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Publications: Publications


Energy metabolism modulates the regulatory impact of activators on gene expression.

Qiao, S., Bernasek, S., Gallagher, K.D., O'Connell, J., Yamada, S., Bagheri, N., Amaral, L.A.N., and R.W. Carthew

Development 151 (1): dev201986. (2024) [DOI]

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Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila.

Bernasek, S.M., Hur, S.J., Peláez, N., Boisclair Lachance, J.-F., Bakker, R., Tejedor Navarro, H., Sanchez-Luege, N., Amaral, L.A.N., Bagheri, N., Rebay, I. and R.W. Carthew

Development 150 (8): dev201467 (2023) [DOI]

Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila.

Liu, A., O'Connell, J., Wall, F., and R.W. Carthew

eLife 12:RP91572. (2023) [DOI]

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Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye.

Gallagher KD, Mani M, and Carthew RW.

eLife 2022;11:e72806. (2022) [DOI]

CRISPR/Cas9 mediated precise and efficient genome editing in Drosophila.
Nyberg KG, and Carthew RW. In:
Drosophila Methods and Protocols, Methods in Molecular Biology Third Edition (ed. C. Dahmann) pp. 135-156. Springer Publishing. (2022) [DOI]

Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate.
Giri R, Brady S, Papadopoulos, DK, and Carthew RW.
iScience 25, 105097 (2022) [DOI]

Invading viral DNA triggers dsRNA synthesis by RNA Polymerase II to activate antiviral RNA interference in Drosophila.
de Faria IJS, Aguiar ERGR, Olmo RP, Alves da Silva J, Daeffler L, Carthew RW, Imler, J-L, and Marques JT.
Cell Reports 39, 110976. (2022) [DOI]

Ratio-based sensing of two transcription factors regulates the transit to differentiation.
Bernasek SM, Hur SJ, Peláez N, Boisclair Lachance J-F, Bakker R, Tejedor Navarro H, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I, and Carthew RW.
BioRxiv (2022) [DOI]

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Global constraints within the developmental program of the Drosophila wing.

Alba V, Carthew JE, Carthew RW, and Mani M.

eLife 2021;10:e66750. (2021) [DOI]

Gene regulation and cellular metabolism: An essential partnership.

Carthew RW.

Trends in Genetics 37, 389-400. (2021) [DOI]

MicroRNA regulation of glucose and lipid metabolism.

Agbu P, and Carthew RW.

Nature Reviews Molecular and Cell Biology  22, 425-438. (2021) [DOI]



MicroRNA miR-7 regulates secretion of insulin-like peptides.

Agbu P, Cassidy JJ, Braverman J, Jacobson A, and Carthew, RW.

Endocrinology 161, 1-15. (2020) [DOI]

The effector mechanism of siRNA Spherical Nucleic Acids.

Yamankurt G, Stawicki J, Posadas DM, Nguyen JQ, Carthew RW, and Mirkin CA.

Proceedings of the National Academy of Sciences USA 117, 1312-1320. (2020) [DOI]

Ordered patterning of the sensory system is susceptible to stochastic features of gene expression.

Giri R, Papadopoulos DK, Posadas DM, Potluri H, Tomancak P, Mani M, and Carthew RW.

eLife 2020;9:e53638. (2020) [DOI]

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila.

Bernasek S, Peláez N.Carthew RW, Bagheri N, and Amaral LAN.

PLoS Computational Biology (2020) [DOI]

The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts.

Bakker R, Mani M, and Carthew RW.

eLife 2020;9:e56076. (2020) [DOI]

A pipeline for precise and efficient genome editing by sgRNA-Cas9 RNPs in Drosophila. 

Nyberg KG, Nguyen J, Kwon Y-J, Blythe S, Beitel GJ, and Carthew RW.

