Leiron Ferrarese, Jean-Sébastien Jouhanneau, Michiel W H Remme, Jens Kremkow, Gergely Katona, Balázs Rózsa, Susanne Schreiber, James F A Poulet, 2018, Dendrite-Specific Amplification of Weak Synaptic Input during Network Activity In Vivo. Cell Rep, 24, 3455-3465.e5 (abstract) (full text)

Evert Bosdriesz, Anirudh Prahallad, Bertram Klinger, Anja Sieber, Astrid Bosma, René Bernards, Nils Blüthgen, Lodewyk F A Wessels, 2018, Comparative Network Reconstruction using mixed integer programming. Bioinformatics, 34, i997-i1004 (abstract) (full text)

Franziska Witzel, Nils Blüthgen, 2018, When More Is Less: Dual Phosphorylation Protects Signaling Off State against Overexpression. Biophys. J., 115, 1383-1392 (abstract) (full text)

Martina Michalikova, Michiel W H Remme, Richard Kempter, 2018, Extracellular waveforms reveal an axonal origin of spikelets in pyramidal neurons. J. Neurophysiol., 120, 1484-1495 (abstract) (full text)

Bharath Ananthasubramaniam, Axel Diernfellner, Michael Brunner, Hanspeter Herzel, 2018, Ultradian Rhythms in the Transcriptome of Neurospora crassa. iScience, 9, 475-486 (abstract) (full text)

Rukeia El-Athman, Angela Relógio, 2018, Escaping Circadian Regulation: An Emerging Hallmark of Cancer? Cell Syst, 6, 266-267 (abstract) (full text)

Rolf Apweiler, Tim Beissbarth, Michael R Berthold, Nils Blüthgen, Yvonne Burmeister, Olaf Dammann, Andreas Deutsch, Friedrich Feuerhake, Andre Franke, Jan Hasenauer, Steve Hoffmann, Thomas Höfer, Peter Lm Jansen, Lars Kaderali, Ursula Klingmüller, Ina Koch, Oliver Kohlbacher, Lars Kuepfer, Frank Lammert, Dieter Maier, Nico Pfeifer, Nicole Radde, Markus Rehm, Ingo Roeder, Julio Saez-Rodriguez, Ulrich Sax, Bernd Schmeck, Andreas Schuppert, Bernd Seilheimer, Fabian J Theis, Julio Vera, Olaf Wolkenhauer, 2018, Whither systems medicine? Exp. Mol. Med., 50, e453 (abstract) (full text)

Christian Beck, Henning Knoop, Ralf Steuer, 2018, Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes. PLoS Genet., 14, e1007239 (abstract) (full text)

Roman Zug, Peter Hammerstein, 2018, Evolution of reproductive parasites with direct fitness benefits. Heredity (Edinb), 120, 266-281 (abstract) (full text)

J Patrick Pett, Matthew Kondoff, Grigory Bordyugov, Achim Kramer, Hanspeter Herzel, 2018, Co-existing feedback loops generate tissue-specific circadian rhythms. Life Sci Alliance, 1, e201800078 (abstract) (full text)

Christopher T Monk, Matthieu Barbier, Pawel Romanczuk, James R Watson, Josep Alós, Shinnosuke Nakayama, Daniel I Rubenstein, Simon A Levin, Robert Arlinghaus, 2018, How ecology shapes exploitation: a framework to predict the behavioural response of human and animal foragers along exploration-exploitation trade-offs. Ecol. Lett., 21, 779-793 (abstract) (full text)

Mónica Abreu, Alireza Basti, Nikolai Genov, Gianluigi Mazzoccoli, Angela Relógio, 2018, The reciprocal interplay between TNFα and the circadian clock impacts on cell proliferation and migration in Hodgkin lymphoma cells. Sci Rep, 8, 11474 (abstract) (full text)

Johannes Meisig, Nils Blüthgen, 2018, The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 373, (abstract) (full text)

Patricio Godoy, Wolfgang Schmidt-Heck, Birte Hellwig, Patrick Nell, David Feuerborn, Jörg Rahnenführer, Kathrin Kattler, Jörn Walter, Nils Blüthgen, Jan G Hengstler, 2018, Assessment of stem cell differentiation based on genome-wide expression profiles. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 373, (abstract) (full text)

Luise Fuhr, Rukeia El-Athman, Rosella Scrima, Olga Cela, Annalucia Carbone, Henning Knoop, Yin Li, Karen Hoffmann, Mikko O Laukkanen, Francesco Corcione, Ralf Steuer, Thomas F Meyer, Gianluigi Mazzoccoli, Nazzareno Capitanio, Angela Relógio, 2018, The Circadian Clock Regulates Metabolic Phenotype Rewiring Via HKDC1 and Modulates Tumor Progression and Drug Response in Colorectal Cancer. EBioMedicine, 33, 105-121 (abstract) (full text)

Rukeia El-Athman, Luise Fuhr, Angela Relógio, 2018, A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine, 33, 68-81 (abstract) (full text)

Christoph Schmal, Erik D Herzog, Hanspeter Herzel, 2018, Measuring Relative Coupling Strength in Circadian Systems. J. Biol. Rhythms, 33, 84-98 (abstract) (full text)

Gina Polo, Carlos Mera Acosta, Marcelo B Labruna, Fernando Ferreira, Dirk Brockmann, 2018, Hosts mobility and spatial spread of Rickettsia rickettsii. PLoS Comput. Biol., 14, e1006636 (abstract) (full text)

Michiel W H Remme, John Rinzel, Susanne Schreiber, 2018, Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection. PLoS Comput. Biol., 14, e1006612 (abstract) (full text)

Mathurin Dorel, Bertram Klinger, Torsten Gross, Anja Sieber, Anirudh Prahallad, Evert Bosdriesz, Lodewyk F A Wessels, Nils Blüthgen, 2018, Modelling signalling networks from perturbation data. Bioinformatics, 34, 4079-4086 (abstract) (full text)

Isao T Tokuda, Daisuke Ono, Sato Honma, Ken-Ichi Honma, Hanspeter Herzel, 2018, Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors. PLoS Comput. Biol., 14, e1006607 (abstract) (full text)

André Holzbecher, Richard Kempter, 2018, Interneuronal gap junctions increase synchrony and robustness of hippocampal ripple oscillations. Eur. J. Neurosci., 48, 3446-3465 (abstract) (full text)

Nicole Wittenbrink, Bharath Ananthasubramaniam, Mirjam Münch, Barbara Koller, Bert Maier, Charlotte Weschke, Frederik Bes, Jan de Zeeuw, Claudia Nowozin, Amely Wahnschaffe, Sophia Wisniewski, Mandy Zaleska, Osnat Bartok, Reut Ashwal-Fluss, Hedwig Lammert, Hanspeter Herzel, Michael Hummel, Sebastian Kadener, Dieter Kunz, Achim Kramer, 2018, High-accuracy determination of internal circadian time from a single blood sample. J. Clin. Invest., 128, 3826-3839 (abstract) (full text)

E Besray Unal, Christina Kiel, Hannah Benisty, Andrew Campbell, Karen Pickering, Nils Blüthgen, Owen J Sansom, Luis Serrano, 2018, Systems level expression correlation of Ras GTPase regulators. Cell Commun. Signal, 16, 46 (abstract) (full text)

David Bierbach, Tim Landgraf, Pawel Romanczuk, Juliane Lukas, Hai Nguyen, Max Wolf, Jens Krause, 2018, Using a robotic fish to investigate individual differences in social responsiveness in the guppy. R Soc Open Sci, 5, 181026 (abstract) (full text)

Paula T Kuokkanen, Go Ashida, Anna Kraemer, Thomas McColgan, Kazuo Funabiki, Hermann Wagner, Christine Köppl, Catherine E Carr, Richard Kempter, 2018, Contribution of action potentials to the extracellular field potential in the nucleus laminaris of barn owl. J. Neurophysiol., 119, 1422-1436 (abstract) (full text)

Bertram Klinger, Nils Blüthgen, 2018, Reverse engineering gene regulatory networks by modular response analysis - a benchmark. Essays Biochem., 62, 535-547 (abstract) (full text)

Jihwan Myung, Christoph Schmal, Sungho Hong, Yoshiaki Tsukizawa, Pia Rose, Yong Zhang, Michael J Holtzman, Erik De Schutter, Hanspeter Herzel, Grigory Bordyugov, Toru Takumi, 2018, The choroid plexus is an important circadian clock component. Nat Commun, 9, 1062 (abstract) (full text)

Michael Schubert, Bertram Klinger, Martina Klünemann, Anja Sieber, Florian Uhlitz, Sascha Sauer, Mathew J Garnett, Nils Blüthgen, Julio Saez-Rodriguez, 2018, Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun, 9, 20 (abstract) (full text)

Stefano Castellana, Tommaso Mazza, Daniele Capocefalo, Nikolai Genov, Tommaso Biagini, Caterina Fusilli, Felix Scholkmann, Angela Relógio, John B Hogenesch, Gianluigi Mazzoccoli, 2018, Systematic Analysis of Mouse Genome Reveals Distinct Evolutionary and Functional Properties Among Circadian and Ultradian Genes. Front Physiol, 9, 1178 (abstract) (full text)

Ute Abraham, Julia Katharina Schlichting, Achim Kramer, Hanspeter Herzel, 2018, Quantitative analysis of circadian single cell oscillations in response to temperature. PLoS ONE, 13, e0190004 (abstract) (full text)

Laura Cantini, Laurence Calzone, Loredana Martignetti, Mattias Rydenfelt, Nils Blüthgen, Emmanuel Barillot, Andrei Zinovyev, 2018, Classification of gene signatures for their information value and functional redundancy. NPJ Syst Biol Appl, 4, 2 (abstract) (full text)

Florian Uhlitz, Anja Sieber, Emanuel Wyler, Raphaela Fritsche-Guenther, Johannes Meisig, Markus Landthaler, Bertram Klinger, Nils Blüthgen, 2017, An immediate-late gene expression module decodes ERK signal duration. Mol. Syst. Biol., 13, 944 (abstract)

Noreen van der Linden, Tom Cornelis, Dorien M Kimenai, Lieke J J Klinkenberg, Judith M Hilderink, Sarah Lück, Elisabeth J R Litjens, Frederique E C M Peeters, Alexander S Streng, Tobias Breidthardt, Luc J C van Loon, Otto Bekers, Jeroen P Kooman, Pål O Westermark, Christian Mueller, Steven J R Meex, 2017, Origin of Cardiac Troponin T Elevations in Chronic Kidney Disease. Circulation, 136, 1073-1075 (abstract) (full text)

Thomas McColgan, Ji Liu, Paula Tuulia Kuokkanen, Catherine Emily Carr, Hermann Wagner, Richard Kempter, 2017, Dipolar extracellular potentials generated by axonal projections. Elife, 6, (abstract) (full text)

Evrim B Ünal, Florian Uhlitz, Nils Blüthgen, 2017, A compendium of ERK targets. FEBS Lett., 591, 2607-2615 (abstract) (full text)

Tiziano D'Albis, Richard Kempter, 2017, A single-cell spiking model for the origin of grid-cell patterns. PLoS Comput. Biol., 13, e1005782 (abstract) (full text)

