An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures. - Ina Koch; Thomas Lengauer; Egon Wanke (J. Comput. Biol., 1996)

Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method. - Ina Koch; Thomas Lengauer (ISMB, 1997)

Simulation and analysis of metabolic networks by time-dependent Petri nets. - Ina Koch; Stefan Schuster; Monika Heiner (German Conference on Bioinformatics, 1999)

Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae. - Stefan Schuster; Thomas Pfeiffer 004; Ferdinand Moldenhauer; Ina Koch; Thomas Dandekar (German Conference on Bioinformatics, 2000)

Enumerating all connected maximal common subgraphs in two graphs. - Ina Koch (Theor. Comput. Sci., 2001)

Theoretical analysis of alternative splice forms using computational methods. - Stéphanie Boué; Martin Vingron; Evgenia V. Kriventseva; Ina Koch (ECCB, 2002)

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. - Stefan Schuster; Thomas Pfeiffer 004; Ferdinand Moldenhauer; Ina Koch; Thomas Dandekar (Bioinform., 2002)

Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. - Monika Heiner; Ina Koch; Jürgen Will (CMSB, 2003)

Steady state analysis of metabolic pathways using Petri nets. - Klaus Voss; Monika Heiner; Ina Koch (Silico Biol., 2003)

Petri Net Based Model Validation in Systems Biology. - Monika Heiner; Ina Koch (ICATPN, 2004)

Columba: Multidimensional Data Integration of Protein Annotations. - Kristian Rother; Heiko Müller 001; Silke Trißl; Ina Koch; Thomas Steinke 001; Robert Preissner; Cornelius Frömmel; Ulf Leser (DILS, 2004)

PTGL - a web-based database application for protein topologies. - Patrick May; Stefan Barthel; Ina Koch (Bioinform., 2004)

STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks. - Ina Koch; Markus Schüler; Monika Heiner (Silico Biol., 2004)

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. - Ina Koch; Björn H. Junker; Monika Heiner (Bioinform., 2005)

Columba: an integrated database of proteins, structures, and annotations. - Silke Trißl; Kristian Rother; Heiko Müller 001; Thomas Steinke 001; Ina Koch; Robert Preissner; Cornelius Frömmel; Ulf Leser (BMC Bioinform., 2005)

Time Petri Nets for Modelling and Analysis of Biochemical Networks. - Louchka Popova-Zeugmann; Monika Heiner; Ina Koch (Fundam. Informaticae, 2005)

Application of Petri net based analysis techniques to signal transduction pathways. - Andrea Sackmann; Monika Heiner; Ina Koch (BMC Bioinform., 2006)

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. - Maurice Scheer; Frank Klawonn; Richard Münch; Andreas Grote; Karsten Hiller; Claudia Choi; Ina Koch; Max Schobert; Elisabeth Härtig; Ulrich Klages; Dieter Jahn (Nucleic Acids Res., 2006)

An analysis of the Petri net based model of the human body iron homeostasis process. - Andrea Sackmann; Dorota Formanowicz; Piotr Formanowicz; Ina Koch; Jacek Blazewicz (Comput. Biol. Chem., 2007)

A review of bioinformatics education in Germany. - Ina Koch; Georg Fuellen (Briefings Bioinform., 2008)

Petri net modelling of gene regulation of the Duchenne muscular dystrophy. - Stefanie Grunwald; Astrid Speer; Jörg Ackermann 001; Ina Koch (Biosyst., 2008)

Modularization of biochemical networks based on classification of Petri net t-invariants. - Eva Grafahrend-Belau; Falk Schreiber; Monika Heiner; Andrea Sackmann; Björn H. Junker; Stefanie Grunwald; Astrid Speer; Katja Winder; Ina Koch (BMC Bioinform., 2008)

Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. - Jeanice Kielbassa; Ralf H. Bortfeldt; Stefan Schuster; Ina Koch (Comput. Biol. Chem., 2009)

Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach. - Ralf H. Bortfeldt; Stefan Schuster; Ina Koch (Silico Biol., 2010)

PTGL: a database for secondary structure-based protein topologies. - Patrick May; Annika Kreuchwig; Thomas Steinke 001; Ina Koch (Nucleic Acids Res., 2010)

