Publications
2022
Zaffagni, Michela, Jenna M. Harris, Ines L. Patop, Nagarjuna Reddy Pamudurti, Sinead Nguyen, and Sebastian Kadener. "SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome." Elife 11 (2022): e71945. [Web]
Pamudurti, Nagarjuna Reddy, Ines Lucia Patop, Aishwarya Krishnamoorthy, Osnat Bartok, Roni Maya, Noam Lerner, Reut Ashwall-Fluss, Jacob Vinay Vikas Konakondla, Tsevi Beatus, and Sebastian Kadener. "circMbl functions in cis and in trans to regulate gene expression and physiology in a tissue-specific fashion." Cell Reports 39, no. 4 (2022): 110740. [Web]
Torres-Mendez, Antonio, Sinziana Pop, Sophie Bonnal, Isabel Almudi, Alida Avola, Ruairi JV Roberts, Chiara Paolantoni et al. "Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals." Science advances 8, no. 4 (2022): eabk0445. [Web]
Nielsen, Anne F., Albrecht Bindereif, Irene Bozzoni, Mor Hanan, Thomas B. Hansen, Manuel Irimia, Sebastian Kadener et al. "Best practice standards for circular RNA research." Nature Methods (2022): 1-13. [Web]
Herman, Neta, Sebastian Kadener, and Sagiv Shifman. "The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes." in Press EMBO Reports (2022). [Web]
Rigal, Joyce, Ane Martin Anduaga, Elena Bitman, Emma Rivellese, Sebastian Kadener, and Michael T. Marr. "Artificially stimulating retrotransposon activity increases mortality and accelerates a subset of aging phenotypes in Drosophila." bioRxiv (2022). Elife 11 (2022): eLife.80169 [Web]
2021
Avigayel Rabin,Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel, Sebastian Kadener "SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Genome Biol 22, 277 (2021). https://doi.org/10.1186/s13059-021-02497-7 [Web]
Neta Herman, Sebastian Kadener, Sagiv Shifman "The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes" bioRxiv 2021.03.08.434270; doi: https://doi.org/10.1101/2021.03.08.434270 [Web]
Michela Zaffagni, Jenna M Harris, Ines L Patop, Nagarjuna Reddy Pamudurti, Sinead Nguyen, Sebastian Kadener "SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome" bioRxiv 2021.07.02.450964; doi: https://doi.org/10.1101/2021.07.02.450964 [Web]
Antonio Torres-Méndez, Sinziana Pop, Sophie Bonnal, Isabel Almudi, Alida Avola, Ruairí J V Roberts, Chiara Paolantoni, Ana Alcaina, Ane Martín-Anduaga, Irmgard U Haussmann, Violeta Morin, Fernando Casares, Matthias Soller, Sebastian Kadener, Jean-Yves Roignant, Lucia Prieto-Godino, Manuel Irimia "Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals" bioRxiv 2021.02.24.432780; doi: https://doi.org/10.1101/2021.02.24.432780 [Web]
Aishwarya Krishnamoorthy and Sebastian Kadener "Using Drosophila to uncover molecular and physiological functions of circRNAs", Methods. 2021 Apr 24;S1046-2023(21)00108-0. doi: 10.1016/j.ymeth.2021.04.016 [Web]
Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. "Extensive tissue-specific expression variation and novel regulators underlying circadian behavior", Sci Adv. 2021 Jan 29;7(5):eabc3781. doi: 10.1126/sciadv.abc3781. Print 2021 Jan. [Web]
2020
Raghuvir Viswanatha, Michela Zaffagni, Jonathan Zirin, Norbert Perrimon, Sebastian Kadener "CRISPR-Cas13 mediated Knock Down in Drosophila cultured cells" bioRxiv 2020.11.01.364166; doi: https://doi.org/10.1101/2020.11.01.364166 [Web]
Tzu-Chun Chen, Marc Tallo-Parra, Qian M Cao, Sebastian Kadener, René Böttcher, Gemma Pérez-Vilaró, Pakpoom Boonchuen, Kunlaya Somboonwiwat, Juana Díez, Peter Sarnow. "Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells" PLoS pathogens e1008346 [Web]
