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Hastreiter, S. et al.: Inductive and selective effects of GSK3 and MEK inhibition on nanog heterogeneity in embryonic stem cells. Stem Cell Rep. 10, 58-69 (2018)
Buggenthin, F. et al.: Prospective identification of hematopoietic lineage choice by deep learning. Nat. Methods, DOI: 10.1038/nmeth.4182 (2017)
Hilsenbeck, O.* et al.: fastER: A user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy. Bioinformatics 33, 2020-2028 (2017)
Feigelman, J. et al.: 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. et al.: Software tools for single-cell tracking and quantification of cellular and molecular properties. Nat. Biotechnol. 34, 703-706 (2016)
Hoppe, P.S. et al.: Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios. Nature 535, 299-302 (2016)
Filipczyk, A. et al.: 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)
Grote, J.* et al.: Evidence of autoinducer-dependent and autoinducer-independent heterogeneous gene expression in Sinorhizobium fredii NGR234. Appl. Environ. Microbiol. 80, 5572-5582 (2014)
Khakhutskyy, V.* et al.: Centroid clustering of cellular lineage trees. Lecture Notes Comp. Sci. 8649, 15-29 (2014)
Schwarzfischer, M.: Quantification and analysis of single-cell protein dynamics in stem cells using time-lapse microscopy. München, Technische Universität, Fakultät Wissenschaftszentrum Weihenstephan, Diss., 2014
Buggenthin, F. et al.: An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy. BMC Bioinformatics 14:297 (2013)
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)
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)
Schwarzfischer, M. et al.: 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-
Schwarzfischer, M.: Single-cell analysis of multipotente hematopoietic progenitor cells. München, Technische Universität & Ludwig-Maximilians-Universität, Fakultät für Informatik, Diplom-Arbeit, 2009, 70 S.