Angerer, P. ; Simon, L. ; Tritschler, S. ; Wolf, F. ; Fischer, D. ; Theis, F.J.
Single cells make big data: New challenges and opportunities in transcriptomics.
Curr. Opin. Syst. Biol. 4, 85-91 (2017)
Ballnus, B. ; Hug, S. ; Hatz, K.* ; Görlitz, L.* ; Hasenauer, J. ; Theis, F.J.
Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems.
BMC Syst. Biol. 11:63 (2017)
Bartel, S. ; Schulz, N. ; Alessandrini, F. ; Schamberger, A.C. ; Pagel, P.* ; Theis, F.J. ; Milger, K. ; Nößner, E. ; Stick, S.M.* ; Kicic, A.* ; Eickelberg, O. ; Freishtat, R.J.* ; Krauss-Etschmann, S.
Pulmonary microRNA profiles identify involvement of Creb1 and Sec14l3 in bronchial epithelial changes in allergic asthma.
Sci. Rep. 7:46026 (2017)
Benedetti, E. ; Pučić-Baković, M.* ; Keser, T.* ; Wahl, A. ; Hassinen, A.* ; Yang, J.Y.* ; Liu, L.* ; Trbojević-Akmačić, I.* ; Razdorov, G.* ; Štambuk, J.* ; Klarić, L.* ; Ugrina, I.* ; Selman, M.H.J.* ; Wuhrer, M.* ; Rudan, I.* ; Polasek, O.* ; Hayward, C.* ; Grallert, H. ; Strauch, K. ; Peters, A. ; Meitinger, T. ; Gieger, C. ; Vilaj, M.* ; Boons, G.J.* ; Moremen, K.W.* ; Ovchinnikova, T.* ; Bovin, N.* ; Kellokumpu, S.* ; Theis, F.J. ; Lauc, G.* ; Krumsiek, J.
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway.
Nat. Commun. 8:1483 (2017)
Blasi, T. ; Buettner, F. ; Strasser, M. ; Marr, C. ; Theis, F.J.
CgCorrect: A method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics.
Phys. Biol. 14:036001 (2017)
Budde, M.* ; Kondofersky, I. ; Adorjan, K.* ; Aldinger, F.* ; Anderson-Schmidt, H.* ; Andlauer, T.F.* ; Flatau, L.* ; Gade, K.* ; Heilbronner, U.* ; Kalman, J.* ; Papiol, S.* ; Theis, F.J. ; Falkai, P.* ; Müller, N.S. ; Schulze, T.G.*
Integrating polygenic allele burden information and phenomic data to characterize complex disease trajectories in severe mental illness.
Eur. Neuropsychopharmacol. 27, 3, S406 (2017)
Buggenthin, F. ; Buettner, F. ; Hoppe, P.S.* ; Endele, M. ; Kroiss, M. ; Strasser, M. ; Schwarzfischer, M. ; Loeffler, D. ; Kokkaliaris, K.D. ; Hilsenbeck, O. ; Schroeder, T. ; Theis, F.J. ; Marr, C.
Prospective identification of hematopoietic lineage choice by deep learning.
Nat. Methods, DOI: 10.1038/nmeth.4182 (2017)
Chlis, N.-K. ; Wolf, F. ; Theis, F.J.
Model-based branching point detection in single-cell data by K-Branches clustering.
Bioinformatics 33, 3211-3219 (2017)
Comes, A.* ; Aldinger, F.* ; Kondofersky, I. ; Adorjan, K.* ; Anderson-Schmidt, H.* ; Andlauer, T.F.* ; Budde, M.* ; Gade, K.* ; Heilbronner, U.* ; Kalman, J.* ; Papiol, S.* ; Theis, F.J. ; Falkai, P.* ; Müller, N.S. ; Schulze, T.G.*
Polygenic burden analysis of longitudinal clusters of quality of life and functioning in patients with severe mental illness.
Eur. Neuropsychopharmacol. 27, 3, S408-S409 (2017)
Conlon, T.M. ; Hackl, M. ; Bartel, J. ; Krumsiek, J. ; Irmler, M. ; Beckers, J. ; Theis, F.J. ; Eickelberg, O.* ; Yildirim, A.Ö.
2d cross-omics integrated enrichment analysis of human and mice COPD lungs reveal novel pathological mechanisms of disease progression.
Am. J. Respir. Crit. Care Med. 195 (2017)
Dirmeier, S.* ; Fuchs, C. ; Müller, N.S. ; Theis, F.J.
netReg: Network-regularized linear models for biological association studies.
Bioinformatics, DOI: 10.1093/bioinformatics/btx677 (2017)
Eulenberg, P. ; Köhler, N. ; Blasi, T. ; Filby, A.* ; Carpenter, A.E.* ; Rees, P.* ; Theis, F.J.° ; Wolf, F.°
Reconstructing cell cycle and disease progression using deep learning.
Nat. Commun. 8:463 (2017)
Florea, A.M.* ; Varghese, E.* ; McCallum, J.E.* ; Mahgoub, S.* ; Helmy, I.* ; Varghese, S.* ; Gopinath, N.* ; Sass, S. ; Theis, F.J. ; Reifenberger, G.* ; Büsselberg, D.*
Calcium-regulatory proteins as modulators of chemotherapy in human neuroblastoma.
Oncotarget 8, 22876-22893 (2017)
Förster, K. ; Sass, S. ; Ehrhardt, H.* ; Mous, D.S.* ; Rottier, R.J.* ; Oak, P. ; Schulze, A.* ; Flemmer, A.W.* ; Gronbach, J.* ; Hübener, C.* ; Desai, T.* ; Eickelberg, O. ; Theis, F.J. ; Hilgendorff, A.
Early identification of bronchopulmonary dysplasia using novel biomarkers by proteomic screening.
Am. J. Respir. Crit. Care Med., DOI: 10.1164/rccm.201706-1218LE (2017)
Fröhlich, F. ; Kaltenbacher, B.* ; Theis, F.J. ; Hasenauer, J.
Scalable parameter estimation for genome-scale biochemical reaction networks.
PLoS Comput. Biol. 13:e1005331 (2017)
Frohnert, B.I.* ; Laimighofer, M. ; Krumsiek, J. ; Theis, F.J. ; Winkler, C. ; Norris, J.M.* ; Ziegler, A.-G. ; Rewers, M.J.* ; Steck, A.K.*
Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young.
Pediatr. Diabetes, DOI: 10.1111/pedi.12543 (2017)
Garzorz-Stark, N. ; Krause, L. ; Lauffer, F. ; Atenhan, A. ; Thomas, J. ; Theis, F.J. ; Müller, N.S. ; Biedermann, T.* ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.
The imiquimod model as a model for psoriasis and/or eczema in humans?
Exp. Dermatol. 26, E68-E68 (2017)
Garzorz-Stark, N.* ; Lauffer, F.* ; Krause, L. ; Gross, O.* ; Traidl-Hoffmann, C.* ; Theis, F.J. ; Schmidt-Weber, C.* ; Biedermann, T.* ; Eyerich, S.* ; Eyerich, K.*
TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans.
J. Invest. Dermatol. 137, S275-S275 (2017)
Garzorz-Stark, N.* ; Lauffer, F.* ; Krause, L. ; Thomas, J. ; Atenhan, A. ; Franz, R.* ; Roenneberg, S.* ; Boehner, A.* ; Jargosch, M. ; Batra, R. ; Müller, N.S. ; Haak, S. ; Groß, C.* ; Groß, O.* ; Traidl-Hoffmann, C. ; Theis, F.J. ; Schmidt-Weber, C.B. ; Biedermann, T.* ; Eyerich, S. ; Eyerich, K.*
TLR7/8 agonists stimulate plasmacytoid dendritic cells to initiate a Th17-deviated acute contact dermatitis in humans.
J. Allergy Clin. Immunol., DOI: 10.1016/j.jaci.2017.07.045 (2017)
Heilbronner, U.* ; Jain, G.* ; Kaurani, L.* ; Kondofersky, I. ; Budde, M.* ; Gade, K.* ; Kalman, J.* ; Adorjan, K.* ; Aldinger, F.* ; Anderson-Schmidt, H.* ; Müller, N.S. ; Theis, F.J. ; Falkai, P.* ; Fischer, A.* ; Schulze, T.G.*
The role of micrornas in the course of severe mental disorders.
Eur. Neuropsychopharmacol. 27, 3, S456-S457 (2017)
Hilgendorff, A. ; Foerster, K.* ; Sass, S. ; Stoecklein, S.* ; Dietrich, O.* ; Pomschar, A.* ; Schulze, A.* ; Huebener, C.* ; Theis, F.J. ; Erhardt, H.* ; Flemmer, A.W.* ; Ertl-Wagner, B.*
Discrimination of pulmonary changes in neonatal chronic lung disease by a new Mri score.
Am. J. Respir. Crit. Care Med. 195 (2017)
Hilsenbeck, O.*° ; Schwarzfischer, M. ; Loeffler, D.* ; Dimopoulos, S.* ; Hastreiter, S.* ; Marr, C. ; Theis, F.J. ; Schroeder, T.*°
fastER: A user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy.
Bioinformatics 33, 2020-2028 (2017)
Hölter, S. ; Dalke, C. ; Garrett, L. ; Ung, M.-C. ; Kunze, S. ; Hladik, D* ; Neff, F. ; Rößler, U.* ; Hornhardt, S.* ; Theis, F.J. ; Unger, K. ; Tapio, S.* ; Graw, J.
Long-term effects of low doses of ionizing radiation on the eye and the brain in mice.
Poster: Low Vision and the Brain, 24-26 November 2017, Berlin. (2017)
Jagiella, N. ; Rickert, D. ; Theis, F.J. ; Hasenauer, J.
Parallelization and high-performance computing enables automated statistical inference of multi-scale models.
Cell Syst. 4, 194–206.e9 (2017)
Kazeroonian, A.° ; Theis, F.J. ; Hasenauer, J.°
A scalable moment-closure approximation for large-scale biochemical reaction networks.
Bioinformatics 33, i293-i300 (2017)
Krautenbacher, N. ; Theis, F.J. ; Fuchs, C.
Correcting classifiers for sample selection bias in two-phase case-control studies.
Comput. Math. Methods Med. 2017:7847531 (2017)
Krendl, C. ; Shaposhnikov, D. ; Rishko, V. ; Ori, C. ; Ziegenhain, C.* ; Sass, S. ; Simon, L. ; Müller, N.S. ; Straub, T.* ; Brooks, K.E.* ; Chavez, S.L.* ; Enard, W.* ; Theis, F.J.* ; Drukker, M.
GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency.
Proc. Natl. Acad. Sci. U.S.A. 114, E9579-E9588 (2017)
Kuepper, M.K.* ; Thomas, J. ; Krause, L. ; Müller, N.S. ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, K.* ; Eyerich, S. ; Garzorz-Stark, N.*
Characterization of multiple B cell subsets in peripheral blood and skin biopsies of psoriasis patients identifies a correlation of plasma and regulatory B cells and disease severity.
Exp. Dermatol. 26, E69-E70 (2017)
Lauffer, F.* ; Krause, L. ; Franz, R.* ; Garzorz-Stark, N.* ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Interface dermatitis shows a distinctive molecular signature independent from individual disease background.
