Publications by the Kaessmann Lab
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Fallahshahroudi, A., Rodriguez-Montes, L., Yousefi Taemeh, S., Trost, N., Tellez Jr., M., Ballantyne, Idoko-Akoh, A., Taylor, L., Sherman, A., Sorato, E., Johnsson, M., Cardoso Moreira, M., McGrew, M., and Kaessmann, H. (2024) A male-essential microRNA is key for avian sex chromosome dosage compensation. bioRxiv [Preprint]. https://doi.org/10.1101/2024.03.06.581755 Sepp, M., Leiss, K., Murat, F., Okonechnikov, K., Joshi, P., Leushkin, E., Spänig, L., Mbengue, N., Schneider, C., Schmidt, J., Trost, N., Schauer, M., Khaitovich, P., Lisgo, S., Palkovits, M., Giere, P., Kutscher, L. M., Anders, S., Cardoso-Moreira, M., Sarropoulos, I., Pfister, S. M., and Kaessmann, H. (2023) Cellular development and evolution of the mammalian cerebellum. Nature 625:788-796. URL Rodríguez-Montes, L., Ovchinnikova, S., Yuan, X., Studer, T., Sarropoulos, I., Anders, S., Kaessmann, H.*, and Cardoso-Moreira, M.* (2023) Sex-biased gene expression across mammalian organ development and evolution. Science 382:6670. *joint senior author. URL Lamanna, F., Hervas-Sotomayor, F, Oel, A.P., Jandzik, D., Sobrido-Cameán, D., Santos-Durán, G.N., Martik, M.L., Stundl, J., Green, S.A., Brüning, T., Mößinger, K., Schmidt, J., Schneider, C., Sepp, M., Murat, F., Smith, J.J., Bronner, M.E., Rodicio, M.C., Barreiro-Iglesias, A., Medeiros, D.M., Arendt, D., and Kaessmann, H. (2023) A lamprey neural cell type atlas illuminates the origins of the vertebrate brain. Nat. Ecol. Evol. 10:1714-1728. URL Okonechnikov, K., Joshi, P., Sepp, M., Leiss, K., Sarropoulos, I., Murat, F., Sill, M., Beck, P., Chan, K.C., Korshunov, A., Sahm, F., Deng, M.Y., Sturm, D., DeSisto, J., Donson, A.M., Foreman, N.K., Green, A.L., Robinson, G., Orr, B.A., Gao, Q., Darrow, E., Hadley, J.L., Northcott, P.A., Gojo, J., Kawauchi, D., Hovestadt, V., Filbin, M.G., von Deimling, A., Zuckermann, M., Pajtler, K.W., Kool, M., Jones, D.T.W., Jäger, N., Kutscher, L.M., Kaessmann, H.*, Pfister, S.M.* (2023) Mapping pediatric brain tumors to their origins in the developing cerebellum. Neuro Oncol. 25(10):1895-1909. *joint senior authors. URL Trost, N., Mbengue, N., Kaessmann, H. (2023) The molecular evolution of mammalian spermatogenesis. Cell Dev. 175: 203865. URL Müller, M., Eghbalian, R., Boeckel, J.-N., Frese, K.S., Haas, J., Kayvanpour, E., Sedaghat-Hamedani, F., Lackner, M.K., Tugrul, O.F., Ruppert, T., Tappu, R., Martins Bordalo, D., Kneuer, J.M., Piekarek, A., Herch, S., Schudy, S., Keller, A., Grammes, N., Bischof, C., Klinke, A., Cardoso-Moreira, M., Kaessmann, H., Katus, H.A., Frey, N., Steinmetz, L.M., and Meder, B. (2022) NIMA-related kinase 9 regulates the phosphorylation of the essential myosin light chain in the heart. Nat. Commun. 13:6209. URL Zhang, F., Raabe C.A., Cardoso-Moreira, M., Brosius J., Kaessmann, H., and Schmitz, J. (2022) ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement. Genomics 114:110434. URL Murat, F., Mbengue, N., Boeg Winge, S., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Riera Belles, M., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S., Marques-Bonet, T., Grützner, F., Almstrup, K., Heide Schierup, M., Kaessmann, H. (2022) The molecular evolution of spermatogenesis across mammals. Nature 613:308-316. URL Bauersachs, H.G., Bengtson, C.P., Weiss, U., Hellwig. A., García-Vilela, C., Zaremba, B., Kaessmann, H., Pruunsild, P., Bading, H. (2021) N-methyl-d-aspartate Receptor-mediated Preconditioning Mitigates Excitotoxicity in Human induced Pluripotent Stem Cell-derived Brain Organoids. Neuroscience 484:83-97. URL Gruhl, F., Janich, P., Kaessmann, H., and Gatfield, D. (2021) Circular RNA repertoires are associated with evolutionarily young transposable elements. Elife 10: e67991. URL Sarropoulos, I., Sepp, M., Frömel, R., Leiss, K., Trost, N., Leushkin, E., Okonechnikov, K., Joshi, P., Giere, P., Kutscher, L.M., Cardoso-Moreira, M., Pfister, S.M., and Kaessmann, H. (2021) Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science 373: eabg4696. URL Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M., and Kaessmann, H. (2021) Alternative splicing during mammalian organ development. Nat. Genet. 