Prof. Dr. Mihaela Zavolan

González, Asier, Pandey, Muskan, Schlusser, Niels, Rahaman, Sayanur, Ataman, Meric, Mittal, Nitish, Schmidt, Alexander, Becskei, Attila, & Zavolan, Mihaela. (2025). Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines [Journal-article]. Scientific Data, 12(1). https://doi.org/10.1038/s41597-025-05861-5

Balajti, Máté, Kandhari, Rohan, Juric,Boris, Zavolan, Mihaela, & Kanitz, Alexander. (2025). HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries. Bioinformatics, 41(3). https://doi.org/10.1093/bioinformatics/btaf076

Tintignac, Lionel, Mittal, Nitish, Alam, Shahidul, Ataman, Meric, Ertuna, Yusuf I., Bock, Thomas, Erne, Beat, Zavolan, Mihaela, & Sinnreich, Michael. (2025). Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.02.10.636994

Moon, Youngbin, Herrmann, Christina J, Mironov, Aleksei, & Zavolan, Mihaela. (2025). PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data [Journal-article]. Nucleic Acids Research, 53(D1), D197–D204. https://doi.org/10.1093/nar/gkae1043

Schlusser, Niels, González, Asier, Pandey, Muskan, & Zavolan, Mihaela. (2024). Current limitations in predicting mRNA translation with deep learning models. Genome Biology, 25(1). https://doi.org/10.1186/s13059-024-03369-6

Schaefer, Thorsten, Mittal, Nitish, Wang, Hui, Ataman, Meric, Candido, Silvia, Lötscher, Jonas, Velychko, Sergiy, Tintignac, Lionel, Bock, Thomas, Börsch, Anastasiya, Baßler, Jochen, Rao, Tata Nageswara, Zmajkovic, Jakub, Roffeis, Sarah, Löliger, Jordan, Jacob, Francis, Dumlin, Alain, Schürch, Christoph, Schmidt, Alexander, et al. (2024). Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate. Cell Reports, 43(10). https://doi.org/10.1016/j.celrep.2024.114807

Mittal, Nitish, Ataman, Meric, Tintignac, Lionel, Ham, Daniel J., Jörin, Lena, Schmidt, Alexander, Sinnreich, Michael, Ruegg, Markus A., & Zavolan, Mihaela. (2024). Calorie restriction and rapamycin distinctly restore non-canonical ORF translation in the muscles of aging mice [Journal-article]. Npj Regenerative Medicine, 9(1). https://doi.org/10.1038/s41536-024-00369-9

Banerjee, Arka, Ataman, Meric, Smialek, Maciej Jerzy, Mookherjee, Debdatto, Rabl, Julius, Mironov, Aleksei, Mues, Lea, Enkler, Ludovic, Coto-Llerena, Mairene, Schmidt, Alexander, Boehringer, Daniel, Piscuoglio, Salvatore, Spang, Anne, Mittal, Nitish, & Zavolan, Mihaela. (2024). Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains [Journal-article]. Nucleic Acids Research, 52(15), 9028–9048. https://doi.org/10.1093/nar/gkae630

Ataman, Meric, Mittal, Nitish, Tintignac, Lionel, Schmidt, Alexander, Ham, Daniel J., González, Asier, Ruegg, Markus A., & Zavolan, Mihaela. (2024). Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles [Journal-article]. Communications Biology, 7(1). https://doi.org/10.1038/s42003-024-06679-4

Karasu, Mehmet E., Jahnke, Leonard, Joseph, Brian J., Amerzhanova, Yerkezhan, Mironov, Aleksei, Shu, Xuan, Schröder, Markus S., Gvozdenovic, Ana, Sala, Irene, Zavolan, Mihaela, Jonas, Stefanie, & Corn, Jacob E. (2024). CCAR1 promotes DNA repair via alternative splicing. Molecular Cell, 84(14), 2634–2647. https://doi.org/10.1016/j.molcel.2024.06.011

Katsantoni, Maria, Gypas, Foivos, Herrmann, Christina J, Burri, Dominik, Bąk, Maciej, Iborra, Paula, Agarwal, Krish, Ataman, Meriç, Balajti, Máté, Pozzan, Noè, Schlusser, Niels, Moon, Youngbin, Mironov, Aleksei, Börsch, Anastasiya, Zavolan, Mihaela, & Kanitz, Alexander. (2024). ZARP: A user-friendly and versatile RNA-seq analysis workflow [Journal-article]. F1000Research, 13, 533. https://doi.org/10.12688/f1000research.149237.1

Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024). MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer [Journal-article]. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-48046-1

Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024, March 21). Supplementary Results. https://doi.org/10.5281/zenodo.10849750

Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024). MAPP. Nature Communications, 15(1). https://doi.org/10.5281/zenodo.10845501

Mironov, Aleksei, Franchitti, Lorenzo, Ghosh, Shreemoyee, Ritz, Marie-Francoise, Hutter, Gregor, De Bortoli, Michele, & Zavolan, Mihaela. (2024). Leveraging multi-omics data to infer regulators of mRNA 3’ end processing in glioblastoma. Frontiers in Molecular Biosciences, 11. https://doi.org/10.3389/fmolb.2024.1363933

Schlusser, Niels, & Zavolan, Mihaela. (2024). On the limits of inferring biophysical parameters of RBP-RNA interactions from in vitro RNA Bind’n Seq data. F1000Research, 12. https://doi.org/10.12688/f1000research.135164.2

Bryce-Smith, Sam, Burri, Dominik, Gazzara, Matthew R., Herrmann, Christina J., Danecka, Weronika, Fitzsimmons, Christina M., Wan, Yuk Kei, Zhuang, Farica, Fansler, Mervin M., Fernández, José M., Ferret, Meritxell, Gonzalez-Uriarte, Asier, Haynes, Samuel, Herdman, Chelsea, Kanitz, Alexander, Katsantoni, Maria, Marini, Federico, McDonnel, Euan, Nicolet, Ben, et al. (2023). Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data [Journal-article]. RNA, 29(12), 1839–1855. https://doi.org/10.1261/rna.079849.123

Bohmann, Dirk, O’Connell, Mary, Frendewey, David, Gerber, André, Hernandez, Nouria, Krämer, Angela, Minvielle-Sebastia, Lionel, Shaw, Peter, Wahle, Elmar, & Zavolan, Mihaela. (2023). Walter Keller (1938-2023): a tribute from his mentees. RNA, 29(9), v–xiii. https://doi.org/10.1261/rna.079742.123

de Smalen, Laura M., Börsch, Anastasiya, Leuchtmann, Aurel B., Gill, Jonathan F., Ritz, Danilo, Zavolan, Mihaela, & Handschin, Christoph. (2023). Impaired age-associated mitochondrial translation is mitigated by exercise and PGC-1α. Proceedings of the National Academy of Sciences (PNAS), 120(36), e2302360120. https://doi.org/10.1073/pnas.2302360120

Katsantoni, Maria, van Nimwegen, Erik, & Zavolan, Mihaela. (2023). Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biology, 24(1), 77. https://doi.org/10.1186/s13059-023-02913-0

Moon, Youngbin, Burri, Dominik, & Zavolan, Mihaela. (2023). Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR genomics and bioinformatics, 5(3), lqad079. https://doi.org/10.1093/nargab/lqad079

Seyres, Denis, Gorka, Oliver, Schmidt, Ralf, Marone, Romina, Zavolan, Mihaela, & Jeker, Lukas T. (2023). T helper cells exhibit a dynamic and reversible 3’UTR landscape [Posted-content]. Rna, 4(30), 418. https://doi.org/10.1261/rna.079897.123

Katsantoni, Maria, van Nimwegen, Erik, & Zavolan, Mihaela. (2022). Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs [Posted-content]. bioRxiv. https://doi.org/10.1101/2022.07.06.498949

Breda, Jeremie, Banerjee, Arka, Jayachandran, Rajesh, Pieters, Jean, & Zavolan, Mihaela. (2022). A novel approach to single cell analysis to reveal intrinsic differences in immune marker expression in unstimulated macrophages from BALB/c and C57BL/6 mouse strains [Posted-content]. bioRxiv. https://doi.org/10.1101/2022.05.29.493868

Ham DJ, Börsch A, Chojnowska K, Lin S, Leuchtmann AB, Ham AS, Thürkauf M, Delezie J, Furrer R, Burri D, Sinnreich M, Handschin C, Tintignac LA, Zavolan M, Mittal N, & Rüegg MA. (2022). Author Correction: Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. (Patent No. 1). 13(1), Article 1. https://doi.org/10.1038/s41467-022-30189-8

