Publications

Giusti S., Pino N., Pannunzio C., Ogando M., Armando N., Garrett A., Zimprich A., Becker L., Gimeno M., Lukin J., Merino F., Pardi1B., Pedroncini O., Di Mauro G., Gailus Durner V., Fuchs H., Hrabe de Angelis M., Patop I., Turck C., Deussing J., Vogt Weisenhorn D., Jahn O., Kadener S., Hölter S., Brose N., Giesert F., Wurst W., Marin-Burgin A. and Refojo D. “A brain-enriched circular RNA controls excitatory neurotransmission and restricts sensitivity to aversive stimuli”. Science Advances, in press (2024). [Link]

Patop I., Canori M. and S Kadener. “In Vivo Tissue-Specific Knockdown of circRNAs Using shRNAs in Drosophila melanogaster” Circular RNAs (2024), 161- 172. [Link]

Schmal C., Maier B., Ashwal-Fluss R., Bartok O., Finger A., Bange T., Koutsouli S., Robles M., Kadener S., Herzel H and Kramer A. “Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock”. PLoS biology 21 (6), e3002164 [Link]

Patop I, Anduaga A., Bussi I., Ceriani M. and Kadener S. “Organismal landscape of clock cells and circadian gene expression in Drosophila”. [Link]

Torres-Méndez, A., Pop, S., Bonnal, S., Almudi, I., Avola, A., Roberts, R. J. V., … Others. (2022). Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals. Science Advances. [Link]

Zaffagni, M., Harris, J. M., Patop, I. L., Pamudurti, N. R., Nguyen, S., & Kadener, S. (2022). SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. eLife. [Link]

Herman, N., Kadener, S., & Shifman, S. (2022) The chromatin factor ROW cooperates with BEAF-32 in regulating long-range inducible genes , EMBO Reports. [Link]

Pamudurti, Nagarjuna Reddy, Patop, I. L., Krishnamoorthy, A., Bartok, O., Maya, R., Lerner, N., … Kadener, S. (2022). circMbl functions in cis and in trans to
regulate gene expression and physiology in a tissue-specific fashion. Cell Reports. [Link]

Rigal, J., Anduaga, A. M., Bitman, E., Rivellese, E., Kadener, S., & Marr, M. T. (2022). Artificially stimulating retrotransposon activity increases mortality and accelerates a subset of aging phenotypes in Drosophila. eLife. [Link]

Litovchenko, M., Meireles-Filho, A. C. A., Frochaux, M. V., Bevers, R. P. J., Prunotto, A., Anduaga, A. M., … Others. (2021). Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. Science Advances. [Link]

Krishnamoorthy, A., & Kadener, S. (2021). Using Drosophila to uncover molecular and physiological functions of circRNAs. Methods.[Link]

Rabin, A., Zaffagni, M., Ashwal-Fluss, R., Patop, I. L., Jajoo, A., Shenzis, S., … Kadener, S. (2021). SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Genome Biology. [Link]

Schmal, C., Maier, B., Ashwal-Fluss, R., Bartok, O., Finger, A.-M., Bange, T., … Others. (2021). An integrative omics approach reveals posttranscriptional mechanisms underlying circadian temperature compensation. bioRxiv, 2021–2010.

Hanan M., Simchovitz A., Yayon N.,Vaknine S., Cohen‐Fultheim R., Karmon M., Madrer N., Rohrlich T., Maman M., Bennett E., Greenberg D., Meshorer E., Levanon E., Soreq H. and Kadener S. “A Parkinson's disease CircRNAs Resource reveals a link between circ SLC 8A1 and oxidative stress”. EMBO Mol Medicine 12 (2020).

Pamudurti N., Patop I., Krishnamoorthy A., Ashwal-Fluss R., Bartok O., Kadener S. “An in vivo strategy for knockdown of circular RNAs”. Cell Discovery 6 (2020).

Chen T., Tallo-Parra M., Cao Q., Kadener S., Böttcher R., Pérez-Vilaró G., Boonchuen P., Somboonwiwat K., Díez J., Sarnow P. “Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells”. PLoS Pathogens 16 (2020).

Simchovitz A., Hanan M., Yayon N., Lee S., Bennett E., Greenberg D., Kadener S., Soreq H. “A lncRNA survey finds increases in neuroprotective LINC‐PINT in Parkinson’s disease substantia nigra”. Aging Cell, e13115 (2020).

 Viswanatha R., Zaffagni M., Zirin J., Perrimon N.*, Kadener S.* “CRISPR-Cas13 mediated Knock Down in Drosophila cultured cells.”, bioRxiv (2020).

Foley L., Ling J., Joshi R., Evantal N., S Kadener S., Emery P “Drosophila PSI controls circadian period and the phase of circadian behavior under temperature cycle via tim splicing”. eLife 8 (2019).

Anduaga A. * , Evantal N. * , Patop I., Bartok O., Weiss R., Kadener S. “Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila”. eLife 8 (2019).

Simchovitz A., Hanan M., Niederhoffer N., Madrer N., Yayon N., Bennett E., Greenberg D., Kadener S. and Soreq H. “NEAT1 is overexpressed in Parkinson’s disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress”. FASEB Journal 33 (2019).

Patop I., Wust S. and Kadener S. “Past, present and future of circRNAs”. Review. EMBO J. 38 (2019).

 Zaffagni M. and Kadener S. “Craving for Introns”. Comment. Molecular Cell 73 (2019).

Zhu Z., Ortiz T., Mezan S., Kadener S. and Blau J. “Transcription of a plasticity gene is activated by neuronal hyperpolarization”. Preprint deposited in bioRxiv (2019).

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 (2018).

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”. Curr. Biol 28 (2018).

Patop I. and Kadener S. “circRNAs in Cancer”. Curr. Opin Genet Dev. 48 (2018).

 Hanan M., Soreq H. and Kadener S. “CircRNAs in the brain”. RNA Biology 14 (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 13 (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 Acid Research 45 (2017).

Levin-Klein R., Fraenkel S., Lichtenstein M., Matheson L., Bartok O., Nevo Y., Kadener S., Corcoran A., Cedar H., Bergman Y. “Clonally stable V K allelic choice instructs Ig K repertoire”. Nature Comm. 8: 15575 (2017).

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 (2017).

 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 7 (2016).

Mezan S., Feuz JD, Deplancke B. and Kadener S. “PDF signaling is an integral part of the Drosophila circadian molecular oscillator”. Cell Reports 17 (2016).

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 (2016).

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 (2016).

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 (2017).

 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 Sebastian Kadener, PhD 9 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).

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).

 Bartok O., Teesalu M., Pandey V., Hanan M., Poukkula M., Havula E., Moussaieff A., Vodala S., Nahmias Y., Kadener S.* and Hietakangas V.* “The transcription factor Cabut coordiantes energy metabolism and the circadian clock in response to sugar sensing”. * Corresponding authors. EMBO J. 34 (2015).

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).

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 (2015).

 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).

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).