Selected publications

2024

  • Pomreinke, AP, Müller, P (2024). Zebrafish nampt-a mutants are viable despite perturbed primitive hematopoiesis. Hereditas 161, 14. doi.org/10.1186/s41065-024-00318-y
  • Kögler AC, Müller P (2024). Modes and motifs in multicellular communication. Cell Systems, 15:1–3 (https://authors.elsevier.com/a/1iRk28YyDfmxdX).
  • Knabl, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife 13:e80803.

2023

  • Toulany N, Morales-Navarrete H, Čapek D, Grathwohl J, Ünalan M, Müller P (2023). Uncovering developmental time and tempo using deep learning. Nature Methods, 20:2000-2010.
  • Ullrich T, Pollmann C, Ritter M, Haaf J, Aghaallaei N, Tesakov I, El-Riz M, Maksymenko K, Hatskovska V, Kandabarau S, Klimiankou M, Lengerke C, Welte K, Hernandez-Alvarez B, Müller P, Lupas A, Piehler J, Skokowa J, ElGamacy M (2023). Tuning of granulopoietic signaling by de novo designed agonists. bioRxiv 2023.11.25.568662.
  • Čapek D, Safroshkin M, Morales-Navarrete H, Toulany N, Arutyunuv G, Kurzbach A, Bihler J, Hagauer J, Kick S, Jones F, Jordan B, Müller P (2023). EmbryoNet: Using deep learning to link embryonic phenotypes to signaling pathways. Nature Methods, 20:815–823.
  • Maksymenko K, Maurer A, Aghaallaei N, Barry C, Borbarán-Bravo N, Ullrich T, Dijkstra TMH, Hernandez Alvarez B, Müller P, Lupas AN, Skokowa J, ElGamacy M (2023). The design of functional proteins using tensorized energy calculations. Cell Reports Methods, 3:100560.
  • Müller P et al. (2023). AI identifies developmental defects and drug mechanisms in embryos. Nature Methods, 20:793–794.

2022

  • Morales-Navarrete H, Müller P (2022). Gastrulation: Nodal signaling controls ordered collective cell migration. Current Biology, 32:R1354-R1356.
  • Kuhn T, Landge AN, Mörsdorf D, Coßmann J, Gerstenecker J, Čapek D, Müller P, Gebhardt JCM (2022). Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model. Nature Communications, 13:6101.
  • Knabl, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Müller P, Genikhovich G (2022). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. bioRxiv 2022.06.03.494682.
  • Skokowa J, Hernandez Alvarez B, Coles M, Ritter M, Nasri M, Haaf J, Aghaallaei N, Xu Y, Mir P, Krahl AC, Rogers KW, Maksymenko K, Bajoghli B, Welte K, Lupas AN, Müller P, ElGamacy M (2022). A topological refactoring design strategy yields highly stable granulopoietic proteins. Nature Communications, 13:2948.
  • Preiß H, Kögler AC, Mörsdorf D, Čapek D, Soh GH, Rogers KW, Morales-Navarrete H, Almuedo-Castillo M, Müller P (2022). Regulation of Nodal signaling propagation by receptor interactions and positive feedback. eLife, 11:e66397.

2021

  • Soh GH, Kögler AC, Müller P (2021). A simple and effective transplantation device for zebrafish embryos. J Vis Exp, doi:10.3791/62767.
  • Čapek D, Ünalan M, Müller P (2021). Wie Tiere sich selbst konstruieren. BIOspektrum, 27:473-477.

2020

  • Rogers KW, ElGamacy M, Jordan BM, Müller P (2020). Optogenetic investigation of BMP target gene expression diversity. eLife, 9:e58641.
  • Soh GH, Pomreinke AP, Müller P (2020). Integration of Nodal and BMP signaling by mutual signaling effector antagonism. Cell Reports, 31:107487.
  • Hernandez Alvarez B, Skokowa J, Coles M, Mir P, Nasri M, Maksymenko K, Weidmann L, Rogers KW, Welte K, Lupas AN, Müller P, ElGamacy M (2020). Design of novel granulopoietic proteins by topological rescaffolding. PLOS Biology, 18:e3000919.
  • Böffert R, Businger R, Preiß H, Ehmann D, Truffault V, Simon C, Ruetalo N, Hamprecht K, Müller P, Wehkamp J, Schindler M (2020). The human α-defensin-derived peptide HD5(1-9) inhibits cellular attachment and entry of human cytomegalovirus. Antiviral Research, 177:104779.
  • Müller P, El-Sherif E (2020). A systems-level view of pattern formation mechanisms in development. Developmental Biology 460:1.
  • Ünalan M, Müller P (2020). Painting flowers with MYBs. Current Biology, 5:227-229.
  • Rogers KW, Müller P (2020). Optogenetic approaches to investigate spatiotemporal signaling during development. Current Topics in Developmental Biology, 137:37-77.
  • Landge AN, Jordan BM, Diego X, Müller P (2020). Pattern formation mechanisms of self-organizing reaction-diffusion systems. Developmental Biology 460:2-11.