Exp. Dermatol. 26, E61-E61 (2017)
Lauffer, F.* ; Jargosch, M.* ; Krause, L. ; Garzorz-Stark, N.* ; Franz, R.* ; Roenneberg, S.* ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C. ; Eyerich, S. ; Eyerich, K.*
Interface Dermatitis is characterized by a type I immune response and an epidermal reaction to IFN-gamma and TNF-alpha.
J. Invest. Dermatol. 137, S254-S254 (2017)
Milger, K. ; Götschke, J. ; Krause, L. ; Nathan, P. ; Alessandrini, F. ; Tufman, A.* ; Fischer, R.* ; Bartel, S.* ; Theis, F.J. ; Behr, J.* ; Dehmel, S. ; Müller, N.S. ; Kneidinger, N.* ; Krauss-Etschmann, S.
Identification of a plasma miRNA biomarker-signature for allergic asthma: A translational approach.
Allergy 72, 1962-1971 (2017)
Molnos, S. ; Baumbach, C. ; Wahl, S. ; Müller-Nurasyid, M. ; Strauch, K. ; Wang-Sattler, R. ; Waldenberger, M. ; Meitinger, T. ; Adamski, J. ; Kastenmüller, G. ; Suhre, K. ; Peters, A. ; Grallert, H. ; Theis, F.J. ; Gieger, C.
pulver: An R package for parallel untra-rapid p-value computation for linear regression interaction terms.
BMC Bioinformatics 18:429 (2017)
Peng, T. ; Thorn, K.* ; Schroeder, T.* ; Wang, L.* ; Theis, F.J. ; Marr, C. ; Navab, N.*
A BaSiC tool for background and shading correction of optical microscopy images.
Nat. Commun. 8:14836 (2017)
Piasecka, J.* ; Hennig, H. ; Theis, F.J. ; Rees, P.* ; Summers, H.D.* ; Thornton, C.A.*
Label free identification of peripheral blood eosinophils using high-throughput imaging flow cytometry.
J. Allergy Clin. Immunol. 139, AB163-AB163 (2017)
Regev, A.* ; Teichmann, S.A.* ; Lander, E.S.* ; Amit, I.* ; Benoist, C.* ; Birney, E.* ; Bodenmiller, B.* ; Campbell, P.J.* ; Carninci, P.* ; Clatworthy, M.* ; Clevers, H.* ; Deplancke, B.* ; Dunham, I.* ; Eberwine, J.* ; Eils, R.* ; Enard, W.* ; Farmer, A.* ; Fugger, L.* ; Göttgens, B.* ; Hacohen, N.* ; Haniffa, M.* ; Hemberg, M.* ; Kim, S.K.* ; Klenerman, P.* ; Kriegstein, A.* ; Lein, E.* ; Linnarsson, S.* ; Lundberg, E.* ; Lundeberg, J.* ; Majumder, P.* ; Marioni, J.C.* ; Merad, M.* ; Mhlanga, M.* ; Nawijn, M.C.* ; Netea, M.* ; Nolan, G.* ; Pe'er, D.* ; Phillipakis, A.* ; Ponting, C.P.* ; Quake, S.R.* ; Reik, W.* ; Rozenblatt-Rosen, O.* ; Sanes, J.R.* ; Satija, R.* ; Schumacher, T.N.* ; Shalek, A.K.* ; Shapiro, E.* ; Sharma, P.* ; Shin, J.W.* ; Stegle, O.* ; Stratton, M.R.* ; Stubbington, M.J.T.* ; Theis, F.J. ; Uhlén, M.* ; van Oudenaarden, A.* ; Wagner, A.* ; Watt, F.M.* ; Weissman, J.S.* ; Wold, B.J.* ; Xavier, R.J.* ; Yosef, N.*
Science Forum: The human cell atlas.
eLife 6:e27041 (2017)
Schulte, E.* ; Kondofersky, I. ; Budde, M.* ; Adorjan, K.* ; Aldinger, F.* ; Anderson-Schmidt, H.* ; Andlauer, T.F.* ; Gade, K.* ; Heilbronner, U.* ; Kalman, J.* ; Papiol, S.* ; Theis, F.J. ; Falkai, P.* ; Müller, N.S. ; Schulze, T.G.*
Polygenic burden analysis of longitudinal clusters of psychopathological features in a cross-diagnostic group of individuals with severe mental illness.
Eur. Neuropsychopharmacol. 27, 3, S401-S402 (2017)
Senís, E.* ; Mockenhaupt, S.* ; Rupp, D.* ; Bauer, T.* ; Paramasivam, N.* ; Knapp, B. ; Gronych, J.* ; Grosse, S.D.* ; Windisch, M.P.* ; Schmidt, F.* ; Theis, F.J. ; Eils, R.* ; Lichter, P.* ; Schlesner, M.* ; Bartenschlager, R.* ; Grimm, D.*
TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus.
Nucleic Acids Res. 45:e3 (2017)
Sobotta, S.* ; Raue, A.* ; Huang, X.* ; Vanlier, J.* ; Jünger, A.* ; Bohl, S.* ; Albrecht, U.* ; Hahnel, M.J.* ; Wolf, S.* ; Müller, N.S. ; D'Alessandro, L.A.* ; Mueller-Bohl, S.* ; Boehm, M.E.* ; Lucarelli, P.* ; Bonefas, S.* ; Damm, G.* ; Seehofer, D.* ; Lehmann, W.D.* ; Rose-John, S.* ; van der Hoeven, F.* ; Gretz, N.* ; Theis, F.J. ; Ehlting, C.* ; Bode, J.G.* ; Timmer, J.*° ; Schilling, M.*° ; Klingmüller, U.*°
Model based targeting of IL-6-induced inflammatory responses in cultured primary hepatocytes to improve application of the JAK inhibitor ruxolitinib.
Front. Physiol. 8:775 (2017)
Theis, F.J.
Network inference from glycoproteomics data reveals new reactions in the IgG glycosylation pathway.
Poster: 12th Jenner Glycobiology and Medicine Symposium, 6-9 May 2017, Dubrovnik, Croatia. (2017)
Theis, F.J. ; Ninkovic, J. ; Hauck, S.M. ; Götz, M. ; Lepko, T. ; Steiner-Mezzadri, A. ; Büttner, M. ; Murenu, E.* ; Cernilogar, F.M.* ; Schotta, G.*
The role of chromatin associated protein Hmgb2 in setting up permissive chromatin states for direct glia to neuron conversion.
Poster: Embo Meeting, 07-10 September 17, Alicante. (2017)
Tritschler, S. ; Theis, F.J. ; Lickert, H. ; Böttcher, A.
Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas.
Mol. Metab. 6, 974-990 (2017)
von Toerne, C. ; Laimighofer, M. ; Achenbach, P. ; Beyerlein, A. ; de Las Heras Gala, T. ; Krumsiek, J. ; Theis, F.J. ; Ziegler, A.-G.° ; Hauck, S.M.°
Peptide serum markers in islet autoantibody-positive children.
Diabetologia 60, 287-295 (2017)
Angerer, P. ; Haghverdi, L. ; Büttner, M. ; Theis, F.J. ; Marr, C. ; Buettner, F.
Destiny: Diffusion maps for large-scale single-cell data in R.
Bioinformatics 32, 1241-1243 (2016)
Blasi, T. ; Hennig, H.* ; Summers, H.D.* ; Theis, F.J. ; Cerveira, J.* ; Patterson, J.O.* ; Davies, D.* ; Filby, A.* ; Carpenter, A.E.*° ; Rees, P.*°
Label-free cell cycle analysis for high-throughput imaging flow cytometry.
Nat. Commun. 7:10256 (2016)
Blasi, T. ; Feller, C.*° ; Feigelman, J. ; Hasenauer, J. ; Imhof, A.* ; Theis, F.J. ; Becker, P.B.* ; Marr, C.°
Combinatorial histone acetylation patterns are generated by motif-specific reactions.
Cell Syst. 2, 49-58 (2016)
Bortsova, G. ; Sterr, M. ; Wang, L. ; Milletari, F.* ; Navab, N.* ; Böttcher, A. ; Lickert, H. ; Theis, F.J.° ; Peng, T.°
Mitosis detection in intestinal crypt images with hough forest and conditional random fields.
Lecture Notes Comp. Sci. 10019, 287-295 (2016)
Carpenter, A.*# ; Eddy, S.E.* ; Flicek, P.* ; Gymrek, M.* ; Hammell, M.* ; Jaqaman, K.* ; Jenkins, J.* ; Koller, D.* ; Lappalainen, T.* ; Oshlack, A.* ; Shamir, R.* ; Singh, M.* ; Teichmann, S.* ; Theis, F.J.# ; Troyanskaya, O.*
What is the key best practice for collaborating with a computational biologist?
Cell Syst. 3, 7-11 (2016)
Conlon, T.M. ; Bartel, J. ; Ballweg, K. ; Günter, S. ; Prehn, C. ; Krumsiek, J. ; Meiners, S. ; Theis, F.J. ; Adamski, J. ; Eickelberg, O. ; Yildirim, A.Ö.
Metabolomics screening identifies reduced L-carnitine to be associated with progressive emphysema.
Clin. Sci. 130, 273-287 (2016)
Feigelman, J. ; Ganscha, S. ; Hastreiter, S.* ; Schwarzfischer, M. ; Filipczyk, A.* ; Schröder, T.* ; Theis, F.J. ; Marr, C. ; Claassen, M.
Analysis of cell lineage trees by exact bayesian inference identifies negative autoregulation of nanog in mouse embryonic stem cells.
Cell Syst. 3, 480-490 (2016)
Fiedler, A. ; Raeth, S.* ; Theis, F.J. ; Hausser, A.* ; Hasenauer, J.
Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints.
BMC Syst. Biol. 10:80 (2016)
Fröhlich, F. ; Thomas, P.* ; Kazeroonian, A. ; Theis, F.J. ; Grima, R.*° ; Hasenauer, J.°
Inference for stochastic chemical kinetics using moment equations and system size expansion.
PLoS Comput. Biol. 12:e1005030 (2016)
Fröhlich, F. ; Shadrin, A.* ; Kessler, T.* ; Wierling, C.* ; Heinig, M. ; Theis, F.J. ; Lange, B.M.* ; Lehrach, H.* ; Hasenauer, J.
Large-scale modeling of cancer signaling: Mechanistic modeling meets Big Data.
Eur. J. Cancer 68, S44-S44 (2016)
Fröhlich, F. ; Theis, F.J. ; Rädler, J.O.* ; Hasenauer, J.
Parameter estimation for dynamical systems with discrete events and logical operations.
Bioinformatics 33, 1049-1056 (2016)
Garzorz-Stark, N.*# ; Krause, L.# ; Lauffer, F.* ; Atenhan, A. ; Thomas, J. ; Stark, S.P. ; Franz, R.* ; Weidinger, S.* ; Balato, A.* ; Müller, N.S. ; Theis, F.J. ; Ring, J.* ; Schmidt-Weber, C.B. ; Biedermann, T.* ; Eyerich, S. ; Eyerich, K.*
A novel molecular disease classifier for psoriasis and eczema.
Exp. Dermatol. 25, 767-774 (2016)
Geissen, E.M.*° ; Hasenauer, J. ; Heinrich, S.* ; Hauf, S.* ; Theis, F.J. ; Radde, N.*°
MEMO - multi-experiment mixture model analysis of censored data.