Bak, Maciej, van Nimwegen, Erik, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2022). Frequent co-regulation of splicing and polyadenylation by RNA-binding proteins inferred with MAPP [Posted-content]. bioRxiv. https://doi.org/10.1101/2022.01.09.475576

Breda, Jeremie, Banerjee, Arka, Jayachandran, Rajesh, Pieters, Jean, & Zavolan, Mihaela. (2022). A novel approach to single-cell analysis reveals intrinsic differences in immune marker expression in unstimulated BALB/c and C57BL/6 macrophages. FEBS Letters, 596(20), 2630–2643. https://doi.org/10.1002/1873-3468.14478

Ghosh, Souvik, Ataman, Meric, Bak, Maciej, Börsch, Anastasiya, Schmidt, Alexander, Buczak, Katarzyna, Martin, Georges, Dimitriades, Beatrice, Herrmann, Christina J., Kanitz, Alexander, & Zavolan, Mihaela. (2022). CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Research, 50(6), 3096–3114. https://doi.org/10.1093/nar/gkac114

Ham, Daniel J., Börsch, Anastasiya, Chojnowska, Kathrin, Lin, Shuo, Leuchtmann, Aurel B., Ham, Alexander S., Thürkauf, Marco, Delezie, Julien, Furrer, Regula, Burri, Dominik, Sinnreich, Michael, Handschin, Christoph, Tintignac, Lionel A., Zavolan, Mihaela, Mittal, Nitish, & Rüegg, Markus A. (2022). Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. Nature Communications, 13(1), 2025. https://doi.org/10.1038/s41467-022-29714-6

Kaiser, Marco S., Milan, Giulia, Ham, Daniel J., Lin, Shuo, Oliveri, Filippo, Chojnowska, Kathrin, Tintignac, Lionel A., Mittal, Nitish, Zimmerli, Christian E., Glass, David J., Zavolan, Mihaela, & Rüegg, Markus A. (2022). Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis. Communications Biology, 5(1), 1141. https://doi.org/10.1038/s42003-022-04097-y

Pignatti, Emanuele, Altinkilic, Emre Murat, Bräutigam, Konstantin, Grössl, Michael, Perren, Aurel, Zavolan, Mihaela, & Flück, Christa E. (2022). Cholesterol deprivation drives DHEA biosynthesis in human adrenals. Endocrinology, 163(7), bqac076. https://doi.org/10.1210/endocr/bqac076

Streese, Lukas, Demougin, Philippe, Iborra, Paula, Kanitz, Alexander, Deiseroth, Arne, Kröpfl, Julia M., Schmidt-Trucksäss, Arno, Zavolan, Mihaela, & Hanssen, Henner. (2022). Untargeted sequencing of circulating microRNAs in a healthy and diseased older population. Scientific Reports, 12(1), 2991. https://doi.org/10.1038/s41598-022-06956-4

Hafner, Markus, Katsantoni, Maria, Köster, Tino, Marks, James, Mukherjee, Joyita, Staiger, Dorothee, Ule, Jernej, & Zavolan, Mihaela. (2021). CLIP and complementary methods. Nature Reviews Methods Primers, 1(1). https://doi.org/10.1038/s43586-021-00018-1

Katsantoni, Maria, Gypas, Foivos, Herrmann, Christina J., Burri, Dominik, Bak, Maciej, Iborra, Paula, Agarwal, Krish, Ataman, Meric, Börsch, Anastasiya, Zavolan, Mihaela, & Kanitz, Alexander. (2021). ZARP: An automated workflow for processing of RNA-seq data [Posted-content]. bioRxiv. https://doi.org/10.1101/2021.11.18.469017

Burri, Dominik, & Zavolan, Mihaela. (2021). Shortening of 3’ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism [Posted-content]. bioRxiv. https://doi.org/10.1101/2021.06.30.450496

Karousis, Evangelos D., Gypas, Foivos, Zavolan, Mihaela, & Mühlemann, Oliver. (2021). Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells [Posted-content]. bioRxiv. https://doi.org/10.1101/2021.04.30.442116

Börsch, Anastasiya, Ham, Daniel J., Mittal, Nitish, Tintignac, Lionel A., Migliavacca, Eugenia, Feige, Jérôme N., Rüegg, Markus A., & Zavolan, Mihaela. (2021). Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Communications Biology, 4(1), 194. https://doi.org/10.1038/s42003-021-01723-z

Börsch, Anastasiya, & Zavolan, Mihaela. (2021). Transcription factor motif activity as a biomarker of muscle aging. American journal of aging science and research, 2(1), 19–23.

