Publications 2017 to 2022

Jurado, S., Fedl, AS., Jaritz, M., Kostanova-Poliakova, D., Malin, SG., Mullighan, CG., Strehl, S., Fischer, M., Busslinger, M. (2022)
The PAX5-JAK2 translocation acts as dual-hit mutation that promotes aggressive B-cell leukemia via nuclear STAT5 activation.
EMBO J.

Kaiser, FMP., Gruenbacher, S., Oyaga, MR., Nio, E., Jaritz, M., Sun, Q., van der Zwaag, W., Kreidl, E., Zopf, LM., Dalm, VASH., Pel, J., Gaiser, C., van der Vliet, R., Wahl, L., Rietman, A., Hill, L., Leca, I., Driessen, G., Laffeber, C., Brooks, A., Katsikis, PD., Lebbink, JHG., Tachibana, K., van der Burg, M., De Zeeuw, CI., Badura, A., Busslinger, M. (2022)
Biallelic PAX5 mutations cause hypogammaglobulinemia, sensorimotor deficits, and autism spectrum disorder.
J Exp Med. 

Pinter, T., Fischer, M., Schäfer, M., Fellner, M., Jude, J., Zuber, J., Busslinger, M., Wöhner, M. (2022)
Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development.
Front Immunol. 

Rauschmeier, R., Reinhardt, A., Gustafsson, C., Glaros, V., Artemov, AV., Dunst, J., Taneja, R., Adameyko, I., Månsson, R., Busslinger, M., Kreslavsky, T. (2022)
Bhlhe40 function in activated B and TFH cells restrains the GC reaction and prevents lymphomagenesis.
J Exp Med. 

Wöhner, M., Pinter, T., Bönelt, P., Hagelkruys, A., Kostanova-Poliakova, D., Stadlmann, J., Konieczny, SF., Fischer, M., Jaritz, M., Busslinger, M. (2022)
The Xbp1-regulated transcription factor Mist1 restricts antibody secretion by restraining Blimp1 expression in plasma cells.
Front Immunol. 

Calderón, L., Schindler, K., Malin, SG., Schebesta, A., Sun, Q., Schwickert, T., Alberti, C., Fischer, M., Jaritz, M., Tagoh, H., Ebert, A., Minnich, M., Liston, A., Cochella, L., Busslinger, M. (2021)
Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.
Sci Immunol. 

Fali, T., Aychek, T., Ferhat, M., Jouzeau, JY., Busslinger, M., Moulin, D., Eberl, G. (2021)
Metabolic regulation by PPARγ is required for IL-33-mediated activation of ILC2s in lung and adipose tissue.
Mucosal Immunol. 

Glaros, V., Rauschmeier, R., Artemov, AV., Reinhardt, A., Ols, S., Emmanouilidi, A., Gustafsson, C., You, Y., Mirabello, C., Björklund, ÅK., Perez, L., King, NP., Månsson, R., Angeletti, D., Loré, K., Adameyko, I., Busslinger, M., Kreslavsky, T. (2021)
Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.
Immunity. 

Hagelkruys, A., Wirnsberger, G., Stadlmann, J., Wöhner, M., Horrer, M., Vilagos, B., Jonsson, G., Kogler, M., Tortola, L., Novatchkova, M., Bönelt, P., Hoffmann, D., Koglgruber, R., Steffen, U., Schett, G., Busslinger, M., Bergthaler, A., Klein, C., Penninger, JM. (2021)
A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans.
J Exp Med.

Hill, L., Ebert, A., Jaritz, M., Wutz, G., Nagasaka, K., Tagoh, H., Kostanova-Poliakova, D., Schindler, K., Sun, Q., Bönelt, P., Fischer, M., Peters, JM., Busslinger, M. (2020)
Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion.
Nature. 

Liu, GJ., Jaritz, M., Wöhner, M., Agerer, B., Bergthaler, A., Malin, SG., Busslinger, M. (2020)
Repression of the B cell identity factor Pax5 is not required for plasma cell development.
J Exp Med. 

Bönelt, P., Wöhner, M., Minnich, M., Tagoh, H., Fischer, M., Jaritz, M., Kavirayani, A., Garimella, M., Karlsson, MC., Busslinger, M. (2019)
Precocious expression of Blimp1 in B cells causes autoimmune disease with increased self-reactive plasma cells.
EMBO J. 

Cronin, SJF., Seehus, C., Weidinger, A., Talbot, S., Reissig, S., Seifert, M., Pierson, Y., McNeill, E., Longhi, MS., Turnes, BL., Kreslavsky, T., Kogler, M., Hoffmann, D., Ticevic, M., da Luz Scheffer, D., Tortola, L., Cikes, D., Jais, A., Rangachari, M., Rao, S., Paolino, M., Novatchkova, M., Aichinger, M., Barrett, L., Latremoliere, A., Wirnsberger, G., Lametschwandtner, G., Busslinger, M., Zicha, S., Latini, A., Robson, SC., Waisman, A., Andrews, N., Costigan, M., Channon, KM., Weiss, G., Kozlov, AV., Tebbe, M., Johnsson, K., Woolf, CJ., Penninger, JM. (2019)
Publisher Correction: The metabolite BH4 controls T cell proliferation in autoimmunity and cancer.
Nature. 

Durai, V., Bagadia, P., Granja, JM., Satpathy, AT., Kulkarni, DH., Davidson, JT., Wu, R., Patel, SJ., Iwata, A., Liu, TT., Huang, X., Briseño, CG., Grajales-Reyes, GE., Wöhner, M., Tagoh, H., Kee, BL., Newberry, RD., Busslinger, M., Chang, HY., Murphy, TL., Murphy, KM. (2019)
Cryptic activation of an Irf8 enhancer governs cDC1 fate specification.
Nat Immunol. 

Holzmann, J., Politi, AZ., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., Stocsits, RR., Busslinger, GA., Novák, B., Mechtler, K., Davidson, IF., Ellenberg, J., Peters, JM. (2019)
Absolute quantification of cohesin, CTCF and their regulators in human cells.
Elife.

Hagelkruys, A., Wirnsberger, G., Stadlmann, J., Wöhner, M., Horrer, M., Vilagos, B., Jonsson, G., Kogler, M., Tortola, L., Novatchkova, M., Bönelt, P., Hoffmann, D., Koglgruber, R., Steffen, U., Schett, G., Busslinger, M., Bergthaler, A., Klein, C., Penninger, JM. (2021)
A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans.
J Exp Med.

