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Abdelilah-Seyfried, Salim

Macrophage development from hematopoietic stem cells requires PU.1 coordinated microRNA expression.
Ghani, S., Riemke, P., Schoenheit, J., Lenze, D., Stumm, J., Hoogenkamp, M., Lagendijk, A., Heinz, S., Bonifer, C., Bakkers, J., Abdelilah-Seyfried, S., Hummel, M. and Rosenbauer, F.
Blood 118 (8): 2275-2284. 25 August 2011

Akalin, Altuna (BIMSB)

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

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

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification.
Delgado-Benito, V., Berruezo-Llacuna, M., Altwasser, R., Winkler, W., Sundaravinayagam, D., Balasubramanian, S., Caganova, M., Graf, R., Rahjouei, A., Henke, M.T., Driesner, M., Keller, L., Prigione, A., Janz, M., Akalin, A. and Di Virgilio, M.
Journal of Experimental Medicine 217 (10): e20200137. 5 October 2020

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.
Fornes, O., Jia, A., Kuehn, H.S., Min, Q., Pannicke, U., Schleussner, N., Thouenon, R., Yu, Z., de Los Angeles Astbury, M., Biggs, C.M., Galicchio, M., Garcia-Campos, J.A., Gismondi, S., Gonzalez Villarreal, G., Hildebrand, K.J., Hönig, M., Hou, J., Moshous, D., Pittaluga, S., Qian, X., Rozmus, J., Schulz, A.S., Staines-Boone, A.T., Sun, B., Sun, J., Uwe, S., Venegas-Montoya, E., Wang, W., Wang, X., Ying, W., Zhai, X., Zhou, Q., Akalin, A., André, I., Barth, T.F.E., Baumann, B., Brüstle, A., Burgio, G., Bustamante, J.C., Casanova, J.L., Casarotto, M.G., Cavazzana, M., Chentout, L., Cockburn, I.A., Costanza, M., Cui, C., Daumke, O., Del Bel, K.L., Eibel, H., Feng, X., Franke, V., Gebhardt, J.C.M., Götz, A., Grunwald, S., Hoareau, B., Hughes, T.R., Jacobsen, E.M., Janz, M., Jolma, A., Lagresle-Peyrou, C., Lai, N., Li, Y., Lin, S., Lu, H.Y., Lugo-Reyes, S.O., Meng, X., Möller, P., Moreno-Corona, N., Niemela, J.E., Novakovsky, G., Perez-Caraballo, J.J., Picard, C., Poggi, L., Puig-Lombardi, M.E., Randall, K.L., Reisser, A., Schmitt, Y., Seneviratne, S., Sharma, M., Stoddard, J., Sundararaj, S., Sutton, H., Tran, L.Q., Wang, Y., Wasserman, W.W., Wen, Z., Winkler, W., Xiong, E., Yang, A.W.H., Yu, M., Zhang, L., Zhang, H., Zhao, Q., Zhen, X., Enders, A., Kracker, S., Martinez-Barricarte, R., Mathas, S., Rosenzweig, S.D., Schwarz, K., Turvey, S.E. and Wang, J.Y.
Science Immunology 8 (79): eade7953. January 2023

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
Karabacak Calviello, A., Hirsekorn, A., Wurmus, R., Yusuf, D. and Ohler, U.
Genome Biology 20 (1): 42. 21 February 2019

Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence.
Kolesnichenko, M., Mikuda, N., Höpken, U.E., Kärgel, E., Uyar, B., Tufan, A.B., Milanovic, M., Sun, W., Krahn, I., Schleich, K., von Hoff, L., Hinz, M., Willenbrock, M., Jungmann, S., Akalin, A., Lee, S., Schmidt-Ullrich, R., Schmitt, C.A. and Scheidereit, C.
EMBO Journal 40 (6): e104296. 15 March 2021

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E., Ofenbauer, A., Bulut, S.I., Uyar, B., Baytek, G., Sommermeier, A., Seelk, S., He, M., Hirsekorn, A., Vucicevic, D., Akalin, A., Diecke, S., Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W., Akalin, A. and Ohler, U.
Nature Machine Intelligence 4 (2): 162-168. February 2022

Deep learning for genomics using Janggu.
Kopp, W., Monti, R., Tamburrini, A., Ohler, U. and Akalin, A.
Nature Communications 11 (1): 3488. 13 July 2020

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
Menzel, L., Zschummel, M., Crowley, T., Franke, V., Grau, M., Ulbricht, C., Hauser, A., Siffrin, V., Bajénoff, M., Acton, S.E., Akalin, A., Lenz, G., Willimsky, G., Höpken, U.E. and Rehm, A.
Cell Reports 37 (4): 109878. 26 October 2021

Degrons in cancer.
Meszaros, B., Kumar, M., Gibson, T.J., Uyar, B. and Dosztanyi, Z.
Science Signaling 10 (470): eaak9982. 14 March 2017

Mutations in disordered regions can cause disease by creating dileucine motifs.
Meyer, K., Kirchner, M., Uyar, B., Cheng, J.Y., Russo, G., Hernandez-Miranda, L.R., Szymborska, A., Zauber, H., Rudolph, I.M., Willnow, T.E., Akalin, A., Haucke, V., Gerhardt, H., Birchmeier, C., Kühn, R., Krauss, M., Diecke, S., Pascual, J.M. and Selbach, M.
Cell 175 (1): 239-253. 20 September 2018

The IκB kinase complex is a regulator of mRNA stability.
Mikuda, N., Kolesnichenko, M., Beaudette, P., Popp, O., Uyar, B., Sun, W., Tufan, A.B., Perder, B., Akalin, A., Chen, W., Mertins, P., Dittmar, G., Hinz, M. and Scheidereit, C.
EMBO Journal 37 (24): e98658. 14 December 2018

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N., Wessels, H.H., Lebedeva, S., Sajek, M., Ghanbari, M., Garzia, A., Munteanu, A., Yusuf, D., Farazi, T., Hoell, J.I., Akat, K.M., Akalin, A., Tuschl, T. and Ohler, U.
Nucleic Acids Research 47 (2): 570-581. 25 January 2019

The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans.
Müthel, S., Uyar, B., He, M., Krause, A., Vitrinel, B., Bulut, S., Vasiljevic, D., Marchal, I., Kempa, S., Akalin, A. and Tursun, B.
Aging Cell 18 (6): e13012. December 2019

Herpesviruses mimic zygotic genome activation to promote viral replication.
Neugebauer, E., Walter, S., Tan, J., Drayman, N., Franke, V., van Gent, M., Pennisi, S., Veratti, P., Stein, K.S., Welker, I., Tay, S., Verjans, G.M.G.M., Timmers, H.T.M., Akalin, A., Landthaler, M., Ensser, A., Wyler, E. and Full, F.
Nature Communications 16 (1): 710. 16 January 2025

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions.
Rrustemi, T., Meyer, K., Roske, Y., Uyar, B., Akalin, A., Imami, K., Ishihama, Y., Daumke, O. and Selbach, M.
Nature Communications 15 (1): 3146. 11 April 2024

Transcriptional reprogramming by mutated IRF4 in lymphoma.
Schleussner, N., Cauchy, P., Franke, V., Giefing, M., Fornes, O., Vankadari, N., Assi, S.A., Costanza, M., Weniger, M.A., Akalin, A., Anagnostopoulos, I., Bukur, T., Casarotto, M.G., Damm, F., Daumke, O., Edginton-White, B., Gebhardt, J.C.M., Grau, M., Grunwald, S., Hansmann, M.L., Hartmann, S., Huber, L., Kärgel, E., Lusatis, S., Noerenberg, D., Obier, N., Pannicke, U., Fischer, A., Reisser, A., Rosenwald, A., Schwarz, K., Sundararaj, S., Weilemann, A., Winkler, W., Xu, W., Lenz, G., Rajewsky, K., Wasserman, W.W., Cockerill, P.N., Scheidereit, C., Siebert, R., Küppers, R., Grosschedl, R., Janz, M., Bonifer, C. and Mathas, S.
Nature Communications 14 (1): 6947. 7 November 2023

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Milojkovic, A., Anders, K., Schröck, E., Sauer, S., Uyar, B., Akalin, A., Martínez-Reyes, I. and Blankenstein, T.
bioRxiv : 2024.07.13.603369. 17 July 2024

Disintegration of the NuRD complex in primary human muscle stem cells in critical illness myopathy.
Schneider, J., Sundaravinayagam, D., Blume, A., Marg, A., Grunwald, S., Metzler, E., Escobar, H., Müthel, S., Wang, H., Wollersheim, T., Weber-Carstens, S., Akalin, A., Di Virgilio, M., Tursun, B. and Spuler, S.
International Journal of Molecular Sciences 24 (3): 2772. 1 February 2023

Functional interplay of Epstein-Barr virus oncoproteins in a mouse model of B cell lymphomagenesis.
Sommermann, T., Yasuda, T., Ronen, J., Wirtz, T., Weber, T., Sack, U., Caeser, R., Zhang, J., Li, X., Chu, V.T., Jauch, A., Unger, K., Hodson, D.J., Akalin, A. and Rajewsky, K.
Proceedings of the National Academy of Sciences of the United States of America 117 (25): 14421-14432. 23 June 2020

DNA virus infections shape transposable elements activity in vitro and in vivo.
Tan, J., Franke, V., Neugebauer, E., Lagisquet, J., Kuderna, A.K., Walter, S., Landthaler, M., Ensser, A., Stamminger, T., Gramberg, T., Akalin, A., Wyler, E. and Full, F.
bioRxiv : 2024.04.18.589901. 19 April 2024

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B., Yusuf, D., Wurmus, R., Rajewsky, N., Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

Global identification of functional microRNA-mRNA interactions in Drosophila.
Wessels, H.H., Lebedeva, S., Hirsekorn, A., Wurmus, R., Akalin, A., Mukherjee, N. and Ohler, U.
Nature Communications 10 (1): 1626. 9 April 2019

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program.
Wyler, E., Franke, V., Menegatti, J., Kocks, C., Boltengagen, A., Praktiknjo, S., Walch-Rückheim, B., Bosse, J., Rajewsky, N., Grässer, F., Akalin, A. and Landthaler, M.
Nature Communications 10 (1): 4878. 25 October 2019

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E., Menegatti, J., Franke, V., Kocks, C., Boltengagen, A., Hennig, T., Theil, K., Rutkowski, A., Ferrai, C., Baer, L., Kermas, L., Friedel, C., Rajewsky, N., Akalin, A., Dölken, L., Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

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

Autocrine LTA signaling drives NF-κB and JAK-STAT activity and myeloid gene expression in Hodgkin lymphoma.
von Hoff, L., Kärgel, E., Franke, V., McShane, E., Schulz-Beiss, K.W., Patone, G., Schleussner, N., Kolesnichenko, M., Hübner, N., Daumke, O., Selbach, M., Akalin, A., Mathas, S. and Scheidereit, C.
Blood 133 (13): 1489-1494. 28 March 2019

Alexander, Christiane

Characterization of protein-binding to the spinach chloroplast psbA mRNA 5' untranslated region.
Alexander, C., Faber, N. and Klaff, P.
Nucleic Acids Research 26 (10): 2265-2272. 15 May 1998

Altmüller, Janine (BIMSB/BIH)

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Activation of gp130 signaling in T cells drives T(H)17-mediated multi-organ autoimmunity.
Baumgartner, F., Bamopoulos, S.A., Faletti, L., Hsiao, H.J., Holz, M., Gonzalez-Menendez, I., Solé-Boldo, L., Horne, A., Gosavi, S., Özerdem, C., Singh, N., Liebig, S., Ramamoorthy, S., Lehmann, M., Demel, U., Kühl, A.A., Wartewig, T., Ruland, J., Wunderlich, F.T., Schick, M., Walther, W., Rose-John, S., Haas, S., Quintanilla-Martinez, L., Feske, S., Ehl, S., Glauben, R. and Keller, U.
Science Signaling 17 (824): eadc9662. 20 February 2024

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R., Conrad, T., Stöber, M.C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Kasack, K., Brückner, L., van Leen, E., Helmsauer, K., Dorado Garcia, H., Stefanova, M.E., Hung, K.L., Bei, Y., Schmelz, K., Lodrini, M., Mundlos, S., Chang, H.Y., Deubzer, H.E., Sauer, S., Eggert, A., Schulte, J.H., Schwarz, R.F., Haase, K., Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 2023

An autochthonous mouse model of Myd88- and BCL2-driven diffuse large B-cell lymphoma reveals actionable molecular vulnerabilities.
Flümann, R., Rehkämper, T., Nieper, P., Pfeiffer, P., Holzem, A., Klein, S., Bhatia, S., Kochanek, M., Kisis, I., Pelzer, B.W., Ahlert, H., Hauer, J., da Palma Guerreiro, A., Ryan, J.A., Reimann, M., Riabinska, A., Wiederstein, J., Krüger, M., Deckert, M., Altmüller, J., Klatt, A.R., Frenzel, L.P., Pasqualucci, L., Béguelin, W., Melnick, A.M., Sander, S., Montesinos-Rongen, M., Brunn, A., Lohneis, P., Büttner, R., Kashkar, H., Borkhardt, A., Letai, A., Persigehl, T., Peifer, M., Schmitt, C.A., Reinhardt, H.C. and Knittel, G.
Blood Cancer Discovery 2 (1): 70-91. January 2021

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4(+) T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Horn, V., Cancino, C.A., Steinheuer, L.M., Obermayer, B., Fritz, K., Nguyen, A.L., Juhran, K.S., Plattner, C., Bösel, D., Oldenburg, L., Burns, M., Schulz, A.R., Saliutina, M., Mantzivi, E., Lissner, D., Conrad, T., Mashreghi, M.F., Zundler, S., Sonnenberg, E., Schumann, M., Haag, L.M., Beule, D., Flatz, L., Trjanoski, Z., D'Haens, G., Weidinger, C., Mei, H.E., Siegmund, B., Thurley, K. and Hegazy, A.N.
Gastroenterology 28 September 2024 (In Press)

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart, Torsten, Belhaj, S., Tawalbeh, E., Nagels, D., Fröhlich, Y., Finzer, P., Ciruela, P., Sabrià, A., Herrero, M., Andrés, C., Antón, A., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., Nicolai, J., Stiller, M., Blum, J., Lange, C., Adelmann, C., Schroer, B., Osmers, U., Grice, C., Kirfel, P.P., Jomaa, H., Strelow, D., Hülse, L., Pigulla, M., Kreuzer, P., Tyshaieva, A., Weber, J., Wienemann, T., Kohns Vasconcelos, M., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Scholz, C.J., Jazmati, N., Göbels, K., Zotz, R., Pfeffer, K., Timm, J., Ehlkes, L., Walker, A. and Dilthey, A.T.
Eurosurveillance 27 (43): 2101089. 27 October 2022

Single cell RNA-sequencing-based analysis of CD4(+) T-cell subset-specific susceptibility to transcriptional modulation by HIV-1 latency-reversing agents.
Kazmierski, J., Postmus, D., Wyler, E., Fischer, C., Jansen, J., Meixenberger, K., Vitcetz, S.N., Sohn, M., Sauer, S., Bannert, N., Landthaler, M. and Goffinet, C.
bioRxiv : 2020.05.04.075119. 5 May 2020

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer, B., Knoll, R., Bonaguro, L., ToVinh, M., Raabe, J., Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K.M., Rieke, G.J., Bischoff, J., Monin, M.B., Hoffmeister, C., Schlabe, S., De Domenico, E., Reusch, N., Händler, K., Reynolds, G., Blüthgen, N., Hack, G., Finnemann, C., Nischalke, H.D., Strassburg, C.P., Stephenson, E., Su, Y., Gardner, L., Yuan, D., Chen, D., Goldman, J., Rosenstiel, P., Schmidt, S.V., Latz, E., Hrusovsky, K., Ball, A.J., Johnson, J.M., Koenig, P.A., Schmidt, F.I., Haniffa, M., Heath, J.R., Kümmerer, B.M., Keitel, V., Jensen, B., Stubbemann, P., Kurth, F., Sander, L.E., Sawitzki, B., Aschenbrenner, A.C., Schultze, J.L. and Nattermann, J.
Immunity 54 (11): 2650-2669. 9 November 2021

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

Effective inhibitor removal from wastewater samples increases sensitivity of RT-dPCR and sequencing analyses and enhances the stability of wastewater-based surveillance.
Linzner, N., Bartel, A., Schumacher, V., Grau, J.H., Wyler, E., Preuß, H., Garske, S., Bitzegeio, J., Kirst, E.B., Liere, K., Hoppe, S., Borodina, T.A., Altmüller, J., Landthaler, M., Meixner, M., Sagebiel, D. and Böckelmann, U.
Microorganisms 12 (12): 2475. December 2024

Tongue immune compartment analysis reveals spatial macrophage heterogeneity.
Lyras, E.M., Zimmermann, K., Wagner, L.K., Dörr, D., Klose, C.S.N, Fischer, C., Jung, S., Yona, S., Hovav, A.H., Stenzel, W., Dommerich, S., Conrad, T., Leutz, A. and Mildner, A.
eLife 11 : 77490. 24 June 2022

A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
Neuschulz, A., Bakina, O., Badillo Lisakowski, V., Olivares-Chauvet, P., Conrad, T., Gotthardt, M., Kettenmann, H. and Junker, J.P.
Molecular Systems Biology 19 (2): e11147. 10 February 2023

Senescent syncytiotrophoblast secretion during early onset preeclampsia.
Nonn, O., Debnath, O., Valdes, D.S., Sallinger, K., Secener, A.K., Fischer, C., Tiesmeyer, S., Nimo, J., Kuenzer, T., Ulrich, J., Maxian, T., Knöfler, M., Karau, P., Bartolomaeus, H., Kroneis, T., Frolova, A., Neuper, L., Haase, N., Malt, A., Müller-Bötticher, N., Kräker, K., Kedziora, S., Forstner, D., Eils, R., Schmidt-Ullrich, R., Haider, S., Verlohren, S., Stern, C., Sugulle, M., Jones, S., Thilaganathan, B., Kaitu'u-Lino, T.J., Tong, S., Huppertz, B., El-Heliebi, A., Staff, A.C., Coscia, F., Müller, D.N., Dechend, R., Gauster, M., Ishaque, N. and Herse, F.
Hypertension 23 October 2024 (In Press)

Maternal angiotensin increases placental leptin in early gestation via an alternative renin-angiotensin system pathway: suggesting a link to preeclampsia.
Nonn, O., Fischer, C., Geisberger, S., El-Heliebi, A., Kroneis, T., Forstner, D., Desoye, G., Staff, A.C., Sugulle, M., Dechend, R., Pecks, U., Kollmann, M., Stern, C., Cartwright, J.E., Whitley, G.S., Thilaganathan, B., Wadsack, C., Huppertz, B., Herse, F. and Gauster, M.
Hypertension 77 (5): 1723-1736. May 2021

Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.
Obermayer, B., Keilholz, L., Conrad, T., Frentsch, M., Blau, I.W., Vuong, L., Lesch, S., Movasshagi, K., Tietze-Stolley, C., Loyal, L., Henze, L., Penack, O., Stervbo, U., Babel, N., Haas, S., Beule, D., Bullinger, L., Wittenbecher, F. and Na, I.K.
Frontiers in Immunology 14 : 1114368. 10 February 2023