Breda, Jérémie, Zavolan, Mihaela, & van Nimwegen, Erik. (2021). Bayesian inference of gene expression states from single-cell RNA-seq data. Nature Biotechnology, 39(8), 1008–1016. https://doi.org/10.1038/s41587-021-00875-x

Burri, Dominik, & Zavolan, Mihaela. (2021). Shortening of 3p UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA (New York, N.Y.), 27(12), 1459–1470. https://doi.org/10.1261/rna.078886.121

Cléry, Antoine, Krepl, Miroslav, Nguyen, Cristina K. X., Moursy, Ahmed, Jorjani, Hadi, Katsantoni, Maria, Okoniewski, Michal, Mittal, Nitish, Zavolan, Mihaela, Sponer, Jiri, & Allain, Frédéric H.-T. (2021). Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing. Nature Communications, 12(1), 428. https://doi.org/10.1038/s41467-020-20481-w

Coto-Llerena, Mairene, Tosti, Nadia, Taha-Mehlitz, Stephanie, Kancherla, Venkatesh, Paradiso, Viola, Gallon, John, Bianco, Gaia, Garofoli, Andrea, Ghosh, Souvik, Tang, Fengyuan, Ercan, Caner, Christofori, Gerhard M., Matter, Matthias S., Droeser, Raoul A., Zavolan, Mihaela, Soysal, Savas D., von Flüe, Markus, Kollmar, Otto, Terracciano, Luigi M., et al. (2021). Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members. Hepatology Communications, 5(4), 661–674. https://doi.org/10.1002/hep4.1656

Ghosh, Souvik, Börsch, Anastasiya, Ghosh, Shreemoyee, & Zavolan, Mihaela. (2021). The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics, 22(1), 238. https://doi.org/10.1186/s12864-021-07532-2

Ham, Daniel J., Börsch, Anastasyia, Chojnowska, Kathrin, Lin, Shuo, Leuchtmann, Aurel B., Ham, Alexander S., Thürkauf, Marco, Delezie, Julien, Furrer, Regula, Burri, Dominik, Sinnreich, Michael, Handschin, Christoph, Tintignac, Lionel A., Zavolan, Mihaela, Mittal, Nitish, & Rüegg, Markus A. (2021). Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. bioRxiv. https://doi.org/10.1101/2021.05.28.446097

Karousis, Evangelos D., Gypas, Foivos, Zavolan, Mihaela, & Mühlemann, Oliver. (2021). Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. Genome Biology, 22(1), 223. https://doi.org/10.1186/s13059-021-02439-3

Ghosh, Souvik, Börsch, Anastasiya, & Zavolan, Mihaela. (2020). The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins [Posted-content]. bioRxiv. https://doi.org/10.1101/2020.07.18.191395

Ghosh, Souvik, Guimaraes, Joao C., Lanzafame, Manuela, Schmidt, Alexander, Syed, Afzal Pasha, Dimitriades, Beatrice, Börsch, Anastasiya, Ghosh, Shreemoyee, Mittal, Nitish, Montavon, Thomas, Correia, Ana Luisa, Danner, Johannes, Meister, Gunter, Terracciano, Luigi M., Pfeffer, Sébastien, Piscuoglio, Salvatore, & Zavolan, Mihaela. (2020). Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. The EMBO Journal, 39(18), e103922. https://doi.org/10.15252/embj.2019103922

Gruber, Andreas J., & Zavolan, Mihaela. (2020). Reply to ‘A different perspective on alternative cleavage and polyadenylation’. Nature Reviews. Genetics, 21(1), 63–64. https://doi.org/10.1038/s41576-019-0199-y

Guimaraes, Joao C., Mittal, Nitish, Gnann, Alexandra, Jedlinski, Dominik, Riba, Andrea, Buczak, Katarzyna, Schmidt, Alexander, & Zavolan, Mihaela. (2020). A rare codon-based translational program of cell proliferation. Genome Biology, 21(1), 44. https://doi.org/10.1186/s13059-020-1943-5

Ham, Daniel J., Börsch, Anastasiya, Lin, Shuo, Thürkauf, Marco, Weihrauch, Martin, Reinhard, Judith R., Delezie, Julien, Battilana, Fabienne, Wang, Xueyong, Kaiser, Marco S., Guridi, Maitea, Sinnreich, Michael, Rich, Mark M., Mittal, Nitish, Tintignac, Lionel A., Handschin, Christoph, Zavolan, Mihaela, & Rüegg, Markus A. (2020). The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. Nature Communications, 11(1), 4510. https://doi.org/10.1038/s41467-020-18140-1

