Browse by Research Team

2025

Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.
Pentimalli, T.M., Schallenberg, S., León-Periñán, D., Legnini, I., Theurillat, I., Thomas, G., Boltengagen, A., Fritzsche, S., Nimo, J., Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M.T., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F., Woehler, A., Karaiskos, N., Klauschen, F. and Rajewsky, N.
Cell Systems : 101261. 11 April 2025 (In Press)

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kügelgen, N., Ludwik, K.A., Mendonsa, S., Römer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Efendic, F., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
NAR Molecular Medicine 2 (2): ugaf005. April 2025

2024

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kuegelgen, N., Ludwik, K., Mendonsa, S., Roemer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
bioRxiv : 2024.08.17.607965. 17 August 2024

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A., Kim, S.J., Thomas, G., Farsi, Z., Zolotarov, G., Dube, G., Deter, A., Bahry, E., Georgii, E., Woehler, A., Piwecka, M. and Rajewsky, N.
EMBO Reports 25 (7): 3039. July 2024

MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution.
Mertens, T.F., Liebheit, A.T., Ehl, J., Köhler, R., Rakhymzhan, A., Woehler, A., Katthän, L., Ebel, G., Liublin, W., Kasapi, A., Triantafyllopoulou, A., Schulz, T.J., Niesner, R.A. and Hauser, A.E.
Nature Communications 15 (1): 1764. 26 February 2024

2023

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Rybak-Wolf, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Kempa, S., Zinzen, R., Woehler, A. and Rajewsky, N.
Nature Methods 20 (10): 1544-1552. October 2023

Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein, E.D., Ruffault, P.L., Misios, A., Osman, K.L., Li, H., Greenberg, R.S., Thompson, R., Song, K., Dietrich, S., Li, X., Vladimirov, N., Woehler, A., Brunet, J.F., Zampieri, N., Kühn, R., Liberles, S.D., Jia, S., Lewin, G.R., Rajewsky, N., Lever, T.E. and Birchmeier, C.
Neuron 111 (14): 2184-2200.e7. 19 July 2023

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A., Wyler, E., Pentimalli, T.M., Legnini, I., Oliveras Martinez, A., Glažar, P., Loewa, A., Kim, S.J., Kaufer, B.B., Woehler, A., Landthaler, M. and Rajewsky, N.
Nature Microbiology 8 (7): 1252-1266. July 2023

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
Lin, M., Hartl, K., Heuberger, J., Beccaceci, G., Berger, H., Li, H., Liu, L., Müllerke, S., Conrad, T., Heymann, F., Woehler, A., Tacke, F., Rajewsky, N. and Sigal, M.
Nature Communications 14 (1): 3025. 25 May 2023

A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish.
Huljev, K., Shamipour, S., Pinheiro, D., Preusser, F., Steccari, I., Sommer, C.M., Naik, S. and Heisenberg, C.P.
Developmental Cell 58 (7): 582-596.e7. 10 April 2023

2022

RS-FISH: precise, interactive, fast, and scalable FISH spot detection.
Bahry, E., Breimann, L., Zouinkhi, M., Epstein, L., Kolyvanov, K., Mamrak, N., King, B., Long, Xi, Harrington, K.I.S., Lionnet, T. and Preibisch, S.
Nature Methods 19 (12): 1563-1567. December 2022

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.
Reichart, D., Lindberg, E.L., Maatz, H., Miranda, A.M.A., Viveiros, A., Shvetsov, N., Gärtner, A., Nadelmann, E.R., Lee, M., Kanemaru, K., Ruiz-Orera, J., Strohmenger, V., DeLaughter, D.M., Patone, G., Zhang, H., Woehler, A., Lippert, C., Kim, Y., Adami, E., Gorham, J.M., Barnett, S.N., Brown, K., Buchan, R.J., Chowdhury, R.A., Constantinou, C., Cranley, J., Felkin, L.E., Fox, H., Ghauri, A., Gummert, J., Kanda, M., Li, R., Mach, L., McDonough, B., Samari, S., Shahriaran, F., Yapp, C., Stanasiuk, C., Theotokis, P.I., Theis, F.J., van den Bogaerdt, A., Wakimoto, H., Ware, J.S., Worth, C.L., Barton, P.J.R., Lee, Y.A., Teichmann, S.A., Milting, H., Noseda, M., Oudit, G.Y., Heinig, M., Seidman, J.G., Hubner, N. and Seidman, C.E.
Science 377 (6606): eabo1984. 5 August 2022

Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice.
Schepanski, S., Chini, M., Sternemann, V., Urbschat, C., Thiele, K., Sun, T., Zhao, Y., Poburski, M., Woestemeier, A., Thieme, M.T., Zazara, D.E., Alawi, M., Fischer, N., Heeren, J., Vladimirov, N., Woehler, A., Puelles, V.G., Bonn, S., Gagliani, N., Hanganu-Opatz, I.L. and Arck, P.C.
Nature Communications 13 (1): 4571. 5 August 2022

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

2021

Dual-view light-sheet imaging through a tilted glass interface using a deformable mirror.
Vladimirov, N., Preusser, F., Wisniewski, J., Yaniv, Z., Desai, R.A., Woehler, A. and Preibisch, S.
Biomedical Optics Express 12 (4): 2186-2203. 1 April 2021

Single synapse glutamate imaging reveals multiple levels of release mode regulation in mammalian synapses.
Farsi, Z., Walde, M., Klementowicz, A.E., Paraskevopoulou, F. and Woehler, A.
iScience 24 (1): 101909. 22 January 2021

2020

Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration.
Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z., Ludwig, C.F., Novarino, G., López-Cayuqueo, K.I., Planells-Cases, R. and Jentsch, T.J.
EMBO Journal 39 (9): e103358. 4 May 2020

2019

Teashirt 1 (Tshz1) is essential for the development, survival and function of hypoglossal and phrenic motor neurons in mouse.
Chaimowicz, C., Ruffault, P.L., Chéret, C., Woehler, A., Zampieri, N., Fortin, G., Garratt, A.N. and Birchmeier, C.
Development 146 (17): dev174045. 6 September 2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.
Ciolli Mattioli, C., Rom, A., Franke, V., Imami, K., Arrey, G., Terne, M., Woehler, A., Akalin, A., Ulitsky, I. and Chekulaeva, M.
Nucleic Acids Research 47 (5): 2560-2573. 18 March 2019

2018

Clathrin coat controls synaptic vesicle acidification by blocking vacuolar ATPase activity.
Farsi, Z., Gowrisankaran, S., Krunic, M., Rammner, B., Woehler, A., Lafer, E.M., Mim, C., Jahn, R. and Milosevic, I.
eLife 7 : e32569. 13 April 2018

2017

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A., van den Bruck, D., Ciolli Mattioli, C., Franke, V., Imami, K., McShane, E., Moreno-Estelles, M., Calviello, L., Filipchyk, A., Peguero-Sanchez, E., Müller, T., Woehler, A., Birchmeier, C., Merino, E., Rajewsky, N., Ohler, U., Mazzoni, E.O., Selbach, M., Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

Proton electrochemical gradient: driving and regulating neurotransmitter uptake.
Farsi, Z., Jahn, R. and Woehler, A.
BioEssays 39 (5): 1600240. May 2017

Engineering an achromatic Bessel beam using a phase-only spatial light modulator and an iterative Fourier transformation algorithm.
Walde, M., Jost, A., Wicker, K. and Heintzmann, R.
Optics Communications 383 : 64-68. 15 January 2017

Imaging activity-dependent signaling dynamics at the neuronal synapse using FRET-based biosensors.
Farsi, Z. and Woehler, A.
Methods in Molecular Biology 1538 : 261-275. 2017

2016

Superpriming of synaptic vesicles as a common basis for intersynapse variability and modulation of synaptic strength.
Taschenberger, H., Woehler, A. and Neher, E.
Proceedings of the National Academy of Sciences of the United States of America 113 (31): E4548-E4557. 2 August 2016