Mutational dynamics between primary and relapse neuroblastomas.
Schramm, A., Köster, J., Assenov, Y., Althoff, K., Peifer, M., Mahlow, E., Odersky, A., Beisser, D., Ernst, C., Henssen, A.G., Stephan, H., Schröder, C., Heukamp, L., Engesser, A., Kahlert, Y., Theissen, J., Hero, B., Roels, F., Altmüller, J., Nürnberg, P., Astrahantseff, K., Gloeckner, C., De Preter, K., Plass, C., Lee, S., Lode, H.N., Henrich, K.O., Gartlgruber, M., Speleman, F., Schmezer, P., Westermann, F., Rahmann, S., Fischer, M., Eggert, A. and Schulte, J.H.
Nature Genetics 47 (8): 872-877. August 2015

Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice.
Spielmann, M., Kakar, N., Tayebi, N., Leettola, C., Nürnberg, G., Sowada, N., Lupiáñez, D.G., Harabula, I., Flöttmann, R., Horn, D., Chan, W.L., Wittler, L., Yilmaz, R., Altmüller, J., Thiele, H., van Bokhoven, H., Schwartz, C.E., Nürnberg, P., Bowie, J.U., Ahmad, J., Kubisch, C., Mundlos, S. and Borck, G.
Genome Research 26 (2): 183-191. February 2016

Intercellular extrachromosomal DNA copy-number heterogeneity drives neuroblastoma cell state diversity.
Stöber, M.C., Chamorro González, R., Brückner, L., Conrad, T., Wittstruck, N., Szymansky, A., Eggert, A., Schulte, J.H., Koche, R.P., Henssen, A.G., Schwarz, R.F. and Haase, K.
Cell Reports 43 (9): 114711. 24 September 2024

A local subset of mesenchymal cells expressing the transcription factor Osr1 orchestrates lymph node initiation.
Vallecillo-García, P., Orgeur, M., Comai, G., Poehle-Kronnawitter, S., Fischer, C., Gloger, M., Dumas, C.E., Giesecke-Thiel, C., Sauer, S., Tajbakhsh, S., Höpken, U.E. and Stricker, S.
Immunity 56 (6): 1204-1219. 13 June 2023

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M.P., Thielen, A., Kolbe-Busch, S., Göbels, K., Zotz, R., Pfeffer, K., Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal, S., Schultze, H., Shastry, K.L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N.A., Ktena, S., Tran, F., Bitzer, M., Ossowski, S., Casadei, N., Herr, C., Petersheim, D., Behrends, U., Kern, F., Fehlmann, T., Schommers, P., Lehmann, C., Augustin, M., Rybniker, J., Altmüller, J., Mishra, N., Bernardes, J.P., Krämer, B., Bonaguro, L., Schulte-Schrepping, J., De Domenico, E., Siever, C., Kraut, M., Desai, M., Monnet, B., Saridaki, M., Siegel, C.M., Drews, A., Nuesch-Germano, M., Theis, H., Heyckendorf, J., Schreiber, S., Kim-Hellmuth, S., Nattermann, J., Skowasch, D., Kurth, I., Keller, A., Bals, R., Nürnberg, P., Rieß, O., Rosenstiel, P., Netea, M.G., Theis, F., Mukherjee, S., Backes, M., Aschenbrenner, A.C., Ulas, T., Breteler, M.M.B., Giamarellos-Bourboulis, E.J., Kox, M., Becker, M., Cheran, S., Woodacre, M.S., Goh, E.L. and Schultze, J.L.
Nature 594 (7862): 265-270. 10 June 2021

Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater.
Wyler, E., Lauber, C., Manukyan, A., Deter, A., Quedenau, C., Teixeira Alves, L.G., Wylezich, C., Borodina, T., Seitz, S., Altmüller, J. and Landthaler, M.
Environment International 190 : 108875. August 2024

The Wnt-driven Mll1 epigenome regulates salivary gland and head and neck cancer.
Zhu, Q., Fang, L., Heuberger, J., Kranz, A., Schipper, J., Scheckenbach, K., Oliveira Vidal, R., Sunaga-Franze, D.Y., Müller, M., Wulf-Goldenberg, A., Sauer, S. and Birchmeier, W.
Cell Reports 26 (2): 415-428. 8 January 2019

Andrade Navarro, Miguel

Mining the literature: new methods to exploit keyword profiles.
Andrade-Navarro, M.A.
Genome Medicine 4 (10): 81. 30 October 2012

A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.
Andrade-Navarro, M.A., Kanji, F., Palii, C.G., Brand, M., Atkins, H. and Perez-Iratxeta, C.
BMC Biotechnology 13 (1): 80. 3 October 2013

Peer2ref: a peer-reviewer finding web tool that uses author disambiguation.
Andrade-Navarro, M.A., Palidwor, G.A. and Perez-Iratxeta, C.
BioData Mining 5 (1): 14. 7 September 2012

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva, A., Fontaine, J.F., Donnard, E.R., Stussi, F., Ortega, J.M. and Andrade-Navarro, M.A.
BMC Bioinformatics 12 (1): 435. 9 November 2011

PRC1-mediated gene silencing in pluripotent ES cells: function and evolution.
Becker, M., Mah, N., Zdzieblo, D., Li, X., Mer, A.S., Andrade-Navarro, M.A. and Mueller, A.M.
Epigenetics and Human Health 2015 : 141-166. 18 November 2014

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen, S., Leddin, M., Andrade-Navarro, M.A. and Mah, N.
Bioinformatics 30 (10): 1484-1485. 15 May 2014

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction.
Broeske, A.M., Vockentanz, L., Kharazi, S., Huska, M.R., Mancini, E., Scheller, M., Kuhl, C., Enns, A., Prinz, M., Jaenisch, R., Nerlov, C., Leutz, A., Andrade-Navarro, M.A., Jacobsen, S.E. and Rosenbauer, F.
Nature Genetics 41 (11): 1207-1215. November 2009

Arabidopsis KCBP interacts with AIR9 but stays in the cortical division zone throughout mitosis via its MyTH4-FERM domain.
Buschmann, H., Dols, J., Kopischke, S., Pena, E.J., Andrade-Navarro, M.A., Heinlein, M., Szymanski, D.B., Zachgo, S., Doonan, J.H. and Lloyd, C.W.
Journal of Cell Science 28 (11): 2033-2046. 1 June 2015

Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2.
Cerdá-Esteban, N., Naumann, H., Ruzittu, S., Mah, N., Pongrac, I.M., Cozzitorto, C., Hommel, A., Andrade-Navarro, M.A., Bonifacio, E. and Spagnoli, F.M.
Nature Communications 8 : 14127. 13 February 2017

Identification of 2-[4-[(4-methoxyphenyl)methoxy]-phenyl]acetonitrile and derivatives as potent Oct3/4 inducers.
Cheng, X., Dimou, E., Alborzinia, H., Wenke, F., Goehring, A., Reuter, S., Mah, N., Fuchs, H., Andrade-Navarro, M.A., Adjaye, J., Gul, S., Harms, C., Utikal, J., Klipp, E., Mrowka, R. and Woelfl, S.
Journal of Medicinal Chemistry 58 (12): 4976-4983. 25 June 2015

Ethyl 2-((4-chlorophenyl)amino)thiazole-4-carboxylate and derivatives are potent inducers of Oct3/4.
Cheng, X., Yoshida, H., Raoofi, D., Saleh, S., Alborzinia, H., Wenke, F., Goehring, A., Reuter, S., Mah, N., Fuchs, H.R., Andrade-Navarro, M.A., Adjaye, J., Gul, S., Utikal, J., Mrowka, R. and Woelfl, S.
Journal of Medicinal Chemistry 58 (1): 5742-5750. 13 August 2015

Preimplantation development regulatory pathway construction through a text-mining approach.
Donnard, E., Barbosa-Silva, A., Guedes, R.L., Fernandes, G.R., Velloso, H., Kohn, M.J., Andrade-Navarro, M.A. and Ortega, J.M.
BMC Genomics 12 (Suppl 4): S3. 22 December 2011

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma.
Fehlker, M., Huska, M.R., Joens, T., Andrade-Navarro, M.A. and Kemmner, W.
BMC Cancer 14 (1): 64. 5 February 2014

Assessment of curated phenotype mining in neuropsychiatric disorder literature.
Fontaine, J.F., Priller, J., Spruth, E., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
Methods 74 : 90-96. March 2015

PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Fournier, D. and Andrade-Navarro, M.A.
Bioinformatics 27 (18): 2605-2606. 15 September 2011

Emergence and evolution of the renin-angiotensin-aldosterone system.
Fournier, D., Luft, F.C., Bader, M., Ganten, D. and Andrade-Navarro, M.A.
Journal of Molecular Medicine 90 (5): 495-508. May 2012

Functional and genomic analyses of α-solenoid proteins.
Fournier, D., Palidwor, G.A., Shcherbinin, S., Szengel, A., Schaefer, M.H., Perez-Iratxeta, C. and Andrade-Navarro, M.A.
PLoS ONE 8 (11): e79894. 21 November 2013

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data.
Gebhardt, M.L., Mer, A.S. and Andrade-Navarro, M.A.
BMC Research Notes 8 (1): 157. 16 April 2015

Similarity in targets with REST points to neural and glioblastoma related miRNAs.
Gebhardt, M.L., Reuter, S., Mrowka, R. and Andrade-Navarro, M.A.
Nucleic Acids Research 42 (9): 5436-5446. 14 May 2014

Alkemio: association of chemicals with biomedical topics by text and data mining.
Gijon-Correas, J.A., Andrade-Navarro, M.A. and Fontaine, J.F.
Nucleic Acids Research 42 (W1): W422-W429. 1 July 2014

Bio++: efficient extensible libraries and tools for computational molecular evolution.
Gueguen, L., Gaillard, S., Boussau, B., Gouy, M., Groussin, M., Rochette, N.C., Bigot, T., Fournier, D., Pouyet, F., Cahais, V., Bernard, A., Scornavacca, C., Nabholz, B., Haudry, A., Dachary, L., Galtier, N., Belkhir, K. and Dutheil, J.Y.
Molecular Biology and Evolution 30 (8): 1745-1750. August 2013

Alterations of pre-mRNA splicing in human inflammatory bowel disease.
Haesler, R., Kerick, M., Mah, N., Hultschig, C., Richter, G., Bretz, F., Sina, C., Lehrach, H., Nietfeld, W., Schreiber, S. and Rosenstiel, P.
European Journal of Cell Biology 90 (6-7): 603-611. June 2011

A role for GPx3 in activity of normal and leukemia stem cells.
Herault, O., Hope, K.J., Deneault, E., Mayotte, N., Chagraoui, J., Wilhelm, B.T., Cellot, S., Sauvageau, M., Andrade-Navarro, M.A., Hebert, J. and Sauvageau, G.
Journal of Experimental Medicine 209 (5): 895-901. 7 May 2012

DNA microarray and miRNA analyses reinforce the classification of follicular thyroid tumors.
Jacques, C., Guillotin, D., Fontaine, J.F., Franc, B., Mirebeau-Prunier, D., Fleury, A., Malthiery, Y. and Savagner, F.
Journal of Clinical Endocrinology and Metabolism 98 (5): E981-E989. May 2013

Computational approaches to discovering noncoding RNA.
Krzyzanowski, P.M., Muro, E.M. and Andrade-Navarro, M.A.
Wiley Interdisciplinary Reviews: RNA 3 (4): 567-579. July 2012

A customized class of functions for modeling and clustering gene expression profiles in embryonic stem cells.
Li, S., Andrade-Navarro, M. and Sankoff, D.
Lecture Notes in Computer Science 5167 : 92-103. 2008

Tissue specific subnetworks and characteristics of publicly available human protein interaction databases.
Lopes, T.J., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.F., Neumann, G., Andrade-Navarro, M.A., Kawaoka, Y. and Kitano, H.
Bioinformatics 27 (17): 2414-2421. 1 September 2011

Prediction of protein secondary structure from circular dichroism using theoretically derived spectra.
Louis-Jeune, C., Andrade-Navarro, M.A. and Perez-Iratxeta, C.
Proteins: Structure, Function, and Bioinformatics 80 (2): 374-381. February 2012

In vivo effects on intron retention and exon skipping by the U2AF large subunit and SF1/BBP in the nematode Caenorhabditis elegans.
Ma, L., Tan, Z., Teng, Y., Hoersch, S. and Horvitz, H.R.
RNA 17 (12): 2201-2211. December 2011

A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in caenorhabditis elegans.
Mansisidor, A.R., Cecere, G., Hoersch, S., Jensen, M.B., Kawli, T., Kennedy, L.M., Chavez, V., Tan, M.W., Lieb, J.D. and Grishok, A.
PLoS Genetics 7 (9): e1002299. September 2011

Comparative genomics identification of a novel set of temporally regulated hedgehog target genes in the retina.
McNeill, B., Perez-Iratxeta, C., Mazerolle, C., Furimsky, M., Mishina, Y., Andrade-Navarro, M.A. and Wallace, V.A.
Molecular and Cellular Neuroscience 49 (3): 333-340. March 2012

A novel approach for protein subcellular location prediction using amino acid exposure.
Mer, A.S. and Andrade-Navarro, M.A.
BMC Bioinformatics 14 (1): 342. 28 November 2013

Estrogen-related receptor alpha modulates lactate dehydrogenase activity in thyroid tumors.
Mirebeau-Prunier, D., Le Pennec, S., Jacques, C., Fontaine, J.F., Gueguen, N., Boutet-Bouzamondo, N., Donnart, A., Malthiery, Y. and Savagner, F.
PLoS ONE 8 (3): e58683. 13 March 2013

Natural antisense transcripts within pseudogenes: an EST survey.
Muro, E.M. and Andrade-Navarro, M.A.
In: Non-coding RNAs and epigenetic regulation of gene expression : drivers of natural selection. Caister Academic Press, Norfolk, 99-108. ISBN 978-1-904455-94-3 February 2012

Functional evidence of post-transcriptional regulation by pseudogenes.
Muro, E.M., Mah, N. and Andrade-Navarro, M.A.
Biochimie 93 (11): 1916-1921. November 2011

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons.
Muro, E.M., Mah, N., Moreno-Hagelsieb, G. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (5): 1732-1738. 1 March 2011

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.
Naba, A., Clauser, K.R., Hoersch, S., Liu, H., Carr, S.A. and Hynes, R.O.
Molecular & Cellular Proteomics 11 (4): M111.014647. 1 April 2012

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.
Neves, M., Damaschun, A., Mah, N., Lekschas, F., Seltmann, S., Stachelscheid, H., Fontaine, J.F., Kurtz, A. and Leser, U.
Database 2013 (2013): bat020. 18 April 2013

ROMO1 is an essential redox-dependent regulator of mitochondrial dynamics.
Norton, M., Ng, A.C., Baird, S., Dumoulin, A., Shutt, T., Mah, N., Andrade-Navarro, M.A., McBride, H.M. and Screaton, R.A.
Science Signaling 7 (310): ra10. 28 January 2014

Using cited references to improve the retrieval of related biomedical documents.
Ortuno, F.M., Rojas, I., Andrade-Navarro, M.A. and Fontaine, J.F.
BMC Bioinformatics 14 : 113. 27 March 2013

A reference guide for tree analysis and visualization.
Pavlopoulos, G.A., Soldatos, T.G., Barbosa-Silva, A. and Schneider, R.
BioData Mining 3 : 1. 22 February 2010

Towards completion of the Earth's proteome.
Perez-Iratxeta, C., Palidwor, G. and Andrade-Navarro, M.A.
EMBO Reports 8 (12): 1135-1141. 1 December 2007

Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1.
Petrakis, S., Rasko, T., Russ, J., Friedrich, R.P., Stroedicke, M., Riechers, S.P., Muehlenberg, K., Moeller, A., Reinhardt, A., Vinayagam, A., Schaefer, M.H., Boutros, M., Tricoire, H., Andrade-Navarro, M.A. and Wanker, E.E.
PLoS Genetics 8 (8): e1002897. 16 August 2012

Aggregation of polyQ-extended proteins is promoted by interaction with their natural coiled-coil partners.
Petrakis, S., Schaefer, M.H., Wanker, E.E. and Andrade-Navarro, M.A.
BioEssays 35 (6): 503-507. June 2013

Myeloid leukemia with transdifferentiation plasticity developing from T-cell progenitors.
Riemke, P., Czeh, M., Fischer, J., Walter, C., Ghani, S., Zepper, M., Agelopoulos, K., Lettermann, S., Gebhardt, M.L., Mah, N., Weilemann, A., Grau, M., Groening, V., Haferlach, T., Lenze, D., Delwel, R., Prinz, M., Andrade-Navarro, M.A., Lenz, G., Dugas, M., Mueller-Tidow, C. and Rosenbauer, F.
EMBO Journal 35 (22): 2399-2416. 15 November 2016

CXCL5 limits macrophage foam cell formation in atherosclerosis.
Rousselle, A., Qadri, F., Leukel, L., Yilmaz, R., Fontaine, J.F., Sihn, G., Bader, M., Ahluwalia, A. and Duchene, J.
Journal of Clinical Investigation 123 (3): 1343-1347. 1 March 2013

The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily.
Sanchez-Pulido, L. and Andrade-Navarro, M.A.
BMC Biochemistry 8 : 23. 8 November 2007

Paired sage-microarray expression data sets reveal antisense transcripts differentially expressed in embryonic stem cell differentiation.
Sandie, R., Porter, C.J., Palidwor, G.A., Price, F., Krzyzanowski, P.M., Muro, E.M., Hoersch, S., Smith, M., Campbell, P.A., Perez-Iratxeta, C., Rudnicki, M.A. and Andrade-Navarro, M.A.
In: Computational Biology of Embryonic Stem Cells. Bentham, Oak Park, 193-215. ISBN 978-1-608-05025-3 2012

HIPPIE: integrating protein interaction networks with experiment based quality scores.
Schaefer, M.H., Fontaine, J.F., Vinayagam, A., Porras, P., Wanker, E.E. and Andrade-Navarro, M.A.
PLoS ONE 7 (2): e31826. 14 February 2012

Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.
Schaefer, M.H., Lopes, T.J.S., Mah, N., Shoemaker, J.E., Matsuoka, Y., Fontaine, J.F., Louis-Jeune, C., Eisfeld, A.J., Neumann, G., Perez-Iratxeta, C., Kawaoka, Y., Kitano, H. and Andrade-Navarro, M.A.
PLoS Computational Biology 9 (1): e1002860. 3 January 2013

Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks.
Schaefer, M.H., Wanker, E.E. and Andrade-Navarro, M.A.
Nucleic Acids Research 40 (10): 4273-4287. 1 May 2012

SPON2, a newly identified target gene of MACC1, drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival.
Schmid, F., Wang, Q., Huska, M.R., Andrade-Navarro, M.A., Lemm, M., Fichtner, I., Dahlmann, M., Kobelt, D., Walther, W., Smith, J., Schlag, P.M. and Stein, U.
Oncogene 35 (46): 5942-5952. 17 November 2016

PU.1 level-directed chromatin structure remodeling at the Irf8 gene drives dendritic cell commitment.
Schönheit, J., Kuhl, C., Gebhardt, M.L., Klett, F.F., Riemke, P., Scheller, M., Huang, G., Naumann, R., Leutz, A., Stocking, C., Priller, J., Andrade-Navarro, M.A. and Rosenbauer, F.
Cell Reports 3 (5): 1617-1628. 30 May 2013

