@article{10.1371/journal.pone.0242177,
author = {Thomos, Miguel AND Wurzel, Patrick AND Scharf, Sonja AND Koch, Ina AND Hansmann, Martin-Leo},
journal = {PLOS ONE},
title = {3D investigation shows walls and wall-like structures around human germinal centres, probably regulating T- and B-cell entry and exit},
year = {2020},
month = {11},
volume = {15},
url = {https://doi.org/10.1371/journal.pone.0242177},
pages = {1-11},
number = {11},
doi = {10.1371/journal.pone.0242177}
}
@article{10.1093/bioinformatics/btaa706,
author = {Wolf, Jan Niclas and Keßler, Marcus and Ackermann, Jörg and Koch, Ina},
title = "{PTGL: extension to graph-based topologies of cryo-EM data for large protein structures}",
journal = {Bioinformatics},
year = {2020},
month = {08},
doi = {10.1093/bioinformatics/btaa706},
url = {https://doi.org/10.1093/bioinformatics/btaa706},
note = {btaa706},
}
@Article{Bernatz2020,
author={Bernatz, Simon
and Ackermann, J{\"o}rg
and Mandel, Philipp
and Kaltenbach, Benjamin
and Zhdanovich, Yauheniya
and Harter, Patrick N.
and D{\"o}ring, Claudia
and Hammerstingl, Renate
and Bodelle, Boris
and Smith, Kevin
and Bucher, Andreas
and Albrecht, Moritz
and Rosbach, Nicolas
and Basten, Lajos
and Yel, Ibrahim
and Wenzel, Mike
and Bankov, Katrin
and Koch, Ina
and Chun, Felix K.-H.
and K{\"o}llermann, Jens
and Wild, Peter J.
and Vogl, Thomas J.},
title={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},
journal={European Radiology},
year={2020},
month={Jul},
doi={10.1007/s00330-020-07064-5},
url={https://doi.org/10.1007/s00330-020-07064-5}
}
@Article{Yousaf2020,
author={Yousaf, Afsheen
and Waltes, Regina
and Haslinger, Denise
and Klauck, Sabine M.
and Duketis, Eftichia
and Sachse, Michael
and Voran, Anette
and Biscaldi, Monica
and Schulte-R{\"u}ther, Martin
and Cichon, Sven
and N{\"o}then, Markus
and Ackermann, J{\"o}rg
and Koch, Ina
and Freitag, Christine M.
and Chiocchetti, Andreas G.},
title={Quantitative genome-wide association study of six phenotypic subdomains identifies novel genome-wide significant variants in autism spectrum disorder},
journal={Translational Psychiatry},
year={2020},
volume={10},
number={1},
pages={215},
doi={10.1038/s41398-020-00906-2},
url={https://doi.org/10.1038/s41398-020-00906-2}
}
@article{10.1371/journal.pcbi.1007516,
author = {Hannig, Jennifer AND Schäfer, Hendrik AND Ackermann, Jörg AND Hebel, Marie AND Schäfer, Tim AND Döring, Claudia AND Hartmann, Sylvia AND Hansmann, Martin-Leo AND Koch, Ina},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma},
year = {2020},
month = {01},
volume = {16},
url = {https://doi.org/10.1371/journal.pcbi.1007516},
pages = {1-21},
number = {1},
doi = {10.1371/journal.pcbi.1007516}
}
@Inbook{Koch2020,
author="Koch, Ina
and Philipp, Oliver
and Hamann, Andrea
and Osiewacz, Heinz",
editor="Canzar, Stefan
and Ringeling, Francisca Rojas",
title="Reconstruction of Protein--Protein Interaction Networks Using Homology-Based Search: Application to the Autophagy Pathway of Aging in Podospora anserina",
bookTitle="Protein-Protein Interaction Networks: Methods and Protocols ",
year="2020",
publisher="Springer US",
address="New York, NY",
pages="45--55",
isbn="978-1-4939-9873-9",
doi="10.1007/978-1-4939-9873-9_4",
url="https://doi.org/10.1007/978-1-4939-9873-9_4"
}
@Article{Liebers2019,
author={Liebers, Julia
and Wurzel, Patrick
and Reisinger, Kerstin Bianca
and Hansmann, Martin-Leo},
title={3D image analysis reveals differences of CD30 positive cells and network formation in reactive and malignant human lymphoid tissue (classical Hodgkin Lymphoma)},
journal={PloS one},
year={2019},
volume={14},
number={10},
pages={e0224156-e0224156},