Hasler, Daniele, Meduri, Rajyalakshmi, Bąk, Maciej, Lehmann, Gerhard, Heizinger, Leonhard, Wang, Xin, Li, Zhi-Tong, Sement, François M., Bruckmann, Astrid, Dock-Bregeon, Anne-Catherine, Merkl, Rainer, Kalb, Reinhard, Grauer, Eva, Kunstmann, Erdmute, Zavolan, Mihaela, Liu, Mo-Fang, Fischer, Utz, & Meister, Gunter. (2020). The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Molecular Cell, 77(5), 1014–1031. https://doi.org/10.1016/j.molcel.2020.01.001

Ho-Xuan, Hung, Lehmann, Gerhard, Glazar, Petar, Gypas, Foivos, Eichner, Norbert, Heizler, Kevin, Schlitt, Hans Jürgen, Zavolan, Mihaela, Rajewsky, Nikolaus, Meister, Gunter, & Hackl, Christina. (2020). Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy. Cancers, 13(1), 49. https://doi.org/10.3390/cancers13010049

Jutzi, Daniel, Campagne, Sébastien, Schmidt, Ralf, Reber, Stefan, Mechtersheimer, Jonas, Gypas, Foivos, Schweingruber, Christoph, Colombo, Martino, von Schroetter, Christine, Loughlin, Fionna E., Devoy, Anny, Hedlund, Eva, Zavolan, Mihaela, Allain, Frédéric H.-T., & Ruepp, Marc-David. (2020). Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis. Nature Communications, 11(1), 6341. https://doi.org/10.1038/s41467-020-20191-3

Liko, Dritan, Rzepiela, Andrzej, Vukojevic, Vanja, Zavolan, Mihaela, & Hall, Michael N. (2020). Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs. Proceedings of the National Academy of Sciences, 117(3), 1524–1532. https://doi.org/10.1073/pnas.1918931117

Breda, Jérémie, Zavolan, Mihaela, & van Nimwegen, Erik. (2019). Bayesian inference of the gene expression states of single cells from scRNA-seq data [Posted-content]. bioRxiv. https://doi.org/10.1101/2019.12.28.889956

Ghosh, Souvik, Guimaraes, Joao C, Lanzafame, Manuela, Schmidt, Alexander, Syed, Afzal Pasha, Dimitriades, Beatrice, Börsch, Anastasiya, Ghosh, Shreemoyee, Correia, Ana Luisa, Danner, Johannes, Meister, Gunter, Terracciano, Luigi M., Piscuoglio, Salvatore, & Zavolan, Mihaela. (2019). AGO1x prevents dsRNA-induced interferon signaling to promote breast cancer cell proliferation [Posted-content]. bioRxiv. https://doi.org/10.1101/603506

Gruber, Andreas J., & Zavolan, Mihaela. (2019). Alternative cleavage and polyadenylation in health and disease. Nature Reviews. Genetics, 20(10), 599–614. https://doi.org/10.1038/s41576-019-0145-z

Herrmann, Christina J., Schmidt, Ralf, Kanitz, Alexander, Artimo, Panu, Gruber, Andreas J., & Zavolan, Mihaela. (2019). PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing. Nucleic Acids Research, 48(D1), D174–D179. https://doi.org/10.1093/nar/gkz918

Kanitz, Alexander, Syed, Afzal Pasha, Kaji, Keisuke, & Zavolan, Mihaela. (2019). Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics, 20(1), 100. https://doi.org/10.1186/s12864-019-5438-2

Păunescu, Virgil, Zavolan, Mihaela, & Oprea, Tudor. (2019). In memoriam: Francisc Schneider (1933-2017). Journal of Cellular and Molecular Medicine, 23(4), 3045–3046. https://doi.org/10.1111/jcmm.14173

Riba, Andrea, Di Nanni, Noemi, Mittal, Nitish, Arhné, Erik, Schmidt, Alexander, & Zavolan, Mihaela. (2019). Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proceedings of the National Academy of Sciences, 116(30), 15023–15032. https://doi.org/10.1073/pnas.1817299116

