Peer-reviewed Journal Articles
An * indicates equal contribution or joint correspondence
2024
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Tamer Butto*, Monika Chanu Chongtham*, Kanak Mungikar*, Dewi Hartwich, Matthias Linke, Nicolas Ruffini, Konstantin Radyushkin, Susann Schweiger, Jennifer Winter and Susanne Gerber: Characterization of transcriptional profiles associated with stress-induced neuronal activation in Arc-GFP mice. Nature Molecular Psychiatry, https://doi.org/10.1038/s41380-024-02555-z (2024).
IF: 13.5
- Charlotte Hewel, Hanno Schmidt, Stefan Runkel, Wolfgang Kohnen, Susann Schweiger-Seemann, Andre Michel, Sven-Ernoe Bikar, Bodo Plachter, Thomas Hankeln, Matthias Linke, Susanne Gerber: Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case. Journal of Medical Virology, https://doi.org/10.1002/jmv.29610 (2024)
IF: 12.8
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Mohit Navandar, Constance Vennin, Beat Lutz and Susanne Gerber: lncRNA expression and regulation across different brain regions in primates. Accepted for publication in Nature Scientific Data (2024)
IF: 10.8
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Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer, Stefan Mündnich, Anna Wierczeiko, Kristina Friedland, Mark Helm, Marie-Luise Winz and Susanne Gerber Real-time transcriptomic profiling in distinct experimental conditions. https://www.biorxiv.org/content/10.1101/2024.03.26.586831v1
- Nicolas Ruffini*, Saleh Altahini*, Stephan Weißbach*, Nico Weber, Jonas Milkovits, Anna Wierczeiko, Hendrik Backhaus, Albrecht Stroh, ViNe-Seg: Deep-Learning assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface, Bioinformatics, 2024, btae177, https://doi.org/10.1093/bioinformatics/btae177
IF: 5.8
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Marko Jörg, Johanna E. Plehn, Marco Kristen, Marc Lander, Lukas Walz, Christine Lietz, Julie Wijns, Florian Pichot, Liliana Rojas-Charry, Katja M. Wirtz Martin, Nicolas Ruffini, Nastasja Kreim, Susanne Gerber, Yuri Motorin, Kristina Endres, Walter Rossmanith, Axel Methner, Mark Helm, Kristina Friedland: N1-methylation of adenosine (m1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer’s disease. Nature Molecular Psychiatry (2024).
IF: 13.5 -
Irina Kovlyagina, Anna Wierczeiko, Hristo Todorov, Eric Jacobi, Margarita Tevosian, Jakob von Engelhardt, Susanne Gerber*, Beat Lutz*. Freezing responses during prolonged threat memory retrieval reflect trait-like anxiety endophenotypes in female and male inbred mice. Accepted for publication in PLOS Biology https://doi.org/10.1101/2023.11.22.568236 (2023).
IF: 9.8
2023
- Min-Kyeung Choi, Alex Cook, Kanak Mungikar, Helen Eachus, Anna Tochwin, Matthias Linke, Susanne Gerber, Soojin Ryu. Lifelong molecular consequences of high Glucocorticoids exposure during development bioRxiv, doi: https://doi.org/10.1101/2023.11.22.568236 (2023).
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Hristo Todorov, Stephan Weißbach, Laura Schlichtholz, Hanna Mueller, Dewi Hartwich, Susanne Gerber*, Jennifer Winter* Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex. bioRxiv, doi: https://doi.org/10.1101/2023.11.22.568236 (2023).
- Florian U. Fischer, Susanne Gerber, Oliver Tüscher, "The Alzheimer’s Disease Neuroimaging Initiative": A mathematical model of the Alzheimer’s Disease biomarker cascade demonstrates statistical pitfalls in identifying neurobiological surrogates of cognitive reserve BioRxiv (2023).
