Sonja Nowotschin, PhD

Senior Research Scientist

Pictured: Sonja Nowotschin

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Education & Training

2014-present: Senior Research Scientist, Developmental Biology Program, Sloan Kettering Institute (lab of Kat Hadjantonakis)

2011–2014: Research Associate, Developmental Biology Program, Sloan Kettering Institute (lab of Kat Hadjantonakis)

2006–2011: Postdoctoral Fellow, Developmental Biology Program, Sloan Kettering Institute (lab of Kat Hadjantonakis)

2005–2006: Postdoctoral Fellow, Albert Einstein College of Medicine (lab of Bernice Morrow)

2002–2005: Graduate studies, University of Karlsruhe, Germany and Albert Einstein College of Medicine, New York (lab of Bernice Morrow)

Research Interests

My research interests are centered on investigating mechanisms of tissue morphogenesis and cell lineage patterning at the time of gastrulation. I use the mouse embryo, embryo-derived and pluripotent stem cells as mammalian model systems. The goal of my work is to formulate a blueprint for understanding analogous events in human development.

My studies specifically focus on the mechanisms driving cell fate decisions towards mesoderm and/or endoderm, the transitions between epithelial and mesenchymal (EMT & MET) states, and how these events are coordinated during embryonic development at gastrulation.

Optical imaging, single-cell transcriptomics, mouse genetics and embryology, and stem cell methods are central approaches that I use.


Recent Publications

Visit PubMed for a full listing of Sonja Nowotschin’s journal articles

Wu T, Hadjantonakis AK, Nowotschin S. Visualizing endoderm cell populations and their dynamics in the mouse embryo with a Hex-tdTomato reporter. Biology Open. 6(5):678-687. PMID: 28288969. PMCID: PMC5450328.

Wang Q., Zou Y., Nowotschin S., Kim SY., Li Q., Soh CL., Xi Q., Zhang C., Su J., Shu W., Huangfu D., Hadjantonakis AK., Massague J. The p53 Family Coordinates Wnt and Nodal Inputs in Mesendodermal Differentiation of Embryonic Stem Cells. Cell Stem Cell. 20(10:70-86). PMID: 27889317. PMCID: PMC5218926

Costello I., Nowotschin S., Sun X., Mould AW., Hadjantonakis AK., Bikoff, EK., Robertson EJ. Lhx1 functions together with Otx2, Foxa2 and the Ldb1 chromatin looping machinery to govern anterior mesendoderm, node and midline development. Genes and Development. 29(20);2108-22. PMID: 26494787. PMCID: PMC4617976

Viotti M., Nowotschin S. and Hadjantonakis AK. (2014) SOX17 links gut endoderm morphogenesis and germ layer segregation.  Nature Cell Biology. 16(12):1146-56. PMID:25419850. PMCID: PMC4250291

Nowotschin S., Costello I., Piliszek A., Kwon GS., Mao CA., Klein WH., Robertson EJ., Hadjantonakis AK. (2013) The T-box transcription factor Eomesodermin is essential for AVE induction in the mouse embryo. Genes & Development. 27(9):997-1002. PMID: 23651855. PMCID: PMC3656330


Nowotschin S, Costello I, Piliszek A, Kwon GS, Mao CA, Klein WH, Robertson EJ, Hadjantonakis AK. The T-box transcription factor Eomesodermin is essential for AVE induction in the mouse embryo. Genes Dev. 2013 27(9):997-1002.

Nowotschin S, Xenopoulos P, Schrode N, Hadjantonakis AK. A bright single-cell resolution live imaging reporter of Notch signaling in the mouse. BMC Dev Biol. 2013 13:15.

Nowotschin S, Ferrer-Vaquer A, Concepcion D, Papaioannou VE, Hadjantonakis AK. Interaction of Wnt3a, Msgn1 and Tbx6 in neural versus paraxial mesoderm lineage commitment and paraxial mesoderm differentiation in the mouse embryo. Dev Biol. 2012 367(1):1-14.

Xenopoulos P, Nowotschin S, Hadjantonakis AK. Live imaging fluorescent proteins in early mouse embryos. Methods Enzymol. 2012;506:361-89.

Viotti M, Nowotschin S, Hadjantonakis AK. Afp::mCherry, a red fluorescent transgenic reporter of the mouse visceral endoderm. Genesis. 2011 49(3):124-33.

Isern J, He Z, Fraser ST, Nowotschin S, Ferrer-Vaquer A, Moore R, Hadjantonakis AK, Schulz V, Tuck D, Gallagher PG, Baron MH. Single-lineage transcriptome analysis reveals key regulatory pathways in primitive erythroid progenitors in the mouse embryo. Blood. 2011 117(18):4924-34.

Santella A, Du Z, Nowotschin S, Hadjantonakis AK, Bao Z. A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. BMC Bioinformatics. 2010 11:580.

Nowotschin S, Ferrer-Vaquer A, Hadjantonakis AK. Imaging mouse development with confocal time-lapse microscopy. Methods Enzymol. 2010; 476:351-77.

Nowotschin S, Hadjantonakis AK. Cellular dynamics in the early mouse embryo: from axis formation to gastrulation. Curr Opin Genet Dev. 2010 20(4):420-7.

Nowotschin S, Hadjantonakis AK. Photomodulatable fluorescent proteins for imaging cell dynamics and cell fate. Organogenesis. 2009 5(4):135-44.

Nowotschin S, Hadjantonakis AK.Use of KikGR a photoconvertible green-to-red fluorescent protein for cell labeling and lineage analysis in ES cells and mouse embryos.

BMC Dev Biol. 2009 9:49.

Nowotschin S, Eakin GS, Hadjantonakis AK. Dual transgene strategy for live visualization of chromatin and plasma membrane dynamics in murine embryonic stem cells and embryonic tissues. Genesis. 2009 47(5):330-6.

Nowotschin S, Eakin GS, Hadjantonakis AK. Live-imaging fluorescent proteins in mouse embryos: multi-dimensional, multi-spectral perspectives. Trends Biotechnol. 2009 27(5):266-76.

Liao J, Aggarwal VS, Nowotschin S, Bondarev A, Lipner S, Morrow BE. Identification of downstream genetic pathways of Tbx1 in the second heart field.

Dev Biol. 2008 Apr 15;316(2):524-37.

Nowotschin S, Liao J, Gage PJ, Epstein JA, Campione M, Morrow BE. Tbx1 affects asymmetric cardiac morphogenesis by regulating Pitx2 in the secondary heart field. Development. 2006 133(8):1565-73.

Arnold JS, Werling U, Braunstein EM, Liao J, Nowotschin S, Edelmann W, Hebert JM, Morrow BE. Inactivation of Tbx1 in the pharyngeal endoderm results in 22q11DS malformations. Development. 2006 133(5):977-87.

Liao J, Kochilas L, Nowotschin S, Arnold JS, Aggarwal VS, Epstein JA, Brown MC, Adams J, Morrow BE. Full spectrum of malformations in velo-cardio-facial syndrome/DiGeorge syndrome mouse models by altering Tbx1 dosage. Hum Mol Genet. 2004 13(15):1577-85.

Raft S, Nowotschin S, Liao J, Morrow BE. Suppression of neural fate and control of inner ear morphogenesis by Tbx1. Development. 2004 131(8):1801-12.

Campione M, Steinbeisser H, Schweickert A, Deissler K, van Bebber F, Lowe LA, Nowotschin S, Viebahn C, Haffter P, Kuehn MR, Blum M. The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. Development. 1999 126(6):1225-34.