Novikov, A., Fu, Y., Huang, W., Freeman, B., Patel, R., van Ginkel, C., Koepsell, H., Busslinger, M., Onishi, A., Nespoux, J., Vallon, V. (2019)
SGLT2 inhibition and renal urate excretion: role of luminal glucose, GLUT9, and URAT1.
Am J Physiol Renal Physiol. 

Rauschmeier, R., Gustafsson, C., Reinhardt, A., A-Gonzalez, N., Tortola, L., Cansever, D., Subramanian, S., Taneja, R., Rossner, MJ., Sieweke, MH., Greter, M., Månsson, R., Busslinger, M., Kreslavsky, T. (2019)
Bhlhe40 and Bhlhe41 transcription factors regulate alveolar macrophage self-renewal and identity.
EMBO J. 

Schwickert, TA., Tagoh, H., Schindler, K., Fischer, M., Jaritz, M., Busslinger, M. (2019)
Ikaros prevents autoimmunity by controlling anergy and Toll-like receptor signaling in B cells.
Nat Immunol.

Ayata, P., Badimon, A., Strasburger, HJ., Duff, MK., Montgomery, SE., Loh, YE., Ebert, A., Pimenova, AA., Ramirez, BR., Chan, AT., Sullivan, JM., Purushothaman, I., Scarpa, JR., Goate, AM., Busslinger, M., Shen, L., Losic, B., Schaefer, A. (2018)
Epigenetic regulation of brain region-specific microglia clearance activity.
Nat Neurosci. 

Cronin, SJF., Seehus, C., Weidinger, A., Talbot, S., Reissig, S., Seifert, M., Pierson, Y., McNeill, E., Longhi, MS., Turnes, BL., Kreslavsky, T., Kogler, M., Hoffmann, D., Ticevic, M., da Luz Scheffer, D., Tortola, L., Cikes, D., Jais, A., Rangachari, M., Rao, S., Paolino, M., Novatchkova, M., Aichinger, M., Barrett, L., Latremoliere, A., Wirnsberger, G., Lametschwandtner, G., Busslinger, M., Zicha, S., Latini, A., Robson, SC., Waisman, A., Andrews, N., Costigan, M., Channon, KM., Weiss, G., Kozlov, AV., Tebbe, M., Johnsson, K., Woolf, CJ., Penninger, JM. (2018)
The metabolite BH4 controls T cell proliferation in autoimmunity and cancer.
Nature. 

Fujimura, N., Kuzelova, A., Ebert, A., Strnad, H., Lachova, J., Machon, O., Busslinger, M., Kozmik, Z. (2018)
Polycomb repression complex 2 is required for the maintenance of retinal progenitor cells and balanced retinal differentiation.
Dev Biol. 

Kreslavsky, T., Wong, JB., Fischer, M., Skok, JA., Busslinger, M. (2018)
Control of B-1a cell development by instructive BCR signaling.
Curr Opin Immunol. 

Busslinger, GA., Stocsits, RR., van der Lelij, P., Axelsson, E., Tedeschi, A., Galjart, N., Peters, JM. (2017)
Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl.
Nature. 

Gu, YF., Cohn, S., Christie, A., McKenzie, T., Wolff, N., Do, QN., Madhuranthakam, AJ., Pedrosa, I., Wang, T., Dey, A., Busslinger, M., Xie, XJ., Hammer, RE., McKay, RM., Kapur, P., Brugarolas, J. (2017)
Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade.
Cancer Discov. 

Kreslavsky, T., Vilagos, B., Tagoh, H., Poliakova, DK., Schwickert, TA., Wöhner, M., Jaritz, M., Weiss, S., Taneja, R., Rossner, MJ., Busslinger, M. (2017)
Essential role for the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells.
Nat Immunol. 

Smeenk, L., Fischer, M., Jurado, S., Jaritz, M., Azaryan, A., Werner, B., Roth, M., Zuber, J., Stanulla, M., den Boer, ML., Mullighan, CG., Strehl, S., Busslinger, M. (2017)
Molecular role of the PAX5-ETV6 oncoprotein in promoting B-cell acute lymphoblastic leukemia.
EMBO J. 

Cable, J., Weber-Ban, E., Clausen, T., Walters, KJ., Sharon, M., Finley, DJ., Gu, Y., Hanna, J., Feng, Y., Martens, S., Simonsen, A., Hansen, M., Zhang, H., Goodwin, JM., Reggio, A., Chang, C., Ge, L., Schulman, BA., Deshaies, RJ., Dikic, I., Harper, JW., Wertz, IE., Thomä, NH., Słabicki, M., Frydman, J., Jakob, U., David, DC., Bennett, EJ., Bertozzi, CR., Sardana, R., Eapen, VV., Carra, S. (2022)
Targeted protein degradation: from small molecules to complex organelles-a Keystone Symposia report.
Ann N Y Acad Sci. 

Hawkins, PME., Hoi, DM., Cheung, CY., Wang, T., Quan, D., Sasi, VM., Liu, DY., Linington, RG., Jackson, CJ., Oehlers, SH., Cook, GM., Britton, WJ., Clausen, T., Payne, RJ. (2022)
Potent Bactericidal Antimycobacterials Targeting the Chaperone ClpC1 Based on the Depsipeptide Natural Products Ecumicin and Ohmyungsamycin A.
J Med Chem.

Ihara, M., Yamamoto, Y., Hattori, Y., Liu, W., Kobayashi, H., Ishiyama, H., Yoshimoto, T., Miyawaki, S., Clausen, T., Bang, OY., Steinberg, GK., Tournier-Lasserve, E., Koizumi, A. (2022)
Moyamoya disease: diagnosis and interventions.
Lancet Neurol.

Morreale, FE., Kleine, S., Leodolter, J., Junker, S., Hoi, DM., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., Guha, S., Podlesainski, D., Kazmaier, U., Boehmelt, G., Weinstabl, H., Rumpel, K., Schmiedel, VM., Hartl, M., Haselbach, D., Meinhart, A., Kaiser, M., Clausen, T. (2022)
BacPROTACs mediate targeted protein degradation in bacteria.
Cell.

Rey, J., Breiden, M., Lux, V., Bluemke, A., Steindel, M., Ripkens, K., Möllers, B., Bravo Rodriguez, K., Boisguerin, P., Volkmer, R., Mieres-Perez, J., Clausen, T., Sanchez-Garcia, E., Ehrmann, M. (2022)
An allosteric HTRA1-calpain 2 complex with restricted activation profile.
Proc Natl Acad Sci U S A. 

