Peter J Oefner

Peter J Oefner

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Peter J Oefner

Publications by authors named "Peter J Oefner"

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Loss-Function Learning for Digital Tissue Deconvolution.

J Comput Biol 2020 Jan 29. Epub 2020 Jan 29.

Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1089/cmb.2019.0462DOI Listing
January 2020

DTD: An R Package for Digital Tissue Deconvolution.

J Comput Biol 2020 Jan 29. Epub 2020 Jan 29.

Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1089/cmb.2019.0469DOI Listing
January 2020

Quantification and C-Tracer analysis of total reduced glutathione by HPLC-QTOFMS/MS.

Anal Chim Acta 2019 Nov 3;1080:127-137. Epub 2019 Jul 3.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.aca.2019.07.001DOI Listing
November 2019

Potential biomarkers to predict outcome of faecal microbiota transfer for recurrent Clostridioides difficile infection.

Dig Liver Dis 2019 07 26;51(7):944-951. Epub 2019 Jan 26.

Department I of Internal Medicine, University Hospital of Cologne, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15908658193004
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http://dx.doi.org/10.1016/j.dld.2019.01.012DOI Listing
July 2019

Degradation of D-2-hydroxyglutarate in the presence of isocitrate dehydrogenase mutations.

Sci Rep 2019 May 15;9(1):7436. Epub 2019 May 15.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.

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http://dx.doi.org/10.1038/s41598-019-43891-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6520482PMC
May 2019

A Novel Metabolic Signature To Predict the Requirement of Dialysis or Renal Transplantation in Patients with Chronic Kidney Disease.

J Proteome Res 2019 04 12;18(4):1796-1805. Epub 2019 Mar 12.

Institute of Genetic Epidemiology, Department of Biometry, Epidemiology, and Medical Bioinformatics, Faculty of Medicine and Medical Center , University of Freiburg , Freiburg 79106 , Germany.

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http://dx.doi.org/10.1021/acs.jproteome.8b00983DOI Listing
April 2019

Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma.

BMC Cancer 2019 Apr 5;19(1):322. Epub 2019 Apr 5.

Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany.

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http://dx.doi.org/10.1186/s12885-019-5537-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451309PMC
April 2019

Limitation of TCA Cycle Intermediates Represents an Oxygen-Independent Nutritional Antibacterial Effector Mechanism of Macrophages.

Cell Rep 2019 03;26(13):3502-3510.e6

Mikrobiologisches Institut, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.02.103DOI Listing
March 2019

Serotonin and tryptophan metabolites, autoantibodies and gut microbiome in APECED.

Endocr Connect 2019 Jan;8(1):69-77

Department of Dermatology, Allergology and Venereology, University of Helsinki, and Helsinki University Central Hospital, Helsinki, Finland.

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https://ec.bioscientifica.com/view/journals/ec/aop/ec-18-051
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http://dx.doi.org/10.1530/EC-18-0513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365670PMC
January 2019

Amino Acid Analysis in Physiological Samples by GC-MS with Propyl Chloroformate Derivatization and iTRAQ-LC-MS/MS.

Methods Mol Biol 2019 ;2030:173-190

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-9639-1_14DOI Listing
January 2019

Systematic Evaluation of Non-Uniform Sampling Parameters in the Targeted Analysis of Urine Metabolites by H,H 2D NMR Spectroscopy.

Sci Rep 2018 03 9;8(1):4249. Epub 2018 Mar 9.

Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.

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http://dx.doi.org/10.1038/s41598-018-22541-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844889PMC
March 2018

From Discovery to Translation: Characterization of C-Mannosyltryptophan and Pseudouridine as Markers of Kidney Function.

Sci Rep 2017 12 12;7(1):17400. Epub 2017 Dec 12.

Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Hugstetter Str. 49, 79106, Freiburg, Germany.

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http://dx.doi.org/10.1038/s41598-017-17107-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727198PMC
December 2017

Srebp-controlled glucose metabolism is essential for NK cell functional responses.

Nat Immunol 2017 Nov 18;18(11):1197-1206. Epub 2017 Sep 18.

School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland.

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http://dx.doi.org/10.1038/ni.3838DOI Listing
November 2017

Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints.

J Proteome Res 2017 10 7;16(10):3596-3605. Epub 2017 Sep 7.