doi={10.1371/journal.pone.0224156},
url={https://www.ncbi.nlm.nih.gov/pubmed/31648255}
}
@article{OSWALD2019769,
title = "3D analysis of morphological alterations of the fibroblastic reticular cells in reactive and neoplastic human lymph nodes",
journal = "Acta Histochemica",
volume = "121",
number = "7",
pages = "769 - 775",
year = "2019",
doi = "https://doi.org/10.1016/j.acthis.2019.07.002",
url = "http://www.sciencedirect.com/science/article/pii/S006512811930114X",
author = "Marvin Siegfried Oswald and Patrick Wurzel and Martin-Leo Hansmann",
}
@Article{Trösemeier2019,
author={Tr{\"o}semeier, Jan-Hendrik
and Rudorf, Sophia
and Loessner, Holger
and Hofner, Benjamin
and Reuter, Andreas
and Schulenborg, Thomas
and Koch, Ina
and Bekeredjian-Ding, Isabelle
and Lipowsky, Reinhard
and Kamp, Christel},
title={Optimizing the dynamics of protein expression},
journal={Scientific Reports},
year={2019},
volume={9},
number={1},
pages={7511},
doi={10.1038/s41598-019-43857-5},
url={https://doi.org/10.1038/s41598-019-43857-5}
}
@Inbook{Koch2019,
author="Koch, Ina",
editor="Reisig, Wolfgang
and Rozenberg, Grzegorz",
title="Petri Nets in Systems Biology: Transition Invariants, Maximal Common Transition Sets, Transition Clusters, Mauritius Maps, and MonaLisa",
bookTitle="Carl Adam Petri: Ideas, Personality, Impact",
year="2019",
publisher="Springer International Publishing",
address="Cham",
pages="217--226",
isbn="978-3-319-96154-5",
doi="10.1007/978-3-319-96154-5_26",
url="https://doi.org/10.1007/978-3-319-96154-5_26"
}
@article{doi:10.1111/plb.12839,
author = {Hsueh, Y.-C. and Nicolaisen, K. and Gross, L. E. and Nöthen, J. and Schauer, N. and Vojta, L. and Ertel, F. and Koch, I. and Ladig, R. and Fulgosi, H. and Fernie, A. R. and Schleiff, E.},
title = {The outer membrane Omp85-like protein P39 influences metabolic homeostasis in mature Arabidopsis thaliana},
journal = {Plant Biology},
volume = {20},
number = {5},
pages = {825-833},
doi = {10.1111/plb.12839},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/plb.12839},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/plb.12839},
year = {2018}
}
@article{10.1093/bioinformatics/bty700,
author = {Hannig, Jennifer and Giese, Heiko and Schweizer, Börje and Amstein, Leonie and Ackermann, Jörg and Koch, Ina},
title = "{isiKnock: in silico knockouts in signaling pathways}",
journal = {Bioinformatics},
volume = {35},
number = {5},
pages = {892-894},
year = {2018},
month = {08},
doi = {10.1093/bioinformatics/bty700},
url = {https://doi.org/10.1093/bioinformatics/bty700},
eprint = {http://oup.prod.sis.lan/bioinformatics/article-pdf/35/5/892/27994994/bty700.pdf},
}
@Article{Singh2018,
author={Singh, Simranjit
and L{\"a}mmle, Simon
and Giese, Heiko
and K{\"a}mmerer, Susanne
and Meyer-Roxlau, Stefanie
and Alfar, Ezzaldin Ahmed
and Dihazi, Hassan
and Guan, Kaomei
and El-Armouche, Ali
and Richter, Florian},
title={The reduced activity of PP-1{\alpha} under redox stress condition is a consequence of GSH-mediated transient disulfide formation},
journal={Scientific Reports},
year={2018},
volume={8},
number={1},
pages={17711},
doi={10.1038/s41598-018-36267-6},
url={https://doi.org/10.1038/s41598-018-36267-6}
}
@article{doi:10.1093/bioinformatics/bty700,
author = {Hannig, Jennifer and Giese, Heiko and Schweizer, Börje and Amstein, Leonie and Ackermann, Jörg and Koch, Ina},
title = {isiKnock: in silico knockouts in signaling pathways},
journal = {Bioinformatics},
pages = {bty700},
year = {2018},
doi = {10.1093/bioinformatics/bty700},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty700},
}
@article {Scheidel313858,
