Publications by the Kaessmann Lab

Our work appeared on the cover of:

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Graphical Abstract

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.

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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.

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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.*

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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.

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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.

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The molecular evolution of mammalian spermatogenesis

Cells & Development 2023

Trost, N., Mbengue, N., Kaessmann, H.

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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.

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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.

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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.

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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.

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Circular RNA repertoires are associated with evolutionarily young transposable elements

eLife 2021

Gruhl, F., Janich, P., Kaessmann, H., Gatfield, D.

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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.

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Alternative splicing during mammalian organ development

Nature Genetics 2021

Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M., Kaessmann, H.

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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.

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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.

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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.

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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.

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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.

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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.

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Developmental dynamics of lncRNAs across mammalian organs and species

Nature 2019

Sarropoulos, I., Marin, R., Cardoso-Moreira, M., Kaessmann, H.

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Repurposing of promoters and enhancers during mammalian evolution

Nature Communications 2018

Carelli, F.N., Liechti, A., Halbert, J., Warnefors, M., Kaessmann, H.

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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.

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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.

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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.

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The evolution of duplicate gene expression in mammalian organs

Genome Research 2017

Guschanski, K., Warnefors, M., Kaessmann, H.

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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.

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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.

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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.

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Evolutionary dynamics of coding and non-coding transcriptomes

Nature Reviews Genetics 2014

Necsulea, A., Kaessmann, H.

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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.

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Conserved microRNA editing in mammalian evolution, development and disease

Genome Biology 2014

Warnefors, M., Liechti, A., Halbert, J., Valloton, D., Kaessmann, H.

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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.

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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.

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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.

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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.

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Evolution of the Correlation between Expression Divergence and Protein Divergence in Mammals

Genome Biology and Evolution 2013

Warnefors, M., Kaessmann, H.

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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.

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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.

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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.

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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.

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Origins, evolution, and phenotypic impact of new genes

Genome Research 2010

Kaessmann, H.

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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.

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The emergence of new genes on the young therian X

Trends in Genetics 2009

Potrzebowski, L., Vinckenbosch, N., Kaessmann, H.

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More Than Just a Copy

Science 2009

Kaessmann, H.

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Evolutionary Origin and Functions of Retrogene Introns

Molecular Biology and Evolution 2009

Fablet, M., Bueno, M., Potrzebowski, L., Kaessmann, H.

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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.

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RNA-based gene duplication: mechanistic and evolutionary insights

Nature Reviews Genetics 2008

Kaessmann, H., Vinckenbosch, N., Long, M.

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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.

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Mating system and avpr1a promoter variation in primates

Biology Letters 2008

Rosso, L., Keller, L., Kaessmann, H., Hammond, R.L.

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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.

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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.

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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.

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Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation

PLoS Biology 2008

Brawand, D., Wahli, W., Kaessmann, H.

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Functional diversification of duplicate genes through subcellular adaptation of encoded proteins

Genome Biology 2008

Marques, A.C., Vinckenbosch, N., Brawand, D., Kaessmann, H.

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Antiretroviral Activity of Ancestral TRIM5α

Journal of Virology 2008

Goldschmidt, V., Ciuffi, A., Ortiz, M., Brawand, D., Muñoz, M., Kaessmann, H., Telenti, A.

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Splicing and the Evolution of Proteins in Mammals

PLoS Biology 2007

Parmley, J.L., Urrutia, A.O., Potrzebowski, L., Kaessmann, H., Hurst, L.D.

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Evolutionary simulations to detect functional lineage-specific genes

Bioinformatics 2006

Dupanloup, I., Kaessmann, H.

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Evolutionary fate of retroposed gene copies in the human genome

Proceedings of the National Academy of Sciences 2006

Vinckenbosch, N., Dupanloup, I., Kaessmann, H.

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Patterns of evolution of host proteins involved in retroviral pathogenesis

Retrovirology 2006

Ortiz, M., Bleiber, G., Martinez, R., Kaessmann, H., Telenti, A.

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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.

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Nature 2004

International Chicken Genome Sequencing Consortium (Kaessmann, H. - member)

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Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux

Nature Genetics 2004

Burki, F., Kaessmann, H.

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Sex Chromosomes and Male Functions: Where Do New Genes Go?

Cell Cycle 2004

Betran, E., Emerson, J., Kaessmann, H., Long, M.

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Extensive Gene Traffic on the Mammalian X Chromosome

Science 2004

Emerson, J.J., Kaessmann, H., Betrán, E., Long, M.

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Human and Chimpanzee Nucleotide Diversity. In: Encyclopedia of the human genome

Nature Publishing Group 2003

Kaessmann, H. Edited by Cooper, David N.

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Signatures of Domain Shuffling in the Human Genome

Genome Research 2002

Kaessmann, H., Zöllner, S., Nekrutenko, A., Li, W.

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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.

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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.

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The genetical history of humans and the great apes

Journal of Internal Medicine 2002

KAESSMANN, H., PAABO, S.

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Die Frühzeit des Menschen: Zurück zu den Wurzeln

Biologie in unserer Zeit 2002

Schrenk, F., Brommage, G., Kaessmann, H.

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Great ape DNA sequences reveal a reduced diversity and an expansion in humans

Nature Genetics 2001

Kaessmann, H., Wiebe, V., Weiss, G., Pääbo, S.

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Mitochondrial genome variation and the origin of modern humans

Nature 2000

Ingman, M., Kaessmann, H., Pääbo, S., Gyllensten, U.

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Extensive Nuclear DNA Sequence Diversity Among Chimpanzees

Science 1999

Kaessmann, H., Wiebe, V., Pääbo, S.

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