Ina Koch

Ina Koch

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Ina Koch

Publications by authors named "Ina Koch"

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Reconstruction of Protein-Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina.

Methods Mol Biol 2020 ;2074:45-55

Department of Biosciences, Molecular Developmental Biology, Institute of Molecular Biosciences and Cluster of Excellence Frankfurt, "Macromolecular Complexes", Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1007/978-1-4939-9873-9_4DOI Listing
January 2020

Comprehensive clinical profiling of the Gauting locoregional lung adenocarcinoma donors.

Cancer Med 2019 Apr 25;8(4):1486-1499. Epub 2019 Feb 25.

Comprehensive Pneumology Center and Institute for Lung Biology and Disease, University Hospital, Ludwig-Maximilians University of Munich (LMU) and Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), Munich, Bavaria, Germany.

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http://dx.doi.org/10.1002/cam4.2031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488114PMC
April 2019

Quality assessment of tissue samples stored in a specialized human lung biobank.

PLoS One 2019 4;14(4):e0203977. Epub 2019 Apr 4.

Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, Gauting and German Center for Lung Research - DZL, Munich, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0203977PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448820PMC
April 2019

isiKnock: in silico knockouts in signaling pathways.

Bioinformatics 2019 Mar;35(5):892-894

Department of Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty700DOI Listing
March 2019

Protein super-secondary structure and quaternary structure topology: theoretical description and application.

Curr Opin Struct Biol 2018 06 17;50:134-143. Epub 2018 Mar 17.

Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, 60325 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1016/j.sbi.2018.02.005DOI Listing
June 2018

Common functional variants of the glutamatergic system in Autism spectrum disorder with high and low intellectual abilities.

J Neural Transm (Vienna) 2018 02 16;125(2):259-271. Epub 2017 Nov 16.

Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence Frankfurt, University Hospital Frankfurt, Goethe University, Deutschordenstraße 50, 60258, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1007/s00702-017-1813-9DOI Listing
February 2018

Manatee invariants reveal functional pathways in signaling networks.

BMC Syst Biol 2017 Jul 28;11(1):72. Epub 2017 Jul 28.

Molecular Bioinformatics, Institute of Computer Science, Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.

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http://dx.doi.org/10.1186/s12918-017-0448-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534052PMC
July 2017

Modeling the Metabolism of : Application of Network Decomposition and Network Reduction in the Context of Petri Nets.

Front Genet 2017 30;8:85. Epub 2017 Jun 30.

Department of Biosciences, Institute of Molecular Biosciences, Molecular Cell Biology of Plants, Cluster of Excellence "Macromolecular Complexes", Goethe-University FrankfurtFrankfurt am Main, Germany.

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http://dx.doi.org/10.3389/fgene.2017.00085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491931PMC
June 2017

The autophagy interaction network of the aging model Podospora anserina.

BMC Bioinformatics 2017 Mar 27;18(1):196. Epub 2017 Mar 27.

Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics and Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, Frankfurt am Main, 60325, Germany.

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http://dx.doi.org/10.1186/s12859-017-1603-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369006PMC
March 2017

In Silico Knockout Studies of Xenophagic Capturing of Salmonella.

PLoS Comput Biol 2016 12 1;12(12):e1005200. Epub 2016 Dec 1.

Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131900PMC
December 2016

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.

Bioinformatics 2016 05 5;32(9):1427-9. Epub 2016 Jan 5.

Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics & Cluster of Excellence 'Macromolecular Complexes', Goethe-University, Frankfurt am Main, Germany and.

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http://dx.doi.org/10.1093/bioinformatics/btv765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848400PMC
May 2016

Petri nets for steady state analysis of metabolic systems.

Stud Health Technol Inform 2011 ;162:56-76

Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) [GMD], Sankt Augustin, Germany.

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April 2016

STEPP - Search Tool for Exploration of Petri net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks.

Stud Health Technol Inform 2011 ;162:113-21

Technical University of Applied Sciences Berlin, FBV, WG Bioinformatics, Seestr. 64, 13347 Berlin, Germany, Tel.: +49 (0)30 4504 3972; Fax: +49 (0)30 4504 3959; E-mail: {ina.koch,

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April 2016

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

Stud Health Technol Inform 2011 ;162:244-78

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

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April 2016

The new protein topology graph library web server.

Bioinformatics 2016 Feb 6;32(3):474-6. Epub 2015 Oct 6.

Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and.

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http://dx.doi.org/10.1093/bioinformatics/btv574DOI Listing
February 2016

CD30 cell graphs of Hodgkin lymphoma are not scale-free--an image analysis approach.

Bioinformatics 2016 Jan 11;32(1):122-9. Epub 2015 Sep 11.

Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence Macromolecular Complexes, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main and.