Christoph Schmal, Jihwan Myung, Hanspeter Herzel, Grigory Bordyugov, 2017, Moran's I quantifies spatio-temporal pattern formation in neural imaging data. Bioinformatics, 33, 3072-3079 (abstract) (full text)

Benjamin F Maier, Dirk Brockmann, 2017, Cover time for random walks on arbitrary complex networks. Phys Rev E, 96, 042307 (abstract) (full text)

Michael E Hughes, Katherine C Abruzzi, Ravi Allada, Ron Anafi, Alaaddin Bulak Arpat, Gad Asher, Pierre Baldi, Charissa de Bekker, Deborah Bell-Pedersen, Justin Blau, Steve Brown, M Fernanda Ceriani, Zheng Chen, Joanna C Chiu, Juergen Cox, Alexander M Crowell, Jason P DeBruyne, Derk-Jan Dijk, Luciano DiTacchio, Francis J Doyle, Giles E Duffield, Jay C Dunlap, Kristin Eckel-Mahan, Karyn A Esser, Garret A FitzGerald, Daniel B Forger, Lauren J Francey, Ying-Hui Fu, Frédéric Gachon, David Gatfield, Paul de Goede, Susan S Golden, Carla Green, John Harer, Stacey Harmer, Jeff Haspel, Michael H Hastings, Hanspeter Herzel, Erik D Herzog, Christy Hoffmann, Christian Hong, Jacob J Hughey, Jennifer M Hurley, Horacio O de la Iglesia, Carl Johnson, Steve A Kay, Nobuya Koike, Karl Kornacker, Achim Kramer, Katja Lamia, Tanya Leise, Scott A Lewis, Jiajia Li, Xiaodong Li, Andrew C Liu, Jennifer J Loros, Tami A Martino, Jerome S Menet, Martha Merrow, Andrew J Millar, Todd Mockler, Felix Naef, Emi Nagoshi, Michael N Nitabach, Maria Olmedo, Dmitri A Nusinow, Louis J Ptáček, David Rand, Akhilesh B Reddy, Maria S Robles, Till Roenneberg, Michael Rosbash, Marc D Ruben, Samuel S C Rund, Aziz Sancar, Paolo Sassone-Corsi, Amita Sehgal, Scott Sherrill-Mix, Debra J Skene, Kai-Florian Storch, Joseph S Takahashi, Hiroki R Ueda, Han Wang, Charles Weitz, Pål O Westermark, Herman Wijnen, Ying Xu, Gang Wu, Seung-Hee Yoo, Michael Young, Eric Erquan Zhang, Tomasz Zielinski, John B Hogenesch, 2017, Guidelines for Genome-Scale Analysis of Biological Rhythms. J. Biol. Rhythms, 32, 380-393 (abstract) (full text)

Guido Hermey, Nils Blüthgen, Dietmar Kuhl, 2017, Neuronal activity-regulated alternative mRNA splicing. Int. J. Biochem. Cell Biol., 91, 184-193 (abstract) (full text)

Jochen Winterer, Nikolaus Maier, Christian Wozny, Prateep Beed, Jörg Breustedt, Roberta Evangelista, Yangfan Peng, Tiziano D'Albis, Richard Kempter, Dietmar Schmitz, 2017, Excitatory Microcircuits within Superficial Layers of the Medial Entorhinal Cortex. Cell Rep, 19, 1110-1116 (abstract) (full text)

Florian Uhlitz, Anja Sieber, Emanuel Wyler, Raphaela Fritsche-Guenther, Johannes Meisig, Markus Landthaler, Bertram Klinger, Nils Blüthgen, 2017, An immediate-late gene expression module decodes ERK signal duration. Mol. Syst. Biol., 13, 928 (abstract)

Janina Hesse, Jan-Hendrik Schleimer, Susanne Schreiber, 2017, Qualitative changes in phase-response curve and synchronization at the saddle-node-loop bifurcation. Phys Rev E, 95, 052203 (abstract) (full text)

Marianne Gründel, Henning Knoop, Ralf Steuer, 2017, Activity and functional properties of the isocitrate lyase in the cyanobacterium Cyanothece sp. PCC 7424. Microbiology (Reading, Engl.), 163, 731-744 (abstract) (full text)

Nils Blüthgen, Mirjam van Bentum, Barbara Merz, Dietmar Kuhl, Guido Hermey, 2017, Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo. Sci Rep, 7, 45101 (abstract) (full text)

Yinxiu Zhan, Luca Mariani, Iros Barozzi, Edda G Schulz, Nils Blüthgen, Michael Stadler, Guido Tiana, Luca Giorgetti, 2017, Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res., 27, 479-490 (abstract) (full text)

Federica Eduati, Victoria Doldàn-Martelli, Bertram Klinger, Thomas Cokelaer, Anja Sieber, Fiona Kogera, Mathurin Dorel, Mathew J Garnett, Nils Blüthgen, Julio Saez-Rodriguez, 2017, Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models. Cancer Res., 77, 3364-3375 (abstract) (full text)

Pamela Riemer, Mattias Rydenfelt, Matthias Marks, Karen van Eunen, Kathrin Thedieck, Bernhard G Herrmann, Nils Blüthgen, Christine Sers, Markus Morkel, 2017, Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids. J. Cell Biol., 216, 1567-1577 (abstract) (full text)

Alexandra-M Reimers, Henning Knoop, Alexander Bockmayr, Ralf Steuer, 2017, Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. Proc. Natl. Acad. Sci. U.S.A., , (abstract) (full text)

Nikolay Chenkov, Henning Sprekeler, Richard Kempter, 2017, Memory replay in balanced recurrent networks. PLoS Comput. Biol., 13, e1005359 (abstract) (full text)

David Druzd, Olga Matveeva, Louise Ince, Ute Harrison, Wenyan He, Christoph Schmal, Hanspeter Herzel, Anthony H Tsang, Naoto Kawakami, Alexei Leliavski, Olaf Uhl, Ling Yao, Leif Erik Sander, Chien-Sin Chen, Kerstin Kraus, Alba de Juan, Sophia Martina Hergenhan, Marc Ehlers, Berthold Koletzko, Rainer Haas, Werner Solbach, Henrik Oster, Christoph Scheiermann, 2017, Lymphocyte Circadian Clocks Control Lymph Node Trafficking and Adaptive Immune Responses. Immunity, 46, 120-132 (abstract) (full text)

Flavio Iannelli, Andreas Koher, Dirk Brockmann, Philipp Hövel, Igor M Sokolov, 2017, Effective distances for epidemics spreading on complex networks. Phys Rev E, 95, 012313 (abstract) (full text)

Martina Michalikova, Michiel W H Remme, Richard Kempter, 2017, Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma. PLoS Comput. Biol., 13, e1005237 (abstract) (full text)

David Malatinszky, Ralf Steuer, Patrik R Jones, 2017, A Comprehensively Curated Genome-Scale Two-Cell Model for the Heterocystous Cyanobacterium Anabaena sp. PCC 7120. Plant Physiol., 173, 509-523 (abstract) (full text)

Kevin Thurley, Christopher Herbst, Felix Wesener, Barbara Koller, Thomas Wallach, Bert Maier, Achim Kramer, Pål O Westermark, 2017, Principles for circadian orchestration of metabolic pathways. Proc. Natl. Acad. Sci. U.S.A., 114, 1572-1577 (abstract) (full text)

Rukeia El-Athman, Nikolai N Genov, Jeannine Mazuch, Kaiyang Zhang, Yong Yu, Luise Fuhr, Mónica Abreu, Yin Li, Thomas Wallach, Achim Kramer, Clemens A Schmitt, Angela Relógio, 2017, The Ink4a/Arf locus operates as a regulator of the circadian clock modulating RAS activity. PLoS Biol., 15, e2002940 (abstract) (full text)

Gregor Mönke, Elena Cristiano, Ana Finzel, Dhana Friedrich, Hanspeter Herzel, Martin Falcke, Alexander Loewer, 2017, Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells. Sci Rep, 7, 46571 (abstract) (full text)

Jorge Jaramillo, Richard Kempter, 2017, Phase precession: a neural code underlying episodic memory? Curr. Opin. Neurobiol., 43, 130-138 (abstract) (full text)

Katharina Anna Wilmes, Jan-Hendrik Schleimer, Susanne Schreiber, 2017, Spike-timing dependent inhibitory plasticity to learn a selective gating of backpropagating action potentials. Eur. J. Neurosci., 45, 1032-1043 (abstract) (full text)

Bruno Christ, Uta Dahmen, Karl-Heinz Herrmann, Matthias König, Jürgen R Reichenbach, Tim Ricken, Jana Schleicher, Lars Ole Schwen, Sebastian Vlaic, Navina Waschinsky, 2017, Computational Modeling in Liver Surgery. Front Physiol, 8, 906 (abstract) (full text)

Lucas Böttcher, Olivia Woolley-Meza, Dirk Brockmann, 2017, Temporal dynamics of online petitions. PLoS ONE, 12, e0178062 (abstract) (full text)

Stefanie Westermark, Ralf Steuer, 2016, Toward Multiscale Models of Cyanobacterial Growth: A Modular Approach. Front Bioeng Biotechnol, 4, 95 (abstract) (full text)

Marco Gebiola, Suzanne E Kelly, Peter Hammerstein, Massimo Giorgini, Martha S Hunter, 2016, “Darwin's corollary” and cytoplasmic incompatibility induced by Cardinium may contribute to speciation in Encarsia wasps (Hymenoptera: Aphelinidae). Evolution, 70, 2447-2458 (abstract) (full text)

Alba Diz-Muñoz, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillaume Salbreux, Carl-Philipp Heisenberg, Ewa K Paluch, 2016, Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biol., 14, 74 (abstract) (full text)

Dagmar Waltemath, Jonathan R Karr, Frank T Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Arne T Bittig, Paulo E Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S Costa, Joseph Cursons, Tobias Czauderna, Arthur P Goldberg, Harold F Gomez, Jens Hahn, Tuure Hameri, Daniel F Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knupfer, Matthias Konig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M Varusai, Leandro H Watanabe, Florian Wendland, Markus Wolfien, James T Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber, 2016, Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans Biomed Eng, 63, 2007-14 (abstract) (full text)

Christian H Gabriel, Fridolin Gross, Martin Karl, Heike Stephanowitz, Anna Floriane Hennig, Melanie Weber, Stefanie Gryzik, Ivo Bachmann, Katharina Hecklau, Jürgen Wienands, Johannes Schuchhardt, Hanspeter Herzel, Andreas Radbruch, Eberhard Krause, Ria Baumgrass, 2016, Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells. J. Biol. Chem., 291, 24172-24187 (abstract) (full text)

Vaibhav Shinde, Sureshkumar Perumal Srinivasan, Margit Henry, Tamara Rotshteyn, Jürgen Hescheler, Jörg Rahnenführer, Marianna Grinberg, Johannes Meisig, Nils Blüthgen, Tanja Waldmann, Marcel Leist, Jan Georg Hengstler, Agapios Sachinidis, 2016, Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells. Stem Cell Res Ther, 7, 190 (abstract) (full text)

