Publications of Prof. Fabian Theis

2018

  • Castañeda-Tamez, Paulina; Ramírez-Peris, Jimena; Pérez-Velázquez, Judith; Kuttler, Christina; Jalalimanesh, Ammar; Saucedo-Mora, Miguel Á.; Jiménez-Cortés, J. Guillermo; Maeda, Toshinari; González, Yael; Tomás, María; Wood, Thomas K.; García-Contreras, Rodolfo: Pyocyanin Restricts Social Cheating in Pseudomonas aeruginosa. Frontiers in Microbiology 9, 2018, 1348 more…
  • Jalalimanesh, Ammar; Kuttler, Christina; Garc{í}a-Contreras, Rodolfo; Pérez-Velázquez, Judith: An Agent-Based Model to Study Selection of Pseudomonas aeruginosa Quorum Sensing by Pyocyanin: A Multidisciplinary Perspective on Bacterial Communication. In: Olivares-Quiroz, Luis; Resendis-Antonio, Osbaldo (Ed.): Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues. Springer International Publishing, 2018, 133--147 more…
  • Pérez-Velázquez, Judith; Hense, Burkhard A.: Differential Equations Models to Study Quorum Sensing. In: Leoni, Livia; Rampioni, Giordano (Ed.): Quorum Sensing: Methods and Protocols. Springer New York, 2018, 253--271 more…

2017

  • Ballnus, Benjamin; Hug, Sabine; Hatz, Kathrin; Görlitz, Linus; Hasenauer, Jan; Theis, Fabian J.: Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. BMC Systems Biology 11 (1), 2017 more…
  • Bartel, Sabine; Schulz, Nikola; Alessandrini, Francesca; Schamberger, Andrea C.; Pagel, Philipp; Theis, Fabian J.; Milger, Katrin; Noessner, Elfriede; Stick, Stephen M.; Kicic, Anthony; Eickelberg, Oliver; Freishtat, Robert J.; Krauss-Etschmann, Susanne: Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma. Scientific Reports 7, 2017, 46026 more…
  • Blasi, Thomas; Buettner, Florian; Strasser, Michael K; Marr, Carsten; Theis, Fabian J: cgCorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics. Physical Biology 14 (3), 2017, 036001 more…
  • Buggenthin, Felix; Buettner, Florian; Hoppe, Philipp S; Endele, Max; Kroiss, Manuel; Strasser, Michael; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hilsenbeck, Oliver; Schroeder, Timm; Theis, Fabian J; Marr, Carsten: Prospective identification of hematopoietic lineage choice by deep learning. Nature Methods 14 (4), 2017, 403-406 more…
  • Chlis, Nikolaos K.; Wolf, F. Alexander; Theis, Fabian J.: Model-based branching point detection in single-cell data by K-branches clustering. Bioinformatics, 2017 more…
  • Florea, Ana-Maria; Varghese, Elizabeth; McCallum, Jennifer E.; Mahgoub, Safa; Helmy, Irfan; Varghese, Sharon; Gopinath, Neha; Sass, Steffen; Theis, Fabian J.; Reifenberger, Guido; Büsselberg, Dietrich: Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma. Oncotarget, 2017 more…
  • Frohnert, Brigitte I; Laimighofer, Michael; Krumsiek, Jan; Theis, Fabian J; Winkler, Christiane; Norris, Jill M; Ziegler, Anette-Gabriele; Rewers, Marian J; Steck, Andrea K: Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young. Pediatric Diabetes, 2017 more…
  • Fröhlich, Fabian; Kaltenbacher, Barbara; Theis, Fabian J.; Hasenauer, Jan: Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLOS Computational Biology 13 (1), 2017, e1005331 more…
  • Hilsenbeck, Oliver; Schwarzfischer, Michael; Loeffler, Dirk; Dimopoulos, Sotiris; Hastreiter, Simon; Marr, Carsten; Theis, Fabian J.; Schroeder, Timm: fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinformatics 33 (13), 2017, 2020-2028 more…
  • Jagiella, Nick; Rickert, Dennis; Theis, Fabian J.; Hasenauer, Jan: Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models. Cell Systems 4 (2), 2017, 194-206.e9 more…
  • Milger, K.; Götschke, J.; Krause, L.; Nathan, P.; Alessandrini, F.; Tufman, A.; Fischer, R.; Bartel, S.; Theis, F. J.; Behr, J.; Dehmel, S.; Mueller, N. S.; Kneidinger, N.; Krauss-Etschmann, S.: Identification of a plasma miRNA biomarker signature for allergic asthma: A translational approach. Allergy, 2017 more…
  • Peng, Tingying; Thorn, Kurt; Schroeder, Timm; Wang, Lichao; Theis, Fabian J.; Marr, Carsten; Navab, Nassir: A BaSiC tool for background and shading correction of optical microscopy images. Nature Communications 8, 2017, 14836 more…
  • Saucedo-Mora, Miguel A.; Castañeda-Tamez, Paulina; Cazares, Adrián; Pérez-Velázquez, Judith; Hense, Burkhard A.; Cazares, Daniel; Figueroa, Wendy; Carballo, Marco; Guarneros, Gabriel; Pérez-Eretza, Berenice; Cruz, Nelby; Nishiyama, Yoshito; Maeda, Toshinari; Belmont-Díaz, Javier A.; Wood, Thomas K.; García-Contreras, Rodolfo: Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa. Frontiers in Microbiology 8, 2017, 1669 more…
  • Schneider, Marc; Christopoulos, Petros; Muley, Thomas; Warth, Arne; Klingmueller, Ursula; Thomas, Michael; Herth, Felix; Dienemann, Hendrik; Mueller, Nikola; Theis, Fabian; Meister, Michael: AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients. International Journal of Oncology, 2017 more…
  • Stoecker, Katharina; Sass, Steffen; Theis, Fabian J.; Hauner, Hans; Pfaffl, Michael W.: Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data. Biomolecular Detection and Quantification 11, 2017, 31-44 more…