- Anna Wierczeiko, Matthias Linke, Johannes Peter Friedrich, Jan Koch, Andreas Schwarting, Andreas Krause, Susanne Gerber, Alexander Gerber: "A call for gene expression analysis in whole blood of patients with RA as biomarker for RA-ILD", Journal of Rheumatology (2023)
IF: 4.7
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Alexander Ewerling, Isa Graebling, Anna Wierczeiko, Elisa Kotzurek, Susanne Foitzik, Susanne Gerber, Thomas J. Colgan and Helen May-Simera: Analysis of human BBS protein homologues in insects support alternative non-ciliary functions.
bioRxiv (2023) -
Käseberg S., Bertin M.#, Menon R.#, Gabassi E.#, Todorov H.#, Frank S., Brennenstuhl H., Lohrer B., Winter J., Krummeich J., Winkler J., Winner B., Weis E., Hartwich D., Diederich S., Luck K., Gerber S., Lunt P., Berninger B., Falk S., Schweiger S., Karow M. Dynamic X-chromosomal reactivation enhances female brain resilience. bioRxiv (2023).
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Anna Wierczeiko, Stefan Pastore, Stefan Mündnich, Anne Busch, Vincent Dietrich, Mark Helm, Tamer Butto* and Susanne Gerber*: NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis. Bioinformatics, btad492, https://doi.org/10.1093/bioinformatics/btad492 (2023).
IF: 6.9
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Margaryta Tevosian, Hristo Todorov, Ermelinda Lomazzo, Laura Bindila, Natsuo Ueda, Davide Bassetti, Davide Warm, Sergei Kirischuk, Heiko J. Luhmann, Susanne Gerber, and Beat Lutz: NAPE-PLD deletion in stress-TRAPed neurons results in an anxiogenic phenotype. Nature Translational Psychiatry, 13, 152, https://doi.org/10.1038/s41398-023-02448-9 (2023).
IF: 7.9
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Tamer Butto, Kanak Mungikar, Peter Baumann, Jennifer Winter, Beat Lutz, Susanne Gerber. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells. 2023, 12(7), 1051; https://doi.org/10.3390/cells12071051
IF: 7.6
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Illia Horenko, Edoardo Vecchi, Juraj Kardos, Olaf Schenk, Andreas Wachter, Terence O’Kane, Patrick Gagliardini and Susanne Gerber: On cheap entropy-sparsified regression learning. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 120 (1) e2214972120, https://doi.org/10.1073/pnas.22149721, (2023).
IF: 12.8
2022
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Anne Marie Busch, Irina Kovlyagina, Beat Lutz, Hristo Todorov,* and Susanne Gerber*: beeRapp: An R Shiny App for automated high-throughput explorative analysis of multivariate behavioral data. Bioinformatics Advances, vbac082, (2022).
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Constance Vennin, Charlotte Hewel, Hristo Todorov, Marlon Wendelmuth, Konstantin Radyushkin, Andre Heimbach, Illia Horenko, Sarah Ayash, Marianne Müller, Susann Schweiger, Susanne Gerber and Beat Lutz. A Resilience-Related Glial-Neurovascular Network Is Transcriptionally Activated after Chronic Social Defeat in Male Mice. Cells, 11(21), 3405; https://doi.org/10.3390/cells11213405 (2022).
IF: 7.6
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, Stephan Lea . CollembolAI, a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities preserved in fluid. Methods in Ecology and Evolution, https://doi.org/10.1111/2041-210X.14001 (2022)
- IF: 8.4
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Leonie Frommherz, Katalin Komlosi, Charlotte Hewel, Julia Kopp, Malin Dewenter, Andreas Zimmer, Oliver Bartsch, Matthias Linke, Kristin Technau-Hafsi, Susanne Gerber, Judith Fischer and Cristina Has: Acral ichthyosis associated with amino acid substitution in the C-terminus of keratin 2. Journal of European Academy of Dermatology Venereology (2022)
IF: 9.2
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Illia Horenko*, Lukáš Pospíšil, Edoardo Vecchi, Steffen Albrecht, Alexander Gerber, Beate Rehbock, Albrecht Stroh and Susanne Gerber*: Low-Cost Probabilistic 3D Denoising with Applications for Ultra-Low-Radiation Computed Tomography. Journal of Imaging, 8(6),156; https://doi.org/10.3390/jimaging8060156 (2022)
IF: 3.4 -
Nicolas Ruffini*, Susanne Klingenberg*, Raoul Heese, Susann Schweiger and Susanne Gerber: The big picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. Frontiers in Aging Neuroscience. https://doi.org/10.3389/fnagi.2022.866886 (2022).