Franziska Fuhrmann, Timo Lischke, Fridolin Gross, Tobias Scheel, Laura Bauer, Khalid Wasim Kalim, Andreas Radbruch, Hanspeter Herzel, Andreas Hutloff, Ria Baumgrass, 2016, Adequate immune response ensured by binary IL-2 and graded CD25 expression in a murine transfer model. Elife, 5, (abstract) (full text)

Katharina Baum, Antonio Z Politi, Bente Kofahl, Ralf Steuer, Jana Wolf, 2016, Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations. PLoS Comput. Biol., 12, e1005298 (abstract) (full text)

James E Herbert-Read, Pawel Romanczuk, Stefan Krause, Daniel Strömbom, Pierre Couillaud, Paolo Domenici, Ralf H J M Kurvers, Stefano Marras, John F Steffensen, Alexander D M Wilson, Jens Krause, 2016, Correction to 'Proto-cooperation: group hunting sailfish improve hunting success by alternating attacks on grouping prey'. Proc. Biol. Sci., 283, (abstract) (full text)

J Patrick Pett, Anja Korenčič, Felix Wesener, Achim Kramer, Hanspeter Herzel, 2016, Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator. PLoS Comput. Biol., 12, e1005266 (abstract) (full text)

Jan-Hendrik Schleimer, Susanne Schreiber, 2016, Homeostasis: How Neurons Achieve Temperature Invariance. Curr. Biol., 26, R1141-R1143 (abstract) (full text)

James E Herbert-Read, Pawel Romanczuk, Stefan Krause, Daniel Strömbom, Pierre Couillaud, Paolo Domenici, Ralf H J M Kurvers, Stefano Marras, John F Steffensen, Alexander D M Wilson, Jens Krause, 2016, Proto-cooperation: group hunting sailfish improve hunting success by alternating attacks on grouping prey. Proc. Biol. Sci., 283, (abstract) (full text)

Alexandra S Klein, José R Donoso, Richard Kempter, Dietmar Schmitz, Prateep Beed, 2016, Early Cortical Changes in Gamma Oscillations in Alzheimer's Disease. Front Syst Neurosci, 10, 83 (abstract) (full text)

Tim Landgraf, David Bierbach, Hai Nguyen, Nadine Muggelberg, Pawel Romanczuk, Jens Krause, 2016, RoboFish: increased acceptance of interactive robotic fish with realistic eyes and natural motion patterns by live Trinidadian guppies. Bioinspir Biomim, 11, 015001 (abstract) (full text)

Patricio Godoy, Agata Widera, Wolfgang Schmidt-Heck, Gisela Campos, Christoph Meyer, Cristina Cadenas, Raymond Reif, Regina Stöber, Seddik Hammad, Larissa Pütter, Kathrin Gianmoena, Rosemarie Marchan, Ahmed Ghallab, Karolina Edlund, Andreas Nüssler, Wolfgang E Thasler, Georg Damm, Daniel Seehofer, Thomas S Weiss, Olaf Dirsch, Uta Dahmen, Rolf Gebhardt, Umesh Chaudhari, Kesavan Meganathan, Agapios Sachinidis, Jens Kelm, Ute Hofmann, René P Zahedi, Reinhard Guthke, Nils Blüthgen, Steven Dooley, Jan G Hengstler, 2016, Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Arch. Toxicol., 90, 2513-29 (abstract) (full text)

Paul F Thaben, Pål O Westermark, 2016, Differential rhythmicity: detecting altered rhythmicity in biological data. Bioinformatics, 32, 2800-8 (full text) (abstract)

John M McNamara, Sasha R X Dall, Peter Hammerstein, Olof Leimar, 2016, Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments. Ecol. Lett., 19, 1267-76 (full text) (abstract)

Tomáš Zavřel, Jan Červený, Henning Knoop, Ralf Steuer, 2016, Optimizing cyanobacterial product synthesis: Meeting the challenges. Bioengineered, 7, 490-496 (abstract) (full text)

Agata Michna, Herbert Braselmann, Martin Selmansberger, Anne Dietz, Julia Hess, Maria Gomolka, Sabine Hornhardt, Nils Blüthgen, Horst Zitzelsberger, Kristian Unger, 2016, Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data. PLoS ONE, 11, e0160791 (full text) (abstract)

Pål O Westermark, 2016, Linking Core Promoter Classes to Circadian Transcription. PLoS Genet., 12, e1006231 (full text) (abstract)

Christian Laut Ebbesen, Eric Torsten Reifenstein, Qiusong Tang, Andrea Burgalossi, Saikat Ray, Susanne Schreiber, Richard Kempter, Michael Brecht, 2016, Cell Type-Specific Differences in Spike Timing and Spike Shape in the Rat Parasubiculum and Superficial Medial Entorhinal Cortex. Cell Rep, 16, 1005-15 (full text) (abstract)

Olof Leimar, Sasha R X Dall, Peter Hammerstein, John M McNamara, 2016, Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments. PLoS Comput. Biol., 12, e1005006 (full text) (abstract)

Catherine Carr, Go Ashida, Hermann Wagner, Thomas McColgan, Richard Kempter, 2016, The Role of Conduction Delay in Creating Sensitivity to Interaural Time Differences. Adv. Exp. Med. Biol., 894, 189-96 (full text) (abstract)

Raphaela Fritsche-Guenther, Franziska Witzel, Stefan Kempa, Tilman Brummer, Christine Sers, Nils Blüthgen, 2016, Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis. Oncotarget, 7, 7960-9 (abstract) (full text)

Nadine Rohwer, Fabian Bindel, Christina Grimm, Suling J Lin, Jessica Wappler, Bertram Klinger, Nils Blüthgen, Ilona Du Bois, Bernd Schmeck, Hans Lehrach, Marjo de Graauw, Emanuel Goncalves, Julio Saez-Rodriguez, Patrick Tan, Heike I Grabsch, Alessandro Prigione, Stefan Kempa, Thorsten Cramer, 2016, Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget, 7, 6693-710 (abstract) (full text)

Katharina A Wilmes, Henning Sprekeler, Susanne Schreiber, 2016, Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons. PLoS Comput. Biol., 12, e1004768 (full text) (abstract)

Lisa Hoelting, Stefanie Klima, Christiaan Karreman, Marianna Grinberg, Johannes Meisig, Margit Henry, Tamara Rotshteyn, Jörg Rahnenführer, Nils Blüthgen, Agapios Sachinidis, Tanja Waldmann, Marcel Leist, 2016, Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants. Stem Cells Transl Med, 5, 476-87 (abstract) (full text)

Eric T Reifenstein, Christian L Ebbesen, Qiusong Tang, Michael Brecht, Susanne Schreiber, Richard Kempter, 2016, Cell-Type Specific Phase Precession in Layer II of the Medial Entorhinal Cortex. J. Neurosci., 36, 2283-8 (full text) (abstract)

Christian T Herbst, Jakob Unger, Hanspeter Herzel, Jan G Švec, Jörg Lohscheller, 2016, Phasegram Analysis of Vocal Fold Vibration Documented With Laryngeal High-speed Video Endoscopy. J Voice, 30, 771.e1-771.e15 (abstract) (full text)

Sarah Lück, Pål O Westermark, 2016, Circadian mRNA expression: insights from modeling and transcriptomics. Cell. Mol. Life Sci., 73, 497-521 (abstract) (full text)

Tomáš Zavřel, Henning Knoop, Ralf Steuer, Patrik R Jones, Jan Červený, Martin Trtílek, 2016, A quantitative evaluation of ethylene production in the recombinant cyanobacterium Synechocystis sp. PCC 6803 harboring the ethylene-forming enzyme by membrane inlet mass spectrometry. Bioresour. Technol., 202, 142-51 (abstract) (full text)

Peter Hammerstein, Ronald Noë, 2016, Biological trade and markets. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 371, (full text) (abstract)

Nadine Dreser, Bastian Zimmer, Christian Dietz, Elena Sügis, Giorgia Pallocca, Johanna Nyffeler, Johannes Meisig, Nils Blüthgen, Michael R Berthold, Tanja Waldmann, Marcel Leist, 2015, Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling. Neurotoxicology, 50, 56-70 (abstract) (full text)

Jonas J Staudacher, Isabel S Naarmann-de Vries, Stefanie J Ujvari, Bertram Klinger, Mumtaz Kasim, Edgar Benko, Antje Ostareck-Lederer, Dirk H Ostareck, Anja Bondke Persson, Stephan Lorenzen, Jochen C Meier, Nils Blüthgen, Pontus B Persson, Alexandra Henrion-Caude, Ralf Mrowka, Michael Fähling, 2015, Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Res., 43, 3219-3236 (full text) (abstract)

Philippe Thomas, Pawel Durek, Illés Solt, Bertram Klinger, Franziska Witzel, Pascal Schulthess, Yvonne Mayer, Domonkos Tikk, Nils Blüthgen, Ulf Leser, 2015, Computer-assisted curation of a human regulatory core network from the biological literature. Bioinformatics, 31, 1258-1266 (full text) (abstract)

Zhuo Fang, Katharina Hecklau, Fridolin Gross, Ivo Bachmann, Melanie Venzke, Martin Karl, Johannes Schuchhardt, Andreas Radbruch, Hanspeter Herzel, Ria Baumgrass, 2015, Transcription factor co-occupied regions in the murine genome constitute T-helper-cell subtype-specific enhancers. Eur. J. Immunol., 45, 3150-7 (abstract) (full text)

Stefan Müller, Georg Regensburger, Ralf Steuer, 2015, Resource allocation in metabolic networks: kinetic optimization and approximations by FBA. Biochem. Soc. Trans., 43, 1195-200 (full text) (abstract)

Nils Blüthgen, 2015, Signaling output: it's all about timing and feedbacks. Mol. Syst. Biol., 11, 843 (abstract)

Kerstin Abshagen, Matthias König, Andreas Hoppe, Isabell Müller, Matthias Ebert, Honglei Weng, Herrmann-Georg Holzhütter, Ulrich M Zanger, Johannes Bode, Brigitte Vollmar, Maria Thomas, Steven Dooley, 2015, Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice. BMC Syst Biol, 9, 83 (abstract) (full text)

Isao T Tokuda, Daisuke Ono, Bharath Ananthasubramaniam, Sato Honma, Ken-Ichi Honma, Hanspeter Herzel, 2015, Coupling Controls the Synchrony of Clock Cells in Development and Knockouts. Biophys. J., 109, 2159-70 (full text) (abstract)

Sven Blankenburg, Wei Wu, Benjamin Lindner, Susanne Schreiber, 2015, Information filtering in resonant neurons. J Comput Neurosci, 39, 349-70 (abstract) (full text)

Endre T Somogyi, Jean-Marie Bouteiller, James A Glazier, Matthias König, J Kyle Medley, Maciej H Swat, Herbert M Sauro, 2015, libRoadRunner: a high performance SBML simulation and analysis library. Bioinformatics, 31, 3315-21 (abstract) (full text)

Florian Rau, Jan Clemens, Victor Naumov, R Matthias Hennig, Susanne Schreiber, 2015, Firing-rate resonances in the peripheral auditory system of the cricket, Gryllus bimaculatus. J. Comp. Physiol. A Neuroethol. Sens. Neural. Behav. Physiol., 201, 1075-90 (abstract) (full text)