Asanović, I., Strandback, E., Kroupova, A., Pasajlic, D., Meinhart, A., Tsung-Pin, P., Djokovic, N., Anrather, D., Schuetz, T., Suskiewicz, MJ., Sillamaa, S., Köcher, T., Beveridge, R., Nikolic, K., Schleiffer, A., Jinek, M., Hartl, M., Clausen, T., Penninger, J., Macheroux, P., Weitzer, S., Martinez, J. (2021)
The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.
Mol Cell. 

Grabarczyk, DB., Petrova, OA., Deszcz, L., Kurzbauer, R., Murphy, P., Ahel, J., Vogel, A., Gogova, R., Faas, V., Kordic, D., Schleiffer, A., Meinhart, A., Imre, R., Lehner, A., Neuhold, J., Bader, G., Stolt-Bergner, P., Böttcher, J., Wolkerstorfer, B., Fischer, G., Grishkovskaya, I., Haselbach, D., Kessler, D., Clausen, T. (2021)
HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.
Nat Chem Biol.

Hajdusits, B., Suskiewicz, MJ., Hundt, N., Meinhart, A., Kurzbauer, R., Leodolter, J., Kukura, P., Clausen, T. (2021)
McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation.
Elife.

Rodriguez Carvajal, A., Grishkovskaya, I., Gomez Diaz, C., Vogel, A., Sonn-Segev, A., Kushwah, MS., Schodl, K., Deszcz, L., Orban-Nemeth, Z., Sakamoto, S., Mechtler, K., Kukura, P., Clausen, T., Haselbach, D., Ikeda, F. (2021)
The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains.
Elife.

Yelagandula, R., Bykov, A., Vogt, A., Heinen, R., Özkan, E., Strobl, MM., Baar, JC., Uzunova, K., Hajdusits, B., Kordic, D., Suljic, E., Kurtovic-Kozaric, A., Izetbegovic, S., Schaeffer, J., Hufnagl, P., Zoufaly, A., Seitz, T., Födinger, M., Allerberger, F., Stark, A., Cochella, L., Elling, U. (2021)
Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq.
Nat Commun. 

Ahel, J., Lehner, A., Vogel, A., Schleiffer, A., Meinhart, A., Haselbach, D., Clausen, T. (2020)
Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism.
Elife.

Beveridge, R., Kessler, D., Rumpel, K., Ettmayer, P., Meinhart, A., Clausen, T. (2020)
Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy.
ACS Cent Sci. 

Merdanovic, M., Burston, SG., Schmitz, AL., Köcher, S., Knapp, S., Clausen, T., Kaiser, M., Huber, R., Ehrmann, M. (2020)
Activation by substoichiometric inhibition.
Proc Natl Acad Sci U S A. 

Stephani, M., Picchianti, L., Gajic, A., Beveridge, R., Skarwan, E., Sanchez de Medina Hernandez, V., Mohseni, A., Clavel, M., Zeng, Y., Naumann, C., Matuszkiewicz, M., Turco, E., Loefke, C., Li, B., Dürnberger, G., Schutzbier, M., Chen, HT., Abdrakhmanov, A., Savova, A., Chia, KS., Djamei, A., Schaffner, I., Abel, S., Jiang, L., Mechtler, K., Ikeda, F., Martens, S., Clausen, T., Dagdas, Y. (2020)
A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress.
Elife.

Hellerschmied, D., Lehner, A., Franicevic, N., Arnese, R., Johnson, C., Vogel, A., Meinhart, A., Kurzbauer, R., Deszcz, L., Gazda, L., Geeves, M., Clausen, T. (2019)
Molecular features of the UNC-45 chaperone critical for binding and folding muscle myosin.
Nat Commun. 

Hnia, K., Clausen, T., Moog-Lutz, C. (2019)
Shaping Striated Muscles with Ubiquitin Proteasome System in Health and Disease.
Trends Mol Med.

Suskiewicz, MJ., Hajdusits, B., Beveridge, R., Heuck, A., Vu, LD., Kurzbauer, R., Hauer, K., Thoeny, V., Rumpel, K., Mechtler, K., Meinhart, A., Clausen, T. (2019)
Structure of McsB, a protein kinase for regulated arginine phosphorylation.
Nat Chem Biol. 

Hellerschmied, D., Roessler, M., Lehner, A., Gazda, L., Stejskal, K., Imre, R., Mechtler, K., Dammermann, A., Clausen, T. (2018)
UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins.
Nat Commun. 

Ouyang, M., Li, X., Zhao, S., Pu, H., Shen, J., Adam, Z., Clausen, T., Zhang, L. (2017)
The crystal structure of Deg9 reveals a novel octameric-type HtrA protease.
Nat Plants. 
 

Calderón, L., Schindler, K., Malin, SG., Schebesta, A., Sun, Q., Schwickert, T., Alberti, C., Fischer, M., Jaritz, M., Tagoh, H., Ebert, A., Minnich, M., Liston, A., Cochella, L., Busslinger, M. (2021)
Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.
Sci Immunol.

Gutiérrez-Pérez, P., Santillán, EM., Lendl, T., Wang, J., Schrempf, A., Steinacker, TL., Asparuhova, M., Brandstetter, M., Haselbach, D., Cochella, L. (2021)
miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.
Sci Adv. 

Ketting, RF., Cochella, L. (2021)
Concepts and functions of small RNA pathways in C. elegans.
Curr Top Dev Biol. 

Yelagandula, R., Bykov, A., Vogt, A., Heinen, R., Özkan, E., Strobl, MM., Baar, JC., Uzunova, K., Hajdusits, B., Kordic, D., Suljic, E., Kurtovic-Kozaric, A., Izetbegovic, S., Schaeffer, J., Hufnagl, P., Zoufaly, A., Seitz, T., Födinger, M., Allerberger, F., Stark, A., Cochella, L., Elling, U. (2021)
Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq.
Nat Commun. 

Charest, J., Daniele, T., Wang, J., Bykov, A., Mandlbauer, A., Asparuhova, M., Röhsner, J., Gutiérrez-Pérez, P., Cochella, L. (2020)
Combinatorial Action of Temporally Segregated Transcription Factors.
Dev Cell. 

Dexheimer, PJ., Cochella, L. (2020)
MicroRNAs: From Mechanism to Organism.
Front Cell Dev Biol. 

