Publications

Wave gradient background

Selected Cell Competition papers

  • Kiparaki, M. and Baker, N.E. (2023) Ribosomal protein mutations and cell competition: Autonomous and non-autonomous effects on a stress response. Genetics, 224:iyad080. 
  • Baker, N.E., and Montagna, C. (2022). Reducing the aneuploid cell burden: cell competition and the ribosome connection. Dis Models Mech 15:dmm049673. 
  • Kiparaki, M., Khan, C., Folgado Marco, V., Chuen, J., and Baker, N.E. (2022) The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function. Elife, 11: e71705.

  • Ji, Z., Chuen, J., Kiparaki, M. and Baker, N.E. (2021) Cell competition removes segmental aneuploid cells from Drosophila imaginal disc-derived tissues based on ribosomal protein gene dose. Elife, 10:e61172.

  • Baker, N.E. (2020) Emerging mechanisms of cell competition. Nature Reviews Genetics 21; 683-697.
  • Baker, N.E.,Kiparaki, M., and Khan, C. (2019). A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila. Dev Biol 446: 17-19. 
  • Lee, C.-H., Kiparaki, M., Blanco, J., Folgado, V., Ji, Z., Kumar, A., Rimesso, G., and Baker, N.E. (2018) A regulatory response to ribosomal protein mutations controls translation, growth, and cell competition. Dev Cell, 46, 456-469.

  • Kale, A., Ji, Z., Kiparaki, M., Rimesso, G., Flibotte, S., and Baker, N.E. (2018). Ribosomal protein S12e has a distinct function in cell competition. Dev Cell 44, 42-55.


All publications by date

2024

  1. Nair, S. and Baker, N.E. (2024)  Extramacrochaetae regulates Notch signaling in the Drosophila eye through non-apoptotic caspase activity.   Elife 12: RP91988.
  2. Reddy, V., Bhattacharya, A., and Baker, N.E. (2024) The Id protein Extramacrochaetae restrains the E-protein Daughterless to regulate Notch, Rap1, and Sevenless within the R7 equivalence group of the Drosophila eye. Biol Open, 13: bio060124.
  3. Baker, N.E. (2024) Founding the Wnt gene family: how wingless was found to be a positional signal and oncogene homolog. Bioessays 46(2):e2300156

2023

  1. Kiparaki, M. and Baker, N.E.  (2023)  Protocol for assessing translation in living imaginal discs by O-propar2023gyl puromycin incorporation. STAR Protocols 4: 102653. 
  2. Kiparaki, M. and Baker, N.E. (2023) Ribosomal protein mutations and cell competition: Autonomous and non-autonomous effects on a stress response. Genetics, 224:iyad080. 
  3. Folgado-Marco, V., Ames, K., Chuen, J., Gritsman, K., and Baker, N.E. (2023) Haploinsufficiency of the essential gene RpS12 causes defects in erythropoiesis and hematopoietic stem cell maintenance. Elife 12: e69322. 

2022

  • Kumar, A., and Baker, N.E. (2022) The CRL4 E3 ligase mahjong/DCAF1 controls cell competition through the transcription factor Xrp1, independently of polarity genes. Development 149:dev200795.

  • Baker, N.E., and Montagna, C. (2022). Reducing the aneuploid cell burden: cell competition and the ribosome connection. Dis Models Mech 15:dmm049673. 
  • Kiparaki, M., Khan, C., Folgado Marco, V., Chuen, J., and Baker, N.E. (2022) The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function. Elife, 11: e71705.


2021

  • Ji, Z., Chuen, J., Kiparaki, M. and Baker, N.E. (2021) Cell competition removes segmental aneuploid cells from Drosophila imaginal disc-derived tissues based on ribosomal protein gene dose. Elife, 10:e61172.

  • Quiquand, M., Rimesso, G., Qiao, N., Suo, S., Zhou, C., Slattery, M., White, K.P., Han, J.J., and Baker, N.E. (2021) New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics, 217(4): iyab007.doi: 10.1093/genetics/iyab007.


2020

  • Blanco, J., Cooper, J.C., and Baker, N.E. (2020) Roles of C/EBP class bZip proteins in the growth and cell competition of Rp (“Minute”) mutants in Drosophila (2020). Elife, 9:e50535.

  • Baker, N.E. (2020) Emerging mechanisms of cell competition. Nature Reviews Genetics 21; 683-697.