53:924-935. URL Zhou, Y., Shearwin-Whyatt, L., Li J., Song, Z, Hayakawa ,T., Stevens, D., Fenelon, J.C., Peel, E., Cheng, Y., Pajpach, F., Bradley, N., Suzuki, H., Nikaido, M., Damas, J., Daish, T., Perry, T., Zhu, Z., Geng, Y., Rhie, A., Sims, Y., Wood ,J., Haase ,B,.Mountcastle, J,. Fedrigo, O., Li ,Q,. Yang, H., Wang, J., Johnston, S.D., Phillippy, AM., Howe, K., Jarvis, E.D,. Ryder, O.A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, HA., Graves, J., Belov, K., Renfree, M.B., Grutzner, F., Zhou, Q., Zhang, G. (2021) Platypus and echidna genomes reveal mammalian biology and evolution. Nature doi: 10.1038/s41586-020-03039-0. URL Wang, Z.Y., Leushkin, E., Liechti, A., Ovchinnikova, S., Mößinger, K., Brüning, T., Rummel, C., Grützner, F., Cardoso-Moreira, M., Janich, P., Gatfield, D., Diagouraga, B., de Massy, B., Gill, M.E., Peters, A.H.F.M., Anders, S., and Kaessmann, H. (2020) Transcriptome and translatome co-evolution in mammals. Nature 588: 642-647. URL Ullate-Agote, A., Burgelin, I., Debry, A., Langrez, C., Montagne, F., Peraldi, R., Daraspe, J., Kaessmann, H. and Milinkovitch, MC., Tzika, AC.(2020) Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. Proc Natl Acad Sci USA. 117: 26307-26317. URL Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M., Cooper, D.N., Huber, W., Kaessmann H. (2020) Developmental Gene Expression Differences between Humans and Mammalian Models. Cell Rep. 33: 108308. URL Sobrido-Cameán, D., Yañez-Guerra, L.A., Lamanna, F., Conde-Fernández, C., Kaessmann, H., Elphick, M.R., Anadón, R., Rodicio, M.C., and Barreiro-Iglesias, A. (2019) Galanin in an Agnathan: Precursor Identification and Localisation of Expression in the Brain of the Sea Lamprey Petromyzon marinus. Front Neuroanat. 13: 83. URL Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., Mazin, P.V., Xenarios, I., Harshman, K., Mort, M., Cooper, D.N., Sandi, C., Soares, M.J., Ferreira, P.G., Afonso, S., Carneiro, M., Turner, J.M., VandeBerg, J.L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y.E., and Kaessmann, H. (2019) Gene expression across mammalian organ development. Nature 571: 505-509. URL Sarropoulos, I., Marin, R., Cardoso-Moreira, M., and Kaessmann, H. (2019) Developmental dynamics of lncRNAs across mammalian organs and species. Nature 571: 510-514. URL Carelli, F.N., Liechti, A., Halbert, J., Warnefors, M., Kaessmann, H. (2018) Repurposing of promoters and enhancers during mammalian evolution. Nat. Commun. 9: 4066. URL Smith, J.J., Timoshevskaya, N., Ye, C., Holt, C., Keinath, M.C., Parker, H.J., Cook, M.E., Hess, J.E., Narum, S.R., Lamanna, F., Kaessmann, H., Timoshevskiy, V.A., Waterbury, C.K.M., Saraceno, C., Wiedemann, L.M., Robb, S.M.C., Baker, C., Eichler, E.E., Hockman, D., Sauka-Spengler, T., Yandell, M., Krumlauf, R., Elgar, G., Amemiya, C.T. (2018) The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat. Genet. 50: 270-277. URL Warnefors, M., Mössinger, K., Halbert, J., Studer, T., VandeBerg, J.L., Lindgren, I., Fallahshahroudi, A., Jensen, P., Kaessmann, H. (2017) Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res. 27:1961-1973. URL Carelli, F.N., Hayakawa, T., Go, Y., Imai, H., Warnefors, M., and Kaessmann, H. (2016) The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res. 26: 301-314. URL Wiberg, R.A., Halligan, D.L., Ness, R.W., Necsulea, A., Kaessmann, H., Keightley, P.D. (2015) Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome. Genome Biol. Evol. 7: 2432-2444. URL Zimermann, C., Stévant, I., Borel, C., Conne, B., Pitetti, J.L., Calvel, P., Kaessmann, H., Jégou B, Chalmel F, Nef S. (2015) Research resource: the dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis. Mol. Endocrinol. 