The Computational Systems Biology group works at the interface of Statistical Physics, Systems Biology and Systems Medicine.
Our investigations simultaneously cover ’omics’ data interpretation in Biology and Medicine (e.g., Marr, et al., 2008; Sonnenschein, et al., 2012; Knecht, et al., 2016; Bauer, et al., 2017; Schlicht, et al., 2019; Kosmidis, et al., 2020; ) and theoretical studies of dynamics on graphs (e.g., Marr, et al., 2006; Marr, et al., 2009; Kosmidis, et al., 2015; Fretter, et al., 2017; Moretti, et al., 2020; ).
We have discovered self-organized excitation waves around hubs in complex networks (Müller-Linow, et al., 2008; ) and explored the implications of this finding for Neuroscience (Garcia, et al., 2012; Hütt, et al., 2014; ) and beyond (Moretti, et al., 2020; ).
My group has pioneered the analysis of gene expression data via network coherences (small quantifiers of the match between a network and an expression profile), which has allowed us to better understand the interplay of chromosomal organization and transcriptional regulatory networks in bacterial gene regulation (Marr, et al., 2008; Sonnenschein, et al., 2011; Kosmidis, et al., 2020; ).
Our work on network-based analyses of transcriptome data from clinical cohorts has led to new insight into various diseases, e.g., primary hyperaldosteronism (Sonnenschein, et al., 2012; ), chronic inflammatory diseases of the gut (Knecht, et al., 2016; Häsler, et al., 2017; ) and hepatocellular carcinoma (Perrin-Cocon, et al., 2021; ).
Furthermore, the application of the notion of multilayer networks has allowed us to identify a simple fundamental principle, how a biological system can balance the conflicting requirements of sensitivity and robustness (Klosik, et al., 2017; ).
On a more general level, we have always pursued diverse interdisciplinary applications of concepts from the theory of complex systems and from network science (e.g., to long-distance train connections (Fretter, et al., 2010; ), to industrial production (e.g., Windt, et al., 2011; Becker, et al., 2011; Meyer, et al., 2016; Chankov, et al., 2016; ), to co-authorship networks (Krumov, et al., 2011; Klosik, et al., 2014; ) and networks of scientific disciplines (Lyutov, et al., 2021; ), to psychotherapy dynamics (Schiepek, et al., 2017; Schöller, et al., 2018; ), to networks of scientific hypotheses (Enders, et al., 2018; )).
@article{moretti2020link,
author = {Moretti, Paolo and Hütt, Marc-Thorsten},
journal = {Proceedings of the National Academy of Sciences},
number = {31},
pages = {18332--18340},
publisher = {National Academy of Sciences},
title = {Link-usage asymmetry and collective patterns emerging from rich-club organization of complex networks},
volume = {117},
year = {2020}
}
@article{klosik2017interdependent,
author = {Klosik, David F and Grimbs, Anne and Bornholdt, Stefan and Hütt, Marc-Thorsten},
journal = {Nature communications},
number = {1},
pages = {1--9},
publisher = {Nature Publishing Group},
title = {The interdependent network of gene regulation and metabolism is robust where it needs to be},
volume = {8},
year = {2017}
}
@article{muller2008organization,
author = {Müller-Linow, Mark and Hilgetag, Claus C and Hütt, Marc-Thorsten},
journal = {PLoS computational biology},
number = {9},
pages = {e1000190},
publisher = {Public Library of Science San Francisco, USA},
title = {Organization of excitable dynamics in hierarchical biological networks},
volume = {4},
year = {2008}
}
My textbooks on bioinformatics (Hütt, et al., 2015; ) and on data analysis in Biology (Hütt, 2001; ) bridge the gap between modern theoretical developments and experimental efforts in the Life Sciences.
