Publications of the Institute

Chen, X.; Sailer, C.; Kammer, K. M.; Fursch, J.; Eisele, M. R.; Sakata, E.; Pellarin, R.; Stengel, F.: Mono- and intralink filter (Mi-Filter) to reduce false identifications in cross-linking mass spectrometry data. Analytical Chemistry 94 (51), pp. 17751 - 17756 (2022)

Bhatia, H. S.; Brunner, A.-D.; Oeztuerk, F.; Kapoor, S.; Rong, Z.; Mai, H.; Thielert, M.; Ali, M.; Al-Maskari, R.; Paetzold, J. C. et al.; Kofler, F.; Todorov, M. I.; Molbay, M.; Kolabas, Z. I.; Negwer, M.; Hoeher, L.; Steinke, H.; Dima, A.; Gupta, B.; Kaltenecker, D.; Caliskan, O. S.; Brandt, D.; Krahmer, N.; Mueller, S.; Lichtenthaler, S. F.; Hellal, F.; Bechmann, I.; Menze, B.; Theis, F.; Mann, M.; Ertuerk, A.: Spatial proteomics in three-dimensional intact specimens. Cell 185 (26), pp. 5040 - 5058 (2022)

Tekin, E.; Salditt, A.; Schwintek, P.; Wunnava, S.; Langlais, J.; Saenz, J.; Tang, D.; Schwille, P.; Mast, C.; Braun, D.: Prebiotic foam environments to oligomerize and accumulate RNA. Chembiochem 23 (24), e202200423 (2022)

Vazquez-Blomquist, D.; Hardy-Sosa, A.; Baez, S. C.; Besada, V.; Palomares, S.; Guirola, O.; Ramos, Y.; Wiśniewski, J. R.; Javier Gonzalez, L.; Bello-Rivero, I.: Proteomics and Phospho-Proteomics Profiling of the Co-Formulation of Type I and II Interferons, HeberFERON, in the Glioblastoma-Derived Cell Line U-87 MG. Cells 11 (24), 4068 (2022)

Schmacke, N. A.; O'Duill, F.; Gaidt, M. M.; Szymanska, I.; Kamper, J. M.; Schmid-Burgk, J. L.; Mädler, S. C.; Mackens-Kiani, T.; Kozaki, T.; Chauhan, D. et al.; Nagl, D.; Stafford, C. A.; Harz, H.; Froehlich, A. L.; Pinci, F.; Ginhoux, F.; Beckmann, R.; Mann, M.; Leonhardt, H.; Hornung, V.: IKKO primes inflammasome formation by recruiting NLRP3 to the trans-Golgi network. Immunity 55 (12), pp. 2271 - 2284 (2022)

Baumeister, W.: Cryo-electron tomography: The power of seeing the whole picture. Biochemical and Biophysical Research Communications 633, pp. 26 - 28 (2022)

Kunert, F.; Metzner, F. J.; Jung, J.; Höpfler, M.; Woike, S.; Schall, K.; Kostrewa, D.; Moldt, M.; Chen, J.-X.; Bantele, S. et al.; Pfander, B.; Eustermann, S.; Hopfner, K.-P.: Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Science Advances 8 (49), eadd3189 (2022)

Kohl, L.; Siddique, M. N. A. A.; Bodendorfer, B.; Berger, R.; Preikschat, A.; Daniel, C.; Oelke, M.; Liebler-Tenorio, E.; Schulze-Luehrmann, J.; Mauermeir, M. et al.; Yang, K.-T.; Hayek, I.; Szperlinski, M.; Andrack, J.; Schleicher, U.; Bozec, A.; Kroenke, G.; Murray, P. J.; Wirtz, S.; Yamamoto, M.; Schatz, V.; Jantsch, J.; Oefner, P.; Degrandi, D.; Pfeffer, K.; Mertens-Scholz, K.; Rauber, S.; Bogdan, C.; Dettmer, K.; Luehrmann, A.; Lang, R.: Macrophages inhibit Coxiella burnetii by the ACOD1-itaconate pathway for containment of Q fever. EMBO Molecular Medicine 15 (2), e15931 (2022)

Kong, S.; Gong, P.; Zeng, W.-F.; Jiang, B.; Hou, X.; Zhang, Y.; Zhao, H.; Liu, M.; Yan, G.; Zhou, X. et al.; Qiao, X.; Wu, M.; Yang, P.; Liu, C.; Cao, W.: pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level. Nature Communications 13 (1), 7539 (2022)