author = {Scheidel, Jennifer and Giese, Heiko and Schweizer, Boerje and Amstein, Leonie and Ackermann, Joerg and Koch, Ina},
title = {isiKnock: in silico knockouts in biochemical pathways},
year = {2018},
doi = {10.1101/313858},
URL = {https://www.biorxiv.org/content/early/2018/05/04/313858},
eprint = {https://www.biorxiv.org/content/early/2018/05/04/313858.full.pdf},
journal = {bioRxiv}
}
@article{Apweiler2018Mar,
author = {Apweiler, Rolf and Beissbarth, Tim and Berthold, Michael R. and Blüthgen, Nils and Burmeister, Yvonne and Dammann, Olaf and Deutsch, Andreas and Feuerhake, Friedrich and Franke, Andre and Hasenauer, Jan and Hoffmann, Steve and Höfer, Thomas and Jansen, Peter LM and Kaderali, Lars and Klingmüller, Ursula and Koch, Ina and Kohlbacher, Oliver and Kuepfer, Lars and Lammert, Frank and Maier, Dieter and Pfeifer, Nico and Radde, Nicole and Rehm, Markus and Roeder, Ingo and Saez-Rodriguez, Julio and Sax, Ulrich and Schmeck, Bernd and Schuppert, Andreas and Seilheimer, Bernd and Theis, Fabian J. and Vera, Julio and Wolkenhauer, Olaf},
title = {{Whither systems medicine?}},
journal = {Exp. Mol. Med.},
volume = {50},
number = {3},
pages = {e453},
year = {2018},
month = {Mar},
issn = {2092-6413},
publisher = {Nature Publishing Group},
doi = {10.1038/emm.2017.290}
}
@article{KOCH2018134,
title = "Protein super-secondary structure and quaternary structure topology: theoretical description and application",
journal = "Current Opinion in Structural Biology",
volume = "50",
pages = "134 - 143",
year = "2018",
doi = "https://doi.org/10.1016/j.sbi.2018.02.005",
url = "http://www.sciencedirect.com/science/article/pii/S0959440X1730115X",
author = "Ina Koch and Tim Schäfer"
}
@article{MRA,
author = {Vic Norris and Ina Koch and Patrick Amar and Francois Kepes and Laurent Janniere},
title = { Hypothesis: Local variations in the speed of individual DNA replication forks determine the phenotype of daughter cells},
journal = {Medical Research Archives},
volume = {5},
number = {12},
year = {2017},
doi = {10.18103/mra.v5i12.1598},
url = {http://www.journals.ke-i.org/index.php/mra/article/view/1598}
}
@article {Scheidel228981,
author = {Scheidel, Jennifer and Schaefer, Hendrik and Ackermann, Joerg and Hebel, Marie and Schaefer, Tim and Doering, Claudia and Hartmann, Sylvia and Hansmann, Martin-Leo and Koch, Ina},
title = {Bioinformatics analysis quantifies neighborhood preferences of cancer cells in Hodgkin lymphoma.},
year = {2017},
doi = {10.1101/228981},
URL = {https://www.biorxiv.org/content/early/2017/12/04/228981},
eprint = {https://www.biorxiv.org/content/early/2017/12/04/228981.full.pdf},
journal = {bioRxiv}
}
@Article{Todorov2017,
author="Todorov, Hristo
and Janssen, Inka
and Honndorf, Stefanie
and Bause, Daniela
and Gottschalk, Antje
and Baasner, Silke
and Volkert, Thomas
and Faerber, Valentin
and Stover, John F.
and Westphal, Martin
and Ellger, Bj{\"o}rn",
title="Clinical significance and risk factors for new onset and recurring atrial fibrillation following cardiac surgery - a retrospective data analysis",
journal="BMC Anesthesiology",
year="2017",
month="Dec",
day="02",
volume="17",
number="1",
pages="163",
doi="10.1186/s12871-017-0455-7",
url="https://doi.org/10.1186/s12871-017-0455-7"
}
@Article{C7CP07194A,
author ="Ackermann, Joerg and Hogreve, H.",
title ="Stability and spectral properties of the dication Ne2+2",
journal ="Phys. Chem. Chem. Phys.",
year ="2017",
volume ="19",
issue ="48",
pages ="32433-32442"
publisher ="The Royal Society of Chemistry",
doi ="10.1039/C7CP07194A",
url ="http://dx.doi.org/10.1039/C7CP07194A",
}
@Article{Chiocchetti2017,
author="Chiocchetti, Andreas G.