@article{marr2008dissecting,
author = {Marr, Carsten and Geertz, Marcel and Hütt, Marc-Thorsten and Muskhelishvili, Georgi},
journal = {BMC systems biology},
number = {1},
pages = {1--9},
publisher = {BioMed Central},
title = {Dissecting the logical types of network control in gene expression profiles},
volume = {2},
year = {2008}
}
@article{sonnenschein2012network,
author = {Sonnenschein, Nikolaus and Golib Dzib, José Felipe and Lesne, Annick and Eilebrecht, Sebastian and Boulkroun, Sheerazed and Zennaro, Maria-Christina and Benecke, Arndt and Hütt, Marc-Thorsten},
journal = {BMC systems biology},
number = {1},
pages = {1--13},
publisher = {BioMed Central},
title = {A network perspective on metabolic inconsistency},
volume = {6},
year = {2012}
}
@article{knecht2016distinct,
author = {Knecht, Carolin and Fretter, Christoph and Rosenstiel, Philip and Krawczak, Michael and Hütt, Marc-Thorsten},
journal = {Scientific reports},
number = {1},
pages = {1--11},
publisher = {Nature Publishing Group},
title = {Distinct metabolic network states manifest in the gene expression profiles of pediatric inflammatory bowel disease patients and controls},
volume = {6},
year = {2016}
}
@article{bauer2017interdisciplinary,
author = {Bauer, Christian R and Knecht, Carolin and Fretter, Christoph and Baum, Benjamin and Jendrossek, Sandra and Rühlemann, Malte and Heinsen, Femke-Anouska and Umbach, Nadine and Grimbacher, Bodo and Franke, Andre and others},
journal = {Briefings in bioinformatics},
number = {3},
pages = {479--487},
publisher = {Oxford University Press},
title = {Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases},
volume = {18},
year = {2017}
}
@article{schlicht2019metabolic,
author = {Schlicht, Kristina and Nyczka, Piotr and Caliebe, Amke and Freitag-Wolf, Sandra and Claringbould, Annique and Franke, Lude and Võsa, Urmo and Kardia, Sharon LR and Smith, Jennifer A and Zhao, Wei and others},
journal = {Human genetics},
number = {4},
pages = {375--388},
publisher = {Springer Berlin Heidelberg},
title = {The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus},
volume = {138},
year = {2019}
}
@article{kosmidis2020chromosomal,
author = {Kosmidis, Kosmas and Jablonski, Kim Philipp and Muskhelishvili, Georgi and Hütt, Marc-Thorsten},
journal = {NPJ systems biology and applications},
number = {1},
pages = {1--9},
publisher = {Nature Publishing Group},
title = {Chromosomal origin of replication coordinates logically distinct types of bacterial genetic regulation},
volume = {6},
year = {2020}
}
@article{marr2006similar,
author = {Marr, Carsten and Hütt, Marc-Thorsten},
journal = {Physics Letters A},
number = {5},
pages = {302--305},
publisher = {Elsevier},
title = {Similar impact of topological and dynamic noise on complex patterns},
volume = {349},
year = {2006}
}
@article{marr2009outer,
author = {Marr, Carsten and Hütt, Marc-Thorsten},
journal = {Physics Letters A},
number = {5},
pages = {546--549},
publisher = {Elsevier},
title = {Outer-totalistic cellular automata on graphs},
volume = {373},
year = {2009}
}
@article{kosmidis2015network,
author = {Kosmidis, Kosmas and Beber, Moritz and Hütt, Marc-Thorsten},
journal = {Advances in Complex Systems},
number = {01n02},
pages = {1550007},
publisher = {World Scientific Publishing Company},
title = {Network heterogeneity and node capacity lead to heterogeneous scaling of fluctuations in random walks on graphs},
volume = {18},
year = {2015}
}
@article{fretter2017topological,
author = {Fretter, Christoph and Lesne, Annick and Hilgetag, Claus C and Hütt, Marc-Thorsten},
journal = {Scientific reports},
number = {1},
pages = {1--11},
publisher = {Nature Publishing Group},
title = {Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs},
volume = {7},
year = {2017}
}
@article{moretti2020link,
author = {Moretti, Paolo and Hütt, Marc-Thorsten},
journal = {Proceedings of the National Academy of Sciences},
number = {31},