Mor Hanan, Alon Simchovitz, Nadav Yayon, Shani Vaknine, Roni Cohen‐Fultheim, Miriam Karmon, Nimrod Madrer, Talia Miriam Rohrlich, Moria Maman, Estelle R Bennett, David S Greenberg, Eran Meshorer, Erez Y Levanon, Hermona Soreq, Sebastian Kadener. "A Parkinson's disease Circ RNAs Resource reveals a link between circ SLC8A1 and oxidative stress" EMBO Molecular Medicine e11942 [Web]
Alon Simchovitz, Mor Hanan, Nadav Yayon, Songhua Lee, Estelle R Bennett, David S Greenberg, Sebastian Kadener, Hermona Soreq. "A lncRNA survey finds increases in neuroprotective LINC‐PINT in Parkinson’s disease substantia nigra" Aging Cell e13115[Web]
Nagarjuna Reddy Pamudurti, Ines Lucia Patop, Aishwarya Krishnamoorthy, Reut Ashwal-Fluss, Osnat Bartok, Sebastian Kadener. "An in vivo strategy for knockdown of circular RNAs" bioRxiv [Web]
2019
Michela Zaffagni, Sebastian Kadener. "Craving for Introns" Mol Cell 73(6) 1095-1096(2019) [Web]
Patop IL, Wüst S, Kadener S. "Past, present, and future of circRNAs" EMBO J. 38(16) e100836(2019) [Web]
Martin Anduaga A, Evantal N, Patop IL, Bartok O, Weiss R, Kadener S. "Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila" Elife. 8 e44642(2019) [Web]
Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. "NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress" FASEB J. 33(10) 11223-11234(2019) [Web]
Foley LE, Ling J, Joshi R, Evantal N, Kadener S, Emery P. "Drosophila PSI controls circadian period and the phase of circadian behavior under temperature cycle via tim splicing" Elife. 8 e50063(2019) [Web]
Sebastian Kadener, Avigayel Rabin, Reut Ashwal-Fluss, Shlomo Shenzis, Daniela Apelblat "A comprehensive pipeline for accurate annotation and quantification of circRNAs" bioRxiv (2019) [Web]
2018
Naveh Evantal, Ane Martin Anduaga, Osnat Bartok, Ines Lucia Patop, Ron Weiss, Sebastian Kadener. "Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila" BioRxiv 503409 (2018) [Web]
Nagarjuna Reddy Pamudurti, Vinay Vikas Konakondla-Jacob, Aishwarya Krishnamoorthy, Reut Ashwal-Fluss, Osnat Bartok, Stas Wust, Katerina Seitz, Roni Maya, Noam Lerner, Ines Lucia Patop, Silvio Rizzoli, Tsevi Beautus, Sebastian Kadener. "An in vivo knockdown strategy reveals multiple functions for circMbl" BioRxiv 504282 (2018) [Web]
Wittenbrink N, Ananthasubramaniam B, Münch M, Koller B, Maier B, Weschke C, Bes F, de Zeeuw J, Nowozin C, Wahnschaffe A, Wisniewski S, Zaleska M, Bartok O, Ashwal-Fluss R, Lammert H, Herzel H, Hummel M, Kadener S, Kunz D, Kramer A. "High-accuracy determination of internal circadian time from a single blood sample" The Journal of Clinical Investigation, 128(9):3826-3839 (2018)[Web]
Chatterjee A, Lamaze A, De J, Mena W, Chélot E, Martin B, Hardin P, Kadener S, Emery P, Rouyer F. "Reconfiguration of a Multi-oscillator Network by Light in the Drosophila Circadian Clock" Current Biology, 28(13):2007-2017(2018)[Web]
Patop IL, Kadener S. “CircRNAs in Cancer” Current Opinion in Genetics & Development, 48:121-127 (2018) [Web]
2017
Buchumenski I, Bartok O, Ashwal-Fluss R, Pandey V, Porath HT, Levanon EY, Kadener S. “Dynamic hyper-editing underlies temperature adaptation in Drosophila.” Plos Genetics 10, 1371 (2017) [Web]
Levin-Klein R., Fraenkel S., Lichtenstein M., Matheson L., Bartok O., Nevo Y., Kadener S., Corcoran A., Cedar H., Bergman Y. “Clonally stable VK allelic choice instructs IgK repertoire”. Nature Comm. 8, 15575 (2017). [Web]
