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Northwestern University Feinberg School of Medicine
Özbudak Lab

Publications

Learn more about the work that we do in the Özbudak Laboratory through our recent publications.

  1. Simsek MF, Saparov D, Keseroglu K, Zinani O, Chandel AS, Dulal B, Sharma BK, Zimik S, Özbudak EM  The vertebrate segmentation clock drives segmentation by stabilizing Dusp phosphatases in zebrafish.  Dev Cell  2024 Nov 19;. pii:S1534-5807(24)00668-3
  2. Chandel AS, Keseroglu K, Özbudak EM  Oscillatory control of embryonic development.  Development  2024 May 01;151(9). pii:dev202191
  3. Koparir A, Lekszas C, Keseroglu K, Rose T, Rappl L, Rad A, Maroofian R, Narendran N, Hasanzadeh A, Karimiani EG  et al.  Zebrafish as a model to investigate a biallelic gain-of-function variant in MSGN1, associated with a novel skeletal dysplasia syndrome.  Hum Genomics  2024 Mar 06;18(1):23. pii:23
  4. McDaniel C, Simsek MF, Chandel AS, Özbudak EM  Spatiotemporal control of pattern formation during somitogenesis.  Sci Adv  2024 Jan 26;10(4):eadk8937. pii:eadk8937
  5. Simsek MF, Özbudak EM  A design logic for sequential segmentation across organisms.  FEBS J  2023 Nov;290(21):5086-5093. doi:10.1111/febs.16899
  6. Keseroglu K, Zinani OQH, Keskin S, Seawall H, Alpay EE, Özbudak EM  Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes.  Nat Commun  2023 Oct 14;14(1):6497. pii:6497
  7. Chandel AS, Stocker M, Özbudak EM  The Role of Fibroblast Growth Factor Signaling in Somitogenesis.  DNA Cell Biol  2023 Oct;42(10):580-584. doi:10.1089/dna.2023.0226
  8. Keseroglu K, Zinani OQH, Özbudak EM  Using single-molecule fluorescence in situ hybridization and immunohistochemistry to count RNA molecules in single cells in zebrafish embryos.  STAR Protoc  2023 Mar 17;4(1):102020. pii:102020
  9. Simsek MF, Özbudak EM  Human stem cell models unravel mechanisms of somite segmentation.  Cell Stem Cell  2023 Mar 02;30(3):246-247. doi:10.1016/j.stem.2023.01.011
  10. Simsek MF, Chandel AS, Saparov D, Zinani OQH, Clason N, Özbudak EM  Periodic inhibition of Erk activity drives sequential somite segmentation.  Nature  2023 Jan;613(7942):153-159. doi:10.1038/s41586-022-05527-x
  11. Simsek MF, Özbudak EM  Patterning principles of morphogen gradients.  Open Biol  2022 Oct;12(10):220224. pii:220224
  12. Zinani OQH, Keseroğlu K, Dey S, Ay A, Singh A, Özbudak EM  Gene copy number and negative feedback differentially regulate transcriptional variability of segmentation clock genes.  iScience  2022 Jul 15;25(7):104579. pii:104579
  13. Zinani OQH, Keseroğlu K, Özbudak EM  Regulatory mechanisms ensuring coordinated expression of functionally related genes.  Trends Genet  2022 Jan;38(1):73-81. doi:10.1016/j.tig.2021.07.008
  14. Simsek MF, Özbudak EM  A 3-D Tail Explant Culture to Study Vertebrate Segmentation in Zebrafish.  J Vis Exp  2021 Jun 30;(172). doi:10.3791/61981
  15. Zinani OQH, Keseroğlu K, Ay A, Özbudak EM  Pairing of segmentation clock genes drives robust pattern formation.  Nature  2021 Jan;589(7842):431-436. doi:10.1038/s41586-020-03055-0
  16. Keskin S, Simsek MF, Vu HT, Yang C, Devoto SH, Ay A, Özbudak EM  Regulatory Network of the Scoliosis-Associated Genes Establishes Rostrocaudal Patterning of Somites in Zebrafish.  iScience  2019 Feb 22;12:247-259. doi:10.1016/j.isci.2019.01.021