Bioinformatics 32, 2464-2472 (2016)
González-Valllinas, M.* ; Albrecht, M.* ; Pitea, A. ; Rodriguez-Paredes, M.* ; Stichel, D.* ; Sass, S. ; Gutekunst, J.* ; Schmitt, J.* ; Muley, T.* ; Meister, M.* ; Warth, A.* ; Schirmacher, P.* ; Theis, F.J. ; Müller, N.S. ; Matthäus, F.* ; Breuhahn, K.*
Abstract 1945: Identification of a miRNA/mRNA network driving non-small cell lung cancer (NSCLC) dissemination.
Cancer Res. 76 (2016)
Haffner, I.* ; Luber, B.* ; Maier, D.* ; Geier, B.* ; Theis, F.J. ; Meyer-Hermann, M.* ; Walch, A.K. ; Kretzschmar, A.K.* ; von Weikersthal, L.F.* ; Knorrenschild, J.R.* ; Schierle, K.* ; Wittekind, C.* ; Lordick, F.*
Clinical validation of response and resistance factor candidates to targeted therapy in Gastric Cancer (GC).
Oncol. Res. Treat. 39, 16-17 (2016)
Haghverdi, L. ; Büttner, M. ; Wolf, F. ; Buettner, F. ; Theis, F.J.
Diffusion pseudotime robustly reconstructs lineage branching.
Nat. Methods 13, 845-848 (2016)
Hilsenbeck, O.# ; Schwarzfischer, M.# ; Skylaki, S.*# ; Schauberger, B. ; Hoppe, P.S.* ; Loeffler, D.* ; Kokkaliaris, K.D.* ; Hastreiter, S.* ; Skylaki, E.* ; Filipczyk, A. ; Strasser, M. ; Buggenthin, F. ; Feigelman, J. ; Krumsiek, J. ; van den Berg, A.J. ; Endele, M. ; Etzrodt, M.* ; Marr, C. ; Theis, F.J.° ; Schroeder, T.°
Software tools for single-cell tracking and quantification of cellular and molecular properties.
Nat. Biotechnol. 34, 703-706 (2016)
Hoppe, P.S. ; Schwarzfischer, M. ; Loeffler, D. ; Kokkaliaris, K.D. ; Hilsenbeck, O. ; Moritz, N. ; Endele, M. ; Filipczyk, A. ; Gambardella, A.* ; Ahmed, N.* ; Etzrodt, M.* ; Coutu, D.L.* ; Rieger, M.A. ; Marr, C. ; Strasser, M. ; Schauberger, B. ; Burtscher, I. ; Ermakova, O.* ; Bürger, A. ; Lickert, H. ; Nerlov, C.* ; Theis, F.J. ; Schroeder, T.
Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.
Nature 535, 299-302 (2016)
Hross, S. ; Fiedler, A. ; Theis, F.J. ; Hasenauer, J.
Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast.
In: (Foundations of Systems Biology in Engineering - FOSBE 2016, 9—12 October 2016, Magdeburg). 2016. 264-269 (IFAC Proc. ; 49-26)
Hug, S. ; Schmidl, D. ; Li, W.B. ; Greiter, M.B. ; Theis, F.J.
Bayesian model selection methods and their application to biological ODE systems.
In: Geris, L.* ; Gomez-Cabrero, D.* [Eds.]: Uncertainty in Biology : A Computational Modeling Approach. Berlin; Heidelberg: Springer, 2016. 243-268 (Stud. Mechanobiol. Tiss. Engineering Biomater. ; 17)
Huypens, P.° ; Sass, S. ; Wu, M. ; Dyckhoff, D. ; Tschöp, M. ; Theis, F.J. ; Marschall, S. ; Hrabě de Angelis, M. ; Beckers, J.*°
Epigenetic germline inheritance of diet-induced obesity and insulin resistance.
Nat. Genet. 48, 497-499 (2016)
Huypens, P.° ; Sass, S. ; Wu, M. ; Dyckhoff, D. ; Tschöp, M. ; Theis, F.J. ; Marschall, S. ; Hrabě de Angelis, M. ; Beckers, J.°
Epigenetic germline inheritance of diet-induced obesity and insulin resistance.
Obstet. Gynecol. Surv. 71, 719-720 (2016)
Jung, B. ; Padula, D. ; Burtscher, I. ; Landerer, C. ; Lutter, D. ; Theis, F.J. ; Messias, A.C. ; Geerlof, A. ; Sattler, M. ; Kremmer, E. ; Boldt, K. ; Ueffing, M. ; Lickert, H.
Pitchfork and Gprasp2 target smoothened to the primary cilium for Hedgehog pathway activation.
PLoS ONE 11:e0149477 (2016)
Kazeroonian, A. ; Fröhlich, F. ; Raue, A.* ; Theis, F.J. ; Hasenauer, J.
CERENA: ChEmical REaction Network Analyzer - a toolbox for the simulation and analysis of stochastic chemical kinetics.
PLoS ONE 11:e0146732 (2016)
Kondofersky, I. ; Theis, F.J. ; Fuchs, C.
Inferring catalysis in biological systems.
IET Syst. Biol. 10, 210-218 (2016)
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 65, 647-657 (2016)
Kong, B.* ; Bruns, P. ; Behler, N.A.* ; Chang, L.* ; Schlitter, A.M.* ; Cao, J.* ; Gewies, A. ; Ruland, J.* ; Fritzsche, S.* ; Valkovskaya, N.* ; Jian, Z.* ; Regel, I.* ; Raulefs, S.* ; Irmler, M. ; Beckers, J. ; Friess, H.* ; Erkan, M.* ; Müller, N.S. ; Roth, S.* ; Hackert, T.* ; Esposito, I.* ; Theis, F.J. ; Kleeff, J.* ; Michalski, C.W.*
Dynamic landscape of pancreatic carcinogenesis reveals early molecular networks of malignancy.
Gut, DOI: 10.1136/gutjnl-2015-310913 (2016)
Kong, B.* ; Bruns, P. ; Behler, N.* ; Schlitter, A.M.* ; Friess, H.* ; Erkan, M.* ; Theis, F.J. ; Esposito, I.* ; Michalski, C.W.* ; Kleeff, J.*
Oncogenic Kras promotes early pancreatic carcinogenesis by perpetuating elements of natural inflammatory response.
Pancreatol. 16, S. 11 (2016)
Krause, L. ; Mourantchanian, V.* ; Brockow, K.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Knapp, B. ; Müller, N.S. ; Eyerich, S.
A computational model to predict severity of atopic eczema from 30 serum proteins.
J. Allergy Clin. Immunol. 138, 1207-1210.e2 (2016)
Krumsiek, J.# ; Bartel, J.# ; Theis, F.J.
Computational approaches for systems metabolomics.
Curr. Opin. Biotechnol. 39, 198-206 (2016)
Kuepper, M.K.* ; Thomas, J. ; Garzorz-Stark, N.* ; Krause, L. ; Müller, N.S. ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, K.* ; Eyerich, S.
Characterization of multiple B cell subsets in peripheral blood of psoriasis patients identifies a correlation of regulatory B cells and disease severity.
J. Invest. Dermatol. 136, S217-S217 (2016)
Laimighofer, M. ; Krumsiek, J. ; Buettner, F.° ; Theis, F.J.°
Unbiased prediction and feature selection in high-dimensional survival regression.
J. Comput. Biol. 23, 279-290 (2016)
Lauffer, F.* ; Krause, L. ; Franz, R.* ; Garzorz-Stark, N.* ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Interface dermatitis shows a distinctive molecular signature independent from individual disease background.
J. Invest. Dermatol. 136, S219-S219 (2016)
Lauffer, F.* ; Krause, L. ; Franz, R.* ; Garzorz-Stark, N.* ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
A distinct molecular signature of interface dermatitis as determined by gene expression analysis combined with disease independent histological phenotyping.
Exp. Dermatol. 25, 30-31 (2016)
Luber, B.* ; Keller, S.* ; Zwingenberger, G.* ; Ebert, K.* ; Maier, D.* ; Geier, B.* ; Theis, F.J. ; Hasenauer, J. ; Huge, S. ; Meyer-Hermann, M. ; Dehghany, J. ; Walch, A.K. ; Aichler, M. ; Lordick, F.* ; Haffner, I.*
Identification of predictive response and resistance factors to targeted therapy in gastric cancer using a systems medicine approach.
Eur. J. Cancer 68, S135-S135 (2016)
Miettinen, J.* ; Illner, K. ; Nordhausen, K.* ; Oja, H.* ; Taskinen, S.* ; Theis, F.J.
Separation of uncorrelated stationary time series using autocovariance matrices.
J. Time Ser. Anal. 37, 337-354 (2016)
Much, D. ; Beyerlein, A. ; Kindt, A. ; Krumsiek, J. ; Stückler, F. ; Rossbauer, M. ; Hofelich, A. ; Wiesenäcker, D. ; Hivner, S. ; Herbst, M. ; Römisch-Margl, W. ; Prehn, C. ; Adamski, J. ; Kastenmüller, G. ; Theis, F.J. ; Ziegler, A.-G. ; Hummel, S.
Lactation is associated with altered metabolomic signatures in women with gestational diabetes.
Diabetologia 59, 2193-2202 (2016)
Much, D. ; Beyerlein, A. ; Kindt, A. ; Krumsiek, J. ; Rossbauerl, M. ; Hofelich, A. ; Hivner, S. ; Herbst, M. ; Römisch-Margl, W. ; Prehn, C. ; Adamski, J. ; Kastenmüller, G. ; Theis, F.J. ; Ziegler, A.-G. ; Hummel, S.
Lactation is associated with altered metabolomic signatures in women with gestational diabetes.
Diabetologia 59, S187-S187 (2016)
Preusse, M. ; Theis, F.J. ; Müller, N.S.
miTALOS v2: Analyzing tissue specific microRNA function.
PLoS ONE 11:e0151771 (2016)
Rolle-Kampczyk, U.E.* ; Krumsiek, J. ; Otto, W.* ; Röder, S.W.* ; Kohajda, T.* ; Borte, M.* ; Theis, F.J. ; Lehmann, I.* ; von Bergen, M.*
Metabolomics reveals effects of maternal smoking on endogenous metabolites from lipid metabolism in cord blood of newborns.
Metabolomics 12:76 (2016)
Sacher, A. ; Theis, F.J.
Von lernfähigen Maschinen lernen.
Laborjournal 7-8, 59-61 (2016)
Sacher, A. ; Theis, F.J.
Einzigartige Zellen: Computerbasierte Methoden verbessern die Einzelzell-Analyse.
Laborpraxis, accepted (2016)
Scheel, C. ; Linnemann, J.R.* ; Miura, H. ; Meixner, L.K. ; Irmier, M.* ; Kloos, U.J.* ; Hirschi, B. ; Bartsch, H.S.* ; Sass, S. ; Beckers, J. ; Theis, F.J. ; Gabka, C.* ; Sotlar, K.*
A force-sensitive organoid assay to quantify regenerative potential of single primary human mammary cells.
Cancer Res. 76:P1-06-02 (2016)
Stoecker, K.* ; Sass, S. ; Theis, F.J. ; Hauner, H.* ; Pfaffl, M.W.*
Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data.