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http://dx.doi.org/10.1093/bioinformatics/btv542DOI Listing
January 2016

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

Metabolites 2015 Dec 17;5(4):766-93. Epub 2015 Dec 17.

Molecular Bioinformatics, Cluster of Excellence "Macromolecular Complexes", Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany.

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http://dx.doi.org/10.3390/metabo5040766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4693194PMC
December 2015

Unsupervised image segmentation for microarray spots with irregular contours and inner holes.

BMC Bioinformatics 2015 Dec 23;16:412. Epub 2015 Dec 23.

Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania.

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http://link.springer.com/content/pdf/10.1186/s12859-015-0842
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http://www.biomedcentral.com/1471-2105/16/412
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http://dx.doi.org/10.1186/s12859-015-0842-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690322PMC
December 2015

Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems.

BMC Bioinformatics 2015 Nov 5;16:371. Epub 2015 Nov 5.

Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.

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http://dx.doi.org/10.1186/s12859-015-0725-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636070PMC
November 2015

Preclinical validation and imaging of Wnt-induced repair in human 3D lung tissue cultures.

Eur Respir J 2015 Oct 30;46(4):1150-66. Epub 2015 Apr 30.

Comprehensive Pneumology Center, Helmholtz Center Munich, Ludwig Maximilians University Munich, University Hospital Grosshadern, Member of the German Center for Lung Research (DZL), Munich, Germany

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http://dx.doi.org/10.1183/09031936.00183214DOI Listing
October 2015

Comprehensive genomic profiles of small cell lung cancer.

Nature 2015 Aug 13;524(7563):47-53. Epub 2015 Jul 13.

1] Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany. [2] Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany.

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http://dx.doi.org/10.1038/nature14664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861069PMC
August 2015

Blood-sampling collection prior to surgery may have a significant influence upon biomarker concentrations measured.

Clin Proteomics 2015 31;12(1):19. Epub 2015 Jul 31.

Translational Research Unit (STF), Thoraxklinik, University of Heidelberg, Amalienstr. 5, 69126 Heidelberg, Germany ; Translational Lung Research Centre Heidelberg (TLRC-H), German Centre for Lung Research (DZL), Heidelberg, Germany.

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http://dx.doi.org/10.1186/s12014-015-9093-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521486PMC
August 2015

MONALISA for stochastic simulations of Petri net models of biochemical systems.

BMC Bioinformatics 2015 Jul 10;16:215. Epub 2015 Jul 10.

Department of Molecular Bioinformatics, Institute of Computer Science, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany.

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http://dx.doi.org/10.1186/s12859-015-0596-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496887PMC
July 2015

APADB: a database for alternative polyadenylation and microRNA regulation events.

Database (Oxford) 2014 22;2014. Epub 2014 Jul 22.

Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.

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http://dx.doi.org/10.1093/database/bau076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105710PMC
February 2015

NOVA: a software to analyze complexome profiling data.

Bioinformatics 2015 Feb 9;31(3):440-1. Epub 2014 Oct 9.

Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany, Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt "Macromolecular Complexes", Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, Functional Proteomics, SFB815 core unit, Medical School, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany and Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu623DOI Listing
February 2015

A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina.

PLoS One 2013 20;8(12):e83109. Epub 2013 Dec 20.

Molecular Developmental Biology, Institute of Molecular Biosciences, Faculty for Biosciences & Cluster of Excellence 'Macromolecular Complexes', Johann Wolfgang Goethe University, Frankfurt am Main, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083109PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869774PMC
October 2014

Genome scale modeling in systems biology: algorithms and resources.

Curr Genomics 2014 Apr;15(2):130-59

Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Iran;

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http://dx.doi.org/10.2174/1389202915666140319002221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009841PMC
April 2014

QuateXelero: an accelerated exact network motif detection algorithm.

PLoS One 2013 18;8(7):e68073. Epub 2013 Jul 18.

Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068073PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715482PMC
February 2014

Gli1 mediates lung cancer cell proliferation and Sonic Hedgehog-dependent mesenchymal cell activation.

PLoS One 2013 7;8(5):e63226. Epub 2013 May 7.

Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063226PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646741PMC
December 2013

Multiplex profiling of cellular invasion in 3D cell culture models.

PLoS One 2013 9;8(5):e63121. Epub 2013 May 9.

Comprehensive Pneumology Center, University Hospital of the Ludwig-Maximilians-University Munich and Helmholtz Zentrum München, Member of the German Center for Lung Research, Munich, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063121PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650046PMC
December 2013

Image database analysis of Hodgkin lymphoma.

Comput Biol Chem 2013 Oct 10;46:1-7. Epub 2013 May 10.

Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1016/j.compbiolchem.2013.04.003DOI Listing
October 2013

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.