Catherine E Carr, Sahil Shah, Thomas McColgan, Go Ashida, Paula T Kuokkanen, Sandra Brill, Richard Kempter, Hermann Wagner, 2015, Maps of interaural delay in the owl's nucleus laminaris. J. Neurophysiol., 114, 1862-73 (abstract) (full text)

Monika J B Eberhard, Jan-Hendrik Schleimer, Susanne Schreiber, Bernhard Ronacher, 2015, A temperature rise reduces trial-to-trial variability of locust auditory neuron responses. J. Neurophysiol., 114, 1424-37 (abstract) (full text)

Eugen Rempel, Lisa Hoelting, Tanja Waldmann, Nina V Balmer, Stefan Schildknecht, Marianna Grinberg, John Antony Das Gaspar, Vaibhav Shinde, Regina Stöber, Rosemarie Marchan, Christoph van Thriel, Julia Liebing, Johannes Meisig, Nils Blüthgen, Agapios Sachinidis, Jörg Rahnenführer, Jan G Hengstler, Marcel Leist, 2015, A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors. Arch. Toxicol., 89, 1599-618 (full text) (abstract)

Philipp Erdrich, Ralf Steuer, Steffen Klamt, 2015, An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. BMC Syst Biol, 9, 48 (full text) (abstract)

Franziska Witzel, Raphaela Fritsche-Guenther, Nadine Lehmann, Anja Sieber, Nils Blüthgen, 2015, Analysis of impedance-based cellular growth assays. Bioinformatics, 31, 2705-12 (full text) (abstract)

Christoph Schmal, Jihwan Myung, Hanspeter Herzel, Grigory Bordyugov, 2015, Corrigendum: A Theoretical Study on Seasonality. Front Neurol, 6, 159 (full text) (abstract)

Tiziano D'Albis, Jorge Jaramillo, Henning Sprekeler, Richard Kempter, 2015, Inheritance of Hippocampal Place Fields Through Hebbian Learning: Effects of Theta Modulation and Phase Precession on Structure Formation. Neural Comput, 27, 1624-72 (full text) (abstract)

Yasuhiro Murakawa, Michael Hinz, Janina Mothes, Anja Schuetz, Michael Uhl, Emanuel Wyler, Tomoharu Yasuda, Guido Mastrobuoni, Caroline C Friedel, Lars Dölken, Stefan Kempa, Marc Schmidt-Supprian, Nils Blüthgen, Rolf Backofen, Udo Heinemann, Jana Wolf, Claus Scheidereit, Markus Landthaler, 2015, RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. Nat Commun, 6, 7367 (full text) (abstract)

Grigory Bordyugov, Ute Abraham, Adrian Granada, Pia Rose, Katharina Imkeller, Achim Kramer, Hanspeter Herzel, 2015, Tuning the phase of circadian entrainment. J R Soc Interface, 12, (full text) (abstract)

Pascal Schulthess, Alexandra Löffler, Silvia Vetter, Luisa Kreft, Michael Schwarz, Albert Braeuning, Nils Blüthgen, 2015, Signal integration by the CYP1A1 promoter - a quantitative study. Nucleic Acids Res., 43, 5318-30 (full text) (abstract)

Martyn Amos, Ilka Maria Axmann, Nils Blüthgen, Fernando de la Cruz, Alfonso Jaramillo, Alfonso Rodriguez-Paton, Friedrich Simmel, 2015, Bacterial computing with engineered populations. Philos Trans A Math Phys Eng Sci, 373, (full text) (abstract)

Friederike Klemke, Antje Baier, Henning Knoop, Ramona Kern, Jiri Jablonsky, Gabriele Beyer, Thomas Volkmer, Ralf Steuer, Wolfgang Lockau, Martin Hagemann, 2015, Identification of the light-independent phosphoserine pathway as an additional source of serine in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology (Reading, Engl.), 161, 1050-60 (full text) (abstract)

Christoph Schmal, Jihwan Myung, Hanspeter Herzel, Grigory Bordyugov, 2015, A theoretical study on seasonality. Front Neurol, 6, 94 (full text) (abstract)

Robert Lehmann, Liam Childs, Philippe Thomas, Monica Abreu, Luise Fuhr, Hanspeter Herzel, Ulf Leser, Angela Relógio, 2015, Assembly of a comprehensive regulatory network for the Mammalian circadian clock: a bioinformatics approach. PLoS ONE, 10, e0126283 (full text) (abstract)

Henning Knoop, Ralf Steuer, 2015, A computational analysis of stoichiometric constraints and trade-offs in cyanobacterial biofuel production. Front Bioeng Biotechnol, 3, 47 (full text) (abstract)

Daniel K Wells, Yishan Chuang, Louis M Knapp, Dirk Brockmann, William L Kath, Joshua N Leonard, 2015, Spatial and functional heterogeneities shape collective behavior of tumor-immune networks. PLoS Comput. Biol., 11, e1004181 (full text) (abstract)

Janina Hesse, Susanne Schreiber, 2015, Externalization of neuronal somata as an evolutionary strategy for energy economization. Curr. Biol., 25, R324-5 (full text) (abstract)

Philippe Bastiaens, Marc R Birtwistle, Nils Blüthgen, Frank J Bruggeman, Kwang-Hyun Cho, Carlo Cosentino, Alberto de la Fuente, Jan B Hoek, Anatoly Kiyatkin, Steffen Klamt, Walter Kolch, Stefan Legewie, Pedro Mendes, Takashi Naka, Tapesh Santra, Eduardo Sontag, Hans V Westerhoff, Boris N Kholodenko, 2015, Silence on the relevant literature and errors in implementation. Nat. Biotechnol., 33, 336-9 (full text) (abstract)

Jörn M Schmiedel, Sandy L Klemm, Yannan Zheng, Apratim Sahay, Nils Blüthgen, Debora S Marks, Alexander van Oudenaarden, 2015, Gene expression. MicroRNA control of protein expression noise. Science, 348, 128-32 (full text) (abstract)

Petra Ritter, Jan Born, Michael Brecht, Hubert R Dinse, Uwe Heinemann, Burkhard Pleger, Dietmar Schmitz, Susanne Schreiber, Arno Villringer, Richard Kempter, 2015, State-dependencies of learning across brain scales. Front Comput Neurosci, 9, 1 (full text) (abstract)

Bartosz Teleńczuk, Stuart N Baker, Richard Kempter, Gabriel Curio, 2015, Correlates of a single cortical action potential in the epidural EEG. Neuroimage, 109, 357-67 (abstract) (full text)

Roman Zug, Peter Hammerstein, 2015, Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biol Rev Camb Philos Soc, 90, 89-111 (abstract) (full text)

Paul F Thaben, Pål O Westermark, 2014, Detecting rhythms in time series with RAIN. J. Biol. Rhythms, 29, 391-400 (abstract) (full text)

Sarah Lück, Kevin Thurley, Paul F Thaben, Pål O Westermark, 2014, Rhythmic degradation explains and unifies circadian transcriptome and proteome data. Cell Rep, 9, 741-51 (full text) (abstract)

Philipp Erdrich, Henning Knoop, Ralf Steuer, Steffen Klamt, 2014, Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling. Microb. Cell Fact., 13, 128 (full text) (abstract)

Ettore Murabito, Malkhey Verma, Martijn Bekker, Domenico Bellomo, Hans V Westerhoff, Bas Teusink, Ralf Steuer, 2014, Monte-Carlo Modeling of the Central Carbon Metabolism of Lactococcus lactis: Insights into Metabolic Regulation. PLoS ONE, 9, e106453 (full text) (abstract)

Monica Killig, Birte Friedrichs, Johannes Meisig, Chiara Gentilini, Nils Blüthgen, Christoph Loddenkemper, Myriam Labopin, Nadezda Basara, Christian Pfrepper, Dietger W Niederwieser, Lutz Uharek, Chiara Romagnani, 2014, Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation. Eur. J. Immunol., 44, 2822-34 (abstract) (full text)

Astrid G Petzoldt, Yü-Hien Lee, Omid Khorramshahi, Eric Reynolds, Andrew J R Plested, Hanspeter Herzel, Stephan J Sigrist, 2014, Gating characteristics control glutamate receptor distribution and trafficking in vivo. Curr. Biol., 24, 2059-65 (full text) (abstract)

Bharath Ananthasubramaniam, Hanspeter Herzel, 2014, Positive feedback promotes oscillations in negative feedback loops. PLoS ONE, 9, e104761 (full text) (abstract)

Robert Lehmann, Rainer Machné, Hanspeter Herzel, 2014, The structural code of cyanobacterial genomes. Nucleic Acids Res., 42, 8873-83 (full text) (abstract)

Bertram Klinger, Nils Blüthgen, 2014, Consequences of feedback in signal transduction for targeted therapies. Biochem. Soc. Trans., 42, 770-5 (full text) (abstract)

Christian Beck, Stefanie Hertel, Anne Rediger, Robert Lehmann, Anika Wiegard, Adrian Kölsch, Beate Heilmann, Jens Georg, Wolfgang R Hess, Ilka M Axmann, 2014, Daily expression pattern of protein-encoding genes and small noncoding RNAs in synechocystis sp. strain PCC 6803. Appl. Environ. Microbiol., 80, 5195-206 (full text) (abstract)

Ana C L Guerreiro, Marco Benevento, Robert Lehmann, Bas van Breukelen, Harm Post, Piero Giansanti, A F Maarten Altelaar, Ilka M Axmann, Albert J R Heck, 2014, Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Mol. Cell Proteomics, 13, 2042-55 (full text) (abstract)

Anja Korenčič, Rok Košir, Grigory Bordyugov, Robert Lehmann, Damjana Rozman, Hanspeter Herzel, 2014, Timing of circadian genes in mammalian tissues. Sci Rep, 4, 5782 (full text) (abstract)

Eric Reifenstein, Martin Stemmler, Andreas V M Herz, Richard Kempter, Susanne Schreiber, 2014, Movement dependence and layer specificity of entorhinal phase precession in two-dimensional environments. PLoS ONE, 9, e100638 (full text) (abstract)

Ilka M Axmann, Stefanie Hertel, Anika Wiegard, Anja K Dörrich, Annegret Wilde, 2014, Diversity of KaiC-based timing systems in marine Cyanobacteria. Mar Genomics, 14, 3-16 (abstract) (full text)

Angela Relógio, Philippe Thomas, Paula Medina-Pérez, Silke Reischl, Sander Bervoets, Ewa Gloc, Pamela Riemer, Shila Mang-Fatehi, Bert Maier, Reinhold Schäfer, Ulf Leser, Hanspeter Herzel, Achim Kramer, Christine Sers, 2014, Ras-mediated deregulation of the circadian clock in cancer. PLoS Genet., 10, e1004338 (full text) (abstract)

Jorge Jaramillo, Robert Schmidt, Richard Kempter, 2014, Modeling inheritance of phase precession in the hippocampal formation. J. Neurosci., 34, 7715-31 (full text) (abstract)

Frederic A Roemschied, Monika Jb Eberhard, Jan-Hendrik Schleimer, Bernhard Ronacher, Susanne Schreiber, 2014, Cell-intrinsic mechanisms of temperature compensation in a grasshopper sensory receptor neuron. Elife, 3, e02078 (abstract)