IF: 5.7 -
Malena dos Santos Guilherme, TheodoraTsoutsouli, Monika Chanu Chongtham, Jennifer Winter Susanne Gerber, Marianne Müller, Kristina Endres: Selective targeting of chronic social stress-induced activated neurons identifies neurogenesis-related genes to be associated with resilience in female mice. Psychoneuroendocrinology (2022)
IF: 4.9 -
Susanne Gerber*, Lucas Pospisil, Stanislav Sys, Charlotte Hewel, Ali Torkamani and Illia Horenko*: Co-inference of data mislabeling reveals improved models in genomics and breast cancer diagnostics, Frontiers in Artificial Intelligence, 4 (193 ) https://doi.org/10.3389/frai.2021.739432, (2022)
2021
- Nicolas Ruffini, Marianne Müller, Ulrich Schmitt and Susanne Gerber: IntelliPy: A GUI for analyzing IntelliCage data. Bioinformatics, https://doi.org/10.1093/bioinformatics/btab682 (2021)
IF: 6.9 -
Henning Formes, Joanna Pimenta Bernardes, Amrit Mann, Franziska Bayer, Giulia Pontarollo, Klytaimnistra Kiouptsi, Katrin Schäfer, Sebastian Attig, Teodora Nikolova, Thomas Hofmann, Jörn Schattenberg, Hristo Todorov, Susanne Gerber, Philip Rosenstiel, Tobias Bopp, Felix Sommer and Christoph Reinhardt: The gut microbiota instructs the hepatic endothelial cell transcriptom. iScience, 24 (10), (2021)
IF: 5.5
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Diego Pascual Cuadrado, Hristo Todorov, Raissa Lerner, Larglinda Islami, Laura Bindila, Susanne Gerber, Beat Lutz: Long-term molecular differences between resilient and susceptible mice after a single traumatic exposure. British Journal of Pharmacology, https://doi.org/10.1111/bph.15697 (2021)
IF: 9.47 -
Malena dos Santos Guilherme, Theodora Tsoutsouli, Hristo Todorov, Sina Teifel, Susanne Gerber* and Kristina Endres*. (2021)
IF: 6.6
- mTOR inhibition in primary neurons and the developing brain represses transcription of cholesterol biosynthesis genes and alters cholesterol levels. International Journal of Molecular Sciences, 22 (11), 6034 (2021)
IF: 6.2 -
, , , , , , , , ,, , ,Genomic basis of drought resistance in Fagus sylvatica. eLife, 10:e65532 (2021)
IF: 8.7
- Monika Chongtham, Tamer Butto, Kanak Mungikar, Susanne Gerber* and Jennifer Winter*: INTACT vs. FANS for cell-type-specific nuclei isolation: A comprehensive qualitative and quantitative comparison, International Journal of Molecular Sciences, 2(10), 5335; https://doi.org/10.3390/ijms22105335 (2021)
IF: 6.2
- Diego Pascual Cuadrado, Anna Wierczeiko, Charlotte Hewel, Susanne Gerber and Beat Lutz: Dichotomic hippocampal transcriptome after glutamatergic versus GABAergic deletion of the cannabinoid CB1 receptor, Frontiers In Synaptic Neuroscience, 13:660718. doi: 10.3389/fnsyn.2021.660718 (2021)
IF: 4.5 -
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Anna Wierczeiko, Lena Gammel, Konstantin Radyushkin, Vu Thu Thuy Nguyen Hristo Todorov, Susanne Gerber*, Kristina Endres*. Voluntary Wheel Running Did Not Alter Gene Expression in 5xFAD Mice, but in Wild-Type Animals Exclusively After One-Day Exercise Bout, Cells 10(3), 693; https://doi.org/10.3390/cells10030693 (2021)