2019

  • Čapek D, Müller P (2019). Positional information and tissue scaling during development and regeneration. Development, 146:dev177709.
  • Morishima T, Krahl AC, Nasri M, Xu Y, Aghaallaei N, Findik B, Klimiankou M, Ritter M, Hartmann MD, Gloeckner CJ, Stefańczyk S, Lindner C, Oswald B, Bernhard R, Hähnel K, Hermanutz-Klein U, Ebinger M, Handgretinger R, Casadei N, Welte K, Andre M, Müller P, Bajoghli B, Skokowa J (2019). LMO2 activation by deacetylation is indispensable for hematopoiesis and T-ALL leukemogenesis. Blood, 134:1159-1175.
  • Mörsdorf D, Müller P (2019). Tuning protein diffusivity with membrane tethers. Biochemistry, 58:177-181.
  • Prummel KD, Hess C, Nieuwenhuize S, Parker HJ, Rogers KW, Kozmikova I, Racioppi C, Brombacher EC, Czarkwiani A, Knapp D, Burger S, Chiavacci E, Shah G, Burger A, Huisken J, Yun MH, Christiaen L, Kozmik Z, Müller P, Bronner M, Krumlauf R, Mosimann C (2019). A conserved regulatory program initiates lateral plate mesoderm emergence across chordates. Nature Communications, 10:3857.
  • Rogers KW, Müller P (2019). Nodal and BMP dispersal during early zebrafish development. Developmental Biology, 447:17-23.

2018

  • Almuedo-Castillo M, Bläßle A, Mörsdorf D, Marcon L, Soh GH, Rogers KW, Schier AF, Müller P (2018). Scale-invariant patterning by size-dependent inhibition of Nodal signalling. Nature Cell Biology, 20:1032-1042.  
  • Soh GH, Müller P (2018). FRAP analysis of extracellular diffusion in zebrafish embryos. Methods Mol Biol, 1863:107-124. 
  • Piragyte I, Clapes T, Polyzou A, Geltink RIK, Lefkopoulos S, Yin N, Cauchy P, Curtis JD, Klaeylé L, Langa X, Beckmann CCA, Wlodarski MW, Müller P, Van Essen D, Rambold A, Kapp FG, Mione M, Buescher JM, Pearce EL, Polyzos A, Trompouki E (2018). A metabolic interplay coordinated by HLX regulates myeloid differentiation and AML through partly overlapping pathways. Nature Communications, 9:3090. 
  • Diego X, Marcon L, Müller P, Sharpe J (2018). Key features of Turing systems are determined purely by network topology. Phys. Rev. X, 8:021071. 
  • Bläßle A, Soh G, Braun T, Mörsdorf D, Preiß H, Jordan BM, Müller P (2018). Quantitative diffusion measurements using the open-source software PyFRAP. Nature Communications, 9:1582. 
  • Ramachandran A, Vizan P, Debipriya D, Chakravarty P, Vogt J, Rogers KW, Müller P, Hinck AP, Sapkota GP, Hill CS (2018). TGF-β uses a novel mode of receptor activation to phosphorylate SMAD1/5 and induce epithelial-to-mesenchymal transition. eLife, 7:e31756. 

2017

  • Pomreinke AP, Soh GH, Rogers KW, Bergmann JK, Bläßle AJ, Müller P (2017). Dynamics of BMP signaling and distribution during zebrafish dorsal-ventral patterning. eLife, 6:e25861. 
  • Donovan P, Dubey OA, Kallioinen S, Rogers KW, Muehlethaler K, Müller P, Rimoldi D, Constam DB (2017). Paracrine Activin-A signaling promotes melanoma growth and metastasis through immune evasion. J Invest Dermatol, 137:2578-2587. 

2016

  • Marcon L, Diego X, Sharpe J, Müller P (2016). High-throughput mathematical analysis identifies Turing networks for patterning with equally diffusing signals. eLife, 5:e14022. 
  • Sako K, Pradhan SJ, Barone V, Inglés-Prieto Á, Müller P, Ruprecht V, Capek D, Galande S, Janovjak H, Heisenberg CP (2016). Optogenetic control of Nodal signaling reveals a temporal pattern of Nodal signaling regulating cell fate specification during gastrulation. Cell Reports,16:866-877.
  • Müller P, Nüsslein-Volhard C (2016). Obituary: Hans Meinhardt (1938-2016). Development, 143:1231-1233. 

