten im Blutungssaft der Rebe mittelsNext Generation Sequencing. Die Bodenkultur: Journal of Land Management, Food and Environment
Genome Sequencing: Turco, S., Mazzaglia, A., Drais, M.I. et al. Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae. Sci Rep
Cell-free DNA sequencing: M. Jimenez-Blanco Bravo, M. Crespo-Leiro, M. Garcia-Cosio, L. Perez-Gomez, R. Lopez-Vilella, C. Ortiz Bautista, M. Farrero Torres, A. Maestro Benedicto, B. Diaz Molina, C. Diez. Donor-Derived Cell-Free DNA as a Potential Biomarker for Acute Cellular Rejection Surveillance (FreeDNA-CAR Study). The Journal of Heart and Lung Transplantation
Metagenome sequencing: Vassileva I., Baev V., Yahubyan G., Apostolova-Kuzova E., Angelov A., Koprinarova M.. Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols. Food Technology and Biotechnology
Microbiome profiling: Mendes, M.; Moreira, I.S.; Moreira, P.; Pintado, M.; Castro, P.M.L. Bioaugmentation of Aerobic Granular Sludge with Dye-Decolorizing Yeast for Textile Industrial Wastewater. Processes
Microbiome profiling: Cabreros C., Vermi Aizza Corpuz M, Castrogiovanni F., Borea L., Sandionigi A., Vigliotta G., Ballesteros F., Puig S., Hasan S., Korshin G., Belgiorno V., Buonerba A., Naddeo V., Unraveling microbial community by next-generation sequencing in living membrane bioreactors for wastewater treatment,
Science of The Total Environment
Transcriptome sequencing: Loxha, L.; Ibrahim, N.K.; Stasche, A.S.; Cinar, B.; Dolgner, T.; Niessen, J.; Schreek, S.; Fehlhaber, B.; Forster, M.; Stanulla, M.; et al. GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells. Int. J. Mol. Sci.
16S rRNA sequencing: Rötzer, V.; Wenderlein, J.; Wiesinger, A.; Versen, F.; Rauch, E.; Straubinger, R.K.; Zeiler, E. Bovine Udder Health: From Standard Diagnostic Methods to New Approaches—A Practical Investigation of Various Udder Health Parameters in Combination with 16S rRNA Sequencing. Microorganisms
INVIEW Oncoprofiling: Master Thesis from Johanna Svensson: Genetic profiling in non-small cell lung cancer. To predict response to immunotherapy
Transcriptome sequencing: Arnold, N.D.; Garbe, D.; Brück, T.B. Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp. Mar. Drugs
Transcriptome sequencing: Cuyutupa, V.R., Moser, D., Diedrich, V. et al. Blood transcriptomics mirror regulatory mechanisms during hibernation—a comparative analysis of the Djungarian hamster with other mammalian species. Pflugers Arch - Eur J Physiol
Transcriptome and plasmid sequencing: Heieck, K., Arnold, N.D. & Brück, T.B. Metabolic stress constrains microbial L-cysteine production in Escherichia coli by accelerating transposition through mobile genetic elements. Microb Cell Fact
Genome sequencing: Farlow, A.J.; Rupasinghe, D.B.; Naji, K.M.; Capon, R.J.; Spiteller, D. Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria. Microorganisms
Genome sequencing: Marzec-Grządziel, A.; Gałązka, A. Sequencing of the Whole Genome of a Bacterium of the Genus Achromobacter Reveals Its Potential for Xenobiotics Biodegradation. Agriculture
2022
Genome Seq (ONT/Illm): Valenti V, Saracchi M, Degradi L, Kunova A, Cortesi P, Pasquali M., A Genome Resource for Ciborinia camelliae, the Causal Agent of Camellia Flower Blight, Molecular Plant-Microbe Interactions
INVIEW Virus: Holicki C., Bergmann F.; Stoek F.; Schulz A., Groschup M., Ziegler U., Sadeghi B., Expedited retrieval of high-quality Usutu virus genomes via Nanopore sequencing with and without target enrichment, Front. Microbiol
SARS-CoV-2 research: Chrysostomou A., Vranchen B., Haralambous C., Alexandrou M., Aristokleous A., Christodoulou C., Gregoriou I., Ioannides M., Kalakouta O., Karagiannis C., Koumbaris G., Loizides C., Mendris M., Papastergiou P., Patasalis P., Pieridou D., Richter J., Schmitt M., Shammas C., Stylianou D., Themistokleuos G., the COMESSAR Network, Lemey P., Kostrikis L. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses
Transcriptome sequencing: Schulze M., Kumar Y.,Rattay M.,Niemann J.,Wijffels R.H., Martens D.E. Transcriptomic analysis reveals mode of action of butyric acid supplementation in an intensified CHO cell fed-batch process. Biotechnology & Bioengineering
INVIEW Oncoprofiling: Siesing, C., Petersson, A., Ulfarsdottir, T. et al. Delineating the intra-patient heterogeneity of molecular alterations in treatment-naïve colorectal cancer with peritoneal carcinomatosis. Mod Pathol
Methylation analysis: Shcherbakov D, Nigri M, Akbergenov R, Brilkova M, Mantovani M, Petit PI, Grimm A, Karol AA, Teo Y, Sanchón AC, Kumar Y, Eckert A, Thiam K, Seebeck P, Wolfer DP, Böttger EC. Premature aging in mice with error-prone protein synthesis. Sci Adv.
INVIEW CRISPR Check: Kaeuferle et al. Genome-wide off-target analyses of CRISPR/Cas9-mediated T-cell receptor engineering in primary human T cells. Clinical & Translational Immunology
Whole Genome Sequencing: Turco et al. Complete genome assembly of the levan-positive strain PVFi1 of Pseudomonas savastanoi pv. savastanoi isolated from olive knots in Central Italy. Environmental Microbiology Reports
Transcriptome sequencing: Hühn et al. Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells. Molecular Oncology
Whole Genome Sequencing: Nikodinoska et al. Whole genome sequence data of Lactiplantibacillus plantarum IMI 507,027. Sciene Direct
SARS-CoV-2 research: Mahajan et al. Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India
2021
Transcriptome sequencing: Pust et al., Direct RNA nanopore sequencing of Pseudomonas aeruginosa clone C transcriptomes
Genome sequencing: Lilge et al., Draft Genome Sequence of the Type Strain Bacillus subtilis subsp. subtilis DSM10
Amplicon sequencing: Hailu et al., Insight into microbial community diversity and composition of two-stage anaerobic digestion: Focusing methanogenic stage
Exome sequencing: Meyer et al., Single-Center Prospective Cohort Study on the Histopathology, Genotype, and Postsurgical Outcomes of Patients With Primary Aldosteronism
Amplicon sequencing: Vinay et al., Effect of Bacillus spp. on the composition of gut microbiota in early life stages of Indian white shrimp, Penaeus indicus
Transcriptome sequencing: Cartagena et al., Comparative transcriptome analysis of root types in salt tolerant and sensitive rice varieties in response to salinity stress
Genome sequencing: Bamouh et al., Draft Genome Sequence of the Capripoxvirus Vaccine Strain KSGP 0240, Reisolated from Cattle
Genome sequencing: Cornet et al., The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach
Amplicon sequencing: Vilperte et al., Development of a multiplex amplicon-sequencing assay to detect low-frequency mutations in poinsettia (Euphorbia pulcherrima) breeding programmes
Amplicon sequencing: Subedi et al., Developing Chenopodium ficifolium as a potential B genome diploid model system for genetic characterization and improvement of allotetraploid quinoa (Chenopodium quinoa)
Transcriptome sequencing: Robertson et al., Increased immune activation and signs of neuronal injury in HIV-negative people on preexposure prophylaxis
Transcriptome sequencing: Anzai et al., TMEM180 contributes to SW480 human colorectal cancer cell proliferation through intra-cellular metabolic pathways
Transcriptome sequencing: Woock et al., Serine residues 726 and 780 have nonredundant roles regulating STAT5a activity in luminal breast cancer
Bisulfite sequencing: Gegner et al., Complete Metamorphosis in Manduca sexta Involves Specific Changes in DNA Methylation Patterns