Biomol. Detect. Quantif. 11, 31-44 (2016)
Stojcheva, N.* ; Schechtmann, G.* ; Sass, S. ; Roth, P.* ; Florea, A.M.* ; Stefanski, A.* ; Stühler, K.* ; Wolter, M.* ; Müller, N.S. ; Theis, F.J. ; Weller, M.G.* ; Reifenberger, G.* ; Happold, C.*
MicroRNA-138 promotes acquired alkylator resistance in glioblastoma by targeting the Bcl-2-interacting mediator BIM.
Oncotarget 7, 12937-12950 (2016)
Styczynski, M.P.*° ; Theis, F.J.°
Systems biology - the intersection of experiments and computation, underpinning biotechnology.
Curr. Opin. Biotechnol. 39, IV-VI (2016)
Theis, F.J.
Das ist der Zyklus der Systembiologie.
Laborjournal 23, 22-25 (2016)
Theis, F.J.
Zelle unter Beobachtung: "Mit der Software können wir die Entwicklung im Video studieren".
MEDICA Magazin, accepted (2016)
Thomas, J. ; Garzorz-Stark, N.* ; Kuepper, L.* ; Krause, L. ; Müller, N.S. ; Biedermann, T.* ; Theis, F.J. ; Schmidt-Weber, C.B. ; Eyerich, K.* ; Eyerich, S.
Characterization of multiple B cell subsets in peripheral blood of psoriasis patients identifies a correlation of plasma and regulatory B cells with disease severity.
Exp. Dermatol. 25, 27-28 (2016)
Willmann, S.# ; Müller, N.S.# ; Engert, S. ; Sterr, M. ; Burtscher, I. ; Raducanu, A. ; Irmler, M. ; Beckers, J. ; Sass, S. ; Theis, F.J. ; Lickert, H.
The global gene expression profile of the secondary transition during pancreatic development.
Mech. Dev. 139, 51-64 (2016)
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 Immunol. 9, 917-926 (2016)
Barbosa, J.S. ; Sanchez-Gonzalez, R. ; di Giaimo, R. ; Baumgart, E.V. ; Theis, F.J. ; Götz, M. ; Ninkovic, J.
Live imaging of adult neural stem cell behavior in the intact and injured zebrafish brain.
Science 348, 789-793 (2015)
Bartel, J.# ; Krumsiek, J.# ; Schramm, K. ; Adamski, J. ; Gieger, C. ; Herder, C.* ; Carstensen, M.* ; Peters, A. ; Rathmann, W.* ; Roden, M.* ; Strauch, K. ; Suhre, K. ; Kastenmüller, G. ; Prokisch, H. ; Theis, F.J.
The human blood metabolome-transcriptome interface.
PLoS Genet. 11:e1005274 (2015)
Buettner, F.# ; Natarajan, K.N.*# ; Casale, F.P.* ; Proserpio, V.* ; Scialdone, A.* ; Theis, F.J. ; Teichmann, S.A.* ; Marioni, J.C.*° ; Stegle, O.*°
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Nat. Biotechnol. 33, 155-160 (2015)
Calzolari, F. ; Michel, J. ; Baumgart, E.V. ; Theis, F.J. ; Götz, M.° ; Ninkovic, J.°
Fast clonal expansion and limited neural stem cell self-renewal in the adult subependymal zone.
Nat. Neurosci. 18, 490-492 (2015)
Cappetta, M. ; Lauri, A. ; Myklatun, A. ; Haghverdi, L. ; Marr, C. ; Theis, F.J. ; Westmeyer, G.G.
Analysis of brain network activity patterns at the cell-circuit level.
Vortrag: EMIM European Molecular Imaging Meeting, 18-20 March 2015, Tübingen. (2015)
Cappetta, M. ; Lauri, A. ; Myklatun, A. ; Haghverdi, L. ; Marr, C. ; Theis, F.J. ; Westmeyer, G.G.
Neuroimaging of photoaversive responses in partially restrained zebrafish larvae.
Vortrag: European Molecular Imaging Meeting, 18-20 May 2015, Tuebingen, Germany. (2015)
Do, K.T. ; Kastenmüller, G. ; Mook-Kanamori, D.O.* ; Yousri, N.A.* ; Theis, F.J. ; Suhre, K. ; Krumsiek, J.
Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva.
J. Proteome Res. 14, 1183-1194 (2015)
Filipczyk, A.# ; Marr, C.# ; Hastreiter, S.# ; Feigelman, J. ; Schwarzfischer, M. ; Hoppe, P.S. ; Loeffler, D. ; Kokkaliaris, K.D. ; Endele, M. ; Schauberger, B. ; Hilsenbeck, O. ; Skylaki, S. ; Hasenauer, J. ; Anastassiadis, K.* ; Theis, F.J.° ; Schroeder, T.°
Network plasticity of pluripotency transcription factors in embryonic stem cells.
Nat. Cell Biol. 17, 1235-1246 (2015)
Garzorz, N.V.* ; Krause, L. ; Lauffer, F.* ; Atenhan, A.* ; Thomas, J.* ; Theis, F.J. ; Biedermann, T.* ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Molecular diagnostics of psoriasis and eczema-a novel approach to establish personalised therapy.
J. Invest. Dermatol. 135, S1 (2015)
Haghverdi, L. ; Buettner, F. ; Theis, F.J.
Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Bioinformatics 31, 2989-2998 (2015)
Hasenauer, J. ; Jagiella, N. ; Hross, S. ; Theis, F.J.
Data-driven modelling of biological multi-scale processes.
J. Coupled Syst. Multiscale Dyn. 3, 101-121 (2015)
Helmbrecht, M.S.# ; Soellner, H.# ; Castiblanco-Urbina, M.A. ; Winzeck, S. ; Sundermeier, J. ; Theis, F.J. ; Fouad, K.* ; Huber, A.B.
A critical period for postnatal adaptive plasticity in a model of motor axon miswiring.
PLoS ONE 10:e0123643 (2015)
Hug, S.° ; Schwarzfischer, M. ; Hasenauer, J. ; Marr, C. ; Theis, F.J.°
An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule.
Stat. Comp. 26, 663-677 (2015)
Illner, K. ; Miettinen, J.* ; Fuchs, C. ; Taskinen, S.* ; Nordhausen, K.* ; Oja, H.* ; Theis, F.J.
Model selection using limiting distributions of second-order blind source separation algorithms.
Signal Process. 113, 95-103 (2015)
Ilmonen, P.* ; Nordhausen, K.* ; Oja, H.* ; Theis, F.J.
An affine equivariant robust second-order BSS method.
Lecture Notes Comp. Sci. 9237, 328-335 (2015)
Kondofersky, I. ; Fuchs, C. ; Theis, F.J.
Identifying latent dynamic components in biological systems.
IET Syst. Biol. 9, 193-203 (2015)
Kong, B.* ; Bruns, P. ; Raulefs, S.* ; Rieder, S.* ; Paul, L.* ; da Costa, O.P.* ; Buch, T.* ; Theis, F.J. ; Michalski, C.W.* ; Kleeff, J.*
Metabolism gene signatures and surgical site infections in abdominal surgery.
Int. J. Surg. 14, 67-74 (2015)
Krumsiek, J.# ; Mittelstraß, K.# ; Do, K.T. ; Stückler, F. ; Ried, J.S. ; Adamski, J. ; Peters, A. ; Illig, T.* ; Kronenberg, F.* ; Friedrich, N.* ; Nauck, M.* ; Pietzner, M.* ; Mook-Kanamori, D.O.* ; Suhre, K. ; Gieger, C. ; Grallert, H. ; Theis, F.J.° ; Kastenmüller, G.°
Gender-specific pathway differences in the human serum metabolome.
Metabolomics 11, 1815-1833 (2015)
Linnemann, J. ; Miura, H. ; Meixner, L.K. ; Irmler, M. ; Kloos, U. ; Hirschi, B. ; Bartsch, H.S.* ; Sass, S. ; Beckers, J. ; Theis, F.J. ; Gabka, C.* ; Sotlar, K.* ; Scheel, C.
Quantification of regenerative potential in primary human mammary epithelial cells.
Development 142, 3239-3251 (2015)
Loos, C. ; Marr, C. ; Theis, F.J. ; Hasenauer, J.
Approximate bayesian computation for stochastic single-cell time-lapse data using multivariate test statistics.
Lecture Notes Comp. Sci. 9308, 52-63 (2015)
Marr, C.° ; Hasenauer, J.° ; Theis, F.J.°
Models and methods for systems biology and systems medicine: The Institute of Computational Biology at the Helmholtz Zentrum München.
Systembiologie.de 9, 40-43 (2015)
Masserdotti, G.# ; Gillotin, S.*# ; Sutor, B.* ; Drechsel, D.* ; Irmler, M. ; Jørgensen, H.F.* ; Sass, S. ; Theis, F.J. ; Beckers, J. ; Berninger, B.* ; Guillemot, F.*° ; Götz, M.°
Transcriptional mechanisms of proneural factors and REST in regulating neuronal reprogramming of astrocytes.
Cell Stem Cell 17, 74-88 (2015)
Meyer, S.U.* ; Sass, S. ; Müller, N.S. ; Krebs, S.* ; Bauersachs, S.* ; Kaiser, S.* ; Blum, H.* ; Thirion, C.* ; Krause, S.* ; Theis, F.J. ; Pfaffl, M.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:e0135284 (2015)
Moignard, V.* ; Woodhouse, S.* ; Haghverdi, L. ; Lilly, A.J.* ; Tanaka, Y.* ; Wilkinson, A.C.* ; Buettner, F. ; Macaulay, I.C.* ; Jawaid, W.* ; Diamanti, E.* ; Nishikawa, S.I.* ; Piterman, N.* ; Kouskoff, V.* ; Theis, F.J. ; Fisher, J.*° ; Gottgens, B.*°
Decoding the regulatory network of early blood development from single-cell gene expression measurements.
Nat. Biotechnol. 33, 269-276 (2015)
Müller, S.* ; Raulefs, S.* ; Bruns, P.* ; Afonso-Grunz, F.* ; Plötner, A.* ; Thermann, R.* ; Jager, C.* ; Schlitter, A.M.* ; Kong, B.* ; Regel, I.* ; Roth, W.K.* ; Rotter, B.* ; Hoffmeier, K.* ; Kahl, G.F.* ; Koch, I.* ; Theis, F.J. ; Kleeff, J.* ; Winter, P.* ; Michalski, C.W.*
Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer.
Mol. Cancer 14:94 (2015)
Müller, S.* ; Raulefs, S.* ; Bruns, P.* ; Afonso-Grunz, F.* ; Plötner, A.* ; Thermann, R.* ; Jager, C.* ; Schlitter, A.M.* ; Kong, B.* ; Regel, I.* ; Roth, W.K.* ; Rotter, B.* ; Hoffmeier, K.* ; Kahl, G.F.* ; Koch, I.* ; Theis, F.J. ; Kleeff, J.* ; Winter, P.* ; Michalski, C.W.*
Erratum to: Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer.
Mol. Cancer 14:144 (2015)
Ocone, A. ; Haghverdi, L. ; Müller, N.S. ; Theis, F.J.
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.
Bioinformatics 31, i89-i96 (2015)
Preusse, M. ; Marr, C. ; Saunders, S.* ; Maticzka, D.* ; Lickert, H. ; Backofen, R.* ; Theis, F.J.
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins.