Sendoel, Ataman, Subasic, Deni, Ducoli, Luca, Keller, Martin, Michel, Erich, Kohler, Ines, Singh, Kapil Dev, Zheng, Xue, Brümmer, Anneke, Imig, Jochen, Kishore, Shivendra, Wu, Yibo, Kanitz, Alexander, Kaech, Andres, Mittal, Nitish, Matia-González, Ana M., Gerber, André P., Zavolan, Mihaela, Aebersold, Ruedi, et al. (2019). MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death & Differentiation Subscription, 26(10), 2157–2178. https://doi.org/10.1038/s41418-019-0291-z

Riba, Andrea, Nanni, Noemi Di, Mittal, Nitish, Arhné, Erik, Schmidt, Alexander, & Zavolan, Mihaela. (2018). Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates [Posted-content]. bioRxiv. https://doi.org/10.1101/465914

Essig, Katharina, Kronbeck, Nina, Guimaraes, Joao C., Lohs, Claudia, Schlundt, Andreas, Hoffmann, Anne, Behrens, Gesine, Brenner, Sven, Kowalska, Joanna, Lopez-Rodriguez, Cristina, Jemielity, Jacek, Holtmann, Helmut, Reiche, Kristin, Hackermüller, Jörg, Sattler, Michael, Zavolan, Mihaela, & Heissmeyer, Vigo. (2018). Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation. Nature Communications, 9(1), 3810. https://doi.org/10.1038/s41467-018-06184-3

Gruber, Andreas J., Gypas, Foivos, Riba, Andrea, Schmidt, Ralf, & Zavolan, Mihaela. (2018). Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. Nature Methods, 15(10), 832–836. https://doi.org/10.1038/s41592-018-0114-z

Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, & Zavolan, Mihaela. (2018). Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC. Genome Biology, 19(1), 44. https://doi.org/10.1186/s13059-018-1415-3

Riba, Andrea, Osella, Matteo, Caselle, Michele, & Zavolan, Mihaela. (2018). Biophysical Analysis of miRNA-Dependent Gene Regulation. In RNA Technologies (pp. 257–273). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-319-92967-5_13

Rzepiela, Andrzej J., Ghosh, Souvik, Breda, Jeremie, Vina-Vilaseca, Arnau, Syed, Afzal P., Gruber, Andreas J., Eschbach, Katja, Beisel, Christian, van Nimwegen, Erik, & Zavolan, Mihaela. (2018). Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Molecular Systems Biology, 14(8), e8266. https://doi.org/10.15252/msb.20188266

Schaefer, T., Candido, S., Mittal, N., Wang, H., Bock, T., Schmidt, A., Tata, N. R., Zmajkovic, J., Bassler, J., Kunze, R., Hurt, E., Zaehres, H., Zavolan, M., & Lengerke, C. (2018). Unexpected roles of the stem cell factor SOX2 in protein translation in cancer cells [Abstract]. Jahrestagung der Deutschen, Österreichischen und Schweizerischen Gesellschaften für Hämatologie und Medizinische Onkologie, 236. https://doi.org/10.1159/000492737

Zavolan, Mihaela, & Gerber, André P. (2018). Mirroring the multifaceted role of RNA and its partners in gene expression. FEBS Letters, 592(17), 2825–2827. https://doi.org/10.1002/1873-3468.13230

Zavolan, Mihaela, & Kanitz, Alexander. (2018). RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Current Opinion in Cell Biology, 52, 8–13. https://doi.org/10.1016/j.ceb.2017.12.002

Pachkov, Mikhail, Balwierz, Piotr J, Arnold, Phil, Gruber, Andreas J, Zavolan, Mihaela, & van Nimwegen, Erik. (2017). ISMARA: Completely automated inference of gene regulatory networks from high-throughput data [Posted-content]. PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.3328v1

Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, & Zavolan, Mihaela. (2017). Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC [Posted-content]. bioRxiv. https://doi.org/10.1101/195958

Dimitrova, Yoana, Gruber, Andreas J., Mittal, Nitish, Ghosh, Souvik, Dimitriades, Beatrice, Mathow, Daniel, Grandy, William Aaron, Christofori, Gerhard, & Zavolan, Mihaela. (2017). TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biology Direct, 12(1), 8. https://doi.org/10.1186/s13062-017-0180-7