pages = {18332--18340},
publisher = {National Academy of Sciences},
title = {Link-usage asymmetry and collective patterns emerging from rich-club organization of complex networks},
volume = {117},
year = {2020}
}
@article{muller2008organization,
author = {Müller-Linow, Mark and Hilgetag, Claus C and Hütt, Marc-Thorsten},
journal = {PLoS computational biology},
number = {9},
pages = {e1000190},
publisher = {Public Library of Science San Francisco, USA},
title = {Organization of excitable dynamics in hierarchical biological networks},
volume = {4},
year = {2008}
}
@article{garcia2012building,
author = {Garcia, Guadalupe Clara and Lesne, Annick and Hütt, Marc-Thorsten and Hilgetag, Claus C},
journal = {Frontiers in computational neuroscience},
pages = {50},
publisher = {Frontiers},
title = {Building blocks of self-sustained activity in a simple deterministic model of excitable neural networks},
volume = {6},
year = {2012}
}
@article{hutt2014perspective,
author = {Hütt, Marc-Thorsten and Kaiser, Marcus and Hilgetag, Claus C},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
number = {1653},
pages = {20130522},
publisher = {The Royal Society},
title = {Perspective: network-guided pattern formation of neural dynamics},
volume = {369},
year = {2014}
}
@article{sonnenschein2011analog,
author = {Sonnenschein, Nikolaus and Geertz, Marcel and Muskhelishvili, Georgi and Hütt, Marc-Thorsten},
journal = {BMC systems biology},
number = {1},
pages = {1--13},
publisher = {BioMed Central},
title = {Analog regulation of metabolic demand},
volume = {5},
year = {2011}
}
@article{sonnenschein2012topological,
author = {Sonnenschein, Nikolaus and Marr, Carsten and Hütt, Marc-Thorsten},
journal = {Metabolites},
number = {3},
pages = {632--647},
publisher = {Molecular Diversity Preservation International},
title = {A topological characterization of medium-dependent essential metabolic reactions},
volume = {2},
year = {2012}
}
@article{hasler2017uncoupling,
author = {Häsler, Robert and Sheibani-Tezerji, Raheleh and Sinha, Anupam and Barann, Matthias and Rehman, Ateequr and Esser, Daniela and Aden, Konrad and Knecht, Carolin and Brandt, Berenice and Nikolaus, Susanna and others},
journal = {Gut},
number = {12},
pages = {2087--2097},
publisher = {BMJ Publishing Group},
title = {Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease},
volume = {66},
year = {2017}
}
@article{perrin2021hexokinase,
author = {Perrin-Cocon, Laure and Vidalain, Pierre-Olivier and Jacquemin, Clémence and Aublin-Gex, Anne and Olmstead, Keedrian and Panthu, Baptiste and Rautureau, Gilles Jeans Philippe and André, Patrice and Nyczka, Piotr and Hütt, Marc-Thorsten and others},
journal = {Communications biology},
number = {1},
pages = {1--15},
publisher = {Nature Publishing Group},
title = {A hexokinase isoenzyme switch in human liver cancer cells promotes lipogenesis and enhances innate immunity},
volume = {4},
year = {2021}
}
@article{klosik2017interdependent,
author = {Klosik, David F and Grimbs, Anne and Bornholdt, Stefan and Hütt, Marc-Thorsten},
journal = {Nature communications},
number = {1},
pages = {1--9},
publisher = {Nature Publishing Group},
title = {The interdependent network of gene regulation and metabolism is robust where it needs to be},
volume = {8},
year = {2017}
}
@article{fretter2010phase,
author = {Fretter, Christoph and Krumov, Lachezar and Weihe, Karsten and Müller-Hannemann, Matthias and Hütt, M-T},
journal = {The European Physical Journal B},
number = {2},
pages = {281--289},
publisher = {Springer-Verlag},
title = {Phase synchronization in railway timetables},
volume = {77},
year = {2010}
}
@article{windt2011exploring,
author = {Windt, Katja and Hütt, Marc-Thorsten},
journal = {CIRP annals},
number = {1},
pages = {473--476},
publisher = {Elsevier},
title = {Exploring due date reliability in production systems using data mining methods adapted from gene expression analysis},