Juliane Manitz, Thomas Kneib, Martin Schlather, Dirk Helbing, Dirk Brockmann, 2014, Origin Detection During Food-borne Disease Outbreaks - A Case Study of the 2011 EHEC/HUS Outbreak in Germany. PLoS Curr, 6, (full text) (abstract)

Arndt Telschow, Kirsten Hilgenboecker, Peter Hammerstein, John H Werren, 2014, Dobzhansky-muller and wolbachia-induced incompatibilities in a diploid genetic system. PLoS ONE, 9, e95488 (full text) (abstract)

Bharath Ananthasubramaniam, Erik D Herzog, Hanspeter Herzel, 2014, Timing of neuropeptide coupling determines synchrony and entrainment in the mammalian circadian clock. PLoS Comput. Biol., 10, e1003565 (full text) (abstract)

Stefan Müller, Georg Regensburger, Ralf Steuer, 2014, Enzyme allocation problems in kinetic metabolic networks: optimal solutions are elementary flux modes. J. Theor. Biol., 347, 182-90 (abstract) (full text)

Philippe Lemey, Andrew Rambaut, Trevor Bedford, Nuno Faria, Filip Bielejec, Guy Baele, Colin A Russell, Derek J Smith, Oliver G Pybus, Dirk Brockmann, Marc A Suchard, 2014, Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLoS Pathog., 10, e1003932 (full text) (abstract)

Willi Gottstein, Stefan Müller, Hanspeter Herzel, Ralf Steuer, 2014, Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. BioSystems, 117, 68-76 (abstract) (full text)

Edda G Schulz, Johannes Meisig, Tomonori Nakamura, Ikuhiro Okamoto, Anja Sieber, Christel Picard, Maud Borensztein, Mitinori Saitou, Nils Blüthgen, Edith Heard, 2014, The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network. Cell Stem Cell, 14, 203-16 (full text) (abstract)

Joost Snijder, Rebecca J Burnley, Anika Wiegard, Adrien S J Melquiond, Alexandre M J J Bonvin, Ilka M Axmann, Albert J R Heck, 2014, Insight into cyanobacterial circadian timing from structural details of the KaiB-KaiC interaction. Proc. Natl. Acad. Sci. U.S.A., 111, 1379-84 (full text) (abstract)

Gijsbert D A Werner, Joan E Strassmann, Aniek B F Ivens, Daniel J P Engelmoer, Erik Verbruggen, David C Queller, Ronald Noë, Nancy Collins Johnson, Peter Hammerstein, E Toby Kiers, 2014, Evolution of microbial markets. Proc. Natl. Acad. Sci. U.S.A., 111, 1237-44 (full text) (abstract)

Dirk Brockmann, Dirk Helbing, 2013, The hidden geometry of complex, network-driven contagion phenomena. Science, 342, 1337-42 (full text) (abstract)

Stefanie Hertel, Reimo Zoschke, Laura Neumann, Yujiao Qu, Ilka M Axmann, Christian Schmitz-Linneweber, 2013, Multiple checkpoints for the expression of the chloroplast-encoded splicing factor MatK. Plant Physiol., 163, 1686-98 (full text) (abstract)

Ekaterina Zhuchkova, Michiel W H Remme, Susanne Schreiber, 2013, Somatic versus dendritic resonance: differential filtering of inputs through non-uniform distributions of active conductances. PLoS ONE, 8, e78908 (full text) (abstract)

Guido Hermey, Claudia Mahlke, Jakob J Gutzmann, Jörg Schreiber, Nils Blüthgen, Dietmar Kuhl, 2013, Genome-wide profiling of the activity-dependent hippocampal transcriptome. PLoS ONE, 8, e76903 (full text) (abstract)

Lloyd P Sanders, Bo Söderberg, Dirk Brockmann, Tobias Ambjörnsson, 2013, Perturbative solution to susceptible-infected-susceptible epidemics on networks. Phys Rev E Stat Nonlin Soft Matter Phys, 88, 032713 (abstract)

Olivia Woolley-Meza, Daniel Grady, Christian Thiemann, James P Bagrow, Dirk Brockmann, 2013, Eyjafjallajökull and 9/11: the impact of large-scale disasters on worldwide mobility. PLoS ONE, 8, e69829 (full text) (abstract)

Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer, 2013, Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803. PLoS Comput. Biol., 9, e1003081 (full text) (abstract)

Paula T Kuokkanen, Go Ashida, Catherine E Carr, Hermann Wagner, Richard Kempter, 2013, Linear summation in the barn owl's brainstem underlies responses to interaural time differences. J. Neurophysiol., 110, 117-30 (abstract) (full text)

Timor Glatzer, Monica Killig, Johannes Meisig, Isabelle Ommert, Merlin Luetke-Eversloh, Marina Babic, Daniela Paclik, Nils Blüthgen, Rainer Seidl, Claudia Seifarth, Jörn Gröne, Minoo Lenarz, Katharina Stölzel, Dominik Fugmann, Angel Porgador, Anja Hauser, Alexander Karlas, Chiara Romagnani, 2013, RORγt⁺ innate lymphoid cells acquire a proinflammatory program upon engagement of the activating receptor NKp44. Immunity, 38, 1223-35 (full text) (abstract)

Kajetan Bentele, Paul Saffert, Robert Rauscher, Zoya Ignatova, Nils Blüthgen, 2013, Efficient translation initiation dictates codon usage at gene start. Mol. Syst. Biol., 9, 675 (full text) (abstract)

Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka Axmann, Ralf Steuer, 2013, How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis. BMC Bioinformatics, 14, 133 (full text) (abstract)

Bertram Klinger, Anja Sieber, Raphaela Fritsche-Guenther, Franziska Witzel, Leanne Berry, Dirk Schumacher, Yibing Yan, Pawel Durek, Mark Merchant, Reinhold Schäfer, Christine Sers, Nils Blüthgen, 2013, Network quantification of EGFR signaling unveils potential for targeted combination therapy. Mol. Syst. Biol., 9, 673 (full text) (abstract)

Nils Blüthgen, Stefan Legewie, 2013, Robustness of signal transduction pathways. Cell. Mol. Life Sci., 70, 2259-69 (full text) (abstract)

Catherine Carr, Sahil Shah, Go Ashida, Thomas McColgan, Hermann Wagner, Paula T Kuokkanen, Richard Kempter, Christine Köppl, 2013, Maps of ITD in the nucleus laminaris of the barn owl. Adv. Exp. Med. Biol., 787, 215-22 (full text) (abstract)

Christian T Herbst, Hanspeter Herzel, Jan G Svec, Megan T Wyman, W Tecumseh Fitch, 2013, Visualization of system dynamics using phasegrams. J R Soc Interface, 10, 20130288 (full text) (abstract)

Anika Wiegard, Anja K Dörrich, Hans-Tobias Deinzer, Christian Beck, Annegret Wilde, Julia Holtzendorff, Ilka M Axmann, 2013, Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence. Microbiology (Reading, Engl.), 159, 948-58 (full text) (abstract)

Pål O Westermark, Hanspeter Herzel, 2013, Mechanism for 12 hr rhythm generation by the circadian clock. Cell Rep, 3, 1228-38 (full text) (abstract)

Adrián E Granada, Grigory Bordyugov, Achim Kramer, Hanspeter Herzel, 2013, Human chronotypes from a theoretical perspective. PLoS ONE, 8, e59464 (full text) (abstract)

Stefanie Hertel, Christian Brettschneider, Ilka M Axmann, 2013, Revealing a two-loop transcriptional feedback mechanism in the cyanobacterial circadian clock. PLoS Comput. Biol., 9, e1002966 (full text) (abstract)

Maria Pangalos, José R Donoso, Jochen Winterer, Aleksandar R Zivkovic, Richard Kempter, Nikolaus Maier, Dietmar Schmitz, 2013, Recruitment of oriens-lacunosum-moleculare interneurons during hippocampal ripples. Proc. Natl. Acad. Sci. U.S.A., 110, 4398-403 (full text) (abstract)

Benjamin Bossan, Peter Hammerstein, Arnulf Koehncke, 2013, We were all young once: an intragenomic perspective on parent-offspring conflict. Proc. Biol. Sci., 280, 20122637 (full text) (abstract)

Franziska Witzel, Louise Maddison, Nils Blüthgen, 2012, How scaffolds shape MAPK signaling: what we know and opportunities for systems approaches. Front Physiol, 3, 475 (full text) (abstract)

Go Ashida, Kazuo Funabiki, Paula T Kuokkanen, Richard Kempter, Catherine E Carr, 2012, Signal-to-noise ratio in the membrane potential of the owl's auditory coincidence detectors. J. Neurophysiol., 108, 2837-45 (full text) (abstract)

Anja Korenčič, Grigory Bordyugov, Rok Košir, Damjana Rozman, Marko Goličnik, Hanspeter Herzel, 2012, The interplay of cis-regulatory elements rules circadian rhythms in mouse liver. PLoS ONE, 7, e46835 (full text) (abstract)

Jari Kämäräinen, Henning Knoop, Natalie J Stanford, Fernando Guerrero, M Kalim Akhtar, Eva-Mari Aro, Ralf Steuer, Patrik R Jones, 2012, Physiological tolerance and stoichiometric potential of cyanobacteria for hydrocarbon fuel production. J. Biotechnol., 162, 67-74 (full text) (abstract)

Michael Fähling, Anja Bondke Persson, Bertram Klinger, Edgar Benko, Andreas Steege, Mumtaz Kasim, Andreas Patzak, Pontus B Persson, Gunter Wolf, Nils Blüthgen, Ralf Mrowka, 2012, Multilevel regulation of HIF-1 signaling by TTP. Mol. Biol. Cell, 23, 4129-41 (full text) (abstract)

Anne Rediger, René Geissen, Benedikt Steuten, Beate Heilmann, Rolf Wagner, Ilka M Axmann, 2012, 6S RNA - an old issue became blue-green. Microbiology (Reading, Engl.), 158, 2480-91 (full text) (abstract)

Dmitry Zarubin, Ekaterina Zhuchkova, Susanne Schreiber, 2012, Effects of cooperative ion-channel interactions on the dynamics of excitable membranes. Phys Rev E Stat Nonlin Soft Matter Phys, 85, 061904 (abstract)

Hanna Bendfeldt, Manuela Benary, Tobias Scheel, Kerstin Steinbrink, Andreas Radbruch, Hanspeter Herzel, Ria Baumgrass, 2012, IL-2 Expression in Activated Human Memory FOXP3(+) Cells Critically Depends on the Cellular Levels of FOXP3 as Well as of Four Transcription Factors of  T Cell Activation. Front Immunol, 3, 264 (full text) (abstract)

Jörn Matthias Schmiedel, Ilka Maria Axmann, Stefan Legewie, 2012, Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS ONE, 7, e42296 (full text) (abstract)

Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen, Reinhold Schäfer, 2012, Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. Mol. Syst. Biol., 8, 601 (full text) (abstract)

Roman Zug, Peter Hammerstein, 2012, Still a host of hosts for Wolbachia: analysis of recent data suggests that 40% of terrestrial arthropod species are infected. PLoS ONE, 7, e38544 (full text) (abstract)