2015

  • Bläßle A, Müller P (2015). PyFDAP: Automated analysis of Fluorescence Decay After Photoconversion (FDAP) experiments. Bioinformatics, 15:972-974. 
  • Rogers KW, Bläßle A, Schier AF, Müller P (2015). Measuring protein stability in living zebrafish embryos using Fluorescence Decay After Photoconversion (FDAP). J Vis Exp, 95:52266. 

Before 2015

  • Müller P, Rogers KW, Shuizi RY, Brand M, Schier AF (2013). Morphogen transport. Development, 140:1621-1638.
  • Müller P, Rogers KW, Jordan BM, Lee JS, Robson D, Ramanathan S, Schier AF (2012). Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system. Science, 336:721-724.
  • Xu C, Fan ZP, Müller P, Fogley R, DiBiase A, Trompouki E, Unternaehrer J, Xong F, Torregroza I, Evans T, Megason SG, Daley GQ, Schier AF, Young RA, Zon LI (2012). Nanog regulates endoderm formation through the Mxtx2-Nodal pathway. Dev Cell, 22:625-638.
  • Müller P, Pugazhendhi D, Zeidler MP (2012). Modulation of human JAK/STAT pathway signalling by functionally conserved regulators. JAK-STAT, 1:34-43.
  • Müller P, Schier AF (2011). Extracellular movement of signaling molecules. Dev Cell, 21:145-158.
  • Müller P, Boutros M, Zeidler MP (2008). Identification of JAK/STAT pathway regulators - Insights from RNAi screens. Semin Cell Dev Biol, 19:360-369.
  • Ginsberg M, Czeko E, Müller P, Ren Z, ChenX, Darnell JE Jr. (2007). Amino acid residues required for physical and cooperative interaction of STAT3 and AP-1 proteins c-Jun and c-Fos. Mol Cell Biol, 27:6300-6308.
  • Dietz GP, Valbuena C, Dietz B, Meuer K, Müller P, Weishaupt JH, Bähr M (2006). Application of a blood-brain-barrier-penetrating form of GDNF in a mouse model for Parkinson’s disease. Brain Res, 1082:61-66.
  • Müller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M (2005). Identification of JAK/STAT signaling components by genome-wide RNA interference. Nature, 436:871-875.

The full publication list can be found on Google Scholar and ORCID 

The KOPS (Konstanz Online Publication System) repository entries below provide links to the full texts of our publications.

Publication list

  • Article
  • Book
  • Dissertation
  • Thesis
  • Proceedings
  • Other
  • Link to full text
  • Link to original publication
  •    
    Müller, Patrick; Kuttenkeuler, David; Gesellchen, Viola; Zeidler, Martin P.; Boutros, Michael (2005): Identification of JAK/STAT signalling components by genome-wide RNA interference
    Müller, Patrick, Kuttenkeuler, David, Gesellchen, Viola, Zeidler, Martin P. & Boutros, Michael. Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 436, 871–875 (2005).

    Identification of JAK/STAT signalling components by genome-wide RNA interference

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    Signalling pathways mediating the transduction of information between cells are essential for development, cellular differentiation and homeostasis. Their dysregulation is also frequently associated with human malignancies. The Janus tyrosine kinase/signal transducer and activator of transcription (JAK/STAT) pathway represents one such signalling cascade whose evolutionarily conserved roles include cell proliferation and haematopoiesis. Here we describe a systematic genome-wide survey for genes required for JAK/STAT pathway activity. Analysis of 20,026 RNA interference (RNAi)-induced phenotypes in cultured Drosophila melanogaster haemocyte-like cells identified interacting genes encoding 4 known and 86 previously uncharacterized proteins. Subsequently, cell-based epistasis experiments were used to classify these proteins on the basis of their interaction with known components of the signalling cascade. In addition to multiple human disease gene homologues, we have found the tyrosine phosphatase Ptp61F and the Drosophila homologue of BRWD3, a bromo-domain-containing protein disrupted in leukaemia. Moreover, in vivo analysis demonstrates that disrupted dBRWD3 and overexpressed Ptp61F function as suppressors of leukaemia-like blood cell tumours. This screen represents a comprehensive identification of novel loci required for JAK/STAT signalling and provides molecular insights into an important pathway relevant for human cancer. Human homologues of identified pathway modifiers may constitute targets for therapeutic interventions.

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