2019

  • Baker, N.E.,Kiparaki, M., and Khan, C. (2019). A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila. Dev Biol 446: 17-19. 
  • Ji, Z., Kiparaki, M., Folgado, V., Kumar, A., Blanco, J. Rimesso, G., Liu, Y., Zheng, D., and Baker, N.E. (2019) Drosophila RpS12 controls translation, growth, and cell competition through Xrp1. PLoS Genetics, 15(12):e1008513.

  • Wang, L.-H. and Baker, N.E. (2019) Salvador-Warts-Hippo pathway regulates sensory organ development via caspase-dependent non-apoptotic signaling. Cell Death & Disease 10 669.

  • Li, K. and Baker, N.E. (2019) Transcriptional and post-transcriptional regulation of extra macrochaetae during Drosophila adult peripheral neurogenesis. Dev Biol 449: 41-51.


2018

  • Lee, C.-H., Kiparaki, M., Blanco, J., Folgado, V., Ji, Z., Kumar, A., Rimesso, G., and Baker, N.E. (2018) A regulatory response to ribosomal protein mutations controls translation, growth, and cell competition. Dev Cell, 46, 456-469.

  • Wang, L.-H. and Baker, N.E. (2018) Spatial regulation of expanded transcription in the Drosophila wing imaginal disc. PLoS One 13,e0201317.
  • Li, K., and Baker, N.E. (2018) Regulation of the Drosophila ID protein Extra Macrochaetae by proneural dimerization partners. Elife 7: e33967.

  • Kale, A., Ji, Z., Kiparaki, M., Rimesso, G., Flibotte, S., and Baker, N.E. (2018). Ribosomal protein S12e has a distinct function in cell competition. Dev Cell 44, 42-55.

  • Kale, A., and Baker, N.E. (2018) Tumor evolution: multiple induction mechanisms for cell competition. Molecular and Cellular Oncology 5: e1481812.
  • Baker, N.E., and Brown, N.L. All in the family: neuronal diversity and proneural bHLH genes. (2018) Development, 145: dev159426. 

2017

  • Bhattacharya, A., Li, K., Quiquand, M., Rimesso, G., and Baker, N.E. (2017). The Notch pathway regulates the Second Mitotic Wave cell cycle independently of bHLH proteins. Dev Biol 431, 309-320.

  • Baker, N.E. (2017). Patterning the eye: a role for the cell cycle? Dev Biol 430, 263-5.
  • Baker, N.E. (2017). Mechanisms of cell competition emerging from Drosophila studies. Curr Opin Cell Biol 48, 40-46.

2016

  • Kale, A., Rimesso, G. and Baker, N.E. (2016). Local cell death changes the orientation of cell division in the developing Drosophila wing imaginal disc without using Fat or Dachsous as orienting signals. PLoS One 11: e0167637.

  • Lee, C.-H., Rimesso, G., Reynolds, D., Cai, J. and Baker, N.E. (2016). Whole genome sequencing and iPLEX MassARRAY genotyping map an EMS-induced mutation affecting cell competition in Drosophila melanogaster. G3(Bethesda) 6:3207-3217.

  • Baker, N.E. and Kale, A. (2016). Ribosomal protein mutations: apoptosis, cell competition and cancer. Mol Cell Oncol 3:1, e1029065. 

2006-2015

  • Kale, A., Li, W., Lee, C.-H. and Baker, N.E. (2015) Apoptotic mechanisms during competition of ribosomal protein mutant cells: roles of the initiator caspases Dronc and Dream/Strica. Cell Death Different 22:1300-1312.

  • Wang, L.-H. and Baker, N.E. (2015) E-proteins and Id-proteins: helix-loop-helix partners in development and disease. Dev Cell 35: 269-280.
  • Wang, L.-H. and Baker, N.E. (2015) Salvador-Warts-Hippo pathway in a developmental checkpoint monitoring Helix-Loop-Helix proteins. Dev Cell 32:.191-202.

  • Fullard, J.F. and Baker, N.E. (2015) Signaling by the engulfment receptor Draper: a screen in Drosophila melanogaster implicates cytoskeletal regulators, Jun N-terminal Kinase, and Yorkie. Genetics, 199:117-134.

  • Baker, N.E. and Jenny, A. (2014). Metabolism and the other fat: a protocadherin in mitochondria. Cell 158: 1240-1. 
  • Baker, N.E., Li, K., Quiquand, M., Ruggiero, R., and Wang, L.-H. (2014). Eye development. Methods 68: 252-9. 
  • Baker, N.E. (2013) Developmental regulation of nucleolus size during Drosophila eye development. PLoS ONE 8:e58266.

