Reinhard Guthke

Reinhard Guthke

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Reinhard Guthke

Reinhard Guthke

Publications by authors named "Reinhard Guthke"

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Comparative Genomics of Serial Isolates and the Rapid Acquisition of Echinocandin Resistance during Therapy.

Antimicrob Agents Chemother 2019 02 29;63(2). Epub 2019 Jan 29.

National Reference Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany

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http://aac.asm.org/lookup/doi/10.1128/AAC.01628-18
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http://dx.doi.org/10.1128/AAC.01628-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355595PMC
February 2019

Proteomics of Conidia-containing Phagolysosomes Identifies Processes Governing Immune Evasion.

Mol Cell Proteomics 2018 06 5;17(6):1084-1096. Epub 2018 Mar 5.

From the ‡Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany;

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http://dx.doi.org/10.1074/mcp.RA117.000069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986250PMC
June 2018

Impairing L-Threonine Catabolism Promotes Healthspan through Methylglyoxal-Mediated Proteohormesis.

Cell Metab 2018 04 15;27(4):914-925.e5. Epub 2018 Mar 15.

Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2018.02.004DOI Listing
April 2018

Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales.

Front Microbiol 2018 13;9:217. Epub 2018 Feb 13.

Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2018.00217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819561PMC
February 2018

DeltaMS: a tool to track isotopologues in GC- and LC-MS data.

Metabolomics 2018 02 27;14(4):41. Epub 2018 Feb 27.

Department of Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena,, Lessingstr. 8, 07743, Jena, Germany.

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http://dx.doi.org/10.1007/s11306-018-1336-xDOI Listing
February 2018

Zonation of hepatic fat accumulation: insights from mathematical modelling of nutrient gradients and fatty acid uptake.

J R Soc Interface 2017 08;14(133)

Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany.

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http://dx.doi.org/10.1098/rsif.2017.0443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5582132PMC
August 2017

Global Transcriptional Response of Human Liver Cells to Ethanol Stress of Different Strength Reveals Hormetic Behavior.

Alcohol Clin Exp Res 2017 May 27;41(5):883-894. Epub 2017 Mar 27.

Bioreactor Group , Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.

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http://dx.doi.org/10.1111/acer.13361DOI Listing
May 2017

Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions.

Brief Funct Genomics 2017 03;16(2):57-69

Leibniz-Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute, Jena, Germany.

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http://dx.doi.org/10.1093/bfgp/elv064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439285PMC
March 2017

Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells.

Front Microbiol 2017 23;8:270. Epub 2017 Feb 23.

Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2017.00270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322194PMC
February 2017

Candida albicans infection leads to barrier breakdown and a MAPK/NF-κB mediated stress response in the intestinal epithelial cell line C2BBe1.

Cell Microbiol 2016 07 26;18(7):889-904. Epub 2016 Feb 26.

Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.

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http://dx.doi.org/10.1111/cmi.12566DOI Listing
July 2016

Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence.

Biol Res 2016 Jul 28;49(1):34. Epub 2016 Jul 28.

Leibniz Institute for Age Research-Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.

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http://dx.doi.org/10.1186/s40659-016-0095-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4963952PMC
July 2016

Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus.

PLoS One 2015 10;10(9):e0136932. Epub 2015 Sep 10.

Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Str. 23, 07745, Jena, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136932PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565559PMC
May 2016

Proteomic Profiling of Serological Responses to Aspergillus fumigatus Antigens in Patients with Invasive Aspergillosis.

J Proteome Res 2016 05 24;15(5):1580-91. Epub 2016 Mar 24.

Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI) , 07745 Jena, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.6b00042DOI Listing
May 2016

Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens.

Front Microbiol 2016 22;7:570. Epub 2016 Apr 22.

Research Group Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2016.00570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4840211PMC
May 2016

Data- and knowledge-based modeling of gene regulatory networks: an update.

EXCLI J 2015 2;14:346-78. Epub 2015 Mar 2.

Research Group Systems Biology / Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

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http://www.excli.de/vol14/Guthke_02032015_proof.pdf
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http://dx.doi.org/10.17179/excli2015-168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817425PMC
April 2016

How to Predict Molecular Interactions between Species?

