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ORCIDIna Koch
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- affiliation: Johann Wolfgang Goethe University, Institute of Computer Science, Frankfurt am Main, Germany
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2020 – today
- 2024
[j48]Florian J. Gisdon
, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch:
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. Bioinform. 40(3) (2024)- 2023
- [j47]Yauheniya Zhdanovich, Jörg Ackermann, Peter J. Wild, Jens Köllermann, Katrin Bankov, Claudia Döring, Nadine Flinner, Henning Reis, Mike Wenzel, Benedikt Höh, Philipp Mandel, Thomas J. Vogl, Patrick Harter, Katharina Filipski, Ina Koch, Simon Bernatz:
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology. BMC Bioinform. 24(1): 1 (2023) - [j46]Simon Bernatz, Ines Böth, Jörg Ackermann, Iris Burck, Scherwin Mahmoudi, Lukas Lenga, Simon S. Martin, Jan-Erik Scholtz, Vitali Koch, Leon D. Grünewald, Ina Koch, Timo Stöver, Peter J. Wild, Ria Winkelmann, Thomas J. Vogl, Daniel Pinto dos Santos:
Radiomics for therapy-specific head and neck squamous cell carcinoma survival prognostication (part I). BMC Medical Imaging 23(1): 71 (2023) - [j45]Julienne Siptroth, Olga Moskalenko, Carsten Krumbiegel, Jörg Ackermann, Ina Koch, Heike Pospisil:
Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks. Discov. Artif. Intell. 3(1) (2023) - 2022
- [j44]Kira Trares, Jörg Ackermann, Ina Koch:
The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets. Biosyst. 211: 104564 (2022) - [j43]Aaron W. Sievering, Peter Wohlmuth, Nele Geßler, Melanie A. Gunawardene, Klaus Herrlinger, Berthold Bein, Dirk Arnold, Martin Bergmann, Lorenz Nowak, Christian Gloeckner, Ina Koch, Martin Bachmann, Christoph U. Herborn, Axel Stang:
Comparison of machine learning methods with logistic regression analysis in creating predictive models for risk of critical in-hospital events in COVID-19 patients on hospital admission. BMC Medical Informatics Decis. Mak. 22(1): 309 (2022) - [j42]Leonie Amstein, Jörg Ackermann, Jennifer Hannig, Ivan Dikic, Simone Fulda, Ina Koch:
Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis. PLoS Comput. Biol. 18(8) (2022) - 2021
- [j41]Jan Niclas Wolf, Marcus Keßler, Jörg Ackermann, Ina Koch:
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. Bioinform. 37(7): 1032-1034 (2021) - [j40]Scherwin Mahmoudi, Simon S. Martin, Jörg Ackermann, Yauheniya Zhdanovich, Ina Koch, Thomas J. Vogl, Moritz H. Albrecht, Lukas Lenga, Simon Bernatz:
Potential of high dimensional radiomic features to assess blood components in intraaortic vessels in non-contrast CT scans. BMC Medical Imaging 21(1): 123 (2021) - 2020
- [j39]Jennifer Hannig, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. PLoS Comput. Biol. 16(1) (2020) - [p4]Ina Koch, Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz:
Reconstruction of Protein-Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina. Protein-Protein Interaction Networks 2020: 45-55
2010 – 2019
- 2019
- [j38]Jennifer Hannig, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch:
isiKnock: in silico knockouts in signaling pathways. Bioinform. 35(5): 892-894 (2019) - [p3]Ina Koch:
Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa. Carl Adam Petri: Ideas, Personality, Impact 2019: 217-226 - 2017
- [j37]Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz, Ina Koch:
The autophagy interaction network of the aging model Podospora anserina. BMC Bioinform. 18(1): 196:1-196:15 (2017) - [j36]Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic, Ina Koch:
Manatee invariants reveal functional pathways in signaling networks. BMC Syst. Biol. 11(1): 72:1-72:11 (2017) - 2016