Dexheimer, PJ., Wang, J., Cochella, L. (2020)
Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans.
Curr Biol. 

Finger, F., Ottens, F., Springhorn, A., Drexel, T., Proksch, L., Metz, S., Cochella, L., Hoppe, T. (2020)
Author Correction: Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signalling.
Nat Metab. 

Finger, F., Ottens, F., Springhorn, A., Drexel, T., Proksch, L., Metz, S., Cochella, L., Hoppe, T. (2019)
Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signalling.
Nature Metabolism. 

Hong, RL., Riebesell, M., Bumbarger, DJ., Cook, SJ., Carstensen, HR., Sarpolaki, T., Cochella, L., Castrejon, J., Moreno, E., Sieriebriennikov, B., Hobert, O., Sommer, RJ. (2019)
Evolution of neuronal anatomy and circuitry in two highly divergent nematode species.
Elife.

Alberti, C., Manzenreither, RA., Sowemimo, I., Burkard, TR., Wang, J., Mahofsky, K., Ameres, SL., Cochella, L. (2018)
Cell-type specific sequencing of microRNAs from complex animal tissues.
Nat Methods. 

Alberti, C., Cochella, L. (2017)
A framework for understanding the roles of miRNAs in animal development.
Development. 
 

Kandolf, S., Grishkovskaya, I., Belačić, K., Bolhuis, DL., Amann, S., Foster, B., Imre, R., Mechtler, K., Schleiffer, A., Tagare, HD., Zhong, ED., Meinhart, A., Brown, NG., Haselbach, D. (2022)
Cryo-EM structure of the plant 26S proteasome.
Plant Commun. 

Morreale, FE., Kleine, S., Leodolter, J., Junker, S., Hoi, DM., Ovchinnikov, S., Okun, A., Kley, J., Kurzbauer, R., Junk, L., Guha, S., Podlesainski, D., Kazmaier, U., Boehmelt, G., Weinstabl, H., Rumpel, K., Schmiedel, VM., Hartl, M., Haselbach, D., Meinhart, A., Kaiser, M., Clausen, T. (2022)
BacPROTACs mediate targeted protein degradation in bacteria.
Cell.

Pechincha, C., Groessl, S., Kalis, R., de Almeida, M., Zanotti, A., Wittmann, M., Schneider, M., de Campos, RP., Rieser, S., Brandstetter, M., Schleiffer, A., Müller-Decker, K., Helm, D., Jabs, S., Haselbach, D., Lemberg, MK., Zuber, J., Palm, W. (2022)
Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins.
Science. 

Prattes, M., Grishkovskaya, I., Hodirnau, VV., Hetzmannseder, C., Zisser, G., Sailer, C., Kargas, V., Loibl, M., Gerhalter, M., Kofler, L., Warren, AJ., Stengel, F., Haselbach, D., Bergler, H. (2022)
Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.
Nat Struct Mol Biol. 

de Almeida, M., Hinterndorfer, M., Brunner, H., Grishkovskaya, I., Singh, K., Schleiffer, A., Jude, J., Deswal, S., Kalis, R., Vunjak, M., Lendl, T., Imre, R., Roitinger, E., Neumann, T., Kandolf, S., Schutzbier, M., Mechtler, K., Versteeg, GA., Haselbach, D., Zuber, J. (2021)
AKIRIN2 controls the nuclear import of proteasomes in vertebrates.
Nature. 

Grabarczyk, DB., Petrova, OA., Deszcz, L., Kurzbauer, R., Murphy, P., Ahel, J., Vogel, A., Gogova, R., Faas, V., Kordic, D., Schleiffer, A., Meinhart, A., Imre, R., Lehner, A., Neuhold, J., Bader, G., Stolt-Bergner, P., Böttcher, J., Wolkerstorfer, B., Fischer, G., Grishkovskaya, I., Haselbach, D., Kessler, D., Clausen, T. (2021)
HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain.
Nat Chem Biol.

Gutiérrez-Pérez, P., Santillán, EM., Lendl, T., Wang, J., Schrempf, A., Steinacker, TL., Asparuhova, M., Brandstetter, M., Haselbach, D., Cochella, L. (2021)
miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.
Sci Adv.

Prattes, M., Grishkovskaya, I., Hodirnau, VV., Rössler, I., Klein, I., Hetzmannseder, C., Zisser, G., Gruber, CC., Gruber, K., Haselbach, D., Bergler, H. (2021)
Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine.
Nat Commun. 

Rodriguez Carvajal, A., Grishkovskaya, I., Gomez Diaz, C., Vogel, A., Sonn-Segev, A., Kushwah, MS., Schodl, K., Deszcz, L., Orban-Nemeth, Z., Sakamoto, S., Mechtler, K., Kukura, P., Clausen, T., Haselbach, D., Ikeda, F. (2021)
The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains.
Elife.

Schimpf, J., Oppermann, S., Gerasimova, T., Santos Seica, AF., Hellwig, P., Grishkovskaya, I., Wohlwend, D., Haselbach, D., Friedrich, T. (2021)
Structure of the peripheral arm of a minimalistic respiratory complex I.
Structure.

Ahel, J., Lehner, A., Vogel, A., Schleiffer, A., Meinhart, A., Haselbach, D., Clausen, T. (2020)
Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism.
Elife.

Sonn-Segev, A., Belacic, K., Bodrug, T., Young, G., Van der Linden, RT., Schulman, BA., Schimpf, J., Friedrich, T., Dip, PV., Schwartz, TU., Bauer, B., Peters, JM., Struwe, WB., Benesch, JLP., Brown, NG., Haselbach, D., Kukura, P. (2020)
Quantifying the heterogeneity of macromolecular machines by mass photometry.
Nat Commun. 

Prajapati, S., Haselbach, D., Wittig, S., Patel, MS., Chari, A., Schmidt, C., Stark, H., Tittmann, K. (2019)
Structural and Functional Analyses of the Human PDH Complex Suggest a "Division-of-Labor" Mechanism by Local E1 and E3 Clusters.
Structure. 

Watson, ER., Grace, CRR., Zhang, W., Miller, DJ., Davidson, IF., Prabu, JR., Yu, S., Bolhuis, DL., Kulko, ET., Vollrath, R., Haselbach, D., Stark, H., Peters, JM., Brown, NG., Sidhu, SS., Schulman, BA. (2019)
Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site.
Proc Natl Acad Sci U S A. 