2016

  • What Is the Key Best Practice for Collaborating with a Computational Biologist? Cell Systems 3 (1), 2016, 7-11 more…
  • Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J.; Becker, Peter B.; Marr, Carsten: Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions. Cell Systems, 2016, 49-58 more…
  • Blasi, Thomas; Hennig, Holger; Summers, Huw D.; Theis, Fabian J.; Cerveira, Joana; Patterson, James O.; Davies, Derek; Filby, Andrew; Carpenter, Anne E.; Rees, Paul: Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications 7, 2016, 10256 more…
  • Feigelman, Justin; Ganscha, Stefan; Hastreiter, Simon; Schwarzfischer, Michael; Filipczyk, Adam; Schroeder, Timm; Theis, Fabian J.; Marr, Carsten; Claassen, Manfred: Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells. Cell Systems 3 (5), 2016, 480-490.e13 more…
  • Fiedler, Anna; Raeth, Sebastian; Theis, Fabian J.; Hausser, Angelika; Hasenauer, Jan: Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. BMC Systems Biology 10 (1), 2016 more…
  • Fröhlich, Fabian; Theis, Fabian J.; Rädler, Joachim O.; Hasenauer, Jan: Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 2016, btw764 more…
  • Fröhlich, Fabian; Thomas, Philipp; Kazeroonian, Atefeh; Theis, Fabian J.; Grima, Ramon; Hasenauer, Jan: Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLOS Computational Biology 12 (7), 2016, e1005030 more…
  • Garzorz-Stark, Natalie; Krause, Linda; Lauffer, Felix; Atenhan, Anne; Thomas, Jenny; Stark, Sebastian P.; Franz, Regina; Weidinger, Stephan; Balato, Anna; Mueller, Nikola S.; Theis, Fabian J.; Ring, Johannes; Schmidt-Weber, Carsten B.; Biedermann, Tilo; Eyerich, Stefanie; Eyerich, Kilian: A novel molecular disease classifier for psoriasis and eczema. Experimental Dermatology 25 (10), 2016, 767-774 more…
  • Geissen, Eva-Maria; Hasenauer, Jan; Heinrich, Stephanie; Hauf, Silke; Theis, Fabian J.; Radde, Nicole E.: MEMO: multi-experiment mixture model analysis of censored data. Bioinformatics 32 (16), 2016, 2464-2472 more…
  • Haghverdi, Laleh; Büttner, Maren; Wolf, F Alexander; Buettner, Florian; Theis, Fabian J: Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods 13 (10), 2016, 845-848 more…
  • Hilsenbeck, Oliver; Schwarzfischer, Michael; Skylaki, Stavroula; Schauberger, Bernhard; Hoppe, Philipp S; Loeffler, Dirk; Kokkaliaris, Konstantinos D; Hastreiter, Simon; Skylaki, Eleni; Filipczyk, Adam; Strasser, Michael; Buggenthin, Felix; Feigelman, Justin S; Krumsiek, Jan; van den Berg, Adrianus J J; Endele, Max; Etzrodt, Martin; Marr, Carsten; Theis, Fabian J; Schroeder, Timm: Software tools for single-cell tracking and quantification of cellular and molecular properties. Nature Biotechnology 34 (7), 2016, 703-706 more…
  • Hoppe, Philipp S.; Schwarzfischer, Michael; Loeffler, Dirk; Kokkaliaris, Konstantinos D.; Hilsenbeck, Oliver; Moritz, Nadine; Endele, Max; Filipczyk, Adam; Gambardella, Adriana; Ahmed, Nouraiz; Etzrodt, Martin; Coutu, Daniel L.; Rieger, Michael A.; Marr, Carsten; Strasser, Michael K.; Schauberger, Bernhard; Burtscher, Ingo; Ermakova, Olga; Bürger, Antje; Lickert, Heiko; Nerlov, Claus; Theis, Fabian J.; Schroeder, Timm: Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature 535 (7611), 2016, 299-302 more…
  • Huypens, Peter; Sass, Steffen; Wu, Moya; Dyckhoff, Daniela; Tschöp, Matthias; Theis, Fabian; Marschall, Susan; de Angelis, Martin Hrabě; Beckers, Johannes: Epigenetic germline inheritance of diet-induced obesity and insulin resistance. Nature Genetics 48 (5), 2016, 497-499 more…
  • Jung, Bomi; Padula, Daniela; Burtscher, Ingo; Landerer, Cedric; Lutter, Dominik; Theis, Fabian; Messias, Ana C.; Geerlof, Arie; Sattler, Michael; Kremmer, Elisabeth; Boldt, Karsten; Ueffing, Marius; Lickert, Heiko: Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation. PLOS ONE 11, 2016, e0149477 more…
  • Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan: CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics. PLOS ONE 11, 2016, e0146732 more…
  • Kondofersky, Ivan; Theis, Fabian J.; Fuchs, Christiane: Inferring catalysis in biological systems. IET Systems Biology 10 (6), 2016, 210-218 more…
  • Kong, Bo; Bruns, Philipp; Behler, Nora A; Chang, Ligong; Schlitter, Anna Melissa; Cao, Jing; Gewies, Andreas; Ruland, Jürgen; Fritzsche, Sina; Valkovskaya, Nataliya; Jian, Ziying; Regel, Ivonne; Raulefs, Susanne; Irmler, Martin; Beckers, Johannes; Friess, Helmut; Erkan, Mert; Mueller, Nikola S; Roth, Susanne; Hackert, Thilo; Esposito, Irene; Theis, Fabian J; Kleeff, Jörg; Michalski, Christoph W: Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy. Gut, 2016, gutjnl-2015-310913 more…
  • Krause, Linda; Mourantchanian, Vagkan; Brockow, Knut; Theis, Fabian J.; Schmidt-Weber, Carsten B.; Knapp, Bettina; Mueller, Nikola S.; Eyerich, Stefanie: A computational model to predict severity of atopic eczema from 30 serum proteins. Journal of Allergy and Clinical Immunology 138 (4), 2016, 1207-1210.e2 more…
  • Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J: Computational approaches for systems metabolomics. Current Opinion in Biotechnology 39, 2016, 198-206 more…
  • Laimighofer, Michael; Krumsiek, Jan; Buettner, Florian; Theis, Fabian J.: Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. Journal of Computational Biology 23, 2016, 279-290 more…
  • Much, Daniela; Beyerlein, Andreas; Kindt, Alida; Krumsiek, Jan; Stückler, Ferdinand; Rossbauer, Michaela; Hofelich, Anna; Wiesenäcker, David; Hivner, Susanne; Herbst, Melanie; Römisch-Margl, Werner; Prehn, Cornelia; Adamski, Jerzy; Kastenmüller, Gabi; Theis, Fabian; Ziegler, Anette-G.; Hummel, Sandra: Lactation is associated with altered metabolomic signatures in women with gestational diabetes. Diabetologia 59 (10), 2016, 2193-2202 more…
  • Mund, A.; Kuttler, C.; Pérez-Velázquez, J.; Hense, B.A.: An age-dependent model to analyse the evolutionary stability of bacterial quorum sensing. Journal of Theoretical Biology 405, 2016, 104-115 more…
  • Preusse, Martin; Theis, Fabian J.; Mueller, Nikola S.: miTALOS v2: Analyzing Tissue Specific microRNA Function. PLOS ONE 11, 2016, e0151771 more…
  • Pérez-Velázquez, Judith; Gevertz, Jana L.; Karolak, Aleksandra; Rejniak, Katarzyna A.: Microenvironmental Niches and Sanctuaries: A Route to Acquired Resistance. In: Rejniak, Katarzyna A. (Ed.): Systems Biology of Tumor Microenvironment: Quantitative Modeling and Simulations. Springer International Publishing, 2016, 149--164 more…
  • Pérez-Velázquez, Judith; Gölgeli, Meltem; García-Contreras, Rodolfo: Mathematical Modelling of Bacterial Quorum Sensing: A Review. Bulletin of Mathematical Biology, 2016 more…
  • Rolle-Kampczyk, Ulrike E.; Krumsiek, Jan; Otto, Wolfgang; Röder, Stefan W.; Kohajda, Tibor; Borte, Michael; Theis, Fabian; Lehmann, Irina; von Bergen, M.: Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns. Metabolomics 12, 2016 more…
  • Sacher, A.; Theis. F. J.: Von lernfähigen Maschinen lernen. Laborjournal (7-8), 2016, 59-61 more…
  • Senís, Elena; Mockenhaupt, Stefan; Rupp, Daniel; Bauer, Tobias; Paramasivam, Nagarajan; Knapp, Bettina; Gronych, Jan; Grosse, Stefanie; Windisch, Marc P.; Schmidt, Florian; Theis, Fabian J.; Eils, Roland; Lichter, Peter; Schlesner, Matthias; Bartenschlager, Ralf; Grimm, Dirk: TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus. Nucleic Acids Research 45 (1), 2016, e3-e3 more…
  • Stojcheva, Nina; Schechtmann, Gennadi; Sass, Steffen; Roth, Patrick; Florea, Ana-Maria; Stefanski, Anja; Stühler, Kai; Wolter, Marietta; Müller, Nikola S.; Theis, Fabian J.; Weller, Michael; Reifenberger, Guido; Happold, Caroline: MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM. Oncotarget 7 (11), 2016, 12937-12950 more…
  • Styczynski, Mark P; Theis, Fabian J: Editorial overview: Systems biology-the intersection of experiments and computation, underpinning biotechnology. Current Opinion in Biotechnology 39, 2016, iv-vi more…
  • Sánchez-Garduño, Faustino; Pérez-Velázquez, Judith: Reactive-Diffusive-Advective Traveling Waves in a Family of Degenerate Nonlinear Equations. The Scientific World Journal 2016, 2016, 1-21 more…
  • Theis, F; Corbacioglu, A; Gaidzik, V I; Paschka, P; Weber, D; Bullinger, L; Heuser, M; Ganser, A; Thol, F; Schlegelberger, B; Göhring, G; Köhne, C-H; Germing, U; Brossart, P; Horst, H-A; Haase, D; Götze, K; Ringhoffer, M; Fiedler, W; Nachbaur, D; Kindler, T; Held, G; Lübbert, M; Wattad, M; Salih, H R; Krauter, J; Döhner, H; Schlenk, R F; Döhner, K: Clinical impact of GATA2 mutations in acute myeloid leukemia patients harboring CEBPA mutations: a study of the AML study group. Leukemia 30 (11), 2016, 2248-2250 more…
  • Willmann, Stefanie J.; Mueller, Nikola S.; Engert, Silvia; Sterr, Michael; Burtscher, Ingo; Raducanu, Aurelia; Irmler, Martin; Beckers, Johannes; Sass, Steffen; Theis, Fabian J.; Lickert, Heiko: The global gene expression profile of the secondary transition during pancreatic development. Mechanisms of Development 139, 2016, 51-64 more…
  • von Toerne, Christine; Laimighofer, Michael; Achenbach, Peter; Beyerlein, Andreas; de las Heras Gala, Tonia; Krumsiek, Jan; Theis, Fabian J.; Ziegler, Anette G.; Hauck, Stefanie M.: Peptide serum markers in islet autoantibody-positive children. Diabetologia 60 (2), 2016, 287-295 more…

