Publications of E Bornberg-Bauer

Coban, A.; Bornberg-Bauer, E.; Kemena, C.: Tracing the paths of modular evolution by quantifying rearrangement events of protein domains. BMC Ecology and Evolution 25 (1), 6 (2025)

Iyengar, B.; Grandchamp, A.; Bornberg-Bauer, E.: How antisense transcripts can evolve to encode novel proteins. Nature Communications 15 (1), 6187 (2024)

Lebherz, K.; Iyengar, B.; Bornberg-Bauer, E.: Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution. Genome Biology and Evolution 16 (7), evae129 (2024)

Lebherz, M.; Fouks, B.; Schmidt, J.; Bornberg-Bauer, E.; Grandchamp, A.: DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs. Genome Biology and Evolution 16 (7), evae134 (2024)

Makova, K.; Pickett, B.; Harris, G.; Hartley, R.; Cechova, M.; Pal, K.; Nurk, S.; Yoo, D.; Li, Q.; Hebbar, P. et al.; McGrath, B.; Antonacci, F.; Aubel, M.; Biddanda, A.; Borchers, M.; Bornberg-Bauer, E.; Bouffard, G.; Brooks, S.; Carbone, L.; Carrel, L.; Carroll, A.; Chang, P.-C.; Chin, C.-S.; Cook, D.; Craig, S.; de Gennaro, L.; Diekhans, M.; Dutra, A.; Garcia, P.; Grady, P.; Green, R.; Haddad, D.; Hallast, P.; Harvey, W.; Hickey, G.; Hillis, D.; Hoyt , S.; Jeong, H.; Kamali, K.; Kosakovsky Pond, S.; LaPolice, T.; Lee, C.; Lewis, A.; Loh, Y.-H.; Masterson, P.; McGarvey, K.; McCoy, R.; Medvedev, P.; Miga, K.; Munson , K.; Pak, E.; Paten, B.; Pinto, B.; Potapova, T.; Rhie, A.; Rocha, J.; Ryabov, F.; Ryder, O.; Sacco, S.; Shafin, K.; Shepelev, V.; Slon, V.; Solar, S.; Storer, J.; Sudmant, P.; Sweetalana; Sweeten, A.; Tassia, M.; Thibaud-Nissen, F.; Ventura, M.; Wilson, M.; Young, A.; Zeng, A.; Zhang, X.; Szpiech, Z.; Huber, C.; Gerton, J.; Yi, S.; Schatz, M.; Alexandrov, I.; Koren, S.; O'Neill, R.; Eichler, E.; Phillippy, A.: The complete sequence and comparative analysis of ape sex chromosomes. Nature 630 (8016), pp. 401 - 411 (2024)

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 16 (4), evae069 (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), pp. 274 - 287 (2024)

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)

Thorburn, D.-M.; Sagonas, K.; Binzer-Panchal, M.; Chain, F.; Feulner, P.; Bornberg-Bauer, E.; Reusch, T.; Samonte-Padilla, I.; Milinski, M.; Lenz, T. et al.; Eizaguirre, C.: Origin matters: Using a local reference genome improves measures in population genomics. Molecular Ecology Resources 23 (7), pp. 1706 - 1723 (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)

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)

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)

Aubel, M.; Eicholt, L.; Bornberg-Bauer, E.: Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning. F1000Research (2023)

Aubel, M.; Bornberg-Bauer, E.: Introducing creative destruction as a mechanism in protein evolution. Proceedings of the National Academy of Sciences of the United States of America 120 (6), e2220460120 (2023)

Post, F.; Bornberg-Bauer, E.; Vasseur-Cognet, M.; Harrison, M.: More effective transposon regulation in fertile, long-lived termite queens than in sterile workers. Molecular Ecology 32 (2), pp. 369 - 380 (2023)

Coban, A.; Bornberg-Bauer, E.; Kemena, C.: Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins. Journal of Molecular Evolution: the Journal of the International Society of Molecular Evolution 90 (6), pp. 418 - 428 (2022)

Eenink, B.; Kaminski, T.; Bornberg-Bauer, E.; Jose, J.; Hollfelder, F.; van Loo, B.: Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli. Microbial Biotechnology 15 (11), pp. 2845 - 2853 (2022)

Berger, J.; Legendre, F.; Zelosko, K.-M.; Harrison, M.; Grandcolas, P.; Bornberg-Bauer, E.; Fouks, B.: Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression. Genes 13 (11), 1948 (2022)

Eicholt, L.; Aubel, M.; Berk, K.; Bornberg-Bauer, E.; Lange, A.: Heterologous expression of naturally evolved putative de novo proteins with chaperones. Protein Science 31 (8), e4371 (2022)