Genome sequencing: Schwendener et al., Complete Circular Genome Sequence of a mecB- and mecD-Containing Strain of Macrococcus canis
Transcriptome sequencing: Lukicheva et al., Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species
Transcriptome sequencing: Wittig et al., Two Brassica napus cultivars differ in gene expression, but not in their response to submergence
Genome sequencing: Ezemokwe et al., Complete Genome Sequence of Pseudomonas Phage Zikora
NGSelect Amplicon 2ndPCR: Kluesner et al., MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq
Genome sequencing: Leao et al., Occurrence of a Rare Multidrug Resistant Escherichia coli Coharboring blaCTX-M-32 and blaCTX-M-2 Genes in a Bovine
Genome sequencing: Moriniere et al., In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes
Genome sequencing: Kawahara et al., Francisellosis of Yesso scallops Mizuhopecten yessoensis in Japan is caused by a novel type of Francisella halioticida
Transcriptome sequencing: Lenz et al., All-trans retinoic acid induces synaptopodin-dependent metaplasticity in mouse dentate granule cells
Gras-Di sequencing: Doganlar et al., Development of single nucleotide polymorphism markers using genotyping by sequencing technique for determination of genetic diversity and population structure in hazelnut
2020
Genome sequencing: Jones, Du, Bernstein, Meyer, Hoppe, Schilling, Ableitner, Juling, Dick, Strauss, Bienefeld. Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee. Ecol Evol. (2020)
Library preparation: J F Hess, T A Kohl, M Kotrová, K Rönsch, T Paprotka, V Mohr, T Hutzenlaub, M Brüggemann, R Zengerle, S Niemann, N Paust. Library preparation for next generation sequencing: A review of automation strategies, Biotechnol Adv
Genome sequencing: Kawahara et al., Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131
Lentiviral gene therapy: Kohn DB, Booth C, Kang EM, Pai SY, Shaw KL, Santilli G, Armant M, Buckland KF, Choi U, De Ravin SS, Dorsey MJ, Kuo CY, Leon-Rico D, Rivat C, Izotova N, Gilmour K, Snell K, Dip JX, Darwish J, Morris EC, Terrazas D, Wang LD, Bauser CA, Paprotka T, Kuhns DB, Gregg J, Raymond HE, Everett JK, Honnet G, Biasco L, Newburger PE, Bushman FD, Grez M, Gaspar HB, Williams DA, Malech HL, Galy A, Thrasher AJ; Net4CGD consortium. Lentiviral gene therapy for X-linked chronic granulomatous disease. Nat Med. 2020 Feb;26(2):200-206.
Methylation studies: Nené NR, Barrett J, Jones A, Evans I, Reisel D, Timms JF, Paprotka T, Leimbach A, Franchi D, Colombo N, Bjørge L, Zikan M, Cibula D, Widschwendter M. DNA methylation signatures to predict the cervicovaginal microbiome status. Clin Epigenetics.
Exome sequencing: Mäkelä R, Arjonen A, Härmä V, Rintanen N, Paasonen L, Paprotka T, Rönsch K, Kuopio T, Kononen J, Rantala JK. Ex vivo modelling of drug efficacy in a rare metastatic urachal carcinoma. BMC Cancer.
Whole genome sequencing: Bogliolo M, Pujol R, Aza-Carmona M, Muñoz-Subirana N, Rodriguez-Santiago B, Casado JA, Rio P, Bauser C, Reina-Castillón J, Lopez-Sanchez M, Gonzalez-Quereda L, Gallano P, Catalá A, Ruiz-Llobet A, Badell I, Diaz-Heredia C, Hladun R, Senent L, Argiles B, Bergua Burgues JM, Bañez F, Arrizabalaga B, López Almaraz R, Lopez M, Figuera Á, Molinés A, Pérez de Soto I, Hernando I, Muñoz JA, Del Rosario Marin M, Balmaña J, Stjepanovic N, Carrasco E, Cuesta I, Cosuelo JM, Regueiro A, Moraleda Jimenez J, Galera-Miñarro AM, Rosiñol L, Carrió A, Beléndez-Bieler C, Escudero Soto A, Cela E, de la Mata G, Fernández-Delgado R, Garcia-Pardos MC, Sáez-Villaverde R, Barragaño M, Portugal R, Lendinez F, Hernadez I, Vagace JM, Tapia M, Nieto J, Garcia M, Gonzalez M, Vicho C, Galvez E, Valiente A, Antelo ML, Ancliff P, Garcia F, Dopazo J, Sevilla J, Paprotka T, Pérez-Jurado LA, Bueren J, Surralles J. Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. J Med Genet.