RNA Biol. 12, 998-1009 (2015)
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.J. ; Klingmüller, U.* ; Schöberl, B.* ; Timmer, J.*
Data2Dynamics: A modeling environment tailored to parameter estimation in dynamical systems.
Bioinformatics 31, 3558-3560 (2015)
Sadic, D.* ; Schmidt, K.* ; Groh, S.* ; Kondofersky, I. ; Ellwart, J.W. ; Fuchs, C. ; Theis, F.J. ; Schotta, G.*
Atrx promotes heterochromatin formation at retrotransposons.
EMBO Rep. 16, 836-850 (2015)
Sass, S. ; Buettner, F. ; Müller, N.S. ; Theis, F.J.
RAMONA: A web application for gene set analysis on multilevel omics data.
Bioinformatics 31, 128-130 (2015)
Sass, S.° ; Pitea, A.° ; Unger, K. ; Hess, J. ; Müller, N.S. ; Theis, F.J.°
MicroRNA-target network inference and local network enrichment analysis identify two microRNA clusters with distinct functions in head and neck squamous cell carcinoma.
Int. J. Mol. Sci. 16, 30204-30222 (2015)
Schmidt, J. ; Panzilius, E. ; Bartsch, H.S.* ; Irmler, M. ; Beckers, J. ; Kari, V.* ; Linnemann, J. ; Dragoi, D. ; Hirschi, B. ; Kloos, U. ; Sass, S. ; Theis, F.J. ; Kahlert, S.* ; Johnsen, S.A.* ; Sotlar, K.* ; Scheel, C.
Stem-cell-like properties and epithelial plasticity arise as stable traits after transient Twist1 activation.
Cell Rep. 10, 131-139 (2015)
Schmidt, J. ; Panzilius, E. ; Bartsch, H.* ; Irmler, M. ; Beckers, J. ; Kari, V.* ; Linnemann, J. ; Dragoi, D. ; Hirschi, B. ; Kloos, U. ; Sass, S. ; Theis, F.J. ; Kahlert, S.* ; Johnsen, S.A.* ; Sotlar, K.* ; Scheel, C.
Stem cell-like properties and epithelial plasticity arise as stable traits after transient Twist1-activation .
Vortrag: Frontiers in Stem Cells & Cancer, 29-31 March 2015, Heidelberg. (2015)
Strasser, M. ; Feigelman, J. ; Theis, F.J. ; Marr, C.
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy.
BMC Syst. Biol. 9:61 (2015)
Theis, F.J.° ; Ugelvig, L.V.*° ; Marr, C.° ; Cremer, S.*°
Opposing effects of allogrooming on disease transmission in ant societies.
Philos. Trans. R. Soc. B - Biol. Sci. 370, DOI: 10.1098/rstb.2014.0108 (2015)
Wahl, S.#° ; Vogt, S.*# ; Stückler, F. ; Krumsiek, J. ; Bartel, J. ; Kacprowski, T.* ; Schramm, K. ; Carstensen, M.* ; Rathmann, W.* ; Roden, M.* ; Jourdan, C. ; Kangas, A.J.* ; Soininen, P.* ; Ala-Korpela, M.* ; Nöthlings, U.* ; Boeing, H.* ; Theis, F.J. ; Meisinger, C. ; Waldenberger, M. ; Suhre, K. ; Homuth, G.* ; Gieger, C. ; Kastenmüller, G. ; Illig, T. ; Linseisen, J. ; Peters, A. ; Prokisch, H. ; Herder, C. ; Thorand, B.° ; Grallert, H.°
Multi-omic signature of body weight change: Results from a population-based cohort study.
BMC Med. 13:48 (2015)
Wang, L. ; Belagiannis, V.* ; Marr, C. ; Theis, F.J. ; Yang, G.Z.* ; Navab, N.*
Anatomic-landmark detection using graphical context modelling.
In: Proceedings (12th IEEE International Symposium on Biomedical Imaging, ISBI 2015, 16-19 April 2015, Brooklyn, United States). 2015. 1304-1307
Wilson, N.K.* ; Kent, D.G.* ; Buettner, F. ; Shehata, M.* ; Macaulay, I.C.* ; Calero-Nieto, F.J.* ; Sánchez Castillo, M.* ; Oedekoven, C.A.* ; Diamanti, E.* ; Schulte, R.* ; Ponting, C.P.* ; Voet, T.* ; Caldas, C.* ; Stingl, J.* ; Green, A.R.* ; Theis, F.J. ; Göttgens, B.*
Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations.
Cell Stem Cell 16, 712-724 (2015)
Albrecht, E.# ; Waldenberger, M.# ; Krumsiek, J. ; Evans, A.M.* ; Jeratsch, U. ; Breier, M. ; Adamski, J. ; Koenig, W.* ; Zeilinger, S. ; Fuchs, C. ; Klopp, N. ; Theis, F.J. ; Wichmann, H.-E. ; Suhre, K. ; Illig, T. ; Strauch, K. ; Peters, A. ; Gieger, C. ; Kastenmüller, G. ; Döring, A. ; Meisinger, C.
Metabolite profiling reveals new insights into the regulation of serum urate in humans.
Metabolomics 10, 141-151 (2014)
Bajikar, S.S.*# ; Fuchs, C.# ; Roller, A. ; Theis, F.J.° ; Janes, K.A.*°
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles.
Proc. Natl. Acad. Sci. U.S.A. 111, E626-E635 (2014)
Bartel, S. ; Schulz, N. ; Alessandrini, F. ; Theis, F.J. ; Eickelberg, O. ; Kicic, A.* ; Freishtat, R.J.* ; Krauss-Etschmann, S.
MicroRNA-based identification of epithelial SEC14L3 loss in experimental and human paediatric asthma.
Allergy 69, 40-41 (2014)
Baumann, S.*# ; Rockstroh, M.*# ; Bartel, J. ; Krumsiek, J. ; Otto, W.* ; Jungnickel, H.* ; Potratz, S.* ; Luch, A.* ; Wilscher, E.* ; Theis, F.J. ; von Bergen, M.* ; Tomm, J.M.*
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.
J. Integr. OMICS, DOI: 10.5584/jiomics.v4i1.157 (2014)
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. 51, 403-411 (2014)
Buettner, F. ; Moignard, V.* ; Göttgens, B.* ; Theis, F.J.
Probabilistic PCA of censored data: Accounting for uncertainties in the visualisation of high-throughput single-cell qPCR data.
Bioinformatics 30, 1867-1875 (2014)
Feigelman, J. ; Theis, F.J. ; Marr, C.
MCA: Multiresolution Correlation Analysis, a graphical tool for subpopulation identification in single-cell gene expression data.
BMC Bioinformatics 15:240 (2014)
Fröhlich, F.° ; Theis, F.J.° ; Hasenauer, J.°
Uncertainty analysis for non-identifiable dynamical systems: Profile likelihoods, bootstrapping and more.
Lecture Notes Comp. Sci. 8859, 61-72 (2014)
Fröhlich, F.° ; Hross, S.° ; Theis, F.J.° ; Hasenauer, J.°
Radial basis function approximations of Bayesian parameter posterior densities for uncertainty analysis.
Lecture Notes Comp. Sci. 8859, 73-85 (2014)
Garzorz, N.V.*# ; Quaranta, M.# ; Knapp, B.# ; Mattii, M. ; Andres, C.* ; Theis, F.J. ; Ring, J.* ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Intra-individual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.
J. Invest. Dermatol. 134, S1 (2014)
Garzorz-Stark, N.* ; Knapp, B. ; Quaranta, M. ; Mattii, M. ; Theis, F.J. ; Ring, J.* ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Eczema ≠ eczema: The transcriptional heterogeneity of eczema.
Br. J. Dermatol. 170, E19 (2014)
Hasenauer, J. ; Wolf, V.* ; Kazeroonian, A. ; Theis, F.J.
Method of conditional moments (MCM) for the chemical master equation: A unified framework for the method of moments and hybrid stochastic-deterministic models.
J. Math. Biol. 69, 687-735 (2014)
Hasenauer, J. ; Hasenauer, C.* ; Hucho, T.* ; Theis, F.J.
ODE constrained mixture modelling: A method for unraveling subpopulation structures and dynamics.
PLoS Comput. Biol. 10:e1003686 (2014)
Illner, K. ; Fuchs, C. ; Theis, F.J.
Bayesian blind source separation for data with network structure.
J. Comput. Biol. 21, 855-865 (2014)
Illner, K.° ; Fuchs, C.° ; Theis, F.J.°
Bayesian blind source separation applied to the lymphocyte pathway.
In: Gillli, M.* ; Gonzalez-Rodriguez, G.* ; Nieto-Reyes, A.* [Eds.]: Proccedings (21st International Conference on Computational Statistics (COMPSTAT2014), 19-22 August 2014, Geneva, Switzerland). 2014. 625-632
Illner, K. ; Fuchs, C. ; Theis, F.J.
Single-cell analysis: Biology at high resolution.
Sep. Sci. Appl. 34, 24-26 (2014)
Illner, K. ; Fuchs, C. ; Theis, F.J.
Einzelzellanalysen: Biologie in Hochauflösung.
GIT Fachz. Lab. 9, 28-30 (2014)
Kazeroonian, A.° ; Theis, F.J.° ; Hasenauer, J.°
Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation.
IFAC Proc. 19, 1729-1735 (2014)
Khakhutskyy, V.*° ; Schwarzfischer, M.° ; Hubig, N.° ; Plant, C.° ; Marr, C.° ; Rieger, M.A.*° ; Schröder, T.*° ; Theis, F.J.°
Centroid clustering of cellular lineage trees.
Lecture Notes Comp. Sci. 8649, 15-29 (2014)
Matthes, M.# ; Preusse, M.# ; Zhang, J.# ; Schechter, J. ; Mayer, D. ; Lentes, B. ; Theis, F.J. ; Prakash, N. ; Wurst, W.° ; Trümbach, D.°
Mouse IDGenes: A reference database for genetic interactions in the developing mouse brain.
Database 2014:bau083 (2014)
Meyer, S.U.* ; Stoecker, K.* ; Sass, S. ; Theis, F.J. ; Pfaffl, M.W.*
Posttranscriptional regulatory networks: From expression profiling to integrative analysis of mRNA and microRNA data.
Methods Mol. Biol. 1160, 165-188 (2014)
Moignard, V.* ; Woodhouse, S.* ; Haghverdi, L. ; Lilly, J.* ; Tanaka, Y.* ; Wilkinson, A.* ; Buettner, F. ; Nishikawa, S.* ; Piterman, N.* ; Kouskoff, V.* ; Theis, F.J. ; Fisher, J.* ; Göttgens, B.*
Decoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements.
Exp. Hematol. 42, S52 (2014)
Quaranta, M. ; Knapp, B. ; Theis, F.J. ; Ring, J.* ; Schmidt-Weber, C.B. ; Eyerich, S. ; Eyerich, K.*
Intra-individual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.
Exp. Dermatol. 23, E20 (2014)
Quaranta, M.# ; Knapp, B.# ; Garzorz-Stark, 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.