Christian Beck, Henning Knoop, Ilka M Axmann, Ralf Steuer, 2012, The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics, 13, 56 (full text) (abstract)

Daniel Grady, Christian Thiemann, Dirk Brockmann, 2012, Robust classification of salient links in complex networks. Nat Commun, 3, 864 (full text) (abstract)

Hanna Bendfeldt, Manuela Benary, Tobias Scheel, Stefan Frischbutter, Anna Abajyan, Andreas Radbruch, Hanspeter Herzel, Ria Baumgrass, 2012, Stable IL-2 decision making by endogenous c-Fos amounts in peripheral memory T-helper cells. J. Biol. Chem., 287, 18386-97 (full text) (abstract)

Elphège P Nora, Bryan R Lajoie, Edda G Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L van Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Blüthgen, Job Dekker, Edith Heard, 2012, Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 485, 381-5 (full text) (abstract)

Roland Schaette, Richard Kempter, 2012, Computational models of neurophysiological correlates of tinnitus. Front Syst Neurosci, 6, 34 (full text) (abstract)

Richard Kempter, Christian Leibold, György Buzsáki, Kamran Diba, Robert Schmidt, 2012, Quantifying circular-linear associations: hippocampal phase precession. J. Neurosci. Methods, 207, 113-24 (full text) (abstract)

Eric T Reifenstein, Richard Kempter, Susanne Schreiber, Martin B Stemmler, Andreas V M Herz, 2012, Grid cells in rat entorhinal cortex encode physical space with independent firing fields and phase precession at the single-trial level. Proc. Natl. Acad. Sci. U.S.A., 109, 6301-6 (full text) (abstract)

Dirk Brockmann, 2012, Complex systems: Spotlight on mobility. Nature, 484, 40-1 (full text) (abstract)

Ralf Steuer, Henning Knoop, Rainer Machné, 2012, Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth. J. Exp. Bot., 63, 2259-74 (full text) (abstract)

Mariano A Belluscio, Kenji Mizuseki, Robert Schmidt, Richard Kempter, György Buzsáki, 2012, Cross-frequency phase-phase coupling between θ and γ oscillations in the hippocampus. J. Neurosci., 32, 423-35 (full text) (abstract)

Adrián E Granada, Trinitat Cambras, Antoni Díez-Noguera, Hanspeter Herzel, 2011, Circadian desynchronization. Interface Focus, 1, 153-66 (full text) (abstract)

Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann, 2011, Robust signal processing in living cells. PLoS Comput. Biol., 7, e1002218 (full text) (abstract)

Angela Relógio, Pal O Westermark, Thomas Wallach, Katja Schellenberg, Achim Kramer, Hanspeter Herzel, 2011, Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput. Biol., 7, e1002309 (full text) (abstract)

Nikolaus Maier, Alvaro Tejero-Cantero, Anja L Dorrn, Jochen Winterer, Prateep S Beed, Genela Morris, Richard Kempter, James F A Poulet, Christian Leibold, Dietmar Schmitz, 2011, Coherent phasic excitation during hippocampal ripples. Neuron, 72, 137-52 (full text) (abstract)

Pascal Schulthess, Nils Blüthgen, 2011, From reaction networks to information flow–using modular response analysis to track information in signaling networks. Meth. Enzymol., 500, 397-409 (full text) (abstract)

K Laurence Jost, Sebastian Haase, Daniel Smeets, Nadine Schrode, Jörn M Schmiedel, Bianca Bertulat, Hanspeter Herzel, Marion Cremer, M Cristina Cardoso, 2011, 3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming. Nucleic Acids Res., 39, e113 (full text) (abstract)

Jan Clemens, Olaf Kutzki, Bernhard Ronacher, Susanne Schreiber, Sandra Wohlgemuth, 2011, Efficient transformation of an auditory population code in a small sensory system. Proc. Natl. Acad. Sci. U.S.A., 108, 13812-7 (full text) (abstract)

Anuradha Chauhan, Stephan Lorenzen, Hanspeter Herzel, Samuel Bernard, 2011, Regulation of mammalian cell cycle progression in the regenerating liver. J. Theor. Biol., 283, 103-12 (full text) (abstract)

Raphaela Fritsche-Guenther, Franziska Witzel, Anja Sieber, Ricarda Herr, Nadine Schmidt, Sandra Braun, Tilman Brummer, Christine Sers, Nils Blüthgen, 2011, Strong negative feedback from Erk to Raf confers robustness to MAPK signalling. Mol. Syst. Biol., 7, 489 (full text) (abstract)

Benjamin Bossan, Arnulf Koehncke, Peter Hammerstein, 2011, A new model and method for understanding Wolbachia-induced cytoplasmic incompatibility. PLoS ONE, 6, e19757 (full text) (abstract)

Ettore Murabito, Kieran Smallbone, Jonathan Swinton, Hans V Westerhoff, Ralf Steuer, 2011, A probabilistic approach to identify putative drug targets in biochemical networks. J R Soc Interface, 8, 880-95 (full text) (abstract)

Christian Klotz, Thomas Ziegler, Ana Sofia Figueiredo, Sebastian Rausch, Matthew R Hepworth, Nadja Obsivac, Christine Sers, Roland Lang, Peter Hammerstein, Richard Lucius, Susanne Hartmann, 2011, A helminth immunomodulator exploits host signaling events to regulate cytokine production in macrophages. PLoS Pathog., 7, e1001248 (full text) (abstract)

Marc Päpper, Richard Kempter, Christian Leibold, 2011, Synaptic tagging, evaluation of memories, and the distal reward problem. Learn. Mem., 18, 58-70 (full text) (abstract)

Karsten Jürchott, Ralf-Jürgen Kuban, Till Krech, Nils Blüthgen, Ulrike Stein, Wolfgang Walther, Christian Friese, Szymon M Kiełbasa, Ute Ungethüm, Per Lund, Thomas Knösel, Wolfgang Kemmner, Markus Morkel, Johannes Fritzmann, Peter M Schlag, Walter Birchmeier, Tammo Krueger, Silke Sperling, Christine Sers, Hans-Dieter Royer, Hanspeter Herzel, Reinhold Schäfer, 2010, Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. PLoS Genet., 6, e1001231 (full text) (abstract)

Christian Thiemann, Fabian Theis, Daniel Grady, Rafael Brune, Dirk Brockmann, 2010, The structure of borders in a small world. PLoS ONE, 5, e15422 (full text) (abstract)

Ute Abraham, Adrián E Granada, Pål O Westermark, Markus Heine, Achim Kramer, Hanspeter Herzel, 2010, Coupling governs entrainment range of circadian clocks. Mol. Syst. Biol., 6, 438 (full text) (abstract)

Paula T Kuokkanen, Hermann Wagner, Go Ashida, Catherine E Carr, Richard Kempter, 2010, On the origin of the extracellular field potential in the nucleus laminaris of the barn owl (Tyto alba). J. Neurophysiol., 104, 2274-90 (full text) (abstract)

Roland Schaette, Ovidiu König, Dirk Hornig, Manfred Gross, Richard Kempter, 2010, Acoustic stimulation treatments against tinnitus could be most effective when tinnitus pitch is within the stimulated frequency range. Hear. Res., 269, 95-101 (full text) (abstract)

Henning Knoop, Yvonne Zilliges, Wolfgang Lockau, Ralf Steuer, 2010, The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. Plant Physiol., 154, 410-22 (full text) (abstract)

Olof Leimar, Peter Hammerstein, 2010, Cooperation for direct fitness benefits. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 365, 2619-26 (full text) (abstract)

Christian Brettschneider, Rebecca J Rose, Stefanie Hertel, Ilka M Axmann, Albert J R Heck, Markus Kollmann, 2010, A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock. Mol. Syst. Biol., 6, 389 (full text) (abstract)

Szymon M Kiełbasa, Holger Klein, Helge G Roider, Martin Vingron, Nils Blüthgen, 2010, TransFind–predicting transcriptional regulators for gene sets. Nucleic Acids Res., 38, W275-80 (full text) (abstract)

Jignesh R Parikh, Bertram Klinger, Yu Xia, Jarrod A Marto, Nils Blüthgen, 2010, Discovering causal signaling pathways through gene-expression patterns. Nucleic Acids Res., 38, W109-17 (full text) (abstract)

Szymon M Kiełbasa, Nils Blüthgen, Michael Fähling, Ralf Mrowka, 2010, Targetfinder.org: a resource for systematic discovery of transcription factor target genes. Nucleic Acids Res., 38, W233-8 (full text) (abstract)

Nils Blüthgen, 2010, Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction. Mol Biosyst, 6, 1277-84 (full text) (abstract)

Samuel Bernard, Branka Cajavec Bernard, Francis Lévi, Hanspeter Herzel, 2010, Tumor growth rate determines the timing of optimal chronomodulated treatment schedules. PLoS Comput. Biol., 6, e1000712 (full text) (abstract)

Isao T Tokuda, Marco Zemke, Malte Kob, Hanspeter Herzel, 2010, Biomechanical modeling of register transitions and the role of vocal tract resonators. J. Acoust. Soc. Am., 127, 1528-36 (full text) (abstract)

Yue-Hien Lee, Manuela Benary, Ria Baumgrass, Hanspeter Herzel, 2010, Prediction of regulatory transcription factors in T helper cell differentiation and maintenance. Genome Inform, 22, 84-94 (abstract)

Olaf Wolkenhauer, Charles Auffray, Simone Baltrusch, Nils Blüthgen, Helen Byrne, Marta Cascante, Andrea Ciliberto, Trevor Dale, Dirk Drasdo, David Fell, James E Ferrell, Daniel Gallahan, Robert Gatenby, Ulrich Günther, Brian D Harms, Hanspeter Herzel, Christian Junghanss, Manfred Kunz, Ingeborg van Leeuwen, Philippe Lenormand, Francis Levi, Michael Linnebacher, John Lowengrub, Philip K Maini, Arif Malik, Katja Rateitschak, Owen Sansom, Reinhold Schäfer, Karsten Schürrle, Christine Sers, Santiago Schnell, Darryl Shibata, John Tyson, Julio Vera, Michael White, Boris Zhivotovsky, Robert Jaster, 2010, Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res., 70, 12-3 (full text) (abstract)

Erik Arner, Pål O Westermark, Kirsty L Spalding, Tom Britton, Mikael Rydén, Jonas Frisén, Samuel Bernard, Peter Arner, 2010, Adipocyte turnover: relevance to human adipose tissue morphology. Diabetes, 59, 105-9 (full text) (abstract)

Pål O Westermark, David K Welsh, Hitoshi Okamura, Hanspeter Herzel, 2009, Quantification of circadian rhythms in single cells. PLoS Comput. Biol., 5, e1000580 (full text) (abstract)

Robert Schmidt, Kamran Diba, Christian Leibold, Dietmar Schmitz, György Buzsáki, Richard Kempter, 2009, Single-trial phase precession in the hippocampus. J. Neurosci., 29, 13232-41 (full text) (abstract)

Judith Dannowski, Matthias Flor, Arndt Telschow, Peter Hammerstein, 2009, The effect of sibmating on the infection dynamics of male-killing bacteria. Evolution, 63, 2525-34 (full text) (abstract)