and Yousaf, Afsheen
and Bour, Hannah S.
and Haslinger, Denise
and Waltes, Regina
and Duketis, Eftichia
and Jarczok, Tomas
and Sachse, Michael
and Biscaldi, Monica
and Degenhardt, Franziska
and Herms, Stefan
and Cichon, Sven
and Ackermann, J{\"o}rg
and Koch, Ina
and Klauck, Sabine M.
and Freitag, Christine M.",
title="Common functional variants of the glutamatergic system in Autism spectrum disorder with high and low intellectual abilities",
journal="Journal of Neural Transmission",
year="2017",
doi="10.1007/s00702-017-1813-9",
url="https://doi.org/10.1007/s00702-017-1813-9"
}
@Article{Amstein2017,
author="Amstein, Leonie
and Ackermann, J{\"o}rg
and Scheidel, Jennifer
and Fulda, Simone
and Dikic, Ivan
and Koch, Ina",
title="Manatee invariants reveal functional pathways in signaling networks",
journal="BMC Systems Biology",
year="2017",
month="Jul",
day="28",
volume="11",
number="1",
pages="72",
doi="10.1186/s12918-017-0448-7",
url="https://doi.org/10.1186/s12918-017-0448-7"
}
@ARTICLE{10.3389/fgene.2017.00085,
AUTHOR={Koch, Ina and Nöthen, Joachim and Schleiff, Enrico},
TITLE={Modeling the Metabolism of {\it Arabidopsis thaliana}: Application of Network Decomposition and Network Reduction in the Context of Petri Nets},
JOURNAL={Frontiers in Genetics},
VOLUME={8},
PAGES={85},
YEAR={2017},
URL={http://journal.frontiersin.org/article/10.3389/fgene.2017.00085},
DOI={10.3389/fgene.2017.00085},
}
@Article{Philipp2017,
author="Philipp, Oliver
and Hamann, Andrea
and Osiewacz, Heinz D.
and Koch, Ina",
title="The autophagy interaction network of the aging model Podospora anserina",
journal="BMC Bioinformatics",
year="2017",
volume="18",
number="1",
pages="196",
doi="10.1186/s12859-017-1603-2",
url="http://dx.doi.org/10.1186/s12859-017-1603-2"
}
@ARTICLE{10.3389/fnmol.2017.00043,
AUTHOR={Weingarten, Jens and Weingarten, Melanie and Wegner, Martin and Volknandt, Walter},
TITLE={APP—A Novel Player within the Presynaptic Active Zone Proteome},
JOURNAL={Frontiers in Molecular Neuroscience},
VOLUME={10},
PAGES={43},
YEAR={2017},
URL={http://journal.frontiersin.org/article/10.3389/fnmol.2017.00043},
DOI={10.3389/fnmol.2017.00043},
}
@ARTICLE{10.3389/fnsyn.2017.00001,
AUTHOR={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},
TITLE={APP deletion accounts for age-dependent changes in the bioenergetic metabolism and in hyperphosphorylated CaMKII at stimulated hippocampal presynaptic active zones},
JOURNAL={Frontiers in Synaptic Neuroscience},
VOLUME={9},
PAGES={1},
YEAR={2017},
URL={http://journal.frontiersin.org/article/10.3389/fnsyn.2017.00001},
DOI={10.3389/fnsyn.2017.00001},
}
@article{scheidel_silico_2016,
title = {In {Silico} {Knockout} {Studies} of {Xenophagic} {Capturing} of {Salmonella}},
volume = {12},
issn = {1553-7358},
url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005200},
doi = {10.1371/journal.pcbi.1005200},
number = {12},
urldate = {2016-12-02},
journal = {PLOS Computational Biology},
author = {Scheidel, Jennifer and Amstein, Leonie and Ackermann, J{\"o}rg and Dikic, Ivan and Koch, Ina},
month = dec,
year = {2016},
}
@Inbook{Klawonn2016,
author="Klawonn, Frank
and Wang, Junxi
and Koch, Ina
and Eberhard, J{\"o}rg
and Omar, Mohamed",
editor="Bostr{\"o}m, Henrik
and Knobbe, Arno
and Soares, Carlos
and Papapetrou, Panagiotis",
title="HAUCA Curves for the Evaluation of Biomarker Pilot Studies with Small Sample Sizes and Large Numbers of Features",
bookTitle="Advances in Intelligent Data Analysis XV: 15th International Symposium, IDA 2016, Stockholm, Sweden, October 13-15, 2016, Proceedings",