Haselbach, D., Komarov, I., Agafonov, DE., Hartmuth, K., Graf, B., Dybkov, O., Urlaub, H., Kastner, B., Lührmann, R., Stark, H. (2018)
Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex.
Cell. 

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TCEA1 regulates the proliferative potential of mouse myeloid cells.
Exp Cell Res.

Aarts, M., Georgilis, A., Beniazza, M., Beolchi, P., Banito, A., Carroll, T., Kulisic, M., Kaemena, DF., Dharmalingam, G., Martin, N., Reik, W., Zuber, J., Kaji, K., Chandra, T., Gil, J. (2017)
Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence.
Genes Dev. 

Adams, FF., Heckl, D., Hoffmann, T., Talbot, SR., Kloos, A., Thol, F., Heuser, M., Zuber, J., Schambach, A., Schwarzer, A. (2017)
An optimized lentiviral vector system for conditional RNAi and efficient cloning of microRNA embedded short hairpin RNA libraries.
Biomaterials. 

Greiner, G., Witzeneder, N., Berger, A., Schmetterer, K., Eisenwort, G., Schiefer, AI., Roos, S., Popow-Kraupp, T., Müllauer, L., Zuber, J., Sexl, V., Kenner, L., Sperr, WR., Valent, P., Mayerhofer, M., Hoermann, G. (2017)
CCL2 is a KIT D816V-dependent modulator of the bone marrow microenvironment in systemic mastocytosis.
Blood. 

Hein, N., Cameron, DP., Hannan, KM., Nguyen, NN., Fong, CY., Sornkom, J., Wall, M., Pavy, M., Cullinane, C., Diesch, J., Devlin, JR., George, AJ., Sanij, E., Quin, J., Poortinga, G., Verbrugge, I., Baker, A., Drygin, D., Harrison, SJ., Rozario, JD., Powell, JA., Pitson, SM., Zuber, J., Johnstone, RW., Dawson, MA., Guthridge, MA., Wei, A., McArthur, GA., Pearson, RB., Hannan, RD. (2017)
Inhibition of Pol I transcription treats murine and human AML by targeting the leukemia-initiating cell population.
Blood. 

Herzog, VA., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, TR., Wlotzka, W., von Haeseler, A., Zuber, J., Ameres, SL. (2017)
Thiol-linked alkylation of RNA to assess expression dynamics.
Nat Methods. 

Hogg, SJ., Vervoort, SJ., Deswal, S., Ott, CJ., Li, J., Cluse, LA., Beavis, PA., Darcy, PK., Martin, BP., Spencer, A., Traunbauer, AK., Sadovnik, I., Bauer, K., Valent, P., Bradner, JE., Zuber, J., Shortt, J., Johnstone, RW. (2017)
BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1.
Cell Rep. 

Housden, BE., Muhar, M., Gemberling, M., Gersbach, CA., Stainier, DY., Seydoux, G., Mohr, SE., Zuber, J., Perrimon, N. (2017)
Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.
Nat Rev Genet. 

Jacamo, R., Davis, RE., Ling, X., Sonnylal, S., Wang, Z., Ma, W., Zhang, M., Ruvolo, P., Ruvolo, V., Wang, RY., McQueen, T., Lowe, S., Zuber, J., Kornblau, SM., Konopleva, M., Andreeff, M. (2017)
Tumor Trp53 status and genotype affect the bone marrow microenvironment in acute myeloid leukemia.
Oncotarget. 

MacPherson, S., Horkoff, M., Gravel, C., Hoffmann, T., Zuber, J., Lum, JJ. (2017)
STAT3 Regulation of Citrate Synthase Is Essential during the Initiation of Lymphocyte Cell Growth.
Cell Rep. 

Miller, TE., Liau, BB., Wallace, LC., Morton, AR., Xie, Q., Dixit, D., Factor, DC., Kim, LJY., Morrow, JJ., Wu, Q., Mack, SC., Hubert, CG., Gillespie, SM., Flavahan, WA., Hoffmann, T., Thummalapalli, R., Hemann, MT., Paddison, PJ., Horbinski, CM., Zuber, J., Scacheri, PC., Bernstein, BE., Tesar, PJ., Rich, JN. (2017)
Transcription elongation factors represent in vivo cancer dependencies in glioblastoma.
Nature. 

Palau, A., Garz, AK., Diesch, J., Zwick, A., Malinverni, R., Valero, V., Lappin, K., Casquero, R., Lennartsson, A., Zuber, J., Navarro, T., Mills, KI., Götze, KS., Buschbeck, M. (2017)
Polycomb protein RING1A limits hematopoietic differentiation in myelodysplastic syndromes.
Oncotarget. 

Pelossof, R., Fairchild, L., Huang, CH., Widmer, C., Sreedharan, VT., Sinha, N., Lai, DY., Guan, Y., Premsrirut, PK., Tschaharganeh, DF., Hoffmann, T., Thapar, V., Xiang, Q., Garippa, RJ., Rätsch, G., Zuber, J., Lowe, SW., Leslie, CS., Fellmann, C. (2017)
Prediction of potent shRNAs with a sequential classification algorithm.
Nat Biotechnol. 

Samwer, M., Schneider, MWG., Hoefler, R., Schmalhorst, PS., Jude, JG., Zuber, J., Gerlich, DW. (2017)
DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.
Cell.

Smeenk, L., Fischer, M., Jurado, S., Jaritz, M., Azaryan, A., Werner, B., Roth, M., Zuber, J., Stanulla, M., den Boer, ML., Mullighan, CG., Strehl, S., Busslinger, M. (2017)
Molecular role of the PAX5-ETV6 oncoprotein in promoting B-cell acute lymphoblastic leukemia.
EMBO J.

Taubenschmid, J., Stadlmann, J., Jost, M., Klokk, TI., Rillahan, CD., Leibbrandt, A., Mechtler, K., Paulson, JC., Jude, J., Zuber, J., Sandvig, K., Elling, U., Marquardt, T., Thiel, C., Koerner, C., Penninger, JM. (2017)
A vital sugar code for ricin toxicity.
Cell Res. 

Valerio, DG., Xu, H., Chen, CW., Hoshii, T., Eisold, ME., Delaney, C., Cusan, M., Deshpande, AJ., Huang, CH., Lujambio, A., Zheng, YG., Zuber, J., Pandita, TK., Lowe, SW., Armstrong, SA. (2017)
Histone Acetyltransferase Activity of MOF Is Required for MLL-AF9 Leukemogenesis.
Cancer Res. 

van der Lelij, P., Lieb, S., Jude, J., Wutz, G., Santos, CP., Falkenberg, K., Schlattl, A., Ban, J., Schwentner, R., Hoffmann, T., Kovar, H., Real, FX., Waldman, T., Pearson, MA., Kraut, N., Peters, JM., Zuber, J., Petronczki, M. (2017)
Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts.
Elife.

