Publications

Altendorfer, E.; Mundlos, S.; Mayer, A.: A transcription coupling model for how enhancers communicate with their target genes. Nature Structural & Molecular Biology 32 (4), pp. 598 - 606 (2025)

Müller, J. M.; Altendorfer, E.; Freier, S.; Moos, K.; Mayer, A.; Tresch, A.: Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives. NAR: genomics and bioinformatics 7 (1), Article lqaf006 (2025)

Ulicevic, J.; Shao, Z.; Jasnovidova, O.; Bressin, A.; Gajos, M.; Ng, A. H.; Annaldasula, S.; Meierhofer, D.; Church, G. M.; Busskamp, V. et al.; Mayer, A.: Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation. Molecular Systems Biology 20 (7), pp. 767 - 798 (2024)

Bressin, A.; Jasnovidova, O.; Arnold, M.; Altendorfer, E.; Trajkovski , F.; Kratz, T. A.; Handzlik, J. E.; Hnisz, D.; Mayer, A.: High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nature Communications 14 (1), Article 4971 (2023)

Nabavizadeh, N.; Bressin, A.; Shboul, M.; Moreno Traspas, R.; Chia, P. H.; Bonnard, C.; Szenker-Ravi, E.; Saribas, B.; Beillard, E.; Altunoglu, U. et al.; Hojati, Z.; Drutman, S.; Freier, S.; El-Khateeb, M.; Fathallah, R.; Casanova, J.-L.; Soror, W.; Arafat, A.; Escande-Beillard, N.; Mayer, A.; Reversade, B.: A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. Embo Molecular Medicine 15 (2), Article e16478 (2023)

Eischer, N.; Arnold, M.; Mayer, A.: Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. Wiley interdisciplinary reviews: WIREs RNA 14 (1), e1734 (2023)

Altendorfer, E.; Mochalova, Y.; Mayer, A.: BRD4: a general regulator of transcription elongation. Transcription 13 (1-3), pp. 70 - 81 (2022)

Bressin, A.; Mayer, A.: Neue Einblicke in die Genregulation mittels funktioneller Multiomik. Biospektrum 28 (3), pp. 276 - 278 (2022)

Arnold, M.; Bressin, A.; Jasnovidova, O.; Meierhofer, D.; Mayer, A.: A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination. Molecular Cell 81 (17), pp. 3589 - 3603 (2021)

Gajos, M.; Jasnovidova, O.; van Bömmel, A.; Freier, S.; Vingron, M.; Mayer, A.: Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Research (London) 49 (8), pp. 4402 - 4420 (2021)

Annaldasula, S.; Gajos, M.; Mayer, A.: IsoTV: processing and visualizing functional features of translated transcript isoforms. Bioinformatics 37 (18), pp. 3070 - 3072 (2021)

Real, F. M.; Haas, S. A.; Franchini, P.; Xiong, P.; Simakov, O.; Kuhl, H.; Schöpflin, R.; Heller, D.; Moeinzadeh, M. H.; Heinrich, V. et al.; Krannich , T.; Bressin, A.; Hartmann, M. F.; Wudy, S. A.; Dechmann, D. K. N.; Hurtado, A.; Barrionuevo, F. J.; Schindler, M.; Harabula, I.; Osterwalder, M.; Hiller, M.; Wittler, L.; Visel, A.; Timmermann, B.; Meyer, A.; Vingron, M.; Jiménez, R.; Mundlos, S.; Lupiáñez, D. G.: The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 370 (6513), pp. 208 - 214 (2020)

Mayer, A.: Genome Transcription Regulation During Cell Differentiation. Scientia 133, pp. 6 - 9 (2020)

Winter, G. E.; Mayer, A.; Buckley, D. L.; Erb, M. A.; Roderick, J. E.; Vittori, S.; Reyes,, J. M.; di Iulio, J.; Souza, A.; Ott, C. J. et al.; Roberts, J. M.; Zeid, R.; Scott, T. G.; Paulk, J.; Lachance, K.; Olson, C. M.; Dastjerdi, S.; Bauer, S.; Lin, C. Y.; Gray, N. S.; Kelliher, M. A.; Churchman, L. S.; Bradner, J. E.: BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Molecular Cell 67 (1), pp. 5 - 18 (2017)

Mayer, A.; Landry, H. M.; Churchman, L. S.: Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Current Opinion in Cell Biology 46, pp. 72 - 80 (2017)

Mayer, A.; Churchman, L. S.: Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing. Nature Protocols 11 (4), pp. 813 - 433 (2016)

Jasnovidova, O.; Arnold, M.; Mayer, A.: Illuminating enhancer transcription at nucleotide resolution with native elongating transcript sequencing (NET-Seq). In: Enhancers and Promoters - Methods and Protocols (Methods in Molecular Biology ; 2351), Vol. 2351, pp. 41 - 65 (Ed. Borggrefe, T.). Humana, New York, NY (2021)

Mayer, A.; Churchman, L. S.: A detailed protocol for subcellular RNA sequencing (subRNA-seq). In: Current Protocols in Molecular Biology, Vol. Suppl. 120, pp. 4.29.1 - 4.29.18 (Ed. Ausubel, F. M.). John Wiley & Sons, Inc., Hoboken, NJ (2017)

Bressin, A. S.: A Multi-Omics Analysis of Transcription Control by BRD4. Dissertation, ix, 205 pp. (2023)

Gajos, M.: Analysis of the determinants of Pol II pausing. Dissertation, vi, 125 pp. (2022)