Current Publications
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes
Bioinformatics, 2024, btae112, https://doi.org/10.1093/bioinformatics/btae112
Inhalation of panaxadiol alleviates lung inflammation via inhibiting TNFA/TNFAR and IL7/IL7R signalling between macrophages and epithelial cells
Journal of Ginseng Research 48(1):77-88, 2024, https://doi.org/10.1016/j.jgr.2023.09.002
Does dual-energy computed tomography material decomposition improve radiomics capability to predict survival in head and neck squamous cell carcinoma patients? A preliminary investigation.
Journal of Computer Assisted Tomography 48(2):323-333, 3/4 10-1097, 2024, DOI: 10.1097/RCT.0000000000001551
Universality of Form: The Case of Retinal Cone Photoreceptor Mosaics.
Entropy 25 (5):766, 2023, https://doi.org/10.3390/e25050766
Thermodynamic properties of non-Hermitian Nambu–Jona-Lasinio models
Physical Review D 107 (1):016015, 2023, https://doi.org/10.1103/PhysRevD.107.016015
The RHOA Mutation G17V Does Not Lead to Increased Migration of Human Malignant T Cells but Is Associated with Matrix Remodelling.
Cancers 15:3226, 2023, doi: 10.3390/cancers15123226
Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV2 infection.
PLoS ONE 18(11): e0287725, 2023, https://doi.org/10.1371/journal.pone.0287725
Three-dimensional human germinal centers of different sizes in patients diagnosed with lymphadenitis show comparative constant relative volumes of B cells, T cells, follicular dendritic cells, and macrophages.
Acta Histochemica, 125(7):152075, 2023, https://doi.org/10.1016/j.acthis.2023.152075
Bernatz S, Böth I, Ackermann, J, Burck I, Mahmoudi S, Lenga L, Simon S. Martin SS, Scholtz J-E, Koch V, Grünewald LD, Koch I, Stöver T, Wild PJ, Winkelmann R, Vogl TJ, Dos Santos DP
Radiomics for therapy-specific head and neck squamous cell carcinoma survival prognostication (part I).
BMC Medical Imaging 23(1):1-15, 2023, https://doi.org/10.1186/s12880-023-01034-1
Stochastic modeling of the dynamics of Salmonella infection of epithelial cells.
bioRxiv, 2023-04, 2023, https://doi.org/10.1101/2023.04.02.535247
Siptroth J, Moskalenko O, Krumbiegel C, Ackermann J, Koch I, Pospisil H
Investigation of metabolic pathways from gut microbiome analyses regarding type 2 diabetes mellitus using artificial neural networks.
Discover Artificial Intelligence 3:1-9, 2023, https://doi.org/10.1007/s44163-023-00064-6
Ren Y, Song Z, Rieser J, Ackermann J, Koch I, Lv X, Ji T, Cai X
USP15 Represses Hepatocellular Carcinoma Progression by Regulation of Pathways of Cell Proliferation and Cell Migration: A System Biology Analysis.
Cancers 15:1371, 2023, https://doi.org/10.3390/cancers15051371
Bernatz S, Koch V, Dos Santos D Pinto, Ackermann J, Grünewald LD, Weitkamp I, Yel I, Martin SS, Lenga L, Scholtz J-E, Vogl TJ, Mahmoudi S
Comparison of radiomics models and dual-energy material decomposition to stratify abdominal lymphoma in contrast-enhanced CT
International Journal of Computer Assisted Radiology and Surgery 1-11, 2023, https://doi.org/10.1007/s11548-023-02854-w
Mahmoudi S, Bernatz S , Ackermann J, Koch V, Dos Santos D Pinto, Grünewald LD, Yel I, Martin SS, Scholtz J-E, Stehle A, Walter D, Zeuzem S, Wild PJ, Vogl TJ, Kinzler MN
Computed Tomography Radiomics to Differentiate Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma
Clinical Oncology 35(5):e312-e318, 2023, https://doi.org/10.1016/j.clon.2023.01.018
Hansmann M-L, Klauschen F., Samek W., Müller K-R, Donnadieu E, Scharf S, Hartmann S, Koch I, Ackermann J, Pantanowitz L, Schäfer H, Wurzel P
Imaging bridges pathology and radiology.
