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. ; 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)
Dragoi, D. ; Krattenmacher, A. ; Mishra, V.K.* ; Schmidt, J. ; Kloos, U. ; Meixner, L.K. ; Hauck, S.M. ; Buggenthin, F. ; Schwartz, D. ; Marr, C. ; Johnsen, S.A.* ; Scheel, C.
Twist1 induces distinct cell states depending on TGFBR1-activation.
Oncotarget 7, 30396-30407 (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)
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)
Marr, C. ; Zhou, J.X.* ; Huang, S.*
Single-cell gene expression profiling and cell state dynamics: Collecting data, correlating data points and connecting the dots.
Curr. Opin. Biotechnol. 39, 207-214 (2016)
Mishra, M. ; Schmitt, S. ; Wang, L. ; Strasser, M. ; Marr, C. ; Navab, N.* ; Zischka, H. ; Peng, T.
Structure-based assessment of cancerous mitochondria using deep networks.
In: Proceedings (Proceedings / IEEE 13th International Symposium on Biomedical Imaging (ISBI), 13-16 April 2016, Prague, Czech Republic). IEEE, 2016.
Feigelman, J.° ; Popovic, N.* ; Marr, C.°
A case study on the use of scale separation-based analytical propagators for parameter inference in models of stochastic gene regulation.
J. Coupled Syst. Multiscale Dyn. 3, 164-173 (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)
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)
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)
Popovic, N.* ; Marr, C. ; Swain, P.S.*
A geometric analysis of fast-slow models for stochastic gene expression.
J. Math. Biol. 72, 87-122 (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)
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)
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
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)
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)
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)
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)
Marr, C. ; Hütt, M.-T.*
Cellular automata on graphs: Topological properties of ER graphs evolved towards low-entropy dynamics.
Entropy 14, 993-1010 (2012)
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)
Sonnenschein, N.* ; Marr, C. ; Hütt, M.-T.*
A topological characterization of medium-dependent essential metabolic reactions.
Metabolites 2, 632-647 (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)
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.# ; Marr, C.# ; Schroeder, T. ; Theis, F.J.
Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network.
PLoS ONE 6:e22649 (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-
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)
Liebovitch, L.S.* ; Shehadeh, L.A.* ; Jirsa, V.K.* ; Hütt, M.-T.* ; Marr, C.
Determining the properties of gene regulatory networks from expression data.
In: Das, S.* ; Caragea, D.* ; Welch, S.* ; Hsu, W.H.* [Eds.]: Handbook of Research on Computational Methodologies in Gene Regulatory Networks. IGI Global, 2010. 405-428
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)
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)
Marr, C. ; Hütt, M.-T.*
Outer-totalistic cellular automata on graphs.
Phys. Lett. A 373, 546-549 (2009)
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)
Marr, C. ; Geertz, M.* ; Hütt, M.-T.* ; Muskhelisvili, G.*
Dissecting the logical types of network control in gene expression profiles.
BMC Syst. Biol. 2:18 (2008)
Marr, C.* ; Müller-Linow, M.* ; Hütt, M.-T.*
Regularizing capacity of metabolic networks.
Phys. Rev. E 75:041917 (2007)
Marr, C.* ; Hütt, M.-T.*
Similar impact of topological and dynamic noise on complex patterns.
Phys. Lett. A 349, 302-305 (2006)
Beige, A.* ; Cable, H.* ; Marr, C.* ; Knight, P.*
Speeding up gate operations through dissipation.
Laser Phys. 15, 162-169 (2005)
Marr, C.* ; Hütt, M.-T.*
Topology regulates pattern formation capacity of binary cellular automata on graphs.
Physica A 354, 641-662 (2005)
Marr, C.* ; Beige, A.* ; Rempe, G.*
Entangled-state preparation via dissipation-assisted adiabatic passages.
Phys. Rev. A 68:033817 (2003)