Single-vesicle imaging reveals different transport mechanisms between glutamatergic and GABAergic vesicles.
Farsi, Z., Preobraschenski, J., van den Bogaart, G., Riedel, D., Jahn, R. and Woehler, A.
Science 351 (6276): 981-984. 26 February 2016

2015

The Green Gut: chlorophyll degradation in the gut of Spodoptera littoralis.
Badgaa, A., Büchler, R., Wielsch, N., Walde, M., Heintzmann, R., Pauchet, Y., Svatos, A., Ploss, K. and Boland, W.
Journal of Chemical Ecology 41 (11): 965-974. November 2015

2014

Calcium-buffering effects of gluconate and nucleotides, as determined by a novel fluorimetric titration method.
Woehler, A., Lin, K.H. and Neher, E.
Journal of Physiology 592 (22): 4863-4875. 15 November 2014

Vinculin binding angle in podosomes revealed by high resolution microscopy.
Walde, M., Monypenny, J., Heintzmann, R., Jones, G.E. and Cox, S.
PLoS ONE 9 (2): e88251. 11 February 2014

2013

Blocking endocytosis enhances short-term synaptic depression under conditions of normal availability of vesicles.
Hua, Y., Woehler, A., Kahms, M., Haucke, V., Neher, E. and Klingauf, J.
Neuron 80 (2): 343-349. 16 October 2013

Functional analysis of PEX13 mutation in a Zellweger syndrome spectrum patient reveals novel homooligomerization of PEX13 and its role in human peroxisome biogenesis.
Krause, C., Rosewich, H., Woehler, A. and Gärtner, J.
Human Molecular Genetics 22 (19): 3844-3857. 1 October 2013

Simultaneous quantitative live cell imaging of multiple FRET-based biosensors.
Woehler, A.
PLoS ONE 8 (4): e61096. 16 April 2013

2012

Quantitative intensity-based FRET approaches - a comparative snapshot.
Zeug, A., Woehler, A., Neher, E. and Ponimaskin, E.
Biophysical Journal 103 (9): 1821-1827. 7 November 2012

Heterodimerization of serotonin receptors 5-HT1A and 5-HT7 differentially regulates receptor signalling and trafficking.
Renner, U., Zeug, A., Woehler, A., Niebert, M., Dityatev, A., Dityateva, G., Gorinski, N., Guseva, D., Abdel-Galil, D., Froehlich, M., Doering, F., Wischmeyer, E., Richter, D.W., Neher, E. and Ponimaskin, E.G.
Journal of Cell Science 125 (Pt 10): 2486-2499. 15 May 2012

2010

Signal/noise analysis of FRET-based sensors.
Woehler, A., Wlodarczyk, J. and Neher, E.
Biophysical Journal 99 (7): 2344-2354. 6 October 2010

2009

G protein - mediated signaling: same receptor, multiple effectors.
Woehler, A. and Ponimaskin, E.G.
Current Molecular Pharmacology 2 (3): 237-248. November 2009

Specific oligomerization of the 5-HT1A receptor in the plasma membrane.
Woehler, A., Wlodarczyk, J. and Ponimaskin, E.G.
Glycoconjugate Journal 26 (6): 749-756. August 2009

2008

Stimulation- and palmitoylation-dependent changes in oligomeric conformation of serotonin 5-HT1A receptors.
Kobe, F., Renner, U., Woehler, A., Wlodarczyk, J., Papusheva, E., Bao, G., Zeug, A., Richter, D., Neher, E. and Ponimaskin, E.
Biochimica et Biophysica Acta - Molecular Cell Research 1783 (8): 1503-1516. August 2008

Analysis of FRET signals in the presence of free donors and acceptors.
Wlodarczyk, J., Woehler, A., Kobe, F., Ponimaskin, E., Zeug, A. and Neher, E.
Biophysical Journal 94 (3): 986-1000. 1 February 2008