Ina Koch

64 papers A 1B 1C 1Journal 50Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Computational analysis of IL-6/IL-22 signaling in liver disease.
Biosyst.
Marcus Keßler, Lara Klemt, Marius Kirchner, Jörg Ackermann, Heiko Mühl, Christoph Welsch, Ina Koch
2024 J jnl
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes.
Bioinform.
Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch
2023 J jnl
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology.
BMC Bioinform.
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
2023 J jnl
Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks.
Discov. Artif. Intell.
Julienne Siptroth, Olga Moskalenko, Carsten Krumbiegel, Jörg Ackermann, Ina Koch, Heike Pospisil
2023 J jnl
Radiomics for therapy-specific head and neck squamous cell carcinoma survival prognostication (part I).
BMC Medical Imaging
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
2022 J jnl
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.
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
2022 J jnl
Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis.
PLoS Comput. Biol.
Leonie Amstein, Jörg Ackermann, Jennifer Hannig, Ivan Dikic, Simone Fulda, Ina Koch
2022 J jnl
The canonical and non-canonical NF-κB pathways and their crosstalk: A comparative study based on Petri nets.
Biosyst.
Kira Trares, Jörg Ackermann, Ina Koch
2021 J jnl
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures.
Bioinform.
Jan Niclas Wolf, Marcus Keßler, Jörg Ackermann, Ina Koch
2021 J jnl
Potential of high dimensional radiomic features to assess blood components in intraaortic vessels in non-contrast CT scans.
BMC Medical Imaging
Scherwin Mahmoudi, Simon S. Martin, Jörg Ackermann, Yauheniya Zhdanovich, Ina Koch, Thomas J. Vogl, Moritz H. Albrecht, Lukas Lenga, Simon Bernatz
2020 J jnl
Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma.
PLoS Comput. Biol.
Jennifer Hannig, Hendrik Schäfer, Jörg Ackermann, Marie Hebel, Tim Schäfer, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch
2020 — ch.
Reconstruction of Protein-Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in
Protein-Protein Interaction Networks
Ina Koch, Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz
2019 — ch.
Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa.
Carl Adam Petri: Ideas, Personality, Impact
Ina Koch
2019 J jnl
isiKnock: in silico knockouts in signaling pathways.
Bioinform.
Jennifer Hannig, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch
2017 J jnl
Manatee invariants reveal functional pathways in signaling networks.
BMC Syst. Biol.
Leonie Amstein, Jörg Ackermann, Jennifer Scheidel, Simone Fulda, Ivan Dikic, Ina Koch
2017 J jnl
The autophagy interaction network of the aging model Podospora anserina.
BMC Bioinform.
Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz, Ina Koch
2016 J jnl
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.
PLoS Comput. Biol.
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
2016 J jnl
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach.
Bioinform.
Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch
2016 B conf
HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features.
IDA
Frank Klawonn, Junxi Wang, Ina Koch, Jörg Eberhard, Mohamed Omar
2016 J jnl
In Silico Knockout Studies of Xenophagic Capturing of Salmonella.
PLoS Comput. Biol.
Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch
2016 — ch.
Introduction.
Modeling in Systems Biology, The Petri Net Approach
Ina Koch, Falk Schreiber
2016 J jnl
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.
Bioinform.
Oliver Philipp, Heinz D. Osiewacz, Ina Koch
2016 — ch.
Quantitative Analysis.
Modeling in Systems Biology, The Petri Net Approach
Jörg Ackermann, Ina Koch
2016 J jnl
The new protein topology graph library web server.
Bioinform.
Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, Ina Koch
2015 J jnl
Cluster analysis and visualization techniques for large datasets in complexome profiling.
PeerJ Prepr.
Heiko Giese, Jörg Ackermann, Ulrich Brandt, Ilka Wittig, Ina Koch
2015 J jnl
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems.
BMC Bioinform.
Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch
2015 J jnl
MONALISA for stochastic simulations of Petri net models of biochemical systems.
BMC Bioinform.
Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch
2015 J jnl
NOVA: a software to analyze complexome profiling data.
Bioinform.
Heiko Giese, Jörg Ackermann, Heinrich Heide, Lea Bleier, Stefan Dröse, Ilka Wittig, Ulrich Brandt, Ina Koch
2015 J jnl
Petri nets in systems biology.
Softw. Syst. Model.
Ina Koch
2015 J jnl
Unsupervised image segmentation for microarray spots with irregular contours and inner holes.
BMC Bioinform.
Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch, Ovidiu Balacescu
2014 J jnl
APADB: a database for alternative polyadenylation and microRNA regulation events.
Database J. Biol. Databases Curation
Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter
2014 J jnl
Petri Nets in the Biosciences.
it Inf. Technol.