Journal of Pathology Informatics 14:100298, 2023, https://doi.org/10.1016/j.jpi.2023.100298)
Scharf S, Ackermann J, Bender L, Wurzel P, Schäfer H, Hansmann M-L, Koch I
Holistic view on the structure of immune response: Petri net model.
Biomedicines, Special Issue: Pathomechanisms of Disturbances Underlying Chronic Disorders, 11(2):432, 2023, https://doi.org/10.3390/biomedicines11020452
Bernatz S, Elenberger O, Ackermann J, Lenga L, Martin S, Scholtz J-E, Koch V, Grünewald LD, Herrmann Y, Kinzler MN, Stehle A, Koch I, Zeuzem S, Bankov K, Reis H, Flinner N, Schulze F, Wild PJ, Hammerstingl R, Eichler K, Gruber-Rouh T, Vog TJ, dos Santos DP, Mahmoudi S
CT-radiomics and clinical risk scores for response and overall survival prognostication in TACE HCC patients.
Scientific Reports 13:533, 2023, https://doi.org/10.1038/s41598-023-27714-0
Siptroth J, Moskalenko O, Krumbiegel C, Ackermann J, Koch I, and Pospisil H
Variation of butyrate production in the gut microbiome in type 2 diabetes patients.
International Microbiology, 2023, https://doi.org/10.1007/s10123-023-00324-6
Zhdanovich Y, Ackermann J, Wild PJ, Kollermann J, Bankov K, Döring C, Flinne N, Reis H, Wenzel M, Hoh B, Mandel Ph, Vogl TJ, Harter P, Filipski K, Koch I, Bernatz S
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology.
BMC Bioinformatics 24:1, 2023, https://doi.org/10.1186/s12859-022-05124-9
Mahmoudi S, Koch V, dos Santos DP, Ackermann J, Grünewald L, Weitkamp I, Yel I., Martin S, Albrecht M, Scholtz J, Vogl T, Bernatz S
Imaging biomarkers to stratify lymph node metastases in abdominal CT – Is radiomics superior to dual-energy material decomposition?
European Journal of Radiology Open, 10:100459, 2023, https://doi.org/10.1016/j.ejro.2022.100459
Sayeed SD, Wolf JN, Koch I, Song G
Protein Fold Classification using Graph Neural Network and Protein Topology Graph.
bioRxiv, 2022-08, 2023, https://doi.org/10.1101/2022.08.10.503436
Wagner P, Strodthoff N, Wurzel P, Marban A, Scharf S, Schäfer H, Seegerer Ph, Loth A, Hartmann S, Klauschen F, Müller KR, Samek W, Hansmann M-L
New definitions of human lymphoid and follicular cell entities in lymphatic tissue by machine learning.
Scientific Reports, 12(1):1-13, 2023, https://doi.org/10.1038/s41598-022-18097-9
Amstein L, Ackermann J, Hannig J ,Đikić I, Fulda S, Koch I
Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways using Petri nets.
PLOS Computational Biology 18(8):e1010383, 2022, https://doi.org/10.1371/journal.pcbi.1010383
Bernatz S, Weitkamp I, Scholtz J, Koch V, Grünewald L, Mader C, Ackermann J, Albrecht M, Martin S, Vogl T, Mahmoudi S
Quantitative analysis of in-TIPS thrombosis in abdominal CT.
European Journal of Radiology Open 9, 2022, https://doi.org/10.1016/j.ejro.2022.100405
Trares K, Ackermann J, Koch I
The canonical and non-canonical NF-κB pathways and their crosstalk: a comparative study based on Petri nets.
Biosystems 211, 2022, https://doi.org/10.1016/j.biosystems.2021.104564
Deli A, Scharf S, Steiner Y, Bein J, Hansmann M-L, Hartmann S
3D analyses reveal T cells with activated nuclear features in T-cell/histiocyte-rich large B-cell lymphoma.