Essig, Katharina, Hu, Desheng, Guimaraes, Joao C., Alterauge, Dominik, Edelmann, Stephanie, Raj, Timsse, Kranich, Jan, Behrens, Gesine, Heiseke, Alexander, Floess, Stefan, Klein, Juliane, Maiser, Andreas, Marschall, Susan, Hrabĕ de Angelis, Martin, Leonhardt, Heinrich, Calkhoven, Cornelis F., Noessner, Elfriede, Brocker, Thomas, Huehn, Jochen, et al. (2017). Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells. Immunity, 47(6), 1067–1082. https://doi.org/10.1016/j.immuni.2017.11.008

Gumienny, Rafal, Jedlinski, Dominik J., Schmidt, Alexander, Gypas, Foivos, Martin, Georges, Vina-Vilaseca, Arnau, & Zavolan, Mihaela. (2017). High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Research, 45(5), 2341–2353. https://doi.org/10.1093/nar/gkw1321

Martin, Georges, Schmidt, Ralf, Gruber, Andreas J., Ghosh, Souvik, Keller, Walter, & Zavolan, Mihaela. (2017). 3′ End Sequencing Library Preparation with A-seq2. Journal of Visualized Experiments, 128, e56129. https://doi.org/10.3791/56129

Mittal, Nitish, Guimaraes, Joao C., Gross, Thomas, Schmidt, Alexander, Vina-Vilaseca, Arnau, Nedialkova, Danny D., Aeschimann, Florian, Leidel, Sebastian A., Spang, Anne, & Zavolan, Mihaela. (2017). The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature Communications, 8(457), 1–12. https://doi.org/10.1038/s41467-017-00539-y

Omidi, Saeed, Zavolan, Mihaela, Pachkov, Mikhail, Breda, Jeremie, Berger, Severin, & van Nimwegen, Erik. (2017). Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13(7), e1005176. https://doi.org/10.1371/journal.pcbi.1005176

Riba, Andrea, Emmenlauer, Mario, Chen, Amy, Sigoillot, Frederic, Cong, Feng, Dehio, Christoph, Jenkins, Jeremy, & Zavolan, Mihaela. (2017). Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell Systems, 4(2), 182–193. https://doi.org/10.1016/j.cels.2017.01.011

Zavolan, Mihaela, & Graveley, Brenton R. (2017). RNAs: dynamic and mutable. Genome Biology, 18(1), 226. https://doi.org/10.1186/s13059-017-1361-5

Omidi, Saeed, Zavolan, Mihaela, Pachkov, Mikhail, Breda, Jeremie, Berger, Severin, & Nimwegen, Erik van. (2016). Automated Incorporation of Pairwise Dependency in Transcription Factor Binding Site Prediction Using Dinucleotide Weight Tensors [Posted-content]. bioRxiv. https://doi.org/10.1101/078212

Gumienny, Rafal, Jedlinski, Dominik, Martin, Georges, Vina-Villaseca, Arnau, & Zavolan, Mihaela. (2016). High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. [Posted-content]. bioRxiv. https://doi.org/10.1101/037259

Gruber, Andreas J., Schmidt, Ralf, Gruber, Andreas R., Martin, Georges, Ghosh, Souvik, Belmadani, Manuel, Keller, Walter, & Zavolan, Mihaela. (2016). A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome Research, 26(8), 1145–1159. https://doi.org/10.1101/gr.202432.115

Guimaraes, Joao C., & Zavolan, Mihaela. (2016). Patterns of ribosomal protein expression specify normal and malignant human cells. Genome Biology, 17(1), 236. https://doi.org/10.1186/s13059-016-1104-z

Janowski, Robert, Heinz, Gitta A, Schlundt, Andreas, Wommelsdorf, Nina, Brenner, Sven, Gruber, Andreas R, Blank, Michael, Buch, Thorsten, Buhmann, Raymund, Zavolan, Mihaela, Niessing, Dierk, Heissmeyer, Vigo, & Sattler, Michael. (2016). Roquin recognizes a non-canonical hexaloop structure in the 3′-UTR of Ox40. Nature Communications, 7, 11032. https://doi.org/10.1038/ncomms11032

Jorjani, Hadi, Kehr, Stephanie, Jedlinski, Dominik J., Gumienny, Rafal, Hertel, Jana, Stadler, Peter F., Zavolan, Mihaela, & Gruber, Andreas R. (2016). An updated human snoRNAome. Nucleic Acids Research, 44(11), 5068–5082. https://doi.org/10.1093/nar/gkw386

