Identification of old coding regions disproves the hominoid de novo status of genes
Nature Ecology & Evolution 2024
Leushkin, E., Kaessmann, H.
Rhesus macaque as a model for sex-biased neurological diseases
Cell Genomics 2024
Rodríguez-Montes, L., Kaessmann, H.
Developmental origins and evolution of pallial cell types and structures in birds
bioRXiv (Preprint) 2024
Zaremba, B., Fallahshahroudi, A., Schneider, C., Schmidt, J., Sarropoulos, I., Leushkin, E., Berki, B., Van Poucke, E., Jensen, P., Senovilla-Ganzo, R., Hervas-Sotomayor, F., Trost, N., Lamanna, F., Sepp, M., García-Moreno, F., and Kaessmann, H.
A male-essential microRNA is key for avian sex chromosome dosage compensation
bioRxiv [Preprint] 2024
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.
Cellular development and evolution of the mammalian cerebellum
Nature 2023
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.
Sex-biased gene expression across mammalian organ development and evolution
Science 2023
Rodríguez-Montes, L., Ovchinnikova, S., Yuan, X., Studer, T., Sarropoulos, I., Anders, S., Kaessmann, H.*, and Cardoso-Moreira, M.*
A lamprey neural cell type atlas illuminates the origins of the vertebrate brain
Nature Ecology & Evolution 2023
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., Kaessmann, H.
Mapping pediatric brain tumors to their origins in the developing cerebellum
Neuro-Oncology 2023
Okonechnikov, K., Joshi, P., Sepp, M., Leiss, K., Sarropoulos, I., Murat, F., Sill, M., Beck, P., Chan, K.C., Korshunov, A., Sah, 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.
The molecular evolution of mammalian spermatogenesis
Cells & Development 2023
Trost, N., Mbengue, N., Kaessmann, H.
The molecular evolution of spermatogenesis across mammals
Nature 2022
Murat, F., Mbengue, N., Winge, S.B., Trefzer, T., Leushkin, E., Sepp, M., Cardoso-Moreira, M., Schmidt, J., Schneider, C., Mößinger, K., Brüning, T., Lamanna, F., Belles, M.R., Conrad, C., Kondova, I., Bontrop, R., Behr, R., Khaitovich, P., Pääbo, S., Marques-Bonet, T., Grützner, F., Almstrup, K., Schierup, M.H., Kaessmann, H.
NIMA-related kinase 9 regulates the phosphorylation of the essential myosin light chain in the heart
Nature Communications 2022
Müller, M., Eghbalian, R., Boeckel, J., 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., Meder, B.
ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement
Genomics 2022
Zhang, F., Raabe, C.A., Cardoso-Moreira, M., Brosius, J., Kaessmann, H., Schmitz, J.
N-methyl-d-aspartate Receptor-mediated Preconditioning Mitigates Excitotoxicity in Human Induced Pluripotent Stem Cell-derived Brain Organoids
Neuroscience 2022
Bauersachs, H.G., Bengtson, C.P., Weiss, U., Hellwig, A., García-Vilela, C., Zaremba, B., Kaessmann, H., Pruunsild, P., Bading, H.
Circular RNA repertoires are associated with evolutionarily young transposable elements
eLife 2021
Gruhl, F., Janich, P., Kaessmann, H., Gatfield, D.
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
Science 2021
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., Kaessmann, H.
Alternative splicing during mammalian organ development
Nature Genetics 2021
Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M., Kaessmann, H.
Platypus and echidna genomes reveal mammalian biology and evolution
Nature 2021
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, A.M., Howe, K., Jarvis, E.D., Ryder, O.A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H.A., Graves, J., Belov, K., Renfree, M.B., Grutzner, F., Zhou, Q., Zhang, G.
Transcriptome and translatome co-evolution in mammals
Nature 2020
Wang, Z., 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., Kaessmann, H.
Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles
Proceedings of the National Academy of Sciences 2020
Ullate-Agote, A., Burgelin, I., Debry, A., Langrez, C., Montange, F., Peraldi, R., Daraspe, J., Kaessmann, H., Milinkovitch, M.C., Tzika, A.C.
Developmental Gene Expression Differences between Humans and Mammalian Models
Cell Reports 2020
Cardoso-Moreira, M., Sarropoulos, I., Velten, B., Mort, M., Cooper, D.N., Huber, W., Kaessmann, H.
Galanin in an Agnathan: Precursor Identification and Localisation of Expression in the Brain of the Sea Lamprey Petromyzon marinus
Frontiers in Neuroanatomy 2019
Sobrido-Cameán, D., Yáñez-Guerra, L.A., Lamanna, F., Conde-Fernández, C., Kaessmann, H., Elphick, M.R., Anadón, R., Rodicio, M.C., Barreiro-Iglesias, A.