Pamudurti N., Bartok O., Jens O., Ashwal-Fluss R., Stottmeister C., Ruhe L., Hanan M., Wyler E., Perez-Hernandez D., Ramberger E., Shenzis S., Samson M., Dittmar G., Landthaler M., Chekulaeva M., Rajewsky N. and Kadener S. “Translation of circRNAs”. Molecular Cell 66(1), 9-21 (2017). [Web]
- Featured in Molecular Cell 66(1), 1-2 (2017)
- Feature in Science 355 (6332), 1363 (2017).
- Featured in Nature Reviews Genetics 18, 272-273 (2017).
- Featured in Cell Research 27, 724-725 (2017)
Afik S. 1, Bartok O. 1, Artyomov M., Shishkin A., Kadri S., Zhu X., Gutman M., Garber M.* and Kadener S.* “Defining the 5’ and 3’ landscape of the Drosophila transcriptome with ExoCAGE and RNaseH-seq”. Nucleic Acids Research 47(11): e95; 1-16 (2017). [Web]
2016
Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. “Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells”. Stem Cell Reports 8(7), 927-940 (2016). [Web]
Mezan S., Feuz JD, Deplancke B. and Kadener S. “PDF signaling is an integral part of the Drosophila circadian molecular oscillator”. Cell Reports 17(3), 708-719 (2016). [Web]
Hanan M., Soreq H. and Kadener S. “CircRNAs in the brain”. RNA Biology Nov28:1-7 (2016).[Web]
Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. “End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data”. Genome Research 26(10), 1397-1410 (2016).[Web]
Chikne V.*, Doniger T.*, Bartok O.*, Eliaz D.*, Cohen Chalamish S., Tschudi C., Unger R., Hashem Y., Kadener S. and Michaeli S. “Pseudouridylation in Trypanosoma brucei rRNA is developmentally regulated in positions critical for ribosome function”. Scientific Reports 6, 25296:1-13 (2016).[Web]
2015
Tattikota SG., Rathjen T., Hausser J., Khedkar A., Kabra UD., Pandey V., Sury M., Wessels HH., Mollet IG., Eliasson L., Selbach M., Zinzen RP., Zavolan M., Kadener S, Tschöp MH, Jastroch M, Friedländer MR., Poy MN. “miR-184 regulates pancreatic β-Cell function according to glucose metabolism”. J. Biol. Chem. 290 (2015).[Web]
Rybak-Wolf A., Stottmeister C., Glazar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Ohman M., Refojo D., Kadener S. and Rajewsky N. “Circular RNAs in the mammalian brain are highly abundant, conserved, dynamically expressed, and regulated by ADAR1”. Molecular Cell 58 (2015).[Web]
Bartok O., Teesalu M., Pandey V., Hanan M., Poukkula M., Havula E., Moussaieff A., Vodala S., Nahmias Y., Kadener S.* and Hietakangas V.* “Cabut-dependent repressive branch of the sugar sensing transcriptional network regulates glyceroneogenesis”. * Corresponding authors. EMBO J. 34 (2015).[Web]
Lerner I.*, Bartok O.*, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. “Clk post-transcriptional control denoises circadian transcription in time and space”. Nature Communications 6 (2015).[Web]
Stelzer Y., Bar S., Bartok O., Afik S., Ronen D., Kadener S.* and Benvenisty N.* “Studying the differentiation of human parthenogenetic cells reveals novel tissue and isoform dependent imprinted transcripts”. * Corresponding authors. Cell Reports 11(2):308 (2015).[Web]
2014
Ashwal-Fluss R., Meyer M., Pamudurti N.R., Ivanov A., Bartok O., Evantal N., Hanan M., Memczak S., Rajewsky N.* and Kadener S.* “CircRNA biogenesis and canonical splicing compete with each other” . Molecular Cell 55:172 (2014).[Web]
- Featured in Cell, 159(1), October 2014.