  • Ruggiero, R., Kale, A., Thomas, B., and Baker, N.E. (2012). Mitosis in neurons: Roughex and Anaphase Promoting Complex maintain cell cycle exit to prevent cytokinetic and axonal defects in Drosophila photoreceptor neurons. PLoS Genetics, 8: e1003049.

  • Bhattacharya, A., and Baker, N.E. (2012). The role of the bHLH protein Hairy in morphogenetic furrow progression in the developing Drosophila eye. PLoS ONE, 7: e47503.

  • Bhattacharya, A., and Baker, N.E. (2011). A network of broadly-expressed HLH genes regulates tissue-specific cell fates. Cell, 147: 881-892.

  • Lubensky, D.K.*, Penninton, M.W., Shraiman, B., and Baker, N.E. (2011). A dynamical model of ommatidial crystal formation. Proc Natl Acad Sci, 108: 11145-11150.

  • Baker, N.E., and Firth, L.C. (2011). Retinal Determination Genes function along with cell-cell signals to regulate Drosophila eye development: examples of multi-layered regulation by Master Regulators. Bioessays, 33: 538-546. 
  • Baker, N.E. (2011). Proximodistal patterning in the Drosophila leg: models and mutations. Genetics 187: 1003-1010.
  • Baker, N.E. (2011). Cell competition. Curr Biol 21: R11-15.
  • Sidyelyeva, G., Wegener, C., Schoenfeld, B.P., Bell, A.J., Baker, N.E., McBride, S.M.J.,and Fricker, L.D.M.* (2010) Individual Carboxypeptidase D domains have both redundant and unique function in Drosophila development and behavior. Cell Mol Life Sci 67: 2991-3004.

  • Firth, L.C.. Bhattacharya, A., and Baker, N.E. (2010) Cell cycle arrest by a gradient of Dpp signaling during Drosophila eye development. BMC Dev Biol 10:28.

  • Li, W., Kale, A., and Baker, N.E. (2009) Oriented cell division as a response to cell death and cell competition. Curr. Biol. 19 1821-1826.

  • Baker, N.E., Bhattacharya, A., and Firth, L.C. (2009) Regulation of Hh signal transduction as Drosophila eye differentiation progresses.  Dev. Biol. 335, 356-366
.
  • Firth, L.C. and Baker, N.E. (2009) Retinal determination genes as targets and possible effectors of extracellular signals. Dev. Biol. 327, 366-375.

  • Bhattacharya, A. and Baker, N.E. (2009) The HLH protein Extramacrochaetae is required for R7 and cone cell fates in the Drosophila eye Dev. Biol. 327, 288-300.
  • Fullard, J.F., Kale, A., and Baker, N.E. (2009). Clearance of apoptotic corpses. Apoptosis, 14: 1029-37.
  • Pei, Z. and Baker, N.E. (2008). Competition between Delta and the Abruptex domain of Notch, BMC Developmental Biology, 8: 4.

  • Firth, L.C., and Baker, N.E. (2007) Spitz from the retina regulates genes transcribed in the Second Mitotic Wave, peripodial epithelium, glia and plasmatocytes of the Drosophila eye imaginal disc. Dev Biol, 307, 521-538. 

  • Baker, N.E. and Li, W. (2008) Cell competition and its possible relation to cancer. Cancer Research 68: 5505-5507.
  • Li, W. and Baker, N.E. (2007) The active role of corpse engulfment pathways during cell competition. Fly 1, 274-278.
  • Li, W. and Baker, N.E. (2007) Engulfment is required for cell competition. Cell, 129, 1215-1225.

  • Tyler, D. and Baker, N.E.(2007) expanded and fat regulate growth and differentiation in the Drosophila eye through multiple signaling pathways. Dev. Biol. 305, 187-201.

  • Tyler, D., Li, W., Zhuo, N., Pellock, B., and Baker, N.E. (2007) Genes affecting cell competition. Genetics, 175, 643-657.

  • Baker, N.E. (2007) Patterning signals and proliferation in Drosophila imaginal discs. Curr. Opin. Genet Dev, 17, 287-293.
  • Sidyelyeva, G., Baker, N.E., and Fricker, L.D. (2006). Characterization of the molecular basis of the Drosophila mutations in Carboxypeptidase D. Effect on enzyme activity and expression. J Biol Chem 281, 13844-13852.
  • Firth, L.C., Li, W., Zhang, H., and Baker, N.E. (2006). Analyses of RAS regulation of eye development in Drosophila melanogaster. Meth. Enzymol., 407, 711-721.
  • Yang, L. and Baker, N.E. (2006). Notch activity opposes Ras-induced differentiation during the Second Mitotic Wave of the developing Drosophila eye. BMC Developmental Biology 6:8.