2019
INVIEW Liquid Biopsy Oncoprofiling: Alunni-Fabbroni M, Rönsch K, Huber T, Cyran CC, Seidensticker M, Mayerle J, Pech M, Basu B, Verslype C, Benckert J, Malfertheiner P, Ricke J. Circulating DNA as prognostic biomarker in patients with advanced hepatocellular carcinoma: a translational exploratory study from the SORAMIC trial. J Transl Med.
Transcriptome sequencing: Golfier et al., Distinct and overlapping functions of Miscanthus sinensis MYB transcription factors SCM1 and MYB103 in lignin biosynthesis. BioRxiv (2019)
Cancer research: Nené NR, Reisel D, Leimbach A, Franchi D, Jones A, Evans I, Knapp S, Ryan A, Ghazali S, Timms JF, Paprotka T, Bjørge L, Zikan M, Cibula D, Colombo N, Widschwendter M. Association between the cervicovaginal microbiome, BRCA1 mutation status, and risk of ovarian cancer: a case-control study. Lancet Oncol.
Genome sequencing: Ravi K., et al., Physiological characterization and sequence analysis of a syringate-consuming Actinobacterium, Bioresource technology (2019)
Genome sequencing: Aliyu H, Gorte O, Neumann A, Ochsenreither K. Draft genome sequence of the oleaginous yeast Saitozyma podzolica (syn. Cryptococcus podzolicus) DSM 27192. Microbiol Resour Announc 8:e01676-18 (2019)
Microbiome sequencing: Palakawong Na Ayudthaya S, et al., Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples, Current Microbiology (2019)
Metagenome sequencing: Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.), Microbiome Journal (2019)
Genome sequencing: Le Roy T., et al., Butyricimonas faecalis sp. nov., isolated from human faeces and emended description of the genus Butyricimonas, International Journal of Systematic and Evolutionary Microbiology (2019)
2018
Microbiome sequencing: Jensen A, et al., Unique subgingival microbiota associated with periodontitis in cirrhosis patients. Nature Scientific Reports (2018)
Transcriptome sequencing: Bell P.A, et al., Mesencephalic astrocyte-derived neurotropic factor is an important factor in chondrocyte ER homeostasis, Cell Stress and Chaperones (2018)
Microbiome sequencing: Teixeira C, et al., Barley Products of Different Fiber Composition Selectively Change Microbiota Composition in Rats, Molecular Nutrition and Food Research (2018)
Transcriptome sequencing: Janus P, et al., Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes, Cellular Signalling (2018)
Amplicon sequencing: Köhler J. M., et al., The Local Ecological Memory of Soil: Majority and Minority Components of Bacterial Communities in Prehistorical Urns from Schöps (Germany), Environmental Research (2018)
Genome sequencing: Cartwright J. F., et al., Highly sensitive detection of mutations in CHO cell recombinant DNA using multi-parallel single molecule real-time DNA sequencing; Biotechnology & Bioengineering (2018)
Genome sequencing: Salsano C., et al., Complete Genome Sequence of the Polymyxin E (Colistin)-Producing Paenibacillus sp. Strain B-LR, Microbiology Resource Announcements (2018)
Amplicon sequencing: Summerer A., et al., Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions, Human Genetics (2018)
2017
Amplicon analysis: Kappel K., Haase I., Käppel C., Sotelo C.G. and Schröder U., Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments. Food Chemistry (2017); http://dx.doi.org/10.1016/j.foodchem.2017.04.178
Amplicon analysis: Langer J.A.F. et al., Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak. PLoS One (2017); doi:10.1371/journal.pone.0175808