year="2016",
publisher="Springer International Publishing",
address="Cham",
pages="356--367",
isbn="978-3-319-46349-0",
doi="10.1007/978-3-319-46349-0_31",
url="http://dx.doi.org/10.1007/978-3-319-46349-0_31"
}
@article{Strecker2016,
author = "Valentina Strecker and Zibirnisa Kadeer and Juliana Heidler and Cristina Maria Cruciat and Heike Angerer and Heiko Giese and Kathy Pfeiffer and Rosemary A. Stuart and Ilka Wittig",
title = "Supercomplex-associated Cox26 protein binds to cytochrome c oxidase ",
journal = "Biochimica et Biophysica Acta (BBA) - Molecular Cell Research ",
year = "2016",
doi = "http://dx.doi.org/10.1016/j.bbamcr.2016.04.012",
url = "http://www.sciencedirect.com/science/article/pii/S016748891630101X",
}
@article{10.1371/journal.pcbi.1004832,
author = {Laßek, Melanie AND Weingarten, Jens AND Wegner, Martin AND Mueller, Benjamin F. AND Rohmer, Marion AND Baeumlisberger, Dominic AND Arrey, Tabiwang N. AND Hick, Meike AND Ackermann, Jörg AND Acker-Palmer, Amparo AND Koch, Ina AND Müller, Ulrike AND Karas, Michael AND Volknandt, Walter},
journal = {PLoS Comput Biol},
publisher = {Public Library of Science},
title = {APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone},
year = {2016},
month = {04},
volume = {12},
url = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004832},
pages = {1-22},
number = {4},
doi = {10.1371/journal.pcbi.1004832}
@article{Philipp01052016,
author = {Philipp, Oliver and Osiewacz, Heinz D. and Koch, Ina},
title = {Path2PPI: an R package to predict protein–protein interaction networks for a set of proteins},
volume = {32},
number = {9},
pages = {1427-1429},
year = {2016},
doi = {10.1093/bioinformatics/btv765},
URL = {http://bioinformatics.oxfordjournals.org/content/32/9/1427.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/32/9/1427.full.pdf+html},
journal = {Bioinformatics}
}
@article{lasek_amyloid_2016,
title = {The {Amyloid} {Precursor} {Protein}{\textemdash}{A} {Novel} {Player} within the {Molecular} {Array} of {Presynaptic} {Nanomachines}},
volume = {7},
url = {http://journal.frontiersin.org/article/10.3389/fnsyn.2015.00021},
doi = {10.3389/fnsyn.2015.00021},
journal = {Frontiers in Synaptic Neuroscience},
author = {La{\ss}ek, Melanie and Weingarten, Jens and Wegner, Martin and Volknandt, Walter},
month = jan,
year = {2016}
}
@article{Schäfer01012016,
author = {Sch{\"a}fer, Hendrik and Sch{\"a}fer, Tim and Ackermann, J{\"o}rg and Dichter, Norbert and D{\"o}ring, Claudia and Hartmann, Sylvia and Hansmann, Martin-Leo and Koch, Ina},
title = {CD30 cell graphs of Hodgkin lymphoma are not scale-free—an image analysis approach},
volume = {32},
number = {1},
pages = {122-129},
year = {2016},
doi = {10.1093/bioinformatics/btv542},
URL = {http://bioinformatics.oxfordjournals.org/content/32/1/122.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/32/1/122.full.pdf+html},
journal = {Bioinformatics}
}
@article{Schäfer01022016,
author = {Schäfer, Tim and Scheck, Andreas and Bruneß, Daniel and May, Patrick and Koch, Ina},
title = {The new protein topology graph library web server},
volume = {32},
number = {3},
pages = {474-476},
year = {2016},
doi = {10.1093/bioinformatics/btv574},
URL = {http://bioinformatics.oxfordjournals.org/content/32/3/474.abstract},
eprint = {http://bioinformatics.oxfordjournals.org/content/32/3/474.full.pdf+html},
journal = {Bioinformatics}
}
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}
@article{Belean2015,
author="Belean, Bogdan