Modern Pathology, 2022, https://doi.org/10.1038/s41379-022-01016-8
Hartmann S, Scharf S, Steiner Y, Loth A, Donnadieu E, Flinner N, Poeschel V, Angel S, Bewarder M, Bein J, Brunnberg U, Bozzato A, Schick B, Stilgenbauer S, Bohle R, Thurner L, Hansmann M-L
Landscape of 4D cell interaction in Hodgkin and Non-Hodgkin lymphomas.
Cancers 13(29): 5208, 2021, https://doi.org/10.3390/cancers13205208
Giese H, Meisterknecht J, Heidler J, Wittig I
Mitochondrial Complexome Profiling.
In: Minczuk M., Rorbach J. (eds) Mitochondrial Gene Expression. Methods in Molecular Biology 2192: 269-285, 2021, https://doi.org/10.1007/978-1-0716-0834-0_19
Tao M, Luo J, Gu T, Yu X, Song Z, Jun Y, Gu H, Han K, Huang X, Yu W, Sun S, Zhang Z, Liu L, Chen X, Zhang L, Luo C, Wang Q
LPCAT1 reprogramming cholesterol metabolism promotes the progression of esophageal squamous cell carcinoma.
Cell Death & Disease, 12: 845, 2021, https://doi.org/10.1038/s41419-021-04132-6
Mahmoudi S, Martin S, Ackermann J, Zhdanovich Y, Koch I, Vogl T, Albrecht M, Lenga L, Bernatz S
Potential of high dimensional radiomic features to assess blood components in intraaortic vessels in non-contrast CT scans.
BMC Medical Imaging, 21:123, 2021, https://doi.org/10.1186/s12880-021-00654-9
Lumer L, Wurzel P, Scharf S, Schäfer H, Ackermann J, Koch I, Hansmann M-L
3D connectomes of reactive and neoplastic CD30 positive lymphoid cells and surrounding cell type.
Acta Histochemica, 123(5):151750, 2021, https://doi.org/10.1016/j.acthis.2021.151750
Bernatz S, Zhdanovich Y, Ackermann J, Koch I, Wild P, dos Santos DP, Vogl T, Kaltenbach B, Rosbach N
Impact of rescanning and repositioning on radiomic features employing a multi-object phantom in magnetic resonance imaging.
Scientific Reports, 11:14248, 2021, https://doi.org/10.1038/s41598-021-93756-x
Bernatz S, Mahmoudi S, Martin S, Burck I, Vogl T, Ackermann J, Stöver T, Balster S, Gröger M
Differences in mastoid and middle-ear cavity opacification in CT between intensive care patients and patients with acute mastoiditis requiring surgical treatment.
European Journal of Radiology 8:100365, 2021, https://doi.org/10.1016/j.ejro.2021.100365
Koch I, Miguel Andrade-Navarro M, Schulz MH, Zarnack K
Bioinformatics in theory and application – highlights of the 36th German Conference on Bioinformatics
Biololgical Chemistry 402(8):869–870, 2021, https://doi.org/10.1515/hsz-2021-0298
Keßler M, Wittig I, Ackermann J, Koch I
Prediction and Analysis of Redox-Sensitive Cysteines Using Machine Learning and Statistical Methods
Biological Chemistry 402(8):925–935, 2021, https://doi.org/10.1515/hsz-2020-0321
Wurzel P, Ackermann J, Schäfer H, Scharf S, Hansmann M-L, Koch I
Detection of follicular regions in actin-stained whole slide images of the human lymph node by shock filter
Biological Chemistry 402(8):991-999, 2021, https://doi.org/10.1515/hsz-2020-0178
Thomos M, Wurzel P, Scharf S, Koch I, Hansmann M
3D investigation shows walls and wall-like structures around human germinal centres, probably regulating T- and B-cell entry and exit
PLoS One 15(11): e0242177 ,2020, https://doi.org/10.1371/journal.pone.0242177
Wolf J, Keßler M, Ackermann J, Koch I
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures
Bioinformatics 37(7):1032–1034, 2020, https://doi.org/10.1093/bioinformatics/btaa706
Bernatz S, Ackermann J, Mandel P, Kaltenbach B, Zhdanovich Y, Harter PN, Döring C, Hammerstingl R, Bodelle B, Smith K, Bucher A, Albrecht M, Rosbach N, Basten L, Yel I, Wenzel M, Bankov K, Koch I, Chun FK-H, Köllermann J, Wild PJ, Vogl, TJ.