Department of Physics, University of Regensburg , Universitätsstraße 31, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.7b00325DOI Listing
October 2017

Quantification of Metabolites by NMR Spectroscopy in the Presence of Protein.

J Proteome Res 2017 04 24;16(4):1784-1796. Epub 2017 Mar 24.

Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.7b00057DOI Listing
April 2017

Biological and clinical significance of tryptophan-catabolizing enzymes in cutaneous T-cell lymphomas.

Oncoimmunology 2017 10;6(3):e1273310. Epub 2017 Feb 10.

Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital , Helsinki, Finland.

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http://dx.doi.org/10.1080/2162402X.2016.1273310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384345PMC
February 2017

Antithymocyte Globulin Induces a Tolerogenic Phenotype in Human Dendritic Cells.

Int J Mol Sci 2016 Dec 11;17(12). Epub 2016 Dec 11.

Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany.

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http://www.mdpi.com/1422-0067/17/12/2081
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http://dx.doi.org/10.3390/ijms17122081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187881PMC
December 2016

Testing Suitability of Cell Cultures for SILAC-Experiments Using SWATH-Mass Spectrometry.

Methods Mol Biol 2016 ;1394:101-108

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053, Regensburg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-3341-9_8DOI Listing
October 2016

Optimizing the SWATH-MS-workflow for label-free proteomics.

J Proteomics 2016 08 21;145:137-140. Epub 2016 Apr 21.

Institute of Functional Genomics, University of Regensburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jprot.2016.04.021DOI Listing
August 2016

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria.

Microbiome 2016 06 21;4(1):28. Epub 2016 Jun 21.

Chair of Statistical Bioinformatics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.

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http://dx.doi.org/10.1186/s40168-016-0175-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915049PMC
June 2016

Renal Fanconi Syndrome Is Caused by a Mistargeting-Based Mitochondriopathy.

Cell Rep 2016 05 5;15(7):1423-1429. Epub 2016 May 5.

Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.04.037DOI Listing
May 2016

Ferritin-Mediated Iron Sequestration Stabilizes Hypoxia-Inducible Factor-1α upon LPS Activation in the Presence of Ample Oxygen.

Cell Rep 2015 Dec 25;13(10):2048-55. Epub 2015 Nov 25.

Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054 Erlangen, Germany; Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg and University of Regensburg, 93053 Regensburg, Germany. Electronic address:

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http://www.cell.com/cms/attachment/2041386719/2055161577/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S221112471501292
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http://dx.doi.org/10.1016/j.celrep.2015.11.005DOI Listing
December 2015

Enhanced metabolite profiling using a redesigned atmospheric pressure chemical ionization source for gas chromatography coupled to high-resolution time-of-flight mass spectrometry.

Anal Bioanal Chem 2015 Sep 21;407(22):6669-80. Epub 2015 Jun 21.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053, Regensburg, Germany.

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http://dx.doi.org/10.1007/s00216-015-8824-xDOI Listing
September 2015

Data Normalization of (1)H NMR Metabolite Fingerprinting Data Sets in the Presence of Unbalanced Metabolite Regulation.

J Proteome Res 2015 Aug 22;14(8):3217-28. Epub 2015 Jul 22.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.5b00192DOI Listing
August 2015

Identification of Plasma Metabolites Prognostic of Acute Kidney Injury after Cardiac Surgery with Cardiopulmonary Bypass.

J Proteome Res 2015 Jul 12;14(7):2897-905. Epub 2015 Jun 12.

†Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.5b00219DOI Listing
July 2015

Polymorphisms within the APOBR gene are highly associated with milk levels of prognostic ketosis biomarkers in dairy cows.

Physiol Genomics 2015 Apr 10;47(4):129-37. Epub 2015 Feb 10.

Institute of Animal Breeding and Husbandry, Christian Albrecht University, Kiel, Germany; and.

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http://dx.doi.org/10.1152/physiolgenomics.00126.2014DOI Listing
April 2015

Selenophosphate synthetase in the male accessory glands of an insect without selenoproteins.

J Insect Physiol 2014 Dec 11;71:46-51. Epub 2014 Oct 11.

Biologie I, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jinsphys.2014.09.012DOI Listing
December 2014

Collagen XVI induces expression of MMP9 via modulation of AP-1 transcription factors and facilitates invasion of oral squamous cell carcinoma.