CELDA - an ontology for the comprehensive representation of cells in complex systems.
Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J.F., Nguyen-Dobinsky, T.N., Leser, U. and Kurtz, A.
BMC Bioinformatics 14 : 228. 17 July 2013

Comparison of inter- and intraspecies variation in humans and fruit flies.
Shih, J., Hodge, R. and Andrade-Navarro, M.A.
Genomics Data 3 : 49-54. March 2015

Recognition of 2'-O-methylated 3'-end of piRNA by the PAZ domain of a piwi protein.
Simon, B., Kirkpatrick, J.P., Eckhardt, S., Reuter, M., Rocha, E.A., Andrade-Navarro, M.A., Sehr, P., Pillai, R.S. and Carlomagno, T.
Structure 19 (2): 172-180. 9 February 2011

Caipirini: using gene sets to rank literature.
Soldatos, T.G., O'Donoghue, S.I., Satagopam, V.P., Barbosa-Silva, A., Pavlopoulos, G.A., Wanderley-Nogueira, A.C., Soares-Cavalcanti, N.M. and Schneider, R.
BioData Mining 5 (1): 1. 1 February 2012

CellFinder: a cell data repository.
Stachelscheid, H., Seltmann, S., Lekschas, F., Fontaine, J.F., Mah, N., Neves, M., Andrade-Navarro, M.A., Leser, U. and Kurtz, A.
Nucleic Acids Research 42 (1): D950-D958. 1 January 2014

Armadillo motifs involved in vesicular transport.
Striegl, H., Andrade-Navarro, M.A. and Heinemann, U.
PLoS ONE 5 (2): e8991. 1 February 2010

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity.
Stroedicke, M., Bounab, Y., Strempel, N., Klockmeier, K., Yigit, S., Friedrich, R.P., Chaurasia, G., Li, S., Hesse, F., Riechers, S.P., Russ, J., Nicoletti, C., Boeddrich, A., Wiglenda, T., Haenig, C., Schnoegl, S., Fournier, D., Graham, R.K., Hayden, M.R., Sigrist, S., Bates, G.P., Priller, J., Andrade-Navarro, M.A., Futschik, M.E. and Wanker, E.E.
Genome Research 25 (5): 701-713. May 2015

Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen.
Suratanee, A., Schaefer, M.H., Betts, M.J., Soons, Z., Mannsperger, H., Harder, N., Oswald, M., Gipp, M., Ramminger, E., Marcus, G., Männer, R., Rohr, K., Wanker, E., Russell, R.B., Andrade-Navarro, M.A., Eils, R. and König, R.
PLoS Computational Biology 10 (9): e1003814. 25 September 2014

Development and application of a DNA microarray-based yeast two-hybrid system.
Suter, B., Fontaine, J.F., Yildirimman, R., Raskó, T., Schaefer, M.H., Rasche, A., Porras, P., Vázquez-Álvarez, B.M., Russ, J., Rau, K., Foulle, R., Zenkner, M., Saar, K., Herwig, R., Andrade-Navarro, M.A. and Wanker, E.E.
Nucleic Acids Research 41 (3): 1496-507. 1 February 2013

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure.
Vlassi, M., Brauns, K. and Andrade-Navarro, M.A.
BMC Structural Biology 13 (1): 17. 2 October 2013

Identification of LRRC8 heteromers as an essential component of the volume-regulated anion channel VRAC.
Voss, F.K., Ullrich, F., Muench, J., Lazarow, K., Lutter, D., Mah, N., Andrade-Navarro, M.A., von Kries, J.P., Stauber, T. and Jentsch, T.J.
Science 344 (6184): 634-638. 9 May 2014

In silico screening for pathogenesis related-2 gene candidates in Vigna uguiculata transcriptome.
Wanderley-Nogueira, A.C., Da Mota Soares-Cavalcanti, N., Belarmino, L.C., Barbosa-Silva, A., Kido, E.A., Do Monte, S.J.H., Pandolfi, V., Calsa-Junior, T. and Benko-Iseppon, A.M.
Lecture Notes in Computer Science 6160 : 70-81. 2010

uORFdb - a comprehensive literature database on eukaryotic uORF biology.
Wethmar, K., Barbosa-Silva, A., Andrade-Navarro, M.A. and Leutz, A.
Nucleic Acids Research 42 (1): D60-D67. 1 January 2014

Comprehensive translational control of tyrosine kinase expression by upstream open reading frames.
Wethmar, K., Schulz, J., Muro, E.M., Talyan, S., Andrade-Navarro, M.A. and Leutz, A.
Oncogene 35 (13): 1736-1742. 31 March 2016

Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.
Zhang, G., Hoersch, S., Amsterdam, A., Whittaker, C.A., Beert, E., Catchen, J.M., Farrington, S., Postlethwait, J.H., Legius, E., Hopkins, N. and Lees, J.A.
PLoS Genetics 9 (8): e1003734. August 2013

Highly aneuploid zebrafish malignant peripheral nerve sheath tumors have genetic alterations similar to human cancers.
Zhang, G., Hoersch, S., Amsterdam, A., Whittaker, C.A., Lees, J.A. and Hopkins, N.
Proceedings of the National Academy of Sciences of the United States of America 107 (39): 16940-16945. 28 September 2010

A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: dominant roles of p50 and p52 revealed by genome-wide analyses.
de Oliveira, K.A.P., Kaergel, E., Heinig, M., Fontaine, J.F., Patone, G., Muro, E.M., Mathas, S., Hummel, M., Andrade-Navarro, M.A., Hübner, N. and Scheidereit, C.
Genome Medicine 8 (1): 28. 17 March 2016

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations.
von Eichborn, J., Dunkel, M., Gohlke, B.O., Preissner, S.C., Hoffmann, M.F., Bauer, J.M.J., Armstrong, J.D., Schaefer, M.H., Andrade-Navarro, M.A., Le Novere, N., Croning, M.D.R., Grant, S.G.N., van Nierop, P., Smit, A.B. and Preissner, R.
Nucleic Acids Research 41 (D1): D834-D840. 1 January 2013

Bader, Michael

Inter-individual and inter-strain differences in cognitive and social abilities of Dark Agouti and Wistar Han rats.
Alonso, L., Peeva, P., Ramos-Prats, A., Alenina, N., Winter, Y. and Rivalan, M.
Behavioural Brain Research 377 : 112188. 13 January 2020

Elevated sortilin expression discriminates functional from non-functional neuroendocrine tumors and enables therapeutic targeting.
Bolduan, F., Wetzel, A., Giesecke, Y., Eichhorn, I., Alenina, N., Bader, M., Willnow, T.E., Wiedenmann, B. and Sigal, M.
Frontiers in Endocrinology 15 : 1331231. 17 April 2024

Inhibition of the NLRP3/IL-1β axis protects against sepsis-induced cardiomyopathy.
Busch, K., Kny, M., Huang, N., Klassert, T.E., Stock, M., Hahn, A., Graeger, S., Todiras, M., Schmidt, S., Chamling, B., Willenbrock, M., Groß, S., Biedenweg, D., Heuser, A., Scheidereit, C., Butter, C., Felix, S.B., Otto, O., Luft, F.C., Slevogt, H. and Fielitz, J.
Journal of Cachexia Sarcopenia and Muscle 12 (6): 1653-1668. December 2021

Hyperphenylalaninemia and serotonin deficiency in Dnajc12-deficient mice.
Cao, Y., Popp, O., Milani, N., Qadri, F., Kühn, R., Mertins, P., Bader, M. and Alenina, N.
Communications Biology 7 (1): 1641. 18 December 2024

Emergence and evolution of the renin-angiotensin-aldosterone system.
Fournier, D., Luft, F.C., Bader, M., Ganten, D. and Andrade-Navarro, M.A.
Journal of Molecular Medicine 90 (5): 495-508. May 2012

Serum amyloid A1 mediates myotube atrophy via Toll-like receptors.
Hahn, A., Kny, M., Pablo-Tortola, C., Todiras, M., Willenbrock, M., Schmidt, S., Schmoeckel, K., Jorde, I., Nowak, M., Jarosch, E., Sommer, T., Bröker, B.M., Felix, S.B., Scheidereit, C., Weber-Carstens, S., Butter, C., Luft, F.C. and Fielitz, J.
Journal of Cachexia Sarcopenia and Muscle 11 (1): 103-119. February 2020

Distinguishing features of microglia- and monocyte-derived macrophages after stroke.
Kronenberg, G., Uhlemann, R., Richter, N., Klempin, F., Wegner, S., Staerck, L., Wolf, S., Uckert, W., Kettenmann, H., Endres, M. and Gertz, K.
Acta Neuropathologica 135 (4): 551. April 2018

CXCL5 limits macrophage foam cell formation in atherosclerosis.
Rousselle, A., Qadri, F., Leukel, L., Yilmaz, R., Fontaine, J.F., Sihn, G., Bader, M., Ahluwalia, A. and Duchene, J.
Journal of Clinical Investigation 123 (3): 1343-1347. 1 March 2013

Structure-based design of xanthine-benzimidazole derivatives as novel and potent tryptophan hydroxylase inhibitors.
Specker, E., Matthes, S., Wesolowski, R., Schütz, A., Grohmann, M., Alenina, N., Pleimes, D., Mallow, K., Neuenschwander, M., Gogolin, A., Weise, M., Pfeifer, J., Ziebart, N., Heinemann, U., von Kries, J.P., Nazaré, M. and Bader, M.
Journal of Medicinal Chemistry 65 (16): 11126-11149. 25 August 2022

Structure-based design of xanthine-imidazopyridines and -imidazothiazoles as highly potent and in vivo efficacious tryptophan hydroxylase inhibitors.
Specker, E., Wesolowski, R., Schütz, A., Matthes, S., Mallow, K., Wasinska-Kalwa, M., Winkler, L., Oder, A., Alenina, N., Pleimes, D., von Kries, J.P., Heinemann, U., Bader, M. and Nazaré, M.
Journal of Medicinal Chemistry 66 (21): 14866-14896. 9 November 2023

The transcription factor grainyhead-like 2 regulates the molecular composition of the epithelial apical junctional complex.
Werth, M., Walentin, K., Aue, A., Schoenheit, J., Wuebken, A., Pode-Shakked, N., Vilianovitch, L., Erdmann, B., Dekel, B., Bader, M., Barasch, J., Rosenbauer, F., Luft, F.C. and Schmidt-Ott, K.M.
Development 137 (22): 3835-3845. November 2010

Bargou, Ralf C.

CD38 low IgG-secreting cells are precursors of various CD38 high-expressing plasma cell populations.
Arce, S., Luger, E., Muehlinghaus, G., Cassese, G., Hauser, A., Horst, A., Lehnert, K., Odendahl, M., Hoenemann, D., Heller, K.D., Kleinschmidt, H., Berek, C., Doerner, T., Krenn, V., Hiepe, F., Bargou, R., Radbruch, A. and Manz, R.A.
Journal of Leukocyte Biology 75 : 1022-1028. 1 January 2004

Combined disruption of both the MEK/ERK and the IL-6R/STAT3 pathways is required to induce apoptosis of multiple myeloma cells in the presence of bone marrow stromal cells.
Chatterjee, M., Stuehmer, T., Herrmann, P., Bommert, K., Doerken, B. and Bargou, R.C.
Blood 104 (12): 3712-3721. 1 January 2004

T cell costimulus-independent and very efficacious inhibition of tumor growth in mice bearing subcutaneous or leukemic human B cell lymphoma xenografts by a CD19-/CD3-bispecific single-chain antibody construct1.
Dreier, T., Baeuerle, P.A., Fichtner, I., Gruen, M., Schlereth, B., Lorenczewski, G., Kufer, P., Lutterbuese, R., Riethmueller, G., Gjorstrup, P. and Bargou, R.C.
Journal of Immunology 170 (8): 4397-4402. 15 April 2003

T-cell-mediated lysis of B cells induced by a CD19xCD3 bispecific single-chain antibody is perforin dependent and death receptor independent.
Gruen, M., Bommert, K. and Bargou, R.C.
Cancer Immunology Immunotherapy 53 (7): 625-632. 1 January 2004

A novel recombinant bispecific single-chain antibody, bscWue-1 x CD3, induces T-cell-mediated cytotoxicity towards human multiple myeloma cells.
Hoenemann, D., Kufer, P., Rimpler, M.M., Chatterjee, M., Friedl, S., Riecher, F., Bommert, K., Doerken, B. and Bargou, R.C.
Leukemia 18 (3): 636-644. 1 January 2004

Jagged1-induced notch signaling drives proliferation of multiple myeloma cells.
Jundt, F., Schulze-Proebsting, K., Anagnostopoulos, I., Muehlinghaus, G., Chatterjee, M., Mathas, S., Bargou, R.C., Manz, R., Stein, H. and Doerken, B.
Blood 103 (9): 3511-3515. 1 January 2004

PI3-K/AKT/FKHR and MAPK signaling cascades are redundantly stimulated by a variety of cytokines and contribute independently to proliferation and survival of multiple myeloma cells.
Lentzsch, S., Chatterjee, M., Gries, M., Bommert, K., Gollasch, H., Doerken, B. and Bargou, R.C.
Leukemia 18 (11): 1883-1890. 1 January 2004

Macrophage inflammatory protein 1-alpha (MIP-1alpha) triggers migration and signaling cascades mediating survival and proliferation in multiple myeloma (MM) cells.
Lentzsch, S., Gries, M., Janz, M., Bargou, R., Doerken, B. and Mapara, M.Y.
Blood 101 (9): 3568-3573. 1 May 2003

Efficient elimination of chronic lymphocytic leukaemia B cells by autologous T cells with a bispecific anti-CD19/anti-CD3 single-chain antibody construct.
Loeffler, A., Gruen, M., Wuchter, C., Schriever, F., Kufer, P., Dreier, T., Hanakam, F., Baeuerle, P.A., Bommert, K., Karawajew, L., Doerken, B. and Bargou, R.C.
Leukemia 17 (5): 900-909. May 2003

Behlke, Joachim

Oligomeric structure of mammalian purine nucleoside phosphorylase in solution determined by analytical ultracentrifugation.
Behlke, J., Koellner, G. and Bzowska, A.
Zeitschrift fuer Naturforschung C, A Journal of Biosciences 60 (11-12): 927-931. November 2005

Protein crystallization with and without precipitants.
Behlke, J., Marg, A. and Paeschke, M.
Journal of Applied Crystallography 30 (5/1): 559-560. 1 October 1997

Enhanced resolution of sedimentation coefficient distribution profiles by extrapolation to infinite time.
Behlke, J. and Ristau, O.
European Biophysics Journal 39 (3): 449-455. February 2010

Molecular mass determination by sedimentation velocity experiments and direct fitting of the concentration profiles.
Behlke, J. and Ristau, O.
Biophysical Journal 72 (1): 428-434. January 1997

Self-association of adrenodoxin studied by using analytical ultracentrifugation.
Behlke, J., Ristau, O., Mueller, E.C., Hannemann, F. and Bernhardt, R.
Biophysical Chemistry 125 (1): 159-165. January 2007

In vitro and in vivo stability of the epsilon2zeta2 protein complex of the broad host-range Streptococcus pyogenes pSM19035 addiction system.
Camacho, A.G., Misselwitz, R., Behlke, J., Ayora, S., Welfle, K., Meinhart, A., Lara, B., Saenger, W., Welfle, H. and Alonso, J.C.
Biological Chemistry 383 (11): 1701-1713. November 2002

X-ray structure of engineered human Aortic Preferentially Expressed Protein-1 (APEG-1).
Manjasetty, B.A., Niesen, F.H., Scheich, C., Roske, Y., Goetz, F., Behlke, J., Sievert, V., Heinemann, U. and Buessow, K.
BMC Structural Biology 5 (14): 21. 14 December 2005

Crystal structures of human saposins C and D: implications for lipid recognition and membrane interactions.
Rossmann, M., Schultz-Heienbrok, R., Behlke, J., Remmel, N., Alings, C., Sandhoff, K., Saenger, W. and Maier, T.
Structure 16 (5): 809-817. 7 May 2008

Structural and functional characterization of human Iba proteins.
Schulze, J.O., Quedenau, C., Roske, Y., Adam, T., Schueler, H., Behlke, J., Turnbull, A.P., Sievert, V., Scheich, C., Mueller, U., Heinemann, U. and Buessow, K.
FEBS Journal 275 (18): 4627-4640. September 2008

CopR binds and bends its target DNA: a footprinting and fluorescence resonance energy transfer study.
Steinmetzer, K., Behlke, J., Brantl, S. and Lorenz, M.
Nucleic Acids Research 30 (9): 2052-2060. 1 May 2002

Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization.
Turnbull, A.P., Kuemmel, D., Prinz, B., Holz, C., Schultchen, J., Lang, C., Niesen, F.H., Hofmann, K.P., Delbrueck, H., Behlke, J., Mueller, E.C., Jarosch, E., Sommer, T. and Heinemann, U.
EMBO Journal 24 (5): 875-884. 1 January 2005

Beitraege zur Struktur und Funktion des kleinen Saeuger-Stressproteins HSP25 unter besonderer Beruecksichtigung der Wechselwirkung mit Actin.
Wieske, M.
UNSPECIFIED thesis, UNSPECIFIED. 22 September 1998

Bergmann, Martin W.

