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Technische Universität München
Technische Universität München


Prof. Dr. Fabian Theis

Technische Universität München

Lehrstuhl für Mathematische Modellierung biologischer Systeme (Prof. Theis)

Postadresse

Postal:
Boltzmannstr. 3
85748 Garching b. München

© Matthias Tunger Photodesign

Curriculum Vitae

Fabian Theis is Director of Helmholtz Munich Computational Health Center and Scientific Director of the Helmholtz Artificial Intelligence Cooperation Unit (HelmholtzAI) which was launched in 2019. He is a Full Professor at the Technical University of Munich, holding the chair ‘Mathematical Modelling of Biological Systems’, Associate Faculty at the Welcome Trust Sanger Institute, and Adjunct Faculty at the Northwestern University, Department of Medicine.

During his academic career, Fabian Theis obtained MSc degrees in Mathematics and Physics at the University of Regensburg in 2000. He received a Ph.D. degree in Physics from the same university in 2002 and a Ph.D. in Computer Science from the University of Granada in 2003. He worked as visiting researcher at the Department of Architecture and Computer Technology (University of Granada, Spain), at the RIKEN Brain Science Institute (Wako, Japan), at FAMU-FSU (Florida State University, USA), and TUAT’s Laboratory for Signal and Image Processing (Tokyo, Japan), and headed the ‘signal processing & information theory’ group at the Institute of Biophysics (Regensburg, Germany). In 2006, he started working as a Bernstein fellow leading a junior research group at the Bernstein Center for Computational Neuroscience, located at the Max Planck Institute for Dynamics and Self-Organisation at Göttingen. In the summer of 2007, Fabian Theis became working group head of CMB at the Institute of Bioinformatics at the Helmholtz Center Munich. In the spring of 2009, he became an associate Professor for Mathematics in Systems Biology at the Math Department of the TU Munich. 2009-2014 he was a member of the ‘Young Academy’ (founded by the Berlin-Brandenburg Academy of Sciences and Humanities and the German Academy of Natural Scientists Leopoldina) and was awarded an ERC starting grant in 2010. 

In 2017 he was awarded the Erwin Schrödinger prize together within an interdisciplinary team at ETH Zürich. In 2021, Fabian Theis was honored with the Hamburg Science Award, the most highly endowed prize of a science academy in Germany. Fabian Theis is part of and also coordinates various consortia (i.e. sparse2big involving 8 Helmholtz Centers) and founded the network SingleCellOmics Germany (SCOG). Furthermore, he coordinates 2019 launched Munich School for Data Science (MUDS) and is co-directing the ELLIS Munich Unit, the local hub of the European Machine Learning network ELLIS. Since 2020, he has been co-chair of the Bavarian AI Council of the Bavarian Ministry for Science and Art and supports the TUM with his expertise as a start-up Ambassador and as a core member of the Munich Data Science Institute (MDSI).
Professor Dr. Dr. Fabian Theis receives one of the prestigious Advanced Grants from the European Research Council (ERC) for his project "DeepCell".

Additionally, Fabian Theis was accepted for membership in the European Molecular Biology Organization (EMBO) in July 2022 and was appointed to the Board of Directors of Human Cell Atlas, Inc.

Fabian Theis received one of the prestigious Advanced Grants from the European Research Council (ERC) for his project "DeepCell" as well as the Gottfried Wilhelm Leibniz Prize 2023 – the most prestigious research award in Germany.

Publications

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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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Chlis, Nikolaos K.; Wolf, F. Alexander; Theis, Fabian J.: Model-based branching point detection in single-cell data by K-branches clustering. Bioinformatics, 2017 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )

2016

  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Fröhlich, Fabian; Theis, Fabian J.; Rädler, Joachim O.; Hasenauer, Jan: Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 2016, btw764 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Kondofersky, Ivan; Theis, Fabian J.; Fuchs, Christiane: Inferring catalysis in biological systems. IET Systems Biology 10 (6), 2016, 210-218 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Krumsiek, Jan; Bartel, Jörg; Theis, Fabian J: Computational approaches for systems metabolomics. Current Opinion in Biotechnology 39, 2016, 198-206 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Preusse, Martin; Theis, Fabian J.; Mueller, Nikola S.: miTALOS v2: Analyzing Tissue Specific microRNA Function. PLOS ONE 11, 2016, e0151771 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Sacher, A.; Theis. F. J.: Von lernfähigen Maschinen lernen. Laborjournal (7-8), 2016, 59-61 mehr… BibTeX
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )

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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Haghverdi, L.; Buettner, F.; Theis, F. J.: Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics, 2015 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 (anderer Eintrag) mehr… BibTeX Volltext ( DOI )
  • Kondofersky, Ivan; Fuchs, Christiane; Theis, Fabian J.: Identifying latent dynamic components in biological systems. IET Systems Biology, 2015 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )

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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 (anderer Eintrag) mehr… BibTeX Volltext ( DOI )
  • 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 (anderer Eintrag) mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • Illner, K.; Fuchs, C.; Theis, F. J.: Single-cell analysis: Biology at high resolution. Separation - Science & Applications (34), 2014, 24-26 mehr… BibTeX
  • Illner, K.; Fuchs, C.; Theis, F. J.: Einzelzellanalysen: Biologie in Hochauflösung. GIT Labor-Fachzeitschrift (9), 2014, 28-30 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX
  • 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 (anderer Eintrag) mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 (anderer Eintrag) mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX Volltext ( DOI )

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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Bartel, J.; Krumsiek, J.; Theis, F. J.: Statistical methods for the analysis of high-throughput metabolomics data. Comp. Struc. Biotech. J. 4 (5), 2013 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX Volltext ( DOI )
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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. (Hrsg.): Springer, 2013, 57-84 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Vehlow, C.; Hasenauer, J.; Theis, F. J.; Weiskopf, D.: Visualizing edge-edge relations in graphs. , 2013, 201-208 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX

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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Cichocki, A.; Theis, F. J.; Yeredor, A.; Zibulevsky, M.: Preface. Lecture Notes Comp. Sci. 7191, 2012, V-VII mehr… BibTeX
  • 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. (Hrsg.): Springer, 2012, 169-208 mehr… BibTeX
  • Gutch, H. W.; Gruber, P.; Yeredor, A.; Theis, F. J.: ICA over finite fields - separability and algorithms. Signal Process. 92 (8), 2012, 1796-1808 mehr… BibTeX
  • Gutch, H. W.; Theis, F. J.: Uniqueness of linear factorizations into independent subspaces. J. Multivar. Anal. 112, 2012, 48-62 mehr… BibTeX
  • Gutch, H. W.; Theis, F. J.: To infinity and beyond: On ICA over Hilbert Spaces. , Springer, 2012 mehr… BibTeX
  • Hug, S.; Theis, F. J.: Bayesian inference of latent causes in gene regulatory dynamics. , Springer, 2012 mehr… BibTeX
  • Illner, K.; Fuchs, C.; Theis, F. J.: Blind source separation using latent gaussian graphical models. , Tampere International Center for Signal Processing, 2012 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Krumsiek, J.; Stückler, F.; Kastenmüller, G.; Theis, F. J.: Systems biology meets metabolism. In: Suhre, K. (Hrsg.): Springer, 2012, 281-313 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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. (Hrsg.): Springer, 2012, 247-260 mehr… BibTeX
  • 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 mehr… BibTeX
  • Meyer-Bäse, A.; Cappendijk, S.; Theis, F. J.: Uncertain gene regulatory networks simplified by gramian-based approach. , CSREA Press, 2012 mehr… BibTeX
  • Nordhausen, K.; Gutch, H. W.; Oja, H.; Theis, F. J.: Joint diagonalization of several scatter matrices for ICA. , Springer, 2012 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Ruepp, A.; Kowarsch, A.; Theis, F. J.: PhenomiR: MicroRNAs in human diseases and biological processes. Methods Mol. Biol. 822, 2012, 249-260 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Theis, F. J.: Bayesian fuzzy clustering of colored graphs. , Springer, 2012 mehr… BibTeX
  • 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 mehr… BibTeX

