Publications

All publications

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1. Gossmann, T. I., & Waxman, D. (2022). Correcting bias in allele frequency estimates due to an observation threshold: A markov chain analysis. Genome Biology and Evolution, 14(4). https://doi.org/10.1093/gbe/evac047

2. Mavreas, K., Gossmann, T. I., & Waxman, D. (2022). Loss and fixation of strongly favoured new variants: Understanding and extending haldane’s result via the wrightfisher model. Biosystems, 221, 104759. https://doi.org/10.1016/j.biosystems.2022.104759

3. Muenzner, J., Trébulle, P., Agostini, F., Messner, C. B., Steger, M., Lehmann, A., Caudal, E., Egger, A.-S., Amari, F., Barthel, N., Chiara, M. D., Mülleder, M., Demichev, V., Liti, G., Schacherer, J., Gossmann, T., Berman, J., & Ralser, M. (2022). The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids. https://doi.org/10.1101/2022.04.06.487392

4. Vendrami, D. L. J., Gossmann, T. I., Chakarov, N., Paijmans, A. J., Litzke, V., Eyre-Walker, A., Forcada, J., & Hoffman, J. I. (2022). Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution, 14(7). https://doi.org/10.1093/gbe/evac104

5. Hildebrand, F., Gossmann, T. I., Frioux, C., Özkurt, E., Myers, P. N., Ferretti, P., Kuhn, M., Bahram, M., Nielsen, H. B., & Bork, P. (2021). Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2021.05.008

6. Junker, N., & Gossmann, T. I. (2021). Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution, 9. https://doi.org/10.3389/fevo.2021.666564

7. Strømland, Øyvind, Kallio, J. P., Pschibul, A., Skoge, R. H., Harardóttir, H. M., Sverkeli, L. J., Heinekamp, T., Kniemeyer, O., Migaud, M., Makarov, M. V., Toni I. Gossmann, Brakhage, A. A., & Ziegler, M. (2021). Discovery of fungal surface NADases predominantly present in pathogenic species. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-21307-z

8. Waterman, J. M., Gossmann, T. I., Brandler, O., & Koprowski, J. L. (2021). Editorial: Ecological, behavioral and genomic consequences in the rodent family sciuridae: Why are squirrels so diverse? 9. https://doi.org/10.3389/fevo.2021.765558

9. Yusuf, L., Heatley, M. C., Palmer, J. P. G., Barton, H. J., Cooney, C. R., & Toni I. Gossmann. (2020). Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome Research. https://doi.org/10.1101/gr.255752.119

10. Toni I. Gossmann, & Ralser, M. (2020). Marmota marmota. Trends in Genetics. https://doi.org/10.1016/j.tig.2020.01.006

11. Bockwoldt, M., Houry, D., Niere, M., Gossmann, Toni I., Reinartz, I., Schug, A., Ziegler, M., & Heiland, I. (2019). Identification of evolutionary and kinetic drivers of NAD-dependent signaling. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1902346116

12. Hildebrand, F., Moitinho-Silva, L., Blasche, S., Jahn, M. T., Toni I Gossmann, Huerta-Cepas, J., Hercog, R., Luetge, M., Bahram, M., Pryszlak, A., Alves, R. J., Waszak, S. M., Zhu, A., Ye, L., Costea, P. I., Aalvink, S., Belzer, C., Forslund, S. K., Sunagawa, S., … Bork, P. (2019). Antibiotics-induced monodominance of a novel gut bacterial order. Gut, gutjnl-2018-317715. https://doi.org/10.1136/gutjnl-2018-317715

13. Karr, T. L., Southern, H., Rosenow, M. A., Toni I. Gossmann, & Snook, R. R. (2019). The old and the new: Discovery proteomics identifies putative novel seminal fluid proteins in Drosophila. Molecular & Cellular Proteomics, mcp.RA118.001098. https://doi.org/10.1074/mcp.ra118.001098

14. Kinsella, C. M., Ruiz-Ruano, F. J., Dion-Côté, A.-M., Charles, A. J., Gossmann, T. I., Cabrero, J., Kappei, D., Hemmings, N., Simons, M. J. P., Camacho, J. P. M., Forstmeier, W., & Suh, A. (2019). Programmed DNA elimination of germline development genes in songbirds. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-13427-4

15. Laine, V. N., Gossmann, Toni I, Oers, K. van, Visser, M. E., & Groenen, M. A. M. (2019). Exploring the unmapped DNA and RNA reads in a songbird genome. BMC Genomics, 20, 19. https://doi.org/10.1186/s12864-018-5378-2

16. Toni I. Gossmann, Shanmugasundram, A., Börno, S., Duvaux, L., Lemaire, C., Kuhl, H., Klages, S., Roberts, L. D., Schade, S., Gostner, J. M., Hildebrand, F., Vowinckel, J., Bichet, C., Mülleder, M., Calvani, E., Zelezniak, A., Griffin, J. L., Bork, P., Allaine, D., … Ralser, M. (2019). Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Current Biology. https://doi.org/10.1016/j.cub.2019.04.020

17. Afanasyeva, A., Bockwoldt, M., Cooney, C. R., Heiland, I., & Gossmann, Toni I. (2018). Human long intrinsically disordered protein regions are frequent targets of positive selection. Genome Research, 28, 975–982. https://doi.org/10.1101/gr.232645.117

18. Toni I. Gossmann, Bockwoldt, M., Diringer, L., Schwarz, F., & Schumann, V.-F. (2018). Evidence for Strong Fixation Bias at 4-fold Degenerate Sites Across Genes in the Great Tit Genome. Frontiers in Ecology and Evolution, 6. https://doi.org/10.3389/fevo.2018.00203

19. Corcoran, P., Gossmann, Toni I, Barton, H. J., Slate, J., & Zeng, K. (2017). Determinants of the efficacy of natural selection on coding and noncoding variability in two passerine species. Genome Biology and Evolution.

