Publications
^{_{Protein Evolution}}

Aubel, M.; Buchel, F.; Heames, B.; Jones, A.; Honc, O.; Bornberg-Bauer, E.; Hlouchova, K.: High-throughput selection of human de novo-emerged sORFs with high folding potential. Genome Biology and Evolution Epub ahead (2024)

Mantovani, O.; Haffner, M.; Walke, P.; Elshereef, A.; Wagner, B.; Petras, D.; Forchhammer, K.; Selim, K.; Hagemann, M.: The redox-sensitive R-loop of the carbon control protein SbtB contributes to the regulation of the cyanobacterial CCM. Scientific Reports 14 (1), 7885 (2024)

Röhl, A.; Netz, E.; Kohlbacher, O.; Elhabashy, H.: CLAUDIO: Automated structural analysis of cross-linking data. Bioinformatics 40 (4), btae146 (2024)

Shevalev, O.; Bischof, L.; Sapegin, A.; Bunev, A.; Grigoreva, O.; Kantin , G.; Kalinin, S.; Hartmann, M.: Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. European Journal of Medicinal Chemistry 270, 116328 (2024)

Luthringer, R.; Raphalen, M.; Guerra, C.; Colin, S.; Martinho, C.; Zheng, M.; Hoshino, M.; Badis, Y.; Lipinska, A.; Haas, F. et al.; Barrera-Redondo, J.; Alva, V.; Coelho, S.: Repeated co-option of HMG-box genes for sex determination in brown algae and animals. Science 283 (6689), eadk5466 (2024)

Grandchamp, A.; Czuppon, P.; Bornberg-Bauer, E.: Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster. Nucleic Acids Research 52 (1), S. 274 - 287 (2024)

Hartmann, M.: TRIM for Tissue Specificity. ACS Medicinal Chemistry Letters 15 (1), S. 4 - 5 (2024)

Winski, A.; Ludwiczak, J.; Orlowska, M.; Madaj, R.; Kaminski, K.; Dunin-Horkawicz, S.: AlphaFold2 captures the conformational landscape of the HAMP signaling domain. Protein Science 33 (1), e4846 (2024)

Alexander, L.; Durairaj, J.; Kryshtafovych, A.; Abriata, L.; Bayo, Y.; Bhabha, G.; Breyton, C.; Caulton, S.; Chen, J.; Degroux, S. et al.; Ekiert, D.; Erlandsen, B.; Freddolino, P.; Gilzer, D.; Greening, C.; Grimes, J.; Grinter, R.; Gurusaran, M.; Hartmann, M.; Hitchman, C.; Keown, J.; Kropp, A.; Kursula, P.; Lovering, A.; Lemaitre, B.; Lia, A.; Liu, S.; Logotheti, M.; Lu, S.; Markússon, S.; Miller, M.; Minasov, G.; Niemann, H.; Opazo, F.; Phillips jr, G.; Davies, O.; Rommelaere, S.; Rosas-Lemus, M.; Roversi, P.; Satchell, K.; Smith, N.; Wilson, M.; Wu, K.-L.; Xia, X.; Xiao, H.; Zhang, W.; Zhou, Z.; Fidelis, K.; Topf, M.; Moult, J.; Schwede, T.: Protein target highlights in CASP15: Analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics 91 (12), S. 1571 - 1599 (2023)

Bharat, T.; Tocheva, E.; Alva, V.: The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan. Proceedings of the National Academy of Sciences of the United States of America 120 (51), e2305338120 (2023)

Joiner, J.; Steinchen, W.; Mozer, N.; Kronenberger, T.; Bange, G.; Poso, A.; Wagner, S.; Hartmann, M.: HilE represses the activity of the Salmonella virulence regulator HilD via a mechanism distinct from that of intestinal long-chain fatty acids. The Journal of Biological Chemistry 299 (12), 105387 (2023)

Fonseca Lopez, F.; Miao, J.; Damjanovic, J.; Bischof, L.; Braun, M.; Ling, Y.; Hartmann, M.; Lin, Y.-S.; Kritzer, J.: Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. Journal of Chemical Information and Modeling 63 (21), S. 6925 - 6937 (2023)

Smug, B.; Szczepaniak, K.; Riocha, E.; Dunin-Horkawicz, S.; Mostowy, R.: Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts. Nature Communications 14 (1), 7460 (2023)

Steinebach, C.; Bricelj, A.; Murgai, A.; Sosič, I.; Bischof, L.; Ng, Y.; Heim, C.; Maiwald, S.; Proj, M.; Voget, R. et al.; Feller, F.; Košmrlj, J.; Sapozhnikova, V.; Schmidt, A.; Zuleeg, M.; Lemnitzer, P.; Mertins, P.; Hansen, F.; Gütschow, M.; Krönke, J.; Hartmann, M.: Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. Current Medicinal Chemistry 66 (21), S. 14513 - 14543 (2023)

Aubel, M.; Eicholt, L.; Bornberg-Bauer, E.; Lange, A.: Wie de novo entstandene Proteine im Labor exprimiert werden können. Biospektrum 29 (6), S. 629 - 632 (2023)

Kaminski, K.; Ludwiczak, J.; Pawlicki, K.; Alva, V.; Dunin-Horkawicz, S.: pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. Bioinformatics 39 (10), btad579 (2023)

Zibat, A.; Zhang, X.; Dickmanns, A.; Stegmann, K.; Dobbelstein, A.; Alachram, H.; Soliwoda, R.; Salinas, G.; Görlich, D.; Kschischo, M. et al.; Wollnik, B.; Dobbelstein, M.: N4-hydroxycytidine, the active compound of Molnupiravir, promotes SARS-CoV-2 mutagenesis and escape from a neutralizing nanobody. iScience 26 (10), 107786 (2023)

Fouks, B.; Harrison, M.; Mikhailova, A.; Marchal, E.; English, S.; Carruthers, M.; Jennings, E.; Pippel, M.; Attardo, G.; Benoit, B. et al.; Bornberg-Bauer, E.; Tobe, S.: Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond. iScience 26 (10), 107832 (2023)

Martinez-Goikoetxea, M.; Lupas, A.: New protein families with hendecad coiled coils in the proteome of life. Journal of Structural Biology 215 (3), 108007 (2023)

Maksymenko, K.; Maurer, A.; Aghaallaei, N.; Barry, C.; Borbarán-Bravo, N.; Ullrich, T.; Dijkstra, T.; Hernandez-Alvarez, B.; Müller, P.; Lupas, A. et al.; Skokowa, J.; ElGamacy, M.: The design of functional proteins using tensorized energy calculations. Cell Reports Methods 3 (8), 100560 (2023)