Wutz, G., Várnai, C., Nagasaka, K., Cisneros, DA., Stocsits, RR., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, MJ., Walther, N., Koch, B., Kueblbeck, M., Ellenberg, J., Zuber, J., Fraser, P., Peters, JM. (2017)
Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.
EMBO J. 
 

Colleagues in the scientific core facilities often are co-authors in publications listed above. Sometimes, they also contribute to papers without the involvement of an IMP research group. Group leaders that transfer to other institutions can remain IMP-affiliated as “adjunct investigators” for a limited transition phase. Papers of such cases are listed below. 

Andreev, VI., Yu, C., Wang, J., Schnabl, J., Tirian, L., Gehre, M., Handler, D., Duchek, P., Novatchkova, M., Baumgartner, L., Meixner, K., Sienski, G., Patel, DJ., Brennecke, J. (2022)
Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery.
Nat Struct Mol Biol. 

Eichmüller, OL., Corsini, NS., Vértesy, Á., Morassut, I., Scholl, T., Gruber, VE., Peer, AM., Chu, J., Novatchkova, M., Hainfellner, JA., Paredes, MF., Feucht, M., Knoblich, JA. (2022)
Amplification of human interneuron progenitors promotes brain tumors and neurological defects.
Science. 

Hagelkruys, A., Horrer, M., Taubenschmid-Stowers, J., Kavirayani, A., Novatchkova, M., Orthofer, M., Pai, TP., Cikes, D., Zhuk, S., Balmaña, M., Esk, C., Koglgruber, R., Moeseneder, P., Lazovic, J., Zopf, LM., Cronin, SJF., Elling, U., Knoblich, JA., Penninger, JM. (2022)
The HUSH complex controls brain architecture and protocadherin fidelity.
Sci Adv. 

Kagawa, H., Javali, A., Heidari Khoei, H., Sommer, TM., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Rivron, N. (2022)
Protocol for Human Blastoids Modeling Blastocyst Development and Implantation.
J Vis Exp. 

Matzinger, M., Vasiu, A., Madalinski, M., Müller, F., Stanek, F., Mechtler, K. (2022)
Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows.
Nat Commun. 

Pajenda, S., Wagner, L., Gerges, D., Herkner, H., Tevdoradze, T., Mechtler, K., Schmidt, A., Winnicki, W. (2022)
Urinary Collectrin (TMEM27) as Novel Marker for Acute Kidney Injury.
Life.

Platanitis, E., Gruener, S., Ravi Sundar Jose Geetha, A., Boccuni, L., Vogt, A., Novatchkova, M., Sommer, A., Barozzi, I., Müller, M., Decker, T. (2022)
Interferons reshape the 3D conformation and accessibility of macrophage chromatin.
iScience. 

Stejskal, K., Jeff, OB., Matzinger, M., Dürnberger, G., Boychenko, A., Jacobs, P., Mechtler, K. (2022)
Deep Proteome Profiling with Reduced Carryover Using Superficially Porous Microfabricated nanoLC Columns.
Anal Chem.

Vértesy, Á., Eichmüller, OL., Naas, J., Novatchkova, M., Esk, C., Balmaña, M., Ladstaetter, S., Bock, C., von Haeseler, A., Knoblich, JA. (2022)
Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets.
EMBO J. 

Zheng, R., Stejskal, K., Pynn, C., Mechtler, K., Boychenko, A. (2022)
Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS.
J Proteome Res. 

Alexander, RG., Mintz, RJ., Custodio, PJ., Macknik, SL., Vaziri, A., Venkatakrishnan, A., Gindina, S., Martinez-Conde, S. (2021)
Gaze mechanisms enabling the detection of faint stars in the night sky.
Eur J Neurosci. 

Böhm, M., Killinger, K., Dudziak, A., Pant, P., Jänen, K., Hohoff, S., Mechtler, K., Örd, M., Loog, M., Sanchez-Garcia, E., Westermann, S. (2021)
Cdc4 phospho-degrons allow differential regulation of Ame1CENP-U protein stability across the cell cycle.
Elife.

Chiva, C., Mendes Maia, T., Panse, C., Stejskal, K., Douché, T., Matondo, M., Loew, D., Helm, D., Rettel, M., Mechtler, K., Impens, F., Nanni, P., Shevchenko, A., Sabidó, E. (2021)
Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users.
EMBO Rep. 

Ctortecka, C., Krššáková, G., Stejskal, K., Penninger, JM., Mendjan, S., Mechtler, K., Stadlmann, J. (2021)
Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition.
Mol Cell Proteomics. 

Ctortecka, C., Stejskal, K., Krššáková, G., Mendjan, S., Mechtler, K. (2021)
Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics.
Anal Chem.

Dorfer, V., Strobl, M., Winkler, S., Mechtler, K. (2021)
MS Amanda 2.0: Advancements in the standalone implementation.
Rapid Commun Mass Spectrom. 

Hofbauer, P., Jahnel, SM., Papai, N., Giesshammer, M., Deyett, A., Schmidt, C., Penc, M., Tavernini, K., Grdseloff, N., Meledeth, C., Ginistrelli, LC., Ctortecka, C., Šalic, Š., Novatchkova, M., Mendjan, S. (2021)
Cardioids reveal self-organizing principles of human cardiogenesis.
Cell. 

Hoffmann, D., Mereiter, S., Jin Oh, Y., Monteil, V., Elder, E., Zhu, R., Canena, D., Hain, L., Laurent, E., Grünwald-Gruber, C., Klausberger, M., Jonsson, G., Kellner, MJ., Novatchkova, M., Ticevic, M., Chabloz, A., Wirnsberger, G., Hagelkruys, A., Altmann, F., Mach, L., Stadlmann, J., Oostenbrink, C., Mirazimi, A., Hinterdorfer, P., Penninger, JM. (2021)
Identification of lectin receptors for conserved SARS-CoV-2 glycosylation sites.
EMBO J.

Hornbachner, R., Lackner, A., Papuchova, H., Haider, S., Knöfler, M., Mechtler, K., Latos, PA. (2021)
MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells.
Proc Natl Acad Sci U S A.