29: 627-642. URL Necsulea, A. and Kaessmann, H. (2014) Evolutionary dynamics of coding and noncoding transcriptomes. Nat. Rev. Genet. 5: 734-48. URL Zimmermann, C., Romero, Y., Warnefors, M., Bilican, A., Borel, C., Smith, L.B., Kotaja, N., Kaessmann, H., and Nef, S. (2014) Germ Cell-Specific Targeting of DICER or DGCR8 reveals a novel role for endo-siRNAs in the progression of mammalian spermatogenesis and male fertility. PLoS One 9: e107023. URL Warnefors, M., Liechti, A., Halbert, J., Valloton, D., and Kaessmann, H. (2014) Conserved miRNA editing in mammalian evolution, development and disease. Genome Biol. 15: R83. URL Ettema, T.J., Lindås, A.C., Hjort, K., Poplawski A.B., Kaessmann, H., Grogan, D.W., Kelman, Z., Andersson, A.F., Pelve, E.A., Lundgren, M., and Svärd, S.G. (2014) Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle. Mol. Microbiol. 92: 903-909. URL Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grützner, F., and Kaessmann, H. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508: 488-493. URL Cover, News & Views (Nature) Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grützner, F., and Kaessmann, H. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640. URL Soumillon, M., Necsulea, A., Weier, M., Brawand, D., Zhang, X., Gu, H., Barthès, P., Kokkinaki, M., Nef, S., Gnirke, A., Dym, M., de Massy, B., Mikkelsen, T.S., and Kaessmann, H. (2013) Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell Rep. 3: 2179-2190. URL Warnefors, M. and Kaessmann, H. (2013) Evolution of the correlation between expression divergence and protein divergence in mammals. Genome Biol. Evol. 5: 1324-1325. URL Meunier, J., Lemoine, F., Soumillon, M., Liechti, A., Weier, M., Guschanski, K., Hu, H., Khaitovich, P., and Kaessmann, H. (2013) Birth and expression evolution of mammalian microRNA genes. Genome Res. 23: 34-45. URL Julien, P., Brawand, D., Soumillon, M., Necsulea, A., Liechti, A., Schütz, F., Daish, T., Grützner, F., and Kaessmann, H. (2012) Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol. 5: e1001328. URL Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F.W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348. URL News & Views (Mol. Syst. Biol.) Romero, Y., Meikar, O., Papaioannou, M.D., Conne, B., Grey, C., Weier, M., Pralong, F., De Massy, B., Kaessmann, H., Vassalli, J.D., Kotaja, N., Nef, S. (2011) Dicer1 depletion in male germ cells leads to infertility due to cumulative meiotic and spermiogenic defects. PLoS One 6: e25241. URL Croset, V., Rytz, R., Cummins, S.F., Budd, A., Brawand, D., Kaessmann, H., Gibson, T.J., and Benton, R. (2010) Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction. PLoS Genet. 6: e1001064. URL Kaessmann, H. (2010) Origins, evolution and phenotypic impact of new genes. Genome Res. 20: 1313-1326. URL Pradervand, S., Weber, J., Lemoine, F., Consales, F., Paillusson, A., Dupasquier, M., Thomas, J., Richter, H., Kaessmann, H., Beaudoing, E., Hagenbüchle, O., and Harshman, K. (2010) Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 48: 219-222. URL Potrzebowski, L., Vinckenbosch, N., and Kaessmann, H. (2010) The emergence of new genes on the young therian X. Trends Genet. 26: 1-4. URL Fablet, M., Bueno, M., Potrzebowski, L., and Kaessmann, H. (2009) Evolutionary origin and functions of retrogene introns. Mol. Biol. Evol. 26: 2147-2156. URL Kaessmann, H. (2009) More than just a copy. Science 325: 958-959. URL Henrichsen, C. N., Vinckenbosch, N., Zollner, S., Chaignat, E., Pradervand, S., Schutz, F., Ruedi, M., *Kaessmann, H., and *Reymond, A. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat. Genet. 41: 424-429. URL Kaessmann, H., Vinckenbosch, N., and Long, M.: RNA-based gene duplication: mechanistic and evolutionary insights. (2009) Nat. Rev. Genet. 10: 19-31. URL Brawand, D., Wahli, W. and Kaessmann, H. (2008) Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 3: e63. URL Cover, Commentary (PLoS Biol.) Goldschmidt, V., Ciuffi, A., Ortiz, M., Brawand, D., Munoz, M., *Kaessmann, H. and *Telenti, A. (2008) Anti–Retroviral Activity of Ancestral TRIM5α. J. Virol. 82: 2089–2096. URL