Gene expression across mammalian organ development
Nature 2019
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.A., VandeBerg, J.L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y.E., Kaessmann, H.
Developmental dynamics of lncRNAs across mammalian organs and species
Nature 2019
Sarropoulos, I., Marin, R., Cardoso-Moreira, M., Kaessmann, H.
Repurposing of promoters and enhancers during mammalian evolution
Nature Communications 2018
Carelli, F.N., Liechti, A., Halbert, J., Warnefors, M., Kaessmann, H.
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution
Nature Genetics 2018
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.
Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
Genome Research 2017
Marin, R., Cortez, D., Lamanna, F., Pradeepa, M.M., Leushkin, E., Julien, P., Liechti, A., Halbert, J., Brüning, T., Mössinger, K., Trefzer, T., Conrad, C., Kerver, H.N., Wade, J., Tschopp, P., Kaessmann, H.
Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
Genome Research 2017
Warnefors, M., Mössinger, K., Halbert, J., Studer, T., VandeBerg, J.L., Lindgren, I., Fallahshahroudi, A., Jensen, P., Kaessmann, H.
The evolution of duplicate gene expression in mammalian organs
Genome Research 2017
Guschanski, K., Warnefors, M., Kaessmann, H.
The life history of retrocopies illuminates the evolution of new mammalian genes
Genome Research 2016
Carelli, F.N., Hayakawa, T., Go, Y., Imai, H., Warnefors, M., Kaessmann, H.
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome
Genome Biology and Evolution 2015
Wiberg, R.A.W., Halligan, D.L., Ness, R.W., Necsulea, A., Kaessmann, H., Keightley, P.D.
Research Resource: The Dynamic Transcriptional Profile of Sertoli Cells During the Progression of Spermatogenesis
Molecular Endocrinology 2015
Zimmermann, C., Stévant, I., Borel, C., Conne, B., Pitetti, J., Calvel, P., Kaessmann, H., Jégou, B., Chalmel, F., Nef, S.
Evolutionary dynamics of coding and non-coding transcriptomes
Nature Reviews Genetics 2014
Necsulea, A., Kaessmann, H.
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 2014
Zimmermann, C., Romero, Y., Warnefors, M., Bilican, A., Borel, C., Smith, L.B., Kotaja, N., Kaessmann, H., Nef, S.
Conserved microRNA editing in mammalian evolution, development and disease
Genome Biology 2014
Warnefors, M., Liechti, A., Halbert, J., Valloton, D., Kaessmann, H.
Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle
Molecular Microbiology 2014
Ettema, T.J.G., Lindås, A., Hjort, K., Poplawski, A.B., Kaessmann, H., Grogan, D.W., Kelman, Z., Andersson, A.F., Pelve, E.A., Lundgren, M., Svärd, S.G.
Origins and functional evolution of Y chromosomes across mammals
Nature 2014
Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grützner, F., Kaessmann, H.
The evolution of lncRNA repertoires and expression patterns in tetrapods
Nature 2014
Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grützner, F., Kaessmann, H.
Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
Cell Reports 2013
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., Kaessmann, H.
Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals
Genome Biology and Evolution 2013
Warnefors, M., Kaessmann, H.
Birth and expression evolution of mammalian microRNA genes
Genome Research 2012
Meunier, J., Lemoine, F., Soumillon, M., Liechti, A., Weier, M., Guschanski, K., Hu, H., Khaitovich, P., Kaessmann, H.
The evolution of gene expression levels in mammalian organs
Nature 2011
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., Kaessmann, H.
Dicer1 Depletion in Male Germ Cells Leads to Infertility Due to Cumulative Meiotic and Spermiogenic Defects
PLoS ONE 2011
Romero, Y., Meikar, O., Papaioannou, M.D., Conne, B., Grey, C., Weier, M., Pralong, F., De Massy, B., Kaessmann, H., Vassalli, J., Kotaja, N., Nef, S.
Ancient Protostome Origin of Chemosensory Ionotropic Glutamate Receptors and the Evolution of Insect Taste and Olfaction
PLoS Genetics 2010
Croset, V., Rytz, R., Cummins, S.F., Budd, A., Brawand, D., Kaessmann, H., Gibson, T.J., Benton, R.
Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs
BioTechniques 2010
Pradervand, S., Weber, J., Lemoine, F., Consales, F., Paillusson, A., Dupasquier, M., Thomas, J., Richter, H., Kaessmann, H., Beaudoing, E., Hagenbüchle, O., Harshman, K.
The emergence of new genes on the young therian X
Trends in Genetics 2009
Potrzebowski, L., Vinckenbosch, N., Kaessmann, H.
Evolutionary Origin and Functions of Retrogene Introns
Molecular Biology and Evolution 2009
Fablet, M., Bueno, M., Potrzebowski, L., Kaessmann, H.