Schink, S.; Ammar, C.; Chang, Y.-F.; Zimmer, R.; Basan, M.: Analysis of proteome adaptation reveals a key role of the bacterial envelope in starvation survival. Molecular Systems Biology 18 (12), e11160 (2022)

Zivanov, J.; Otón, J.; Ke, Z.; von Kügelgen, A.; Pyle, E.; Qu, K.; Morado, D.; Castaño-Díez, D.; Zanetti, G.; Bharat, T. A. et al.; Briggs, J. A. G.; Scheres, S. H.: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife 11, e83724 (2022)

Sherpa, D.; Mueller, J.; Karayel, Ö.; Xu, P.; Yao, Y.; Chrustowicz, J.; Gottemukkala, K. V.; Baumann, C. A.; Gross, A.; Czarnecki, O. et al.; Zhang, W.; Gu, J.; Nilvebrant, J.; Sidhu, S. S.; Murray, P. J.; Mann, M.; Weiss, M. J.; Schulman, B. A.; Alpi, A. F.: Modular UBE2H-CTLH E2-E3 complexes regulate erythroid maturation. eLife 11, e77937 (2022)

Brüggenthies, J. B.; Fiore, A.; Russier, M.; Bitsina, C.; Brötzmann, J.; Kordes, S.; Menninger, S.; Wolf, A.; Conti, E.; Eickhoff, J. E. et al.; Murray, P. J.: A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling. Journal of Biological Chemistry 298 (12), 102629 (2022)

Wirth, A.-K.; Wange, L.; Vosberg, S.; Henrich, K.-O.; Rausch, C.; Oezdemir, E.; Zeller, C. M.; Richter, D.; Feuchtinger, T.; Kaller, M. et al.; Hermeking, H.; Greif, P. A.; Senft, D.; Jurinovic, V.; Bahrami, E.; Jayavelu, A. K.; Westermann, F.; Mann, M.; Enard, W.; Herold, T.; Jeremias, I.: In vivo PDX CRISPR/Cas9 screens reveal mutual therapeutic targets to overcome heterogeneous acquired chemo-resistance. Leukemia 36 (9), pp. 2863 - 2874 (2022)

Stasi, M.; Monferrer, A.; Babl, L.; Wunnava, S.; Dirscherl, C. F.; Braun, D.; Schwille, P.; Dietz, H.; Boekhoven, J.: Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle. Journal of the American Chemical Society 144, pp. 21939 - 21947 (2022)

Langley, C.; Tatsis, E.; Hong, B.; Nakamura, Y.; Paetz, C.; Stevenson, C. E. M.; Basquin, J.; Lawson, D. M.; Caputi, L.; O'Connor, S. E.: Expansion of the catalytic repertoire of alcohol dehydrogenases in plant metabolism. Angewandte Chemie International Edition 61 (48), e202210934 (2022)

Gassler, J.; Kobayashi, W.; Gáspár, I.; Ruangroengkulrith, S.; Mohanan, A.; Gómez Hernández, L.; Kravchenko, P.; Kümmecke, M.; Lalic, A.; Rifel, N. et al.; Ashburn, R. J.; Zaczek, M.; Vallot, A.; Cuenca Rico, L.; Ladstätter, S.; Tachibana, K.: Zygotic genome activation by the totipotency pioneer factor Nr5a2. Science 378 (6626), pp. 1305 - 1315 (2022)

Zeng, W.-F.; Zhou, X.-X.; Willems, S.; Ammar, C.; Wahle, M.; Bludau, I.; Voytik, E.; Strauss, M. T.; Mann, M.: AlphaPeptDeep: A modular deep learning framework to predict peptide properties for proteomics. Nature Communications 13 (1), 7238 (2022)

Berg, A.; Gräber, M.; Schmutzler, S.; Hoffmann, R.; Berg, T.: A High-Throughput Fluorescence Polarization-Based Assay for the SH2 Domain of STAT4. Methods and protocols 5 (6), 93 (2022)

Fazel, M.; Wester, M. J.; Schodt, D. J.; Cruz, S. R.; Strauss, S.; Schueder, F.; Schlichthärle, T.; Gillette, J. M.; Lidke, D. S.; Rieger, B. et al.; Jungmann, R.; Lidke, K. A.: High-precision estimation of emitter positions using Bayesian grouping of localizations. Nature Communications 13 (1), 7152 (2022)