Comparison of Machine Learning Algorithms to predict Clinically Significant Prostate Cancer of the Peripheral Zone with multiparametric MRI using Clinical Assessment Categories and Radiomic Features
European Radiology 30: 6757–6769, 2020, https://doi.org/10.1007/s00330-020-07064-5
Yousaf A, Waltes R, Haslinger D, Klauck S, Duketis E, Sachse M, Voran A, Biscaldi M, Schulte-Rüther M, Cichon S, Nöthen M, Ackermann J, Koch I, Freitag C, Chiocchetti A
Quantitative genome-wide association study of six phenotypic subdomains identifies novel genome-wide significant variants in Autism Spectrum Disorder
Translational Psychiatry, 10(1):215, 2020, https://doi.org/10.1038/s41398-020-00906-2
Hannig J, Schäfer H, Ackermann J, Hebel M, Schäfer T, Döring C, Hartmann S, Hansmann M-L, Koch I
Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma
PLoS Computational Biology, 16(1), 2020, https://doi.org/10.1371/journal.pcbi.1007516
Schäfer H, Hansmann M-L, Koch I
Lymph Node Landscapes
pp. 28-29
Rieser J, Ackermann J, Koch I
Green Protein Interaction Wheel
pp. 112-113
Rieser J, Bruneß D, Ackermann J, Koch I
Interacting Spider Webs
pp. 136-138
In: Matthäus F, Matthäus S, Harris S, Hillen T (Eds.)
The Art of Theoretical Biology, Systems Biology and Bioinformatics, Springer, 2020, ISBN 978-3-030-33470-3
Koch I, Philipp O, Hamann A, Osiewacz A
Reconstruction of Protein–Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina
Methods in Molecular Biology 2074:45-55, 2020, https://doi.org/10.1007/978-1-4939-9873-9_4
Liebers J, Wurzel P, Reisinger K, Hansmann M-L
3D image analysis reveals differences of CD30 positive cells and network formation in reactive and malignant human lymphoid tissue (classical Hodgkin Lymphoma)
PLoS One 14(10):e0224156, 2019, https://doi.org/10.1371/journal.pone.0224156
Oswald M, Wurzel P, Hansmann M-L
3D analysis of morphological alterations of the fibroblastic reticular cells in reactive and neoplastic human lymph nodes
Acta Histochemica 121(7):769-775, 2019, https://doi.org/10.1016/j.acthis.2019.07.002
Trösemeier J, Rudorf S, Loessner H, Hofner B, Reuter A, Schulenborg T, Koch I, Bekeredjian-Ding I, Lipowsky R, Kamp C
Optimizing the dynamics of protein expression
Scientific Reports 9:7511, 2019, https://doi.org/10.1038/s41598-019-43857-5
Koch I
Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa
In: Carl Adam Petri: Ideas, Personality, Impact pp 217-226, 2019, https://doi.org/10.1007/978-3-319-96154-5_26
Hannig J, Giese H, Schweizer B, Amstein L, Ackermann J, Koch I
isiKnock: in silico knockouts in biochemical pathways
Bioinformatics 35(5): 892–894, 2019, https://doi.org/10.1093/bioinformatics/bty700
Hsueh Y‐C, Nicolaisen K, Gross L, Nöthen J, Schauer N, Vojta L, Ertel F, Koch I, Ladig R, Fulgosi H, Fernie A, Schleiff E
The outer membrane Omp85‐like protein P39 influences metabolic homeostasis in mature Arabidopsis thaliana
Plant Biology 20(5): 825-833, 2018, https://doi.org/10.1111/plb.12839
Singh S, Lämmle S, Giese H, Kämmerer S, Meyer-Roxlau S, Alfar E, Dihazi H, Guan K, El-Armouche A, Richter F
The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Scientific Reports 8: 177112018, 2018, https://doi.org/10.1038/s41598-018-36267-6
Scheidel J, Giese H, Schweizer B, Amstein L, Ackermann J, Koch I
isiKnock: in silico knockouts in biochemical pathways
bioRxiv, 2018, https://doi.org/10.1101/313858
Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, ... Koch I, Olaf Wolkenhauer O
Whither systems medicine?