Epigenetics: Widschwendter, Evan, Jones, Ghazali, Reisel, Ryan, Gentry-Maharaj, Zikan, Cibula, Eichner, Alunni-Fabbroni, Koch, Janni, Paprotka, Wittenberger, Menon, Wahl, Rack, Lempiäinen. Methylation patterns in serum DNA for early identification of disseminated breast cancer. Genome Med (2017)
Transcriptome sequencing: Akagi et al., RNA-Seq analysis of human cell lines established from normal and neoplastic esophageal squamous epithelium
Epigenetics: Widschwendter, Zikan, Wahl, Lempiäinen, Paprotka, Evans, Jones, Ghazali, Reisel, Eichner, Rujan, Yang, Teschendorff, Ryan Cibula Menon, Wittenberger. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med (2017)
Whole genome sequencing: Guachalla LM, Stojkovic K, Hartl K, Kaszowska M, Kumar Y, Wahl B, Paprotka T, Nagy E, Lukasiewicz J, Nagy G, Szijártó V. Discovery of monoclonal antibodies cross-reactive to novel subserotypes of K. pneumoniae O3. Sci Rep.
2016
Genome analysis: Sollars, E. et al., Genome sequence and genetic diversity of European ash trees. Nature (2016); doi:10.1038/nature20786
Academia meets Industry: Schäfer C, Paprotka T, Heitzer E, Eccleston M, Noe J, Holdenrieder S, Diehl F, Thierry A. Academia Meets Industry. Adv Exp Med Biol.
2015
Genome analysis: Sato, K. et al., Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis. Scientific Reports, 5:16894
Microbiome Profiling: Mahé F, Mayor J, Bunge J, Chi J, Siemensmeyer T, Stoeck T, Wahl B, Paprotka T, Filker S, Dunthorn M. Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys. J Eukaryot Microbiol.
Amplicon analysis: Lange, A., Schilling E., Strittmatter A. et al., AmpliconDuo: A split-sample filtering protocol for high-throughput amplicon sequencing of microbial communities. PLOS One 10(11)
Genome analysis: Tourasse, N. et al., The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. BMC Genomics, vol. 16:580
Microbiome Profiling: Mahé F, Mayor J, Bunge J, Chi J, Siemensmeyer T, Stoeck T, Wahl B, Paprotka T, Filker S, Dunthorn M. Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys. J Eukaryot Microbiol.
Transcriptome analysis: Kwasiborski, A. et al., Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum. Heredity
Amplicon analysis: Köberl, M. et al., Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America. Frontiers in microbiology 6
Genome analysis: Shimomura, M. et al., The Glycine max cv. enrei genome for improvement of Japanese soybean cultivars. Intern. Journal of Genomics, vol. 2015 (358127)
Amplicon analysis: Tambadou, F. et al., Characterization of the colistin (polymyxin E1 and E2) biosynthetic gene cluster. Archives of Microbiology
2014
Amplicon analysis: Schiml, S. et al., The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J. 80 (6)
Genome analysis: Moura AE., Janse van Rensburg C., Pilot M., Tehrani A., et al. Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum. MolBiolEvol 5(1121-31)
Genome analysis: Stoeckle, B. et al., Identification of 10 polymorphic microsatellite loci in the high montane gastropod Semilimax kotulae using high-throughput sequence data. Molluscan Research 34(1)
INVIEW Epigenome: Wittenberger T, Sleigh S, Reisel D, Zikan M, Wahl B, Alunni-Fabbroni M, Jones A, Evans I, Koch J, Paprotka T, Lempiäinen H, Rujan T, Rack B, Cibula D, Widschwendter M. DNA methylation markers for early detection of women's cancer: promise and challenges. Epigenomics.