Sci. Transl. Med. 6:244ra90 (2014)
Quaranta, M. ; Eyerich, S. ; Knapp, B. ; Nasorri, F.* ; Scarponi, C.* ; Mattii, M. ; Garzorz-Stark, N.* ; Harlfinger, A.T.* ; Jaeger, T.* ; Grosber, M.* ; Pennino, D. ; Mempel, M.* ; Schnopp, C.* ; Theis, F.J. ; Albanesi, C.* ; Cavani, A.* ; Schmidt-Weber, C.B. ; Ring, J.* ; Eyerich, K.*
Allergic contact dermatitis in psoriasis patients: Typical, delayed, and non-interacting.
PLoS ONE 9:e101814 (2014)
Quaranta, M.* ; Knapp, B. ; Garzoz, 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 opposing immune reaction in psoriasis and eczema.
Br. J. Dermatol. 171, E135 (2014)
Reversat, A.* ; Buggenthin, F. ; Merrin, J.* ; Leithner, A.* ; de Vries, I.* ; Theis, F.J. ; Marr, C. ; Sixt, M.*
Morphodynamic analysis of T lymphocyte migration in confined microenvironments.
Mol. Biol. Cell 25:P537 (2014)
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.
Hum. Mol. Genet. 23, 5847-5857 (2014)
Röck, K.* ; Tigges, J.* ; Sass, S. ; Schütze, A.* ; Florea, A.M.* ; Fender, A.C.* ; Theis, F.J. ; Krutmann, J.* ; Boege, F.* ; Fritsche, E.* ; Reifenberger, G.* ; Fischer, J.W.*
miR-23a-3p causes cellular senescence by targeting hyaluronan synthase2: Possible implication for skin aging.
J. Invest. Dermatol. 135, 369-377 (2014)
Shin, S.Y.*# ; Fauman, E.B.*# ; Petersen, A.-K.# ; Krumsiek, J.# ; Santos, R.* ; Huang, J.* ; Arnold, M. ; Erte, I.* ; Forgetta, V.* ; Yang, T.P.* ; Walter, K.* ; Menni, C.* ; Chen, L.* ; Vasquez, L.* ; Valdes, A.M.* ; Hyde, C.L.* ; Wang, V.* ; Ziemek, D.* ; Roberts, P.* ; Xi, L.* ; Grundberg, E.* ; Waldenberger, M. ; Richards, J.B.* ; Mohney, R.P.* ; Milburn, M.V.* ; John, S.L.* ; Trimmer, J.* ; Theis, F.J. ; Overington, J.P.* ; Suhre, K. ; Brosnan, M.J.* ; Gieger, C. ; Kastenmüller, G.° ; Spector, T.D.*° ; Soranzo, N.*°
An atlas of genetic influences on human blood metabolites.
Nat. Genet. 46, 543-550 (2014)
Thalheimer, F.B.* ; Wingert, S.* ; de Giacomo, P.* ; Haetscher, N.* ; Rehage, M.* ; Brill, B.* ; Theis, F.J. ; Hennighausen, L.* ; Schroeder, T.* ; Rieger, M.A.*
Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells.
Stem Cell Rep. 3, 34-43 (2014)
Thalheimer, F.B.* ; Wingert, S.* ; de Giacomo, P.* ; Haetscher, N.* ; Brill, B.* ; Theis, F.J. ; Hennighausen, L.* ; Schroeder, T.* ; Rieger, M.*
Cytokine-regulated GADD45G induces differentiation and lineage selection in hematopoietic stem cells.
Exp. Hematol. 42, S57 (2014)
Vinnikov, I.A.*° ; Hajdukiewicz, K.* ; Reymann, J.* ; Beneke, J.* ; Czajkowski, R.* ; Roth, L.C.* ; Novak, M.* ; Roller, A. ; Dörner, N.* ; Starkuviene, V.* ; Theis, F.J. ; Erfle, H.* ; Schütz, G.* ; Grinevich, V.*° ; Konopka, W.*°
Hypothalamic miR-103 protects from hyperphagic obesity in mice.
J. Neurosci. 34, 10659-10674 (2014)
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 6, 856-878 (2014)
Winkler, C.# ; Krumsiek, J.# ; Buettner, F. ; Angermüller, C. ; Giannopoulou, E.Z. ; Theis, F.J. ; Ziegler, A.-G.° ; Bonifacio, E.°
Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.
Diabetologia 57, 2521-2529 (2014)
Winkler, C. ; Krumsiek, J. ; Buettner, F. ; Angermüller, C. ; Giannopoulou, E.Z. ; Theis, F.J. ; Ziegler, A.-G. ; Bonifacio, E.
Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.
Diabetologia 58, 206 (2014)
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, 514-525 (2014)
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, 1299-1309 (2013)
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, 2216-2226 (2013)
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, 580-586 (2013)
Bartel, J. ; Krumsiek, J. ; Theis, F.J.
Statistical methods for the analysis of high-throughput metabolomics data.
Comp. Struc. Biotech. J. 4:e201301009 (2013)
Bartel, S. ; Schulz, N. ; Theis, F.J. ; Alessandrini, F. ; Takenaka, S. ; Eickelberg, O. ; Krauss-Etschmann, S.
SEC14L3 is de-regulated in murine experimental asthma via miRNA-mediated down-regulation of CREB.
Allergy 68, 233-233 (2013)
Bartel, S. ; Schulz, N. ; Theis, F.J. ; Alessandrini, F. ; Takenaka, S. ; Eickelberg, O. ; Krauss-Etschmann, S.
miRNA-based identification of SEC14L3 deregulation in murine experimental asthma.
Eur. Respir. J. 42 (2013)
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 14:297 (2013)
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. 7:48 (2013)
Hock, S. ; Hasenauer, J. ; Theis, F.J.
Modeling of 2D diffusion processes based on microscopy data: Parameter estimation and practical identifiability analysis.
BMC Bioinformatics 14:S7 (2013)
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, 293-304 (2013)
Kazeroonian, A.° ; Hasenauer, J.° ; Theis, F.J.°
Parameter estimation for stochastic biochemical processes: A comparison of moment equation and fintie state projection.
In: Autio, R.* ; Shmulevich, I.* ; Strimmer, K.* ; Wiuf, C.* ; Sarbu, S.* ; Yli-Harja, O.* [Eds.]: Proceedings of the WCSB 2013 (10th International Workshop on Computational Systems Biology, 10 - 12 June 2013, Tampere, Finland). Tampere: Tampere International Center for Signal Processing, 2013. 66-73 (TICSP Series ; 63)
Kong, B.* ; Wu, W.* ; Cheng, T.* ; Schlitter, A.M.* ; Bruns, P. ; Jaeger, C.* ; Regel, I.* ; Raulefs, S.* ; Behler, N.* ; Irmler, M. ; Beckers, J. ; Erkan, M.* ; Theis, F.J. ; Esposito, I.* ; Kleeff, J.* ; Michalski, C.W.*
Identification and characterization of an Aldh1a3-positive subtype of pancreatic ductal adenocarcinoma mediated by oncogenic Krasg12d/Erk-Mtor axis.
Pancreas 42, 1360-1361 (2013)
Kong, B.* ; Behler, N.* ; Bruns, P. ; Schlitter, A.M.* ; Valkovska, N.* ; Fritzsche, S.* ; Raulefs, S.* ; Regel, I.* ; Erkan, M.* ; Theis, F.J. ; Esposito, I.* ; Kleeff, J.* ; Michalski, C.W.*
Pancreatic progenitor expansion, mesenchymal cell proliferation and inflammation are required during early carcinogenesis.
Pancreas 42, 1360 (2013)
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.* ; Woodward, O.M.* ; Okada, Y.* ; Tin, A.* ; Müller, C.* ; Oldmeadow, C.* ; Putku, M.* ; Czamara, D.* ; Kraft, P.* ; Frogheri, L.* ; Thun, G.A.* ; Grotevendt, A.* ; Gislason, G.K.* ; Harris, T.B.* ; Launer, L.J.* ; McArdle, P.* ; Shuldiner, A.R.* ; Boerwinkle, E.* ; Coresh, J.* ; Schmidt, H.* ; Schallert, M.* ; Martin, N.G.* ; Montgomery, G.W.* ; Kubo, M.* ; Nakamura, Y.* ; Munroe, P.B.* ; Samani, N.J.* ; Jacobs, D.R. J.r.* ; Liu, K.* ; D'Adamo, P.* ; Ulivi, S.* ; Rotter, J.I.* ; Psaty, B.M.* ; Vollenweider, P.* ; Waeber, G.* ; Campbell, S.* ; Devuyst, O.* ; Navarro, P.* ; Kolcic, I.* ; Hastie, N.* ; Balkau, B.* ; Froguel, P.* ; Esko, T.* ; Salumets, A.* ; Khaw, K.T.* ; Langenberg, C.* ; Wareham, N.J.* ; Isaacs, A.* ; Kraja, A.* ; Zhang, Q.* ; Wild, P.S.* ; Scott, R.J.* ; Holliday, E.G.* ; Org, E.* ; Viigimaa, M.* ; Bandinelli, S.* ; Metter, J.E.* ; Lupo, A.* ; Trabetti, E.* ; Sorice, R.* ; Döring, A. ; Lattka, E. ; Strauch, K. ; Theis, F.J. ; Waldenberger, M. ; Wichmann, H.-E. ; Davies, G.* ; Gow, A.J.* ; Bruinenberg, M.* ; LifeLines Cohort Study ; Stolk, R.P.* ; Kooner, J.S.* ; Zhang, W.* ; Winkelmann, B.R.* ; Boehm, B.O.* ; Lucae, S.* ; Penninx, B.W.* ; Smit, J.H.* ; Curhan, G.* ; Mudgal, P.* ; Plenge, R.M.* ; Portas, L.* ; Persico, I.* ; Kirin, M.* ; Wilson, J.F.* ; Leach, I.M.* ; van Gilst, W.H.* ; Goel, A.* ; Ongen, H.* ; Hofman, A.* ; Rivadeneira, F.* ; Uitterlinden, A.G.* ; Imboden, M.* ; von Eckardstein, A.* ; Cucca, F.* ; Nagaraja, R.* ; Piras, M.G.* ; Nauck, M.* ; Schurmann, C.* ; Budde, K.* ; Ernst, F.* ; Farrington, S.M.* ; Theodoratou, E.* ; Prokopenko, I.* ; Stumvoll, M.* ; Jula, A.* ; Perola, M.* ; Salomaa, V.* ; Shin, S.Y.* ; Spector, T.D.* ; Sala, C.* ; Ridker, P.M.* ; Kähönen, M.* ; Viikari, J.* ; Hengstenberg, C.* ; Nelson, C.P.* ; Gieger, C. ; CARDIoGRAM Consortium (Wichmann, H.-E. ; Illig, T. ; Döring, A. ; Meisinger, C. ; Klopp, N. ; Peters, A. ; Meitinger, T.) ; DIAGRAM Consortium (Huth, C. ; Thorand, B. ; Meitinger, T. ; Gieger, C. ; Klopp, N. ; Grallert, H. ; Wichmann, H.-E. ; Illig, T. ; Petersen, A.-K.) ; ICBP Consortium ; MAGIC Investigators (Wichmann, H.-E. ; Illig, T. ; Meisinger, C. ; Gieger, C. ; Thorand, B. ; Grallert, H.) ; Meschia, J.F.* ; Nalls, M.A.* ; Sharma, P.* ; Singleton, A.B.* ; Kamatani, N.* ; Zeller, T.* ; Burnier, M.* ; Attia, J.* ; Laan, M.* ; Klopp, N. ; Hillege, H.L.* ; Kloiber, S.* ; Choi, H.* ; Pirastu, M.* ; Tore, S.* ; Probst-Hensch, N.M.* ; Völzke, H.* ; Gudnason, V.* ; Parsa, A.* ; Schmidt, R.* ; Whitfield, J.B.* ; Fornage, M.* ; Gasparini, P.* ; Siscovick, D.S.* ; Polasek, O.* ; Campbell, H.* ; Rudan, I.* ; Bouatia-Naji, N.* ; Metspalu, A.* ; Loos, R.J.* ; van Duijn, C.M.* ; Borecki, I.B.* ; Ferrucci, L.* ; Gambaro, G.* ; Deary, I.J.* ; Wolffenbuttel, B.H.* ; Chambers, J.C.* ; Marz, W.* ; Pramstaller, P.P.* ; Snieder, H.* ; Gyllensten, U.* ; Wright, A.F.* ; Navis, G.* ; Watkins, H.* ; Witteman, J.C.* ; Sanna, S.* ; Schipf, S.* ; Dunlop, M.G.* ; Tönjes, A.* ; Ripatti, S.* ; Soranzo, N.* ; Toniolo, D.* ; Chasman, D.I.* ; Raitakari, O.* ; Kao, W.H.* ; Ciullo, M.* ; Fox, C.S.* ; Caulfield, M.* ; Bochud, M.*
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
Nat. Genet. 45, 145-154 (2013)
Kuruoglu, E.E.* ; Theis, F.J.