IF: 7.6
- Davi Rodrigues, Karin Everschor-Sitte, Susanne Gerber and Illia Horenko. A deeper look into natural sciences with physics-based and data-driven measures. iScience Volume 24 (Issue 3), https://doi.org/10.1016/j.isci.2021.102171 (2021)
IF: 5.5
- Stephan Weißbach, Stanislav Sys, Charlotte Hewel, Hristo Todorov, Susann Schweiger, Jennifer Winter, Markus Pfenninger, Ali Torkamani, Doug Evans, Joachim Burger Karin Everschor-Sitte, Helen May-Simera and Susanne Gerber. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines. BMC Genomics 22, 62 (2021)
IF: 4.0 -
Halina Binde Doria, Cosima Caliendo, Susanne Gerber and Markus Pfenninger: Photoperiod is an important seasonal selection factor in Chironomus riparius. Biological Journal of the Linnean Society,blab147, https://doi.org/10.1093/biolinnean/blab147(2021)
IF: 2.3
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Illia Horenko, Lukas Pospisil, Edoardo Vecchi, Steffen Albrecht, Alexander Gerber, Beate Rehbock, Albrecht Stroh and Susanne Gerber: Quality-preserving low-cost probabilistic 3D denoising with applications to Computed Tomograpy doi: https://doi.org/10.1101/2021.08.10.455778
2020
- Nicolas Ruffini, Susanne Klingenberg, Susann Schweiger and Susanne Gerber. Common Factors in Neurodegeneration: A Meta-Study revealing Shared Patterns on a Multi-Omics Scale, Cells 9(12), 2642, https://doi.org/10.3390/cells9122642, (2020)
IF: 7.6
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- Susanne Gerber, Lukas Pospisil, Mohit Navandar and Illia Horenko:Low-cost scalable discretization, prediction and feature selection for complex systems, Science Advances, Vol. 6, no. 5, eaaw0961 DOI: 10.1126/sciadv.aaw0961 (2020)
IF: 14.1
- Laura Domingo-Rodriguez, Inigo Ruiz de Azua, Eduardo Dominguez, Eric Senabre, Irene Serra,Sami Kummer, Mohit Navandar, Sarah Baddenhausen, Clementine Hofmann, Raul Andero, Susanne Gerber, Marta Navarrete, Mara Dierssen, Beat Lutz, Elena Martín-García &Rafael Maldonado: A specific prelimbic-nucleus accumbens pathway controls resilience versus vulnerability to food addiction. Nature Communications 11, 782 (2020).
IF: 17.7
- Caroline Fischer, Heiko Endle, Lana Schumann, Annett Wilken-Schmitz, Julia Kaiser, Susanne Gerber, Christina F. Vogelaar, Mirko H.H. Schmidt, Robert Nitsch, Isabel Snodgrass, Dominique Thomas, Johannes Vogt, Irmgard Tegeder. Prevention of age-associated neuronal hyperexcitability with improved learning and attention upon knockout or antagonism of LPAR2. Cellular and Molecular Life Sciences https://doi.org/10.1007/s00018-020-03553-4 (2020).
IF: 9.3
- Klytaimnistra Kiouptsi, Giulia Pontarollo, Hristo Todorov, Johannes Braun, Sven Jäckel, Thomas Koeck, Franziska Bayer, Cornelia Karwot, Angelica Karpi, Susanne Gerber, Yvonne Jansen, Philipp Wild, Wolfram Ruf, Andreas Daiber, Emiel van der Vorst, Christian Weber, Yvonne Döring, Christoph Reinhardt. Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice. Gut Microbes https://www.tandfonline.com/doi/full/10.1080/19490976.2020.1767463 (2020).