Kagawa, H., Javali, A., Khoei, HH., Sommer, TM., Sestini, G., Novatchkova, M., Scholte Op Reimer, Y., Castel, G., Bruneau, A., Maenhoudt, N., Lammers, J., Loubersac, S., Freour, T., Vankelecom, H., David, L., Rivron, N. (2021)
Human blastoids model blastocyst development and implantation.
Nature.

Krenn, V., Bosone, C., Burkard, TR., Spanier, J., Kalinke, U., Calistri, A., Salata, C., Rilo Christoff, R., Pestana Garcez, P., Mirazimi, A., Knoblich, JA. (2021)
Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly.
Cell Stem Cell. 

Matzinger, M., Mechtler, K. (2021)
Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks in Vivo.
J Proteome Res.

Miletic, S., Fahrenkamp, D., Goessweiner-Mohr, N., Wald, J., Pantel, M., Vesper, O., Kotov, V., Marlovits, TC. (2021)
Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation.
Nat Commun.

Paolino, M., Koglgruber, R., Cronin, SJF., Uribesalgo, I., Rauscher, E., Harreiter, J., Schuster, M., Bancher-Todesca, D., Pranjic, B., Novatchkova, M., Fededa, JP., White, AJ., Sigl, V., Dekan, S., Penz, T., Bock, C., Kenner, L., Holländer, GA., Anderson, G., Kautzky-Willer, A., Penninger, JM. (2021)
RANK links thymic regulatory T cells to fetal loss and gestational diabetes in pregnancy.
Nature. 

Pirklbauer, GJ., Stieger, CE., Matzinger, M., Winkler, S., Mechtler, K., Dorfer, V. (2021)
MS Annika: A New Cross-Linking Search Engine.
J Proteome Res.

Stejskal, K., Op de Beeck, J., Dürnberger, G., Jacobs, P., Mechtler, K. (2021)
Ultrasensitive NanoLC-MS of Subnanogram Protein Samples Using Second Generation Micropillar Array LC Technology with Orbitrap Exploris 480 and FAIMS PRO.
Anal Chem. 

Velkova, M., Silva, N., Dello Stritto, MR., Schleiffer, A., Barraud, P., Hartl, M., Jantsch, V. (2021)
Caenorhabditis elegans RMI2 functional homolog-2 (RMIF-2) and RMI1 (RMH-1) have both overlapping and distinct meiotic functions within the BTR complex.
PLoS Genet. 

Waidmann, S., Petutschnig, E., Rozhon, W., Molnár, G., Popova, O., Mechtler, K., Jonak, C. (2021)
GSK3-mediated phosphorylation of DEK3 regulates chromatin accessibility and stress tolerance in Arabidopsis.
FEBS J.

Winter, N., Novatchkova, M., Bachmair, A. (2021)
Cellular Control of Protein Turnover via the Modification of the Amino Terminus.
Int J Mol Sci. 

Andergassen, D., Muckenhuber, M., Bammer, PC., Kulinski, TM., Theussl, HC., Shimizu, T., Penninger, JM., Pauler, FM., Hudson, QJ. (2020)
Correction: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.
PLoS Genet. 

Beveridge, R., Stadlmann, J., Penninger, JM., Mechtler, K. (2020)
A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes.
Nat Commun. 

Bondarieva, A., Raveendran, K., Telychko, V., Rao, HBDP., Ravindranathan, R., Zorzompokou, C., Finsterbusch, F., Dereli, I., Papanikos, F., Tränkner, D., Schleiffer, A., Fei, JF., Klimova, A., Ito, M., Kulkarni, DS., Roeder, I., Hunter, N., Tóth, A. (2020)
Proline-rich protein PRR19 functions with cyclin-like CNTD1 to promote meiotic crossing over in mouse.
Nat Commun. 

Fennell, LM., Gomez Diaz, C., Deszcz, L., Kavirayani, A., Hoffmann, D., Yanagitani, K., Schleiffer, A., Mechtler, K., Hagelkruys, A., Penninger, J., Ikeda, F. (2020)
Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling.
EMBO J. 

Kogler, M., Tortola, L., Negri, GL., Leopoldi, A., El-Naggar, AM., Mereiter, S., Gomez-Diaz, C., Nitsch, R., Tortora, D., Kavirayani, AM., Gapp, BV., Rao, S., Uribesalgo, I., Hoffmann, D., Cikes, D., Novatchkova, M., Williams, DA., Trent, JM., Ikeda, F., Daugaard, M., Hagelkruys, A., Sorensen, PH., Penninger, JM. (2020)
HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases.
Cancer Res. 

Landskron, L., Bonnay, F., Burkard, TR., Knoblich, JA. (2020)
DigiTAG-a RNA Sequencing Approach to Analyze Transcriptomes of Rare Cell Populations in Drosophila melanogaster.
Bio Protoc. 

Le Goff, S., Keçeli, BN., Jeřábková, H., Heckmann, S., Rutten, T., Cotterell, S., Schubert, V., Roitinger, E., Mechtler, K., Franklin, FCH., Tatout, C., Houben, A., Geelen, D., Probst, AV., Lermontova, I. (2020)
The H3 histone chaperone NASPSIM3 escorts CenH3 in Arabidopsis.
Plant J. 

Lin, Q., Manley, J., Helmreich, M., Schlumm, F., Li, JM., Robson, DN., Engert, F., Schier, A., Nöbauer, T., Vaziri, A. (2020)
Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level.
Cell. 

Matzinger, M., Fischhuber, K., Pölöske, D., Mechtler, K., Heiss, EH. (2020)
AMPK leads to phosphorylation of the transcription factor Nrf2, tuning transactivation of selected target genes.
Redox Biol. 

Matzinger, M., Kandioller, W., Doppler, P., Heiss, EH., Mechtler, K. (2020)
Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides.
J Proteome Res. 

Pinotsis, N., Zielinska, K., Babuta, M., Arolas, JL., Kostan, J., Khan, MB., Schreiner, C., Salmazo, A., Ciccarelli, L., Puchinger, M., Gkougkoulia, EA., Ribeiro, EA., Marlovits, TC., Bhattacharya, A., Djinovic-Carugo, K. (2020)
Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin.
Proc Natl Acad Sci U S A. 

Pinto, PH., Kroupova, A., Schleiffer, A., Mechtler, K., Jinek, M., Weitzer, S., Martinez, J. (2020)
ANGEL2 is a member of the CCR4 family of deadenylases with 2',3'-cyclic phosphatase activity.
Science. 