Beta-catenin downregulation is required for adaptive cardiac remodeling.
Baurand, A., Zelarayan, L., Betney, R., Gehrke, C., Dunger, S., Noack, C., Busjahn, A., Huelsken, J., Taketo, M.M., Birchmeier, W., Dietz, R. and Bergmann, M.W.
Circulation Research 100 (9): 1353-1362. 11 May 2007

Besser, Daniel

Regulation of the urokinase-type plasminogen activator gene by the oncogene Tpr-Met involves GRB2.
Besser, D., Bardelli, A., Didichenko, S., Thelen, M., Comoglio, P.M., Ponzetto, C. and Nagamine, Y.
Oncogene 14 (6): 705-711. 13 February 1997

A single amino acid substitution in the v-Eyk intracellular domain results in activation of Stat3 and enhances cellular transformation.
Besser, D., Bromberg, J.F., Darnell, J.E. and Hanafusa, H.
Molecular and Cellular Biology 19 (2): 1401-1409. February 1999

DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene.
Besser, D., Goetz, F., Schulze-Forster, K., Wagner, H., Kroeger, H. and Simon, D.
FEBS Letters 269 (2): 358-362. 3 September 1990

Elucidation of a signaling pathway induced by FGF-2 leading to uPA gene expression in NIH 3T3 fibroblasts.
Besser, D., Presta, M. and Nagamine, Y.
Cell Growth & Differentiation 6 (8): 1009-1017. August 1995

Urokinase-type plasminogen activator gene regulation by polyomavirus middle-T antigen.
Besser, D., Urich, M., Sakaue, M., Messerschmitt, A., Ballmer-Hofer, K. and Nagamine, Y.
Oncogene 11 (11): 2383-2391. 7 December 1995

Signal transduction and the u-PA/u-PAR system.
Besser, D., Verde, P., Nagamine, Y. and Blasi, F.
Fibrinolysis 10 (4): 215-237. July 1996

Stem cell biology-from basic research to regenerative medicine.
Besser, D.
Journal of Molecular Medicine 90 (7): 731-733. July 2012

Expression of nodal, lefty-A, and lefty-B in undifferentiated human embryonic stem cells requires activation of Smad2/3.
Besser, D.
Journal of Biological Chemistry 279 (43): 45076-45084. 1 January 2004

Replicative aging and differentiation potential of human adipose tissue-derived mesenchymal stromal cells expanded in pooled human or fetal bovine serum.
Bieback, K., Hecker, A., Schlechter, T., Hofmann, I., Brousos, N., Redmer, T., Besser, D., Klueter, H., Mueller, A.M. and Becker, M.
Cytotherapy 14 (5): 570-583. May 2012

Mesenchymal stromal cells (MSCs): science and f(r)iction.
Bieback, K., Wuchter, P., Besser, D., Franke, W., Becker, M., Ott, M., Pacher, M., Ma, N., Stamm, C., Klueter, H., Mueller, A. and Ho, A.D.
Journal of Molecular Medicine 90 (7): 773-782. July 2012

SH2 and SH3-containing adaptor proteins: redundant or independent mediators of intracellular signal transduction.
Birge, R.B., Knudsen, B.S., Besser, D. and Hanafusa, H.
Genes to Cells 1 (7): 595-613. July 1996

Stat3 activation is required for cellular transformation by v-src.
Bromberg, J.F., Horvath, C.M., Besser, D., Lathem, W.W. and Darnell, J.E.
Molecular and Cellular Biology 18 (5): 2553-2558. May 1998

Bone morphogenetic protein-7 release from endogenous neural precursor cells suppresses the tumourigenicity of stem-like glioblastoma cells.
Chirasani, S.R., Sternjak, A., Wend, P., Momma, S., Campos, B., Herrmann, I.M., Graf, D., Mitsiadis, T., Herold-Mende, C., Besser, D., Synowitz, M., Kettenmann, H. and Glass, R.
Brain 133 (Pt 7): 1961-1972. July 2010

Cooperation of two PEA3/AP1 sites in uPA gene induction by TPA and FGF-2.
D'Orazio, D., Besser, D., Marksitzer, R., Kunz, C., Hume, D.A., Kiefer, B. and Nagamine, Y.
Gene 201 (1-2): 179-187. 12 November 1997

FGF2 signaling in mouse embryonic fibroblasts is crucial for self-renewal of embryonic stem cells.
Diecke, S., Quiroga-Negreira, A., Redmer, T. and Besser, D.
Cells Tissues Organs 188 (1-2): 52-61. July 2008

12-O-Tetradecanoylphorbol-13-acetate activates the Ras/extracellular signal-regulated kinase (ERK) signaling pathway upstream of SOS involving serine phosphorylation of Shc in NIH3T3 cells.
El-Shemerly, M.Y., Besser, D., Nagasawa, M. and Nagamine, Y.
Journal of Biological Chemistry 272 (49): 30599-30602. 5 December 1997

A colorectal cancer expression profile that includes transforming growth factor beta inhibitor BAMBI predicts metastatic potential.
Fritzmann, J., Morkel, M., Besser, D., Budczies, J., Kosel, F., Brembeck, F.H., Stein, U., Fichtner, I., Schlag, P.M. and Birchmeier, W.
Gastroenterology 137 (11): 165-175. July 2009

The tyrosine phosphatase Shp2 (PTPN11) directs neuregulin-1/ErbB signaling throughout schwann cell development.
Grossmann, K.S., Wende, H., Paul, F.E., Cheret, C., Garratt, A.N., Zurborg, S., Feinberg, K., Besser, D., Schulz, H., Peles, E., Selbach, M., Birchmeier, W. and Birchmeier, C.
Proceedings of the National Academy of Sciences of the United States of America 106 (39): 16704-16709. 29 September 2009

Two isoforms of human RNA polymerase III with specific functions in cell growth and transformation.
Haurie, V., Durrieu-Gaillard, S., Dumay-Odelot, H., Da Silva, D., Rey, C., Prochazkova, M., Roeder, R.G., Besser, D. and Teichmann, M.
Proceedings of the National Academy of Sciences of the United States of America 107 (9): 4176-4181. 2 March 2010

Cytoskeleton reorganization induces the urokinase-type plasminogen activator gene via the Ras/extracellular signal-regulated kinase (ERK) signaling pathway.
Irigoyen, J.P., Besser, D. and Nagamine, Y.
Journal of Biological Chemistry 272 (3): 1904-1909. 17 January 1997

TGFbeta/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells.
James, D., Levine, A.J., Besser, D. and Hemmati-Brivanlou, A.
Development 132 (6): 1273-1282. March 2005

Homogeneity and persistence of transgene expression by omitting antibiotic selection in cell line isolation.
Kaufman, W.L., Kocman, I., Agrawal, V., Rahn, H.P., Besser, D. and Gossen, M.
Nucleic Acids Research 36 (17): e111. October 2008

Transcriptional regulation of the murine urokinase-type plasminogen activator gene in skeletal myoblasts.
Miralles, F., Ibanez-Tallon, I., Parra, M., Crippa, M., Blasi, F., Besser, D., Nagamine, Y. and Munoz-Canoves, P.
Thrombosis and Haemostasis 81 (5): 767-774. May 1999

E-cadherin is crucial for embryonic stem cell pluripotency and can replace OCT4 during somatic cell reprogramming.
Redmer, T., Diecke, S., Grigoryan, T., Quiroga-Negreira, A., Birchmeier, W. and Besser, D.
EMBO Reports 12 (7): 720-726. 1 July 2011

Where do you come from; where do you go? Pluripotency, differentiation and malfunction of stem cells.
Spagnoli, F.M., Besser, D. and Benitah, S.A.
EMBO Reports 13 (1): 9-11. January 2012

WISP-1 attenuates p53-mediated apoptosis in response to DNA damage through activation of the Akt kinase.
Su, F., Overholtzer, M., Besser, D. and Levine, A.J.
Genes & Development 16 (1): 46-57. 2002

Activation and nuclear translocation of mitogen-activated protein kinases by polyomavirus middle-T or serum depend on phosphatidylinositol 3-kinase.
Urich, M., el Shemerly, M.Y., Besser, D., Nagamine, Y. and Ballmer-Hofer, K.
Journal of Biological Chemistry 270 (49): 29286-29292. 8 December 1995

Protein kinase B beta/Akt2 plays a specific role in muscle differentiation.
Vandromme, M., Rochat, A., Meier, R., Carnac, G., Besser, D., Hemmings, B.A., Fernandez, A. and Lamb, N.J.
Journal of Biological Chemistry 276 (11): 8173-8179. 16 March 2001

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.
Wang, J., Xie, G., Singh, M., Ghanbarian, A.T., Raskó, T., Szvetnik, A., Cai, H., Besser, D., Prigione, A., Fuchs, N.V., Schumann, G.G., Chen, W., Lorincz, M.C., Ivics, Z., Hurst, L.D. and Izsvák, Z.
Nature 516 (7531): 405-409. 18 December 2014

Insulin regulates the activity of forkhead transcription factor Hnf-3beta/Foxa-2 by Akt-mediated phosphorylation and nuclear/cytosolic localization.
Wolfrum, C., Besser, D., Luca, E. and Stoffel, M.
Proceedings of the National Academy of Sciences of the United States of America 100 (20): 11624-11629. 30 September 2003

TRANCE, a TNF family member, activates Akt/PKB through a signaling complex involving TRAF6 and c-Src.
Wong, B.R., Besser, D., Kim, N., Arron, J.R., Vologodskaia, M., Hanafusa, H. and Choi, Y.
Molecular Cell 4 (6): 1041-1049. December 1999

Independent and cooperative activation of chromosomal c-fos promoter by STAT3.
Yang, E., Lerner, L., Besser, D. and Darnell, J.E.
Journal of Biological Chemistry 278 (18): 15794-15799. 2 May 2003

Beule, Dieter (MDC/BIH)

State-of-the-art analytical methods of viral infections in human lung organoids.
Baumgardt, M., Hülsemann, M., Löwa, A., Fatykhova, D., Hoffmann, K., Kessler, M., Mieth, M., Hellwig, K., Frey, D., Langenhagen, A., Voss, A., Obermayer, B., Wyler, E., Dökel, S., Gruber, A.D., Tölch, U., Hippenstiel, S., Hocke, A.C. and Hönzke, K.
PLoS ONE 17 (12): e0276115. 20 December 2022

Leveraging large language models for decision support in personalized oncology.
Benary, M., Wang, X.D., Schmidt, M., Soll, D., Hilfenhaus, G., Nassir, M., Sigler, C., Knödler, M., Keller, U., Beule, D., Keilholz, U., Leser, U. and Rieke, D.T.
JAMA Network Open 6 (11): e2343689. November 2023

Identification and ranking of recurrent neo-epitopes in cancer.
Blanc, E., Holtgrewe, M., Dhamodaran, A., Messerschmidt, C., Willimsky, G., Blankenstein, T. and Beule, D.
BMC Medical Genomics 12 : 171. 27 November 2019

The anti-amyloid compound DO1 decreases plaque pathology and neuroinflammation-related expression changes in 5xFAD transgenic mice.
Boeddrich, A., Babila, J.T., Wiglenda, T., Diez, L., Jacob, M., Nietfeld, W., Huska, M.R., Haenig, C., Groenke, N., Buntru, A., Blanc, E., Meier, J.C., Vannoni, E., Erck, C., Friedrich, B., Martens, H., Neuendorf, N., Schnoegl, S., Wolfer, D.P., Loos, M., Beule, D., Andrade-Navarro, M.A. and Wanker, E.E.
Cell Chemical Biology 26 (1): 109-120. 17 January 2019

WiPP: workflow for improved peak picking for gas chromatography-mass spectrometry (GC-MS) data.
Borgsmüller, N., Gloaguen, Y., Opialla, T., Blanc, E., Sicard, E., Royer, A.L., Le Bizec, B., Durand, S., Migné, C., Pétéra, M., Pujos-Guillot, E., Giacomoni, F., Guitton, Y., Beule, D. and Kirwan, J.
Metabolites 9 (9): 171. 21 August 2019

Frequent ZNF217 mutations lead to transcriptional deregulation of interferon signal transduction via altered chromatin accessibility in B cell lymphoma.
Briest, F., Noerenberg, D., Hennch, C., Yoshida, K., Hablesreiter, R., Nimo, J., Sasca, D., Kirchner, M., Mansouri, L., Inoue, Y., Wiegand, L., Staiger, A.M., Casadei, B., Korkolopoulou, P., Weiner, J., Lopez-Guillermo, A., Warth, A., Schneider, T., Nagy, Á., Klapper, W., Hummel, M., Kanellis, G., Anagnostopoulos, I., Mertins, P., Bullinger, L., Rosenquist, R., Vassilakopoulos, T.P., Ott, G., Ogawa, S. and Damm, F.
Leukemia 37 (11): 2237-2249. November 2023

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert, M., Blanc, E., Thiessen, N., Weber, C., Toedling, J., Monti, R., Dombrowe, V.M., de Biase, M.S., Kaufmann, T.L., Haase, K., Waszak, S.M., Eggert, A., Beule, D., Schulte, J.H., Ohler, U. and Schwarz, R.F.
iScience 27 (10): 110918. 18 October 2024

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
Dorel, M., Klinger, B., Mari, T., Toedling, J., Blanc, E., Messerschmidt, C., Nadler-Holly, M., Ziehm, M., Sieber, A., Hertwig, F., Beule, D., Eggert, A., Schulte, J.H., Selbach, M. and Blüthgen, N.
PLoS Computational Biology 17 (11): e1009515. 4 November 2021

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D., Obermayer, B., Weiner, J.M., Zimmermann, K., Anania, C., Wagner, L.K., Lyras, E.M., Sapozhnikova, V., Lara-Astiaso, D., Prósper, F., Lang, R., Lupiáñez, D.G., Beule, D., Höpken, U.E., Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19.
Essex, M., Millet Pascual-Leone, B.L., Löber, U., Kuhring, M., Zhang, B., Brüning, U., Fritsche-Guenther, R., Krzanowski, M., Fiocca Vernengo, F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thibeault, C., Corman, V.M., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
NPJ Biofilms and Microbiomes 10 (1): 66. 1 August 2024

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M., Pascual-Leone, B.M., Löber, U., Kuhring, M., Zhang, B., Bruening, U., Fritsche-Guenther, R., Krzanowski, M., Vernengo, F.F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thiebeault, C., Corman, V., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Complement activation induces excessive T cell cytotoxicity in severe COVID-19.
Georg, P., Astaburuaga-García, R., Bonaguro, L., Brumhard, S., Michalick, L., Lippert, L.J., Kostevc, T., Gäbel, C., Schneider, M., Streitz, M., Demichev, V., Gemünd, I., Barone, M., Tober-Lau, P., Helbig, E.T., Hillus, D., Petrov, L., Stein, J., Dey, H.P., Paclik, D., Iwert, C., Mülleder, M., Aulakh, S.K., Djudjaj, S., Bülow, R.D., Mei, H.E., Schulz, A.R., Thiel, A., Hippenstiel, S., Saliba, A.E., Eils, R., Lehmann, I., Mall, M.A., Stricker, S., Röhmel, J., Corman, V.M., Beule, D., Wyler, E., Landthaler, M., Obermayer, B., von Stillfried, S., Boor, P., Demir, M., Wesselmann, H., Suttorp, N., Uhrig, A., Müller-Redetzky, H., Nattermann, J., Kuebler, W.M., Meisel, C., Ralser, M., Schultze, J.L., Aschenbrenner, A.C., Thibeault, C., Kurth, F., Sander, L.E., Blüthgen, N. and Sawitzki, B.
Cell 185 (3): 493-512. 3 February 2022

Long-term in vitro expansion ensures increased yield of central memory T cells as perspective for manufacturing challenges.
Herda, S., Heimann, A., Obermayer, B., Ciraolo, E., Althoff, S., Ruß, J., Grunert, C., Busse, A., Bullinger, L., Pezzutto, A., Blankenstein, T., Beule, D. and Na, I.K.
International Journal of Cancer 148 (12): 3097-3110. 15 June 2021

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C., Kocks, C., Leiz, J., Karaiskos, N., Boltengagen, A., Cao, S., Skopnik, C.M., Klocke, J., Hardenberg, J.H., Stockmann, H., Gotthardt, I., Obermayer, B., Haghverdi, L., Wyler, E., Landthaler, M., Bachmann, S., Hocke, A.C., Corman, V., Busch, J., Schneider, W., Himmerkus, N., Bleich, M., Eckardt, K.U., Enghard, P., Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

Human alveolar progenitors generate dual lineage bronchioalveolar organoids.
Hoffmann, K., Obermayer, B., Hönzke, K., Fatykhova, D., Demir, Z., Löwa, A., Teixeira Alves, L.G., Wyler, E., Lopez-Rodriguez, E., Mieth, M., Baumgardt, M., Hoppe, J., Firsching, T.C., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Gruber, A.D., Ochs, M., Landthaler, M., Beule, D., Suttorp, N., Hippenstiel, S., Hocke, A.C. and Kessler, M.
Communications Biology 5 (1): 875. 25 August 2022

Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance.
Holle, J., Bartolomaeus, H., Löber, U., Behrens, F., Bartolomaeus, T.U.P., Anandakumar, H., Wimmer, M., Vu, D.L., Kuhring, M., Brüning, U., Maifeld, A., Geisberger, S., Kempa, S., Schumacher, F., Kleuser, B., Bufler, P., Querfeld, U., Kitschke, S., Engler, D., Kuhrt, L.D., Drechsel, O., Eckardt, K.U., Forslund, S., Thürmer, A., McParland, V., Kirwan, J., Wilck, N. and Mueller, D.
Journal of the American Society of Nephrology 33 (12): 2259-2275. December 2022

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4(+) T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Horn, V., Cancino, C.A., Steinheuer, L.M., Obermayer, B., Fritz, K., Nguyen, A.L., Juhran, K.S., Plattner, C., Bösel, D., Oldenburg, L., Burns, M., Schulz, A.R., Saliutina, M., Mantzivi, E., Lissner, D., Conrad, T., Mashreghi, M.F., Zundler, S., Sonnenberg, E., Schumann, M., Haag, L.M., Beule, D., Flatz, L., Trjanoski, Z., D'Haens, G., Weidinger, C., Mei, H.E., Siegmund, B., Thurley, K. and Hegazy, A.N.
Gastroenterology 28 September 2024 (In Press)

Human lungs show limited permissiveness for SARS-CoV-2 due to scarce ACE2 levels but virus-induced expansion of inflammatory macrophages.
Hönzke, K., Obermayer, B., Mache, C., Fathykova, D., Kessler, M., Dökel, S., Wyler, E., Baumgardt, M., Löwa, A., Hoffmann, K., Graff, P., Schulze, J., Mieth, M., Hellwig, K., Demir, Z., Biere, B., Brunotte, L., Mecate-Zambrano, A., Bushe, J., Dohmen, M., Hinze, C., Elezkurtaj, S., Tönnies, M., Bauer, T.T., Eggeling, S., Tran, H.L., Schneider, P., Neudecker, J., Rückert, J.C., Schmidt-Ott, K.M., Busch, J., Klauschen, F., Horst, D., Radbruch, H., Radke, J., Heppner, F., Corman, V.M., Niemeyer, D., Müller, M.A., Goffinet, C., Mothes, R., Pascual-Reguant, A., Hauser, A.E., Beule, D., Landthaler, M., Ludwig, S., Suttorp, N., Witzenrath, M., Gruber, A.D., Drosten, C., Sander, L.E., Wolff, T., Hippenstiel, S. and Hocke, A.C.
European Respiratory Journal 60 (6): 2102725. 1 December 2022

Tumour ischaemia by interferon-γ resembles physiological blood vessel regression.
Kammertoens, T., Friese, C., Arina, A., Idel, C., Briesemeister, D., Rothe, M., Ivanov, A., Szymborska, A., Patone, G., Kunz, S., Sommermeyer, D., Engels, B., Leisegang, M., Textor, A., Fehling, H.J., Fruttiger, M., Lohoff, M., Herrmann, A., Yu, H., Weichselbaum, R., Uckert, W., Hübner, N., Gerhardt, H., Beule, D., Schreiber, H. and Blankenstein, T.
Nature 545 (7652): 98-102. 4 May 2017

Intestinal retinol saturase is implicated in the development of obesity and epithelial homeostasis upon injury.
Kiefer, M.F., Meng, Y., Yang, N., Vahrenbrink, M., Wulff, S., Li, C., Wowro, S.J., Petricek, K.M., Sommerfeld, M., Flores, R.E., Obermayer, B., Piepelow, K., Klaus, S., Hartl, K., Guillot, A., Tacke, F., Sigal, M. and Schupp, M.
American Journal of Physiology Endocrinology and Metabolism 327 (2): E203-E216. August 2024

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche, R.P., Rodriguez-Fos, E., Helmsauer, K., Burkert, M., MacArthur, I.C., Maag, J., Chamorro, R., Munoz-Perez, N., Puiggròs, M., Dorado Garcia, H., Bei, Y., Röefzaad, C., Bardinet, V., Szymansky, A., Winkler, A., Thole, T., Timme, N., Kasack, K., Fuchs, S., Klironomos, F., Thiessen, N., Blanc, E., Schmelz, K., Künkele, A., Hundsdörfer, P., Rosswog, C., Theissen, J., Beule, D., Deubzer, H., Sauer, S., Toedling, J., Fischer, M., Hertwig, F., Schwarz, R.F., Eggert, A., Torrents, D., Schulte, J.H. and Henssen, A.G.
Nature Genetics 52 (1): 29-34. January 2020

Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L., Krupp, F., Harnett, D., Turko, P., Ambrozkiewicz, M.C., Sprink, T., Imami, K., Günnigmann, M., Zinnall, U., Vieira-Vieira, C.H., Schaub, T., Münster-Wandowski, A., Bürger, J., Borisova, E., Yamamoto, H., Rasin, M.R., Ohler, U., Beule, D., Mielke, T., Tarabykin, V., Landthaler, M., Kramer, G., Vida, I., Selbach, M. and Spahn, C.M.T.
Molecular Cell 81 (2): 304-322. 21 January 2021

Soluble ACE2 correlates with severe COVID-19 and can impair antibody responses.
Lebedin, M., Ratswohl, C., Garg, A., Schips, M., Vazquez Garcia, C., Spatt, L., Thibeault, C., Obermayer, B., Weiner, J., Moreno Velásquez, I., Gerhard, C., Stubbemann, P., Hanitsch, L.G., Pischon, T., Witzenrath, M., Sander, L.E., Kurth, F., Meyer-Hermann, M. and de la Rosa, K.
iScience 27 (3): 109330. 15 March 2024

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19.
Nouailles, G., Wyler, E., Pennitz, P., Postmus, D., Vladimirova, D., Kazmierski, J., Pott, F., Dietert, K., Muelleder, M., Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L.E., Suttorp, N., Ralser, M., Beule, D., Gruber, A.D., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Nature Communications 12 (1): 4869. 11 August 2021

Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19.
Nouailles, Geraldine, Wyler, E., Pennitz, P., Postmus, D., Vladrimirova, D., Kazmierski, J., Pott, F., Dietert, K., Mülleder, M.l, Farztdinov, V., Obermayer, B., Wienhold, S.M., Andreotti, S., Hoefler, T., Sawitzki, B., Drosten, C., Sander, L., Suttorp, N., Ralser, M., Beule, D., Gruber, A., Goffinet, C., Landthaler, M., Trimpert, J. and Witzenrath, M.
Research Square : rs-148392/v1. 28 January 2021

Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation.
Obermayer, B., Keilholz, L., Conrad, T., Frentsch, M., Blau, I.W., Vuong, L., Lesch, S., Movasshagi, K., Tietze-Stolley, C., Loyal, L., Henze, L., Penack, O., Stervbo, U., Babel, N., Haas, S., Beule, D., Bullinger, L., Wittenbecher, F. and Na, I.K.
Frontiers in Immunology 14 : 1114368. 10 February 2023

Multiplexed quantification of four neuroblastoma DNA targets in a single droplet digital PCR reaction.
Peitz, C., Sprüssel, A., Linke, R.B., Astrahantseff, K., Grimaldi, M., Schmelz, K., Toedling, J., Schulte, J.H., Fischer, M., Messerschmidt, C., Beule, D., Keilholz, U., Eggert, A., Deubzer, H.E. and Lodrini, M.
Journal of Molecular Diagnostics 22 (11): 1309-1323. November 2020

A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.
Pennitz, P., Kirsten, H., Friedrich, V.D., Wyler, E., Goekeri, C., Obermayer, B., Heinz, G.A., Mashreghi, M.F., Büttner, M., Trimpert, J., Landthaler, M., Suttorp, N., Hocke, A.C., Hippenstiel, S., Tönnies, M., Scholz, M., Kuebler, W.M., Witzenrath, M., Hoenzke, K. and Nouailles, G.
European Respiratory Review 31 (165): 220056. 30 September 2022

Tracing tumorigenesis in a solid tumor model at single-cell resolution.
Praktiknjo, S.D., Obermayer, B., Zhu, Q., Fang, L., Liu, H., Quinn, H., Stoeckius, M., Kocks, C., Birchmeier, W. and Rajewsky, N.
Nature Communications 11 (1): 991. 20 February 2020

YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer.
Quinn, H.M., Vogel, R., Popp, O., Mertins, P., Lan, L., Messerschmidt, C., Landshammer, A., Lisek, K., Château-Joubert, S., Marangoni, E., Koren, E., Fuchs, Y. and Birchmeier, W.
Cancer Research 81 (8): 2116-2127. April 2021

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.
Rajasekaran, S., Siddiqui, J., Rakijas, J., Nicolay, B., Lin, C., Khan, E., Patel, R., Morris, R., Wyler, E., Boukhali, M., Balasubramanyam, J., Ranjith Kumar, R., Van Rechem, C., Vogel, C., Elchuri, S.V., Landthaler, M., Obermayer, B., Haas, W., Dyson, N. and Miles, W.
Communications Biology 4 (1): 977. 17 August 2021

The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities.
Ramberger, E., Sapozhnikova, V., Ng, Y.L.D., Dolnik, A., Ziehm, M., Popp, O., Sträng, E., Kull, M., Grünschläger, F., Krüger, J., Benary, M., Müller, S., Gao, X., Murgai, A., Haji, M., Schmidt, A., Lutz, R., Nogai, A., Braune, J., Laue, D., Langer, C., Khandanpour, C., Bassermann, F., Döhner, H., Engelhardt, M., Straka, C., Hundemer, M., Beule, D., Haas, S., Keller, U., Einsele, H., Bullinger, L., Knop, S., Mertins, P. and Krönke, J.
Nature Cancer 5 (8): 1267-1284. August 2024

Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutated salivary duct carcinoma.
Rieke, D.T., Schröder, S., Schafhausen, P., Blanc, E., Zuljan, E., von der Emde, B., Beule, D., Keller, U., Keilholz, U. and Klinghammer, K.
Frontiers in Oncology 13 : 1107134. 2023

Mutational topography reflects clinical neuroblastoma heterogeneity.
Rodriguez-Fos, E., Planas-Fèlix, M., Burkert, M., Puiggròs, M., Toedling, J., Thiessen, N., Blanc, E., Szymansky, A., Hertwig, F., Ishaque, N., Beule, D., Torrents, D., Eggert, A., Koche, R.P., Schwarz, R.F., Haase, K., Schulte, J.H. and Henssen, A.G.
Cell Genomics 3 (10): 100402. 11 October 2023

SigsPack, a package for cancer mutational signatures.
Schumann, F., Blanc, E., Messerschmidt, C., Blankenstein, T., Busse, A. and Beule, D.
BMC Bioinformatics 20 (1): 450. 2 September 2019

Reflection of neuroblastoma intratumor heterogeneity in the new OHC-NB1 disease model.
Thole, T.M., Toedling, J., Sprüssel, A., Pfeil, S., Savelyeva, L., Capper, D., Messerschmidt, C., Beule, D., Groeneveld-Krentz, S., Eckert, C., Gambara, G., Henssen, A.G., Finkler, S., Schulte, J.H., Sieber, A., Bluethgen, N., Regenbrecht, C.R.A., Künkele, A., Lodrini, M., Eggert, A. and Deubzer, H.E.
International Journal of Cancer 146 (4): 1031-1041. 15 February 2020

Comparable CD8(+) T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals.
Tranter, E., Frentsch, M., Hütter-Krönke, M.L., Vuong, G.L., Busch, D., Loyal, L., Henze, L., Rosnev, S., Blau, I.W., Thiel, A., Beule, D., Bullinger, L., Obermayer, B. and Na, I.K.
Journal of Medical Virology 96 (3): e29539. March 2024

Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer.
Uhlitz, F., Bischoff, P., Peidli, S., Sieber, A., Trinks, A., Lüthen, M., Obermayer, B., Blanc, E., Ruchiy, Y., Sell, T., Mamlouk, S., Arsie, R., Wei, T.T., Klotz-Noack, K., Schwarz, R.F., Sawitzki, B., Kamphues, C., Beule, D., Landthaler, M., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
EMBO Molecular Medicine 13 (10): e14123. 7 October 2021

Immune phenotypes and target antigens of clonally expanded bone marrow T cells in treatment-naïve multiple myeloma.
Welters, C., Lammoglia Cobo, M.F., Stein, C.A., Hsu, M.T., Ben Hamza, A., Penter, L., Chen, X., Buccitelli, C., Popp, O., Mertins, P., Dietze, K., Bullinger, L., Moosmann, A., Blanc, E., Beule, D., Gerbitz, A., Strobel, J., Hackstein, H., Rahn, H.P., Dornmair, K., Blankenstein, T. and Hansmann, L.
Cancer Immunology Research 10 (11): 1407-1419. 1 November 2022

Mouse models of human multiple myeloma subgroups.
Winkler, W., Farré Díaz, C., Blanc, E., Napieczynska, H., Langner, P., Werner, M., Walter, B., Wollert-Wulf, B., Yasuda, T., Heuser, A., Beule, D., Mathas, S., Anagnostopoulos, I., Rosenwald, A., Rajewsky, K. and Janz, M.
Proceedings of the National Academy of Sciences of the United States of America 120 (10): e2219439120. 7 March 2023

EBAG9-silencing exerts an immune checkpoint function without aggravating adverse effects.
Wirges, A., Bunse, M., Joedicke, J.J., Blanc, E., Gudipati, V., Moles, M.W., Shiku, H., Beule, D., Huppa, J.B., Höpken, U.E. and Rehm, A.
Molecular Therapy 30 (11): 3358-3378. 2 November 2022

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

Tumour mutational burden and survival with molecularly matched therapy.
de Bortoli, T., Benary, M., Horak, P., Lamping, M., Stintzing, S., Tinhofer, I., Leyvraz, S., Schäfer, R., Klauschen, F., Keller, U., Stenzinger, A., Fröhling, S., Kurzrock, R., Keilholz, U., Rieke, D.T. and Jelas, I.
European Journal of Cancer 190 : 112925. September 2023

Bielka, Heinz

Arnold Graffi (1910-2006) : A pioneer of experimental cancer research.
Wunderlich, V. and Bielka, H.
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Bimmler, Marion

Antibodies to the alpha(1)-adrenergic receptor cause vascular impairments in rat brain as demonstrated by magnetic resonance angiography.
Karczewski, P., Pohlmann, A., Wagenhaus, B., Wisbrun, N., Hempel, P., Lemke, B., Kunze, R., Niendorf, T. and Bimmler, M.
PLoS ONE 7 (7): e41602. 30 July 2012

Birchmeier, Walter

Gab1 and Mapk signaling are essential in the hair cycle and hair follicle stem cell quiescence.
Akilli Öztürk, Ö., Pakula, H., Chmielowiec, J., Qi, J., Stein, S., Lan, L., Sasaki, Y., Rajewsky, K. and Birchmeier, W.
Cell Reports 13 (3): 561-572. 20 October 2015

Loss of epidermal Evi/Wls results in a phenotype resembling psoriasiform dermatitis.
Augustin, I., Gross, J., Baumann, D., Korn, C., Kerr, G., Grigoryan, T., Mauch, C., Birchmeier, W. and Boutros, M.
Journal of Experimental Medicine 210 (9): 1761-1777. 26 August 2013

Role of β-catenin in synaptic vesicle localization and presynaptic assembly.
Bamji, S.X., Shimazu, K., Kimes, N., Huelsken, J., Birchmeier, W., Lu, B. and Reichardt, L.F.
Neuron 40 (4): 719-731. November 2003

Establishment of kidney cancer organoid cultures.
Bauer, D., Birchmeier, W. and Fendler, A.
Research Square : rs.3.pex-911. 12 May 2020

Beta-catenin downregulation is required for adaptive cardiac remodeling.
Baurand, A., Zelarayan, L., Betney, R., Gehrke, C., Dunger, S., Noack, C., Busjahn, A., Huelsken, J., Taketo, M.M., Birchmeier, W., Dietz, R. and Bergmann, M.W.
Circulation Research 100 (9): 1353-1362. 11 May 2007

Control of beta-catenin signaling in tumor development.
Behrens, J.
Annals of the New York Academy of Sciences 910 : 21-35. June 2000

Functional interaction of an axin homolog, conductin, with beta-catenin, APC, and GSK3beta.
Behrens, J., Jerchow, B.A., Wuertele, M., Grimm, J., Asbrand, C., Wirtz, R., Kuehl, M., Wedlich, D. and Birchmeier, W.
Science 280 (5363): 596-599. 24 April 1998

Functional interaction of beta-catenin with the transcription factor LEF-1.
Behrens, J., von Kries, J.P., Kuehl, M., Bruhn, L., Wedlich, D., Grosschedl, R. and Birchmeier, W.
Nature 382 (6592): 638-642. 15 August 1996

Expression of nodal, lefty-A, and lefty-B in undifferentiated human embryonic stem cells requires activation of Smad2/3.
Besser, D.
Journal of Biological Chemistry 279 (43): 45076-45084. 1 January 2004

Hormonal induction of functional differentiation and mammary-derived growth inhibitor expression in cultured mouse mammary gland explants.
Binas, B., Spitzer, E., Zschiesche, W., Erdmann, B., Kurtz, A., Mueller, T., Niemann, C., Blenau, W. and Grosse, R.
In Vitro Cellular & Developmental Biology 28A (9-10): 625-634. September 1992

Molecular aspects of mesenchymal-epithelial interactions.
Birchmeier, C. and Birchmeier, W.
Annual Review of Cell Biology 9 : 511-540. 1993

Met, metastasis, motility and more.
Birchmeier, C., Birchmeier, W., Gherardi, E. and Vande Woude, G.F.
Nature Reviews Molecular Cell Biology 4 (12): 915-925. December 2003

Orchestrating Wnt signalling for metabolic liver zonation.
Birchmeier, W.
Nature Cell Biology 18 (5): 463-465. May 2016

Stem cells: Orphan receptors find a home.
Birchmeier, W.
Nature 476 (7360): 287-288. 18 August 2011

Cell adhesion and signal transduction in cancer.
Birchmeier, W.
EMBO Reports 6 (5): 413-417. 1 January 2005

Mittel zur Beeinflussung der Zelldifferenzierung und seine Verwendung.
Birchmeier, W.
DE19509792A1. 19 September 1996

Cadherin expression in carcinomas: role in the formation of cell junctions and the prevention of invasiveness.
Birchmeier, W. and Behrens, J.
Biochimica et Biophysica Acta 1198 (1): 11-26. 27 May 1994

The role of Irf6 in tooth epithelial invagination.
Blackburn, J., Ohazama, A., Kawasaki, K., Otsuka-Tanaka, Y., Liu, B., Honda, K., Rountree, R.B., Hu, Y., Kawasaki, M., Birchmeier, W., Schmidt-Ullrich, R., Kinoshita, A., Schutte, B.C., Hammond, N.L., Dixon, M.J. and Sharpe, P.T.
Developmental Biology 365 (1): 61-70. 1 May 2012

Balancing cell adhesion and Wnt signaling, the key role of beta-catenin.
Brembeck, F.H., Rosario, M. and Birchmeier, W.
Current Opinion in Genetics & Development 16 (1): 51-59. February 2006

Essential role of BCL9-2 in the switch between beta-catenin's adhesive and transcriptional functions.
Brembeck, F.H., Schwarz-Romond, T., Bakkers, J., Wilhelm, S., Hammerschmidt, M. and Birchmeier, W.
Genes & Development 18 (18): 2225-2230. 15 September 2004

BCL9-2 promotes early stages of intestinal tumor progression.
Brembeck, F.H., Wiese, M., Zatula, N., Grigoryan, T., Dai, Y., Fritzmann, J. and Birchmeier, W.
Gastroenterology 141 (4): 1359-1370. October 2011

Hepatocyte growth factor/scatter factor induces a variety of tissue-specific morphogenic programs in epithelial cells.
Brinkmann, V., Foroutan, H., Sachs, M., Weidner, K.M. and Birchmeier, W.
Journal of Cell Biology 131 (6 Pt. 1): 1573-1586. December 1995

NF-κB determines Paneth versus goblet cell fate decision in the small intestine.
Brischetto, C., Krieger, K., Klotz, C., Krahn, I., Kunz, S., Kolesnichenko, M., Mucka, P., Heuberger, J., Scheidereit, C. and Schmidt-Ullrich, R.
Development 148 (21): dev199683. November 2021

Piwi-interacting RNAs as novel prognostic markers in clear cell renal cell carcinomas.
Busch, J., Ralla, B., Jung, M., Wotschofsky, Z., Trujillo-Arribas, E., Schwabe, P., Kilic, E., Fendler, A. and Jung, K.
Journal of Experimental & Clinical Cancer Research 34 (1): 61. 14 June 2015

Sodium current deficit and arrhythmogenesis in a murine model of plakophilin-2 haploinsufficiency.
Cerrone, M., Noorman, M., Lin, X., Chkourko, H., Liang, F.X., van der Nagel, R., Hund, T., Birchmeier, W., Mohler, P., van Veen, T.A., van Rijen, H.V. and Delmar, M.
Cardiovascular Research 95 (4): 460-468. 1 September 2012

Bone morphogenetic protein-7 release from endogenous neural precursor cells suppresses the tumourigenicity of stem-like glioblastoma cells.
Chirasani, S.R., Sternjak, A., Wend, P., Momma, S., Campos, B., Herrmann, I.M., Graf, D., Mitsiadis, T., Herold-Mende, C., Besser, D., Synowitz, M., Kettenmann, H. and Glass, R.
Brain 133 (Pt 7): 1961-1972. July 2010

c-Met is essential for wound healing in the skin.
Chmielowiec, J., Borowiak, M., Morkel, M., Stradal, T., Munz, B., Werner, S., Wehland, J., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 177 (1): 151-162. 9 April 2007

Helicobacter pylori CagA protein targets the c-Met receptor and enhances the motogenic response.
Churin, Y., Al Ghoul, L., Kepp, O., Meyer, T.E., Birchmeier, W. and Naumann, M.
Journal of Cell Biology 161 (2): 249-255. 28 April 2003

The A-kinase anchoring protein (AKAP) glycogen synthase kinase 3β interaction protein (GSKIP) regulates β-catenin through its interactions with both protein kinase A (PKA) and GSK3β.
Dema, A., Schröter, M.F., Perets, E., Skroblin, P., Moutty, M.C., Deàk, V.A., Birchmeier, W. and Klussmann, E.
Journal of Biological Chemistry 291 (37): 19618-19630. 9 September 2016

FGF2 signaling in mouse embryonic fibroblasts is crucial for self-renewal of embryonic stem cells.
Diecke, S., Quiroga-Negreira, A., Redmer, T. and Besser, D.
Cells Tissues Organs 188 (1-2): 52-61. July 2008

From totipotent embryonic stem cells to spontaneously contracting smooth muscle cells: a retinoic acid and db-cAMP in vitro differentiation model.
Drab, M., Haller, H., Bychkov, R., Erdmann, B., Lindschau, C., Haase, H., Morano, I., Luft, F.C. and Wobus, A.M.
FASEB Journal 11 (11): 905-915. September 1997

A small-molecule antagonist of the β-catenin/TCF4 interaction blocks the self-renewal of cancer stem cells and suppresses tumorigenesis.
Fang, L., Zhu, Q., Neuenschwander, M., Specker, E., Wulf-Goldenberg, A., Weis, W.I., von Kries, J.P. and Birchmeier, W.
Cancer Research 76 (4): 891-901. 15 February 2016