- [j35]Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach. Bioinform. 32(1): 122-129 (2016) - [j34]Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, Ina Koch:
The new protein topology graph library web server. Bioinform. 32(3): 474-476 (2016) - [j33]Oliver Philipp, Heinz D. Osiewacz, Ina Koch:
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. Bioinform. 32(9): 1427-1429 (2016) - [j32]Melanie Laßek, Jens Weingarten, Martin Wegner, Benjamin F. Mueller, Marion Rohmer, Dominic Baeumlisberger, Tabiwang N. Arrey, Meike Hick, Jörg Ackermann, Amparo Acker-Palmer, Ina Koch, Ulrike Müller, Michael Karas, Walter Volknandt:
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. PLoS Comput. Biol. 12(4) (2016) - [j31]Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch:
In Silico Knockout Studies of Xenophagic Capturing of Salmonella. PLoS Comput. Biol. 12(12) (2016) - [c9]Frank Klawonn, Junxi Wang, Ina Koch, Jörg Eberhard, Mohamed Omar:
HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features. IDA 2016: 356-367 - [p2]Ina Koch, Falk Schreiber:
Introduction. Modeling in Systems Biology, The Petri Net Approach 2016: 3-18 - [p1]Jörg Ackermann, Ina Koch:
Quantitative Analysis. Modeling in Systems Biology, The Petri Net Approach 2016: 153-178 - 2015
- [j30]Heiko Giese, Jörg Ackermann, Heinrich Heide, Lea Bleier, Stefan Dröse, Ilka Wittig, Ulrich Brandt, Ina Koch:
NOVA: a software to analyze complexome profiling data. Bioinform. 31(3): 440-441 (2015) - [j29]Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch:
MONALISA for stochastic simulations of Petri net models of biochemical systems. BMC Bioinform. 16: 215:1-215:11 (2015) - [j28]Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch:
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems. BMC Bioinform. 16: 371:1 (2015) - [j27]Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch, Ovidiu Balacescu:
Unsupervised image segmentation for microarray spots with irregular contours and inner holes. BMC Bioinform. 16: 412:1-412:12 (2015) - [j26]Ina Koch:
Petri nets in systems biology. Softw. Syst. Model. 14(2): 703-710 (2015) - [i1]Heiko Giese, Jörg Ackermann, Ulrich Brandt, Ilka Wittig, Ina Koch:
Cluster analysis and visualization techniques for large datasets in complexome profiling. PeerJ Prepr. 3: e1303 (2015) - 2014
- [j25]Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter:
APADB: a database for alternative polyadenylation and microRNA regulation events. Database J. Biol. Databases Curation 2014 (2014) - [j24]Ina Koch:
Petrinetze in der Systembiologie. Inform. Spektrum 37(3): 211-219 (2014) - [j23]Ina Koch, Wolfgang Reisig, Falk Schreiber:
Petri Nets in the Biosciences. it Inf. Technol. 56(2): 43-45 (2014) - 2013
- [j22]Jens Einloft, Jörg Ackermann, Joachim Nöthen, Ina Koch:
MonaLisa - visualization and analysis of functional modules in biochemical networks. Bioinform. 29(11): 1469-1470 (2013) - [j21]Sören Müller, Lukas Rycak, Peter Winter, Günter Kahl, Ina Koch, Björn Rotter:
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinform. 29(20): 2651-2652 (2013) - [j20]Tim Schäfer, Hendrik Schäfer, Alexander Schmitz, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
Image database analysis of Hodgkin lymphoma. Comput. Biol. Chem. 46: 1-7 (2013) - 2012
- [j19]Susann Vorberg, Ina Koch, Christian Buning:
Sodium dependent glucose transporter (SGLT) 1 / 2 - elucidating inhibitor SAR and selectivity using homology modelling and 3D QSAR studies. J. Cheminformatics 4(S-1): 41 (2012) - [c8]Tim Schäfer, Patrick May, Ina Koch:
Computation and Visualization of Protein Topology Graphs Including Ligand Information. GCB 2012: 108-118 - 2011
- [e1]Ina Koch, Wolfgang Reisig, Falk Schreiber:
Modeling in Systems Biology, The Petri Net Approach. Computational Biology 16, Springer 2011, ISBN 978-1-84996-473-9 [contents] - 2010