Xie, W., Sowemimo, I., Hayashi, R., Wang, J., Burkard, TR., Brennecke, J., Ameres, SL., Patel, DJ. (2020)
Structure-function analysis of microRNA 3'-end trimming by Nibbler.
Proc Natl Acad Sci U S A. 

Abdusselamoglu, MD., Eroglu, E., Burkard, TR., Knoblich, JA. (2019)
The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop.
Elife.

Andergassen, D., Muckenhuber, M., Bammer, PC., Kulinski, TM., Theussl, HC., Shimizu, T., Penninger, JM., Pauler, FM., Hudson, QJ. (2019)
The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.
PLoS Genet. 

Batki, J., Schnabl, J., Wang, J., Handler, D., Andreev, VI., Stieger, CE., Novatchkova, M., Lampersberger, L., Kauneckaite, K., Xie, W., Mechtler, K., Patel, DJ., Brennecke, J. (2019)
The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Nat Struct Mol Biol. 

Doblmann, J., Dusberger, F., Imre, R., Hudecz, O., Stanek, F., Mechtler, K., Dürnberger, G. (2019)
apQuant: Accurate Label-Free Quantification by Quality Filtering.
J Proteome Res. 

Griss, J., Stanek, F., Hudecz, O., Dürnberger, G., Perez-Riverol, Y., Vizcaíno, JA., Mechtler, K. (2019)
Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.
J Proteome Res. 

Haider, S., Gamperl, M., Burkard, TR., Kunihs, V., Kaindl, U., Junttila, S., Fiala, C., Schmidt, K., Mendjan, S., Knöfler, M., Latos, PA. (2019)
Estrogen Signaling Drives Ciliogenesis in Human Endometrial Organoids.
Endocrinology. 

Iacobucci, C., Piotrowski, C., Aebersold, R., Amaral, BC., Andrews, P., Bernfur, K., Borchers, C., Brodie, NI., Bruce, JE., Cao, Y., Chaignepain, S., Chavez, JD., Claverol, S., Cox, J., Davis, T., Degliesposti, G., Dong, MQ., Edinger, N., Emanuelsson, C., Gay, M., Götze, M., Gomes-Neto, F., Gozzo, FC., Gutierrez, C., Haupt, C., Heck, AJR., Herzog, F., Huang, L., Hoopmann, MR., Kalisman, N., Klykov, O., Kukačka, Z., Liu, F., MacCoss, MJ., Mechtler, K., Mesika, R., Moritz, RL., Nagaraj, N., Nesati, V., Neves-Ferreira, AGC., Ninnis, R., Novák, P., O'Reilly, FJ., Pelzing, M., Petrotchenko, E., Piersimoni, L., Plasencia, M., Pukala, T., Rand, KD., Rappsilber, J., Reichmann, D., Sailer, C., Sarnowski, CP., Scheltema, RA., Schmidt, C., Schriemer, DC., Shi, Y., Skehel, JM., Slavin, M., Sobott, F., Solis-Mezarino, V., Stephanowitz, H., Stengel, F., Stieger, CE., Trabjerg, E., Trnka, M., Vilaseca, M., Viner, R., Xiang, Y., Yilmaz, S., Zelter, A., Ziemianowicz, D., Leitner, A., Sinz, A. (2019)
First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
Anal Chem. 

Papanikos, F., Clément, JAJ., Testa, E., Ravindranathan, R., Grey, C., Dereli, I., Bondarieva, A., Valerio-Cabrera, S., Stanzione, M., Schleiffer, A., Jansa, P., Lustyk, D., Fei, JF., Adams, IR., Forejt, J., Barchi, M., de Massy, B., Toth, A. (2019)
Mouse ANKRD31 Regulates Spatiotemporal Patterning of Meiotic Recombination Initiation and Ensures Recombination between X and Y Sex Chromosomes.
Mol Cell. 

Platanitis, E., Demiroz, D., Schneller, A., Fischer, K., Capelle, C., Hartl, M., Gossenreiter, T., Müller, M., Novatchkova, M., Decker, T. (2019)
A molecular switch from STAT2-IRF9 to ISGF3 underlies interferon-induced gene transcription.
Nat Commun. 

Reiter, T., Knafl, D., Agis, H., Mechtler, K., Wagner, L., Winnicki, W. (2019)
Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders.
PeerJ.

Schmidt, O., Weyer, Y., Baumann, V., Widerin, MA., Eising, S., Angelova, M., Schleiffer, A., Kremser, L., Lindner, H., Peter, M., Fröhlich, F., Teis, D. (2019)
Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism.
EMBO J. 

Stadlmann, J., Hudecz, O., Krššáková, G., Ctortecka, C., Van Raemdonck, G., Op De Beeck, J., Desmet, G., Penninger, JM., Jacobs, P., Mechtler, K. (2019)
Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography.
Anal Chem. 

Stieger, CE., Doppler, P., Mechtler, K. (2019)
Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents.
J Proteome Res. 

Weisenburger, S., Tejera, F., Demas, J., Chen, B., Manley, J., Sparks, FT., Martínez Traub, F., Daigle, T., Zeng, H., Losonczy, A., Vaziri, A. (2019)
Volumetric Ca2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy.
Cell. 

Winnicki, W., Pichler, P., Mechtler, K., Imre, R., Steinmacher, I., Sengölge, G., Knafl, D., Beilhack, G., Wagner, L. (2019)
A novel approach to immunoapheresis of C3a/C3 and proteomic identification of associates.
PeerJ.

Zess, EK., Jensen, C., Cruz-Mireles, N., De la Concepcion, JC., Sklenar, J., Stephani, M., Imre, R., Roitinger, E., Hughes, R., Belhaj, K., Mechtler, K., Menke, FLH., Bozkurt, T., Banfield, MJ., Kamoun, S., Maqbool, A., Dagdas, YF. (2019)
N-terminal β-strand underpins biochemical specialization of an ATG8 isoform.
PLoS Biol. 

Corsini, NS., Peer, AM., Moeseneder, P., Roiuk, M., Burkard, TR., Theussl, HC., Moll, I., Knoblich, JA. (2018)
Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation.
Cell Stem Cell. 

Dorfer, V., Maltsev, S., Winkler, S., Mechtler, K. (2018)
CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction.
J Proteome Res. 

Dorl, S., Winkler, S., Mechtler, K., Dorfer, V. (2018)
PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search.
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