volume = {60},
year = {2011}
}
@article{becker2011flow,
author = {Becker, Till and Beber, Moritz E and Windt, Katja and Hütt, Marc-Thorsten and Helbing, Dirk},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
number = {05},
pages = {P05004},
publisher = {IOP Publishing},
title = {Flow control by periodic devices: a unifying language for the description of traffic, production, and metabolic systems},
volume = {2011},
year = {2011}
}
@article{meyer2016elementary,
author = {Meyer, Mirja and Hütt, Marc-Thorsten and Bendul, Julia},
journal = {International Journal of Production Research},
number = {14},
pages = {4145--4160},
publisher = {Taylor & Francis},
title = {The elementary flux modes of a manufacturing system: a novel approach to explore the relationship of network structure and function},
volume = {54},
year = {2016}
}
@article{chankov2016synchronization,
author = {Chankov, Stanislav and Hütt, Marc-Thorsten and Bendul, Julia},
journal = {International Journal of Production Research},
number = {20},
pages = {6033--6051},
publisher = {Taylor & Francis},
title = {Synchronization in manufacturing systems: quantification and relation to logistics performance},
volume = {54},
year = {2016}
}
@article{krumov2011motifs,
author = {Krumov, Lachezar and Fretter, Christoph and Müller-Hannemann, Matthias and Weihe, Karsten and Hütt, M-T},
journal = {The European Physical Journal B},
number = {4},
pages = {535--540},
publisher = {Springer-Verlag},
title = {Motifs in co-authorship networks and their relation to the impact of scientific publications},
volume = {84},
year = {2011}
}
@article{klosik2014motif,
author = {Klosik, David F and Bornholdt, Stefan and Hütt, Marc-Thorsten},
journal = {Physical Review E},
number = {3},
pages = {032811},
publisher = {American Physical Society},
title = {Motif-based success scores in coauthorship networks are highly sensitive to author name disambiguation},
volume = {90},
year = {2014}
}
@article{lyutov2021machine,
author = {Lyutov, Alexey and Uygun, Yilmaz and Hütt, Marc-Thorsten},
journal = {Scientometrics},
number = {2},
pages = {1173--1186},
publisher = {Springer International Publishing},
title = {Machine learning misclassification of academic publications reveals non-trivial interdependencies of scientific disciplines},
volume = {126},
year = {2021}
}
@article{schiepek2017psychotherapy,
author = {Schiepek, Günter K and Viol, Kathrin and Aichhorn, Wolfgang and Hütt, Marc-Thorsten and Sungler, Katharina and Pincus, David and Schöller, Helmut J},
journal = {Frontiers in Psychology},
pages = {379},
publisher = {Frontiers},
title = {Psychotherapy is chaotic---(not only) in a computational world},
volume = {8},
year = {2017}
}
@article{scholler2018personality,
author = {Schöller, Helmut and Viol, Kathrin and Aichhorn, Wolfgang and Hütt, Marc-Thorsten and Schiepek, Günter},
journal = {Cognitive Neurodynamics},
number = {5},
pages = {441--459},
publisher = {Springer Netherlands},
title = {Personality development in psychotherapy: a synergetic model of state-trait dynamics},
volume = {12},
year = {2018}
}
@article{enders2018drawing,
author = {Enders, Martin and Hütt, Marc-Thorsten and Jeschke, Jonathan M},
journal = {Ecosphere},
number = {3},
pages = {e02146},
title = {Drawing a map of invasion biology based on a network of hypotheses},
volume = {9},
year = {2018}
}
@misc{hutt2015methoden,
author = {Hütt, Marc-Thorsten and Dehnert, Manuel},
date-modified = {2022-02-19 07:49:52 +0100},
publisher = {Springer-Verlag},
title = {Methoden der Bioinformatik: eine Einführung zur Anwendung in Biologie und Medizin},
year = {2015}
}
@incollection{hutt2001dynamical,
author = {Hütt, M-Th and Rascher, U and Lüttge, U},
booktitle = {Emergent Nature: Patterns, Growth and Scaling in the Sciences},
pages = {123--133},
title = {Dynamical Regimes in the Metabolic Cycle of a Higher Plant are Characterized by Different Fractal Dimensions},
year = {2001}
}