Marques, A., Vinckenbosch, N., Brawand, D., and Kaessmann, H. (2008) Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biol. 9: R54. URL Ortiz, M., Kaessmann, H., Zhang, K., Bashirova, A., Carrington, M., Quintana–Murci, L., and Telenti, A. (2008) The evolutionary history of the CD209 (DC–SIGN) family in humans and non–human primates. Genes Immun. 9: 483–492. URL Potrzebowski, L., Vinckenbosch, N., Marques, A., Chalmel, F., Jégou, B., and Kaessmann, H. (2008) Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol. 4: e80. URL Rosso, L., Keller, L., Kaessmann, H., and Hammond, R. (2008) Mating system and avpr1a promoter variation in primates. Biology letters 4: 375–378. URL Rosso, L., Marques, A., Reichert, A., and Kaessmann, H. (2008) Mitochondrial targeting adaptation of the hominoid–specific glutamate dehydrogenase driven by positive Darwinian selection PLoS Genet. 4: e1000150. URL Rosso, L., Marques, A., Weier, M., Lambert, N., Lambot, M.A., Vanderhaeghen, P., and Kaessmann, H. (2008) Birth and rapid subcellular adaptation of a hominoid–specific CDC14 protein. PLoS Biol. 6: e140. URL Cover Parmley, J.L., Potrzebowski, L., Kaessmann, H., and Hurst, L. (2007) Splicing and the evolution of proteins in mammals. PLoS Biol. 5: e26. URL Dupanloup, I. and Kaessmann, H. (2006) Evolutionary simulations to detect functional lineage–specific genes. Bioinformatics 22: 1815–1822. URL Ortiz M, Bleiber G, Martinez R, *Kaessmann H. and *Telenti A. (2006) Patterns of evolution of host proteins involved in retroviral pathogenesis. Retrovirol. 3: 11. URL Vinckenbosch, N., Dupanloup, I. and Kaessmann, H. (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl. Acad. Sci. USA 103: 3220–3225. URL Marques, A., Dupanloup, I., Vinckenbosch, N., Reymond, A., and Kaessmann, H. (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3: e357. URL Cover Betran, E., Kaessmann, H., Emerson, J.J., and Long, M. (2004) Sex chromosomes and male functions – where do new genes go? Cell Cycle 7: 873-875. URL Burki, F. and Kaessmann, H. (2004) Birth and adaptive evolution of a hominoid gene supporting high neurotransmitter flux. Nat. Genet. 10: 1061–1063. URL News & Views (Nature Genetics) International Chicken Genome Sequencing Consortium (Kaessmann H. – member). (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716. URL Cover, News & Views (Nature) Kaessmann, H. (2003) Human and chimpanzee nucleotide diversity. In: Encyclopedia of the human genome. Edited by Cooper, David N.; Nature Publishing Group. Kaessmann, H., Paabo, S. (2002) The genetical history of humans and the great apes. J Intern Med 251: 1-18. URL Kaessmann, H., Zollner, S., Nekrutenko, A., and Li, W. H. (2002) Signatures of domain shuffling in the human genome. Genome Res. 12: 1642-50. URL Kaessmann, H., Zöllner, S., Gustafsson, A. C., Wiebe, V., Laan, M., Lundeberg, J., Uhlen, M., and Paabo, S. (2002) Extensive linkage disequilibrium in small human populations in Eurasia. Am J Hum Genet. 70: 673-85. URL Schrenk, F., Brommage, G., Kaessmann, H. (2002) Die Frühzeit des Menschen: Zurück zu den Wurzeln. Biologie in unserer Zeit 32: 352-359. URL Kaessmann, H., Wiebe, V., Weiss, G., Paabo, S. (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27:155-6. URL Ingman, M., Kaessmann, H., Paabo, S., and Gyllensten, U. (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-13. URL Cover, News & Views (Nature) Kaessmann, H., Wiebe, V., and Paabo, S. (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-62. URL Kaessmann, H., Heissig, F., von Haeseler, A., and Paabo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. 22: 78-81. URL
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