IF: 10.3
- Malena dos Santos Guilherme, Hristo Todorov, Carina Osterhof, Anton Möllerke, Kristina Cub, Thomas Hankeln, Susanne Gerber, Kristina Endres: Impact of acute and chronic amyloid-β peptide exposure on gut microbial commensals in the mouse. Frontiers in Microbiology 11:1008. doi: 10.3389/fmicb.2020.01008 (2020).
IF: 5.6
- Hristo Todorov, Emily Searle-White and Susanne Gerber. Applying univariate vs. multivariate statistics to investigate therapeutic efficacy in (pre)clinical trials: A Monte Carlo simulation study on the example of a controlled preclinical neurotrauma trial. PLOS ONE, 15(3): e0230798; https://doi.org/10.1371/journal.pone.0230798 (2020).
IF: 3.2
- Hristo Todorov, Bettina Kollar, Franziska Bayer, Inês Brandão, Amrit Mann, Julia Mohr, Giulia Pontarollo, Henning Formes, Roland Stauber, Jens M. Kittner, Kristina Endres, Bernhard Watzer, Wolfgang Andreas Nockher, Felix Sommer, Susanne Gerber and Christoph Reinhardt. Alpha-Linolenic Acid-Rich Diet Influences Microbiota Composition and Villus Morphology of the Mouse Small Intestine. Nutrients. 12, 732; doi:10.3390/nu12030732. (2020).
IF: 6.7
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Marlon Wendelmuth, Michael Willam, Hristo Todorov, Konstantin Radyushkin, Susanne Gerber and Susann Schweiger. Dynamic longitudinal behavior in animals exposed to chronic social defeat stress. PLOS ONE. 15(7): e0235268 (2020).
IF: 3.2
2019
- Klytaimnistra Kiouptsi, Sven Jäckel, Giulia Pontarollo, Alexandra Grill, Marijke Kuijpers, Eivor Wilms, Christian Weber, Felix Sommer, Magdolna Nagy, Carlos Neideck, Yvonne Jansen, Stefanie Ascher, Henning Formes, Cornelia Karwot, Franziska Bayer, Bettina Kollar, Saravanan Subramaniam, Michael Molitor, Philip Wenzel, Philip Rosenstiel, Hristo Todorov, Susanne Gerber, Ulrich Walter, Kerstin Jurk, Johan Heemskerk, Emiel van der Vorst, Yvonne Döring, and Christoph Reinhardt: The microbiota promotes arterial thrombosis in low-density lipoprotein receptor-deficient mice. mBio, 10 (5) e02298-19; DOI: 10.1128/mBio.02298-19 (2019).
IF: 7.8
- Charlotte Hewel, Julia Kaiser, Anna Wierczeiko, Jan Linke, Christoph Reinhardt, Kristina Endres and Susanne Gerber: Common miRNA patterns of Alzheimers disease and Parkinsons disease and their putative impact on commensal gut microbiota. Frontiers in Neuroscience, doi: 10.3389/fnins.2019.00113 (2019).
IF: 5.1
2018
- Imputation of posterior linkage probability relations reveals a significant influence of structural 3D constraints on linkage disequilibrium,
- Susanne Gerber, Simon Olsson, Frank Noe and Illia Horenko: A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. Nature Scientific Reports, 8, Article number: 1796, doi:10.1038/s41598-018-19863-4 (2018)
IF: 4.9
- Hristo Todorov, David Fournier and Susanne Gerber: Principal components analysis: theory and application to gene expression data analysis, Genomics and Computational Biology, 4(2) p. e100041, jan. 2018. ISSN 2365-7154 (2018)
- Anna Wierczeiko, David Fournier, Hristo Todorov, Susanne Klingenberg, Kristina Endres and Susanne Gerber: Decoupling of DNA methylation status and gene expression levels in aging individuals, Genomics and Computational Biology, 4(2) p.e100040, jan. 2018. ISSN 2365-7154 (2018)
- Stanislav J. Sys, David Fournier, Illia Horenko, Kristina Endres and Susanne Gerber: Dynamics of SNP associations in relation to Alzheimer’s Disease captured with a new measure of linkage disequilibrium. Genomics and Computational Biology, 4(2) p. e100045, jan. 2018. ISSN 2365-7154 (2018)
2017
- Susanne Gerber and Illia Horenko: Towards a direct and scalable identification of reduced models for categorical processes, Proceedings of the National Academy of Sciences of the United States of America - (PNAS),114 (19) 4863-4868,doi:10.1073/pnas.1612619114 (2017).