Martin, Georges, & Zavolan, Mihaela. (2016). Redesigning CLIP for efficiency, accuracy and speed. Nature Methods, 13(6), 3–482. https://doi.org/10.1038/nmeth.3870

Ustianenko, Dmytro, Pasulka, Josef, Feketova, Zuzana, Bednarik, Lukas, Zigackova, Dagmar, Fortova, Andrea, Zavolan, Mihaela, & Vanacova, Stepanka. (2016). TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs. The EMBO Journal, 35(20), 2179–2191. https://doi.org/10.15252/embj.201694857

Rzepiela, Andrzej Jerzy, Vina-Vilaseca, Arnau, Breda, Jeremie, Ghosh, Souvik, Syed, Afzal P, Gruber, Andreas J, Grandy, William A, Eschbach, Katja, Beisel, Christian, van Nimwegen, Erik, & Zavolan, Mihaela. (2015). Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets [Posted-content]. bioRxiv. https://doi.org/10.1101/035097

Mittal, Nitish, Kunz, Christophe, Gypas, Foivos, Kishore, Shivendra, Martin, Georges, Wenzel, Friedel, Nimwegen, Erik van, Schaer, Primo, & Zavolan, Mihaela. (2015). Ewing sarcoma breakpoint region 1 prevents transcription-associated genome instability [Posted-content]. bioRxiv. https://doi.org/10.1101/034215

Gruber, Andreas J, Schmidt, Ralf, Gruber, Andreas R, Martin, Georges, Ghosh, Souvik, Belmadani, Manuel, Keller, Walter, & Zavolan, Mihaela. (2015). A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation [Posted-content]. bioRxiv. https://doi.org/10.1101/033001

Breda, Jeremie, Rzepiela, Andrzej J, Gumienny, Rafal, van Nimwegen, Erik, & Zavolan, Mihaela. (2015). Quantifying the strength of miRNA-target interactions. Methods, 85, 9–90. https://doi.org/10.1016/j.ymeth.2015.04.012

Gumienny, Rafal, & Zavolan, Mihaela. (2015). Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Research, 43(3), 91–1380. https://doi.org/10.1093/nar/gkv050

Gumienny, Rafal, & Zavolan, Mihaela. (2015). Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. (erratum) [Review of Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. (erratum)]. Nucleic Acids Research, 43, Article 18. https://doi.org/10.1093/nar/gkv924

Imig, Jochen, Brunschweiger, Andreas, Brümmer, Anneke, Guennewig, Boris, Mittal, Nitish, Kishore, Shivendra, Tsikrika, Panagiota, Gerber, André P, Zavolan, Mihaela, & Hall, Jonathan. (2015). miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nature Chemical Biology, 11(2), 14–107. https://doi.org/10.1038/nchembio.1713

Kanitz, Alexander, Gypas, Foivos, Gruber, Andreas J, Gruber, Andreas R, Martin, Georges, & Zavolan, Mihaela. (2015). Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biology, 16, 150. https://doi.org/10.1186/s13059-015-0702-5

Subasic, Deni, Brümmer, Anneke, Wu, Yibo, Pinto, Sérgio Morgado, Imig, Jochen, Keller, Martin, Jovanovic, Marko, Lightfoot, Helen Louise, Nasso, Sara, Goetze, Sandra, Brunner, Erich, Hall, Jonathan, Aebersold, Ruedi, Zavolan, Mihaela, & Hengartner, Michael O. (2015). Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome Research, 25(11), 91–1680. https://doi.org/10.1101/gr.183160.114

Tattikota, Sudhir G, Rathjen, Thomas, Hausser, Jean, Khedkar, Aditya, Kabra, Uma D, Pandey, Varun, Sury, Matthias, Wessels, Hans-Hermann, Mollet, Inês G, Eliasson, Lena, Selbach, Matthias, Zinzen, Robert P, Zavolan, Mihaela, Kadener, Sebastian, Tschöp, Matthias H, Jastroch, Martin, Friedländer, Marc R, & Poy, Matthew N. (2015). miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism. Journal of Biological Chemistry, 290(33), 94–20284. https://doi.org/10.1074/jbc.m115.658625

Zavolan, Mihaela. (2015). Inferring gene expression regulatory networks from high-throughput measurements [Review of Inferring gene expression regulatory networks from high-throughput measurements]. Methods, 85, 1–2. https://doi.org/10.1016/j.ymeth.2015.07.006