1996-2005

  • Firth, L.C. and Baker, N.E. (2005) Extracellular signals responsible for spatially-regulated proliferation in the differentiating Drosophila eye Dev Cell 8, 541-551.
  • Li, Y., and Baker, N.E. (2004). The roles of cis-inactivation by Notch ligands and of neuralized during eye and bristle patterning in Drosophila. BMC Developmental Biology, 4 :5
  • Baker, N.E. (2004). Atonal Points the way – protein-protein interactions and developmental biology. Dev Cell 7:632-634.
  • Shi, W., Stampas, A., Zapata, C., and Baker, N.E. (2003) The pineapple eye gene is required for survival of Drosophila imaginal disc cells. Genetics 165, 1869-1879.
  • Fu, W. and Baker, N.E. (2003) Deciphering synergistic and redundant roles of Hedgehog, Decapentaplegic and Delta that drive the wave of differentiation in Drosophila eye development. Development 130. 5229-5239.
  • Li, Y., Fetchko, M., Lai, Z., and Baker, N.E. (2003). Scabrous and Gp150 are endosomal proteins that regulate Notch activity. Development 130, 2819-2827.
See also Corrigendum Development 131, 5213.
  • Li, Y., Lei, L., Irvine, K., and Baker, N.E. (2003). Notch activity in neural cells triggered by a mutant allele with altered glycosylation. Development 130, 2829-2840.
  • Yang, L. and Baker, N.E. (2003). Cell cycle withdrawal, progression, and cell survival regulation by EGFR and its effectors in the differentiating Drosophila eye. Dev. Cell 4, 359-369.
  • Firth, L.C., and Baker, N.E. (2003). EGF Receptor signaling: a prickly proposition. Curr. Biol. 13. 773-774.
  • Tyler, D. and Baker, N.E. (2003). Size isn’t everything. Bioessays 25, 5-8.
  • Yu, S.-SY., Yoo, S.J., Yang, L., Zapata, C., Srinivasan, A., Hay, B., and Baker, N.E. (2002). A pathway of signals regulating effector and initiator caspases in the developing Drosophila eye. Development 129, 3269-3278.
  • Baker, N.E. (2002). Notch and the patterning of ommatidial founder cells in the developing Drosophila eye. Results and Problems in Cell Differentiation, vol. 37, pp 35-58 (Ed: K. Moses) “Drosophila Eye Development”.
  • Sultan, R., Stampas, A., Goldberg, M.B. and Baker, N.E. (2001)  Drug resistance of bacteria commensal with Drosophila melanogaster in laboratory cultures.  Drosoph. Inf. Serv 84, 175-180.
  • Baker, N.E. and Yu, S.-Y. (2001). The EGF receptor defines domains of cell cycle progression and survival to regulate cell number in the developing Drosophila eye. Cell 104, 699-708. 
  • Yang, L., and Baker, N.E. (2001). Role of the EGFR/Ras/Raf pathway in specification of R8 photoreceptor cells in the Drosophila retina. Development 128, 1183-1191.
  • Li, Y., and Baker, N.E. (2001). Proneural enhancement by Notch overcomes Suppressor-of Hairless repressor function in the developing Drosophila eye. Curr. Biol.11, 330-338.
  • Baker, N.E. (2001). Proliferation, survival, and death in the Drosophila eye. Sem Cell Dev. Biol 12, 499-507.
  • Baker, N.E. (2001). Master Regulatory Genes; telling them what to do. BioEssays, 23, 763-766.
  • Lee, E-C., Yu, S.-Y., and Baker, N.E. (2000) The Scabrous protein can act as an extracellular antagonist of Notch signalling in the Drosophila wing. Curr. Biol 10, 931-934.
  • Baker, N.E. (2000) Notch signaling in the nervous system. Pieces still missing from the puzzle. BioEssays 22, 264-273.
  • Lee, E-C., Yu, S.-Y., Hu, X., Mlodzik, M., and Baker, N.E. (1998). Functional analysis of the Fibrinogen-Related scabrous gene from Drosophila melanogaster identifies potential effector and stimulatory protein domains. Genetics 150, 663-673.
  • Lesokhin, A., Yu, S.-SY., Katz, J., and Baker, N.E. (1999). Several levels of EGF Receptor signalling during photoreceptor specification in Ellipse , wild type, and null mutant Drosophila . Dev. Biol. 205, 129-144.
  • Ligoxygakis, P., Yu, S.-SY., Delidakis, C., and Baker, N.E. (1998). A subset of Notch functions during Drosophila eye development require Su(H) and the E(spl)-C. Development 125, 2893 – 2900.
  • Baker, N.E., and Yu, S. (1998). The R8 photoreceptor equivalence group in Drosophila: fate choice precedes regulation of Delta transcription and is independent of Notch gene dose. Mech. Dev. 74. 3-14. 
  • Baker, N.E., and Yu, S. (1997) Proneural function of neurogenic genes in the developing Drosophila eye. Current Biology,7, 122-132. 
  • Han, J., Baker, N.E., and Rubin, C.S. (1997). Molecular characterization of a novel A Kinase anchor protein from Drosophila melanogaster. J. Biol. Chem, 272, 26611-26619.
  • Baker, N.E., Yu, S, and Han, D. (1996) Evolution of proneural atonal expression through distinct regulatory phases in the developing Drosophila eye. Current Biology, 6, 1290-1301. 
  • Lee, E-C., and Baker, N.E. (1996) Gp300sca is not a high-affinity Notch ligand. Biochemical and Biophysical Research Communications, 225, 720-725. 
  • Lee, E-C., Hu, X., Yu, S.Y., and Baker, N.E. (1996) The scabous gene encodes a secreted glycoprotein dimer and regulates proneural development in Drosophila eyes. Mol. Cell. Biol. 16, 1179-1188.