Fly 14, 34-48. (2020) [DOI]



Repressive gene regulation synchronizes development with cellular metabolism.
Cassidy JJ, Bernasek S, Bakker R, Giri R, Pelaez N, Eder B, Bobrowska A, Bagheri N, Amaral LAN, and Carthew RW.
Cell  178, 980-992. (2019) [DOI]

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Out of the testis: biological impacts of new genes.
Nyberg KG, and Carthew RW.
Genes & Development 31, 1825-1826.(2017) [DOI]

Microprocessor recruitment to elongating RNA Polymerase II Is required for differential expression of microRNAs.
Church VA, Pressman S, Isaji M, Truscott M, Cizmecioglu NT, Buratowski S, Frolov MV, and Carthew RW.
Cell Reports 20, 3123-3134. (2017) [DOI]

MicroRNAs make a difference in cardiovascular robustness.
Bakker R, and Carthew RW.
Developmental Cell 40, 515-516. (2017) [DOI]

RNA interference functions and mechanisms in animals.

Carthew RW.

The Biomedical & Life Sciences Collection, Henry Stewart Talks. (2017)

MicroRNA function in Drosophila melanogaster.

Carthew RW, Agbu P, and Giri R.

Seminars in Cell and Developmental Biology 65, 29-37. (2017) [DOI]



Hexagonal patterning of the insect compound eye: Facet area variation, defects, and disorder.
Kim S, Cassidy JJ, Yang B, Carthew RW,  and Hilgenfeldt S.
Biophysical Journal 111, 2735-2746. (2016) [DOI]

Differential masking of natural genetic variation by miR-9a in Drosophila.
Cassidy JJ, Straughan AJ, and Carthew RW.
Genetics 202, 675-687. (2016) [DOI]

Spindle-E cycling between nuage and cytoplasm is controlled by Qin and Piwi proteins.
Andress A, Bei,Y, Fonslow BR, Giri R, Wu Y, Yates III JR, and Carthew RW.
Journal of Cell Biology 213, 201-211. (2016) [DOI]

MicroRNA function in Drosophila melanogaster.
Carthew, R.W., Agbu, P. and R. Giri
Seminars in Cell and Developmental Biology doi:10.1016/j.semcdb.2016.03.015. (2016) [DOI]

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Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation.
Peláez, N., Gavalda-Miralles, A., Wang, B., Tejedor Navarro, H., Gudjonson, H., Rebay, I.,Dinner, A.R., Katsaggelos, A.K., Amaral, L.A.N. and R. W. Carthew
 eLife 10.7554/eLife.08924. (2015) [DOI]

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MicroRNAs and their roles in developmental canalization.
Posadas, D.M. and R.W. Carthew
Current Opinions in Genetics and Development 27, 1-6. (2014) [DOI]

MicroRNAs suppress cellular phenotypic heterogeneity.
Giri, R. and R.W. Carthew
Cell Cycle 13, 1517-1518. (2014) [DOI]



miR-9a minimizes the phenotypic impact of genomic diversity by buffering a transcription factor.
Cassidy, J.J., Jha, A.R., Posadas, D.M., Giri, R., Venken, K.J.T., Ji, J., Jiang, H., Bellen, H.J., White, K.P. and R.W. Carthew.
Cell 155, 1556-1567 (2013) [DOI]

Functionally diverse microRNA effector complexes are regulated by extracellular signaling.
Wu, P.H., Isaji, M. and R.W. Carthew.
Molecular Cell 52, 113-123 (2013) [DOI]

Functional specialization of the small interfering RNA pathway in response to virus infection.
Marques, J.T., Wang, J-P., Wang, X., Oliveira, K.P., Gao, C., Aguiar, E.R.G.R., Jafari, N. and R.W. Carthew.
PLoS Pathogens 9, e1003579 (2013) [DOI]

Drosophila eye nuclei segmentation based on graph cut and convex shape prior.
Qi, J., Wang, B., Pelaez, N., Rebay, I., Carthew, R.W., Katsaggelos, A.K. and L.A.N. Amaral
IEEE International Conference on Signal Processing 978-1-4799-2341-0/13. (2013) [DOI]

A study of Pointed and Yan reveals new complexity to the regulatory networks downstream of receptor tyrosine kinase signaling.
Boisclair Lachance, J.F., Peláez, N., Cassidy, J.J., Webber, J.L., Rebay, I. and R.W. Carthew.
Developmental Biology DOI: 10.1016/j.ydbio.2013.11.002. (2013) [DOI]