Transcriptome analysis: Boenigk, J. et al., Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure. PloS one 9(4)
Amplicon analysis: Zozomová-Lihová, J. et al., When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine schulzii trigenomic allopolyploid. New Phytologist
Transcriptome analysis: Højland, D. et al., Adaptation of Musca domestica L. field population to laboratory breeding causes transcriptional alterations. PloS one 9(1)
Microbiome Profiling: Pison C, Magnan A, Botturi K, Sève M, Brouard S, Marsland BJ, Ernst F, Paprotka T, Deplanche K, Fritz A, Siroux V, Boissel JP, Corris PA, Auffray C, Nicod LP; SysCLAD consortium. Prediction of chronic lung allograft dysfunction: a systems medicine challenge. Eur Respir J.
Amplicon analysis: Schmidt, R. et al., Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants. Frontiers in microbiology 5
Transcriptome analysis: Merlot, S. et al., The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation. Journal of experimental botany
Genome analysis: Wang, J. et al., Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans. Journal of Antimicrobial Chemotherapy 69
Amplicon analysis: Herlemann et al. Uncoupling of bacterial and terrigenous dissolved organic matter dynamics in decomposition experiments. PLOS One 9(4)
Transcriptome analysis: Safavi-Hemami et al. Diversity of Conotoxin Gene Superfamilies in the Venomous Snail, Conus victoriae. PLoS ONE 9(2)
Genome analysis: Fujinami et al. Genome Sequence of Deep-Sea Denitrifier Pseudomonas sp. Strain MT-1, Isolated from the Mariana Trench. Genome Announc. 2(6)
Transcriptome analysis: Yamauchi et al. Newly Developed SNP-Based Identification Method of Hop Varieties. ASBC 72(4)
Fish-Project: Roche 454 & MiSeq: Haase et al. Species identification by DNA sequencing (Application of Next Generation Sequencing on Food and Feed Analysis). eFOOD-Lab International (2)
Amplicon analysis: Chaillou et al. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. The ISME Journal
Transcriptome analysis: Amich et al. Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus. PLOS One, 9(8)
Amplicon analysis: Wunderlin et al. Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments. Environ. Microbio. Reports
Amplicon analysis: Fauser et al. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. The Plant Journal, 79 (2)
Transcriptome analysis: Shimizu et al. Qualitative de novo analysis of full length cDNA and quantitative analysis of gene expression for common marmoset (Callithrix jacchus) transcriptomes using parallel long-read technology and short-read sequencing. PLOS One, 9(6)
Amplicon analysis: Gomathi et al. Screening of Indigenous Oxalate Degrading Lactic Acid Bacteria from Human Faeces and South Indian Fermented Foods: Assessment of Probiotic Potential. The Scientific World Journal, 648059
Amplicon analysis: Sugiyama et al. Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field. PLOS One 9(6)
Twin testing: Weber-Lehmann, Schilling, Gradl, Richter, Wiehler, Rolf. Finding the needle in the haystack: Differentiating "identical twins in paternity testing and forensics by ultra-deep next generation sequencings. Forensic Sci. Intl.: Genetics
Genome analysis: Bottacini et al. Comparative genomics of the Bifidobacterium breve taxon. BMC Genomics, 15:170
Amplicon analysis: Holler et al. Metagenomic analysis of the stool microbiome in patients receiving allogeneic SCT: Loss of diversity is associated with use of systemic antibiotics and more pronounced in gastrointestinal GvHD. BBMT 01.030
Genome analysis: Takeuchi et al. Complete Genome Sequence of the Biocontrol Strain Pseudomonas protegens Cab57 Discovered in Japan Reveals Strain-Specific Diversity of This Species. PLOS One 9(4)
2013
Genome analysis: Zhurina et al. High-quality draft genome sequence of Bifidobacterium longum E18, isolated from a healthy adult. Genome Announc. 01084-13
Genome analysis: Sabat et al. Novel organization of the arginine catabolic mobile element and staphylococcal cassette chromosome mec composite island and its horizontal transfer between distinct Staphylococcus aureus genotypes. Antimicrob Agents Chemother. 57 (11)