Bioinformatics 2013 Oct 13;29(20):2651-2. Epub 2013 Aug 13.

Plant Molecular Biology, Institute of Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Str.9, 60439 Frankfurt am Main, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, 60438 Frankfurt am Main and Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence, Frankfurt "Macromolecular Complexes", Robert-Mayer-Strasse 11-15, 60325 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt457DOI Listing
October 2013

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

In Silico Biol 2010 ;10(1):89-123

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

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http://dx.doi.org/10.3233/ISB-2010-0419DOI Listing
September 2013

On functional module detection in metabolic networks.

Metabolites 2013 Aug 12;3(3):673-700. Epub 2013 Aug 12.

Molecular Bioinformatics group, Cluster of Excellence "Macromolecular Complexes", Johann Wolfgang Goethe-University Frankfurt (Main), Institute of Computer Science, Robert-Mayer-Strasse 11-15, Frankfurt (Main) 60325, Germany.

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http://dx.doi.org/10.3390/metabo3030673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901286PMC
August 2013

Interleukin-22 is frequently expressed in small- and large-cell lung cancer and promotes growth in chemotherapy-resistant cancer cells.

J Thorac Oncol 2013 Aug;8(8):1032-42

Department of Internal Medicine IV, Division of Clinical Pharmacology and Center of Integrated Protein Science, Ludwig-Maximilians Universität München, Member of the German Center for Lung Research, Munich, Germany.

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http://dx.doi.org/10.1097/JTO.0b013e31829923c8DOI Listing
August 2013

MonaLisa--visualization and analysis of functional modules in biochemical networks.

Bioinformatics 2013 Jun 5;29(11):1469-70. Epub 2013 Apr 5.

Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt 'Macromolecular Complexes', Robert-Mayer-Strasse 11-15, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btt165DOI Listing
June 2013

Hierarchical representation of supersecondary structures using a graph-theoretical approach.

Methods Mol Biol 2013 ;932:7-33

Molecular Bioinformatics Group, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

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http://dx.doi.org/10.1007/978-1-62703-065-6_2DOI Listing
January 2013

Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly complex.

Cell Metab 2012 Oct 13;16(4):538-49. Epub 2012 Sep 13.

Molecular Bioenergetics Group, Medical School, Cluster of Excellence Frankfurt Macromolecular Complexes, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1016/j.cmet.2012.08.009DOI Listing
October 2012

Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks.

Authors:
Ina Koch

Mol Inform 2010 Dec 16;29(12):838-43. Epub 2010 Nov 16.

Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1002/minf.201000086DOI Listing
December 2010

PTGL: a database for secondary structure-based protein topologies.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D326-30. Epub 2009 Nov 11.

Max Planck Institute for Molecular Plant Physiology, Bioinformatics, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.

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http://dx.doi.org/10.1093/nar/gkp980DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808981PMC
January 2010

Efficient shRNA delivery into B and T lymphoma cells using lentiviral vector-mediated transfer.

J Hematop 2009 Mar 19;2(1):9-19. Epub 2008 Nov 19.

Institute of Pathology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.

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http://link.springer.com/10.1007/s12308-008-0020-x
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http://dx.doi.org/10.1007/s12308-008-0020-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713496PMC
March 2009

Atypical chronic myeloid leukemia as defined in the WHO classification is a JAK2 V617F negative neoplasm.

Leuk Res 2008 Dec 13;32(12):1931-5. Epub 2008 Jun 13.

Institute of Pathology, University Hospital Tuebingen, Eberhard-Karls-University, Tuebingen, Germany.

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http://dx.doi.org/10.1016/j.leukres.2008.04.024DOI Listing
December 2008

A review of bioinformatics education in Germany.

Brief Bioinform 2008 May 1;9(3):232-42. Epub 2008 Mar 1.

Technical University of Applied Sciences Berlin, FB VI, Bioinformatics, Seestr. 64, 13347 Berlin.

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http://dx.doi.org/10.1093/bib/bbn006DOI Listing
May 2008

Petri net modelling of gene regulation of the Duchenne muscular dystrophy.

Biosystems 2008 May 10;92(2):189-205. Epub 2008 Mar 10.

Technical University of Applied Sciences Berlin, Department V/VI, Biotechnology/Bioinformatics, Seestr. 64, 13347 Berlin, Germany.

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http://dx.doi.org/10.1016/j.biosystems.2008.02.005DOI Listing
May 2008

Modularization of biochemical networks based on classification of Petri net t-invariants.

BMC Bioinformatics 2008 Feb 8;9:90. Epub 2008 Feb 8.

Technical University of Applied Sciences Berlin, FB VI/FB V, Bioinformatics/Biotechnology, Seestr, 64, 13347 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-9-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2277402PMC
February 2008

An analysis of the Petri net based model of the human body iron homeostasis process.