Computation and Visualization of Protein Topology Graphs Including Ligand Information. - Tim Schäfer; Patrick May; Ina Koch (GCB, 2012)

Sodium dependent glucose transporter (SGLT) 1 / 2 - elucidating inhibitor SAR and selectivity using homology modelling and 3D QSAR studies. - Susann Vorberg; Ina Koch; Christian Buning (J. Cheminformatics, 2012)

MonaLisa - visualization and analysis of functional modules in biochemical networks. - Jens Einloft; Jörg Ackermann 001; Joachim Nöthen; Ina Koch (Bioinform., 2013)

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. - Sören Müller; Lukas Rycak; Peter Winter; Günter Kahl; Ina Koch; Björn Rotter (Bioinform., 2013)

Image database analysis of Hodgkin lymphoma. - Tim Schäfer; Hendrik Schäfer; Alexander Schmitz; Jörg Ackermann 001; Norbert Dichter; Claudia Döring 002; Sylvia Hartmann; Martin-Leo Hansmann; Ina Koch (Comput. Biol. Chem., 2013)

APADB: a database for alternative polyadenylation and microRNA regulation events. - Sören Müller; Lukas Rycak; Fabian Afonso-Grunz; Peter Winter; Adam M. Zawada; Ewa Damrath; Jessica Scheider; Juliane Schmäh; Ina Koch; Günter Kahl; Björn Rotter (Database J. Biol. Databases Curation, 2014)

Petrinetze in der Systembiologie. - Ina Koch (Inform. Spektrum, 2014)

Petri Nets in the Biosciences. - Ina Koch; Wolfgang Reisig; Falk Schreiber (it Inf. Technol., 2014)

NOVA: a software to analyze complexome profiling data. - Heiko Giese; Jörg Ackermann 001; Heinrich Heide; Lea Bleier; Stefan Dröse; Ilka Wittig; Ulrich Brandt; Ina Koch (Bioinform., 2015)

MONALISA for stochastic simulations of Petri net models of biochemical systems. - Pavel Balazki; Klaus Lindauer; Jens Einloft; Jörg Ackermann 001; Ina Koch (BMC Bioinform., 2015)

Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems. - Pavel Balazki; Klaus Lindauer; Jens Einloft; Jörg Ackermann 001; Ina Koch (BMC Bioinform., 2015)

Unsupervised image segmentation for microarray spots with irregular contours and inner holes. - Bogdan Belean; Monica Borda; Jörg Ackermann 001; Ina Koch; Ovidiu Balacescu (BMC Bioinform., 2015)

Cluster analysis and visualization techniques for large datasets in complexome profiling. - Heiko Giese; Jörg Ackermann 001; Ulrich Brandt; Ilka Wittig; Ina Koch (PeerJ Prepr., 2015)

Petri nets in systems biology. - Ina Koch (Softw. Syst. Model., 2015)

HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features. - Frank Klawonn; Junxi Wang; Ina Koch; Jörg Eberhard; Mohamed Omar (IDA, 2016)

Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. - Oliver Philipp; Heinz D. Osiewacz; Ina Koch (Bioinform., 2016)

CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach. - Hendrik Schäfer; Tim Schäfer; Jörg Ackermann 001; Norbert Dichter; Claudia Döring 002; Sylvia Hartmann; Martin-Leo Hansmann; Ina Koch (Bioinform., 2016)

The new protein topology graph library web server. - Tim Schäfer; Andreas Scheck; Daniel Bruneß; Patrick May; Ina Koch (Bioinform., 2016)

APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone. - Melanie Laßek; Jens Weingarten; Martin Wegner; Benjamin F. Mueller; Marion Rohmer; Dominic Baeumlisberger; Tabiwang N. Arrey; Meike Hick; Jörg Ackermann 001; Amparo Acker-Palmer; Ina Koch; Ulrike Müller; et al. (PLoS Comput. Biol., 2016)

In Silico Knockout Studies of Xenophagic Capturing of Salmonella. - Jennifer Scheidel; Leonie Amstein; Jörg Ackermann 001; Ivan Dikic; Ina Koch (PLoS Comput. Biol., 2016)

