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publications:start [2017/04/17 12:16] nilspublications:start [2018/12/28 13:29] (current) nils
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 may be incomplete or could contain papers which are not by ITB may be incomplete or could contain papers which are not by ITB
 authors. //  authors. // 
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 +=== 2018 ===
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30257207%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.celrep.2018.08.088|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30423075%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1093/bioinformatics/bty616|(full text)]] 
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 +Franziska Witzel, Nils Blüthgen, 2018, When More Is Less: Dual Phosphorylation Protects Signaling Off State against Overexpression. Biophys. J., 115,  1383-1392  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30217381%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.bpj.2018.08.019|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29947587%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1152/jn.00463.2017|(full text)]] 
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 +Bharath Ananthasubramaniam, Axel Diernfellner, Michael Brunner, Hanspeter Herzel, 2018, Ultradian Rhythms in the Transcriptome of Neurospora crassa. iScience, 9,  475-486  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30472532%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.isci.2018.11.012|(full text)]] 
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 +Rukeia El-Athman, Angela Relógio, 2018, Escaping Circadian Regulation: An Emerging Hallmark of Cancer? Cell Syst, 6,  266-267  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29596780%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.cels.2018.03.006|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29497170%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/emm.2017.290|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29522508%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pgen.1007239|(full text)]] 
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 +Roman Zug, Peter Hammerstein, 2018, Evolution of reproductive parasites with direct fitness benefits. Heredity (Edinb), 120,  266-281  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29234159%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/s41437-017-0022-5|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30456356%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.26508/lsa.201800078|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29611278%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/ele.12949|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30065253%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/s41598-018-29847-z|(full text)]] 
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 +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,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29786557%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1098/rstb.2017.0222|(full text)]] 
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 +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,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29786556%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1098/rstb.2017.0221|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30005951%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.ebiom.2018.07.002|(full text)]] 
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 +Rukeia El-Athman, Luise Fuhr, Angela Relógio, 2018, A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine, 33,  68-81  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29936137%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.ebiom.2018.06.012|(full text)]] 
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 +Christoph Schmal, Erik D Herzog, Hanspeter Herzel, 2018, Measuring Relative Coupling Strength in Circadian Systems. J. Biol. Rhythms, 33,  84-98  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29219034%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1177/0748730417740467|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30586381%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pcbi.1006636|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30521528%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pcbi.1006612|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29931053%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1093/bioinformatics/bty473|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30532130%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pcbi.1006607|(full text)]] 
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 +André Holzbecher, Richard Kempter, 2018, Interneuronal gap junctions increase synchrony and robustness of hippocampal ripple oscillations. Eur. J. Neurosci., 48,  3446-3465  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30414336%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/ejn.14267|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29953415%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1172/JCI120874|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30111366%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1186/s12964-018-0256-8|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30225087%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1098/rsos.181026|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29357463%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1152/jn.00175.2017|(full text)]] 
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 +Bertram Klinger, Nils Blüthgen, 2018, Reverse engineering gene regulatory networks by modular response analysis - a benchmark. Essays Biochem., 62,  535-547  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30315094%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1042/EBC20180012|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29540683%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/s41467-018-03507-2|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29295995%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/s41467-017-02391-6|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=30190679%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.3389/fphys.2018.01178|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29293562%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pone.0190004|(full text)]] 
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29263798%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/s41540-017-0038-8|(full text)]] 
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 === 2017 === === 2017 ===
  
-Jorge JaramilloRichard Kempter, 2017, Phase precession: a neural code underlying episodic memory? CurrOpinNeurobiol., 43,  130-138  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28390862%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.conb.2017.02.006|(full text)]] +Florian UhlitzAnja Sieber, Emanuel Wyler, Raphaela Fritsche-Guenther, Johannes Meisig, Markus Landthaler, Bertram Klinger, Nils Blüthgen, 2017, An immediate-late gene expression module decodes ERK signal durationMolSyst. Biol., 13,  944  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28947433%5Buid%5D|(abstract)]] 
  