Experimental & Molecular Medicine 50: e453, 2018, https://doi.org/10.1038/emm.2017.290
Koch I, Schäfer T
Protein super-secondary structure and quaternary structure topology: theoretical description and application
Current Opinion in Structural Biology 50: 134–143, 2018, https://doi.org/10.1016/j.sbi.2018.02.005
Norris V, Koch I, Amar P, Kepes F, Janniere L
Hypothesis: Local variations in the speed of individual DNA replication forks determine the phenotype of daughter cells
Medical Research Archives 5: 12, 2017, https://doi.org/10.18103/mra.v5i12.1598
Scheidel J, Schaefer H, Ackermann J, Hebel M, Schaefer T, Doering C, Hartmann S, Hansmann M, Koch I
Bioinformatics analysis quantifies neighborhood preferences of cancer cells in Hodgkin lymphoma
bioRxiv, 2017, https://doi.org/10.1101/228981
Todorov H, Janssen I, Honndorf S, Bause D, Gottschalk A, Baasner S, Volkert T, Faerber V, Stover J, Westphal M, Ellger B
Clinical significance and risk factors for new onset and recurring atrial fibrillation following cardiac surgery - a retrospective data analysis
BMC Anesthesiology, 17:163, 2017, https://doi.org/10.1186/s12871-017-0455-7
Ackermann J, Hogreve J
Stability and spectral properties of the dication Ne22+
Physical Chemistry Chemical Physics (PCCP) 19:32433-32442, 2017, https://doi.org/10.1039/C7CP07194A
Chiocchetti A, Yousaf A, Bour H, Haslinger D, Waltes R, Duketis E, Jarczok T, Sachse M, Biscaldi M, Degenhardt F, Herms S, Cichon S, Ackermann J, Koch I, Klauck S, Freitag C
Common functional variants of the glutamatergic system in Autism Spectrum Disorder with high and low intellectual abilities
Journal of Neural Transmission, 2017, https://doi.org/10.1007/s00702-017-1813-9
Amstein L, Ackermann J, Scheidel J, Fulda S, Dikic I, Koch I
Manatee invariants reveal functional pathways in signaling networks
BMC Systems Biology 11:72, 2017, https://doi.org/10.1186/s12918-017-0448-7
Koch I, Nöthen J, Schleiff E
Modeling the metabolism of Arabidopsis thaliana: application of network decomposition and network reduction in the context of Petri nets
Frontiers in Genetics 8: 85, 2017, https://doi.org/10.3389/fgene.2017.00085
Philipp O, Hamann A, Osiewacz H, Koch I
The autophagy interaction network of the aging model Podospora anserina
BMC Bioinformatics 18: 196, 2017, https://doi.org/10.1186/s12859-017-1603-2
Weingarten J, Weingarten M, Wegner M, Volknandt W
APP—A Novel Player within the Presynaptic Active Zone Proteome
Front. Mol. Neurosci. 10: 43, 2017, https://doi.org/10.3389/fnmol.2017.00043
Laßek M, Weingarten J, Wegner M, Neupärt M, Array T, Harde E, Beckert B, Golghalyani V, Ackermann J, Koch I, Müller U, Karas M, Acker-Palmer A, Volknandt W
APP deletion accounts for age-dependent changes in the bioenergetic metabolism and in hyperphosphorylated CaMKII at stimulated hippocampal presynaptic active zones
Front. Synaptic Neurosci. 9: 1, 2017, https://doi.org/10.3389/fnsyn.2017.00001
Scheidel J, Amstein L, Ackermann J, Dikic I, Koch I
In Silico Knockout Studies of Xenophagic Capturing of Salmonella
PLoS Computational Biology 12(12):e1005200, 2016, https://doi.org/10.1371/journal.pcbi.1005200
Klawonn F, Wang J, Koch I, Eberhard J
HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features
Advances in Intelligent Data Analysis XV, 2016, Vol. 9897 Lecture Notes in Computer Science pp 356-367, https://doi.org/10.1007/978-3-319-46349-0_31