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 mehr… BibTeX
  • 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. (Hrsg.): Bentham Science Publishers, 2011, 157-170 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Krumsiek, J.; Wittmann, D. M.; Theis, F. J.: From discrete to continuous gene regulation models - a tutorial using the odefy toolbox. In: Michalowski, T. (Hrsg.): InTech, 2011, 35-60 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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. (Hrsg.): Bentham Science Publishers, 2011, 26-47 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Müller, N.; Krumsiek, J.; Theis, F. J.; Böhm, C.; Meyer-Bäse, A.: Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells. , SPIE, 2011 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Schwarzfischer, M.; Marr, C.; Krumsiek, J.; Hoppe, P. S.; Schroeder, T.; Theis, F. J.: Efficient fluorescence image normalization for time lapse movies. , MIAAB, 2011 mehr… BibTeX
  • 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 mehr… BibTeX
  • Theis, F. J.; Kawanabe, M.; Müller, K. R.: Uniqueness of non-Gaussianity-based dimension reduction. IEEE Trans. Signal Process. 59 (9), 2011, 4478 - 4482 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Wittmann, D. M.; Theis, F. J.: Dynamic regimes of random fuzzy logic networks. New J. Phys. 13, 2011 mehr… BibTeX

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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Blöchl, F.; Kowarsch, A.; Theis, F. J.: Second-order source separation based on prior knowledge realized in a graph model. , Springer, 2010 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Gutch, H. W.; Gruber, P.; Theis, F. J.: ICA over finite fields. , Springer, 2010 mehr… BibTeX
  • Gutch, H. W.; Maehara, T.; Theis, F. J.: Second order subspace analysis and simple decompositions. , Springer, 2010 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Krumsiek, J.; Pölsterl, S.; Wittmann, D. M.; Theis, F. J.: Odefy - from discrete to continuous models. BMC Bioinformatics 11, 2010, 1-10 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Plant, C.; Theis, F. J.; Meyer-Bäse, A.; Böhm, C.: Information-theoretic model selection for independent components. , Springer, 2010 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • Theis, F. J.; Meyer-Bäse, A.: Foundations of medical imaging and signal recording. In: MIT Press, 2010, 1-28 mehr… BibTeX
  • Theis, F. J.; Müller, N. S.; Plant, C.; Böhm, C.: Robust second-order source separation identifies experimental responses in biomedical imaging. , Springer, 2010 mehr… BibTeX
  • Thiemann, C.; Theis, F. J.; Grady, D.; Brune, R.; Brockmann, D.: The structure of borders in a small world. PLoS ONE 5 (11), 2010 mehr… BibTeX
  • 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 mehr… BibTeX

2009

  • Blöchl, F.; Theis, F. J.: Estimating hidden influences in metabolic and gene regulatory networks. In: Adali, T.; al., et (Hrsg.): Springer, 2009, 387-394 mehr… BibTeX
  • Georgiev, P. G.; Theis, F. J.: Optimization techniques for data representions with biomedical applications. In: Romejin, H. E.; Pardalos, P. M. (Hrsg.): Springer, 2009, 1-38 mehr… BibTeX
  • Gruber, P.; Gutch, H. W.; Theis, F. J.: Hierarchical extraction of independent subspaces of unknown dimensions. In: Adali, T.; al., et (Hrsg.): Springer, 2009, 259-266 mehr… BibTeX
  • 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 mehr… BibTeX
  • Klamt, S.; Haus, U. U.; Theis, F. J.: Hypergraphs and cellular networks. PLoS Comput. Biol. 5 (5), 2009 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 (Hrsg.): Springer, 2009, 354-361 mehr… BibTeX
  • 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 (Hrsg.): Springer, 2009, 548-556 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX

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 mehr… BibTeX
  • 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 mehr… BibTeX
  • 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 mehr… BibTeX

Teaching

Winter term 2022/23

TitleLecturer (assistant)Dates
Advanced Student Seminar: Deep LearningLink
Computational Methods for Single-Cell Biology (Exercise Session) [MA5617]Link
Computational Methods for Single-Cell Biology [MA5617]Link

A list of previous courses can be found on TUMonline.

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