Ina Koch

Publication Activity (10 Years)

Years Active: 1996-2024
Publications (10 Years): 25

Top Topics

Diabetes Mellitus

Systems Biology

Using Artificial Neural Networks

Top Venues

PLoS Comput. Biol.

BMC Medical Imaging

Publications

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)
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)
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) (2023)
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) (2023)
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) (2022)
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 (2022)
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)
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) (2021)
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) (2021)
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)
Jennifer Hannig, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch
isiKnock: in silico knockouts in signaling pathways. Bioinform. 35 (5) (2019)
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) (2017)
Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz, Ina Koch
The autophagy interaction network of the aging model Podospora anserina. BMC Bioinform. 18 (1) (2017)
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) (2016)
Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, Ina Koch
The new protein topology graph library web server. Bioinform. 32 (3) (2016)
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)
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)
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) (2016)
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)
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 (2015)
Heiko Giese, Jörg Ackermann, Ulrich Brandt, Ilka Wittig, Ina Koch
Cluster analysis and visualization techniques for large datasets in complexome profiling. PeerJ Prepr. 3 (2015)
Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann, Ina Koch
MONALISA for stochastic simulations of Petri net models of biochemical systems. BMC Bioinform. 16 (2015)
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 (2015)
Ina Koch
Petri nets in systems biology. Softw. Syst. Model. 14 (2) (2015)
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) (2015)
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)
Ina Koch, Wolfgang Reisig, Falk Schreiber
Petri Nets in the Biosciences. it Inf. Technol. 56 (2) (2014)
Ina Koch
Petrinetze in der Systembiologie. Inform. Spektrum 37 (3) (2014)
Jens Einloft, Jörg Ackermann, Joachim Nöthen, Ina Koch
MonaLisa - visualization and analysis of functional modules in biochemical networks. Bioinform. 29 (11) (2013)
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 (2013)
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) (2013)
Tim Schäfer, Patrick May, Ina Koch
Computation and Visualization of Protein Topology Graphs Including Ligand Information. GCB (2012)
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) (2012)
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) (2010)
Patrick May, Annika Kreuchwig, Thomas Steinke, Ina Koch
PTGL: a database for secondary structure-based protein topologies. Nucleic Acids Res. 38 (Database-Issue) (2010)
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) (2009)
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)
Stefanie Grunwald, Astrid Speer, Jörg Ackermann, Ina Koch
Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosyst. 92 (2) (2008)
Ina Koch, Georg Fuellen
A review of bioinformatics education in Germany. Briefings Bioinform. 9 (3) (2008)
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) (2007)
Andrea Sackmann, Monika Heiner, Ina Koch
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform. 7 (2006)
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) (2006)
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) (2005)
Louchka Popova-Zeugmann, Monika Heiner, Ina Koch
Time Petri Nets for Modelling and Analysis of Biochemical Networks. Fundam. Informaticae 67 (1-3) (2005)
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 (2005)
Patrick May, Stefan Barthel, Ina Koch
PTGL - a web-based database application for protein topologies. Bioinform. 20 (17) (2004)
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) (2004)
Monika Heiner, Ina Koch
Petri Net Based Model Validation in Systems Biology. ICATPN (2004)
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)
Klaus Voss, Monika Heiner, Ina Koch
Steady state analysis of metabolic pathways using Petri nets. Silico Biol. 3 (3) (2003)
Monika Heiner, Ina Koch, Jürgen Will
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis. CMSB (2003)
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) (2002)
Stéphanie Boué, Martin Vingron, Evgenia V. Kriventseva, Ina Koch
Theoretical analysis of alternative splice forms using computational methods. ECCB (2002)
Ina Koch
Enumerating all connected maximal common subgraphs in two graphs. Theor. Comput. Sci. 250 (1-2) (2001)
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)
Ina Koch, Stefan Schuster, Monika Heiner
Simulation and analysis of metabolic networks by time-dependent Petri nets. German Conference on Bioinformatics (1999)
Ina Koch, Thomas Lengauer
Detection of Distant Structural Similarities in a Set of Proteins Using a Fast Graph-Based Method. ISMB (1997)
Ina Koch, Thomas Lengauer, Egon Wanke
An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures. J. Comput. Biol. 3 (2) (1996)