1987-1995

  • Hu, X., Lee, E-C., and Baker, N.E. (1995) Molecular analysis of scabrous mutant alleles from Drosophila indicates a secreted protein with two functional domains. Genetics 141, 607-617.
  • Baker, N.E., and Zitron, A.E. (1995). Drosophila eye development: Notch and Delta amplify a neurogenic pattern conferred on the morphogenetic furrow by scabrous . Mech. Dev. 49, 173-189. 
  • Baker, N.E., Moses, K., Nakahara, D., Ellis, M.C., Carthew, R.W., & Rubin, G.M. (1992). Mutations on the second chromosome affecting the Drosophila eye. J. Neurogenetics. 8, 85-100. 
  • Baker, N.E. & Rubin, G.M. (1992). Ellipse mutations in the Drosophila homologue of the EGF-receptor affect pattern formation, cell division and cell death in eye imaginal discs. Dev.Biol. 150, 381-396. 
  • Baker, N.E., Mlodzik, M., & Rubin, G.M.* (1990). Spacing differentiation in the developing Drosophila eye: a fibrinogen-related lateral inhibitor encoded by scabrous. Science 250, 1370-1377.
  • Mlodzik, M., Baker, N.E., & Rubin, G.M.* (1990). Isolation and expression of scabrous, a gene regulating neurogenesis in Drosophila. Genes Dev. 4, 1848-1861. 
  • Baker, N.E., & Rubin, G.M.* (1989). Effect on eye development of dominant mutations in Drosophila homologue of the EGF-receptor. Nature 340, 150-153.
  • Baker, N.E. (1989). In situ hybrization to whole embryos. Protocol 84 in “Drosophila. A laboratory manual” by M. Ashburner, Cold Spring Harbor Laboratory Press
  • Baker, N. E. (1988). Localization of transcripts from the wingless gene in whole Drosophila embryos. Development 103, 289-298.
  • Martinez-Arias, A., Baker, N. E., & Ingham, P. W. (1988). Role of segment polarity genes in the definition and maintenance of cell states in the Drosophila embryo. Development 103,157-170. 
  • Baker, N. E. (1988). Transcription of the segment-polarity gene wingless in the imaginal discs of Drosophila, and the phenotype of a pupal-lethal wg mutation. Development 102, 489-497.
  • Ingham, P. W., Baker, N. E., & Martinez-Arias, A. (1988). Regulation of segment polarity genes in the Drosophila blastoderm by fushi tarazu and even skipped. Nature 331, 73-75. 
  • Baker, N.E. (1988). Embryonic and imaginal requirements for wingless, a segment-polarity gene in Drosophila. Dev. Biol. 125, 96-108.
  • Baker, N. E. (1987). Molecular cloning of sequences from wingless, a segment- polarity gene in Drosophila; the spatial distribution of a transcript in embryos. EMBO J 6, 1765-1773.