IF: 12.8
2016
- Susanne Gerber, Martina Fröhlich, Hella Lichtenberg-Fraté, Sergey Shabala, Lana Shabala and Edda Klipp: A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae PLoS Comput. Biol. 12 (1), e1004703. doi: 10.1371/journal.pcbi.1004703, PMID: 26815455 (2016).
IF: 4.8
2015
- Susanne Gerber and Illia Horenko: Improving clustering by imposing network information. Science Advances 1(7), e1500163; DOI: 10.1126/sciadv.1500163 (2015).
IF: 14.1
2014
- Susanne Gerber and Illia Horenko: On inference of causality for discrete state models in multiscale context. Proceedings of the National Academy of Sciences of the United States of America (PNAS) - 111 (41) 14651-14656, doi:10.1073/pnas.1410404111,(2014):
IF: 12.8
- Dagmar Hosiner, Susanne Gerber, Hella Lichtenberg-Fraté, Walter Glaser, Christoph Schüller, and Edda Klipp: Impact of acute metal stress in Saccharomyces cerevisiae, PLoS ONE 9(1): e83330. doi:10.1371/journal.pone.0083330 (2014).
IF: 3.2
2011 and before
- Szymon Stoma, Martina Fröhlich, Susanne Gerber and Edda Klipp. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology, BMC Bioinformatics 12:126 (2011).
IF: 3.2
- Susanne Gerber, Guide Hasenbrink, Wouter Hendriksen, Paul van Heusden, Jost Ludwig, Edda Klipp, and Hella Lichtenberg-Frate, Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK_1|2 and P_BMH_1|2 promoter region, Genome Informatics 21 (2009).
IF: 1.4
- Susanne Gerber, Heike Aßmus, Barbara Bakker, and Edda Klipp. Drug-efficacy depends on the inhibitor type and the target position in a metabolic network - a systematic study, J. Theor. Biol. 252(3): 442-455 (2008).
IF: 2.7
Books and Book-Chapter
- Illia Horenko, Susanne Gerber, Terence J. O'Kane, James S. Risbey and Didier P. Monselesan: On inference and validation of causality relations in climate teleconnections. In Nonlinear and Stochastic Climate Dynamics, Cambridge University Press (C. Franzke and T. O'Kane, eds.), (2016)
- Susanne Gerber: Computational investigation of cation induced stress in yeast: Strategies for understanding the complex system of cation homeostasis in the yeast Saccharomyces cerevisia, Book, Südwestdeutscher Verlag für Hochschulschriften, ISBN-10: 3838130774, ISBN-13: 978-3838130774 (2012)
Theses:
- Susanne Gerber: In silico modeling of cation homeostasis in Saccaromyces cerevisiae, PhD thesis, Humboldt University of Berlin, Theoretical Biophysics Group, (2011)
- Susanne Gerber: Modeling and simulation of blood perfusion in human cancer tumors during hyperthermia treatment - Master's thesis, Konrad Zuse Institut, Numerische Analysis und Modellierung, Free University of Berlin, (2007)
- Susanne Gerber: Theoretische Untersuchung zur Wirkung von Inhibitoren in Abhängigkeit von ihrem Angriffsort im metabolischen Netzwerk und ihrem Typ, Bachelor thesis, Kinetic Modelling Group, Max Planck Institute for Molecular Genetics Berlin, Free University of Berlin (2004)