Strecker V, Kadeer Z, Heidler J, Cruciat C, Angerer H, Giese H, Pfeiffer K, Stuart R, Wittig I
Supercomplex-associated Cox26 protein binds to cytochrome c oxidase
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 2016, https://doi.org/10.1016/j.bbamcr.2016.04.012
Laßek M, Weingarten J, Wegner M, Mueller B, Rohmer M, Baeumlisberger D, Arrey T, Hick M, Ackermann J, Acker-Palmer A, Koch I, Müller U, Karas M, Volknandt W
APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone
PLoS Computational Biology, 2016, 12(4): e1004832, https://doi.org/10.1371/journal.pcbi.1004832
Philipp O, Osiewacz H, Koch I
PATH2PPI: an R package to predict protein-protein interaction networks for a set of proteins
Bioinformatics, 2016, 32 (9): 1427-1429, https://doi.org/10.1093/bioinformatics/btv765
Laßek M, Weingarten J, Wegner M, Volknandt W
The amyloid precursor protein – a novel player within the molecular array of presynaptic nanomachines
Frontiers in Synaptic Neuroscience, 2016,7: 21; https://doi.org/10.3389/fnsyn.2015.00021
Schäfer T, Scheck A, Bruneß D, May P, Koch I
The new Protein Topology Graph Library web server
Bioinformatics, 2016, 32 (3): 474-476, https://doi.org/10.1093/bioinformatics/btv574
Schäfer H, Schäfer T, Ackermann J, Dichter N, Döring C, Hartmann S, Hansmann M, Koch I
CD30 cell graphs of Hodgkin lymphoma are not scale-free – An image analysis approach
Bioinformatics, 2016, 32 (1): 122-129, https://doi.org/10.1093/bioinformatics/btv542
Schäfer H
Automated cell detection in whole slide images of classical Hodgkin lymphoma
Der Pathologe, 2015, 36(Suppl 1): 10; doi:10.1007/s00292-015-0028-9
Schäfer T, Schäfer H, Ackermann J, Döring C, Hartmann S, Hansmann M, Koch I
Analysis of the distribution of CD30+ cells in classical Hodgkin lymphoma and lymphadenitis using graph-based methods
Der Pathologe, 2015, 36(Suppl 1): 10-11; doi:10.1007/s00292-015-0028-9
Belean B, Borda M, Ackermann J, Koch I, Balacescu O
Unsupervised Image Segmentation for Microarray Spots with Irregular Contours and Inner Holes
BMC Bioinformatics, 2015, 16: 412; doi:doi:10.1186/s12859-015-0842-3
Scheidel J, Lindauer K, Ackermann J, Koch I
Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System’s Dynamics: The Life Cycle of the Insulin Receptor
Metabolites, 2015, Special Issue Metabolic Flux Analysis, 5: 766-793, doi:10.3390/metabo5040766
Koch I
Petri nets in systems biology
Software & Systems Modeling, 2015, 14(2): 703-710, doi:10.1007/s10270-014-0421-5
Giese H, Ackermann J, Brandt U, Wittig I, Koch I
Cluster analysis and visualization techniques for large datasets in complexome profiling
PeerJ PrePrints 3:e1602, 2015, doi:10.7287/peerj.preprints.1303v1
Balazki P, Lindauer K, Einloft J, Ackermann J, Koch I
MONALISA for stochastic simulations of Petri net models of biochemical systems
BMC Bioinformatics, 2015, 16: 215, doi:10.1186/s12859-015-0596-y
Balazki P, Lindauer K, Einloft J, Ackermann J, Koch I
Erratum to: MONALISA for stochastic simulations of Petri net models of biochemical systems
BMC Bioinformatics, 2015, 16: 371, doi:10.1186/s12859-015-0725-7
Müller S, Raulefs S, Bruns P, Afonso-Grunz F, Plötner A, Thermann R, Jäger C, Schlitter A, Kong B, Regel I, Roth W.K., Rotter B, Hoffmeier K, Kahl G, Koch I, Theis F.J., Kleeff J, Winter P, Michalski C.W.