Adrián E Granada, Hanspeter Herzel, 2009, How to achieve fast entrainment? The timescale to synchronization. PLoS ONE, 4, e7057 (full text) (abstract)

Frank J Bruggeman, Nils Blüthgen, Hans V Westerhoff, 2009, Noise management by molecular networks. PLoS Comput. Biol., 5, e1000506 (full text) (abstract)

Ilka M Axmann, Ulf Dühring, Luiza Seeliger, Anne Arnold, Jens T Vanselow, Achim Kramer, Annegret Wilde, 2009, Biochemical evidence for a timing mechanism in prochlorococcus. J. Bacteriol., 191, 5342-7 (full text) (abstract)

Hermann Wagner, Sandra Brill, Richard Kempter, Catherine E Carr, 2009, Auditory responses in the barn owl's nucleus laminaris to clicks: impulse response and signal analysis of neurophonic potential. J. Neurophysiol., 102, 1227-40 (full text) (abstract)

Ana Sofia Figueiredo, Thomas Höfer, Christian Klotz, Christine Sers, Susanne Hartmann, Richard Lucius, Peter Hammerstein, 2009, Modelling and simulating interleukin-10 production and regulation by macrophages after stimulation with an immunomodulator of parasitic nematodes. FEBS J., 276, 3454-69 (full text) (abstract)

Roland Schaette, Richard Kempter, 2009, Predicting tinnitus pitch from patients' audiograms with a computational model for the development of neuronal hyperactivity. J. Neurophysiol., 101, 3042-52 (full text) (abstract)

Susanne Schreiber, Inés Samengo, Andreas V M Herz, 2009, Two distinct mechanisms shape the reliability of neural responses. J. Neurophysiol., 101, 2239-51 (full text) (abstract)

Katarzyna Bozek, Angela Relógio, Szymon M Kielbasa, Markus Heine, Christof Dame, Achim Kramer, Hanspeter Herzel, 2009, Regulation of clock-controlled genes in mammals. PLoS ONE, 4, e4882 (full text) (abstract)

Nils Blüthgen, Stefan Legewie, Szymon M Kielbasa, Anja Schramme, Oleg Tchernitsa, Jana Keil, Andrea Solf, Martin Vingron, Reinhold Schäfer, Hanspeter Herzel, Christine Sers, 2009, A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts. FEBS J., 276, 1024-35 (full text) (abstract)

Arnulf Koehncke, Arndt Telschow, John H Werren, Peter Hammerstein, 2009, Life and death of an influential passenger: Wolbachia and the evolution of CI-modifiers by their hosts. PLoS ONE, 4, e4425 (full text) (abstract)

Sonja-Verena Albers, Nils-Kåre Birkeland, Arnold J M Driessen, Susanne Gertig, Patrick Haferkamp, Hans-Peter Klenk, Theresa Kouril, Andrea Manica, Trong K Pham, Peter Ruoff, Christa Schleper, Dietmar Schomburg, Kieran J Sharkey, Bettina Siebers, Pawel Sierocinski, Ralf Steuer, John van der Oost, Hans V Westerhoff, Patricia Wieloch, Phillip C Wright, Melanie Zaparty, 2009, SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochem. Soc. Trans., 37, 58-64 (full text) (abstract)

Stefan Legewie, Christine Sers, Hanspeter Herzel, 2009, Kinetic mechanisms for overexpression insensitivity and oncogene cooperation. FEBS Lett., 583, 93-6 (full text) (abstract)

Manuela Benary, Hanna Bendfeldt, Ria Baumgrass, Hanspeter Herzel, 2008, Modeling IL-2 gene expression in human regulatory T cells. Genome Inform, 20, 222-30 (abstract)

Markus J Herrgård, Neil Swainston, Paul Dobson, Warwick B Dunn, K Yalçin Arga, Mikko Arvas, Nils Blüthgen, Simon Borger, Roeland Costenoble, Matthias Heinemann, Michael Hucka, Nicolas Le Novère, Peter Li, Wolfram Liebermeister, Monica L Mo, Ana Paula Oliveira, Dina Petranovic, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasić, Dieter Weichart, Roger Brent, David S Broomhead, Hans V Westerhoff, Betül Kirdar, Merja Penttilä, Edda Klipp, Bernhard Ø Palsson, Uwe Sauer, Stephen G Oliver, Pedro Mendes, Jens Nielsen, Douglas B Kell, 2008, A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol., 26, 1155-60 (full text) (abstract)

Stefan Legewie, Dennis Dienst, Annegret Wilde, Hanspeter Herzel, Ilka M Axmann, 2008, Small RNAs establish delays and temporal thresholds in gene expression. Biophys. J., 95, 3232-8 (full text) (abstract)

Nils Blüthgen, Stefan Legewie, 2008, Systems analysis of MAPK signal transduction. Essays Biochem., 45, 95-107 (full text) (abstract)

Hanspeter Herzel, Nils Blüthgen, 2008, Mathematical models in mammalian cell biology. Genome Biol., 9, 316 (full text) (abstract)

Annamaria Bevilacqua, Stephen J Wilkinson, Richard Dimelow, Ettore Murabito, Samrina Rehman, Maria Nardelli, Karen van Eunen, Sergio Rossell, Frank J Bruggeman, Nils Blüthgen, Dirk De Vos, Jildau Bouwman, Barbara M Bakker, Hans V Westerhoff, 2008, Vertical systems biology: from DNA to flux and back. SEB Exp Biol Ser, 61, 65-91 (abstract)

Yutaka Kobayashi, Peter Hammerstein, Arndt Telschow, 2008, The neutral effective migration rate in a mainland-island context. Theor Popul Biol, 74, 84-92 (full text) (abstract)

Coen P H Elemans, Riccardo Zaccarelli, Hanspeter Herzel, 2008, Biomechanics and control of vocalization in a non-songbird. J R Soc Interface, 5, 691-703 (full text) (abstract)

Roland Schaette, Richard Kempter, 2008, Development of hyperactivity after hearing loss in a computational model of the dorsal cochlear nucleus depends on neuron response type. Hear. Res., 240, 57-72 (full text) (abstract)

Kirsty L Spalding, Erik Arner, Pål O Westermark, Samuel Bernard, Bruce A Buchholz, Olaf Bergmann, Lennart Blomqvist, Johan Hoffstedt, Erik Näslund, Tom Britton, Hernan Concha, Moustapha Hassan, Mikael Rydén, Jonas Frisén, Peter Arner, 2008, Dynamics of fat cell turnover in humans. Nature, 453, 783-7 (full text) (abstract)

Ralf Mrowka, Nils Blüthgen, Michael Fähling, 2008, Seed-based systematic discovery of specific transcription factor target genes. FEBS J., 275, 3178-92 (full text) (abstract)

Anuradha Chauhan, Stefan Legewie, Pål O Westermark, Stephan Lorenzen, Hanspeter Herzel, 2008, A mesoscale model of G1/S phase transition in liver regeneration. J. Theor. Biol., 252, 465-73 (full text) (abstract)

Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff, Nils Blüthgen, 2008, Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol. Syst. Biol., 4, 190 (full text) (abstract)

Roger J Sullivan, Edward H Hagen, Peter Hammerstein, 2008, Revealing the paradox of drug reward in human evolution. Proc. Biol. Sci., 275, 1231-41 (full text) (abstract)

Matthias E Futschik, Hanspeter Herzel, 2008, Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics, 24, 1063-9 (full text) (abstract)

Isao T Tokuda, Jaromir Horácek, Jan G Svec, Hanspeter Herzel, 2008, Bifurcations and chaos in register transitions of excised larynx experiments. Chaos, 18, 013102 (full text) (abstract)

James C W Locke, Pål O Westermark, Achim Kramer, Hanspeter Herzel, 2008, Global parameter search reveals design principles of the mammalian circadian clock. BMC Syst Biol, 2, 22 (full text) (abstract)

Kirsten Hilgenboecker, Peter Hammerstein, Peter Schlattmann, Arndt Telschow, John H Werren, 2008, How many species are infected with Wolbachia?–A statistical analysis of current data. FEMS Microbiol. Lett., 281, 215-20 (full text) (abstract)

Kay Thurley, Christian Leibold, Anja Gundlfinger, Dietmar Schmitz, Richard Kempter, 2008, Phase precession through synaptic facilitation. Neural Comput, 20, 1285-324 (full text) (abstract)

Christian Leibold, Anja Gundlfinger, Robert Schmidt, Kay Thurley, Dietmar Schmitz, Richard Kempter, 2008, Temporal compression mediated by short-term synaptic plasticity. Proc. Natl. Acad. Sci. U.S.A., 105, 4417-22 (full text) (abstract)

Steven A Brown, Dieter Kunz, Amelie Dumas, Pål O Westermark, Katja Vanselow, Amely Tilmann-Wahnschaffe, Hanspeter Herzel, Achim Kramer, 2008, Molecular insights into human daily behavior. Proc. Natl. Acad. Sci. U.S.A., 105, 1602-7 (full text) (abstract)

Christian Leibold, Richard Kempter, 2008, Sparseness constrains the prolongation of memory lifetime via synaptic metaplasticity. Cereb. Cortex, 18, 67-77 (full text) (abstract)

Matthias E Futschik, Anna Tschaut, Gautam Chaurasia, Hanspeter Herzel, 2007, Graph-theoretical comparison reveals structural divergence of human protein interaction networks. Genome Inform, 18, 141-51 (abstract)

Katarzyna Bozek, Szymon M Kiełbasa, Achim Kramer, Hanspeter Herzel, 2007, Promoter analysis of Mammalian clock controlled genes. Genome Inform, 18, 65-74 (abstract)

Ilka M Axmann, Stefan Legewie, Hanspeter Herzel, 2007, A minimal circadian clock model. Genome Inform, 18, 54-64 (abstract)

Szymon M Kiełbasa, Hanspeter Herzel, Ilka M Axmann, 2007, Regulatory elements of marine cyanobacteria. Genome Inform, 18, 1-11 (abstract)

Björn Voss, Gregor Gierga, Ilka M Axmann, Wolfgang R Hess, 2007, A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. BMC Genomics, 8, 375 (full text) (abstract)

Anja Gundlfinger, Christian Leibold, Katja Gebert, Marion Moisel, Dietmar Schmitz, Richard Kempter, 2007, Differential modulation of short-term synaptic dynamics by long-term potentiation at mouse hippocampal mossy fibre synapses. J. Physiol. (Lond.), 585, 853-65 (full text) (abstract)

Ilka M Axmann, Julia Holtzendorff, Björn Voss, Philip Kensche, Wolfgang R Hess, 2007, Two distinct types of 6S RNA in Prochlorococcus. Gene, 406, 69-78 (full text) (abstract)

Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg Holzhütter, Ralf Steuer, 2007, The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Mol. Syst. Biol., 3, 146 (full text) (abstract)

Silke Reischl, Katja Vanselow, Pål O Westermark, Nadine Thierfelder, Bert Maier, Hanspeter Herzel, Achim Kramer, 2007, Beta-TrCP1-mediated degradation of PERIOD2 is essential for circadian dynamics. J. Biol. Rhythms, 22, 375-86 (full text) (abstract)