20. Kappei, D., Scheibe, M., Paszkowski-Rogacz, M., Bluhm, A., Gossmann, Toni I., Dietz, S., Dejung, M., Herlyn, H., Buchholz, F., Mann, M., & Butter, F. (2017). Phylointeractomics reconstructs functional evolution of protein binding. Nature Communications, 8, 14334. https://doi.org/10.1038/ncomms14334

21. Shafiey, H., Gossmann, Toni I, & Waxman, D. (2017). Evolutionary control: Targeted change of allele frequencies in natural populations using externally directed evolution. Journal of Theoretical Biology, 419, 362–374. https://doi.org/10.1016/j.jtbi.2017.01.023

22. Laine, V. N., Gossmann, Toni I, Schachtschneider, K. M., Garroway, C. J., Madsen, O., Verhoeven, K. J. F., Jager, V. de, Megens, H.-J., Warren, W. C., Minx, P., Crooijmans, R. P. M. A., Corcoran, P., Consortium, G. T. H., Sheldon, B. C., Slate, J., Zeng, K., Oers, K. van, Visser, M. E., & Groenen, M. A. M. (2016). Evolutionary signals of selection on cognition from the great tit genome and methylome. Nature Communications, 7, 10474. https://doi.org/10.1038/ncomms10474

23. Zhao, L., Toni I Gossmann, & Waxman, D. (2016). A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity. Journal of Theoretical Biology, 393, 218–228. https://doi.org/10.1016/j.jtbi.2016.01.002

24. Gossmann, Toni I., Saleh, D., Schmid, M. W., Spence, M. A., & Schmid, K. J. (2016). Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes. Molecular Biology and Evolution, 33, 1669–1678. https://doi.org/10.1093/molbev/msw044

25. Gossmann, Toni I, Santure, A. W., Sheldon, B. C., Slate, J., & Zeng, K. (2014). Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biology and Evolution, 6, 2061–2075. https://doi.org/10.1093/gbe/evu157

26. Gossmann, Toni I, Schmid, M. W., Grossniklaus, U., & Schmid, K. J. (2014). Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana. Molecular Biology and Evolution, 31, 574–583. https://doi.org/10.1093/molbev/mst226

27. Gossmann, Toni I, Waxman, D., & Eyre-Walker, A. (2014). Fluctuating selection models and McDonald-Kreitman type analyses. PLoS One, 9, e84540. https://doi.org/10.1371/journal.pone.0084540

28. Gossmann, Toni I, & Ziegler, M. (2014). Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism. DNA Repair, 23, 39–48. https://doi.org/10.1016/j.dnarep.2014.07.005

29. Gossmann, Toni I, Keightley, P. D., & Eyre-Walker, A. (2012). The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Genome Biology and Evolution, 4, 658–667. https://doi.org/10.1093/gbe/evs027

30. Gossmann, Toni I, Ziegler, M., Puntervoll, P., de Figueiredo, L. F., Schuster, S., & Heiland, I. (2012). Two new perspectives on NAD metabolism. GCB 2012 Highlight Abstracts, 5.

31. Gossmann, Toni I, Ziegler, M., Puntervoll, P., de Figueiredo, L. F., Schuster, S., & Heiland, I. (2012). NAD(+) biosynthesis and salvage–a phylogenetic perspective. FEBS Journal, 279, 3355–3363. https://doi.org/10.1111/j.1742-4658.2012.08559.x

32. de Figueiredo, L. F., Gossmann, Toni I, Ziegler, M., & Schuster, S. (2011). Pathway analysis of NAD+ metabolism. Biochemical Journal, 439, 341–348. https://doi.org/10.1042/BJ20110320

33. Gossmann, Toni I, & Schmid, K. J. (2011). Selection-driven divergence after gene duplication in Arabidopsis thaliana. Journal of Molecular Evolution, 73, 153–165. https://doi.org/10.1007/s00239-011-9463-2

34. Gossmann, Toni I, Woolfit, M., & Eyre-Walker, A. (2011). Quantifying the variation in the effective population size within a genome. Genetics, 189, 1389–1402. https://doi.org/10.1534/genetics.111.132654

35. Lau, C., Dölle, C., Gossmann, Toni I, Agledal, L., Niere, M., & Ziegler, M. (2010). Isoform-specific targeting and interaction domains in human nicotinamide mononucleotide adenylyltransferases. Journal of Biological Chemistry, 285, 18868–18876. https://doi.org/10.1074/jbc.M110.107631

36. Gossmann, Toni I, Song, B.-H., Windsor, A. J., Mitchell-Olds, T., Dixon, C. J., Kapralov, M. V., Filatov, D. A., & Eyre-Walker, A. (2010). Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Molecular Biology and Evolution, 27, 1822–1832. https://doi.org/10.1093/molbev/msq079

2023 EvoGen Lab (PI Gossmann).