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Molecular Cancer, 2015, 14: 94, doi:10.1186/s12943-015-0358-5
Müller S, Raulefs S, Bruns P, Afonso-Grunz F, Plötner A, Thermann R, Jäger C, Schlitter A.M., Kong B, Regel I, Roth W.K., Rotter B, Hoffmeier K, Kahl G, Koch I, Theis F.J., Kleeff J, Winter P, Michalski C.W.
Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Molecular Cancer, 2015, 14:144, doi:10.1186/s12943-015-0401-6
Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf K, Schleiff E
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum
Bioinformatics and Biology Insights, 2015, 9: 1-17, doi:10.4137/BBI.S20751
Giese H, Ackermann J, Heide H, Bleier L, Dröse S, Wittig I, Brandt U, Koch I
NOVA: a software to analyze complexome profiling data
Bioinformatics, 2015, 31(3): 440-441, doi: 10.1093/bioinformatics/btu623
Trösemeier J, Lipp S, Lößner H, Koch I, Kamp C
The Right Word in the Right Place? Using an evolutionary model to link codon usage bias to an organism’s fitness.
Chalmers Conferences, 9th European Conference on Mathematical and Theoretical Biology, 2014
Müller S, Rycak L, Afonso-Grunz F, Winter P, Zawada A.M., Damrath E, Scheider J, Schmäh J, Koch I, Kahl G, Rotter B
APADB: a database for alternative polyadenylation and microRNA regulation events
Database, 2014, bau076, doi: 10.1093/database/bau076
Koch I
Petrinetze in der Systembiologie
CLB - Chemie in Labor und Biotechnik, 2014, 64(5-6): 220-228.
Koch I, Reisig W, Schreiber F
Petri Nets in the Biosciences
it - Information Technology, 2014, 56(2): 43-45, doi: 10.1515/itit-2014-1042
Najafi A, Bidkhori G, Bozorgmehr J, Koch I, Masoudi-Nejad A
Genome Scale Modeling in Systems Biology: Algorithms and Resources
Current Genomics, 2014, 15: 130-159, doi:10.2174/1389202915666140319002221
Koch I
Petrinetze in der Systembiologie
Informatik-Spektrum, 2014, 37(3): 211-219, doi:10.1007/s00287-013-0757-1
Philipp O, Hamann A, Servos J, Werner A, Koch I, Osiewacz H
A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina
PLoS ONE 2013, 8(12): e83109, doi: 10.1371/journal.pone.0083109
Amstein L, Schöne N, Fulda S, Koch I
Mathematical Modelling of the Function of Ubiquitylation in TNFR1-Mediated NF-κB Signalling
in Proceedings: "Computational Methods in Systems Biology"
CMSB 2013, 8130: 278-279, doi: 10.1007/978-3-642-40708-6
Müller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B
omiRas: A Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
Bioinformatics 2013, 29(20): 2651-2652, doi:10.1093/bioinformatics/btt457
Koch I, Ackermann J
On Functional Module Detection in Metabolic Networks
in Special Issue: "Metabolism and Systems Biology"
Metabolites 2013, 3(3): 673-700; doi:10.3390/metabo3030673n
Khakabimamaghani S, Sharafuddin I, Dichter N, Koch I, Masoudi-Nejad A
QuateXelero: an accelerated exact network motif detection algorithm
PLoS ONE, 2013, doi:10.1371/journal.pone.0068073
Schäfer T, Schäfer H, Schmitz A, Ackermann J, Dichter N, Döring C, Hartmann S, Hansmann M, Koch I
Image database analysis of Hodgkin lymphoma
Computational Biology and Chemistry, 2013, 46: 1-7, doi: 10.1016/j.compbiolchem.2013.04.003
Einloft J, Ackermann J, Nöthen J, Koch I
MonaLisa - visualization and analysis of functional modules in biochemical networks
Bioinformatics, 2013, 29: 1469-1470
Koch I, Kreuchwig A, May P
Hierarchical representation of super-secondary structures using a graph-theoretical approach
In: Protein supersecondary structure, Kister, Alexander E. (Ed.)