PLoS One 2014 23;9(1):e86777. Epub 2014 Jan 23.

Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany ; Center for Medical Biotechnology, BioPark I, Regensburg, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086777PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900656PMC
September 2014

Continuous water infusion enhances atmospheric pressure chemical ionization of methyl chloroformate derivatives in gas chromatography coupled to time-of-flight mass spectrometry-based metabolomics.

Anal Chem 2014 Sep 3;86(18):9186-95. Epub 2014 Sep 3.

Institute of Functional Genomics, University of Regensburg , Josef-Engert-Strasse 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/ac502133rDOI Listing
September 2014

What identity crisis? Rapidly mutating Y-STRs facilitate differentiation of males.

Authors:
Peter J Oefner

Hum Mutat 2014 Aug;35(8)

Universität Regensburg, Germany.

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http://dx.doi.org/10.1002/humu.22412DOI Listing
August 2014

Regulation and function of the atypical cadherin FAT1 in hepatocellular carcinoma.

Carcinogenesis 2014 Jun 3;35(6):1407-15. Epub 2014 Mar 3.

Department of Internal Medicine I, University Hospital Regensburg, 93053 Regensburg, Germany, Institute of Pharmacy, University of Regensburg, 93053 Regensburg, Germany, Institute of Surgical Pathology, University Hospital Zurich, 8091 Zurich, Switzerland, Institute of Pathology, University Hospital Erlangen, 91054 Erlangen, Germany, Department of Pediatrics and Juvenile Medicine, University Hospital Regensburg, 93053 Regensburg, Germany and Institute of Functional Genomics and Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany

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http://dx.doi.org/10.1093/carcin/bgu054DOI Listing
June 2014

N-cadherin promoter polymorphisms and risk of osteoarthritis.

FASEB J 2014 Feb 22;28(2):683-91. Epub 2013 Oct 22.

2Institute of Pathology, University of Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany.

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http://dx.doi.org/10.1096/fj.13-238295DOI Listing
February 2014

Mistargeting of peroxisomal EHHADH and inherited renal Fanconi's syndrome.

N Engl J Med 2014 Jan;370(2):129-38

From the Centre for Nephrology (E.D.K., H.C.S., D.B., G.J., H.C., A.M.H., R.J.U., R.K.) and Institute of Child Health (D.B., R.K.), University College London, and Biomolecular Medicine, Imperial College London (S.L.R., A.D.W., E.H., J.K.N.) - both in London; the Departments of Medical Cell Biology (M.R., C.B., D.P., C.S., R. Warth), Internal Medicine III (K.R.), Internal Medicine II (S.W.R.), and Molecular and Cellular Anatomy (R. Witzgall) and the Institutes of Functional Genomics (J.R., K.E., N.A., P.J.O., K.D.) and Pathology (J.S.), University of Regensburg, and the Department of Radiology, Barmherzige Brueder Hospital (N.Z.) - all in Regensburg, Germany; the National Human Genome Research Institute (A.H.-W., S.L.R., H.C.S., K.O., I.B., D.M.K., W.A.G., R.K.) and National Heart, Lung, and Blood Institute (Y.I.), National Institutes of Health, Bethesda, MD; the Division of Pediatric Nephrology, University of Florida, Jacksonville (A.T., M.I.); the Genome Biology Department, Australian National University, Canberra, ACT, Australia (M.A.-B.); Kitasato University Medical Center, Saitama, Japan (H.N.); and the Department of Pathology, Northwestern University, Chicago (Y.J., J.K.R.).

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http://dx.doi.org/10.1056/NEJMoa1307581DOI Listing
January 2014

Correlations between milk and plasma levels of amino and carboxylic acids in dairy cows.

J Proteome Res 2013 Nov 23;12(11):5223-32. Epub 2013 Aug 23.

Institute of Functional Genomics, University of Regensburg , Regensburg, Germany.

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http://dx.doi.org/10.1021/pr4006537DOI Listing
November 2013

Distinct metabolic differences between various human cancer and primary cells.

Electrophoresis 2013 Oct 12;34(19):2836-47. Epub 2013 Sep 12.

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1002/elps.201300228DOI Listing
October 2013

Diclofenac inhibits lactate formation and efficiently counteracts local immune suppression in a murine glioma model.