Front Microbiol 2016 31;7:442. Epub 2016 Mar 31.

Research Group Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany.

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http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00
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http://dx.doi.org/10.3389/fmicb.2016.00442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814556PMC
April 2016

Draft Genome Sequences of Fungus Aspergillus calidoustus.

Genome Announc 2016 Mar 10;4(2). Epub 2016 Mar 10.

Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, HKI, Jena, Germany

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http://dx.doi.org/10.1128/genomeA.00102-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786660PMC
March 2016

Editorial: Computational Systems Biology of Pathogen-Host Interactions.

Front Microbiol 2016 4;7:21. Epub 2016 Feb 4.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2016.00021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740391PMC
February 2016

Longitudinal RNA-Seq Analysis of Vertebrate Aging Identifies Mitochondrial Complex I as a Small-Molecule-Sensitive Modifier of Lifespan.

Cell Syst 2016 02 24;2(2):122-32. Epub 2016 Feb 24.

Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; Scuola Normale Superiore, Laboratory of Biology, c/o Istituto di Biofisica del CNR, via Moruzzi 1, 56124 Pisa, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.01.014DOI Listing
February 2016

Computing the various pathways of penicillin synthesis and their molar yields.

Biotechnol Bioeng 2016 Jan 19;113(1):173-81. Epub 2015 Aug 19.

Department of Bioinformatics, University of Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany.

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http://dx.doi.org/10.1002/bit.25694DOI Listing
January 2016

Draft Genome Sequence of the Fungus Penicillium brasilianum MG11.

Genome Announc 2015 Sep 3;3(5). Epub 2015 Sep 3.

Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany Leibniz Junior Research Group-Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Jena, Germany

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http://dx.doi.org/10.1128/genomeA.00724-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559720PMC
September 2015

Hormetic effect of rotenone in primary human fibroblasts.

Immun Ageing 2015 16;12:11. Epub 2015 Sep 16.

Leibniz-Institute for Age Research - Fritz Lipmann Institute e.V. (FLI), Beutenbergstrasse 11, D-07745 Jena, Germany.

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http://dx.doi.org/10.1186/s12979-015-0038-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572608PMC
September 2015

Fuzzy modeling reveals a dynamic self-sustaining network of the GLI transcription factors controlling important metabolic regulators in adult mouse hepatocytes.

Mol Biosyst 2015 Aug;11(8):2190-7

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1039/c5mb00129cDOI Listing
August 2015

A review on computational systems biology of pathogen-host interactions.

Front Microbiol 2015 9;6:235. Epub 2015 Apr 9.

Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena Germany.

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http://dx.doi.org/10.3389/fmicb.2015.00235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391036PMC
April 2015

Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study.

Front Microbiol 2015 11;6:171. Epub 2015 Mar 11.

Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2015.00171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356159PMC
March 2015

FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species.

Bioinformatics 2015 Feb 7;31(3):445-6. Epub 2014 Oct 7.

Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstraße 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btu627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4308660PMC
February 2015

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.

Nucleic Acids Res 2015 Feb 13;43(3):1392-406. Epub 2015 Jan 13.

Septomics Research Center, Fungal Septomics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany National Reference Center for Invasive Mycoses, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany.

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http://dx.doi.org/10.1093/nar/gku1357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330350PMC
February 2015

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.

Front Microbiol 2015 6;6:65. Epub 2015 Feb 6.

Department of Systems Biology and Bioinformatics, Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2015.00065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319478PMC
February 2015

Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417.

Genome Announc 2015 Jan 22;3(1). Epub 2015 Jan 22.

Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01370-14
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http://dx.doi.org/10.1128/genomeA.01370-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319578PMC
January 2015

Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum.

Genome Announc 2015 Jan 22;3(1). Epub 2015 Jan 22.

Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany

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http://dx.doi.org/10.1128/genomeA.01439-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319583PMC
January 2015

Integrated metabolic spatial-temporal model for the prediction of ammonia detoxification during liver damage and regeneration.

Hepatology 2014 Dec 12;60(6):2040-51. Epub 2014 May 12.