The relationship between long-range chromatin occupancy and polymerization of the Drosophila ETS family transcriptional repressor Yan.
Webber, J.L., Zhang, J., Cote, L., Vivekanand, P., Ni,.X., Zhou, J., Nègre, N., Carthew, R.W., White, K.P. and I. Rebay
Genetics 193, 633-649 (2013) [DOI]

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Tobacco calmodulin-like protein provides secondary defense by biding to and directing degradation of virus RNA silencing suppressors.
Nakahara, K., Masuta, C., Yamada, S., Shimura, H., Wada, T.S., Meguro, A., Sueda, K., Goto, K., Sekiguchi, T., Jun, S., Carthew R.W. and I. Uyeda.
Proceedings of the National Academy of Sciences USA 109, 10113-10118 (2012) [DOI]

A systematic genetic screen to dissect the microRNA pathway in Drosophila.
Pressman, S., Reinke, C.A, Wang, X. and R.W. Carthew
Genes Genomes Genetics 2, 437-448 (2012) [DOI]

Biological robustness and the role of microRNAs: a network perspective.
Pelaez, N., and R.W. Carthew
Current Topics in Developmental Biology 99, 237-255 (2012) [DOI]

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Cargo sorting to lysosome-related organelles regulates siRNA-mediated gene silencing.
Harris, D.A., Kim, K., Nakahara, K., Vazquez-Doorman, C. and R.W. Carthew
Journal of Cell Biology 194, 77-87 (2011) [DOI]

Cadherin-dependent cell morphology in an epithelium: constructing a quantitative dynamical model.
Gemp, I., Carthew, R.W. and S. Hilgenfeldt  
PLoS Computational Biology 7, e1002115 (2011) [DOI]



Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila.
Marques, J.T., Kim, K., Wu, P-H., Alleyne, T., Jafari, N. and R.W. Carthew
Nature Structural and Molecular Biology 17, 24-30 (2010) [DOI]

Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
Lu, J., Shen, Y., Carthew, R.W., Wang, S.M. and C.I. Wu
Nature Genetics 42, 9–10 (2010) [DOI]



The endo-siRNA pathway is required for robust development of the Drosophila embryo.
Lucchetta, E.M., Carthew, R.W. and R.F. Ismagilov
PLoS One 4, e7576 (2009) [DOI]

A microRNA imparts robustness against environmental fluctuation during development.
Li, X., Cassidy, J., Reinke, C.A., Fischboeck, S. and R.W. Carthew
Cell 137, 273-282 (2009) [DOI]

Silencing by small RNAs is linked to endosomal trafficking.
Lee, Y.S., Pressman, S., Andress, A.P., Kim, K.,, White, J.L., Cassidy, J.J., Li, X., Lubell, K., Lim, D.H., Cho, I.S., Nakahara, K., Preall, J.B., Bellare, P., Sontheimer, E.J. and R.W. Carthew  
Nature Cell Biology 11, 1150-1156 (2009) [DOI]

Origins and mechanisms of miRNAs and siRNAs.
Carthew, R.W. and E.J. Sontheimer
Cell 136, 642-655 (2009) [DOI]

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Lola regulates cell fate by antagonizing Notch induction in the Drosophila eye.
Zheng, L. and R.W. Carthew
Mechanisms of Development 125, 18-29 (2008) [DOI]

BMP signaling goes post-transcriptional in a microRNA-sort of way.  
Reinke, C.A. and R.W. Carthew  
Developmental Cell 15, 174-175 (2008) [DOI]

The birth and death of microRNA genes in Drosophila.
Lu, J., Shen, Y., Wu, Q., Kumar, S., He, B., Carthew, R.W., Wang, S. and C.I. Wu  
Nature Genetics 40, 351-355 (2008) [DOI]

Adaptive evolution of newly-emerged microRNA genes in Drosophila.
Lu, J., Fu, Y., Kumar, S., Shen, Y., Zeng, K., Carthew, R.W. and C.I. Wu
Molecular Biology and Evolution 25, 929-938 (2008) [DOI]