Beta-catenin regulates P-cadherin expression in mammary basal epithelial cells.
Faraldo, M.M., Teuliere, J., Deugnier, M.A., Birchmeier, W., Huelsken, J., Thiery, J.P., Cano, A. and Glukhova, M.A.
FEBS Letters 581 (5): 831-836. 6 March 2007

Inhibiting WNT and NOTCH in renal cancer stem cells and the implications for human patients.
Fendler, A., Bauer, D., Busch, J., Jung, K., Wulf-Goldenberg, A., Kunz, S., Song, K., Myszczyszyn, A., Elezkurtaj, S., Erguen, B., Jung, S., Chen, W. and Birchmeier, W.
Nature Communications 11 (1): 929. 17 February 2020

The translational potential of microRNAs as biofluid markers of urological tumours.
Fendler, A., Stephan, C., Yousef, G.M., Kristiansen, G. and Jung, K.
Nature Reviews Urology 13 (12): 734-752. December 2016

Keratinocyte-specific ablation of protease-activated receptor-2 prevents gingival inflammation and bone loss in a mouse model of periodontal disease.
Francis, N., Ayodele, B.A., O'Brien-Simpson, N.M., Birchmeier, W., Pike, R.N., Pagel, C.N. and Mackie, E.J.
Cellular Microbiology 20 (11): e12891. November 2018

Circular RNAs: a new class of biomarkers as a rising interest in laboratory medicine.
Franz, A., Rabien, A., Stephan, C., Ralla, B., Fuchs, S., Jung, K. and Fendler, A.
Clinical Chemistry and Laboratory Medicine 56 (12): 1992-2003. December 2018

Circular RNAs in clear cell renal cell carcinoma: their microarray-based identification, analytical validation, and potential use in a clinico-genomic model to improve prognostic accuracy.
Franz, A., Ralla, B., Weickmann, S., Jung, M., Rochow, H., Stephan, C., Erbersdobler, A., Kilic, E., Fendler, A. and Jung, K.
Cancers 11 (10): 1473. 30 September 2019

A colorectal cancer expression profile that includes transforming growth factor beta inhibitor BAMBI predicts metastatic potential.
Fritzmann, J., Morkel, M., Besser, D., Budczies, J., Kosel, F., Brembeck, F.H., Stein, U., Fichtner, I., Schlag, P.M. and Birchmeier, W.
Gastroenterology 137 (11): 165-175. July 2009

Mutations in the desmosomal protein plakophilin-2 are common in arrhythmogenic right ventricular cardiomyopathy.
Gerull, B., Heuser, A., Wichter, T., Paul, M., Basson, C.T., McDermott, D.A., Lerman, B.B., Markowitz, S.M., Ellinor, P.T., MacRae, C.A., Peters, S., Grossmann, K.S., Drenckhahn, J., Michely, B., Sasse-Klaassen, S., Birchmeier, W., Dietz, R., Breithardt, G., Schulze-Bahr, E. and Thierfelder, L.
Nature Genetics 36 (11): 1162-1164. November 2004

Immunohistological analysis of E-cadherin, alpha-, beta- and gamma-catenin expression in colorectal cancer: Implications for cell adhesion and signaling.
Ghadimi, B.M., Behrens, J., Hoffmann, I., Haensch, W., Birchmeier, W. and Schlag, P.M.
European Journal of Cancer 35 (1): 60-65. January 1999

Targeting MET in cancer: rationale and progress.
Gherardi, E., Birchmeier, W., Birchmeier, C. and Woude, G.V.
Nature Reviews Cancer 12 (2): 89-103. February 2012

MLL1 is required for maintenance of intestinal stem cells.
Goveas, N., Waskow, C., Arndt, K., Heuberger, J., Zhang, Q., Alexopoulou, D., Dahl, A., Birchmeier, W., Anastassiadis, K., Stewart, A.F. and Kranz, A.
PLoS Genetics 17 (12): e1009250. 3 December 2021

Molecular signaling mechanisms of axon-glia communication in the peripheral nervous system.
Grigoryan, T. and Birchmeier, W.
BioEssays 37 (5): 502-513. May 2015

Wnt/Rspondin/β-catenin signals control axonal sorting and lineage progression in Schwann cell development.
Grigoryan, T., Stein, S., Qi, J., Wende, H., Garratt, A.N., Nave, K.A., Birchmeier, C. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 110 (45): 18174-18179. 5 November 2013

Deciphering the function of canonical Wnt signals in development and disease: conditional loss- and gain-of-function mutations of beta-catenin in mice.
Grigoryan, T., Wend, P., Klaus, A. and Birchmeier, W.
Genes & Development 22 (17): 2308-2341. 1 September 2008

Novel p62dok family members, dok-4 and dok-5, are substrates of the c-Ret receptor tyrosine kinase and mediate neuronal differentiation.
Grimm, J., Sachs, M., Britsch, S., Di Cesare, S., Schwarz-Romond, T. and Birchmeier, W.
Journal of Cell Biology 154 (2): 345-354. 23 July 2001

The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness.
Grinat, J., Heuberger, J., Vidal, R., Goveas, N., Kosel, F., Berenguer-Llergo, A., Kranz, A., Wulf-Goldenberg, A., Behrens, D., Melcher, B., Sauer, S., Vieth, M., Batlle, E., Stewart, A. and Birchmeier, W.
Nature Communications 11 (1): 6422. 21 December 2020

Epigenetic modifier balances Mapk and Wnt signalling in differentiation of goblet and Paneth cells.
Grinat, J., Kosel, F., Goveas, N., Kranz, A., Alexopoulou, D., Rajewsky, K., Sigal, M., Stewart, A.F. and Heuberger, J.
Life Science Alliance 5 (4): e202101187. April 2022

Selective inhibitors of the protein tyrosine phosphatase SHP2 block cellular motility and growth of cancer cells in vitro and in vivo.
Grosskopf, S., Eckert, C., Arkona, C., Radetzki, S., Böhm, K., Heinemann, U., Wolber, G., von Kries, J.P., Birchmeier, W. and Rademann, J.
ChemMedChem 10 (5): 815-826. May 2015

Requirement of plakophilin 2 for heart morphogenesis and cardiac junction formation.
Grossmann, K.S., Grund, C., Huelsken, J., Behrend, M., Erdmann, B., Franke, W.W. and Birchmeier, W.
Journal of Cell Biology 167 (1): 149-160. 11 October 2004

The tyrosine phosphatase Shp2 in development and cancer.
Grossmann, K.S., Rosario, M., Birchmeier, C. and Birchmeier, W.
Advances in Cancer Research 106 : 53-89. 2010

The tyrosine phosphatase Shp2 (PTPN11) directs neuregulin-1/ErbB signaling throughout schwann cell development.
Grossmann, K.S., Wende, H., Paul, F.E., Cheret, C., Garratt, A.N., Zurborg, S., Feinberg, K., Besser, D., Schulz, H., Peles, E., Selbach, M., Birchmeier, W. and Birchmeier, C.
Proceedings of the National Academy of Sciences of the United States of America 106 (39): 16704-16709. 29 September 2009

Functional involvement of CD44, a family of cell adhesion molecules, in immune responses, tumour progression and haematopoiesis.
Guenthert, U., Schwaerzler, C., Wittig, B., Laman, J., Ruiz, P., Stauder, R., Bloem, A., Smadja-Joffe, F., Zoeller, M. and Rolink, A.
Advances in Experimental Medicine and Biology 451 : 43-49. 1998

Aberrant Wnt/beta-catenin signaling can induce chromosomal instability in colon cancer.
Hadjihannas, M.V., Brueckner, M., Jerchow, B., Birchmeier, W., Dietmaier, W. and Behrens, J.
Proceedings of the National Academy of Sciences of the United States of America 103 (28): 10747-10752. 11 July 2006

Beneficial effect of voluntary physical exercise in Plakophilin2 transgenic mice.
Hammer, K.P., Mustroph, J., Stauber, T., Birchmeier, W., Wagner, S. and Maier, L.S.
PLoS ONE 16 (6): e0252649. 4 June 2021

Two isoforms of human RNA polymerase III with specific functions in cell growth and transformation.
Haurie, V., Durrieu-Gaillard, S., Dumay-Odelot, H., Da Silva, D., Rey, C., Prochazkova, M., Roeder, R.G., Besser, D. and Teichmann, M.
Proceedings of the National Academy of Sciences of the United States of America 107 (9): 4176-4181. 2 March 2010

Shp-2 inhibitors, pharmaceutical compositions comprising them and their use for treating phosphatase-mediated diseases [Shp-2-Inhibitoren, Arzneimittel, die sie enthalten sowie deren Verwendung zur Behandlung von Phosphatasen-vermittelten Krankheiten].
Hellmuth, K. and Birchmeier, W.
EP1728790 ; WO06128909. 6 December 2006

Specific inhibitors of the protein tyrosine phosphatase Shp2 identified by high-throughput docking.
Hellmuth, K., Grosskopf, S., Lum, C.T., Wuertele, M., Roeder, N., von Kries, J.P., Rosario, M., Rademann, J. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 105 (20): 7275-7280. 20 May 2008

Interplay of cadherin-mediated cell adhesion and canonical wnt signaling.
Heuberger, J. and Birchmeier, W.
Cold Spring Harbor Perspectives in Biology 2 (2): a002915. February 2010

Shp2/MAPK signaling controls goblet/paneth cell fate decisions in the intestine.
Heuberger, J., Kosel, F., Qi, J., Grossmann, K.S., Rajewsky, K. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 111 (9): 3472-3477. 4 March 2014

High Yap and Mll1 promote a persistent regenerative cell state induced by Notch signaling and loss of p53.
Heuberger, J., Grinat, J., Kosel, F., Liu, L., Kunz, S., Vidal, R.O., Keil, M., Haybaeck, J., Robine, S., Louvard, D., Regenbrecht, C., Sporbert, A., Sauer, S., von Eyss, B., Sigal, M. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 118 (22): e2019699118. 1 June 2021

A C/EBPα-Wnt connection in gut homeostasis and carcinogenesis.
Heuberger, J., Hill, U., Förster, S., Zimmermann, K., Malchin, V., Kühl, A.A., Stein, U., Vieth, M., Birchmeier, W. and Leutz, A.
Life Science Alliance 2 (1): e201800173. February 2019

Targeting SHP2 phosphatase in breast cancer overcomes RTK-mediated resistance to PI3K inhibitors.
Heynen, G.J.J.E., Lisek, K., Vogel, R., Wulf-Goldenberg, A., Alcaniz, J., Montaudon, E., Marangoni, E. and Birchmeier, W.
Breast Cancer Research 24 (1): 23. 1 April 2022

Canonical Wnt/beta-catenin signaling prevents osteoblasts from differentiating into chondrocytes.
Hill, T.P., Spaeter, D., Taketo, M.M., Birchmeier, W. and Hartmann, C.
Developmental Cell 8 (5): 727-738. 1 May 2005

Multiple roles of mesenchymal beta-catenin during murine limb patterning.
Hill, T.P., Taketo, M.M., Birchmeier, W. and Hartmann, C.
Development 133 (7): 1219-1229. 1 April 2006

Expression of multidrug resistance proteins (Mrps) in astrocytes of the mouse brain: a single cell rt-PCR study.
Hirrlinger, J., Moeller, H., Kirchhoff, F. and Dringen, R.
Neurochemical Research 30 (10): 1237-1244. 1 October 2005

Rap1 regulates the formation of E-cadherin-based cell-cell contacts.
Hogan, C., Serpente, N., Cogram, P., Hosking, C.R., Bialucha, C.U., Feller, S.M., Braga, V.M.M., Birchmeier, W. and Fujita, Y.
Molecular and Cellular Biology 24 (15): 6690-6700. 1 January 2004

Wnt signaling in stem and cancer stem cells.
Holland, J.D., Klaus, A., Garratt, A.N. and Birchmeier, W.
Current Opinion in Cell Biology 25 (2): 254-264. April 2013

Combined Wnt/β-catenin, met, and CXCL12/CXCR4 signals characterize basal breast cancer and predict disease outcome.
Holland, J.D., Györffy, B., Vogel, R., Eckert, K., Valenti, G., Fang, L., Lohneis, P., Elezkurtaj, S., Ziebold, U. and Birchmeier, W.
Cell Reports 5 (5): 1214-1227. 12 December 2013

The transcriptional repressor Glis2 is a novel binding partner for p120 catenin.
Hosking, C.R., Ulloa, F., Hogan, C., Ferber, E., Figueroa, A., Gevaert, K., Birchmeier, W., Briscoe, J. and Fujita, Y.
Molecular Biology of the Cell 18 (5): 1918-1927. 1 May 2007

E-cadherin and APC compete for the interaction with beta-catenin and the cytoskeleton.
Huelsken, J., Birchmeier, W. and Behrens, J.
Journal of Cell Biology 127 (6 Pt. 2): 2061-2069. December 1994

Requirement for beta-catenin in anterior-posterior axis formation in mice.
Huelsken, J., Vogel, R., Brinkmann, V., Erdmann, B., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 148 (3): 567-578. 7 February 2000

beta-Catenin controls hair follicle morphogenesis and stem cell differentiation in the skin.
Huelsken, J., Vogel, R., Erdmann, B., Cotsarelis, G. and Birchmeier, W.
Cell 105 (4): 533-545. 18 May 2001

Plakoglobin is essential for myocardial compliance but dispensable for myofibril insertion into adherens junctions.
Isac, C.M., Ruiz, P., Pfitzmaier, B., Haase, H., Birchmeier, W. and Morano, I.
Journal of Cellular Biochemistry 72 (1): 8-15. 1 January 1999

Continuous tooth generation in mouse is induced by activated epithelial Wnt/β-catenin signaling.
Jaervinen, E., Salazar-Ciudad, I., Birchmeier, W., Taketo, M.M., Jernvall, J. and Thesleff, I.
Proceedings of the National Academy of Sciences of the United States of America 103 (49): 18627-18632. 5 December 2006

Long-term, multilineage hematopoiesis occurs in the combined absence of beta-catenin and gamma-catenin.
Jeannet, G., Scheller, M., Scarpellino, L., Duboux, S., Gardiol, N., Back, J., Kuttler, F., Malanchi, I., Birchmeier, W., Leutz, A., Huelsken, J. and Held, W.
Blood 111 (1): 142-149. 1 January 2008

Genetische Analyse von Conductin durch zielgerichtete Mutagenese in der Maus.
Jerchow, B.
UNSPECIFIED thesis, UNSPECIFIED. 6 May 2003

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells.
Juerchott, K., Kuban, R.J., Krech, T., Blüthgen, N., Stein, U., Walther, W., Friese, C., Kielbasa, S.M., Ungethuem, U., Lund, P., Knoesel, T., Kemmner, W., Morkel, M., Fritzmann, J., Schlag, P.M., Birchmeier, W., Krueger, T., Sperling, S., Sers, C., Royer, H.D., Herzel, H. and Schaefer, R.
PLoS Genetics 6 (12): e1001231. 2 December 2010

Identification of miR-21-5p and miR-210-3p serum levels as biomarkers for patients with papillary renal cell carcinoma: a multicenter analysis.
Kalogirou, C., Ellinger, J., Kristiansen, G., Hatzichristodoulou, G., Kübler, H., Kneitz, B., Busch, J. and Fendler, A.
Translational Andrology and Urology 9 (3): 1314-1322. June 2020

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling.
Kamdem, N., Roske, Y., Kovalskyy, D., Platonov, M.O., Balinskyi, O., Kreuchwig, A., Saupe, J., Fang, L., Diehl, A., Schmieder, P., Krause, G., Rademann, J., Heinemann, U., Birchmeier, W. and Oschkinat, H.
Magnetic Resonance 2 (1): 355-374. 2 June 2021

Homogeneity and persistence of transgene expression by omitting antibiotic selection in cell line isolation.
Kaufman, W.L., Kocman, I., Agrawal, V., Rahn, H.P., Besser, D. and Gossen, M.
Nucleic Acids Research 36 (17): e111. October 2008

Negative regulation of Ros receptor tyrosine kinase signaling: An epithelial function of the SH2 domain protein tyrosine phosphatase SHP-1.
Keilhack, H., Mueller, M., Boehmer, S.A., Frank, C., Weidner, K.M., Birchmeier, W., Ligensa, T., Berndt, A., Kosmehl, H., Gunther, B., Mueller, T., Birchmeier, C. and Boehmer, F.D.
Journal of Cell Biology 152 (2): 325-334. 22 January 2001

Developmental signaling in myocardial progenitor cells: A comprehensive view of Bmp- and Wnt/beta-catenin signaling.
Klaus, A. and Birchmeier, W.
Pediatric Cardiology 30 (5): 609-616. July 2009

Wnt signalling and its impact on development and cancer.
Klaus, A. and Birchmeier, W.
Nature Reviews Cancer 8 (5): 387-398. May 2008

Wnt/beta-catenin and Bmp signals control distinct sets of transcription factors in cardiac progenitor cells.
Klaus, A., Mueller, M., Schulz, H., Saga, Y., Martin, J.F. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 109 (27): 10921-10926. 3 July 2012

Distinct roles of Wnt/beta-catenin and Bmp signaling during early cardiogenesis.
Klaus, A., Saga, Y., Taketo, M.M., Tzahor, E. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 104 (47): 18531-18536. 20 November 2007

Mutations of the Wnt antagonist AXIN2 (Conductin) result in TCF-dependent transcription in medulloblastomas.
Koch, A., Hrychyk, A., Hartmann, W., Waha, A., Mikeska, T., Waha, A., Schueller, U., Soerensen, N., Berthold, F., Goodyer, C.G., Wiestler, O.D., Birchmeier, W., Behrens, J. and Pietsch, T.
International Journal of Cancer 121 (2): 284-291. 15 July 2007

Mutations and elevated transcriptional activity of conductin (AXIN2) in hepatoblastomas.
Koch, A., Weber, N., Waha, A., Hartmann, W., Denkhaus, D., Behrens, J., Birchmeier, W., von Schweinitz, D. and Pietsch, T.
Journal of Pathology 204 (5): 546-554. 1 January 2004

Epicatechin gallate and catechin gallate are superior to epigallocatechin gallate in growth suppression and anti-inflammatory activities in pancreatic tumor cells.
Kuerbitz, C., Heise, D., Redmer, T., Goumas, F., Arlt, A., Lemke, J., Rimbach, G., Kalthoff, H. and Trauzold, A.
Cancer Science 102 (4): 728-734. April 2011

The docking protein Gab1 is an essential component of an indirect mechanism for fibroblast growth factor stimulation of the phosphatidylinositol 3-kinase/Akt antiapoptotic pathway.
Lamothe, B., Yamada, M., Schaeper, U., Birchmeier, W., Lax, I. and Schlessinger, J.
Molecular and Cellular Biology 24 (13): 5657-5666. 1 January 2004

Shp2 signaling suppresses senescence in PyMT-induced mammary gland cancer in mice.
Lan, L., Holland, J.D., Qi, J., Grosskopf, S., Rademann, J., Vogel, R., Gyoerffy, B., Wulf-Goldenberg, A. and Birchmeier, W.
EMBO Journal 34 (11): 1493-1508. 3 June 2015