and Borda, Monica
and Ackermann, J{\"o}rg
and Koch, Ina
and Balacescu, Ovidiu",
title="Unsupervised image segmentation for microarray spots with irregular contours and inner holes",
journal="BMC Bioinformatics",
year="2015",
volume="16",
number="1",
pages="1--12",
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}
@article{scheidel_quasi-steady-state_2015,
title = {Quasi-{Steady}-{State} {Analysis} based on {Structural} {Modules} and {Timed} {Petri} {Net} {Predict} {System}{\textquoteright}s {Dynamics}: {The} {Life} {Cycle} of the {Insulin} {Receptor}},
volume = {5},
url = {http://www.mdpi.com/2218-1989/5/4/766},
doi = {10.3390/metabo5040766},
number = {4},
journal = {Metabolites},
author = {Scheidel, Jennifer and Lindauer, Klaus and Ackermann, J{\"o}rg and Koch, Ina},
month = dec,
year = {2015},
pages = {766--793}
}
@article{koch_petri_2015,
title = {Petri nets in systems biology},
volume = {14},
url = {http://link.springer.com/10.1007/s10270-014-0421-5},
doi = {10.1007/s10270-014-0421-5},
number = {2},
urldate = {2016-01-28},
journal = {Software \& Systems Modeling},
author = {Koch, Ina},
month = may,
year = {2015},
pages = {703--710}
}
@article{heiko_giese_cluster_2015,
title = {Cluster analysis and visualization techniques for large datasets in complexome profiling},
author = {{Heiko Giese} and {J{\"o}rg Ackermann} and {Ulrich Brandt} and {Ilka Wittig} and {Ina Koch}},
year = {2015},
month = {8},
volume = {3},
journal = {PeerJ PrePrints},
url = {https://doi.org/10.7287/peerj.preprints.1303v1},
doi = {10.7287/peerj.preprints.1303v1}
}
@article{balazki_erratum_2015,
title = {Erratum to: {MONALISA} for stochastic simulations of {Petri} net models of biochemical systems},
volume = {16},
shorttitle = {Erratum to},
url = {http://www.biomedcentral.com/1471-2105/16/371},
doi = {10.1186/s12859-015-0725-7},
number = {1},
journal = {BMC Bioinformatics},
author = {Balazki, Pavel and Lindauer, Klaus and Einloft, Jens and Ackermann, J{\"o}rg and Koch, Ina},
month = dec,
year = {2015}
}
@article{balazki_monalisa_2015,
title = {{MONALISA} for stochastic simulations of {Petri} net models of biochemical systems},
volume = {16},
url = {http://www.biomedcentral.com/1471-2105/16/215},
doi = {10.1186/s12859-015-0596-y},
number = {1},
journal = {BMC Bioinformatics},
author = {Balazki, Pavel and Lindauer, Klaus and Einloft, Jens and Ackermann, J{\"o}rg and Koch, Ina},
month = dec,
year = {2015}
}
@article{muller_erratum_2015,
title = {Erratum to: {Next}-generation sequencing reveals novel differentially regulated {mRNAs}, {lncRNAs}, {miRNAs}, {sdRNAs} and a {piRNA} in pancreatic cancer},
volume = {14},
shorttitle = {Erratum to},
url = {http://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-015-0401-6},
doi = {10.1186/s12943-015-0401-6},
number = {1},
journal = {Molecular Cancer},
author = {M{\"u}ller, S{\"o}ren and Raulefs, Susanne and Bruns, Philipp and Afonso-Grunz, Fabian and Pl{\"o}tner, Anne and Thermann, Rolf and J{\"a}ger, Carsten and Schlitter, Anna Melissa and Kong, Bo and Regel, Ivonne and Roth, W Kurt and Rotter, Bj{\"o}rn and Hoffmeier, Klaus and Kahl, G{\"u}nter and Koch, Ina and Theis, Fabian J and Kleeff, J{\"o}rg and Winter, Peter and Michalski, Christoph W},
month = dec,
year = {2015}
}
@article{muller_next-generation_2015,
title = {Next-generation sequencing reveals novel differentially regulated {mRNAs}, {lncRNAs}, {miRNAs}, {sdRNAs} and a {piRNA} in pancreatic cancer},
volume = {14},
url = {http://molecular-cancer.biomedcentral.com/articles/10.1186/s12943-015-0358-5},
