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

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

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)

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)

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)

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)

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)

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)

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)

Comparison of radiomics models and dual-energy material decomposition to decipher abdominal lymphoma in contrast-enhanced CT. - Simon Bernatz; Vitali Koch; Daniel Pinto dos Santos; Jörg Ackermann 001; Leon D. Grünewald; Inga Weitkamp; Ibrahim Yel; Simon S. Martin; Lukas Lenga; Jan-Erik Scholtz; Thomas J. Vogl; Scherwin Mahmoudi (Int. J. Comput. Assist. Radiol. Surg., 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)