Genome analysis: Naito et al. De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. Ibaraki 305-8602
Genome analysis: Mondy et al. Genome Sequence of the Quorum-Quenching Agrobacterium tumefaciens Strain WRT31. GenomeA 10.1270
Amplicon analysis: Wunderlin et al. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. environmental microbiology reports 10.1111
Amplicon analysis: Sauvain et al. Bacterial communities in trace metal contaminated lake sediments are dominated by endospore-forming bacteria. Aquat Sci, 10.1007
Amplicon analysis: Bueche et al. Quantification of Endospore-Forming Firmingcutes by Quantitative PCR with the Functional Gene spo0A. Appl. Environ.Microbiol. 79(17)
Transcriptome analysis: Bizuayehu et al. Characterization of Novel Precursor miRNAs Using Next Generation Sequencing and Prediction of miRNA Targets in Atlantic Halibut. PLOS ONE 8(4)
Amplicon analysis: Sedlácek et al. Enterococcus ureilyticus sp. nov and Enterococcus rotai sp. nov., two urease-producing enterococci from the environment. IJSEM 63(Pt 2)
Transcriptome analysis: D'Agostino et al. Genomic analysis of the native European Solanum species, S. dulcamara. BMC Genomics 14:356
Transcriptome analysis: Gould et al. Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition. International Journal for Parasitology [Epub ahead of print]
Amplicon analysis: Heinrichs et al. Analysis of Black Fungal Biofilms Occurring at Domestic Water Taps (I): Compositional Analysis Using Tag-Encoded FLX Amplicon Pyrosequencing. Mycopathologia 1-11
Transcriptome analysis: Passos M et al. Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycospharella musicola: gene assembly, annotation and marker development. BMC Genomics 14:78
Genome analysis (Cosmids): Chi X et al. The muraminomicin biosynthetic gene cluster and enzymatic formation of the 2-deoxyaminoribosyl appendage. Med. Chem. Commun., 4, 239-243
2012
Amplicon analysis: Matyasek et al. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13:722
Genome analysis: Stoeckle et al. Identification of polymorphic microsatellite loci for the endangered Kagu (Rhynochetos jubatus) by high-throughput sequencing. J Ornithol 153:249-253
Transcriptome analysis: Urbarova et al. Digital Marine Bioprospecting: Mining new neurotoxin drug candidates from the transcriptomes of cold-water sea anemones. Marine Drugs 10(10)
Genome analysis: Witzel et al. Genome sequence of Enterobacter radicincitans DSM16656T, a plant growth-promoting endophyte. J. Bacteriol. vol. 194
Genome analysis: Zischka M et al. Complete genome sequence of the porcine isolate Enterococcus faecalis D32. J Bacteriol. vol. 194
Amplicon analysis: Jacoby et al. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 7:12
Genome analysis: Karczmarczyk M et al. Complete nucleotide sequence of pVQS1 containing a quinolone resistance determinant from Salmonella enterica serovar Virchow associated with foreign travel. J Antimicrob Chemother
Genome analysis: Hauser H, Richter DC et al. Comparative genomic analyses of the Taylorellae. Vet Microbiol. Apr 6
Transcriptome analysis: Mutasa-Göttgens E et al. A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13:99
Genome analysis: Volozhantsev NV et al. Molecular Characterization of Podoviral Bacteriophages Virulent for Clostridium perfringens and Their Comparison with Members of the Picovirinae. PLoS ONE 7(5)
Transcriptome analysis: Hroudova M et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan JellyfishCraspedacusta sowerbyi. PLoS ONE 7(4)
Amplicon analysis: Håkansson Å et al. Blueberry Husks and Probiotics Attenuate Colorectal Inflammation and Oncogenesis, and Liver Injuries in Rats Exposed to Cycling DSS-Treatment. PLoS ONE 7(3)
Genome analysis: Morohoshi T et al. Complete genome sequence and characterization of the N-acylhomoserine lactone-degrading gene of the potato leaf-associated Solibacillus silvestris. J Biosci Bioeng. Jan;113(1):20-5