2015

  • Angerer, Philipp; Haghverdi, Laleh; Büttner, Maren; Theis, Fabian J.; Marr, Carsten; Buettner, Florian: destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32 (8), 2015, 1241-1243 more…
  • Barbosa, J. S.; Sanchez-Gonzalez, R.; Di Giaimo, R.; Baumgart, E. V.; Theis, F. J.; Gotz, M.; Ninkovic, J.: Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain. Science 348 (6236), 2015, 789-793 more…
  • Bartel, Jörg; Krumsiek, Jan; Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.: The Human Blood Metabolome-Transcriptome Interface. PLoS Genet 11, 2015, e1005274 more…
  • Buettner, Florian; Natarajan, Kedar N; Casale, F Paolo; Proserpio, Valentina; Scialdone, Antonio; Theis, Fabian J; Teichmann, Sarah A; Marioni, John C; Stegle, Oliver: Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33, 2015, 155-160 more…
  • Calzolari, Filippo; Michel, Julia; Baumgart, Emily Violette; Theis, Fabian; Götz, Magdalena; Ninkovic, Jovica: Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone. Nature Neuroscience 18, 2015, 490-492 more…
  • Conlon, T. M.; Bartel, J.; Ballweg, K.; Gunter, S.; Prehn, C.; Krumsiek, J.; Meiners, S.; Theis, F. J.; Adamski, J.; Eickelberg, O.; Yildirim, A. O.: Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema. Clinical Science 130, 2015, 273-287 more…
  • Filipczyk, Adam; Marr, Carsten; Hastreiter, Simon; Feigelman, Justin; Schwarzfischer, Michael; Hoppe, Philipp S.; Loeffler, Dirk; Kokkaliaris, Konstantinos D.; Endele, Max; Schauberger, Bernhard; Hilsenbeck, Oliver; Skylaki, Stavroula; Hasenauer, Jan; Anastassiadis, Konstantinos; Theis, Fabian J.; Schroeder, Timm: Network plasticity of pluripotency transcription factors in embryonic stem cells. Nature Cell Biology 17 (10), 2015, 1235-1246 more…
  • Gevertz, Jana L.; Aminzare, Zahra; Norton, Kerri-Ann; Pérez-Velázquez, Judith; Volkening, Alexandria; Rejniak, Katarzyna A.: Emergence of Anti-Cancer Drug Resistance: Exploring the Importance of the Microenvironmental Niche via a Spatial Model. In: The IMA Volumes in Mathematics and its Applications. Springer Science + Business Media, 2015 more…
  • Haghverdi, L.; Buettner, F.; Theis, F. J.: Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics, 2015 more…
  • Hasenauer, J.; Jagiella, N.; Hross, S.; Theis, F. J.: Data-driven modelling of biological multi-scale processes. Journal of Coupled Systems and Multiscale Dynamics, 2015 more…
  • Helmbrecht, Michaela S.; Soellner, Heidi; Castiblanco-Urbina, Maria A.; Winzeck, Stefan; Sundermeier, Julia; Theis, Fabian J.; Fouad, Karim; Huber, Andrea B.: A Critical Period for Postnatal Adaptive Plasticity in a Model of Motor Axon Miswiring. PLOS ONE 10, 2015, e0123643 more…
  • Hug, Sabine; Schmidl, Daniel; Li, Wei Bo; Greiter, Matthias B.; Theis, Fabian J.: Bayesian Model Selection Methods and Their Application to Biological ODE Systems. In: Uncertainty in Biology. Springer Science + Business Media, 2015 more…
  • Hug, Sabine; Schwarzfischer, Michael; Hasenauer, Jan; Marr, Carsten; Theis, Fabian J.: An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule. Statistics and Computing, 2015 more…
  • Illner, Katrin; Miettinen, Jari; Fuchs, Christiane; Taskinen, Sara; Nordhausen, Klaus; Oja, Hannu; Theis, Fabian J.: Model selection using limiting distributions of second-order blind source separation algorithms. Signal Processing 113, 2015, 95-103 more…
  • Ilmonen, Pauliina; Nordhausen, Klaus; Oja, Hannu; Theis, Fabian: An Affine Equivariant Robust Second-Order BSS Method. 2015, 10.1007/978-3-319-22482-4_38(other entry) more…
  • Kondofersky, Ivan; Fuchs, Christiane; Theis, Fabian J.: Identifying latent dynamic components in biological systems. IET Systems Biology, 2015 more…
  • Kong, B.; Wu, W.; Cheng, T.; Schlitter, A. M.; Qian, C.; Bruns, P.; Jian, Z.; Jager, C.; Regel, I.; Raulefs, S.; Behler, N.; Irmler, M.; Beckers, J.; Friess, H.; Erkan, M.; Siveke, J. T.; Tannapfel, A.; Hahn, S. A.; Theis, F. J.; Esposito, I.; Kleeff, J.; Michalski, C. W.: A subset of metastatic pancreatic ductal adenocarcinomas depends quantitatively on oncogenic Kras/Mek/Erk-induced hyperactive mTOR signalling. Gut, 2015 more…
  • Kong, Bo; Bruns, Philipp; Raulefs, Susanne; Rieder, Simon; Paul, Laura; Prazeresda Costa, Olivia; Buch, Thorsten; Theis, Fabian J.; Michalski, Christoph W.; Kleeff, Jörg: Metabolism gene signatures and surgical site infections in abdominal surgery. International Journal of Surgery 14, 2015, 67-74 more…
  • Krumsiek, Jan; Mittelstrass, Kirstin; Do, Kieu Trinh; Stückler, Ferdinand; Ried, Janina; Adamski, Jerzy; Peters, Annette; Illig, Thomas; Kronenberg, Florian; Friedrich, Nele; Nauck, Matthias; Pietzner, Maik; Mook-Kanamori, Dennis O.; Suhre, Karsten; Gieger, Christian; Grallert, Harald; Theis, Fabian J.; Kastenmüller, Gabi: Gender-specific pathway differences in the human serum metabolome. Metabolomics, 2015 more…
  • Linnemann, J. R.; Miura, H.; Meixner, L. K.; Irmler, M.; Kloos, U. J.; Hirschi, B.; Bartsch, H. S.; Sass, S.; Beckers, J.; Theis, F. J.; Gabka, C.; Sotlar, K.; Scheel, C. H.: Quantification of regenerative potential in primary human mammary epithelial cells. Development, 2015 more…
  • Loos, Carolin; Marr, Carsten; Theis, Fabian J.; Hasenauer, Jan: Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. In: Computational Methods in Systems Biology. Springer Science + Business Media, 2015 more…
  • Masserdotti, Giacomo; Gillotin, Sébastien; Sutor, Bernd; Drechsel, Daniela; Irmler, Martin; Jørgensen, Helle F.; Sass, Steffen; Theis, Fabian J.; Beckers, Johannes; Berninger, Benedikt; Guillemot, François; Götz, Magdalena: Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes. Cell Stem Cell 17, 2015, 74-88 more…
  • Meyer, Swanhild U.; Sass, Steffen; Mueller, Nikola S.; Krebs, Stefan; Bauersachs, Stefan; Kaiser, Sebastian; Blum, Helmut; Thirion, Christian; Krause, Sabine; Theis, Fabian J.; Pfaffl, Michael W.: Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1. PLOS ONE 10, 2015, e0135284 more…
  • Miettinen, Jari; Illner, Katrin; Nordhausen, Klaus; Oja, Hannu; Taskinen, Sara; Theis, Fabian J.: Separation of Uncorrelated Stationary time series using Autocovariance Matrices. Journal of Time Series Analysis, 2015, n/a-n/a more…
  • Moignard, Victoria; Woodhouse, Steven; Haghverdi, Laleh; Lilly, Andrew J; Tanaka, Yosuke; Wilkinson, Adam C; Buettner, Florian; Macaulay, Iain C; Jawaid, Wajid; Diamanti, Evangelia; Nishikawa, Shin-Ichi; Piterman, Nir; Kouskoff, Valerie; Theis, Fabian J; Fisher, Jasmin; Göttgens, Berthold: Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol 33, 2015, 269-276 more…
  • Müller, Sören; Raulefs, Susanne; Bruns, Philipp; Afonso-Grunz, Fabian; Plötner, Anne; Thermann, Rolf; Jäger, Carsten; Schlitter, Anna Melissa; Kong, Bo; Regel, Ivonne; Roth, W Kurt; Rotter, Björn; Hoffmeier, Klaus; Kahl, Günter; Koch, Ina; Theis, Fabian J; Kleeff, Jörg; Winter, Peter; Michalski, Christoph W: Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer. Molecular Cancer 14, 2015 more…
  • Müller, Sören; Raulefs, Susanne; Bruns, Philipp; Afonso-Grunz, Fabian; Plötner, Anne; Thermann, Rolf; Jäger, Carsten; Schlitter, Anna Melissa; Kong, Bo; Regel, Ivonne; Roth, W Kurt; Rotter, Björn; Hoffmeier, Klaus; Kahl, Günter; Koch, Ina; Theis, Fabian J; Kleeff, Jörg; Winter, Peter; Michalski, Christoph W: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer. Molecular Cancer 14, 2015 more…
  • Ocone, A.; Haghverdi, L.; Mueller, N. S.; Theis, F. J.: Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinformatics 31 (12), 2015, i89-i96 more…
  • Preusse, Martin; Marr, Carsten; Saunders, Sita; Maticzka, Daniel; Lickert, Heiko; Backofen, Rolf; Theis, Fabian: SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biology 12, 2015, 998-1009 more…
  • Pérez-Velázquez, Judith; Quiñones, Beatriz; Hense, Burkhard A.; Kuttler, Christina: A mathematical model to investigate quorum sensing regulation and its heterogeneity in Pseudomonas syringae on leaves. Ecological Complexity 21, 2015, 128-141 more…
  • Raue, A.; Steiert, B.; Schelker, M.; Kreutz, C.; Maiwald, T.; Hass, H.; Vanlier, J.; Tönsing, C.; Adlung, L.; Engesser, R.; Mader, W.; Heinemann, T.; Hasenauer, J.; Schilling, M.; Höfer, T.; Klipp, E.; Theis, F.; Klingmüller, U.; Schöberl, B.; Timmer, J.: Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems: Fig. 1. Bioinformatics, 2015, btv405 more…
  • Sadic, D.; Schmidt, K.; Groh, S.; Kondofersky, I.; Ellwart, J.; Fuchs, C.; Theis, F. J.; Schotta, G.: Atrx promotes heterochromatin formation at retrotransposons. EMBO reports 16, 2015, 836-850 more…
  • Sass, Steffen; Pitea, Adriana; Unger, Kristian; Hess, Julia; Mueller, Nikola; Theis, Fabian: MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma. IJMS 16 (12), 2015, 30204-30222 more…
  • Schmidt, Johanna M.; Panzilius, Elena; Bartsch, Harald S.; Irmler, Martin; Beckers, Johannes; Kari, Vijayalakshmi; Linnemann, Jelena R.; Dragoi, Diana; Hirschi, Benjamin; Kloos, Uwe J.; Sass, Steffen; Theis, Fabian; Kahlert, Steffen; Johnsen, Steven A.; Sotlar, Karl; Scheel, Christina H.: Stem-Cell-like Properties and Epithelial Plasticity Arise as Stable Traits after Transient Twist1 Activation. Cell Reports 10, 2015, 131-139 more…
  • Strasser, Michael K.; Feigelman, Justin; Theis, Fabian J.; Marr, Carsten: Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. BMC Systems Biology, 2015 more…
  • Theis, F. J.; Ugelvig, L. V.; Marr, C.; Cremer, S.: Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society B: Biological Sciences 370 (1669), 2015, 20140108-20140108 more…
  • Wahl, Simone; Vogt, Susanne; Stückler, Ferdinand; Krumsiek, Jan; Bartel, Jörg; Kacprowski, Tim; Schramm, Katharina; Carstensen, Maren; Rathmann, Wolfgang; Roden, Michael; Jourdan, Carolin; Kangas, Antti J; Soininen, Pasi; Ala-Korpela, Mika; Nöthlings, Ute; Boeing, Heiner; Theis, Fabian J; Meisinger, Christa; Waldenberger, Melanie; Suhre, Karsten; Homuth, Georg; Gieger, Christian; Kastenmüller, Gabi; Illig, Thomas; Linseisen, Jakob; Peters, Annette; Prokisch, Holger; Herder, Christian; Thorand, Barbara; Grallert, Harald: Multi-omic signature of body weight change: results from a population-based cohort study. BMC Medicine 13, 2015 more…
  • Wang, L. ; Belagiannis, V. ; Marr, C. ; Theis, F. ; Guang-Zhong Yang ; Navab, N.: Anatomic-landmark detection using graphical context modelling. 12th International Symposium on Biomedical Imaging, New York, USA, April 16-19, 2015, 2015, 1304-1307 more…
  • Wilson, Nicola K.; Kent, David G.; Buettner, Florian; Shehata, Mona; Macaulay, Iain C.; Calero-Nieto, Fernando J.; Sánchez Castillo, Manuel; Oedekoven, Caroline A.; Diamanti, Evangelia; Schulte, Reiner; Ponting, Chris P.; Voet, Thierry; Caldas, Carlos; Stingl, John; Green, Anthony R.; Theis, Fabian J.; Göttgens, Berthold: Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell 16, 2015, 712-724 more…
  • Zissler, U M; Chaker, A M; Effner, R; Ulrich, M; Guerth, F; Piontek, G; Dietz, K; Regn, M; Knapp, B; Theis, F J; Heine, H; Suttner, K; Schmidt-Weber, C B: Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways. Mucosal Immunology 9 (4), 2015, 917-926 more…