- [j18]Ralf H. Bortfeldt, Stefan Schuster, Ina Koch:
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach. Silico Biol. 10(1-2): 89-123 (2010) - [j17]Patrick May, Annika Kreuchwig, Thomas Steinke, Ina Koch:
PTGL: a database for secondary structure-based protein topologies. Nucleic Acids Res. 38(Database-Issue): 326-330 (2010)
2000 – 2009
- 2009
- [j16]Jeanice Kielbassa, Ralf H. Bortfeldt, Stefan Schuster, Ina Koch:
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Comput. Biol. Chem. 33(1): 46-61 (2009) - 2008
- [j15]Ina Koch, Georg Fuellen:
A review of bioinformatics education in Germany. Briefings Bioinform. 9(3): 232-242 (2008) - [j14]Stefanie Grunwald, Astrid Speer, Jörg Ackermann, Ina Koch:
Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosyst. 92(2): 189-205 (2008) - [j13]Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch:
Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinform. 9 (2008) - 2007
- [j12]Andrea Sackmann, Dorota Formanowicz, Piotr Formanowicz, Ina Koch, Jacek Blazewicz:
An analysis of the Petri net based model of the human body iron homeostasis process. Comput. Biol. Chem. 31(1): 1-10 (2007) - 2006
- [j11]Andrea Sackmann, Monika Heiner, Ina Koch:
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform. 7: 482 (2006) - [j10]Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, Dieter Jahn:
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res. 34(Web-Server-Issue): 510-515 (2006) - 2005
- [j9]Ina Koch, Björn H. Junker, Monika Heiner:
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinform. 21(7): 1219-1226 (2005) - [j8]Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser:
Columba: an integrated database of proteins, structures, and annotations. BMC Bioinform. 6: 81 (2005) - [j7]Louchka Popova-Zeugmann, Monika Heiner, Ina Koch:
Time Petri Nets for Modelling and Analysis of Biochemical Networks. Fundam. Informaticae 67(1-3): 149-162 (2005) - 2004
- [j6]Patrick May, Stefan Barthel, Ina Koch:
PTGL - a web-based database application for protein topologies. Bioinform. 20(17): 3277-3279 (2004) - [j5]Ina Koch, Markus Schüler, Monika Heiner:
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks. Silico Biol. 5(2): 129-137 (2004) - [c7]Monika Heiner, Ina Koch:
Petri Net Based Model Validation in Systems Biology. ICATPN 2004: 216-237 - [c6]Kristian Rother, Heiko Müller, Silke Trißl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser:
Columba: Multidimensional Data Integration of Protein Annotations. DILS 2004: 156-171 - 2003
- [j4]Klaus Voss, Monika Heiner, Ina Koch:
Steady state analysis of metabolic pathways using Petri nets. Silico Biol. 3(3): 367-387 (2003) - [c5]Monika Heiner, Ina Koch, Jürgen Will:
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB 2003: 173 - 2002
- [j3]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinform. 18(2): 351-361 (2002) - [c4]Stéphanie Boué, Martin Vingron, Evgenia V. Kriventseva, Ina Koch:
Theoretical analysis of alternative splice forms using computational methods. ECCB 2002: 65-73 - 2001
- [j2]Ina Koch:
Enumerating all connected maximal common subgraphs in two graphs. Theor. Comput. Sci. 250(1-2): 1-30 (2001) - 2000
- [c3]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae. German Conference on Bioinformatics 2000: 115-120
1990 – 1999
- 1999
- [c2]Ina Koch, Stefan Schuster, Monika Heiner:
Simulation and analysis of metabolic networks by time-dependent Petri nets. German Conference on Bioinformatics 1999: 208-209 - 1997
- [c1]Ina Koch, Thomas Lengauer:
Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method. ISMB 1997: 167-178 - 1996
- [j1]Ina Koch, Thomas Lengauer, Egon Wanke:
An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures. J. Comput. Biol. 3(2): 289-306 (1996)
Coauthor Index
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