2011
Genome analysis: Zhurina et al. Complete genome sequence of Bifidobacterium bifidum S17. J Bacteriol. 193 (1)
Transcriptome analysis: Windisch H et al. Thermal acclimation in Antartic fish: transcriptomic profiling of metabolic pathways. AJP - Regu Physiol 301, 5
Transcriptome analysis: Kinoshita S et al. Deep Sequencing of ESTs from Nacreous and Prismatic Layer Producing Tissues and a Screen for Novel Shell Formation-Related Genes in the Pearl Oyster. PLoS ONE 6(6)
Genome analysis: Amlacher, S. et al. Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 146, July 2011, p 277-289
Genome analysis: Morohoshi, T. et al. Genome sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves. Journal of bacteriology, p. 2072–2073
Transcriptome analysis: Kuzina V. et al. Barbarea vulgaris linkage map and quantitative trait loci for saponins, glucosinolates, hairiness and resistance to the herbivore Phyllotreta nemorum. Phytochemistry. 2011 Feb 72, 2-3
Genome analysis & gap closing services: Schoen, C.,Weber-Lehmann, J., Strittmatter, A., et al. Whole-genome sequence of the transformableNeisseria meningitidisserogroup A strain WUE2594. Journal of Bacteriology (JB), 27-01-2011
2010
Transcriptome analysis: Toulza, E. et al. Gene expression in proliferating cells of the dinoflagellate Alexandrium catenella (Dinophyceae). Applied and Environmental Microbiology, p4521-4529
Amplicon analysis: Medinger, R., Ottenwälder, B. et al. Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of Eukaryotic microorganisms. Molecular Ecology, 19 Suppl. 1: 32-40
Amplicon analysis: Nolte, V., Ottenwälder, B. et al. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology; 19(14):2908-2915
Fosmid sequencing: Beloqui, A., Strittmatter, AW. et al. Diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. Appl Environ Microbiol. 76(17):5934-46. Epub 2010 Jul 9
Transcriptome analysis: Young, N.D. et al. Elucidating the transcriptome of Fasciola hepatica – A key to fundamental and biotechnological discoveries for a neglected parasite. Biotechnology Advances 28, 222-231
Transcriptome analysis: Elmer KR et al. Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times. BMC Biol. 2010 May 12; 8:60
Genome analysis: Nowrousian, M. et al. De novo Assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genetics, April 2010, Volume 6, Issue 4
Transcriptome analysis: Johansen, S.D., Emblem, A., Karlsen, B.O., Okkenhaug, S., Hansen, H., Moum, T., Coucheron, D.H., Seternes, O.M. Approaching marine bioprospecting in hexacorals by RNA deep sequencing. New Biotechnology, March 2010
Before 2010
Genome analysis: De Schutter K., Glinka, S., Weber-Lehmann, J. et al. Genome Sequence of the recombinant protein production hostPichia pastoris. Nature Biotechnology (2009) 27(6), 561-566
Genome analysis: Gordon, P.M. et al. Disease-specific motifs an be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopahties. Nucleic Acids Res (2009) 37(2), 550-556
Genome analysis: Beck, J., Urnovitz, H.B., Riggert, J., Clerici, M., Schütz, E. Profile of circulating DNA in apparently healthy individuals. Clin Chem (2009) 55(4), 730-738
Genome analysis: Steuernagel B. et al. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics 2009, 10:547
Transcriptome analysis: Torres, T.T., Ottenwälder, B. et al. Gene expression profiling by massively parallel sequencing. Genome Research (2008) 18: 172-177
Genome analysis: Waterfield NR, et al. Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts. PNAS (2008)
Transcriptome analysis: Ender, C. et al. A human snoRNA with microRNA-like functions. MolCell (2008)
Transcriptome analysis: Gassler, N., Kopitz, J., Tehrani, A., Ottenwälder, B., et. al. Expression of acyl-CoA synthetase 5 reflects the state of villus architecture in human small intestine. J. Pathol. (2004)
Genome analysis: Horn M. et. al. Illuminating the evolutionary history of chlamydiae. Science (2004)
Transcriptome analysis: Dietrich G. et. al. Transcriptome analysis of Neisseria meningitidis during infection. J Bacteriol. (2003)