  17. Simsek MF, Özbudak EM  Spatial Fold Change of FGF Signaling Encodes Positional Information for Segmental Determination in Zebrafish.  Cell Rep  2018 Jul 03;24(1):66-78.e8. doi:10.1016/j.celrep.2018.06.023
  18. Keskin S, Devakanmalai GS, Kwon SB, Vu HT, Hong Q, Lee YY, Soltani M, Singh A, Ay A, Özbudak EM  Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling.  Cell Rep  2018 May 15;23(7):2175-2185.e4. doi:10.1016/j.celrep.2018.04.069
  19. Racedo SE, Hasten E, Lin M, Devakanmalai GS, Guo T, Ozbudak EM, Cai CL, Zheng D, Morrow BE  Reduced dosage of β-catenin provides significant rescue of cardiac outflow tract anomalies in a Tbx1 conditional null mouse model of 22q11.2 deletion syndrome.  PLoS Genet  2017 Mar;13(3):e1006687. pii:e1006687
  20. Ay A, Holland J, Sperlea A, Devakanmalai GS, Knierer S, Sangervasi S, Stevenson A, Ozbudak EM  Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves.  Development  2014 Nov;141(21):4158-67. doi:10.1242/dev.111930
  21. Ay A, Knierer S, Sperlea A, Holland J, Özbudak EM  Short-lived Her proteins drive robust synchronized oscillations in the zebrafish segmentation clock.  Development  2013 Aug;140(15):3244-53. doi:10.1242/dev.093278
  22. Devakanmalai GS, Zumrut HE, Ozbudak EM  Cited3 activates Mef2c to control muscle cell differentiation and survival.  Biol Open  2013 May 15;2(5):505-14. doi:10.1242/bio.20132550
  23. Hanisch A, Holder MV, Choorapoikayil S, Gajewski M, Özbudak EM, Lewis J  The elongation rate of RNA polymerase II in zebrafish and its significance in the somite segmentation clock.  Development  2013 Jan 15;140(2):444-53. doi:10.1242/dev.077230
  24. Ozbudak EM, Tassy O, Pourquié O  Spatiotemporal compartmentalization of key physiological processes during muscle precursor differentiation.  Proc Natl Acad Sci U S A  2010 Mar 02;107(9):4224-9. doi:10.1073/pnas.0909375107
  25. Ozbudak EM, Pourquié O  The vertebrate segmentation clock: the tip of the iceberg.  Curr Opin Genet Dev  2008 Aug;18(4):317-23. doi:10.1016/j.gde.2008.06.007
  26. Gomez C, Ozbudak EM, Wunderlich J, Baumann D, Lewis J, Pourquié O  Control of segment number in vertebrate embryos.  Nature  2008 Jul 17;454(7202):335-9. doi:10.1038/nature07020
  27. Ozbudak EM, Lewis J  Notch signalling synchronizes the zebrafish segmentation clock but is not needed to create somite boundaries.  PLoS Genet  2008 Feb;4(2):e15. pii:e15
  28. Giudicelli F, Ozbudak EM, Wright GJ, Lewis J  Setting the tempo in development: an investigation of the zebrafish somite clock mechanism.  PLoS Biol  2007 Jun;5(6):e150. pii:e150
  29. Lewis J, Ozbudak EM  Deciphering the somite segmentation clock: beyond mutants and morphants.  Dev Dyn  2007 Jun;236(6):1410-5
  30. Mettetal JT, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A  Predicting stochastic gene expression dynamics in single cells.  Proc Natl Acad Sci U S A  2006 May 09;103(19):7304-9
  31. Ozbudak EM, Becskei A, van Oudenaarden A  A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization.  Dev Cell  2005 Oct;9(4):565-71
  32. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A  Multistability in the lactose utilization network of Escherichia coli.  Nature  2004 Feb 19;427(6976):737-40
  33. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A  Regulation of noise in the expression of a single gene.  Nat Genet  2002 May;31(1):69-73

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