MicroRNA signature helps distinguish early from late biochemical failure in prostate cancer.
Lichner, Z., Fendler, A., Saleh, C., Nasser, A.N., Boles, D., Al-Haddad, S., Kupchak, P., Dharsee, M., Nuin, P.S., Evans, K.R., Jung, K., Stephan, C., Fleshner, N.E. and Yousef, G.M.
Clinical Chemistry 59 (11): 1595-1603. November 2013

Impaired Plakophilin-2 in obesity breaks cell cycle dynamics to breed adipocyte senescence.
Lluch, A., Latorre, J., Serena-Maione, A., Espadas, I., Caballano-Infantes, E., Moreno-Navarrete, J.M., Oliveras-Cañellas, N., Ricart, W., Malagón, M.M., Martin-Montalvo, A., Birchmeier, W., Szymanski, W., Graumann, J., Gómez-Serrano, M., Sommariva, E., Fernández-Real, J.M. and Ortega, F.J.
Nature Communications 14 (1): 5106. 22 August 2023

Diagnostic and prognostic potential of circulating cell-free genomic and mitochondrial DNA fragments in clear cell renal cell carcinoma patients.
Lu, H., Busch, J., Jung, M., Rabenhorst, S., Ralla, B., Kilic, E., Mergemeier, S., Budach, N., Fendler, A. and Jung, K.
Clinica Chimica Acta 452 : 109-119. 15 January 2016

Arrhythmogenic right ventricular cardiomyopathy: moving toward mechanism.
MacRae, C.A., Birchmeier, W. and Thierfelder, L.
Journal of Clinical Investigation 116 (7): 1825-1828. July 2006

Cutaneous cancer stem cell maintenance is dependent on beta-catenin signalling.
Malanchi, I., Peinado, H., Kassen, D., Hussenet, T., Metzger, D., Chambon, P., Huber, M., Hohl, D., Cano, A., Birchmeier, W. and Huelsken, J.
Nature 452 (7187): 650-653. 3 April 2008

Diversin regulates heart formation and gastrulation movements in development.
Moeller, H., Jenny, A., Schaeffer, H.J., Schwarz-Romond, T., Mlodzik, M., Hammerschmidt, M. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 103 (43): 15900-15905. 24 October 2006

Effects of silibinin on growth and invasive properties of human ovarian carcinoma cells through suppression of heregulin/HER3 pathway.
Momeny, M., Ghasemi, R., Valenti, G., Miranda, M., Zekri, A., Zarrinrad, G., Javadikooshesh, S., Yaghmaie, M., Alimoghaddam, K., Ghavamzadeh, A. and Ghaffari, S.H.
Tumor Biology 37 (3): 3913-3923. March 2016

Heregulin-HER3-HER2 signaling promotes matrix metalloproteinase-dependent blood-brain-barrier transendothelial migration of human breast cancer cell lines.
Momeny, M., Saunus, J.M., Marturana, F., McCart Reed, A.E., Black, D., Sala, G., Iacobelli, S., Holland, J.D., Yu, D., Da Silva, L., Simpson, P.T., Khanna, K.K., Chenevix-Trench, G. and Lakhani, S.R.
Oncotarget 6 (6): 3932-3946. 19 February 2015

β-Catenin regulates Cripto- and Wnt3-dependent gene expression programs in mouse axis and mesoderm formation.
Morkel, M., Huelsken, J., Wakamiya, M., Ding, J., van de Wetering, M., Clevers, H., Taketo, M.M., Behringer, R.R., Shen, M.M. and Birchmeier, W.
Development 130 (25): 6283-6294. 1 January 2003

From pyrazolones to azaindoles: evolution of active-site SHP2 inhibitors based on scaffold hopping and bioisosteric replacement.
Mostinski, Y., Heynen, G.J.J.E., López-Alberca, M.P., Paul, J., Miksche, S., Radetzki, S., Schaller, D., Shanina, E., Seyffarth, C., Kolomeets, Y., Ziebart, N., de Schryver, J., Oestreich, S., Neuenschwander, M., Roske, Y., Heinemann, U., Rademacher, C., Volkamer, A., von Kries, J.P., Birchmeier, W. and Nazaré, M.
Journal of Medicinal Chemistry 63 (23): 14780-14804. 10 December 2020

β-catenin is required for specification of proximal/distal cell fate during lung morphogenesis.
Mucenski, M.L., Wert, S.E., Nation, J.M., Loudy, D.E., Huelsken, J., Birchmeier, W., Morrisey, E.E. and Whitsett, J.A.
Journal of Biological Chemistry 278 (41): 40231-40238. 10 October 2003

Mice with renal-specific alterations 1 of stem cell-associated signaling develop symptoms of chronic kidney disease but surprisingly no tumors.
Myszczyszyn, A., Popp, O., Kunz, S., Sporbert, A., Jung, S., Penning, L.C., Fendler, A., Mertins, P. and Birchmeier, W.
PLoS ONE 19 (3): e0282938. 21 March 2024

Sustained epithelial beta-catenin activity induces precocious hair development but disrupts hair follicle down-growth and hair shaft formation.
Naerhi, K., Jaervinen, E., Birchmeier, W., Taketo, M.M., Mikkola, M.L. and Thesleff, I.
Development 135 (6): 1019-1028. March 2008

Reconstitution of mammary gland development in vitro: Requirement of c-met and c-erbB2 signaling for branching and alveolar morphogenesis.
Niemann, C., Brinkmann, V., Spitzer, E., Hartmann, G., Sachs, M., Naundorf, H. and Birchmeier, W.
Journal of Cell Biology 143 (2): 533-545. 19 October 1998

SHP-2 in lymphocytes' cytokine and inhibitory receptor signaling.
Niogret, C., Birchmeier, W. and Guarda, G.
Frontiers in Immunology 10 : 2468. 25 October 2019

Shp-2 is critical for ERK and metabolic engagement downstream of IL-15 receptor in NK cells.
Niogret, C., Miah, S.M.S., Rota, G., Fonta, N.P., Wang, H., Held, W., Birchmeier, W., Sexl, V., Yang, W., Vivier, E., Ho, P.C., Brossay, L. and Guarda, G.
Nature Communications 10 (1): 1444. 29 March 2019

Inverse relation of E-cadherin and autocrine motility factor receptor expression as a prognostic factor in patients with bladder carcinomas.
Otto, T., Birchmeier, W., Schmidt, U., Hinke, A., Schipper, J., Ruebben, H. and Raz, A.
Cancer Research 54 (12): 3120-3123. 15 June 1994

Tracing tumorigenesis in a solid tumor model at single-cell resolution.
Praktiknjo, S.D., Obermayer, B., Zhu, Q., Fang, L., Liu, H., Quinn, H., Stoeckius, M., Kocks, C., Birchmeier, W. and Rajewsky, N.
Nature Communications 11 (1): 991. 20 February 2020

The MEK1 scaffolding protein MP1 regulates cell spreading by integrating PAK1 and Rho signals.
Pullikuth, A., McKinnon, E., Schaeffer, H.J. and Catling, A.D.
Molecular and Cellular Biology 25 (12): 5119-5133. 1 June 2005

Targeting Wnt/β-catenin signaling by TET1/FOXO4 inhibits metastatic spreading and self-renewal of cancer stem cells in gastric cancer.
Qi, J., Cui, D., Wu, Q.N., Zhao, Q., Chen, Z.H., Li, L., Birchmeier, W., Yu, Y. and Tao, R.
Cancers 14 (13): 3232. 30 June 2022

New Wnt/β-catenin target genes promote experimental metastasis and migration of colorectal cancer cells through different signals.
Qi, J., Yu, Y., Akilli Öztürk, Ö., Holland, J.D., Besser, D., Fritzmann, J., Wulf-Goldenberg, A., Eckert, K., Fichtner, I. and Birchmeier, W.
Gut 65 (10): 1690-1701. October 2016

KLF4 functions as an oncogene in promoting cancer stem cell-like characteristics in osteosarcoma cells.
Qi, X.T., Li, Y.L., Zhang, Y.Q., Xu, T., Lu, B., Fang, L., Gao, J.Q., Yu, L.S., Zhu, D.F., Yang, B., He, Q.J. and Ying, M.D.
Acta Pharmacologica Sinica 40 (4): 546-555. April 2019

YAP and β-catenin cooperate to drive oncogenesis in basal breast cancer.
Quinn, H.M., Vogel, R., Popp, O., Mertins, P., Lan, L., Messerschmidt, C., Landshammer, A., Lisek, K., Château-Joubert, S., Marangoni, E., Koren, E., Fuchs, Y. and Birchmeier, W.
Cancer Research 81 (8): 2116-2127. April 2021

miR-9-5p in nephrectomy specimens is a potential predictor of primary resistance to first-line treatment with tyrosine kinase inhibitors in patients with metastatic renal cell carcinoma.
Ralla, B., Busch, J., Flörcken, A., Westermann, J., Zhao, Z., Kilic, E., Weickmann, S., Jung, M., Fendler, A. and Jung, K.
Cancers 10 (9): 321. 10 September 2018

E-cadherin is crucial for embryonic stem cell pluripotency and can replace OCT4 during somatic cell reprogramming.
Redmer, T., Diecke, S., Grigoryan, T., Quiroga-Negreira, A., Birchmeier, W. and Besser, D.
EMBO Reports 12 (7): 720-726. 1 July 2011

Instability of circular RNAs in clinical tissue samples impairs their reliable expression analysis using RT-qPCR: from the myth of their advantage as biomarkers to reality.
Rochow, H., Franz, A., Jung, M., Weickmann, S., Ralla, B., Kilic, E., Stephan, C., Fendler, A. and Jung, K.
Theranostics 10 (20): 9268-9279. 23 July 2020

Circular RNAs and their linear transcripts as diagnostic and prognostic tissue biomarkers in prostate cancer after prostatectomy in combination with clinicopathological factors.
Rochow, H., Jung, M., Weickmann, S., Ralla, B., Stephan, C., Elezkurtaj, S., Kilic, E., Zhao, Z., Jung, K., Fendler, A. and Franz, A.
International Journal of Molecular Sciences 21 (21): E7812. 22 October 2020

Making tubes: Step by step.
Rosario, M. and Birchmeier, W.
Developmental Cell 7 (1): 3-5. 1 July 2004

How to make tubes: signaling by the Met receptor tyrosine kinase.
Rosario, M. and Birchmeier, W.
Trends in Cell Biology 13 (6): 328-335. June 2003

The neurite outgrowth multiadaptor RhoGAP, NOMA-GAP, regulates neurite extension through SHP2 and Cdc42.
Rosario, M., Franke, R., Bednarski, C. and Birchmeier, W.
Journal of Cell Biology 178 (3): 503-516. 30 July 2007

Neocortical dendritic complexity is controlled during development by NOMA-GAP-dependent inhibition of Cdc42 and activation of cofilin.
Rosario, M., Schuster, S., Juettner, R., Parthasarathy, S., Tarabykin, V. and Birchmeier, W.
Genes & Development 26 (15): 1743-1757. 1 August 2012

Shp-2 is dispensable for establishing T cell exhaustion and for PD-1 signaling in vivo.
Rota, G., Niogret, C., Dang, A.T., Barros, C.R., Fonta, N.P., Alfei, F., Morgado, L., Zehn, D., Birchmeier, W., Vivier, E. and Guarda, G.
Cell Reports 23 (1): 39-49. 3 April 2018

Mutant KRAS-driven cancers depend on PTPN11/SHP2 phosphatase.
Ruess, D.A., Heynen, G.J., Ciecielski, K.J., Ai, J., Berninger, A., Kabacaoglu, D., Görgülü, K., Dantes, Z., Wörmann, S.M., Diakopoulos, K.N., Karpathaki, A.F., Kowalska, M., Kaya-Aksoy, E., Song, L., Zeeuw van der Laan, E.A., López-Alberca, M.P., Nazaré, M., Reichert, M., Saur, D., Erkan, M.M., Hopt, U.T., Sainz, B., Birchmeier, W., Schmid, R.M., Lesina, M. and Algül, H.
Nature Medicine 24 (7): 954-960. July 2018

The plakoglobin knock-out mouse: A paradigm for the molecular analysis of cardiac cell junction formation.
Ruiz, P. and Birchmeier, W.
Trends in Cardiovascular Medicine 8 (3): 97-101. April 1998

Targeted mutation of plakoglobin in mice reveals essential functions of desmosomes in the embryonic heart.
Ruiz, P., Brinkmann, V., Ledermann, B., Behrend, M., Grund, C., Thalhammer, C., Vogel, F., Birchmeier, C., Guenthert, U., Franke, W.W. and Birchmeier, W.
Journal of Cell Biology 135 (1): 215-225. October 1996

Essential role of Gab1 for signaling by the c-Met receptor in vivo.
Sachs, M., Brohmann, H., Zechner, D., Mueller, T., Huelsken, J., Walther, I., Schaeper, U., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 150 (6): 1375-1384. 18 September 2000

Motogenic and morphogenic activity of epithelial receptor tyrosine kinases.
Sachs, M., Weidner, K.M., Brinkmann, V., Walther, I., Obermeier, A., Ullrich, A. and Birchmeier, W.
Journal of Cell Biology 133 (5): 1095-1107. 3 June 1996

HGF/SF c-Met signaling in the epithelial-mesenchymal transition and migration of muscle progenitor cells.
Schaeper, U. and Birchmeier, W.
In: Cell Migration in Development and Disease. Wiley-VCH, Weinheim, 191-204. ISBN 3-527-30587-4 1 January 2005

Coupling of Gab1 to c-Met, Grb2, and Shp2 mediates biological responses.
Schaeper, U., Gehring, N.H., Fuchs, K.P., Sachs, M., Kempkes, B. and Birchmeier, W.
Journal of Cell Biology 149 (7): 1419-1432. 26 June 2000

Tyrosine kinases.
Schaeper, U. and Grossmann, K.S.
In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine ; Vol. 2. Springer, Berlin [u.a.], 1951-1959. ISBN 3-540-44244-8 2006

Distinct requirements for Gab1 in Met and EGF receptor signaling in vivo.
Schaeper, U., Vogel, R., Chmielowiec, J., Huelsken, J., Rosario, M. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 104 (39): 15376-15381. 25 September 2007

Hematopoietic stem cell and multilineage defects generated by constitutive beta-catenin activation.
Scheller, M., Huelsken, J., Rosenbauer, F., Taketo, M.M., Birchmeier, W., Tenen, D.G. and Leutz, A.
Nature Immunology 7 (10): 1037-1047. October 2006

The neuronal scaffold protein Shank3 mediates signaling and biological function of the receptor tyrosine kinase Ret in epithelial cells.
Schuetz, G., Rosario, M., Grimm, J., Boeckers, T.M., Gundelfinger, E.D. and Birchmeier, W.
Journal of Cell Biology 167 (5): 945-952. 6 December 2004

MEK Partner 1 (MP1): Regulation of oligomerization in MAP kinase signaling.
Sharma, C., Vomastek, T., Tarcsafalvi, A., Catling, A.D., Schaeffer, H.J., Eblen, S.T. and Weber, M.J.
Journal of Cellular Biochemistry 94 (4): 708-719. 1 January 2005

Activation of MAPK overrides the termination of myelin growth and replaces Nrg1/ErbB3 signals during Schwann cell development and myelination.
Sheean, M.E., McShane, E., Cheret, C., Walcher, J., Müller, T., Wulf-Goldenberg, A., Hoelper, S., Garratt, A.N., Krüger, M., Rajewsky, K., Meijer, D., Birchmeier, W., Lewin, G.R., Selbach, M. and Birchmeier, C.
Genes & Development 28 (3): 290-303. 1 February 2014

Wnt/beta-catenin signaling acts upstream of N-myc, BMP4, and FGF signaling to regulate proximal-distal patterning in the lung.
Shu, W., Guttentag, S., Wang, Z., Andl, T., Ballard, P., Lu, M.M., Piccolo, S., Birchmeier, W., Whitsett, J.A., Millar, S.E. and Morrisey, E.E.
Developmental Biology 283 (1): 226-239. 1 January 2005

Wnt-Fzd signaling sensitizes peripheral sensory neurons via distinct noncanonical pathways.
Simonetti, M., Agarwal, N., Stösser, S., Bali, K.K., Karaulanov, E., Kamble, R., Pospisilova, B., Kurejova, M., Birchmeier, W., Niehrs, C., Heppenstall, P. and Kuner, R.
Neuron 83 (1): 104-121. 2 July 2014

Specific paucity of unmyelinated C-fibers in cutaneous peripheral nerves of the African naked-mole rat: comparative analysis using six species of bathyergidae.
Smith, E.S.J., Purfürst, B., Grigoryan, T., Park, T.J., Bennett, N.C. and Lewin, G.R.
Journal of Comparative Neurology 520 (12): 2785-2803. 15 August 2012

Oxidized LDL-dependent pathway as new pathogenic trigger in arrhythmogenic cardiomyopathy.
Sommariva, E., Stadiotti, I., Casella, M., Catto, V., Dello Russo, A., Carbucicchio, C., Arnaboldi, L., De Metrio, S., Milano, G., Scopece, A., Casaburo, M., Andreini, D., Mushtaq, S., Conte, E., Chiesa, M., Birchmeier, W., Cogliati, E., Paolin, A., König, E., Meraviglia, V., De Musso, M., Volani, C., Cattelan, G., Rauhe, W., Turnu, L., Porro, B., Pedrazzini, M., Camera, M., Corsini, A., Tondo, C., Rossini, A. and Pompilio, G.
EMBO Molecular Medicine 13 (9): e14365. 7 September 2021

Limb development.
Soshnikova, N. and Birchmeier, W.
In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine ; Vol. 1. Springer, Berlin [u.a.], 976-981. ISBN 3-540-44244-8 2006

Genetic interaction between Wnt/β-catenin and BMP receptor signaling during formation of the AER and the dorsal-ventral axis in the limb.
Soshnikova, N., Zechner, D., Huelsken, J., Mishina, Y., Behringer, R.R., Taketo, M.M., Crenshaw, E.B. and Birchmeier, W.
Genes & Development 17 (16): 1963-1968. 1 January 2003

Where do you come from; where do you go? Pluripotency, differentiation and malfunction of stem cells.
Spagnoli, F.M., Besser, D. and Benitah, S.A.
EMBO Reports 13 (1): 9-11. January 2012

The metastasis-associated gene S100A4 is a novel target of beta-catenin/T-cell factor (TCF) signaling in colon cancer.
Stein, U., Arlt, F., Walther, W., Smith, J., Waldman, T., Harris, E.D., Mertins, S.D., Heizmann, C.W., Allard, D., Birchmeier, W., Schlag, P.M. and Shoemaker, R.H.
Gastroenterology 131 (5): 1486-1500. November 2006

MACC1, a newly identified key regulator of HGF-MET signaling, predicts colon cancer metastasis.
Stein, U., Walther, W., Arlt, F., Schwabe, H., Smith, J., Fichtner, I., Birchmeier, W. and Schlag, P.M.
Nature Medicine 15 (1): 59-67. January 2009

A human protein-protein interaction network: a resource for annotating the proteome.
Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoez, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H. and Wanker, E.E.
Cell 122 (6): 957-968. 23 September 2005