Dependent component analysis.
EURASIP J. Adv. Signal Process. 2013:185 (2013)
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.* ; Göttgens, B.*
Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis.
Nat. Cell Biol. 15, 363-372 (2013)
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. Trans. R. Soc. A - Math. Phys. Eng. Sci. 371:20110544 (2013)
Raue, A.# ; Schilling, M.*# ; Bachmann, J.* ; Matteson, A.* ; Schelker, 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:e74335 (2013)
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.* [Eds.]: Systems Biology of Apoptosis. New York: Springer, 2013. 57-84
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, 629-636 (2013)
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, 1125-1135 (2013)
Sass, S.# ; Buettner, F.# ; Müller, N.S. ; Theis, F.J.
A modular framework for gene set analysis integrating multilevel omics data.
Nucleic Acids Res. 41, 9622-9633 (2013)
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, 1-22 (2013)
Schmidl, D.° ; Czado, C.*° ; Hug, S.° ; Theis, F.J.°
Rejoinder on "A vine-copula based adaptive MCMC sampler for efficient inference of dynamical systems".
Bayesian Anal. 8, 33-42 (2013)
Vehlow, C.* ; Hasenauer, J. ; Theis, F.J.° ; Weiskopf, D.*°
Visualizing edge-edge relations in graphs.
In: Proceedings of the 6th IEEE Pacific Visualization Symposium (IEEE PacificVis 2013 : 27.02.-01.03.2013, Sydney, Australia). Sydney, Australia: Univ. Sydney, 2013. 201-208
Vehlow, C.*#° ; Hasenauer, J.#° ; Krämer, A.* ; Raue, A. ; Hug, S. ; Timmer, J.* ; Radde, N.* ; Theis, F.J. ; Weiskopf, D.*
iVUN: Interactive Visualization of Uncertain biochemical reaction Networks.
BMC Bioinformatics 14:S2 (2013)
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, 315-351 (2013)
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. 11:60 (2013)
Theis, F.J. ; Cichocki, A.* ; Yeredor, A.* ; Zibulevsky, M.*[Eds.]
Latent variable analysis and signal separation : 10th International Conference, LVA/ICA 2012, Tel Aviv, Israel, March 12-15, 2012, Proceedings.
Berlin [u.a.]: Springer, 2012. ( ; 7191)
Buettner, F. ; Theis, F.J.
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst.
Bioinformatics 28, i626-i632 (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, 496-505 (2012)
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, 1266-1274 (2012)
Cichocki, A.*° ; Theis, F.J.° ; Yeredor, A.*° ; Zibulevsky, M.*°
Preface.
Lecture Notes Comp. Sci. 7191, V-VII (2012)
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.* [Eds.]: Handbook of Optimization in Complex Networks. Theory and Applications. New York, NJ: Springer, 2012. 169-208 (Optimization and Its Applications ; 57)
Gutch, H.W.* ; Theis, F.J.
Uniqueness of linear factorizations into independent subspaces.
J. Multivar. Anal. 112, 48-62 (2012)
Gutch, H.W.* ; Theis, F.J.
To infinity and beyond: On ICA over Hilbert Spaces.
In: Theis, F.J. ; Cichocki, A.* ; Yeredor, A* ; Zibulevsky, M.* [Eds.]: Proceedings (10th International Conference, LVA/ICA 2012, 12-15 March 2012, Tel Aviv, Israel). Heidelberg: Springer, 2012. 180-187 (Lecture Notes Comp. Sci. ; 7191)
Gutch, H.W.*° ; Gruber, P.*° ; Yeredor, A.*° ; Theis, F.J.°
ICA over finite fields - separability and algorithms.
Signal Process. 92, 1796-1808 (2012)
Hug, S. ; Theis, F.J.
Bayesian inference of latent causes in gene regulatory dynamics.
In: Theis, F.J. ; Cichocki, A.* ; Yeredor, A* ; Zibulevsky, M.* [Eds.]: Proceedings (10th international conference on Latent Variable Analysis and Signal Separation). Heidelberg: Springer, 2012. 520-527 (Lecture Notes Comp. Sci. ; 7191)
Illner, K.° ; Fuchs, C.° ; Theis, F.J.°
Blind source separation using latent gaussian graphical models.
In: Larjo, A.* ; Schober, S.* ; Farhan, M.* ; Bossert, M.* ; Yli-Harja, O.* [Eds.]: Proceedings (Ninth International Workshop on Computational Systems Biology, WCSB 2012, June 4-6, 2012, Ulm, Germany). Tampere, Finnland: Tampere International Center for Signal Processing, 2012. 43-46 (Proc. WCSB ; 61)
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:e40009 (2012)
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:e1001300 (2012)
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, 2607-2619 (2012)
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, 4120-4131 (2012)
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:e1003005 (2012)
Krumsiek, J. ; Stückler, F. ; Kastenmüller, G. ; Theis, F.J.
Systems biology meets metabolism.
In: Suhre, K.* [Eds.]: Genetics Meets Metabolomics: from Experiment to Systems Biology. New York: Springer, 2012. 281-313
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.* [Eds.]: Advances in Systems Biology. New York: Springer, 2012. 247-260 (Adv. Exp. Med. Biol. ; 736)
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, 3488-3500 (2012)
Meyer-Bäse, A.* ; Cappendijk, S.* ; Theis, F.J.
Uncertain gene regulatory networks simplified by gramian-based approach.
In: Arabnia, H.R.* ; Tran, Q.-N.* [Eds.]: Proceedings (2011 International Conference on Bioinformatics & Computational Biology (BIOCOMP '11), 18-21 July 2011, Las Vegas, USA). Athens, GA, USA: CSREA Press, 2012. 751-759
Nordhausen, K.* ; Gutch, H.W.* ; Oja, H.* ; Theis, F.J.
Joint diagonalization of several scatter matrices for ICA.
In: Theis, F.J. ; Cichocki, A.* ; Yeredor, A* ; Zibulevsky, M.* [Eds.]: Proceedings (10th international conference on Latent Variable Analysis and Signal Separation). Heidelberg: Springer, 2012. 172-179 (Lecture Notes in Computer Science ; 7191)
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, 13292-13308 (2012)
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 13:120 (2012)
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.
Adv. Artif. Neural Syst. 2012:962105 (2012)
Ruepp, A. ; Kowarsch, A. ; Theis, F.J.
PhenomiR: MicroRNAs in human diseases and biological processes.
Methods Mol. Biol. 822, 249-260 (2012)
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. 6:95 (2012)
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, 1565-1567 (2012)
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, 19-29 (2012)
Theis, F.J.
Bayesian fuzzy clustering of colored graphs.
In: Theis, F.J. ; Cichocki, A.* ; Yeredor, A* ; Zibulevsky, M.* [Eds.]: Proceedings (10th international conference on Latent Variable Analysis and Signal Separation). Heidelberg: Springer, 2012. 528-535 (Lecture Notes Comp. Sci. ; 7191)
Winkler, C. ; Krumsiek, J. ; Lempainen, J. ; Achenbach, P. ; Grallert, H. ; Giannopoulou, E.Z. ; 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, 549-555 (2012)
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, 135-145 (2011)
Blöchl, F.# ; Wittmann, D.M.# ; Theis, F.J.
Effective parameters determining the information flow in hierarchical biological systems.
Bull. Math. Biol. 73, 706-725 (2011)
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: Górriz, J.M.* ; Lang, E.W.* ; Ramirez, J.* [Eds.]: Recent Advances in Biomedical Signal Processing. Hilversum: Bentham Science Publishers, 2011. 157-170
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 83:046127 (2011)
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, 1742-1758 (2011)
Gutch, H.W.* ; Krumsiek, J. ; Theis, F.J.
An ISA algorithm with unknown group sizes successfully identifies biologically meaningful clusters in metabolomics data.
In: Eur. Signal Process. Conf (19th European Signal Processing Conference, 29 August - 2 September 2011, Barcelona). Barcelona: EUSIPCO, 2011. 1733-1737
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:e26457 (2011)
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, 809-819 (2011)
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. 5:21 (2011)
Krumsiek, J.# ; Marr, C.# ; Schroeder, T. ; Theis, F.J.
Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network.
PLoS ONE 6:e22649 (2011)
Krumsiek, J. ; Wittmann, D.M. ; Theis, F.J.
From discrete to continuous gene regulation models - a tutorial using the odefy toolbox.
Applications of MATLAB in Science and Engineering. Rijeka: InTech, 2011. 35-60
Laaser, I. ; Theis, F.J. ; Hrabě de Angelis, M. ; Kolb, H.-J. ; Adamski, J.
Huge splicing frequency in human Y chromosomal UTY gene.
OMICS 15, 141-154 (2011)
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.* [Eds.]: Recent Advances in Biomedical Signal Processing. Oak Park, IL: Bentham Science Publishers, 2011. 26-47
Lang, E.W.* ; Schachtner, R.* ; Lutter, D.* ; Herold, D.* ; Kodewitz, A.* ; Blöchl, F.* ; Theis, F.J. ; Keck, I.R.* ; Górriz Sáez, J.M.* ; Gomez, P.* ; 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.* [Eds.]: Recent Advances in Biomedical Signal Processing. Sharjah: Bentham Science, 2011. 26-47
Meyer-Bäse, A.* ; Plant, C.* ; Krumsiek, J.* ; Theis, F.J. ; Emmett, M.* ; Conrad, C.A.*
Stability analysis of hybrid stochastic gene regulatory networks.
In: Arabnia, H.R.* ; Tran, Q.-N.* [Eds.]: Proceedings (The 2011 International Conference on Bioinformatics and Computational Biology). Elsevier, 2011. ( ; Proceedings of BIOCOMP'11)
Mittelstraß, K.# ; Ried, J.S.# ; Yu, Z.# ; Krumsiek, J. ; Gieger, C. ; Prehn, C. ; Römisch-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:e1002215 (2011)
Müller, N.S.* ; Krumsiek, J. ; Theis, F.J. ; Böhm, C.* ; Meyer-Bäse, A.*
Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells.
