Centre intégratif de génomique

Equipe principale | CIG Services communs | Groupe Benton | Groupe Fajas | Groupe Fankhauser | Groupe Franken | Groupe Gambetta | Groupe Gatfield | Groupe Larsch | Groupe Michalik | Groupe Reymond | Groupe Roignant | Groupe van Leeuwen | Groupe Vastenhouw | Groupe Vjestica | Plateforme de biostatistique | Plateforme Genomics Technologies Facility (GTF) | Plateforme Protein Analysis Facility (PAF)
Publications | Mémoires et thèses

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36 publications

2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 |
2023
 
ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging.
Snieckute G., Ryder L., Vind A.C., Wu Z., Arendrup F.S., Stoneley M., Chamois S., Martinez-Val A., Leleu M., Dreos R. et al., 2023/12/08. Science, 382 (6675) pp. eadf3208. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1A73F41B8085]
 
Molecular basis of translation termination at noncanonical stop codons in human mitochondria.
Saurer M., Leibundgut M., Nadimpalli H.P., Scaiola A., Schönhut T., Lee R.G., Siira S.J., Rackham O., Dreos R., Lenarčič T. et al., 2023/05/05. Science, 380 (6644) pp. 531-536. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C702F2EE694B]
A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway.
Katsioudi G., Dreos R., Arpa E.S., Gaspari S., Liechti A., Sato M., Gabriel C.H., Kramer A., Brown S.A., Gatfield D., 2023/01/13. Science advances, 9 (2) pp. eade2828. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AAE7ED64F36D]
2022
Ribosome stalling is a signal for metabolic regulation by the ribotoxic stress response.
Snieckute G., Genzor A.V., Vind A.C., Ryder L., Stoneley M., Chamois S., Dreos R., Nordgaard C., Sass F., Blasius M. et al., 2022/12/06. Cell metabolism, 34 (12) pp. 2036-2046.e8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7C7E5C26F023]
Global and precise identification of functional miRNA targets in mESCs by integrative analysis.
Schaefer M., Nabih A., Spies D., Hermes V., Bodak M., Wischnewski H., Stalder P., Ngondo R.P., Liechti L.A., Sajic T. et al., 2022/09/05. EMBO reports, 23 (9) pp. e54762. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C5B40F2C87CA]
A novel Smg6 mouse model reveals regulation of circadian period and daily CRY2 accumulation through the nonsense-mediated mRNA decay pathway
Katsioudi G., Dreos R., Arpa E.S., Gaspari S., Liechti A., Sato M., Gabriel C.H., Kramer A., Brown S.A., Gatfield D., 2022/07/03..
[URN][DOI][serval:BIB_0EAB52392E7A]
 
Recording of Diurnal Gene Expression in Peripheral Organs of Mice Using the RT-Biolumicorder
Katsioudi G., Osorio-Forero A., Sinturel F., Hagedorn C., Kreppel F., Schibler U., Gatfield D., 2022. pp. 217-242 dans Circadian Regulation, Springer US.
[URN][DOI][Pmid][serval:BIB_323DFF4D2B80]
2021
Circular RNA repertoires are associated with evolutionarily young transposable elements.
Gruhl F., Janich P., Kaessmann H., Gatfield D., 2021/09/20. eLife, 10 pp. e67991. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_81B4CC087DBB]
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome.
Bhatt P.R., Scaiola A., Loughran G., Leibundgut M., Kratzel A., Meurs R., Dreos R., O'Connor K.M., McMillan A., Bode J.W. et al., 2021/06/18. Science, 372 (6548) pp. 1306-1313. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AA30EA09AC1E]
2020
Transcriptome and translatome co-evolution in mammals.
Wang Z.Y., Leushkin E., Liechti A., Ovchinnikova S., Mößinger K., Brüning T., Rummel C., Grützner F., Cardoso-Moreira M., Janich P. et al., 2020/12. Nature, 588 (7839) pp. 642-647. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2233C0F2B0FC]
Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing.
Arpat A.B., Liechti A., De Matos M., Dreos R., Janich P., Gatfield D., 2020/07. Genome research, 30 (7) pp. 985-999. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_071D4E7F8B17]
Emerging Roles of Translational Control in Circadian Timekeeping.
Castelo-Szekely V., Gatfield D., 2020/05/29. Journal of molecular biology, 432 (12) pp. 3483-3497. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A85C20DA0A13]
 
Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation.
Tuck A.C., Rankova A., Arpat A.B., Liechti L.A., Hess D., Iesmantavicius V., Castelo-Szekely V., Gatfield D., Bühler M., 2020/03/19. Molecular cell, 77 (6) pp. 1222-1236.e13. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_ED9F802C1F1F]
2019
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock.
Castelo-Szekely V., De Matos M., Tusup M., Pascolo S., Ule J., Gatfield D., 2019/06/04. Nucleic acids research, 47 (10) pp. 5193-5209. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9D401C4DBF9B]
 
Design of in vitro Transcribed mRNA Vectors for Research and Therapy.
Tusup M., French L.E., De Matos M., Gatfield D., Kundig T., Pascolo S., 2019/05/29. Chimia, 73 (6) pp. 391-394. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2CCF1F79C61C]
2018
Repurposing of promoters and enhancers during mammalian evolution.
Carelli F.N., Liechti A., Halbert J., Warnefors M., Kaessmann H., 2018/10/04. Nature communications, 9 (1) p. 4066. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B849DBF5E53D]
Circadian Clocks and UPR: New Twists as the Story Unfolds.
Milev N.B., Gatfield D., 2018/01/08. Developmental cell, 44 (1) pp. 7-9. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C24D87F779D5]
Metabolic oscillations on the circadian time scale in <i>Drosophila</i> cells lacking clock genes.
Rey G., Milev N.B., Valekunja U.K., Ch R., Ray S., Silva Dos Santos M., Nagy A.D., Antrobus R., MacRae J.I., Reddy A.B., 2018. Molecular Systems Biology, 14 (8) pp. e8376. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_92C579221F0E]
2017
Translational contributions to tissue specificity in rhythmic and constitutive gene expression.
Castelo-Szekely V., Arpat A.B., Janich P., Gatfield D., 2017/06/16. Genome biology, 18 (1) p. 116. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3F3B91FFCF68]
 
Diurnal Oscillations in Liver Mass and Cell Size Accompany Ribosome Assembly Cycles.
Sinturel F., Gerber A., Mauvoisin D., Wang J., Gatfield D., Stubblefield J.J., Green C.B., Gachon F., Schibler U., 2017. Cell, 169 (4) pp. 651-663.e14. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_716FC2928A80]
Guidelines for Genome-Scale Analysis of Biological Rhythms.
Hughes M.E., Abruzzi K.C., Allada R., Anafi R., Arpat A.B., Asher G., Baldi P., de Bekker C., Bell-Pedersen D., Blau J. et al., 2017. Journal of Biological Rhythms, 32 (5) pp. 380-393. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_559D1C2C8AB7]
2016
Analyzing the temporal regulation of translation efficiency in mouse liver.
Janich P., Arpat A.B., Castelo-Szekely V., Gatfield D., 2016. Genomics Data, 8 pp. 41-44. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_5DC1F8E190CC]
Translational contributions to tissue-specificity in rhythmic and constitutive gene expression.
Castelo-Szekely V., Arpat A.B., Janich P., Gatfield D., 2016..
[URN][DOI][serval:BIB_5DA00A50C88B]
2015
A neuron-specific deletion of the microRNA-processing enzyme DICER induces severe but transient obesity in mice.
Mang G.M., Pradervand S., Du N.H., Arpat A.B., Preitner F., Wigger L., Gatfield D., Franken P., 2015. PLoS One, 10 (1) pp. e0116760.
[URN][DOI][WoS][Pmid][serval:BIB_470C9DE8C422]
Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.
Janich P., Arpat A.B., Castelo-Szekely V., Lopes M., Gatfield D., 2015. Genome Research, 25 (12) pp. 1848-1859. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5CC6939B3A97]
2014
 
