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Ina 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
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
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
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
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
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
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
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
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
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
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
The autophagy interaction network of the aging model Podospora anserina. BMC Bioinform. 18(1): 196:1-196:15 (2017) - [j36]Leonie Amstein
Manatee invariants reveal functional pathways in signaling networks. BMC Syst. Biol. 11(1): 72:1-72:11 (2017) - 2016
- [j35]Hendrik Schäfer
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach. Bioinform. 32(1): 122-129 (2016) - [j34]Tim Schäfer
The new protein topology graph library web server. Bioinform. 32(3): 474-476 (2016) - [j33]Oliver Philipp, Heinz D. Osiewacz
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
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
In Silico Knockout Studies of Xenophagic Capturing of Salmonella. PLoS Comput. Biol. 12(12) (2016) - [c9]Frank Klawonn
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
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
NOVA: a software to analyze complexome profiling data. Bioinform. 31(3): 440-441 (2015) - [j29]Pavel Balazki
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
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
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
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
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
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
Computation and Visualization of Protein Topology Graphs Including Ligand Information. GCB 2012: 108-118 - 2011
- [e1]Ina Koch
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
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
A review of bioinformatics education in Germany. Briefings Bioinform. 9(3): 232-242 (2008) - [j14]Stefanie Grunwald
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
Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinform. 9 (2008) - 2007
- [j12]Andrea Sackmann, Dorota Formanowicz
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
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform. 7: 482 (2006) - [j10]Maurice Scheer, Frank Klawonn
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
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
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
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
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
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB 2003: 173 - 2002
- [j3]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch
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
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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