2014

  • Bajikar, S. S.; Fuchs, C.; Roller, A.; Theis, F. J.; Janes, K. A.: Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proceedings of the National Academy of Sciences 111, 2014, E626-E635 more…
  • Baumann, S.; Rockstroh, M.; Bartel, J.; Krumsiek, J.; Otto, W.; Jungnickel, H.; Potratz, S.; Luch, A.; Willscher, E.; Theis, F.; von Bergen, M.; Tomm, J.: Subtoxic concentrations of benzo[a]pyrene induce metabolic changes and oxidative stress in non-activated and affect the mTOR pathway in activated Jurkat T cells. Journal of Integrated OMICS 4 (1), 2014, 11-20 more…
  • Buettner, F.; Moignard, V.; Gottgens, B.; Theis, F. J.: Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. Bioinformatics 30 (13), 2014, 1867-1875 more…
  • Do, Kieu Trinh; Kastenmüller, Gabi; Mook-Kanamori, Dennis O.; Yousri, Noha A.; Theis, Fabian J.; Suhre, Karsten; Krumsiek, Jan: Network-Based Approach for Analyzing Intra- and Interfluid Metabolite Associations in Human Blood, Urine, and Saliva. J. Proteome Res., 2014, 141209141645008 more…
  • Feigelman, Justin; Theis, Fabian J; Marr, Carsten: MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data. BMC Bioinformatics 15, 2014, 240 more…
  • Fröhlich, Fabian; Hross, Sabrina; Theis, Fabian J.; Hasenauer, Jan: Radial Basis Function Approximations of Bayesian Parameter Posterior Densities for Uncertainty Analysis. 2014, 10.1007/978-3-319-12982-2_6(other entry) more…
  • Fröhlich, Fabian; Theis, Fabian J.; Hasenauer, Jan: Uncertainty Analysis for Non-identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and More. 2014, 10.1007/978-3-319-12982-2_5(other entry) more…
  • Hasenauer, Jan; Hasenauer, Christine; Hucho, Tim; Theis, Fabian J.: ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics. PLoS Computational Biology 10, 2014, e1003686 more…
  • Illner, K.; Fuchs, C.; Theis, F. J.: Single-cell analysis: Biology at high resolution. Separation - Science & Applications (34), 2014, 24-26 more…
  • Illner, K.; Fuchs, C.; Theis, F. J.: Einzelzellanalysen: Biologie in Hochauflösung. GIT Labor-Fachzeitschrift (9), 2014, 28-30 more…
  • Illner, K.; Fuchs, C.; Theis, F. J.: Bayesian blind source separation applied to the lymphocyte pathway. Proceedings, 201421st International Conference on Computational Statistics (COMPSTAT2014), 625-632 more…
  • Illner, Katrin; Fuchs, Christiane; Theis, Fabian J.: Bayesian Blind Source Separation for Data with Network Structure. Journal of Computational Biology 21 (11), 2014, 855-865 more…
  • Kazeroonian, A.; Theis, F. J.; Hasenauer, J.: Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation. 19th World Congress of the International Federation of Automatic Control, 2014 more…
  • Khakhutskyy, Valeriy; Schwarzfischer, Michael; Hubig, Nina; Plant, Claudia; Marr, Carsten; Rieger, Michael A.; Schroeder, Timm; Theis, Fabian J.: Centroid Clustering of Cellular Lineage Trees. 2014, 10.1007/978-3-319-10265-8_2(other entry) more…
  • Matthes, M.; Preusse, M.; Zhang, J.; Schechter, J.; Mayer, D.; Lentes, B.; Theis, F.; Prakash, N.; Wurst, W.; Trumbach, D.: Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. Database 2014, 2014, bau083-bau083 more…
  • Meyer, Swanhild U.; Stoecker, Katharina; Sass, Steffen; Theis, Fabian J.; Pfaffl, Michael W.: Posttranscriptional Regulatory Networks: From Expression Profiling to Integrative Analysis of mRNA and MicroRNA Data. 2014, 10.1007/978-1-4939-0733-5_15(other entry) more…
  • Quaranta, M.; Knapp, B.; Garzorz, N.; Mattii, M.; Pullabhatla, V.; Pennino, D.; Andres, C.; Traidl-Hoffmann, C.; Cavani, A.; Theis, F. J.; Ring, J.; Schmidt-Weber, C. B.; Eyerich, S.; Eyerich, K.: Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema. Science Translational Medicine (244), 2014, 244ra90-244ra90 more…
  • Quaranta, Maria; Eyerich, Stefanie; Knapp, Bettina; Nasorri, Francesca; Scarponi, Claudia; Mattii, Martina; Garzorz, Natalie; Harlfinger, Anna T.; Jaeger, Teresa; Grosber, Martine; Pennino, Davide; Mempel, Martin; Schnopp, Christina; Theis, Fabian J.; Albanesi, Cristina; Cavani, Andrea; Schmidt-Weber, Carsten B.; Ring, Johannes; Eyerich, Kilian: Allergic Contact Dermatitis in Psoriasis Patients: Typical, Delayed, and Non-Interacting. PLoS ONE, 2014, e101814 more…
  • Ried, J. S.; Shin, S.-Y.; Krumsiek, J.; Illig, T.; Theis, F. J.; Spector, T. D.; Adamski, J.; Wichmann, H.- E.; Strauch, K.; Soranzo, N.; Suhre, K.; Gieger, C.: Novel genetic associations with serum level metabolites identified by phenotype set enrichment analyses. Human Molecular Genetics 23 (21), 2014, 5847-5857 more…
  • Röck, Katharina; Tigges, Julia; Sass, Steffen; Schütze, Alexandra; Florea, Ana-Maria; Fender, Anke C; Theis, Florian J; Krutmann, Jean; Boege, Fritz; Fritsche, Ellen; Reifenberger, Guido; Fischer, Jens W: miR-23a-3p Causes Cellular Senescence by Targeting Hyaluronan Synthase 2: Possible Implication for Skin Aging. J Investig Dermatol 135, 2014, 369-377 more…
  • Sass, S.; Buettner, F.; Mueller, N. S.; Theis, F. J.: RAMONA: a Web application for gene set analysis on multilevel omics data. Bioinformatics 31, 2014, 128-130 more…
  • Shin, So-Youn; Fauman, Eric B; Petersen, Ann-Kristin; Krumsiek, Jan; Santos, Rita; Huang, Jie; Arnold, Matthias; Erte, Idil; Forgetta, Vincenzo; Yang, Tsun-Po; Walter, Klaudia; Menni, Cristina; Chen, Lu; Vasquez, Louella; Valdes, Ana M; Hyde, Craig L; Wang, Vicky; Ziemek, Daniel; Roberts, Phoebe; Xi, Li; Grundberg, Elin; Waldenberger, Melanie; Richards, J Brent; Mohney, Robert P; Milburn, Michael V; John, Sally L; Trimmer, Jeff; Theis, Fabian J; Overington, John P; Suhre, Karsten; Brosnan, M Julia; Gieger, Christian; Kastenmüller, Gabi; Spector, Tim D; Soranzo, Nicole: An atlas of genetic influences on human blood metabolites. Nat Genet 46, 2014, 543-550 more…
  • Thalheimer, Frederic B.; Wingert, Susanne; De Giacomo, Pangrazio; Haetscher, Nadine; Rehage, Maike; Brill, Boris; Theis, Fabian J.; Hennighausen, Lothar; Schroeder, Timm; Rieger, Michael A.: Cytokine-Regulated GADD45G Induces Differentiation and Lineage Selection in Hematopoietic Stem Cells. Stem Cell Reports, 2014, 34-43 more…
  • Vinnikov, I. A.; Hajdukiewicz, K.; Reymann, J.; Beneke, J.; Czajkowski, R.; Roth, L. C.; Novak, M.; Roller, A.; Dorner, N.; Starkuviene, V.; Theis, F. J.; Erfle, H.; Schutz, G.; Grinevich, V.; Konopka, W.: Hypothalamic miR-103 Protects from Hyperphagic Obesity in Mice. Journal of Neuroscience 34 (32), 2014, 10659-10674 more…
  • Waldera-Lupa, D. M.; Kalfalah, F.; Florea, A. M.; Sass, S.; Kruse, F. E.; Rieder, V.; Tigges, J.; Fritsche, E.; Krutmann, J.; Busch, H.; Boerries, M.; Meyer, H. E.; Boege, F.; Theis, F. J.; Reifenberger, G.; Stühler, K.: Proteome-wide analysis reveals an age-associated cellular phenotype of in situ aged human fibroblasts. Aging-US (6), 2014, 856-878 more…
  • Winkler, Christiane; Krumsiek, Jan; Buettner, Florian; Angermüller, Christof; Giannopoulou, Eleni Z.; Theis, Fabian J.; Ziegler, Anette-Gabriele; Bonifacio, Ezio: Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia 58, 2014, 206-206 more…
  • Winkler, Christiane; Krumsiek, Jan; Buettner, Florian; Angermüller, Christof; Giannopoulou, Eleni Z.; Theis, Fabian J.; Ziegler, Anette-Gabriele; Bonifacio, Ezio: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia 57 (12), 2014, 2521-2529 more…
  • Yang, D.; Lutter, D.; Burtscher, I.; Uetzmann, L.; Theis, F. J.; Lickert, H.: miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm. Development 141, 2014, 514-525 more…

