Remy Bruggmann

Remy Bruggmann

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Remy Bruggmann

Remy Bruggmann

Publications by authors named "Remy Bruggmann"

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Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri.

Sci Rep 2019 Nov 5;9(1):16040. Epub 2019 Nov 5.

Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland.

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http://dx.doi.org/10.1038/s41598-019-52572-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6831594PMC
November 2019

Single cell transcriptome atlas of the larval brain.

Elife 2019 11 20;8. Epub 2019 Nov 20.

Department of Biology, University of Fribourg, Fribourg, Switzerland.

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http://dx.doi.org/10.7554/eLife.50354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894929PMC
November 2019

CD8 T cells expand stem and progenitor cells in favorable but not adverse risk acute myeloid leukemia.

Leukemia 2019 Oct 15;33(10):2379-2392. Epub 2019 Mar 15.

Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1038/s41375-019-0441-9DOI Listing
October 2019

Adult sox10 Cardiomyocytes Contribute to Myocardial Regeneration in the Zebrafish.

Cell Rep 2019 Oct;29(4):1041-1054.e5

Spanish National Centre for Cardiovascular Research Carlos III (CNIC-ISCIII), 28029 Madrid, Spain; Institute of Anatomy, University of Bern, 3012 Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.09.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856760PMC
October 2019

Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes.

Int J Syst Evol Microbiol 2019 Mar 28;69(3):652-661. Epub 2019 Jan 28.

2​Laboratory of Fundamental and Applied Research in Chemical Ecology, University of Neuchâtel, Neuchâtel, Switzerland.

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http://dx.doi.org/10.1099/ijsem.0.003154DOI Listing
March 2019

Contribution of epigenetic variation to adaptation in Arabidopsis.

Nat Commun 2018 10 25;9(1):4446. Epub 2018 Oct 25.

Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.

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http://dx.doi.org/10.1038/s41467-018-06932-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6202389PMC
October 2018

Conversion of Methionine to Cysteine in Depends on the Highly Mobile Gene Cluster.

Front Microbiol 2018 17;9:2415. Epub 2018 Oct 17.

Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.

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https://www.frontiersin.org/article/10.3389/fmicb.2018.02415
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http://dx.doi.org/10.3389/fmicb.2018.02415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200037PMC
October 2018

Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians.

Genome Biol Evol 2018 09 1;10(9):2205-2217. Epub 2018 Sep 1.

Department of Biology, Institute of Zoology, University of Fribourg, Switzerland.

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http://dx.doi.org/10.1093/gbe/evy170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125248PMC
September 2018

The genome of Naegleria lovaniensis, the basis for a comparative approach to unravel pathogenicity factors of the human pathogenic amoeba N. fowleri.

BMC Genomics 2018 Sep 5;19(1):654. Epub 2018 Sep 5.

Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland.

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http://dx.doi.org/10.1186/s12864-018-4994-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125883PMC
September 2018

Tumor Necrosis Factor-α Initiates miRNA-mRNA Signaling Cascades in Obstruction-Induced Bladder Dysfunction.

Am J Pathol 2018 08 18;188(8):1847-1864. Epub 2018 Jun 18.

Urology Research Laboratory, Department for BioMedical Research, University of Bern, Bern, Switzerland; Department of Urology, University Hospital, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2018.05.008DOI Listing
August 2018

Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in .

Genetics 2018 08 20;209(4):1167-1181. Epub 2018 Jun 20.

Department of Biology, University of Fribourg, CH-1700, Switzerland

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http://dx.doi.org/10.1534/genetics.118.301106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063240PMC
August 2018

Accumulation of Deleterious Mutations During Bacterial Range Expansions.

Genetics 2017 10 16;207(2):669-684. Epub 2017 Aug 16.

Computational and Molecular Population Genetics, Institute of Ecology an Evolution, University of Berne, 3012, Switzerland

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http://dx.doi.org/10.1534/genetics.117.300144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629331PMC
October 2017

Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.

Proc Natl Acad Sci U S A 2017 10 15;114(40):E8320-E8322. Epub 2017 Sep 15.

Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, CH-8952 Schlieren-Zurich, Switzerland;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1713830114
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http://dx.doi.org/10.1073/pnas.1713830114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635930PMC
October 2017

Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland.

Vet Microbiol 2017 Sep 29;208:137-145. Epub 2017 Jul 29.

NeuroCenter, Division of Neurological Sciences, Vetsuisse Faculty Bern, Bremgartenstrasse 109a, University of Bern, CH 3012 Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.vetmic.2017.07.027DOI Listing
September 2017

Avoiding the pitfalls of gene set enrichment analysis with SetRank.

BMC Bioinformatics 2017 Mar 4;18(1):151. Epub 2017 Mar 4.

Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012, Berne, Switzerland.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s12859-017-1571-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336655PMC
March 2017

The Histidine Decarboxylase Gene Cluster of Was Gained by Horizontal Gene Transfer and Is Mobile within the Species.

Front Microbiol 2017 17;8:218. Epub 2017 Feb 17.

Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern Bern, Switzerland.

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http://dx.doi.org/10.3389/fmicb.2017.00218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313534PMC
February 2017

Characterization and Transcriptomic Analysis of Porcine Blood Conventional and Plasmacytoid Dendritic Cells Reveals Striking Species-Specific Differences.

J Immunol 2016 12 11;197(12):4791-4806. Epub 2016 Nov 11.

Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland;

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http://dx.doi.org/10.4049/jimmunol.1600672DOI Listing
December 2016

Maize Cytolines Unmask Key Nuclear Genes That Are under the Control of Retrograde Signaling Pathways in Plants.

Genome Biol Evol 2016 11 17;8(11):3256-3270. Epub 2016 Nov 17.

Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland

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http://dx.doi.org/10.1093/gbe/evw245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203784PMC
November 2016

Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects.

Food Microbiol 2016 Oct 26;59:213-23. Epub 2016 May 26.

Institute for Food Sciences, Agroscope, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.fm.2016.05.013DOI Listing
October 2016

Full-genome based molecular characterization of encephalitis-associated bovine astroviruses.

Infect Genet Evol 2016 10 1;44:162-168. Epub 2016 Jul 1.

NeuroCenter, Division of Neurological Sciences, Vetsuisse Faculty, University of Bern,Bremgartenstrasse 109a, CH-3012 Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.meegid.2016.06.052DOI Listing
October 2016

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics.

Virology 2016 06 18;493:22-30. Epub 2016 Mar 18.

Neurocenter, Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2016.03.009DOI Listing
June 2016

Clinical sequencing: is WGS the better WES?

Hum Genet 2016 Mar 7;135(3):359-62. Epub 2016 Jan 7.

Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, 8952, Schlieren-Zurich, Switzerland.

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http://dx.doi.org/10.1007/s00439-015-1631-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757617PMC
March 2016

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration.

Cell Host Microbe 2016 Mar;19(3):409-23

Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2016.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826034PMC
March 2016

Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae.

Nat Commun 2016 Feb 11;7:10687. Epub 2016 Feb 11.

Department of Biology, Institute of Zoology, University of Fribourg, Chemin du Musee 10, Fribourg CH-1700, Switzerland.

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http://dx.doi.org/10.1038/ncomms10687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753250PMC
February 2016

Identification of a second encephalitis-associated astrovirus in cattle.

Emerg Microbes Infect 2016 Jan 20;5:e71. Epub 2016 Jan 20.

Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern CH-3012, Switzerland.

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http://dx.doi.org/10.1038/emi.2017.56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603821PMC
January 2016

New insights into the performance of human whole-exome capture platforms.

Nucleic Acids Res 2015 Jun 27;43(11):e76. Epub 2015 Mar 27.

Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich CH-8952, Switzerland Department of Cardiovascular Surgery, University Hospital, Berne CH-3010, Switzerland Zurich Center for Integrative Human Physiology, University of Zurich, Zurich CH-8057, Switzerland

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http://dx.doi.org/10.1093/nar/gkv216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477645PMC
June 2015

Regulation of 11β-hydroxysteroid dehydrogenase type 2 by microRNA.

Hypertension 2014 Oct 30;64(4):860-6. Epub 2014 Jun 30.

From the Department of Nephrology, Hypertension, and Clinical Pharmacology (M.R., T.A., D.M., F.J.F., B.V., B.M.F.) and Department of Biology and Bioinformatics (S.N., R.B.), University of Bern, Bern, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland (S.N.); and Department of Clinical Research, University Hospital Bern, Bern, Switzerland (B.M.F.)

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http://dx.doi.org/10.1161/HYPERTENSIONAHA.114.00002DOI Listing
October 2014

Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe.

J Clin Microbiol 2014 Sep 2;52(9):3318-24. Epub 2014 Jul 2.

Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland

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http://dx.doi.org/10.1128/JCM.01195-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313157PMC
September 2014

In search of epigenetic marks in testes and sperm cells of differentially fed boars.

PLoS One 2013 4;8(11):e78691. Epub 2013 Nov 4.

Department of Biology, Bioinformatics, University of Bern, Berne, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078691PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817071PMC
August 2014

A frameshift mutation in the cubilin gene (CUBN) in Beagles with Imerslund-Gräsbeck syndrome (selective cobalamin malabsorption).

Anim Genet 2014 Feb 27;45(1):148-50. Epub 2013 Oct 27.

Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.

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http://dx.doi.org/10.1111/age.12094DOI Listing
February 2014

Streaming support for data intensive cloud-based sequence analysis.

Biomed Res Int 2013 24;2013:791051. Epub 2013 Apr 24.

Center for Informatics Sciences, Nile University, Giza, Egypt.

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http://dx.doi.org/10.1155/2013/791051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655485PMC
December 2013

SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing.

Genetics 2012 Aug 29;191(4):1381-6. Epub 2012 May 29.

Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland.

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http://dx.doi.org/10.1534/genetics.112.141341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416015PMC
August 2012

Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex.

BMC Genomics 2012 May 4;13:166. Epub 2012 May 4.

Forest Pathology and Dendrology, Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-13-166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434094PMC
May 2012

Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice.

Mol Genet Genomics 2011 Dec 12;286(5-6):433-47. Epub 2011 Nov 12.

Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.

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http://link.springer.com/content/pdf/10.1007/s00438-011-0654
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http://link.springer.com/10.1007/s00438-011-0654-8
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http://dx.doi.org/10.1007/s00438-011-0654-8DOI Listing
December 2011

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems.

BMC Genomics 2011 Jul 8;12:356. Epub 2011 Jul 8.

Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA.

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http://dx.doi.org/10.1186/1471-2164-12-356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143107PMC
July 2011

Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites.

Plant Mol Biol 2006 Nov 29;62(4-5):561-78. Epub 2006 Aug 29.

Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, CH-8000 Zurich, Switzerland.

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http://dx.doi.org/10.1007/s11103-006-9045-7DOI Listing
November 2006

Analysis of epidermis- and mesophyll-specific transcript accumulation in powdery mildew-inoculated wheat leaves.

Plant Mol Biol 2005 May;58(2):247-67

Institute of Plant Biology, University of Zurich, Zürich, Switzerland.

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http://dx.doi.org/10.1007/s11103-005-3099-9DOI Listing
May 2005