doi = {10.1186/s12943-015-0358-5},
number = {1},
journal = {Molecular Cancer},
author = {M{\"u}ller, S{\"o}ren and Raulefs, Susanne and Bruns, Philipp and Afonso-Grunz, Fabian and Pl{\"o}tner, Anne and Thermann, Rolf and J{\"a}ger, Carsten and Schlitter, Anna Melissa and Kong, Bo and Regel, Ivonne and Roth, W Kurt and Rotter, Bj{\"o}rn and Hoffmeier, Klaus and Kahl, G{\"u}nter and Koch, Ina and Theis, Fabian J and Kleeff, J{\"o}rg and Winter, Peter and Michalski, Christoph W},
month = dec,
year = {2015}
}
@article{schleiff_identification_2015,
title = {Identification and {Expression} {Analysis} of {Ribosome} {Biogenesis} {Factor} {Co}-orthologs in {Solanum} lycopersicum},
url = {http://www.la-press.com/identification-and-expression-analysis-of-ribosome-biogenesis-factor-c-article-a4657},
doi = {10.4137/BBI.S20751},
journal = {Bioinformatics and Biology Insights},
author={Stefan Simm, Sotirios Fragkostefanakis, Puneet Paul, Mario Keller, Jens Einloft, Klaus-Dieter Scharf and Enrico Schleiff},
year={2015},
month={02},
volume={9},
pages={1--17},
}
@article{giese_nova:_2015,
title = {{NOVA}: a software to analyze complexome profiling data},
volume = {31},
shorttitle = {{NOVA}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu623},
doi = {10.1093/bioinformatics/btu623},
number = {3},
journal = {Bioinformatics},
author = {Giese, Heiko and Ackermann, J{\"o}rg and Heide, Heinrich and Bleier, Lea and Dr{\"o}se, Stefan and Wittig, Ilka and Brandt, Ulrich and Koch, Ina},
month = feb,
year = {2015},
pages = {440--441}
}
@inproceedings{trosemeier2014right,
title={The Right Word in the Right Place? Using an evolutionary model to link codon usage bias to an organism’s fitness.},
author={Tr{\"o}semeier, Jan-Hendrik and Lipp, Susanne and L{\"o}{\ss}ner, Holger and Koch, Ina and Kamp, Christel},
booktitle={9th European Conference on Mathematical and Theoretical Biology},
year={2014}
}
@article{muller_apadb:_2014,
title = {{APADB}: a database for alternative polyadenylation and {microRNA} regulation events},
volume = {2014},
shorttitle = {{APADB}},
url = {http://database.oxfordjournals.org/cgi/doi/10.1093/database/bau076},
doi = {10.1093/database/bau076},
number = {0},
journal = {Database},
author = {M{\"u}ller, S{\"o}ren and Rycak, Lukas and Afonso-Grunz, Fabian and Winter, Peter and Zawada, Adam M. and Damrath, Ewa and Scheider, Jessica and Schm{\"a}h, Juliane and Koch, Ina and Kahl, G{\"u}nter and Rotter, Bj{\"o}rn},J. and Koch, I. and Kahl, G. and Rotter, B.},
month = jul,
year = {2014},
}
@article{koch_petri_2014,
title = {Petri {Nets} in the {Biosciences}},
volume = {56},
url = {http://www.degruyter.com/view/j/itit.2014.56.issue-2/itit-2014-1042/itit-2014-1042.xml},
doi = {10.1515/itit-2014-1042},
number = {2},
journal = {it {\textendash} Information Technology},
author = {Koch, Ina and Reisig, Wolfgang and Schreiber, Falk},
month = jan,
year = {2014}
}
@article{Najafi_Genome_2014,
Title = {Genome {Scale} {Modeling} In {Systems} {Biology}: {Algorithms} And {Resources}},
Volume = {15},
Shorttitle = {Genome {Scale} {Modeling} In {Systems} {Biology}},
Url = {Http://Www.Eurekaselect.Com/Openurl/Content.Php?Genre=Article&Issn=1389-2029&Volume=15&issue=2&spage=130},
doi = {10.2174/1389202915666140319002221},
number = {2},
journal = {Current Genomics},
author = {Najafi, Ali and Bidkhori, Gholamreza and Bozorgmehr, Joseph and Koch, Ina and Masoudi-Nejad, Ali},
month = apr,
year = {2014},
pages = {130--159}
}
@article{koch_petrinetze_2014,