2013

  • Albrecht, Eva; Waldenberger, Melanie; Krumsiek, Jan; Evans, Anne M.; Jeratsch, Ulli; Breier, Michaela; Adamski, Jerzy; Koenig, Wolfgang; Zeilinger, Sonja; Fuchs, Christiane; Klopp, Norman; Theis, Fabian J.; Wichmann, H.-Erich; Suhre, Karsten; Illig, Thomas; Strauch, Konstantin; Peters, Annette; Gieger, Christian; Kastenmüller, Gabi; Doering, Angela; Meisinger, Christa: Metabolite profiling reveals new insights into the regulation of serum urate in humans. Metabolomics 10, 2013, 141-151 more…
  • Altmaier, E.; Emeny, R. T.; Krumsiek, J.; Lacruz, M. E.; Lukaschek, K.; Häfner, S.; Kastenmüller, G.; Römisch-Margl, W.; Prehn, C.; Mohney, R. P.; Evans, A. M.; Milburn, M. V.; Illig, T.; Adamski, J.; Theis, F. J.; Suhre, K.; Ladwig, K. H.: Metabolomic profiles in individuals with negative affectivity and social inhibition: A population-based study of Type D personality. Psychoneuroendocrinology 38 (8), 2013, 1299-1309 more…
  • Andres, C.; Hasenauer, J.; Ahn, H. S.; Joseph, E. K.; Isensee, J.; Theis, F. J.; Allgöwer, F.; Levine, J. D.; Dib-Hajj, S. D.; Waxman, S. G.; Hucho, T.: Wound-healing growth factor, basic FGF, induces Erk1/2-dependent mechanical hyperalgesia. Pain 154 (10), 2013, 2216-2226 more…
  • Bardehle, S.; Krüger, M.; Buggenthin, F.; Schwausch, J.; Ninkovic, J.; Clevers, H.; Snippert, H. J.; Theis, F. J.; Meyer-Luehmann, M.; Bechmann, I.; Dimou, L.; Götz, M.: Live imaging of astrocyte responses to acute injury reveals selective juxtavascular proliferation. Nat. Neurosci. 16 (5), 2013, 580-586 more…
  • Bartel, J.; Krumsiek, J.; Theis, F. J.: Statistical methods for the analysis of high-throughput metabolomics data. Comp. Struc. Biotech. J. 4 (5), 2013 more…
  • Bonifacio, E.; Krumsiek, J.; Winkler, C.; Theis, F. J.; Ziegler, A. G.: A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion. Acta Diabetol., 2013, 10.1007/s00592-013-0526-2 more…
  • Buggenthin, F.; Marr, C.; Schwarzfischer, M.; Hoppe, P. S.; Hilsenbeck, O.; Schroeder, T.; Theis, F. J.: An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics 14 (1), 2013 more…
  • Hasenauer, J.; Wolf, V.; Kazeroonian, A.; Theis, F. J.: Method of conditional moments (MCM) for the Chemical Master Equation. Journal of Mathematical Biology 69, 2013, 687-735 more…
  • Hock, S.; Hasenauer, J.; Theis, F. J.: Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis. , Biomed Central, 2013 more…
  • Hock, S.; Ng, Y. K.; Hasenauer, J.; Wittmann, D. M.; Lutter, D.; Trümbach, D.; Wurst, W.; Prakash, N.; Theis, F. J.: Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation. BMC Syst. Biol. 7, 2013 more…
  • Hug, S.; Raue, A.; Hasenauer, J.; Bachmann, J.; Klingmüller, U.; Timmer, J.; Theis, F. J.: High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling. Math. Biosci. 246 (2), 2013, 293-304 more…
  • Kazeroonian, A.; Hasenauer, J.; Theis, F.: Parameter estimation for stochastic biochemical processes: A comparison of moment equation and fintie state projection. , Tampere International Center for Signal Processing, 2013 more…
  • Köttgen, A.; Albrecht, E.; Teumer, A.; Vitart, V.; Krumsiek, J.; Hundertmark, C.; Pistis, G.; Ruggiero, D.; O'Seaghdha, C. M.; Haller, T.; Yang, Q.; Tanaka, T.; Johnson, A. D.; Kutalik, Z.; Smith, A. V.; Shi, J.; Struchalin, M.; Middelberg, R. P.; Brown, M. J.; Gaffo, A. L.; Pirastu, N.; Li, G.; Hayward, C.; Zemunik, T.; Huffman, J.; Yengo, L.; Zhao, J. H.; Demirkan, A.; Feitosa, M. F.; Liu, X.; Malerba, G.; Lopez, L. M.; van der Harst, P.; Li, X.; Kleber, M. E.; Hicks, A. A.; Nolte, I. M.; Johansson, A.; Murgia, F.; Wild, S. H.; Bakker, S. J.; Peden, J. F.; Dehghan, A.; Steri, M.; Tenesa, A.; Lagou, V.; Salo, P.; Mangino, M.; Rose, L. M.; Lehtimäki, T. et al.: Genome-wide association analyses identify 18 new loci associated with serum urate concentrations. Nat. Genet. 45 (2), 2013, 145-154 more…
  • Moignard, V.; Macaulay, I. C.; Swiers, G.; Buettner, F.; Schütte, J.; Calero-Nieto, F. J.; Kinston, S.; Joshi, A.; Hannah, R.; Theis, F. J.; Jacobsen, S. E.; de Bruijn, M. F.; Gottgens, B.: Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat. Cell Biol. 15 (4), 2013, 363-372 more…
  • Raue, A.; Kreutz, C.; Theis, F. J.; Timmer, J.: Joining forces of Bayesian and frequentist methodology: A study for inference in the presence of non-identiability. Philos. Transact. R. Soc. A - Math. Phys. Eng. Sci. 371 (1984), 2013 more…
  • Raue, A.; Schilling, M.; Bachmann, J.; Matteson, A.; Schelke, M.; Kaschek, D.; Hug, S.; Kreutz, C.; Harms, B. D.; Theis, F. J.; Klingmüller, U.; Timmer, J.: Lessons learned from quantitative dynamical modeling in systems biology. PLoS One 8 (9), 2013 more…
  • Rickert, D.; Fricker, N.; Lavrik, I. N.; Theis, F. J.: Systematic complexity reduction of signaling models and application to a CD95 signaling model for apoptosis. In: Lavrik, I. N. (Ed.): Springer, 2013, 57-84 more…
  • Ried, J. S.; Baurecht, H.; Stückler, F.; Krumsiek, J.; Gieger, C.; Heinrich, J.; Kabesch, M.; Prehn, C.; Peters, A.; Rodriguez, E.; Schulz, H.; Strauch, K.; Suhre, K.; Wang-Sattler, R.; Wichmann, H. E.; Theis, F. J.; Illig, T.; Adamski, J.; Weidinger, S.: Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma. Allergy 68 (5), 2013, 629-636 more…
  • Rinck, A.; Preusse, M.; Laggerbauer, B.; Lickert, H.; Engelhardt, S.; Theis, F. J.: The human transcriptome is enriched for miRNA-binding sites located in cooperativity-permitting distance. RNA Biol. 10 (7), 2013, 1125-1135 more…
  • Sass, S.; Büttner, F.; Müller, N. S.; Theis, F. J.: A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res. 41 (21), 2013, 9622-9633 more…
  • Schmidl, D.; Czado, C.; Hug, S.; Theis, F. J.: Rejoinder on 'A vine-copula based adaptive MCMC sampler for efficient inference of dynamical systems&quot. Bayesian Anal. 8 (1), 2013, 33-42 more…
  • Schmidl, D.; Czado, C.; Hug, S.; Theis, F. J.: A vine-copula based adaptive MCMC sampler for efficient inference of dynamical systems. Bayesian Anal. 8 (1), 2013, 1-22 more…
  • Vehlow, C.; Hasenauer, J.; Theis, F. J.; Weiskopf, D.: Visualizing edge-edge relations in graphs. , 2013, 201-208 more…
  • Wittmann, D. M.; Hock, S.; Theis, F. J.: Truth-content and phase transitions of random boolean networks with generic logics. SIAM J. Appl. Dyn. Syst. 12 (1), 2013, 315-351 more…
  • Xu, T.; Holzapfel, C.; Dong, X.; Bader, E.; Yu, Z.; Prehn, C.; Perstorfer, K.; Jaremek, M.; Römisch-Margl, W.; Rathmann, W.; Li, Y.; Wichmann, H. E.; Wallaschofski, H.; Ladwig, K. H.; Theis, F. J.; Suhre, K.; Adamski, J.; Illig, T.; Peters, A.; Wang-Sattler, R.: Effects of smoking and smoking cessation on human serum metabolite profile: Results from the KORA cohort study. BMC Med. 11 (1), 2013 more…

