Current Publications

2018

Simranjit Singh, Simon Lämmle, Heiko Giese, Susanne Kämmerer, Stefanie Meyer-Roxlau, Ezzaldin Ahmed Alfar, Hassan Dihazi, Kaomei Guan, Ali El-Armouche, and Florian Richter
The reduced activity of PP-1α under redox stress condition is a consequence of GSH-mediated transient disulfide formation
Nature Scientific Reports2018, 8, 17711 doi: 10.1038/s41598-018-36267-6 | PDFBibTex

Jennifer Hannig, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch
isiKnock: in silico knockouts in biochemical pathways
Bioinformatics, bty700, 2018doi: 10.1093/bioinformatics/bty700 | PDF | BibTex

Jennifer Scheidel, Heiko Giese, Börje Schweizer, Leonie Amstein, Jörg Ackermann, Ina Koch
isiKnock: in silico knockouts in biochemical pathways
bioRxiv2018doi: 10.1101/313858  | PDF | BibTex

Rolf Apweiler, Tim Beissbarth, Michael R Berthold, Nils Blüthgen, Yvonne Burmeister, Olaf Dammann, Andreas Deutsch, ... Ina Koch, and Olaf Wolkenhauer
Whither systems medicine?
Experimental & Molecular Medicine2018, 50, e453 doi: 10.1038/emm.2017.290 | PDFBibTex

Tim Schäfer, and Ina Koch
Protein super-secondary structure and quaternary structure topology: theoretical description and application
Current Opinion in Structural Biology2018, 50:134–143 doi: 10.1016/j.sbi.2018.02.005  | PDFBibTex

2017

Vic Norris, Ina Koch, Patrick Amar, Francois Kepes, Laurent Janniere
Hypothesis: Local variations in the speed of individual DNA replication forks determine the phenotype of daughter cells
Medical Research Archives2017, 5:12 doi: 10.18103/mra.v5i12.15988 | PDFBibTex

Jennifer ScheidelHendrik SchaeferJoerg AckermannMarie HebelTim Schaefer, Claudia Doering, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch
Bioinformatics analysis quantifies neighborhood preferences of cancer cells in Hodgkin lymphoma
bioRxiv2017, doi: 10.1101/228981 | PDFBibTex

Hristo Todorov, Inka Janssen, Stefanie Honndorf, Daniela Bause, Antje Gottschalk, Silke Baasner, Thomas Volkert, Valentin Faerber, John F. Stover, Martin Westphal and Björn Ellger
Clinical significance and risk factors for new onset and recurring atrial fibrillation following cardiac surgery - a retrospective data analysis
BMC Anesthesiology2017, 17:163, doi: 10.1186/s12871-017-0455-7 | PDFBibTex

Jörg Ackermann, Hajo Hogreve
Stability and spectral properties of the dication Ne22+
Physical Chemistry Chemical Physics (PCCP)2017, 19, 32433 - 32442, doi: 10.1039/C7CP07194A | PDF | BibTex

Andreas G. Chiocchetti, Afsheen Yousaf, Hannah S. Bour, Denise Haslinger, Regina Waltes, Eftichia Duketis, Tomasz Jarczok, Michael Sachse, Monica Biscaldi, Franziska Degenhardt, Stefan Herms, Sven Cichon, Jörg AckermannIna Koch, Sabine M. Klauck, Christine M. Freitag
Common functional variants of the glutamatergic system in Autism Spectrum Disorder with high and low intellectual abilities
Journal of Neural Transmission2017, doi: 10.1007/s00702-017-1813-9 | PDF | BibTex

Leonie AmsteinJörg AckermannJennifer Scheidel, Simone Fulda, Ivan Dikic, and Ina Koch
Manatee invariants reveal functional pathways in signaling networks
BMC Systems Biology2017, 11:72 doi: 10.1186/s12918-017-0448-7 | PDF | BibTex

Ina Koch, Joachim Nöthen and Enrico Schleiff
Modeling the metabolism of Arabidopsis thaliana: application of network decomposition and network reduction in the context of Petri nets
Frontiers in Genetics2017, 8:85. doi: 10.3389/fgene.2017.00085 | PDF | BibTex

Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz and Ina Koch
The autophagy interaction network of the aging model Podospora anserina
BMC Bioinformatics2017, 18:196. doi: 10.1186/s12859-017-1603-2 | PDF | BibTex

Weingarten, Jens and Weingarten, Melanie and Wegner, Martin and Volknandt, Walter
APP—A Novel Player within the Presynaptic Active Zone Proteome
Front. Mol. Neurosci2017, 10:43. doi: 10.3389/fnmol.2017.00043 | PDF | BibTex

Laßek, Melanie and Weingarten, Jens and Wegner, Martin and Neupärtl, Moritz and Array, Tabiwang and Harde, Eva and Beckert, Benedikt and Golghalyani, Vahid and Ackermann, Jörg and Koch, Ina and Müller, Ulrike and Karas, Michael and Acker-Palmer, Amparo and Volknandt, Walter
APP deletion accounts for age-dependent changes in the bioenergetic metabolism and in hyperphosphorylated CaMKII at stimulated hippocampal presynaptic active zones
Front. Synaptic Neurosci. 2017, 9:1. doi: 10.3389/fnsyn.2017.00001 | PDF | BibTex

2016

Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, and Ina Koch
In Silico Knockout Studies of Xenophagic Capturing of Salmonella
PLoS Computational Biology2016, 12(12):e1005200, doi: 10.1371/journal.pcbi.1005200 | PDF | BibTex

Frank Klawonn, Junxi Wang, Ina Koch, Jörg Eberhard
HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features
Advances in Intelligent Data Analysis XV2016, Vol. 9897 Lecture Notes in Computer Science pp 356-367 doi:10.1007/978-3-319-46349-0_31 | PDF | BibTeX

Valentina Strecker, Zibirnisa Kadeer, Juliana Heidler, Cristina Maria Cruciat, Heike Angerer, Heiko Giese, Kathy Pfeiffer, Rosemary A. Stuart, Ilka Wittig
Supercomplex-associated Cox26 protein binds to cytochrome c oxidase
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research2016, doi:10.1016/j.bbamcr.2016.04.012 | PDF | BibTeX

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 Computational Biology2016, 12(4): e1004832, doi: 10.1371/journal.pcbi.1004832  | PDF | BibTeX

Oliver Philipp, Heinz D. Osiewacz, and Ina Koch
PATH2PPI: an R package to predict protein-protein interaction networks for a set of proteins
Bioinformatics, 2016, 32 (9): 1427-1429, doi:10.1093/bioinformatics/btv765  | PDFBibTeX

Melanie Laßek, Jens Weingarten, Martin Wegner and Walter Volknandt
The amyloid precursor protein – a novel player within the molecular array of presynaptic nanomachines
Frontiers in Synaptic Neuroscience2016,7:21; doi:10.3389/fnsyn.2015.00021 | PDF | BibTeX

Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, and Ina Koch
The new Protein Topology Graph Library web server
Bioinformatics, 2016, 32 (3): 474-476 doi:10.1093/bioinformatics/btv574 | PDF | BibTeX

Hendrik SchäferTim SchäferJörg AckermannNorbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch
CD30 cell graphs of Hodgkin lymphoma are not scale-free – An image analysis approach
Bioinformatics2016, 32 (1): 122-129 doi:10.1093/bioinformatics/btv542 | PDF | BibTeX

2015

H. Schäfer
Automated cell detection in whole slide images of classical Hodgkin lymphoma
Der Pathologe2015, 36(Suppl 1), page 10; doi:10.1007/s00292-015-0028-9 | PDF | BibTeX

T. Schäfer, H. Schäfer, J. Ackermann, C. Döring, S. Hartmann, M.-L. Hansmann, I. Koch
Analysis of the distribution of CD30 + cells in classical Hodgkin lymphoma and lymphadenitis using graph-based methods
Der Pathologe2015, 36(Suppl 1), page 10-11; doi:10.1007/s00292-015-0028-9 | PDF | BibTeX

Bogdan Belean,  Monica Borda, Jörg Ackermann, Ina Koch, Ovidiu Balacescu
Unsupervised Image Segmentation for Microarray Spots with Irregular Contours and Inner Holes
BMC Bioinformatics2015, 16:412; doi: 10.1186/s12859-015-0842-3 | PDF | BibTeX