UroFors: Konstituierung eines Interessensverbundes fuer Naturwissenschaftler in der urologischen Forschung [UroFors: establishment of an interest group for natural scientists in urological research].
Stope, M.B., Dansranjavin, T., Erb, H., Erdmann, K., Fendler, A., Hoelters, S., Juengel, E., Nitschke, K., Salomo, K., Seidel, P., Skowron, M.A., Wach, S. and Becker, C.
Urologe 56 (4): 515-518. April 2017

Embryonic hair follicle fate change by augmented β-catenin through Shh and Bmp signaling.
Suzuki, K., Yamaguchi, Y., Villacorte, M., Mihara, K., Akiyama, M., Shimizu, H., Taketo, M.M., Nakagata, N., Tsukiyama, T., Yamaguchi, T.P., Birchmeier, W., Kato, S. and Yamada, G.
Development 136 (3): 367-372. February 2009

V-src kinase shifts the cadherin-based cell adhesion from the strong to the weak state and beta-catenin is not required for the shift.
Takeda, H., Nagafuchi, A., Yonemura, S., Tsukita, S., Behrens, J., Birchmeier, W. and Tsukita, S.
Journal of Cell Biology 131 (6 Pt. 2): 1839-1847. December 1995

Role of Epiprofin, a zinc-finger transcription factor, in limb development.
Talamillo, A., Delgado, I., Nakamura, T., de-Vega, S., Yoshitomi, Y., Unda, F., Birchmeier, W., Yamada, Y. and Ros, M.A.
Developmental Biology 337 (2): 363-374. 15 January 2010

beta-catenin-dependent and -independent effects of deltaN-plakoglobin on epidermal growth and differentiation.
Teuliere, J., Faraldo, M.M., Shtutman, M., Birchmeier, W., Huelsken, J., Thiery, J.P. and Glukhova, M.A.
Molecular and Cellular Biology 24 (19): 8649-8661. 1 October 2004

RNF4-dependent oncogene activation by protein stabilization.
Thomas, J.J., Abed, M., Heuberger, J., Novak, R., Zohar, Y., Beltra-Lopez, A.P., Trausch-Azar, J.S., Ilagan, M.X.G., Benhamou, D., Dittmar, G., Kopan, R., Birchmeier, W., Schwartz, A.L. and Orian, A.
Cell Reports 16 (12): 3388-3400. 20 September 2016

The discriminative ability of Prostate Health Index to detect prostate cancer is enhanced in combination with miR-222-3p.
Tölle, A., Jung, K., Friedersdorff, F., Maxeiner, A., Lein, M., Fendler, A. and Stephan, C.
Cancer Biomarkers 30 (4): 381-393. 9 April 2021

Global increase of p16INK4a in APC-deficient mouse liver drives clonal growth of p16INK4a negative tumors.
Ueberham, E., Glöckner, P., Göhler, C., Straub, B.K., Teupser, D., Schönig, K., Braeuning, A., Höhn, A.K., Jerchow, B., Birchmeier, W., Gaunitz, F., Arendt, T., Sansom, O., Gebhardt, R. and Ueberham, U.
Molecular Cancer Research 13 (2): 239-249. February 2015

Cancer stem cells regulate cancer-associated fibroblasts via activation of Hedgehog signaling in mammary gland tumors.
Valenti, G., Quinn, H.M., Heynen, G.J.J.E., Lan, L., Holland, J.D., Vogel, R., Wulf-Goldenberg, A. and Birchmeier, W.
Cancer Research 77 (8): 2134-2147. 15 April 2017

Decreased microglial Wnt/β-catenin signalling drives microglial pro-inflammatory activation in the developing brain.
Van Steenwinckel, J., Schang, A.L., Krishnan, M.L., Degos, V., Delahaye-Duriez, A., Bokobza, C., Csaba, Z., Verdonk, F., Montané, A., Sigaut, S., Hennebert, O., Lebon, S., Schwendimann, L., Le Charpentier, T., Hassan-Abdi, R., Ball, G., Aljabar, P., Saxena, A., Holloway, R.K., Birchmeier, W., Baud, O., Rowitch, D., Miron, V., Chretien, F., Leconte, C., Besson, V.C., Petretto, E.G., Edwards, A.D., Hagberg, H., Soussi-Yanicostas, N., Fleiss, B. and Gressens, P.
Brain 142 (12): 3806-3833. December 2019

Loss of the Wnt/β-catenin pathway in microglia of the developing brain drives pro-inflammatory activation leading to white matter injury.
Van Steenwinckel, J., Schang, A.L., Krishnan, M.L., Degos, V., Delahaye-Duriez, A., Bokobza, C., Verdonk, F., Montane, A., Sigaut, S., Hennebert, O., Lebon, S., Schwendimann, L., Le Charpentier, T., Hassan-Abdi, R., Ball, G., Aljabar, P., Saxena, A., Holloway, R.K., Birchmeier, W., Miron, V., Rowitch, D., Chretien, F., Leconte, C., Besson, V.C., Petretto, E.G., Edwards, A.D., Hagberg, H., Soussi-Yanicostas, N., Fleiss, B. and Gressens, P.
bioRxiv : 334359. 31 May 2018

Concomitant deletion of Ptpn6 and Ptpn11 in T cells fails to improve anticancer responses.
Ventura, P.M.O., Gakovic, M., Fischer, B.A., Spinelli, L., Rota, G., Pathak, S., Khameneh, H.J., Zenobi, A., Thomson, S., Birchmeier, W., Cantrell, D.A. and Guarda, G.
EMBO Reports 23 (11): e55399. 7 November 2022

Spatially restricted stromal Wnt signaling restrains prostate epithelial progenitor growth through direct and indirect mechanisms.
Wei, X., Zhang, L., Zhou, Z., Kwon, O.J., Zhang, Y., Nguyen, H., Dumpit, R., True, L., Nelson, P., Dong, B., Xue, W., Birchmeier, W., Taketo, M.M., Xu, F., Creighton, C.J., Ittmann, M.M. and Xin, L.
Cell Stem Cell 24 (5): 753-768. 2 May 2019

Interaction between Gab1 and the c-Met receptor tyrosine kinase is responsible for epithelial morphogenesis.
Weidner, K.M., Dicesare, S., Sachs, M., Brinkmann, V., Behrens, J. and Birchmeier, W.
Nature 384 (6605): 173-176. 14 November 1996

The Met receptor tyrosine kinase transduces motility, proliferation, andmorphogenic signals of scatter factor/ hepatocyte growth factor in epithelial cells.
Weidner, K.M., Sachs, M. and Birchmeier, W.
Journal of Cell Biology 121 (1): 145-154. April 1993

Wnt/β-catenin signalling induces MLL to create epigenetic changes in salivary gland tumours.
Wend, P., Fang, L., Zhu, Q., Schipper, J.H., Loddenkemper, C., Kosel, F., Brinkmann, V., Eckert, K., Hindersin, S., Holland, J.D., Lehr, S., Kahn, M., Ziebold, U. and Birchmeier, W.
EMBO Journal 32 (14): 1977-1989. 17 July 2013

Wnt signaling in stem and cancer stem cells.
Wend, P., Holland, J.D., Ziebold, U. and Birchmeier, W.
Seminars in Cell & Developmental Biology 21 (8): 855-863. October 2010

Lenalidomide regulates CNS autoimmunity by promoting M2 macrophages polarization.
Weng, Q., Wang, J., Wang, J., Wang, J., Sattar, F., Zhang, Z., Zheng, J., Xu, Z., Zhao, M., Liu, X., Yang, L., Hao, G., Fang, L., Lu, Q.R., Yang, B. and He, Q.
Cell Death & Disease 9 (2): 251. 14 February 2018

The miRNA-kallikrein axis of interaction: a new dimension in the pathogenesis of prostate cancer.
White, N.M.A., Youssef, Y.M., Fendler, A., Stephan, C., Jung, K. and Yousef, G.M.
Biological Chemistry 393 (5): 379-389. May 2012

The LIM domain protein Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signalling.
Wijk, N.V., Witte, F., Feike, A.C., Schambony, A., Birchmeier, W., Mundlos, S. and Stricker, S.
Biochemical and Biophysical Research Communications 390 (2): 211-216. 11 December 2009

The tyrosine phosphatase Shp2 acts downstream of GDNF/Ret in branching morphogenesis of the developing mouse kidney.
Willecke, R., Heuberger, J., Grossmann, K., Michos, O., Schmidt-Ott, K., Walentin, K., Costantini, F. and Birchmeier, W.
Developmental Biology 360 (2): 310-307. 15 December 2011

Developing antagonists for the Met-HGF/SF protein-protein interaction using a fragment-based approach.
Winter, A., Sigurdardottir, A.G., DiCara, D., Valenti, G., Blundell, T.L. and Gherardi, E.
Molecular Cancer Therapeutics 15 (1): 3-14. January 2016

Deletion of beta-catenin impairs T cell development.
Xu, Y., Banerjee, D., Huelsken, J., Birchmeier, W. and Sen, J.M.
Nature Immunology 4 (12): 1177-1182. 1 January 2003

Sequential requirement of hepatocyte growth factor and neuregulin in the morphogenesis and differentiation of the mammary gland.
Yang, Y., Spitzer, E., Meyer, D., Sachs, M., Niemann, C., Hartmann, G., Weidner, K.M., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 131 (1): 215-226. October 1995

Afadin requirement for cytokine expressions in keratinocytes during chemically induced inflammation in mice.
Yoshida, T., Iwata, T., Takai, Y., Birchmeier, W., Yamato, M. and Okano, T.
Genes to Cells 19 (11): 842-852. November 2014

The role of Axin2 in calvarial morphogenesis and craniosynostosis.
Yu, H.M., Jerchow, B., Sheu, T.J., Liu, B., Costantini, F., Puzas, J.E., Birchmeier, W. and Hsu, W.
Development 132 (8): 1995-2005. 1 January 2005

The BCL9-2 proto-oncogene governs estrogen receptor alpha expression in breast tumorigenesis.
Zatula, N., Wiese, M., Bunzendahl, J., Birchmeier, W., Perske, C., Bleckmann, A. and Brembeck, F.H.
Oncotarget 5 (16): 6770-6787. 30 August 2014

Deciphering the function of signaling pathways by tissue specific gene modification in mice.
Zechner, D., Soshnikova, N. and Birchmeier, W.
Zellbiologie Aktuell 30 (1): 6-8. January 2004

Bmp and Wnt/beta-catenin signals control expression of the transcription factor Olig3 and the specification of spinal cord neurons.
Zechner, D., Muller, T., Wende, H., Walther, I., Taketo, M.M., Crenshaw, E.B., Treier, M., Birchmeier, W. and Birchmeier, C.
Developmental Biology 303 (1): 181-190. 1 March 2007

The tyrosine phosphatase SHP2 controls TGFβ-induced STAT3 signaling to regulate fibroblast activation and fibrosis.
Zehender, A., Huang, J., Györfi, A.H., Matei, A.E., Trinh-Minh, T., Xu, X., Li, Y.N., Chen, C.W., Lin, J., Dees, C., Beyer, C., Gelse, K., Zhang, Z.Y., Bergmann, C., Ramming, A., Birchmeier, W., Distler, O., Schett, G. and Distler, J.H.W.
Nature Communications 9 (1): 3259. 14 August 2018

Reciprocal requirements for EDA/EDAR/NF-κB and Wnt/β-catenin signaling pathways in hair follicle induction.
Zhang, Y., Tomann, P., Andl, T., Gallant, N.M., Huelsken, J., Jerchow, B., Birchmeier, W., Paus, R., Piccolo, S., Mikkola, M.L., Morrisey, E.E., Overbeek, P.A., Scheidereit, C., Millar, S.E. and Schmidt-Ullrich, R.
Developmental Cell 17 (1): 49-61. 21 July 2009

A novel predictor tool of biochemical recurrence after radical prostatectomy based on a five-microRNA tissue signature.
Zhao, Z., Weickmann, S., Jung, M., Lein, M., Kilic, E., Stephan, C., Erbersdobler, A., Fendler, A. and Jung, K.
Cancers 11 (10): 1603. 21 October 2019

The Wnt-driven Mll1 epigenome regulates salivary gland and head and neck cancer.
Zhu, Q., Fang, L., Heuberger, J., Kranz, A., Schipper, J., Scheckenbach, K., Oliveira Vidal, R., Sunaga-Franze, D.Y., Müller, M., Wulf-Goldenberg, A., Sauer, S. and Birchmeier, W.
Cell Reports 26 (2): 415-428. 8 January 2019

Tyrosine kinase receptor RON functions downstream of the erythropoietin receptor to induce expansion of erythroid progenitors.
van den Akker, E., van Dijk, T., Parren-van Amelsvoort, M., Grossmann, K.S., Schaeper, U., Toney-Earley, K., Waltz, S.E., Loewenberg, B. and von Lindern, M.
Blood 103 (12): 4457-4465. 1 January 2004

Birchmeier-Kohler, Carmen

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J., Karaiskos, N., Praktiknjo, S.D., Grosswendt, S., Wahle, P., Ruffault, P.L., Ayoub, S., Schreyer, L., Boltengagen, A., Birchmeier, C., Zinzen, R., Kocks, C. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

Molecular aspects of mesenchymal-epithelial interactions.
Birchmeier, C. and Birchmeier, W.
Annual Review of Cell Biology 9 : 511-540. 1993

Met, metastasis, motility and more.
Birchmeier, C., Birchmeier, W., Gherardi, E. and Vande Woude, G.F.
Nature Reviews Molecular Cell Biology 4 (12): 915-925. December 2003

c-Met is essential for wound healing in the skin.
Chmielowiec, J., Borowiak, M., Morkel, M., Stradal, T., Munz, B., Werner, S., Wehland, J., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 177 (1): 151-162. 9 April 2007

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

Molecular identity of proprioceptor subtypes innervating different muscle groups in mice.
Dietrich, S., Company, C., Song, K., Lowenstein, E.D., Riedel, L., Birchmeier, C., Gargiulo, G. and Zampieri, N.
Nature Communications 13 (1): 6867. 11 November 2022

Targeting MET in cancer: rationale and progress.
Gherardi, E., Birchmeier, W., Birchmeier, C. and Woude, G.V.
Nature Reviews Cancer 12 (2): 89-103. February 2012

HDAC4 mutations cause diabetes and induce β-cell FoxO1 nuclear exclusion.
Gong, M., Yu, Y., Liang, L., Vuralli, D., Froehler, S., Kuehnen, P., Du Bois, P., Zhang, J., Cao, A., Liu, Y., Hussain, K., Fielitz, J., Jia, S., Chen, W. and Raile, K.
Molecular Genetics & Genomic Medicine 7 (5): e602. May 2019

Wnt/Rspondin/β-catenin signals control axonal sorting and lineage progression in Schwann cell development.
Grigoryan, T., Stein, S., Qi, J., Wende, H., Garratt, A.N., Nave, K.A., Birchmeier, C. and Birchmeier, W.
Proceedings of the National Academy of Sciences of the United States of America 110 (45): 18174-18179. 5 November 2013

The tyrosine phosphatase Shp2 in development and cancer.
Grossmann, K.S., Rosario, M., Birchmeier, C. and Birchmeier, W.
Advances in Cancer Research 106 : 53-89. 2010

The tyrosine phosphatase Shp2 (PTPN11) directs neuregulin-1/ErbB signaling throughout schwann cell development.
Grossmann, K.S., Wende, H., Paul, F.E., Cheret, C., Garratt, A.N., Zurborg, S., Feinberg, K., Besser, D., Schulz, H., Peles, E., Selbach, M., Birchmeier, W. and Birchmeier, C.
Proceedings of the National Academy of Sciences of the United States of America 106 (39): 16704-16709. 29 September 2009

Requirement for beta-catenin in anterior-posterior axis formation in mice.
Huelsken, J., Vogel, R., Brinkmann, V., Erdmann, B., Birchmeier, C. and Birchmeier, W.
Journal of Cell Biology 148 (3): 567-578. 7 February 2000

Negative regulation of Ros receptor tyrosine kinase signaling: An epithelial function of the SH2 domain protein tyrosine phosphatase SHP-1.
Keilhack, H., Mueller, M., Boehmer, S.A., Frank, C., Weidner, K.M., Birchmeier, W., Ligensa, T., Berndt, A., Kosmehl, H., Gunther, B., Mueller, T., Birchmeier, C. and Boehmer, F.D.
Journal of Cell Biology 152 (2): 325-334. 22 January 2001

Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells.
Kim, M., Wende, H., Walcher, J., Kühnemund, J., Cheret, C., Kempa, S., McShane, E., Selbach, M., Lewin, G.R. and Birchmeier, C.
Genes & Development 32 (9-10): 645-657. 10 May 2018

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat.
Labi, V., Peng, S., Klironomos, F., Munschauer, M., Kastelic, N., Chakraborty, T., Schoeler, K., Derudder, E., Martella, M., Mastrobuoni, G., Hernandez-Miranda, L.R., Lahmann, I., Kocks, C., Birchmeier, C., Kempa, S., Quintanilla-Martinez de Fend, L., Landthaler, M., Rajewsky, N. and Rajewsky, K.
Genes & Development 33 : 23-24. 7 November 2019

Oscillations of MyoD and Hes1 proteins regulate the maintenance of activated muscle stem cells.
Lahmann, I., Bröhl, D., Zyrianova, T., Isomura, A., Czajkowski, M.T., Kapoor, V., Griger, J., Ruffault, P.L., Mademtzoglou, D., Zammit, P.S., Wunderlich, T., Spuler, S., Kühn, R., Preibisch, S., Wolf, J., Kageyama, R. and Birchmeier, C.
Genes & Development 33 (9-10): 524-535. 1 May 2019

An oscillatory network controlling self-renewal of skeletal muscle stem cells.
Lahmann, I., Zhang, Y., Baum, K., Wolf, J. and Birchmeier, C.
Experimental Cell Research 409 (2): 112933. 15 December 2021

Technologies for profiling the impact of genomic variants on transcription factor binding.
Leiz, J., Rutkiewicz, M., Birchmeier, C., Heinemann, U. and Schmidt-Ott, K.M.
Medizinische Genetik 33 (2): 147-155. 14 August 2021

Precise CRISPR-Cas9 gene repair in autologous memory T cells to treat familial hemophagocytic lymphohistiocytosis.
Li, X., Wirtz, T., Weber, T., Lebedin, M., Lowenstein, E.D., Sommermann, T., Zach, A., Yasuda, T., de la Rosa, K., Chu, V.T., Schulte, J.H., Müller, I., Kocks, C. and Rajewsky, K.
Science Immunology 9 (92): eadi0042. 2 February 2024

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

Hepatocarcinogenesis in mice with a conditional knockout of the hepatocyte growth factor receptor c-Met.
Marx-Stoelting, P., Borowiak, M., Knorpp, T., Birchmeier, C., Buchmann, A. and Schwarz, M.
International Journal of Cancer 124 (8): 1767-1772. 15 April 2009

EHD2-mediated restriction of caveolar dynamics regulates cellular fatty acid uptake.
Matthaeus, C., Lahmann, I., Kunz, S., Jonas, W., Melo, A.A., Lehmann, M., Larsson, E., Lundmark, R., Kern, M., Blüher, M., Olschowski, H., Kompa, J., Brügger, B., Müller, D.N., Haucke, V., Schürmann, A., Birchmeier, C. and Daumke, O.
Proceedings of the National Academy of Sciences of the United States of America 117 (13): 7471-7481. 31 March 2020