  
-Federica EduatiVictoria Doldàn-MartelliBertram KlingerThomas CokelaerAnja SieberFiona KogeraMathurin DorelMathew Garnett, Nils Blüthgen, Julio Saez-Rodriguez, 2017, Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic modelsCancer Res., ,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28381545%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1158/0008-5472.CAN-17-0078|(full text)]] +Noreen van der LindenTom CornelisDorien M KimenaiLieke J J KlinkenbergJudith M HilderinkSarah LückElisabeth J R LitjensFrederique E C M Peeters, Alexander S Streng, Tobias Breidthardt, Luc 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28893963%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1161/CIRCULATIONAHA.117.029986|(full text)]]  
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 + 
 +Thomas McColgan, Ji Liu, Paula Tuulia Kuokkanen, Catherine Emily Carr, Hermann Wagner, Richard Kempter, 2017, Dipolar extracellular potentials generated by axonal projections. Elife, 6,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28871959%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.7554/eLife.26106|(full text)]]  
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 + 
 +Evrim B Ünal, Florian Uhlitz, Nils Blüthgen, 2017, A compendium of ERK targets. FEBS Lett., 591,  2607-2615  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28675784%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1002/1873-3468.12740|(full text)]]  
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 +Tiziano D'Albis, Richard Kempter, 2017, A single-cell spiking model for the origin of grid-cell patternsPLoS Comput. Biol., 13 e1005782  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28968386%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pcbi.1005782|(full text)]]  
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 +Christoph Schmal, Jihwan Myung, Hanspeter Herzel, Grigory Bordyugov, 2017, Moran's I quantifies spatio-temporal pattern formation in neural imaging dataBioinformatics, 33,  3072-3079  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28575207%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1093/bioinformatics/btx351|(full text)]]  
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 + 
 +Benjamin F Maier, Dirk Brockmann, 2017, Cover time for random walks on arbitrary complex networks. Phys Rev E, 96,  042307  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29347543%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1103/PhysRevE.96.042307|(full text)]]  
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 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29098954%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1177/0748730417728663|(full text)]]  
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 +Guido Hermey, Nils Blüthgen, Dietmar Kuhl, 2017, Neuronal activity-regulated alternative mRNA splicing. Int. J. Biochem. Cell Biol., 91,  184-193  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28591617%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.biocel.2017.06.002|(full text)]]  
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 + 
 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28494861%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.celrep.2017.04.041|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28468958%5Buid%5D|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28618541%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1103/PhysRevE.95.052203|(full text)]]  
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 + 
 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28516845%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1099/mic.0.000459|(full text)]] 
  
  
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-Flavio IannelliAndreas KoherDirk BrockmannPhilipp HövelIgor M Sokolov, 2017, Effective distances for epidemics spreading on complex networksPhys Rev E95,  012313  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28208446%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1103/PhysRevE.95.012313|(full text)]] +Yinxiu ZhanLuca MarianiIros BarozziEdda G SchulzNils 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28057745%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1101/gr.212803.116|(full text)]] 
  
  
-Kevin ThurleyChristopher Herbst, Felix WesenerBarbara Koller, Thomas WallachBert MaierAchim KramerPål O Westermark, 2017, Principles for circadian orchestration of metabolic pathways. Proc. Natl. Acad. Sci. U.S.A., 114 1572-1577  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28159888%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1073/pnas.1613103114|(full text)]] +Federica EduatiVictoria Doldàn-MartelliBertram Klinger, Thomas CokelaerAnja SieberFiona KogeraMathurin 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28381545%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1158/0008-5472.CAN-17-0078|(full text)]]  
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 + 
 +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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28442534%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1083/jcb.201610058|(full text)]]  
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 +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., ,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28720699%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1073/pnas.1617508114|(full text)]] 
  
  
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 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28087238%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.immuni.2016.12.011|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28087238%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.immuni.2016.12.011|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28208446%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1103/PhysRevE.95.012313|(full text)]] 
  