- Featured in Nature Review Genetics, November 2014.
- Selected for Faculty 1000.
Weiss R., Bartok O., Mezan S., Malka Y and Kadener S. “Synergistic Interactions between the Molecular and Neuronal Circadian Networks Drive Behavioral Circadian Rhythms in Drosophila melanogaster”. PloS Genetics 10:e1004252 (2014).[Web]
2013
Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. “Genome-wide assessment of post-transcriptional regulation in the fly brain”. Frontiers in Molecular Neuroscience 6:49 (2013).[Web]
Bartok O., Kyriacou C., Levine J., Sehgal A. and Kadener S. “Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs”. Proc R. Soc. B. 280:2013001 (2013).[Web]
Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. “A new in vivo model of pantothenate kinase-associated neurodegeneration reveals a surprising role for transcriptional regulation in PKAN pathogenesis”. Frontiers in Cell Neuroscience 7: 146 (2013).[Web]
Melamed Z., Levy A., Ashwal R., Lev-Maor G., Mekahel N., Atias N., Gilad S., Sharan R., Levy C., Kadener S* and Ast G*. “Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions”. * Corresponding authors. Mol. Cell 50:869 (2013).[Web]
2012
Belacortu Y., Weiss R., Kadener S. and Paricio N. “Transcriptional activity and nuclear localization of Cabut, the Drosophila ortholog of vertebrate TGF-β-inducible early-response gene (TIEG) proteins”. PLoS One 7(2):e32004 (2012).[Web]
2011
Belancortu Y., Weiss R., Kadener S. and Paricio N. “Expression of Drosophila cabut during early embryogenesis, dorsal closure and nervous system development”. Gene Expr Patterns 3-4: 190 (2011).[Web]
Bekenstein U. and Kadener S. “What can Drosophila teach us about iron-accumulation neurodegenerative disorders?” J. Neural Trans 118(3):389 (2011).[Web]
2010
Van der Linden A.M., Beverly M., Kadener S., Rodriguez J., Wasserman S., Rosbash M. and Sengupta P. “Genome-Wide Analysis of Light and Temperature-Entrained Circadian Transcripts in C. elegans”. PLoS Biology 8(10):e10000503 (2010).[Web]
2009
Fathallah-Shaykh H.M., Bona J.L. and Kadener S. “Mathematical Model of the Drosophila Circadian Clock: Loop Regulation and Transcriptional Integration”. Biophys J. 97(9): 2399 (2009). Cover article. Selected for Faculty of 1000 (Factor 8 Must read)[Web]
Kadener S., Menet J., Sugino K., Horwich M.D., Weissbein U., Nawathean P., Vagin V., Zamore P., Nelson S. and Rosbash M. “A role for miRNAs in the Drosophila circadian clock”. Genes Dev. 23(8):2179 (2009).[Web]
Kadener S., Rodriguez J., Abruzzi K. and Rosbash M. “Genome-wide identification of targets of the drosha-pasha/DGCR8 complex”. RNA 15(4): 537 (2009). [Web]
2008
Kadener S., Schoer R., Menet J. and Rosbash M. “Circadian transcription contributes to core period determination in Drosophila”. PLOS Biology 6(5): 119 (2008). [Web]