Clinic for Gastroenterology, Hepatology, and Infectiology, Heinrich Heine University, Düsseldorf, Germany.

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http://dx.doi.org/10.1002/hep.27136DOI Listing
December 2014

Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant.

PLoS Genet 2014 Dec 4;10(12):e1004824. Epub 2014 Dec 4.

Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena (HKI), Jena, Germany; Integrated Research and Treatment Center, Sepsis und Sepsisfolgen, Center for Sepsis Control and Care (CSCC), Universitätsklinikum Jena, Germany; Friedrich Schiller University, Jena, Germany.

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https://dx.plos.org/10.1371/journal.pgen.1004824
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http://dx.doi.org/10.1371/journal.pgen.1004824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256171PMC
December 2014

Regulatory networks controlling nitrogen sensing and uptake in Candida albicans.

PLoS One 2014 20;9(3):e92734. Epub 2014 Mar 20.

Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany; Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092734PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961412PMC
November 2014

Extension of life span by impaired glucose metabolism in Caenorhabditis elegans is accompanied by structural rearrangements of the transcriptomic network.

PLoS One 2013 30;8(10):e77776. Epub 2013 Oct 30.

Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077776PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813781PMC
September 2014

The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus.

Mol Microbiol 2014 Aug 7;93(3):539-53. Epub 2014 Jul 7.

Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany; Institute of Microbiology, Friedrich Schiller University, Jena, Germany.

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http://dx.doi.org/10.1111/mmi.12679DOI Listing
August 2014

Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients.

BMC Med Genomics 2014 Jul 3;7:40. Epub 2014 Jul 3.

Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr, 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1186/1755-8794-7-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099018PMC
July 2014

Draft Genome Sequence of Streptomyces iranensis.

Genome Announc 2014 Jul 17;2(4). Epub 2014 Jul 17.

Bioinformatics/Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute (HKI), Jena, Germany

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http://dx.doi.org/10.1128/genomeA.00616-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102860PMC
July 2014

Within-host influenza dynamics: a small-scale mathematical modeling approach.

Biosystems 2014 Apr 11;118:51-9. Epub 2014 Mar 11.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2014.02.004DOI Listing
April 2014

D-Glucosamine supplementation extends life span of nematodes and of ageing mice.

Nat Commun 2014 Apr 8;5:3563. Epub 2014 Apr 8.

1] Energy Metabolism Laboratory, ETH Zürich (Swiss Federal Institute of Technology Zurich), Zürich CH-8603, Switzerland [2] German Institute of Human Nutrition Potsdam-Rehbrücke, D-14558 Nuthetal, Germany [3] Department of Human Nutrition, Institute of Nutrition, University of Jena, D-07743 Jena, Germany.

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http://dx.doi.org/10.1038/ncomms4563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988823PMC
April 2014

Interactive exploration of integrated biological datasets using context-sensitive workflows.

Front Genet 2014 20;5:21. Epub 2014 Feb 20.

Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany.

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http://dx.doi.org/10.3389/fgene.2014.00021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929842PMC
March 2014

Neuronal ROS signaling rather than AMPK/sirtuin-mediated energy sensing links dietary restriction to lifespan extension.

Mol Metab 2013 14;2(2):92-102. Epub 2013 Feb 14.

Department of Human Nutrition, Institute of Nutrition, University of Jena, Jena D-07743, Germany ; Leibniz Graduate School of Aging, Leibniz Institute for Age Research, Fritz-Lipmann-Institute, Jena D-07745, Germany.

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https://linkinghub.elsevier.com/retrieve/pii/S22128778130002
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http://dx.doi.org/10.1016/j.molmet.2013.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817383PMC
November 2013

Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation.

BMC Syst Biol 2013 Nov 12;7:124. Epub 2013 Nov 12.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr, 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1186/1752-0509-7-124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225824PMC
November 2013

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0.

BMC Syst Biol 2013 Jan 2;7. Epub 2013 Jan 2.

Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.

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http://dx.doi.org/10.1186/1752-0509-7-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605253PMC
January 2013

Genome-Wide Scale-Free Network Inference for Candida albicans.

Front Microbiol 2012 16;3:51. Epub 2012 Feb 16.

Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2012.00051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280432PMC
October 2012

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells.

Front Microbiol 2012 12;3:85. Epub 2012 Mar 12.

Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories, Medical University of Vienna Vienna, Austria.

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http://dx.doi.org/10.3389/fmicb.2012.00085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299011PMC
October 2012

Multivariate analysis of flow cytometric data using decision trees.

Front Microbiol 2012 2;3:114. Epub 2012 Apr 2.

Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2012.00114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316995PMC
October 2012

Systems biology of microbial infection.

Front Microbiol 2012 12;3:328. Epub 2012 Sep 12.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute Jena, Germany.

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http://dx.doi.org/10.3389/fmicb.2012.00328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439864PMC
October 2012

Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression.

BMC Genomics 2012 Oct 2;13:519. Epub 2012 Oct 2.

Department of Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Beutenbergstr. 11a, Jena 07745, Germany.

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http://dx.doi.org/10.1186/1471-2164-13-519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505472PMC
October 2012

Sustained liver regeneration after portal vein embolization --a human molecular pilot study.

Dig Liver Dis 2012 Aug 5;44(8):681-8. Epub 2012 May 5.

Department of General and Vascular Surgery, University Hospital Jena, Erlanger Allee 101, Jena, Germany.

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http://dx.doi.org/10.1016/j.dld.2012.04.002DOI Listing
August 2012

4-Hydroxyphenylglycine biosynthesis in Herpetosiphon aurantiacus: a case of gene duplication and catalytic divergence.

Arch Microbiol 2012 Jun 4;194(6):557-66. Epub 2012 Feb 4.

Junior Research Group Secondary Metabolism of Predatory Bacteria, Leibniz Institute for Natural Product Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1007/s00203-012-0789-yDOI Listing
June 2012

Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis.

BMC Med Genomics 2012 Jun 8;5:23. Epub 2012 Jun 8.

Experimental Rheumatology Unit, Department of Orthopedics, University Hospital Jena, Friedrich Schiller University, Jena, Germany.

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http://dx.doi.org/10.1186/1755-8794-5-23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528008PMC
June 2012

Age-dependent regulation of tumor-related microRNAs in the brain of the annual fish Nothobranchius furzeri.

Mech Ageing Dev 2012 May 6;133(5):226-33. Epub 2012 Apr 6.

Biology of Ageing, Leibniz Institute for Age Research, Fritz-Lipmann Institute, Jena, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S004763741200050
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http://dx.doi.org/10.1016/j.mad.2012.03.015DOI Listing
May 2012

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach.

BMC Syst Biol 2012 Jan 19;6. Epub 2012 Jan 19.

Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany.

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http://dx.doi.org/10.1186/1752-0509-6-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305660PMC
January 2012

Effect of L-carnitine on the hepatic transcript profile in piglets as animal model.

Nutr Metab (Lond) 2011 Oct 31;8:76. Epub 2011 Oct 31.

Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany.

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http://dx.doi.org/10.1186/1743-7075-8-76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3216248PMC
October 2011

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.

Mol Syst Biol 2011 Jul 19;7:515. Epub 2011 Jul 19.

Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, Jena, Germany.

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http://dx.doi.org/10.1038/msb.2011.46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159982PMC
July 2011

In silico evidence for gluconeogenesis from fatty acids in humans.

PLoS Comput Biol 2011 Jul 21;7(7):e1002116. Epub 2011 Jul 21.

Department of Bioinformatics, School of Biology and Pharmaceutics, Friedrich Schiller University of Jena, Jena, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1002116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3140964PMC
July 2011

On the way toward systems biology of Aspergillus fumigatus infection.

Int J Med Microbiol 2011 Jun 8;301(5):453-9. Epub 2011 May 8.

Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

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http://dx.doi.org/10.1016/j.ijmm.2011.04.014DOI Listing
June 2011

Automated image analysis of the host-pathogen interaction between phagocytes and Aspergillus fumigatus.

PLoS One 2011 May 5;6(5):e19591. Epub 2011 May 5.

Research Group Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Jena, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088683PMC
May 2011

FungiFun: a web-based application for functional categorization of fungal genes and proteins.