2012

  • Burtscher, I.; Barkey, W.; Schwarzfischer, M.; Theis, F. J.; Lickert, H.: The Sox17-mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development. Genesis 50 (6), 2012, 496-505 more…
  • Büttner, F.; Theis, F. J.: A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics 28 (18), 2012, i626-i632 more…
  • Chursov, A.; Kopetzky, S. J.; Leshchiner, I.; Kondofersky, I.; Theis, F. J.; Frishman, D.; Shneider, A.: Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus. RNA Biol. 9 (10), 2012, 1266-1274 more…
  • Cichocki, A.; Theis, F. J.; Yeredor, A.; Zibulevsky, M.: Preface. Lecture Notes Comp. Sci. 7191, 2012, V-VII more…
  • Grady, D.; Brune, R.; Thiemann, C.; Theis, F. J.; Brockmann, D.: Modularity maximization and tree clustering: Novel ways to determine effective geographic borders. In: Thai, M. T.; Pardalos, P. M. (Ed.): Springer, 2012, 169-208 more…
  • Gutch, H. W.; Gruber, P.; Yeredor, A.; Theis, F. J.: ICA over finite fields - separability and algorithms. Signal Process. 92 (8), 2012, 1796-1808 more…
  • Gutch, H. W.; Theis, F. J.: Uniqueness of linear factorizations into independent subspaces. J. Multivar. Anal. 112, 2012, 48-62 more…
  • Gutch, H. W.; Theis, F. J.: To infinity and beyond: On ICA over Hilbert Spaces. , Springer, 2012 more…
  • Hug, S.; Theis, F. J.: Bayesian inference of latent causes in gene regulatory dynamics. , Springer, 2012 more…
  • Illner, K.; Fuchs, C.; Theis, F. J.: Blind source separation using latent gaussian graphical models. , Tampere International Center for Signal Processing, 2012 more…
  • Jourdan, C.; Petersen, A. K.; Gieger, C.; Döring, A.; Illig, T.; Wang-Sattler, R.; Meisinger, C.; Peters, A.; Adamski, J.; Prehn, C.; Suhre, K.; Altmaier, E.; Kastenmüller, G.; Römisch-Margl, W.; Theis, F. J.; Krumsiek, J.; Wichmann, H. E.; Linseisen, J.: Body fat free mass is associated with the serum metabolite profile in a population-based study. PLoS One 7 (6), 2012 more…
  • Konrad, M.; Vyleta, M. L.; Theis, F. J.; Stock, M.; Tragust, S.; Klatt, M.; Drescher, V.; Marr, C.; Ugelvig, L. V.; Cremer, S.: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. PLoS Biol. 10 (4), 2012 more…
  • Krug, S.; Kastenmüller, G.; Stückler, F.; Rist, M. J.; Skurk, T.; Sailer, M.; Raffler, J.; Römisch-Margl, W.; Adamski, J.; Prehn, C.; Frank, T.; Engel, K. H.; Hofmann, T.; Luy, B.; Zimmermann, R.; Moritz, F.; Schmitt-Kopplin, P.; Krumsiek, J.; Kremer, W.; Huber, F.; Oeh, U.; Theis, F. J.; Szymczak, W.; Hauner, H.; Suhre, K.; Daniel, H.: The dynamic range of the human metabolome revealed by challenges. Faseb J. 26 (6), 2012, 2607-2619 more…
  • Krumsiek, J.; Stückler, F.; Kastenmüller, G.; Theis, F. J.: Systems biology meets metabolism. In: Suhre, K. (Ed.): Springer, 2012, 281-313 more…
  • Krumsiek, J.; Suhre, K.; Evans, A. M.; Mitchell, M. W.; Mohney, R. P.; Milburn, M. V.; Wägele, B.; Römisch-Margl, W.; Illig, T.; Adamski, J.; Gieger, C.; Theis, F. J.; Kastenmüller, G.: Mining the unknown: A systems approach to metabolite identification combining genetic and metabolic information. PLoS Genet. 8 (10), 2012 more…
  • Krumsiek, J.; Suhre, K.; Illig, T.; Adamski, J.; Theis, F. J.: Bayesian independent component analysis recovers pathway signatures from blood metabolomics data. J. Proteome Res. 11 (8), 2012, 4120-4131 more…
  • Lutter, D.; Bruns, P.; Theis, F. J.: An ensemble approach for inferring semi-quantitative regulatory dynamics for the differentiation of mouse embryonic stem cells using prior knowledge. In: Goryanin, I. I.; Goryachev, A. B. (Ed.): Springer, 2012, 247-260 more…
  • Marr, C.; Strasser, M.; Schwarzfischer, M.; Schroeder, T.; Theis, F. J.: Multi-scale modeling of GMP differentiation based on single-cell genealogies. FEBS J. 279 (18), 2012, 3488-3500 more…
  • Meyer-Bäse, A.; Cappendijk, S.; Theis, F. J.: Uncertain gene regulatory networks simplified by gramian-based approach. , CSREA Press, 2012 more…
  • Nordhausen, K.; Gutch, H. W.; Oja, H.; Theis, F. J.: Joint diagonalization of several scatter matrices for ICA. , Springer, 2012 more…
  • Peng, C.; Li, N.; Ng, Y. K.; Zhang, J.; Meier, F.; Theis, F. J.; Merkenschlager, M.; Chen, W.; Wurst, W.; Prakash, N.: A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation. J. Neurosci. 32 (38), 2012, 13292-13308 more…
  • Petersen, A. K.; Krumsiek, J.; Wägele, B.; Theis, F. J.; Wichmann, H. E.; Gieger, C.; Suhre, K.: On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. BMC Bioinformatics 13, 2012 more…
  • Plant, C. C.; Mai Thai, S.; Shao, J.; Theis, F. J.; Meyer-Bäse, A.; Böhm, C.: Measuring non-Gaussianity by phi-transformed and fuzzy histograms. Advances in Artificial Neural Systems 2012, 2012 more…
  • Pérez-Velázquez, J.; Schlicht, R.; Dulla, G.; Hense, B.A.; Kuttler, C.; Lindow, S.E.: Stochastic modeling of Pseudomonas syringae growth in the phyllosphere. Mathematical Biosciences 239 (1), 2012, 106-116 more…
  • Ruepp, A.; Kowarsch, A.; Theis, F. J.: PhenomiR: MicroRNAs in human diseases and biological processes. Methods Mol. Biol. 822, 2012, 249-260 more…
  • Schmidl, D.; Hug, S.; Li, W. B.; Greiter, M. B.; Theis, F. J.: Bayesian model selection validates a biokinetic model for zirconium processing in humans. BMC Syst. Biol. 6, 2012 more…
  • Sterz, K.; Scherer, G.; Krumsiek, J.; Theis, F. J.; Ecker, J.: Identification and quantification of 1-hydroxybutene-2-yl mercapturic acid in human urine by UPLC- HILIC-MS/MS as a novel biomarker for 1,3-butadiene exposure. Chem. Res. Toxicol. 25 (8), 2012, 1565-1567 more…
  • Strasser, M.; Theis, F. J.; Marr, C.: Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression. Biophys. J. 102 (1), 2012, 19-29 more…
  • Theis, F. J.: Bayesian fuzzy clustering of colored graphs. , Springer, 2012 more…
  • Winkler, C.; Krumsiek, J.; Lempainen, J.; Achenbach, P.; Grallert, H.; Giannopoulou, E.; Bunk, M.; Theis, F. J.; Bonifacio, E.; Ziegler, A. G.: A strategy for combining minor genetic susceptibility genes to improve prediction of disease in type 1 diabetes. Genes Immun. 13 (7), 2012, 549-555 more…