  
Line 31: Line 171:
 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27899536%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1104/pp.16.01487|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27899536%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1104/pp.16.01487|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28159888%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1073/pnas.1613103114|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29216180%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pbio.2002940|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28417973%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1038/srep46571|(full text)]] 
 +
 +
 +Jorge Jaramillo, Richard Kempter, 2017, Phase precession: a neural code underlying episodic memory? Curr. Opin. Neurobiol., 43,  130-138  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28390862%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.conb.2017.02.006|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27374316%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/ejn.13326|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=29249974%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.3389/fphys.2017.00906|(full text)]] 
 +
 +
 +Lucas Böttcher, Olivia Woolley-Meza, Dirk Brockmann, 2017, Temporal dynamics of online petitions. PLoS ONE, 12,  e0178062  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=28542492%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1371/journal.pone.0178062|(full text)]] 
  
 === 2016 === === 2016 ===
Line 92: Line 252:
  
 Pål O Westermark, 2016, Linking Core Promoter Classes to Circadian Transcription. PLoS Genet., 12,  e1006231  [[http://dx.doi.org/10.1371/journal.pgen.1006231|(full text)]]  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27504829%5Buid%5D|(abstract)]]  Pål O Westermark, 2016, Linking Core Promoter Classes to Circadian Transcription. PLoS Genet., 12,  e1006231  [[http://dx.doi.org/10.1371/journal.pgen.1006231|(full text)]]  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27504829%5Buid%5D|(abstract)]] 
- 
- 
-Katharina Anna Wilmes, Jan-Hendrik Schleimer, Susanne Schreiber, 2016, Spike-timing dependent inhibitory plasticity to learn a selective gating of backpropagating action potentials. Eur. J. Neurosci., ,    [[http://www.ncbi.nlm.nih.gov/pubmed/?term=27374316%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/ejn.13326|(full text)]]  
  
  
Line 131: Line 288:
  
 Peter Hammerstein, Ronald Noë, 2016, Biological trade and markets. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 371,    [[http://dx.doi.org/10.1098/rstb.2015.0101|(full text)]]  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26729940%5Buid%5D|(abstract)]]  Peter Hammerstein, Ronald Noë, 2016, Biological trade and markets. Philos. Trans. R. Soc. Lond., B, Biol. Sci., 371,    [[http://dx.doi.org/10.1098/rstb.2015.0101|(full text)]]  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26729940%5Buid%5D|(abstract)]] 
- 
- 
- 
- 
  
 === 2015 === === 2015 ===
- 
-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, 2015, Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget, ,    [[http://dx.doi.org/10.18632/oncotarget.6793|(full text)]]  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26760764%5Buid%5D|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26238599%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.neuro.2015.07.008|(full text)]]  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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26238599%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1016/j.neuro.2015.07.008|(full text)]] 
Line 156: Line 307:
  
 Nils Blüthgen, 2015, Signaling output: it's all about timing and feedbacks. Mol. Syst. Biol., 11,  843  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26613962%5Buid%5D|(abstract)]]  Nils Blüthgen, 2015, Signaling output: it's all about timing and feedbacks. Mol. Syst. Biol., 11,  843  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26613962%5Buid%5D|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26589287%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1186/s12918-015-0229-0|(full text)]] 
  
  
Line 162: Line 316:
  
 Sven Blankenburg, Wei Wu, Benjamin Lindner, Susanne Schreiber, 2015, Information filtering in resonant neurons. J Comput Neurosci, 39,  349-70  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26546022%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1007/s10827-015-0580-6|(full text)]]  Sven Blankenburg, Wei Wu, Benjamin Lindner, Susanne Schreiber, 2015, Information filtering in resonant neurons. J Comput Neurosci, 39,  349-70  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26546022%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1007/s10827-015-0580-6|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=26085503%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1093/bioinformatics/btv363|(full text)]] 
  
  
Line 231: Line 388:
  
 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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=24618033%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/brv.12098|(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  [[http://www.ncbi.nlm.nih.gov/pubmed/?term=24618033%5Buid%5D|(abstract)]]  [[http://dx.doi.org/10.1111/brv.12098|(full text)]] 
 +