Fungal Genet Biol 2011 Apr 10;48(4):353-8. Epub 2010 Nov 10.

Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute (HKI), Jena, Germany.

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April 2011

Dietary L-carnitine alters gene expression in skeletal muscle of piglets.

Mol Nutr Food Res 2011 Mar 11;55(3):419-29. Epub 2010 Oct 11.

Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-Universität Gießen, Gießen, Germany.

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http://dx.doi.org/10.1002/mnfr.201000293DOI Listing
March 2011

Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells.

BMC Syst Biol 2010 Nov 4;4:148. Epub 2010 Nov 4.

Leibniz-Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute, Jena, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225834PMC
November 2010

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.

BMC Syst Biol 2010 Aug 18;4:116. Epub 2010 Aug 18.

Systems Biology/Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr, 11a, D-07745 Jena, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936295PMC
August 2010

Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus.

J Proteome Res 2010 Jul;9(7):3427-42

Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.

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http://dx.doi.org/10.1021/pr9010684DOI Listing
July 2010

Missing values in gel-based proteomics.

Proteomics 2010 Mar;10(6):1202-11

Research Group Systems Biology/Bioinformatics, Hans-Knölle-Institute, Jena, Germany.

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http://doi.wiley.com/10.1002/pmic.200800576
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March 2010

Integrative analysis of the heat shock response in Aspergillus fumigatus.

BMC Genomics 2010 Jan 15;11:32. Epub 2010 Jan 15.

Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany.

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http://dx.doi.org/10.1186/1471-2164-11-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820008PMC
January 2010

Heterogeneous expression of suppressor of cytokine signalling 2 (SOCS-2) in liver tissue.

J Anat 2009 Aug 14;215(2):176-83. Epub 2009 May 14.

Institute of Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740965PMC
August 2009

Integrative modeling of transcriptional regulation in response to antirheumatic therapy.

BMC Bioinformatics 2009 Aug 24;10:262. Epub 2009 Aug 24.

Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena, Germany.

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http://dx.doi.org/10.1186/1471-2105-10-262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757030PMC
August 2009

Adapted Boolean network models for extracellular matrix formation.

BMC Syst Biol 2009 Jul 21;3:77. Epub 2009 Jul 21.

Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734845PMC
July 2009

Gene regulatory network inference: data integration in dynamic models-a review.

Biosystems 2009 Apr 27;96(1):86-103. Epub 2008 Dec 27.

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany.

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April 2009

Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus.

Proteomics 2009 Mar;9(5):1407-15

Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute (HKI), Jena, Germany.

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http://dx.doi.org/10.1002/pmic.200800394DOI Listing
March 2009

Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane.

Arthritis Res Ther 2008 22;10(4):R98. Epub 2008 Aug 22.

Department of Orthopedics, Experimental Rheumatology Unit, University Hospital Jena, Waldkrankenhaus Rudolf Elle, Eisenberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575612PMC
February 2009

Molecular discrimination of responders and nonresponders to anti-TNF alpha therapy in rheumatoid arthritis by etanercept.

Arthritis Res Ther 2008 2;10(3):R50. Epub 2008 May 2.

Department of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany.

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http://dx.doi.org/10.1186/ar2419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483439PMC
December 2008

Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions.

J Biotechnol 2008 May 4;135(1):34-44. Epub 2008 Mar 4.

Department of Biotechnology, University of Natural Resources and Applied Life Science, Muthgasse 18, 1190 Vienna, Austria.

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http://dx.doi.org/10.1016/j.jbiotec.2008.02.013DOI Listing
May 2008

Convergence of the proteomic pattern in cancer.

Bioinformatics 2006 Jun 7;22(11):1293-6. Epub 2006 Mar 7.

Core Unit Chip Application (CUCA), Institute of Human Genetics and Anthropology, Friedrich-Schiller-University, 07740 Jena, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btl077DOI Listing
June 2006

Rheumatoid arthritis, a complex multifactorial disease: on the way toward individualized medicine.

Med Res Rev 2006 Jan;26(1):63-87

Proteome Center Rostock, University of Rostock, Rostock, Germany.

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January 2006