2011

  • Baskaran, T.; Blöchl, F.; Brück, T.; Theis, F. J.: The Heckscher-Ohlin model and the network structure of international trade. Int. Rev. Econom. Finance 20 (2), 2011, 135-145 more…
  • Blöchl, F.; Rascle, A.; Kastner, J.; Witzgall, R.; Lang, E. W.; Theis, F. J.: Are we to integrate previous information into microarray analyses? Interpretation of a Lmx1b-knockout experiment. In: Gorriz, J. M.; Lang, E. W.; Ramirez, J. (Ed.): Bentham Science Publishers, 2011, 157-170 more…
  • Blöchl, F.; Theis, F. J.; Vega-Redondo, F.; Fisher, E.: Vertex centralities in input-output networks reveal the structure of modern economies. Phys. Rev. E 83 (4), 2011 more…
  • Blöchl, F.; Wittmann, D. M.; Theis, F. J.: Effective parameters determining the information flow in hierarchical biological systems. Bull. Math. Biol. 73 (4), 2011, 706-725 more…
  • Breindl, C.; Waldherr, S.; Wittmann, D. M.; Theis, F. J.; Allgoewer, F.: Steady-state robustness of qualitative gene regulation networks. Int. J. Robust Nonlin. 21 (15), 2011, 1742-1758 more…
  • Gutch, H. W.; Krumsiek, J.; Theis, F. J.: An ISA algorithm with unknown group sizes successfully identifies biologically meaningful clusters in metabolomics data. , EUSIPCO, 2011 more…
  • Hattersley, J.G.; Pérez-Velázquez, J.; Chappell, M.J.; Bearup, D.; Roper, D.; Dowson, C.; Bugg, T.; Evans, N.D.: Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis. Computer Methods and Programs in Biomedicine 104 (2), 2011, 70-80 more…
  • Hennig, H.; Fleischmann, R.; Fredebohm, A.; Hagmayer, Y.; Nagler, J.; Witt, A.; Theis, F. J.; Geisel, T.: The nature and perception of fluctuations in human musical rhythms. PLoS ONE 6 (10), 2011 more…
  • Kowarsch, A.; Preusse, M.; Marr, C.; Theis, F. J.: miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA 17 (5), 2011, 809-819 more…
  • Krumsiek, J.; Marr, C.; Schroeder, T.; Theis, F. J.: Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network. PLoS One 6 (8), 2011 more…
  • Krumsiek, J.; Suhre, K.; Illig, T.; Adamski, J.; Theis, F. J.: Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst. Biol. 5 (1), 2011 more…
  • Krumsiek, J.; Wittmann, D. M.; Theis, F. J.: From discrete to continuous gene regulation models - a tutorial using the odefy toolbox. In: Michalowski, T. (Ed.): InTech, 2011, 35-60 more…
  • Laaser, I.; Theis, F. J.; Hrabé de Angelis, M.; Kolb, H. J.; Adamski, J.: Huge splicing frequency in human Y chromosomal UTY gene. OMICS 15 (3), 2011, 141-154 more…
  • Lang, E. W.; Schachtner, R.; Lutter, D.; Herold, D.; Kodewitz, A.; Blöchl, F.; Theis, F. J.; Keck, I. R.; Górriz Sáez, J. M.; Gómez Vilda, P.; Tomé, A. M.: Exploratory matrix factorization techniques for large scale biomedical data sets. In: Górriz, J. M.; Lang, E. W.; Ramirez, J. (Ed.): Bentham Science Publishers, 2011, 26-47 more…
  • Meyer-Bäse, A.; Plant, C.; Krumsiek, J.; Theis, F. J.; Emmett, M.; Conrad, C. A.: Stability analysis of hybrid stochastic gene regulatory networks. , Elsevier, 2011 more…
  • Mittelstrass, K.; Ried, J. S.; Yu, Z.; Krumsiek, J.; Gieger, C.; Prehn, C.; Roemisch-Margl, W.; Polonikov, A.; Peters, A.; Theis, F. J.; Meitinger, T.; Kronenberg, F.; Weidinger, S.; Wichmann, H. E.; Suhre, K.; Wang-Sattler, R.; Adamski, J.; Illig, T.: Discovery of sexual dimorphisms in metabolic and genetic biomarkers. PLoS Genet. 7 (8), 2011 more…
  • Müller, N.; Krumsiek, J.; Theis, F. J.; Böhm, C.; Meyer-Bäse, A.: Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells. , SPIE, 2011 more…
  • Raia, V.; Schilling, M.; Böhm, M.; Hahn, B.; Kowarsch, A.; Raue, A.; Sticht, C.; Bohl, S.; Saile, M.; Möller, P.; Gretz, N.; Timmer, J.; Theis, F. J.; Lehmann, W. D.; Lichter, P.; Klingmüller, U.: Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-Cell lymphoma allows prediction of therapeutic targets. Cancer Res. 71 (3), 2011, 693-704 more…
  • Sass, S.; Dietmann, S.; Burk, U. C.; Brabletz, S.; Lutter, D.; Kowarsch, A.; Mayer, K. F. X.; Brabletz, T.; Ruepp, A.; Theis, F. J.; Wang, Y.: MicroRNAs coordinately regulate protein complexes. BMC Syst. Biol. 5, 2011 more…
  • Schwarzfischer, M.; Marr, C.; Krumsiek, J.; Hoppe, P. S.; Schroeder, T.; Theis, F. J.: Efficient fluorescence image normalization for time lapse movies. , MIAAB, 2011 more…
  • Theis, F. J.; Bohl, S.; Klingmüller, U.: Theoretical analysis of time-to-peak responses in biological reaction networks. Bull. Math. Biol. 73, 2011, 978-1003 more…
  • Theis, F. J.; Kawanabe, M.; Müller, K. R.: Uniqueness of non-Gaussianity-based dimension reduction. IEEE Trans. Signal Process. 59 (9), 2011, 4478 - 4482 more…
  • Theis, F. J.; Latif, N.; Wong, P.; Frishman, D.: Complex principal component and correlation structure of 16 yeast genomic variables. Mol. Biol. Evol. 28 (9), 2011, 2501-2512 more…
  • Vincent, E.; Araki, S.; Theis, F. J.; Nolte, G.; Bofill, P.; Sawada, H.; Ozerov, A.; Gowreesunker, V.; Lutter, D.; Duong, N. Q. K.: The signal separation evaluation campaign (2007-2010): Achievements and remaining challenges. Signal Process. 92 (8), 2011, 1928-1936 more…
  • Wittmann, D. M.; Theis, F. J.: Dynamic regimes of random fuzzy logic networks. New J. Phys. 13, 2011 more…