Functional analysis of Dicer-2 missense mutations in the siRNA pathway of Drosophila.
Lim, D-W., Kim, J., Kim, S., Carthew, R.W. and Y.S. Lee  
Biochimiche Biophysical Research Communications 37, 525-530 (2008) [DOI]

Physical modeling of cell geometric order in an epithelial tissue.
Hilgenfeldt, S., Erisken, S. and R.W. Carthew
Proceedings of the National Academy of Sciences USA 105, 907-911 (2008) [DOI]

Cell-type-specific transcription of prospero is controlled by combinatorial signaling in the Drosophila eye.
Hayashi, T., Xu, C. and R.W. Carthew
Development 135, 2787-2796 (2008) [DOI]

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Post transcriptional gene silencing.
Pressman, S., Bei, Y and R.W. Carthew
Cell 130, 570 (2007) [DOI]

A call to arms: co-evolution of animal viruses and host innate immune responses.
Marques J.T. and R.W. Carthew
Trends in Genetics 23, 359-364 (2007) [DOI]

Conversion of pre-RISC to holo-RISC by Ago2 during assembly of RNAi complexes.
Kim K., Lee, Y.S. and R.W. Carthew
RNA 13, 22-29 (2007) [DOI]

Cell adhesion and cortex contractility determine cell patterning in the Drosophila retina.
Käfer, J., Hayashi, T., Marée, A.F.M., Carthew, R.W. and F. Graner
Proceedings of the National Academy of Sciences USA 104, 18549-18554 (2007) [DOI]

Pattern formation in the Drosophila eye.
Carthew R.W.
Current Opinions in Genetics and Development 17, 309-313 (2007) [DOI]

Small RNA-mediated epigenetic modifications.
Bei, Y., Pressman, S. and R.W. Carthew
Cell 130, 665 (2007) [DOI]

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RNA interference directs innate immunity against viruses in adult Drosophila.
Wang X-H., Aliyari R., Li W-X., Li H-W., Kim K., Carthew R.W., Atkinson P. and X-W. Ding
Science 312, 452-454 (2006) [DOI]

The RNAi pathway initiated by Dicer-2 in Drosophila.
Kim K., Lee Y.S., Harris D., Nakahara K. and R.W. Carthew
Cold Spring Harbor Symposia in Quantitative Biology 71, 39-44 (2006) [DOI]

Gene regulation by microRNAs.
Carthew R.W.
Current Opinions in Genetics and Development 16, 203-208 (2006) [DOI]

A new RNA dimension to genome control.
Carthew R.W.  
Science 313, 305-306 (2006) [DOI]

Par-1 kinase establishes cell polarity and functions in Notch signaling in the Drosophila embryo.
Bayraktar J, Zygmunt D. and R.W. Carthew  
Journal of Cell Science 119, 711-721 (2006) [DOI]

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Functional roles of endogenous miRNAs and siRNAs.
Sontheimer E.J. and R.W. Carthew
Cell 122, 9-12 (2005) [DOI]

Targets of microRNA regulation in the Drosophila oocyte proteome.
Nakahara K., Kim K., Sciulli C., Dowd S.R., Minden J.S. and R.W. Carthew
Proceedings of the National Academy of Sciences USA 102, 12023-12028 (2005) [DOI]

A miRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye.
Li X. and R.W. Carthew
Cell 123, 1267-1277 (2005) [DOI]

Stem cell division is regulated by the microRNA pathway.
Hatfield S.D., Shcherbata H.R., Fischer K.A., Nakahara K., Carthew R.W. and H. Ruohola-Baker.
Nature 435, 974-978 (2005) [DOI]

Adhesion proteins and control of cell shape.
Carthew R.W.
Current Opinions in Genetics and Development 15, 358-363 (2005) [DOI]



Argonaute journeys into the heart of RISC.
Sontheimer E.J. and R.W. Carthew
Science 305, 1409-1410 (2004) [DOI]

A Dicer-2-dependent 80S complex cleaves targeted mRNAs during RNAi in Drosophila.
Pham J.W., Pellino J.L., Lee Y.S., Carthew R.W. and E.J. Sontheimer  
Cell 117, 83-94 (2004) [DOI]

Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways.
Lee Y.S., Nakahara K., Pham J.W., Kim K., He Z., Sontheimer E.J. and R.W. Carthew  
Cell 117, 69-81 (2004) [DOI]

Surface mechanics mediate pattern formation in the developing retina.
Hayashi T. and R.W. Carthew
Nature 431, 647-652 (2004) [DOI]

Genome wide survey of protein kinases required for cell cycle progression.
Bettencourt-Dias M., Giet R., Sinka R., Mazumdar A., Lock W.G., Balloux F., Zafiropoulos P.J., Yamaguchi S., Winter S., Carthew R.W., Cooper M., Jones D., Frenz L. and D.M. Glover
Nature 432, 980-987 (2004) [DOI]



Chibby, a nuclear ß-catenin-associated antagonist of the Wnt/Wingless pathway.
Takemaru K-I., Yamaguchi S., Lee Y.S., Zhang Y., Carthew R.W. and R.T. Moon
Nature 422, 905-909 (2003) [DOI]

Making a better RNAi vector for Drosophila: Use of Intron Spacers.
Lee Y.S. and R.W. Carthew
Methods 30, 322-329 (2003) [DOI]



Phyllopod acts as an adaptor protein to link the Sina ubiquitin ligase to the substrate protein Tramtrack.
Li S., Xu C. and R.W. Carthew
Molecular and Cellular Biology 22, 6854-6865 (2002) [DOI]

RNAi is activated during Drosophila oocyte maturation in a manner dependent on aubergine and spindle-E.
Kennerdell J.R., Yamaguchi S. and R.W. Carthew
Genes & Development 16, 1884-1889 (2002) [DOI]



Overlapping activators and repressors delimit transcriptional response to receptor tyrosine kinase signals in the Drosophila eye.
Xu C., Kauffmann R.C., Zhang J., Kladny S. and R.W. Carthew
Cell 103, 87-97 (2000) [DOI]

Heritable gene silencing in Drosophila using double-stranded RNA.
Kennerdell J.R. and R.W. Carthew
Nature Biotechnology 18, 896-898 (2000) [DOI]


Prior to 2000

Ebi regulates epidermal growth factor receptor signaling pathways in Drosophila.
Dong X., Tsuda L., Zavitz K.H., Lin M., Li S., Carthew R.W. and S.L. Zipursky
Genes & Development 13, 954-965 (1999) [DOI]

Interactions between Wingless and DFz2 during Drosophila wing development.
Zhang J. and R.W. Carthew
Development 125, 3075-3085 (1998) [DOI]

Proteasomal regulation of nuclear receptor corepressor-mediated repression.
Zhang J., Guenther M.G., Carthew R.W. and M.A. Lazar
Genes & Development 12, 1775-1780 (1998) [DOI]

Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled2 act in the Wingless pathway.
Kennerdell, J.R. and R.W. Carthew
Cell 95, 1017-1026 (1998) [DOI]

Photoreceptor cell differentiation requires regulated proteolysis of the transcriptional repressor Tramtrack.
Li S., Li Y., Z.-C. Lai and R.W. Carthew
Cell 90, 469-478 (1997) [DOI]

Ras1 signaling and transcriptional competence in the R7 cell of Drosophila.
Kauffmann R.C., Li S., Gallagher P.A., Zhang J. and R.W. Carthew
Genes & Development 10, 2167-2178 (1996) [DOI]

Frizzled regulates mirror-symmetric pattern formation in the Drosophila eye.
Zheng L., Zhang J. and R.W. Carthew
Development 121, 3045-3055 (1995) [DOI]

Activated Drosophila Ras1 is selectively suppressed by isoprenyl transferase inhibitors.
Kauffmann R.C., Qian, Y., Vogt, A., Sebti, S.M., Hamilton, A.D. and R.W. Carthew
Proceedings of the National Academy of Sciences USA 92, 10919-10923 (1995) [DOI]

Identification of genes that interact with the sina gene in Drosophila eye development.
Carthew, R.W., Neufeld, T. and G.M. Rubin
Proceedings of the National Academy of Sciences USA 91, 11689-11693 (1994) [DOI]

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