title = {Petrinetze in der {Systembiologie}},
volume = {37},
url = {http://link.springer.com/10.1007/s00287-013-0757-1},
doi = {10.1007/s00287-013-0757-1},
number = {3},
journal = {Informatik-Spektrum},
author = {Koch, Ina},
month = jun,
year = {2014},
pages = {211--219}
}
@article{Philipp_Genome-Wide_2013,
Title = {A {Genome}-{Wide} {Longitudinal} {Transcriptome} {Analysis} Of The {Aging} {Model} {Podospora} Anserine},
Volume = {8},
Url = {http://Dx.Plos.Org/10.1371/Journal.Pone.0083109},
Doi = {10.1371/Journal.Pone.0083109},
Language = {En},
Number = {12},
Journal = {Plos One},
Author = {Philipp, Oliver And Hamann, Andrea And Servos, J{\"O}Rg And Werner, Alexandra And Koch, Ina And Osiewacz, Heinz D.},
Month = Dec,
Year = {2013},
}
@inproceedings{amstein2013mathematical,
title={Mathematical Modelling of the Function of Ubiquitylation in TNFR1-Mediated NF-$\kappa$B Signalling},
author={Amstein, Leonie and Sch{\"o}ne, Nadine and Fulda, Simone and Koch, Ina},
booktitle={Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings},
volume={8130},
pages={278},
year={2013},
url = {http://link.springer.com/10.1007/978-3-642-40708-6},
doi = {10.1007/978-3-642-40708-6},
publisher = {Springer Berlin Heidelberg},
}
@article{muller_omiras:_2013,
title = {{omiRas}: a {Web} server for differential expression analysis of {miRNAs} derived from small {RNA}-{Seq} data},
volume = {29},
shorttitle = {{omiRas}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btt457},
doi = {10.1093/bioinformatics/btt457},
number = {20},
journal = {Bioinformatics},
author = {Muller, S. and Rycak, L. and Winter, P. and Kahl, G. and Koch, I. and Rotter, B.},
month = oct,
year = {2013},
pages = {2651--2652}
}
@article{koch_functional_2013,
title = {On {Functional} {Module} {Detection} in {Metabolic} {Networks}},
volume = {3},
url = {http://www.mdpi.com/2218-1989/3/3/673/},
doi = {10.3390/metabo3030673},
number = {3},
journal = {Metabolites},
author = {Koch, Ina and Ackermann, J{\"o}rg},
month = aug,
year = {2013},
pages = {673--700}
}
@article{khakabimamaghani_quatexelero:_2013,
title = {{QuateXelero}: {An} {Accelerated} {Exact} {Network} {Motif} {Detection} {Algorithm}},
volume = {8},
shorttitle = {{QuateXelero}},
url = {http://dx.plos.org/10.1371/journal.pone.0068073},
doi = {10.1371/journal.pone.0068073},
number = {7},
journal = {PLoS ONE},
author = {Khakabimamaghani, Sahand and Sharafuddin, Iman and Dichter, Norbert and Koch, Ina and Masoudi-Nejad, Ali},
month = jul,
year = {2013},
}
@article{schafer_image_2013,
title = {Image database analysis of {Hodgkin} lymphoma},
volume = {46},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1476927113000376},
doi = {10.1016/j.compbiolchem.2013.04.003},
journal = {Computational Biology and Chemistry},
author = {Sch{\"a}fer, Tim and Sch{\"a}fer, Hendrik and Schmitz, Alexander and Ackermann, J{\"o}rg and Dichter, Norbert and D{\"o}ring, Claudia and Hartmann, Sylvia and Hansmann, Martin-Leo and Koch, Ina},
month = oct,
year = {2013},
pages = {1--7}
}
@incollection{koch_hierarchical_2012,
title = {Hierarchical {Representation} of {Supersecondary} {Structures} {Using} a {Graph}-{Theoretical} {Approach}},
volume = {932},
isbn = {978-1-62703-064-9 978-1-62703-065-6},
url = {http://link.springer.com/10.1007/978-1-62703-065-6_2},
doi = {10.1007/978-1-62703-065-6_2},
booktitle = {Protein {Supersecondary} {Structures}},
publisher = {Humana Press},
author = {Koch, Ina and Kreuchwig, Annika and May, Patrick},
editor = {Kister, Alexander E.},
year = {2012},
pages = {7--33}
}