Jennifer Scheidel, Klaus Lindauer, Jörg Ackermann, and Ina Koch
Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System’s Dynamics: The Life Cycle of the Insulin Receptor
Metabolites2015, Special Issue Metabolic Flux Analysis, Volume 5, 766-793; doi:10.3390/metabo5040766 | PDF | BibTeX

Ina Koch
Petri nets in systems biology
Software & Systems Modeling2015, Volume 14, Issue 2, pp 703-710; doi:10.1007/s10270-014-0421-5 | PDF | BibTeX

Heiko Giese, Jörg Ackermann, Ulrich Brandt, Ilka Wittig, Ina Koch
Cluster analysis and visualization techniques for large datasets in complexome profiling
PeerJ PrePrints 3:e1602, 2015, doi:10.7287/peerj.preprints.1303v1 | PDF | BibTeX

Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann and Ina Koch
MONALISA for stochastic simulations of Petri net models of biochemical systems
BMC Bioinformatics, 2015, 16:215; doi:10.1186/s12859-015-0596-y | PDF | BibTeX

Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann and Ina Koch
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 | PDF | BibTeX

Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter and Christoph W. Michalski
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 | PDF | BibTeX

Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter and Christoph W. Michalski
Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Molecular Cancer201514:144; doi:10.1186/s12943-015-0401-6 | PDF | BibTeX

Stefan Simm, Sotirios Fragkostefanakis, Puneet Paul, Mario Keller, Jens Einloft, Klaus-Dieter Scharf and  Enrico Schleiff
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 | PDF | BibTeX

Heiko Giese, Jörg Ackermann, Heinrich Heide, Lea Bleier, Stefan Dröse, Ilka Wittig, Ulrich Brandt, and Ina Koch
NOVA: a software to analyze complexome profiling data
Bioinformatics, 2015, 31(3): 440-441, doi: 10.1093/bioinformatics/btu623 | PDF | BibTeX

2014

Jan-Hendrik Trösemeier, Susanne Lipp, Holger Lößner, Ina Koch, Christel Kamp
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, 2014BibTeX

Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, and Björn Rotter
APADB: a database for alternative polyadenylation and microRNA regulation events
Database, 2014, bau076; doi: 10.1093/database/bau076 | PDF | BibTeX

Ina Koch
Petrinetze in der Systembiologie
CLB - Chemie in Labor und Biotechnik, 2014, 64(5-6), 220-228.

Ina Koch and Wolfgang Reisig and Falk Schreiber
Petri Nets in the Biosciences
it - Information Technology, 2014, 56(2), 43-45, doi: 10.1515/itit-2014-1042BibTeX

Ali Najafi, Gholamreza Bidkhori, Joseph H. Bozorgmehr, Ina Koch and Ali Masoudi-Nejad
Genome Scale Modeling in Systems Biology: Algorithms and Resources
Current Genomics, 2014, 15, 130-159; doi:10.2174/1389202915666140319002221 | BibTeX

Ina Koch
Petrinetze in der Systembiologie
Informatik-Spektrum, 2014, 37(3), 211-219. doi: 10.1007/s00287-013-0757-1 | PDF | BibTeX

2013

Oliver Philipp, Andrea Hamann, Jörg Servos, Alexandra Werner, Ina Koch, Heinz D. Osiewacz
A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina
PLoS ONE 8(12): e83109, 2013, doi: 10.1371/journal.pone.0083109 | PDFBibTeX

Leonie Amstein, Nadine Schöne, Simone Fulda, and Ina Koch
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 | PDFBibTeX

Sören Müller, Lukas Rycak, Peter Winter, Günter Kahl, Ina Koch, and Björn Rotter
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 | PDF | BibTeX

Ina Koch, Jörg Ackermann
On Functional Module Detection in Metabolic Networks
in Special Issue: "Metabolism and Systems Biology"
Metabolites 2013, 3(3), 673-700; doi:10.3390/metabo3030673n | PDF | BibTeX

Sahand Khakabimamaghani, Iman Sharafuddin, Norbert Dichter, Ina Koch, Ali Masoudi-Nejad
QuateXelero: an accelerated exact network motif detection algorithm
PLoS ONE, 2013, doi:10.1371/journal.pone.0068073 | PDF | BibTeX

