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Select item 59897251.

Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling

Sevdenur Keskin, Gnanapackiam S. Devakanmalai, Soo Bin Kwon, Ha T. Vu, Qiyuan Hong, Yin Yeng Lee, Mohammad Soltani, Abhyudai Singh, Ahmet Ay, Ertugrul M. Özbudak

Cell Rep. Author manuscript; available in PMC 2018 Jun 6.

Published in final edited form as: Cell Rep. 2018 May 15; 23(7): 2175–2185.e4. doi: 10.1016/j.celrep.2018.04.069

PMCID:: PMC5989725

Abstract Article PDF–1.4M

Select item 57118422.

Small molecule screen in embryonic zebrafish using modular variations to target segmentation

Sandra Richter, Ulrike Schulze, Pavel Tomançak, Andrew C. Oates

Nat Commun. 2017; 8: 1901. Published online 2017 Dec 1. doi: 10.1038/s41467-017-01469-5

PMCID:: PMC5711842

Abstract Article PDF–2.5M

Select item 46544813.

Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling

Robert P. Jenkins, Anja Hanisch, Cristian Soza-Ried, Erik Sahai, Julian Lewis

PLoS Comput Biol. 2015 Nov; 11(11): e1004459. Published online 2015 Nov 20. doi: 10.1371/journal.pcbi.1004459

PMCID:: PMC4654481

Abstract Article PDF–7.5M

Select item 105767764.

Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes

Kemal Keseroglu, Oriana Q. H. Zinani, Sevdenur Keskin, Hannah Seawall, Eslim E. Alpay, Ertuğrul M. Özbudak

Nat Commun. 2023; 14: 6497. Published online 2023 Oct 14. doi: 10.1038/s41467-023-42220-7

PMCID:: PMC10576776

Abstract Article PDF–4.5M

Select item 92500175.

Gene copy number and negative feedback differentially regulate transcriptional variability of segmentation clock genes

Oriana Q.H. Zinani, Kemal Keseroğlu, Supravat Dey, Ahmet Ay, Abhyudai Singh, Ertuğrul M. Özbudak

iScience. 2022 Jul 15; 25(7): 104579. Published online 2022 Jun 11. doi: 10.1016/j.isci.2022.104579

PMCID:: PMC9250017

Abstract Article PDF–2.5M

Select item 79326816.

Segmentation clock gene pairing drives robust pattern formation

Oriana Q.H. Zinani, Kemal Keseroğlu, Ahmet Ay, Ertuğrul M. Özbudak

Nature. Author manuscript; available in PMC 2021 Jun 23.

Published in final edited form as: Nature. 2021 Jan; 589(7842): 431–436. Published online 2020 Dec 23. doi: 10.1038/s41586-020-03055-0

PMCID:: PMC7932681

Abstract Article PDF–1.3M

Select item 76110347.

A Doppler Effect in Embryonic Pattern Formation

Daniele Soroldoni, David J. Jörg, Luis G. Morelli, David L. Richmond, Johannes Schindelin, Frank Jülicher, Andrew C. Oates

Science. Author manuscript; available in PMC 2021 Jun 21.

Published in final edited form as: Science. 2014 Jul 11; 345(6193): 222–5. doi: 10.1126/science.1253089

PMCID:: PMC7611034

Abstract Article PDF–1.1M

Select item 75851218.

Muscle defects due to perturbed somite segmentation contribute to late adult scoliosis

Laura Lleras-Forero, Elis Newham, Stefan Teufel, Koichi Kawakami, Christine Hartmann, Chrissy L. Hammond, Robert D. Knight, Stefan Schulte-Merker

Aging (Albany NY) 2020 Sep 30; 12(18): 18603–18621. Published online 2020 Sep 25. doi: 10.18632/aging.103856

PMCID:: PMC7585121

Abstract Article PDF–1.9M

Select item 17978239.

Repressor Dimerization in the Zebrafish Somitogenesis Clock

Olivier Cinquin

PLoS Comput Biol. 2007 Feb; 3(2): e32. Published online 2007 Feb 16. doi: 10.1371/journal.pcbi.0030032

PMCID:: PMC1797823

Abstract Article PDF–720K

Select item 978998910.

Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation

Ece Özelçi, Erik Mailand, Matthias Rüegg, Andrew C. Oates, Mahmut Selman Sakar

Nat Commun. 2022; 13: 7934. Published online 2022 Dec 24. doi: 10.1038/s41467-022-35632-4

PMCID:: PMC9789989

Abstract Article PDF–7.5M

Select item 705431111.

Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects

Swapnalee Sarmah, Rajneesh Srivastava, Jeanette N. McClintick, Sarath C. Janga, Howard J. Edenberg, James A. Marrs

Sci Rep. 2020; 10: 3951. Published online 2020 Mar 3. doi: 10.1038/s41598-020-59043-x

PMCID:: PMC7054311

Abstract Article PDF–1.8M

Select item 645693412.

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

Shaokun An, Liang Ma, Lin Wan

BMC Genomics. 2019; 20(Suppl 2): 224. Published online 2019 Apr 4. doi: 10.1186/s12864-019-5477-8

PMCID:: PMC6456934

Abstract Article PDF–6.6M

Select item 430289413.

Spatial gradients of protein-level time delays set the pace of the traveling segmentation clock waves

Ahmet Ay, Jack Holland, Adriana Sperlea, Gnanapackiam Sheela Devakanmalai, Stephan Knierer, Sebastian Sangervasi, Angel Stevenson, Ertuğrul M. Özbudak

Development. 2014 Nov; 141(21): 4158–4167. doi: 10.1242/dev.111930

PMCID:: PMC4302894

Abstract Article

Select item 601310014.

Investigation of Islet2a function in zebrafish embryos: Mutants and morphants differ in morphologic phenotypes and gene expression

Rosa L. Moreno, Kristina Williams, Kenneth L. Jones, Angeles B. Ribera

PLoS One. 2018; 13(6): e0199233. Published online 2018 Jun 21. doi: 10.1371/journal.pone.0199233

PMCID:: PMC6013100

Abstract Article PDF–14M

Select item 350052815.

Single cell resolution imaging of the impact of Notch signaling and mitosis on segmentation clock dynamics

Emilie A. Delaune, Paul François, Nathan P. Shih, Sharon L. Amacher

Dev Cell. Author manuscript; available in PMC 2013 Nov 13.

Published in final edited form as: Dev Cell. 2012 Nov 13; 23(5): 995–1005. doi: 10.1016/j.devcel.2012.09.009

PMCID:: PMC3500528

Abstract Article PDF–4.0M

Select item 340411916.

Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit

Christian Schröter, Saúl Ares, Luis G. Morelli, Alina Isakova, Korneel Hens, Daniele Soroldoni, Martin Gajewski, Frank Jülicher, Sebastian J. Maerkl, Bart Deplancke, Andrew C. Oates

PLoS Biol. 2012 Jul; 10(7): e1001364. Published online 2012 Jul 24. doi: 10.1371/journal.pbio.1001364