Ina Koch, Wolfgang Reisig, Falk Schreiber
2014 J jnl
Petrinetze in der Systembiologie.
Inform. Spektrum
Ina Koch
2013 J jnl
Image database analysis of Hodgkin lymphoma.
Comput. Biol. Chem.
Tim Schäfer, Hendrik Schäfer, Alexander Schmitz, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch
2013 J jnl
MonaLisa - visualization and analysis of functional modules in biochemical networks.
Bioinform.
Jens Einloft, Jörg Ackermann, Joachim Nöthen, Ina Koch
2013 J jnl
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.
Bioinform.
Sören Müller, Lukas Rycak, Peter Winter, Günter Kahl, Ina Koch, Björn Rotter
2012 — conf
Computation and Visualization of Protein Topology Graphs Including Ligand Information.
GCB
Tim Schäfer, Patrick May, Ina Koch
2012 J jnl
Sodium dependent glucose transporter (SGLT) 1 / 2 - elucidating inhibitor SAR and selectivity using homology modelling and 3D QSAR studies.
J. Cheminformatics
Susann Vorberg, Ina Koch, Christian Buning
2011 — book
Modeling in Systems Biology, The Petri Net Approach
Ina Koch, Wolfgang Reisig, Falk Schreiber
2010 J jnl
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach.
Silico Biol.
Ralf H. Bortfeldt, Stefan Schuster, Ina Koch
2010 J jnl
PTGL: a database for secondary structure-based protein topologies.
Nucleic Acids Res.
Patrick May, Annika Kreuchwig, Thomas Steinke, Ina Koch
2009 J jnl
Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets.
Comput. Biol. Chem.
Jeanice Kielbassa, Ralf H. Bortfeldt, Stefan Schuster, Ina Koch
2008 J jnl
A review of bioinformatics education in Germany.
Briefings Bioinform.
Ina Koch, Georg Fuellen
2008 J jnl
Modularization of biochemical networks based on classification of Petri net t-invariants.
BMC Bioinform.
Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch
2008 J jnl
Petri net modelling of gene regulation of the Duchenne muscular dystrophy.
Biosyst.
Stefanie Grunwald, Astrid Speer, Jörg Ackermann, Ina Koch
2007 J jnl
An analysis of the Petri net based model of the human body iron homeostasis process.
Comput. Biol. Chem.
Andrea Sackmann, Dorota Formanowicz, Piotr Formanowicz, Ina Koch, Jacek Blazewicz
2006 J jnl
Application of Petri net based analysis techniques to signal transduction pathways.
BMC Bioinform.
Andrea Sackmann, Monika Heiner, Ina Koch
2006 J jnl
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
Nucleic Acids Res.
Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, Dieter Jahn
2005 J jnl
Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.
Bioinform.
Ina Koch, Björn H. Junker, Monika Heiner
2005 J jnl
Columba: an integrated database of proteins, structures, and annotations.
BMC Bioinform.
Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser
2005 J jnl
Time Petri Nets for Modelling and Analysis of Biochemical Networks.
Fundam. Informaticae
Louchka Popova-Zeugmann, Monika Heiner, Ina Koch
2004 — conf
Columba: Multidimensional Data Integration of Protein Annotations.
DILS
Kristian Rother, Heiko Müller, Silke Trißl, Ina Koch, Thomas Steinke, Robert Preissner, Cornelius Frömmel, Ulf Leser
2004 J jnl
PTGL - a web-based database application for protein topologies.
Bioinform.
Patrick May, Stefan Barthel, Ina Koch
2004 — conf
Petri Net Based Model Validation in Systems Biology.
ICATPN
Monika Heiner, Ina Koch
2004 J jnl
STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks.
Silico Biol.
Ina Koch, Markus Schüler, Monika Heiner
2003 — conf
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis.
CMSB
Monika Heiner, Ina Koch, Jürgen Will
2003 J jnl
Steady state analysis of metabolic pathways using Petri nets.
Silico Biol.
Klaus Voss, Monika Heiner, Ina Koch
2002 J jnl
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Bioinform.
Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar
2002 C conf
Theoretical analysis of alternative splice forms using computational methods.
ECCB
Stéphanie Boué, Martin Vingron, Evgenia V. Kriventseva, Ina Koch
2001 J jnl
Enumerating all connected maximal common subgraphs in two graphs.
Theor. Comput. Sci.
Ina Koch
2000 — conf
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae.
German Conference on Bioinformatics
Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar
1999 — conf
Simulation and analysis of metabolic networks by time-dependent Petri nets.
German Conference on Bioinformatics
Ina Koch, Stefan Schuster, Monika Heiner
1997 A conf
Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method.
ISMB
Ina Koch, Thomas Lengauer
1996 J jnl
An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures.
J. Comput. Biol.
Ina Koch, Thomas Lengauer, Egon Wanke