Circadian control of tissue homeostasis and adult stem cells.
Janich P., Meng Q.J., Benitah S.A., 2014. Current Opinion in Cell Biology, 31C pp. 8-15.
[DOI][WoS][Pmid][serval:BIB_B2F8B0C05266]
 
CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.
Yoshitane H., Ozaki H., Terajima H., Du N.H., Suzuki Y., Fujimori T., Kosaka N., Shimba S., Sugano S., Takagi T. et al., 2014. Molecular and Cellular Biology, 34 (10) pp. 1776-1787.
[DOI][WoS][Pmid][serval:BIB_0050828FF1AB]
Human Prominin-1 (CD133) Is Detected in Both Neoplastic and Non-Neoplastic Salivary Gland Diseases and Released into Saliva in a Ubiquitinated Form.
Karbanová J., Laco J., Marzesco A.M., Janich P., Voborníková M., Mokrý J., Fargeas C.A., Huttner W.B., Corbeil D., 2014. PLoS One, 9 (6) pp. e98927.
[URN][DOI][WoS][Pmid][serval:BIB_A4E7FFEB1F1F]
MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale.
Du N.H., Arpat A.B., De Matos M., Gatfield D., 2014. Elife, 3 pp. e02510.
[URN][WoS][Pmid][serval:BIB_9EC4C39CC571]
Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells.
Bieler J., Cannavo R., Gustafson K., Gobet C., Gatfield D., Naef F., 2014. Molecular Systems Biology, 10 (7) p. 739. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_54F704C349C4]
2013
 
Control and host-dependent activation of insect toxin expression in a root-associated biocontrol pseudomonad.
Péchy-Tarr M., Borel N., Kupferschmied P., Turner V., Binggeli O., Radovanovic D., Maurhofer M., Keel C., 2013. Environmental Microbiology, 15 (3) pp. 736-750.
[DOI][WoS][Pmid][serval:BIB_3B8F92118AE5]
 
Functional significance of thermosensitive transient receptor potential melastatin channel 8 (TRPM8) expression in immortalized human corneal endothelial cells.
Mergler S., Mertens C., Valtink M., Reinach P.S., Székely V.C., Slavi N., Garreis F., Abdelmessih S., Türker E., Fels G. et al., 2013. Experimental Eye Research, 116 pp. 337-349.
[DOI][WoS][Pmid][serval:BIB_FD9CAC0000C0]
 
Human epidermal stem cell function is regulated by circadian oscillations.
Janich P., Toufighi K., Solanas G., Luis N.M., Minkwitz S., Serrano L., Lehner B., Benitah S.A., 2013. Cell Stem Cell, 13 (6) pp. 745-753. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A53508AD334C]
2012
 
CAVIN-3 regulates circadian period length and PER:CRY protein abundance and interactions.
Schneider K., Köcher T., Andersin T., Kurzchalia T., Schibler U., Gatfield D., 2012. EMBO Reports, 13 (12) pp. 1138-1144.
[DOI][Pmid][serval:BIB_E261C93B68A9]
2011
 
Mammalian genes are transcribed with widely different bursting kinetics.
Suter D.M., Molina N., Gatfield D., Schneider K., Schibler U., Naef F., 2011. Science, 332 (6028) pp. 472-474.
[DOI][WoS][Pmid][serval:BIB_46FF0CE7D3AB]
2010
MicroRNA-122 modulates the rhythmic expression profile of the circadian deadenylase Nocturnin in mouse liver.
Kojima S., Gatfield D., Esau C.C., Green C.B., 2010. PLoS One, 5 (6) pp. e11264.
[URN][DOI][WoS][Pmid][serval:BIB_553A9D383D3E]
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