Springer Protocols, Humana Press, New York, Methods in Molecular Biology, 2012, 932: 7-33, doi: 10.1007/978-1-62703-065-6_2
Wittig I, Heide H, Bleier L, Schwamb B, Strecker V, Steger M, Ackermann J, Dröse S, Zörnig M, Reichert A, Koch I, Brandt U
Identification of new assembly factors of complex I by complexome profiling
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2012, 1817: S138, doi: 10.1016/j.bbabio.2012.06.363
Schäfer T, May P, Koch I
Computation and Visualization of Protein Topology Graphs Including Ligand Information
German Conference on Bioinformatics 2012, pp. 108-118
Schmitz A, Schäfer T, Schäfer H, Döring C, Ackermann J, Dichter N, Hartmann S, Hansmann M, Koch I
Automated Image Analysis of Hodgkin lymphoma
Dagstuhl Seminar "Structure Discovery in Biology: Motifs, Networks & Phylogenies", 2012
Ackermann J, Einloft J, Nöthen J, Koch I
Reduction techniques for network validation in systems biology
Journal of Theoretical Biology, 2012, 315: 71-80, doi:10.1016/j.jtbi.2012.08.042
Heide H, Bleier L, Steger M, Ackermann J, Dröse S, Schwamb B, Zörnig M, Reichert A, Koch I, Wittig I, Brandt U
Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly (MCIA)
Cell Metabolism, 2012, 16(4): 538-549
Bortfeldt R, Schuster S, Koch I
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach
Studies in Health Technology and Informatics, 2011, 162:244-78 PubMed
Koch I, Schüler M, Heiner M
STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks
Studies in Health Technology and Informatics, 2011, 162:113-21 PubMed
Voss K, Heiner M, Koch I
Petri nets for steady state analysis of metabolic systems
Studies in Health Technology and Informatics, 2011, 162:56-76 PubMed
Petri-Net Book: Modeling in Systems Biology, doi: 10.1007/978-1-84996-474-6
Koch I and Schreiber F
Introduction
In: Modeling in Systems Biology: The Petri Net Approach
Koch I, Reisig W and Schreiber F, Editors
Springer, Computational Biology 16, 2011, pp. 3-18, doi: 10.1007/978-1-84996-474-6_1
Ackermann J and Koch I
Quantitative Analysis
In: Modeling in Systems Biology: The Petri Net Approach
Koch, Reisig W and Schreiber F, Editors
Springer, Computational Biology 16, 2011, pp. 153-178, doi: 10.1007/978-1-84996-474-6_8
Ackermann J and Koch I
Network decomposition in biology - computational challenges
In: Models of Computation in Context, volume 7 of Computability in Europe
Ganchev H, Löwe B, Normann D, Soskov I, and Soskova M, Editors
St. Kliment Ohridski University Press, Sofia, 2011, pp. 39-48
Koch I
Petri Nets and GRN Models
In: Handbook of Research on Computational Methodologies in Gene Regulatory Networks
Eds. Das S, Caragea D, Welch S.M., Hsu W.H., IGI Global Hershey, 2010, chapter 25: 604-637
Koch I, Chaouiya C
Discrete Modelling: Petri Net and Logical Approaches
In: Systems Biology for Signaling Networks, Series: Systems Biology, Vol. 1, Choi, Sangdun (Ed.), Springer, Hardcover ISBN: 978-1-4419-5796-2, 2010, chapter 32: 821-856, doi: 10.1007/978-1-4419-5797-9_32
Bortfeldt R.H., Schuster S, Koch I
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach
In Silico Biology, 2010, 10:135, PubMed
Koch I
Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks
Molecular Informatics , 2010,29 (12): 838-843
May P, Kreuchwig A, Steinke T, Koch I
PTGL: A database for secondary structure-based protein topologies
Nucleic Acids Research 38: D326-D330, 2010, doi:10.1093/nar/gkp980
Ackermann J, Hogreve H
Small dead-time expansion in counting distributions and moments
Nuclear Instruments and Methods in Physics Research A 614(2): 297-302, 2010, doi:10.1016/j.nima.2009.12.038