Int J Cancer 2013 Feb 21;132(4):843-53. Epub 2012 Jul 21.

Department of Neurology, University Medical Centre of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1002/ijc.27712DOI Listing
February 2013

Performance evaluation of algorithms for the classification of metabolic 1H NMR fingerprints.

J Proteome Res 2012 Dec 12;11(12):6242-51. Epub 2012 Nov 12.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/pr3009034DOI Listing
December 2012

State-of-the art data normalization methods improve NMR-based metabolomic analysis.

Metabolomics 2012 Jun 12;8(Suppl 1):146-160. Epub 2011 Aug 12.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1007/s11306-011-0350-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337420PMC
June 2012

Early changes in the liver-soluble proteome from mice fed a nonalcoholic steatohepatitis inducing diet.

Proteomics 2012 May;12(9):1437-51

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, Regensburg, Germany.

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http://doi.wiley.com/10.1002/pmic.201100628
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http://dx.doi.org/10.1002/pmic.201100628DOI Listing
May 2012

Amino acid analysis in physiological samples by GC-MS with propyl chloroformate derivatization and iTRAQ-LC-MS/MS.

Methods Mol Biol 2012 ;828:165-81

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1007/978-1-61779-445-2_15DOI Listing
March 2012

Metabolic fingerprinting using comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

Methods Mol Biol 2012 ;815:399-411

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, Regensburg 93053, Germany.

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http://dx.doi.org/10.1007/978-1-61779-424-7_29DOI Listing
March 2012

Comprehensive two-dimensional gas chromatography in metabolomics.

Anal Bioanal Chem 2012 Feb 17;402(6):1993-2013. Epub 2012 Jan 17.

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1007/s00216-011-5630-yDOI Listing
February 2012

Performance evaluation of gas chromatography-atmospheric pressure chemical ionization-time-of-flight mass spectrometry for metabolic fingerprinting and profiling.

Anal Chem 2011 Oct 9;83(19):7514-22. Epub 2011 Sep 9.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Straße 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/ac201719dDOI Listing
October 2011

Comparison of two algorithmic data processing strategies for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry.

J Chromatogr A 2011 Sep 12;1218(39):7031-8. Epub 2011 Aug 12.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1016/j.chroma.2011.08.006DOI Listing
September 2011

Glucocorticoid-induced alterations in mitochondrial membrane properties and respiration in childhood acute lymphoblastic leukemia.

Biochim Biophys Acta 2011 Jun 13;1807(6):719-25. Epub 2011 Jan 13.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1016/j.bbabio.2010.12.010DOI Listing
June 2011

Metabolite extraction from adherently growing mammalian cells for metabolomics studies: optimization of harvesting and extraction protocols.

Anal Bioanal Chem 2011 Jan 2;399(3):1127-39. Epub 2010 Dec 2.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str. 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1007/s00216-010-4425-xDOI Listing
January 2011

Comparison of serum versus plasma collection in gas chromatography--mass spectrometry-based metabolomics.

Electrophoresis 2010 Jul;31(14):2365-73

Institute of Functional Genomics, University of Regensburg, Regensburg, Germany.

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http://dx.doi.org/10.1002/elps.200900778DOI Listing
July 2010

Quantification of intermediates of the methionine and polyamine metabolism by liquid chromatography-tandem mass spectrometry in cultured tumor cells and liver biopsies.

J Chromatogr A 2010 May 18;1217(19):3282-8. Epub 2010 Jan 18.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1016/j.chroma.2010.01.025DOI Listing
May 2010

Comparison of derivatization and chromatographic methods for GC-MS analysis of amino acid enantiomers in physiological samples.

J Chromatogr B Analyt Technol Biomed Life Sci 2010 May 18;878(15-16):1103-12. Epub 2010 Mar 18.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1016/j.jchromb.2010.03.021DOI Listing
May 2010

ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly.

BMC Bioinformatics 2009 Dec 22;10:440. Epub 2009 Dec 22.

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str, 9, D-93053 Regensburg, Germany.

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http://dx.doi.org/10.1186/1471-2105-10-440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087351PMC
December 2009

Urinary metabolite quantification employing 2D NMR spectroscopy.

Anal Chem 2008 Dec;80(23):9288-97

Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany.

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http://dx.doi.org/10.1021/ac801627cDOI Listing
December 2008