2010

  • Ansorg, M.; Blöchl, F.; zu Castell, W.; Theis, F. J.; Wittmann, D. M.: Gene regulation at the Mid-Hindbrain Boundary: Study of a mathematical model in the stationary limit. Int. J. Biomath. Biostat. 1 (1), 2010, 9-21 more…
  • Araki, S.; Ozerov, A.; Gowreesunker, V.; Sawada, H.; Theis, F. J.; Nolte, G.; Lutter, D.; Duong, N. Q. K.: The 2010 signal separation evaluation campaign (SiSEC2010): Audio source separation. , Springer, 2010 more…
  • Araki, S.; Theis, F. J.; Nolte, G.; Lutter, D.; Ozerov, A.; Gowreesunker, V.; Sawada, H.; Duong, N. Q. K.: The 2010 signal separation evaluation campaign (SiSEC2010): Biomedical source separation. , Springer, 2010 more…
  • Blöchl, F.; Hartsperger, M. L.; Stümpflen, V.; Theis, F. J.: Uncovering the structure of heterogeneus biological data: Fuzzy graph partitioning in the k-partite setting. , Ges. f. Inform., 2010 more…
  • Blöchl, F.; Kowarsch, A.; Theis, F. J.: Second-order source separation based on prior knowledge realized in a graph model. , Springer, 2010 more…
  • Blöchl, F.; Theis, F. J.; Vega-Redondo, F.; Fisher, E. O'N: Which sectors of a modern economy are most central? , ifo Institut für Wirtschaftsforschung e.V., 2010 more…
  • Franke, R.; Theis, F. J.; Klamt, S.: From binary to multivalued to continuous models: The lac operon as a case study. J. Integr. Bioinform. 7 (1), 2010 more…
  • Gutch, H. W.; Gruber, P.; Theis, F. J.: ICA over finite fields. , Springer, 2010 more…
  • Gutch, H. W.; Maehara, T.; Theis, F. J.: Second order subspace analysis and simple decompositions. , Springer, 2010 more…
  • Hartsperger, M. L.; Blöchl, F.; Stümpflen, V.; Theis, F. J.: Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs. BMC Bioinformatics 11, 2010 more…
  • Konopka, W.; Kiryk, A.; Novak, M.; Herwerth, M.; Parkitna, J. R.; Wawrzyniak, M.; Kowarsch, A.; Michaluk, P.; Dzwonek, J.; Arnsperger, T.; Wilczynski, G.; Merkenschlager, M.; Theis, F. J.; Köhr, G.; Kaczmarek, L.; Schütz, G.: MicroRNA loss enhances learning and memory in mice. J. Neurosci. 30 (44), 2010, 14835-14842 more…
  • Kowarsch, A.; Blöchl, F.; Bohl, S.; Saile, M.; Gretz, N.; Klingmüller, U.; Theis, F. J.: Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation. BMC Bioinformatics 11, 2010 more…
  • Kowarsch, A.; Marr, C.; Schmidl, D.; Ruepp, A.; Theis, F. J.: Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways. PLoS ONE 5 (6), 2010 more…
  • Kreuzpointner, L.; Simon, P.; Theis, F. J.: The ad coefficient as a descriptive measure of the within-group agreement of ratings. Brit. J. Math. Stat. Psychol. 63 (2), 2010, 341-360 more…
  • Krumsiek, J.; Pölsterl, S.; Wittmann, D. M.; Theis, F. J.: Odefy - from discrete to continuous models. BMC Bioinformatics 11, 2010, 1-10 more…
  • Lutter, D.; Marr, C.; Krumsiek, J.; Lang, E. W.; Theis, F. J.: Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects. BMC Genomics 11, 2010 more…
  • Marr, C.; Theis, F. J.; Liebovitch, L. S.; Hütt, M. T.: Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. PLoS Comput. Biol. 6 (7), 2010 more…
  • Mewes, H. W.; Ruepp, A.; Theis, F. J.; Rattei, T.; Walter, M. C.; Frishman, D.; Suhre, K.; Spannagl, M.; Mayer, K. F. X.; Stümpflen, V.; Antonov, A.: MIPS: Curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39, 2010, D220-D224 more…
  • Meyer-Bäse, A.; Plant, C.; Cappendijk, S.; Theis, F. J.: Robust stability analysis of multi-time scale genetic regulatory networks under parametric uncertainties. , CSREA Press, 2010 more…
  • Meyer-Bäse, A.; Theis, F. J.; Emmett, M. R.: Robust stability analysis and design under consideration of multiple feedback loops of the tryptophan regulatory network of Escherichia coli. Adv. Exp. Med. Biol. 680, 2010, 189-197 more…
  • Plant, C.; Theis, F. J.; Meyer-Bäse, A.; Böhm, C.: Information-theoretic model selection for independent components. , Springer, 2010 more…
  • Ruepp, A.; Kowarsch, A.; Schmidl, D.; Buggenthin, F.; Brauner, B.; Dunger, I.; Fobo, G.; Frishman, G.; Montrone, C.; Theis, F. J.: PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 11 (1), 2010 more…
  • Theis, F. J.: Colored subspace analysis: Dimension reduction based on a signal's autocorrelation structure. IEEE Trans. Circuits Syst. I-Regul. Pap. 57 (7), 2010, 1463-1474 more…
  • Theis, F. J.; Meyer- Bäse, A.: Biomedical signal analysis: Contemporary methods and applications. MIT Press, 2010 more…
  • Theis, F. J.; Meyer-Bäse, A.: Foundations of medical imaging and signal recording. In: MIT Press, 2010, 1-28 more…
  • Theis, F. J.; Müller, N. S.; Plant, C.; Böhm, C.: Robust second-order source separation identifies experimental responses in biomedical imaging. , Springer, 2010 more…
  • Thiemann, C.; Theis, F. J.; Grady, D.; Brune, R.; Brockmann, D.: The structure of borders in a small world. PLoS ONE 5 (11), 2010 more…
  • Wittmann, D. M.; Marr, C.; Theis, F. J.: Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks. J. Theor. Biol. 266 (3), 2010, 436-448 more…

2009

  • Blöchl, F.; Theis, F. J.: Estimating hidden influences in metabolic and gene regulatory networks. In: Adali, T.; al., et (Ed.): Springer, 2009, 387-394 more…
  • Georgiev, P. G.; Theis, F. J.: Optimization techniques for data representions with biomedical applications. In: Romejin, H. E.; Pardalos, P. M. (Ed.): Springer, 2009, 1-38 more…
  • Gruber, P.; Gutch, H. W.; Theis, F. J.: Hierarchical extraction of independent subspaces of unknown dimensions. In: Adali, T.; al., et (Ed.): Springer, 2009, 259-266 more…
  • Gruber, P.; Meyer-Bäse, A.; Foo, S.; Theis, F. J.: ICA, kernel methods and nonnegativity: New paradigms for dynamical component analysis of fMRI data. Eng. Appl. Artif. Intel. 22 (4-5), 2009, 497-504 more…
  • King, John; Pérez-Velázquez, Judith; Byrne, H.M.: Singular travelling waves in a model for tumour encapsulation. Discrete and Continuous Dynamical Systems 25 (1), 2009, 195-230 more…
  • Klamt, S.; Haus, U. U.; Theis, F. J.: Hypergraphs and cellular networks. PLoS Comput. Biol. 5 (5), 2009 more…
  • Neher, R. A.; Mitkovski, M.; Kirchhoff, F.; Neher, E.; Theis, F. J.; Zeug, A.: Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophys. J. 96 (9), 2009, 3791-3800 more…
  • Pérez-Velázquez, J.; Hattersley, J.G.; Chappell, M.J.; Bearup, D.; Roper, D.; Dowson, C.; Bugg, T.; Evans, N.D.: Indistinguishability and identifiability of kinetic models for the Mur C reaction in peptidoglycan biosynthesis* *EPSRC funded project Indistinguishability analysis for model discrimination in Systems Biology: A Feasibility Study applied to Bacterial Peptidoglycan Biosynthesis (EP/E057535/1). IFAC Proceedings Volumes 42 (12), 2009, 103-108 more…
  • Sánchez-Garduño, Faustino; Maini, Philip K.; Pérez-Velázquez, Judith: A non-linear degenerate equation for direct aggregation and traveling wave dynamics. DCDS-B 13 (2), 2009, 455-487 more…
  • Theis, F. J.; Cason, T. P.; Absil, P. A.: Soft dimension reduction for ICA by joint diagonalization on the Stiefel manifold. In: Adali, T.; al., et (Ed.): Springer, 2009, 354-361 more…
  • Theis, F. J.; Neher, R.; Zeug, A.: Blind decomposition of spectral imaging microscopy: A study on artificial and real test data. In: Adali, T.; al., et (Ed.): Springer, 2009, 548-556 more…
  • Webb, K. J.; Norton, W. H. J.; Trümbach, D.; Meijer, A. H.; Ninkovic, J.; Topp, S.; Heck, D.; Marr, C.; Wurst, W.; Theis, F. J.; Spaink, H. P.; Bally-Cuif, L.: Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol. 10 (7), 2009 more…
  • Wittmann, D. M.; Blöchl, F.; Trümbach, D.; Wurst, W.; Prakash, N.; Theis, F. J.: Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary. PLoS Comput. Biol. 5 (11), 2009 more…
  • Wittmann, D. M.; Krumsiek, J.; Saez-Rodriguez, J.; Lauffenburg, D. A.; Klam, S.; Theis, F. J.: Transforming Boolean models to continuous models: Methodology and application to T-cell receptor signaling. BMC Syst. Biol. 3, 2009 more…
  • Wittmann, D. M.; Schmidl, D.; Blöchl, F.; Theis, F. J.: Reconstruction of graphs based on random walks. Theor. Comput. Sci. 410 (38-40), 2009, 3826-3838 more…

2008

  • Brockmann, D.; Theis, F. J.: Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns. IEEE Pervasive Comput. 7 (4), 2008, 28-35 more…
  • Pérez-Velázquez, J.; Evans, N.D.; Chappell, M.J.; Errington, R.J.; Smith, P.J.; Khan, I.: A Mathematical Model of Cyclin B1 Dynamics at the Single Cell Level in Osteosarcoma Cells. IFAC Proceedings Volumes 41 (2), 2008, 9057-9062 more…
  • Schachtner, R.; Lutter, D.; Knollmüller, P.; Tomé, A. M.; Theis, F. J.; Schmitz, G.; Stetter, M.; Vilda, P. G.; Lang, E. W.: Knowledge-based gene expression classification via matrix factorization. Bioinformatics 24 (15), 2008, 1688-1697 more…
  • Wong, P.; Althammer, S.; Hildebrand, A.; Kirschner, A.; Pagel, P.; Geissler, B.; Smialowski, P.; Blöchl, F.; Oesterheld, M.; Schmidt, T.; Strack, N.; Theis, F. J.; Ruepp, A.; Frishman, D.: An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics 9, 2008 more…