Segmental copy number variation shapes tissue transcriptomes
Nature Genetics 2009
Henrichsen, C.N., Vinckenbosch, N., Zöllner, S., Chaignat, E., Pradervand, S., Schütz, F., Ruedi, M., Kaessmann, H., Reymond, A.
RNA-based gene duplication: mechanistic and evolutionary insights
Nature Reviews Genetics 2008
Kaessmann, H., Vinckenbosch, N., Long, M.
The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates
Genes & Immunity 2008
Ortiz, M., Kaessmann, H., Zhang, K., Bashirova, A., Carrington, M., Quintana-Murci, L., Telenti, A.
Mating system and avpr1a promoter variation in primates
Biology Letters 2008
Rosso, L., Keller, L., Kaessmann, H., Hammond, R.L.
Mitochondrial Targeting Adaptation of the Hominoid-Specific Glutamate Dehydrogenase Driven by Positive Darwinian Selection
PLoS Genetics 2008
Rosso, L., Marques, A.C., Reichert, A.S., Kaessmann, H.
Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein
PLoS Biology 2008
Rosso, L., Marques, A.C., Weier, M., Lambert, N., Lambot, M., Vanderhaeghen, P., Kaessmann, H.
Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes
PLoS Biology 2008
Potrzebowski, L., Vinckenbosch, N., Marques, A.C., Chalmel, F., Jégou, B., Kaessmann, H.
Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation
PLoS Biology 2008
Brawand, D., Wahli, W., Kaessmann, H.
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins
Genome Biology 2008
Marques, A.C., Vinckenbosch, N., Brawand, D., Kaessmann, H.
Antiretroviral Activity of Ancestral TRIM5α
Journal of Virology 2008
Goldschmidt, V., Ciuffi, A., Ortiz, M., Brawand, D., Muñoz, M., Kaessmann, H., Telenti, A.
Splicing and the Evolution of Proteins in Mammals
PLoS Biology 2007
Parmley, J.L., Urrutia, A.O., Potrzebowski, L., Kaessmann, H., Hurst, L.D.
Evolutionary simulations to detect functional lineage-specific genes
Bioinformatics 2006
Dupanloup, I., Kaessmann, H.
Evolutionary fate of retroposed gene copies in the human genome
Proceedings of the National Academy of Sciences 2006
Vinckenbosch, N., Dupanloup, I., Kaessmann, H.
Patterns of evolution of host proteins involved in retroviral pathogenesis
Retrovirology 2006
Ortiz, M., Bleiber, G., Martinez, R., Kaessmann, H., Telenti, A.
Emergence of Young Human Genes after a Burst of Retroposition in Primates
PLoS Biology 2005
Marques, A.C., Dupanloup, I., Vinckenbosch, N., Reymond, A., Kaessmann, H.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Nature 2004
International Chicken Genome Sequencing Consortium (Kaessmann, H. - member)
Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux
Nature Genetics 2004
Burki, F., Kaessmann, H.
Sex Chromosomes and Male Functions: Where Do New Genes Go?
Cell Cycle 2004
Betran, E., Emerson, J., Kaessmann, H., Long, M.
Extensive Gene Traffic on the Mammalian X Chromosome
Science 2004
Emerson, J.J., Kaessmann, H., Betrán, E., Long, M.
Human and Chimpanzee Nucleotide Diversity. In: Encyclopedia of the human genome
Nature Publishing Group 2003
Kaessmann, H. Edited by Cooper, David N.
Signatures of Domain Shuffling in the Human Genome
Genome Research 2002
Kaessmann, H., Zöllner, S., Nekrutenko, A., Li, W.
DNA sequence variation in a non-coding region of low recombination on the human X chromosome
Nature Genetics 2002
Kaessmann, H., Heißig, F., Haeseler, A.v., Pääbo, S.
Extensive Linkage Disequilibrium in Small Human Populations in Eurasia
The American Journal of Human Genetics 2002
Kaessmann, H., Zöllner, S., Gustafsson, A.C., Wiebe, V., Laan, M., Lundeberg, J., Uhlén, M., Pääbo, S.
The genetical history of humans and the great apes
Journal of Internal Medicine 2002
KAESSMANN, H., PAABO, S.
Die Frühzeit des Menschen: Zurück zu den Wurzeln
Biologie in unserer Zeit 2002
Schrenk, F., Brommage, G., Kaessmann, H.
Great ape DNA sequences reveal a reduced diversity and an expansion in humans
Nature Genetics 2001
Kaessmann, H., Wiebe, V., Weiss, G., Pääbo, S.
Mitochondrial genome variation and the origin of modern humans
Nature 2000
Ingman, M., Kaessmann, H., Pääbo, S., Gyllensten, U.
Extensive Nuclear DNA Sequence Diversity Among Chimpanzees
Science 1999