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
Computational Biology and Chemistry2013, 46, 1-7 doi: 10.1016/j.compbiolchem.2013.04.003 | PDF | BibTeX

Jens Einloft, Jörg Ackermann, Joachim Nöthen, and Ina Koch
MonaLisa - visualization and analysis of functional modules in biochemical networks
Bioinformatics, 2013, 29, 1469-1470

Ina Koch, Annika Kreuchwig, and Patrick May
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 932, 2013, 7-33, doi: 10.1007/978-1-62703-065-6_2 | BibTeX

2012

Ilka Wittig, Heinrich Heide, Lea Bleier, Bettina Schwamb, Valentina Strecker, Mirco Steger, Jörg Ackermann, Stefan Dröse, Martin Zörnig, Andreas S. Reichert, Ina Koch, Ulrich Brandt
Identification of new assembly factors of complex I by complexome profiling
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2012, 1817, page S138

Tim Schäfer, Patrick May, and Ina Koch
Computation and Visualization of Protein Topology Graphs Including Ligand Information
German Conference on Bioinformatics 2012, 2012, 108-118

Alexander Schmitz, Tim Schäfer, Hendrik Schäfer, Claudia Döring, Jörg Ackermann, Norbert Dichter, Sylvia Hartmann, Martin-Leo Hansmann, and Ina Koch
Automated Image Analysis of Hodgkin lymphoma
Dagstuhl Seminar "Structure Discovery in Biology: Motifs, Networks & Phylogenies"2012

Jörg Ackermann, Jens Einloft, Joachim Nöthen, and Ina Koch
Reduction techniques for network validation in systems biology
Journal of Theoretical Biology 315, 2012, 71-80

Heinrich Heide, Lea Bleier, Mirco Steger, Jörg Ackermann, Stefan Dröse, Bettina Schwamb, Martin Zörnig, Andreas S. Reichert, Ina Koch, Ilka Wittig, Ulrich Brandt
Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly (MCIA)
Cell Metabolism 16(4), 2012, 538-549

2011

Ralf H. Bortfeldt, Stefan Schuster, Ina Koch
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

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
Studies in Health Technology and Informatics, 2011, 162:113-21 PubMed

Klaus Voss, Monika Heiner, Ina Koch
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

 

Ina Koch and Falk Schreiber
Introduction
In: Modeling in Systems Biology: The Petri Net Approach
Ina Koch, Wolfgang Reisig and Falk Schreiber, Editors
Springer, Computational Biology 162011, 3-18

Jörg Ackermann and Ina Koch
Quantitative Analysis
In: Modeling in Systems Biology: The Petri Net Approach
Ina Koch, Wolfgang Reisig and Falk Schreiber, Editors
Springer, Computational Biology 16, 2011, 153-178

Jörg Ackermann and Ina Koch
Network decomposition in biology - computational challenges
In: Models of Computation in Context, volume 7 of Computability in Europe
H. Ganchev, B. Löwe, D. Normann, I. Soskov, and M. Soskova, Editors
St. Kliment Ohridski University Press, Sofia, 2011, pages 39­48

2010

Ina Koch
Petri Nets and GRN Models
In: Handbook of Research on Computational Methodologies in Gene Regulatory Networks
Eds. Sanjoy Das, Doina Caragea, Stephen M. Welch, William H. Hsu, IGI Global Hershey, 2010, chapter 25:604-637

Ina Koch, Claudine Chaouiya
Discrete Modelling: Petri Net and Logical Approaches
In: Systems Biology for Signaling Networks, Series: Systems Biology, Vol. 1, Choi, Sangdun (Ed.), Springer, 2010chapter 32:821-856 Hardcover ISBN: 978-1-4419-5796-2.

Ralf H. Bortfeldt, Stefan Schuster, Ina Koch
Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach
In Silico Biology 10:1­352010PubMed

Ina Koch
Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks
Molecular Informatics 29 (12):838-8432010

Patrick May, Annika Kreuchwig, Thomas Steinke, Ina Koch
PTGL: A database for secondary structure-based protein topologies
Nucleic Acids Research 38 (Database issue):D326-3302010PubMed

Jörg Ackermann, H. Hogreve
Small dead-time expansion in counting distributions and moments
Nuclear Instruments and Methods in Physics Research, 2010, A 614, 297-302

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