Publications
^{_{Protein Evolution}}

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), pp. 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), pp. 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), pp. 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), pp. 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)

Podobnik, M.; Singh, A.; Fu, Z.; Dooley, C.; Frohnhöfer, H.; Firlej, M.; Stednitz, S.; Elhabashy, H.; Weyand, S.; Weir, J. et al.; Lu, J.; Nüsslein-Volhard, C.; Irion, U.: kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species. Development 150 (16), dev.201627 (2023)

Wu, Y.; Chen, K.-W.; Li, Y.-N.; Qiu, K.-Y.; Lu, G.; Shu, T.; Sun, T.-Y.; Hou , Z.-Q.; Wu, Y.-D.; Yu, L.-J.: Propeptide-Mediated Allosteric Regulation of Xylanase Xyl-1: An Integrated Experimental and Computational Analysis. Journal of Agricultural and Food Chemistry 71 (30), pp. 11692 - 11703 (2023)

Braun, V.; Ratcliff, A.; Celia, H.; Buchanan, S.: Energization of Outer Membrane Transport by the ExbB ExbD Molecular Motor. Journal of Bacteriology 205 (6), e0003523 (2023)

Grandchamp, A.; Kühl, L.; Lebherz, M.; Brüggemann, K.; Parsch, J.; Bornberg-Bauer, E.: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research 33 (6), pp. 872 - 890 (2023)

Fuchs, A.: Specific, sensitive and quantitative protein detection by in-gel fluorescence. Nature Communications 14 (1), 2505 (2023)

Böhning, J.; Dobbelstein, A.; Sulkowski, N.; Eilers, K.; von Kügelgen, A.; Tarafder, A.; Peak-Chew, S.-Y.; Skehel, M.; Alva, V.; Filloux, A. et al.; Bharat, T.: Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa. PLoS Pathogens 19 (4), e1011177 (2023)

Heames, B.; Buchel, F.; Aubel, M.; Tretyachenko, V.; Loginov, D.; Novák, P.; Lange, A.; Bornberg-Bauer, E.; Hlouchová, K.: Experimental characterization of de novo proteins and their unevolved random-sequence counterparts. Nature Ecology & Evolution 7 (4), pp. 570 - 580 (2023)

Iyengar, B.; Bornberg-Bauer, E.: Neutral models of de novo gene emergence suggest that gene evolution has a preferred trajectory. Molecular Biology and Evolution 40 (4), msad079 (2023)