Proc. SPIE 8058:805819 (2011)
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.* ; Lichtner, 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, 693-704 (2011)
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. 5:136 (2011)
Schwarzfischer, M.# ; Marr, C.# ; Krumsiek, J. ; Hoppe, P.S. ; Schroeder, T. ; Theis, F.J.
Efficient fluorescence image normalization for time lapse movies.
In: Proceedings (Microscopic Image Analysis with Applications in Biology, 2nd September 2011, Heidelberg, Germany). Heidelberg: MIAAB, 2011. http://www.miaab.org/miaab-2011-
Theis, F.J.# ; Bohl, S.*# ; Klingmüller, U.*
Theoretical analysis of time-to-peak responses in biological reaction networks.
Bull. Math. Biol. 73, 978-1003 (2011)
Theis, F.J. ; Latif, N.* ; Wong, P. ; Frishman, D.
Complex principal component and correlation structure of 16 yeast genomic variables.
Mol. Biol. Evol. 28, 2501-2512 (2011)
Theis, F.J. ; Kawanabe, M.* ; Müller, K.-R.*
Uniqueness of non-Gaussianity-based dimension reduction.
IEEE Trans. Signal Process. 59, 4478 - 4482 (2011)
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, 1928-1936 (2011)
Wittmann, D.M. ; Theis, F.J.
Dynamic regimes of random fuzzy logic networks.
New J. Phys. 13:013041 (2011)
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, 9-21 (2010)
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.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Latent variable analysis and signal separation (Latent variable analysis and signal separation 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 114-122 (Lecture Notes Comp. Sci. ; 6365)
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.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 123-130 (Lecture Notes Comp. Sci. ; 6365)
Blöchl, F.# ; Kowarsch, A.# ; Theis, F.J.#
Second-order source separation based on prior knowledge realized in a graph model.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 434-441 (Lecture Notes Comp. Sci. ; 6365)
Blöchl, F.# ; Hartsperger, M.L.# ; Stuempflen, V. ; Theis, F.J.
Uncovering the structure of heterogeneus biological data: Fuzzy graph partitioning in the k-partite setting.
In: Schomburg, D.* ; Grote, A.* [Eds.]: Proceedings (German Conference on Bioinformatics 2010). Bonn: Ges. f. Inform., 2010. 31-40 ( ; P-173)
Blöchl, F. ; Theis, F.J. ; Vega-Redondo, F.* ; Fisher, E.O'N.*
Which sectors of a modern economy are most central?
In: Empirical and theoretical methods. München: ifo Institut für Wirtschaftsforschung e.V., 2010. 1-20 (CESifo working paper series ; 3175)
Franke, R.* ; Theis, F.J. ; Klamt, S.*
From binary to multivalued to continuous models: The lac operon as a case study.
J. Integr. Bioinform. 7:151 (2010)
Gutch, H.W.* ; Maehara, T.* ; Theis, F.J.
Second order subspace analysis and simple decompositions.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 370-377 ( ; 6365)
Gutch, H.W.* ; Gruber, P.* ; Theis, F.J.
ICA over finite fields.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 645-652 ( ; 6365)
Hartsperger, M.L.# ; Blöchl, F.# ; Stuempflen, V. ; Theis, F.J.
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs.
BMC Bioinformatics 11:522 (2010)
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, 14835-14842 (2010)
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 11:585 (2010)
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:e11154 (2010)
Kreuzpointner, L.* ; Simon, P.* ; Theis, F.J.
The ad coefficient as a descriptive measure of the within-group agreement of ratings.
Br. J. Math. Stat. Psychol. 63, 341-360 (2010)
Krumsiek, J. ; Pölsterl, S. ; Wittmann, D.M. ; Theis, F.J.
Odefy - from discrete to continuous models.
BMC Bioinformatics 11, 1-10:233 (2010)
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 11:224 (2010)
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, 31:e1000836 (2010)
Mewes, H.-W. ; Ruepp, A. ; Theis, F.J. ; Rattei, T.* ; Walter, M.C. ; Frishman, D. ; Suhre, K. ; Spannagl, M. ; Mayer, K.F.X. ; Stuempflen, V. ; Antonov, A.
MIPS: Curated databases and comprehensive secondary data resources in 2010.
Nucleic Acids Res. 39, 1, D220-D224 (2010)
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, 189-197 (2010)
Meyer-Bäse, A.* ; Plant, C.* ; Cappendijk, S.* ; Theis, F.J.
Robust stability analysis of multi-time scale genetic regulatory networks under parametric uncertainties.
In: Proceedings (BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology). Las Vegas (Nevada): CSREA Press, 2010.
Plant, C.* ; Theis, F.J. ; Meyer-Bäse, A.* ; Böhm, C.*
Information-theoretic model selection for independent components.
In: Vigneron, V.* ; Zarzoso, V.* ; Moreau, E.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Berlin: Springer, 2010. 254-262 (Lecture Notes Comp. Sci. ; 6365)
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:R6 (2010)
Theis, F.J. ; Müller, N.S.* ; Plant, C.* ; Böhm, C.*
Robust second-order source separation identifies experimental responses in biomedical imaging.
In: Vigneron, V.* [Eds.]: Proceedings (Latent variable analysis and signal separation : 9th international conference, 27-30 September 2010, St. Malo, France). Heidelberg: Springer, 2010. 466-473 (LNCS; 6365)
Theis, F.J.
Colored subspace analysis: Dimension reduction based on a signal's autocorrelation structure.
IEEE Trans. Circuits Syst. I-Regul. Pap. 57, 1463-1474 (2010)
Theis, F.J. ; Meyer-Bäse, A.
Foundations of medical imaging and signal recording.
In: Biomedical Signal Analysis - Contemporary Methods and Applications. Cambridge, MA: MIT Press, 2010. 1-28
Theis, F.J. ; Meyer- Bäse, A.*
Biomedical signal analysis: Contemporary methods and applications.
Cambridge, Mass.: MIT Press, 2010. 432 S.
Thiemann, C.* ; Theis, F.J. ; Grady, D.* ; Brune, R.* ; Brockmann, D.*
The structure of borders in a small world.
PLoS ONE 5:e15422 (2010)
Wittmann, D.M. ; Marr, C. ; Theis, F.J.
Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks.
J. Theor. Biol. 266, 436-448 (2010)
Blöchl, F. ; Theis, F.J.
Estimating hidden influences in metabolic and gene regulatory networks.
In: Adali, T.* [Eds.]: Independent Component Analysis and Signal Separation. Berlin: Springer, 2009. 387-394 (Lecture Notes Comp. Sci. ; 5441)
Georgiev, P.G.*° ; Theis, F.J.°
Optimization techniques for data representions with biomedical applications.
In: Romejin, H.E.* ; Pardalos, P.M.* [Eds.]: Handbook of Optimization in Medicine. New York: Springer, 2009. 1-38 (Springer Optimization and Its Applications ; 26)
Georgiev, P.G.* ; Theis, F.J.
Optimization techniques for data representations with biomedical applications.
In: Pardalos, P.M.* ; Romejin, H.E.* [Eds.]: Handbook of Optimization in Medicine. New York: Springer Science + Business Media B.V., 2009. 253-290
Gruber, P.* ; Gutch, H.W.* ; Theis, F.J.
Hierarchical extraction of independent subspaces of unknown dimensions.
In: Adali, T.* [Eds.]: Independent Component Analysis and Signal Separation. Berlin: Springer, 2009. 259-266 (Lecture Notes Comp. Sci. ; 5441)
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, 497-504 (2009)
Klamt, S.* ; Haus, U.-U.* ; Theis, F.J.
Hypergraphs and cellular networks.
PLoS Comput. Biol. 5:e1000385 (2009)
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, 3791-3800 (2009)
Theis, F.J. ; Cason, T.P.* ; Absil, P.A.*
Soft dimension reduction for ICA by joint diagonalization on the Stiefel manifold.
In: Adali, T.* [Eds.]: Independent Component Analysis and Signal Separation. Berlin: Springer, 2009. 354-361 (Lecture Notes Comp. Sci. ; 5441)
Theis, F.J. ; Neher, R.* ; Zeug, A.*
Blind decomposition of spectral imaging microscopy: A study on artificial and real test data.
In: Adali, T.* [Eds.]: Proceedings (Independent Component Analysis and Signal Separation). Berlin: Springer, 2009. 548-556 (Lecture Notes in Computer Science ; 5441)
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:R81 (2009)
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:e1000569 (2009)
Wittmann, D.M. ; Schmidl, D. ; Blöchl, F. ; Theis, F.J.
Reconstruction of graphs based on random walks.
Theor. Comput. Sci. 410, 3826-3838 (2009)
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, 98:98 (2009)
Adamcio, B.*# ; Sargin, D.*# ; Stradomska, A.*# ; Medrihan, L.* ; Gertler, C.* ; Theis, F.J.* ; Zhang, M.* ; Müller, M.* ; Hassouna, I.* ; Hannke, K.* ; Sperling, S.* ; Radyushkin, K.* ; El-Kordi, A.* ; Schulze, L.* ; Ronnenberg, A.* ; Wolf, F.* ; Brose, N.* ; Rhee, J.S.* ; Zhang, W.* ; Ehrenreich, H.*
Erythropoietin enhances hippocampal long-term potentiation and memory.
BMC Biol. 6:37 (2008)
Begemann, M.*# ; Sargin, D.*# ; Rossner, M.J.* ; Bartels, C.* ; Theis, F.J.* ; Wichert, S.P.* ; Stender, N.* ; Fischer, B.* ; Sperling, S.* ; Stawicki, S.* ; Wiedl, A.* ; Falkai, P.* ; Nave, K.A.* ; Ehrenreich, H.*
Episode-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling supports novel treatment approaches.
Mol. Med. 14, 546-552 (2008)
Brockmann, D.* ; Theis, F.J.
Money Circulation, Trackable Items, and the Emergence of Universal Human Mobility Patterns.
IEEE Pervasive Comput. 7, 28-35 (2008)
Lutter, D.* ; Ugocsai, P.* ; Grandl, M.* ; Orso, E.* ; Theis, F.J.* ; Lang, E.W.* ; Schmitz, G.*
Analyzing M-CSF dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis.
BMC Bioinformatics 9:100 (2008)
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, 1688-1697 (2008)
Theis, F.J.* ; Gruber, P.* ; Keck, I.R.* ; Lang, E.W.*
A robust model for spatiotemporal dependencies.
Neurocomp. 71, 2209-2216 (2008)
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 9:629 (2008)
Gutch, H.W.*° ; Theis, F.J.*°
Independent subspace analysis is unique, given irreducibility.
Lecture Notes Comp. Sci. 4666, 49-56 (2007)
Kawanabe, M.* ; Theis, F.J.*
Joint low-rank approximation for extracting non-Gaussian subspaces.
Signal Process. 87, 1890-1903 (2007)
Theis, F.J.* ; Kawanabe, M.*
Colored subspace analysis.
Lecture Notes Comp. Sci. 4666, 121-128 (2007)
Theis, F.J.* ; Georgiev, P.* ; Cichocki, A.*
Robust sparse component analysis based on a generalized Hough transform.
EURASIP J. Adv. Signal Process. 2007:052105 (2007)