Comput Biol Chem 2007 Feb 9;31(1):1-10. Epub 2006 Nov 9.

Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.

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http://dx.doi.org/10.1016/j.compbiolchem.2006.09.005DOI Listing
February 2007

Application of Petri net based analysis techniques to signal transduction pathways.

BMC Bioinformatics 2006 Nov 2;7:482. Epub 2006 Nov 2.

Technical University of Applied Sciences Berlin, Bioinformatics group, Seestr, 64, 13347 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-7-482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1686943PMC
November 2006

STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks.

In Silico Biol 2005 ;5(2):129-37

Seestr. 64, 13347 Berlin, Germany. Email:

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October 2005

Theoretical analysis of alternative splice forms using computational methods.

Bioinformatics 2002 ;18 Suppl 2:S65-73

Max-Planck-Institute for Molecular Genetics, Department Computational Molecular Biology, Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_2.s65DOI Listing
September 2005

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.

Bioinformatics 2005 Apr 16;21(7):1219-26. Epub 2004 Nov 16.

Department of Bioinformatics, Technical University of Applied Sciences Berlin, Seestrasse 64, Berlin, 13347, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bti145DOI Listing
April 2005

Columba: an integrated database of proteins, structures, and annotations.

BMC Bioinformatics 2005 Mar 31;6:81. Epub 2005 Mar 31.

Institute of Informatics, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2105-6-81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087474PMC
March 2005

PTGL--a web-based database application for protein topologies.

Bioinformatics 2004 Nov 24;20(17):3277-9. Epub 2004 Jun 24.

BCB Junior Research Group, ZIB Berlin, Takustr.7, Berlin 14195, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bth367DOI Listing
November 2004

The induction of cytochrome P450 3A5 (CYP3A5) in the human liver and intestine is mediated by the xenobiotic sensors pregnane X receptor (PXR) and constitutively activated receptor (CAR).

J Biol Chem 2004 Sep 12;279(37):38379-85. Epub 2004 Jul 12.

Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, D-70376 Stuttgart, Germany.

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http://dx.doi.org/10.1074/jbc.M404949200DOI Listing
September 2004

Different mechanisms of cyclin D1 overexpression in multiple myeloma revealed by fluorescence in situ hybridization and quantitative analysis of mRNA levels.

Blood 2004 Aug 13;104(4):1120-6. Epub 2004 Apr 13.

Institute of Pathology, GSF-National Research Center for Environment and Health Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.

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http://dx.doi.org/10.1182/blood-2003-11-3837DOI Listing
August 2004

Steady state analysis of metabolic pathways using Petri nets.

In Silico Biol 2003 ;3(3):367-87

Fraunhofer-Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany.

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July 2004

Limited contribution of CYP3A5 to the hepatic 6beta-hydroxylation of testosterone.

Naunyn Schmiedebergs Arch Pharmacol 2004 Jul 1;370(1):71-7. Epub 2004 Jul 1.

Department of Clinical Pharmacology, Georg-August University Göttingen, Robert-Koch Strasse 40, 37099, Germany.

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http://link.springer.com/10.1007/s00210-004-0944-3
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http://dx.doi.org/10.1007/s00210-004-0944-3DOI Listing
July 2004

Model validation of biological pathways using Petri nets--demonstrated for apoptosis.

Biosystems 2004 Jul;75(1-3):15-28

Department of Computer Science, Brandenburg University of Technology Cottbus, Post Box 10 13 44, 03013 Cottbus, Germany.

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http://dx.doi.org/10.1016/j.biosystems.2004.03.003DOI Listing
July 2004

Identification of transcripts from a subtraction library which might be responsible for the mild phenotype in an intrafamilially variable course of Duchenne muscular dystrophy.

Hum Genet 2004 Jan 5;114(2):149-56. Epub 2003 Nov 5.

Department of Neuropediatrics, Charité, Humboldt-University Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

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http://dx.doi.org/10.1007/s00439-003-1041-2DOI Listing
January 2004

Increase of functional diversity by alternative splicing.

Trends Genet 2003 Mar;19(3):124-8

European Bioinformatics Institute (EMBL-EBI), Hinxton Wellcome Trust Genome Campus, Hinxton, Cambridge, UK CB10 1SD.

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http://dx.doi.org/10.1016/S0168-9525(03)00023-4DOI Listing
March 2003

Molecular mechanisms of polymorphic CYP3A7 expression in adult human liver and intestine.

J Biol Chem 2002 Jul 8;277(27):24280-8. Epub 2002 Apr 8.

Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, D-70376 Stuttgart, Germany.

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http://dx.doi.org/10.1074/jbc.M202345200DOI Listing
July 2002