Quantitative Analysis. - Jörg Ackermann 001; Ina Koch (Modeling in Systems Biology, The Petri Net Approach, 2016)

Introduction. - Ina Koch; Falk Schreiber (Modeling in Systems Biology, The Petri Net Approach, 2016)

The autophagy interaction network of the aging model Podospora anserina. - Oliver Philipp; Andrea Hamann; Heinz D. Osiewacz; Ina Koch (BMC Bioinform., 2017)

Manatee invariants reveal functional pathways in signaling networks. - Leonie Amstein; Jörg Ackermann 001; Jennifer Scheidel; Simone Fulda; Ivan Dikic; Ina Koch (BMC Syst. Biol., 2017)

Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa. - Ina Koch (Carl Adam Petri: Ideas, Personality, Impact, 2019)

isiKnock: in silico knockouts in signaling pathways. - Jennifer Hannig; Heiko Giese; Börje Schweizer; Leonie Amstein; Jörg Ackermann 001; Ina Koch (Bioinform., 2019)

Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma. - Jennifer Hannig; Hendrik Schäfer; Jörg Ackermann 001; Marie Hebel; Tim Schäfer; Claudia Döring 002; Sylvia Hartmann; Martin-Leo Hansmann; Ina Koch (PLoS Comput. Biol., 2020)

Reconstruction of Protein-Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina. - Ina Koch; Oliver Philipp; Andrea Hamann; Heinz D. Osiewacz (Protein-Protein Interaction Networks, 2020)

PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. - Jan Niclas Wolf; Marcus Keßler; Jörg Ackermann 001; Ina Koch (Bioinform., 2021)

Potential of high dimensional radiomic features to assess blood components in intraaortic vessels in non-contrast CT scans. - Scherwin Mahmoudi; Simon S. Martin; Jörg Ackermann 001; Yauheniya Zhdanovich; Ina Koch; Thomas J. Vogl; Moritz H. Albrecht; Lukas Lenga; Simon Bernatz (BMC Medical Imaging, 2021)

The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets. - Kira Trares; Jörg Ackermann 001; Ina Koch (Biosyst., 2022)

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. - Aaron W. Sievering; Peter Wohlmuth; Nele Geßler; Melanie A. Gunawardene; Klaus Herrlinger; Berthold Bein; Dirk Arnold 003; Martin Bergmann; Lorenz Nowak; Christian Gloeckner; Ina Koch; Martin Bachmann; et al. (BMC Medical Informatics Decis. Mak., 2022)

Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis. - Leonie Amstein; Jörg Ackermann 001; Jennifer Hannig; Ivan Dikic; Simone Fulda; Ina Koch (PLoS Comput. Biol., 2022)

Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology. - Yauheniya Zhdanovich; Jörg Ackermann 001; Peter J. Wild; Jens Köllermann; Katrin Bankov; Claudia Döring 002; Nadine Flinner; Henning Reis; Mike Wenzel; Benedikt Höh; Philipp Mandel; Thomas J. Vogl; et al. (BMC Bioinform., 2023)

Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks. - Julienne Siptroth; Olga Moskalenko; Carsten Krumbiegel; Jörg Ackermann 001; Ina Koch; Heike Pospisil (Discov. Artif. Intell., 2023)

Radiomics for therapy-specific head and neck squamous cell carcinoma survival prognostication (part I). - Simon Bernatz; Ines Böth; Jörg Ackermann 001; Iris Burck; Scherwin Mahmoudi; Lukas Lenga; Simon S. Martin; Jan-Erik Scholtz; Vitali Koch; Leon D. Grünewald; Ina Koch; Timo Stöver; et al. (BMC Medical Imaging, 2023)

Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. - Florian J. Gisdon; Mariella Zunker; Jan Niclas Wolf; Kai Prüfer; Jörg Ackermann 001; Christoph Welsch; Ina Koch (Bioinform., 2024)

Computational analysis of IL-6/IL-22 signaling in liver disease. - Marcus Keßler; Lara Klemt; Marius Kirchner; Jörg Ackermann 001; Heiko Mühl; Christoph Welsch; Ina Koch (Biosyst., 2025)