Debbie Lindell, Jacob D Jaffe, Maureen L Coleman, Matthias E Futschik, Ilka M Axmann, Trent Rector, Gregory Kettler, Matthew B Sullivan, Robert Steen, Wolfgang R Hess, George M Church, Sallie W Chisholm, 2007, Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature, 449, 83-6 (full text) (abstract)

Stefan Legewie, Birgit Schoeberl, Nils Blüthgen, Hanspeter Herzel, 2007, Competing docking interactions can bring about bistability in the MAPK cascade. Biophys. J., 93, 2279-88 (full text) (abstract)

Ralf Mrowka, Andreas Steege, Charlotte Kaps, Hanspeter Herzel, Bernd J Thiele, Pontus B Persson, Nils Blüthgen, 2007, Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity. Nucleic Acids Res., 35, 5120-9 (full text) (abstract)

Arndt Telschow, Matthias Flor, Yutaka Kobayashi, Peter Hammerstein, John H Werren, 2007, Wolbachia-induced unidirectional cytoplasmic incompatibility and speciation: mainland-island model. PLoS ONE, 2, e701 (full text) (abstract)

Isao T Tokuda, Jaromir Horácek, Jan G Svec, Hanspeter Herzel, 2007, Comparison of biomechanical modeling of register transitions and voice instabilities with excised larynx experiments. J. Acoust. Soc. Am., 122, 519-31 (full text) (abstract)

Ralf Steuer, Adriano Nunes Nesi, Alisdair R Fernie, Thilo Gross, Bernd Blasius, Joachim Selbig, 2007, From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle. Bioinformatics, 23, 1378-85 (full text) (abstract)

Samuel Bernard, Didier Gonze, Branka Cajavec, Hanspeter Herzel, Achim Kramer, 2007, Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput. Biol., 3, e68 (full text) (abstract)

Matthias E Futschik, Gautam Chaurasia, Hanspeter Herzel, 2007, Comparison of human protein-protein interaction maps. Bioinformatics, 23, 605-11 (full text) (abstract)

Sébastien Clodong, Ulf Dühring, Luiza Kronk, Annegret Wilde, Ilka Axmann, Hanspeter Herzel, Markus Kollmann, 2007, Functioning and robustness of a bacterial circadian clock. Mol. Syst. Biol., 3, 90 (full text) (abstract)

Nico Blüthgen, Florian Menzel, Thomas Hovestadt, Brigitte Fiala, Nils Blüthgen, 2007, Specialization, constraints, and conflicting interests in mutualistic networks. Curr. Biol., 17, 341-6 (full text) (abstract)

Pål O Westermark, Jeanette Hellgren Kotaleski, Anneli Björklund, Valdemar Grill, Anders Lansner, 2007, A mathematical model of the mitochondrial NADH shuttles and anaplerosis in the pancreatic beta-cell. Am. J. Physiol. Endocrinol. Metab., 292, E373-93 (full text) (abstract)

Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E Wanker, Matthias E Futschik, 2007, UniHI: an entry gate to the human protein interactome. Nucleic Acids Res., 35, D590-4 (full text) (abstract)

Ralf Steuer, Katja Morgenthal, Wolfram Weckwerth, Joachim Selbig, 2007, A gentle guide to the analysis of metabolomic data. Methods Mol. Biol., 358, 105-26 (abstract) (full text)

Samuel Bernard, Hanspeter Herzel, 2006, Why do cells cycle with a 24 hour period? Genome Inform, 17, 72-9 (abstract)

Gautam Chaurasia, Hanspeter Herzel, Erich E Wanker, Matthias E Futschik, 2006, Systematic functional assessment of human protein-protein interaction maps. Genome Inform, 17, 36-45 (abstract)

Stefan Legewie, Nils Blüthgen, Hanspeter Herzel, 2006, Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput. Biol., 2, e120 (full text) (abstract)

Nils Blüthgen, 2006, Sequestration shapes the response of signal transduction cascades. IUBMB Life, 58, 659-63 (full text) (abstract)

Ovidiu König, Roland Schaette, Richard Kempter, Manfred Gross, 2006, Course of hearing loss and occurrence of tinnitus. Hear. Res., 221, 59-64 (full text) (abstract)

Katja Vanselow, Jens T Vanselow, Pål O Westermark, Silke Reischl, Bert Maier, Thomas Korte, Andreas Herrmann, Hanspeter Herzel, Andreas Schlosser, Achim Kramer, 2006, Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev., 20, 2660-72 (full text) (abstract)

Ralf Steuer, Peter Humburg, Joachim Selbig, 2006, Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics, 7, 380 (full text) (abstract)

Lokesh Kumar, Matthias Futschik, Hanspeter Herzel, 2006, DNA motifs and sequence periodicities. In Silico Biol. (Gedrukt), 6, 71-8 (abstract)

Nico Blüthgen, Florian Menzel, Nils Blüthgen, 2006, Measuring specialization in species interaction networks. BMC Ecol., 6, 9 (full text) (abstract)

Ralf Steuer, 2006, Review: on the analysis and interpretation of correlations in metabolomic data. Brief. Bioinformatics, 7, 151-8 (full text) (abstract)

Ralf Steuer, Thilo Gross, Joachim Selbig, Bernd Blasius, 2006, Structural kinetic modeling of metabolic networks. Proc. Natl. Acad. Sci. U.S.A., 103, 11868-73 (full text) (abstract)

Roland Schaette, Richard Kempter, 2006, Development of tinnitus-related neuronal hyperactivity through homeostatic plasticity after hearing loss: a computational model. Eur. J. Neurosci., 23, 3124-38 (full text) (abstract)

Olof Leimar, Peter Hammerstein, Tom J M Van Dooren, 2006, A new perspective on developmental plasticity and the principles of adaptive morph determination. Am. Nat., 167, 367-76 (full text) (abstract)

Ulf Dühring, Ilka M Axmann, Wolfgang R Hess, Annegret Wilde, 2006, An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc. Natl. Acad. Sci. U.S.A., 103, 7054-8 (full text) (abstract)

Edward H Hagen, Peter Hammerstein, 2006, Game theory and human evolution: a critique of some recent interpretations of experimental games. Theor Popul Biol, 69, 339-48 (full text) (abstract)

Samuel Bernard, Branka Cajavec, Laurent Pujo-Menjouet, Michael C Mackey, Hanspeter Herzel, 2006, Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations. Philos Trans A Math Phys Eng Sci, 364, 1155-70 (full text) (abstract)

Branka Cajavec, Hanspeter Herzel, Samuel Bernard, 2006, Death of neuronal clusters contributes to variance of age at onset in Huntington's disease. Neurogenetics, 7, 21-5 (full text) (abstract)

Christian Leibold, Richard Kempter, 2006, Memory capacity for sequences in a recurrent network with biological constraints. Neural Comput, 18, 904-41 (full text) (abstract)

Nils Blüthgen, Frank J Bruggeman, Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff, Boris N Kholodenko, 2006, Effects of sequestration on signal transduction cascades. FEBS J., 273, 895-906 (full text) (abstract)

Obul Reddy Bandapalli, Martina Geheeb, Dennis Kobelt, Katrin Kuehnle, Sefer Elezkurtaj, Jens Herrmann, Axel M Gressner, Ralf Weiskirchen, Dieter Beule, Nils Blüthgen, Hanspeter Herzel, Claudia Franke, Karsten Brand, 2006, Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases. Int. J. Cancer, 118, 74-89 (full text) (abstract)

Peter Hammerstein, Edward H Hagen, 2005, The second wave of evolutionary economics in biology. Trends Ecol. Evol. (Amst.), 20, 604-9 (full text) (abstract)

Branka Cajavec, Samuel Bernard, Hanspeter Herzel, 2005, Aggregation in Huntington's disease: insights through modelling. Genome Inform, 16, 262-71 (abstract)

Nils Blüthgen, Karsten Brand, Branka Cajavec, Maciej Swat, Hanspeter Herzel, Dieter Beule, 2005, Biological profiling of gene groups utilizing Gene Ontology. Genome Inform, 16, 106-15 (abstract)

Arndt Telschow, Peter Hammerstein, John H Werren, 2005, The effect of Wolbachia versus genetic incompatibilities on reinforcement and speciation. Evolution, 59, 1607-19 (abstract)

Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel, 2005, Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction. PLoS Comput. Biol., 1, e54 (full text) (abstract)

Szymon M Kielbasa, Didier Gonze, Hanspeter Herzel, 2005, Measuring similarities between transcription factor binding sites. BMC Bioinformatics, 6, 237 (full text) (abstract)

Ilka M Axmann, Philip Kensche, Jörg Vogel, Stefan Kohl, Hanspeter Herzel, Wolfgang R Hess, 2005, Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol., 6, R73 (full text) (abstract)

Axel Kowald, Marina Jendrach, Sandra Pohl, Jürgen Bereiter-Hahn, Peter Hammerstein, 2005, On the relevance of mitochondrial fusions for the accumulation of mitochondrial deletion mutants: a modelling study. Aging Cell, 4, 273-83 (full text) (abstract)

David T Blake, Fabrizio Strata, Richard Kempter, Michael M Merzenich, 2005, Experience-dependent plasticity in S1 caused by noncoincident inputs. J. Neurophysiol., 94, 2239-50 (full text) (abstract)

Stefan Legewie, Nils Blüthgen, Hanspeter Herzel, 2005, Quantitative analysis of ultrasensitive responses. FEBS J., 272, 4071-9 (full text) (abstract)

Hermann Wagner, Sandra Brill, Richard Kempter, Catherine E Carr, 2005, Microsecond precision of phase delay in the auditory system of the barn owl. J. Neurophysiol., 94, 1655-8 (full text) (abstract)

Didier Gonze, Samuel Bernard, Christian Waltermann, Achim Kramer, Hanspeter Herzel, 2005, Spontaneous synchronization of coupled circadian oscillators. Biophys. J., 89, 120-9 (full text) (abstract)

Malte Kleinschmidt, Olav Grundmann, Nils Blüthgen, Hans-Ulrich Mösch, Gerhard H Braus, 2005, Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions. Mol. Genet. Genomics, 273, 382-93 (full text) (abstract)

Peter Hammerstein, 2005, Strategic analysis in evolutionary genetics and the theory of games. J. Genet., 84, 7-12 (abstract)

Isao Tokuda, Hanspeter Herzel, 2005, Detecting synchronizations in an asymmetric vocal fold model from time series data. Chaos, 15, 13702 (full text) (abstract)

Florian Geier, Sabine Becker-Weimann, Achim Kramer, Hanspeter Herzel, 2005, Entrainment in a model of the mammalian circadian oscillator. J. Biol. Rhythms, 20, 83-93 (full text) (abstract)

Nils Blüthgen, Szymon M Kiełbasa, Hanspeter Herzel, 2005, Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res., 33, 272-9 (full text) (abstract)

Matthias Truss, Maciej Swat, Szymon M Kielbasa, Reinhold Schäfer, Hanspeter Herzel, Christian Hagemeier, 2005, HuSiDa–the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. Nucleic Acids Res., 33, D108-11 (full text) (abstract)