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Select item 105767761.

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

Article PDF–4.5M

Select item 101022342.

Ripply suppresses Tbx6 to induce dynamic-to-static conversion in somite segmentation

Taijiro Yabe, Koichiro Uriu, Shinji Takada

Nat Commun. 2023; 14: 2115. Published online 2023 Apr 13. doi: 10.1038/s41467-023-37745-w

PMCID:: PMC10102234

Article PDF–13M

Select item 98465773.

Periodic Inhibition of ERK activity Drives Sequential Somite Segmentation

M. Fethullah Simsek, Angad Singh Chandel, Didar Saparov, Oriana Zinani, Nicholas Clason, Ertuğrul M. Özbudak

Nature. Author manuscript; available in PMC 2023 Jul 1.

Published in final edited form as: Nature. 2023 Jan; 613(7942): 153–159. Published online 2022 Dec 14. doi: 10.1038/s41586-022-05527-x

PMCID:: PMC9846577

Article PDF–4.5M

Select item 97899894.

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

Article PDF–7.5M

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

Article PDF–2.5M

Select item 88215936.

Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis

Weiting Zhang, Pierluigi Scerbo, Marine Delagrange, Virginie Candat, Vanessa Mayr, Sophie Vriz, Martin Distel, Bertrand Ducos, David Bensimon

Commun Biol. 2022; 5: 113. Published online 2022 Feb 7. doi: 10.1038/s42003-022-03053-0

PMCID:: PMC8821593

Article PDF–1.9M

Select item 83201837.

Evolution of hes gene family in vertebrates: the hes5 cluster genes have specifically increased in frogs

Aya Kuretani, Takayoshi Yamamoto, Masanori Taira, Tatsuo Michiue

BMC Ecol Evol. 2021; 21: 147. Published online 2021 Jul 29. doi: 10.1186/s12862-021-01879-6

PMCID:: PMC8320183

Article PDF–4.8M

Select item 79326818.

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

Article PDF–1.3M

Select item 76110349.

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

Article PDF–1.1M

Select item 758512110.

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

Article PDF–1.9M

Select item 716037311.

Function of Arl4aa in the Initiation of Hematopoiesis in Zebrafish by Maintaining Golgi Complex Integrity in Hemogenic Endothelium

Yuhan Guo, Bowie Y.L. Cheng, Dandan Wang, Alvin C.H. Ma, Bai-Liang He, Toni K. Man, May P.L. Cheung, Xiangguo Shi, Nelson K.L. Ng, Anskar Y.H. Leung

Stem Cell Reports. 2020 Apr 14; 14(4): 575–589. Published online 2020 Mar 26. doi: 10.1016/j.stemcr.2020.02.012

PMCID:: PMC7160373

Article PDF–6.1M

Select item 705431112.

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

Article PDF–1.8M

Select item 704445113.

Greb1 is required for axial elongation and segmentation in vertebrate embryos

Ravindra Singh Prajapati, Richard Mitter, Annalisa Vezzaro, David Ish-Horowicz

Biol Open. 2020 Feb 15; 9(2): bio047290. Published online 2020 Feb 11. doi: 10.1242/bio.047290

PMCID:: PMC7044451

Article PDF–5.0M

Select item 645693414.

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

Article PDF–6.6M

Select item 636051815.

Regulatory Network of the Scoliosis-Associated Genes Establishes Rostrocaudal Patterning of Somites in Zebrafish

Sevdenur Keskin, M. Fethullah Simsek, Ha T. Vu, Carlton Yang, Stephen H. Devoto, Ahmet Ay, Ertuğrul M. Özbudak

iScience. 2019 Feb 22; 12: 247–259. Published online 2019 Jan 21. doi: 10.1016/j.isci.2019.01.021

PMCID:: PMC6360518

Article PDF–4.8M

Select item 601310016.

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

Article PDF–14M

Select item 600657417.

Identification of Dmrt2a downstream genes during zebrafish early development using a timely controlled approach

Rita Alexandra Pinto, José Almeida-Santos, Raquel Lourenço, Leonor Saúde

BMC Dev Biol. 2018; 18: 14. Published online 2018 Jun 19. doi: 10.1186/s12861-018-0173-5

PMCID:: PMC6006574

Article PDF–3.7M

Select item 598972518.

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

Article PDF–1.4M

Select item 596234119.

Segmentation of the zebrafish axial skeleton relies on notochord sheath cells and not on the segmentation clock

Laura Lleras Forero, Rachna Narayanan, Leonie FA Huitema, Maaike VanBergen, Alexander Apschner, Josi Peterson-Maduro, Ive Logister, Guillaume Valentin, Luis G Morelli, Andrew C Oates, Stefan Schulte-Merker

eLife. 2018; 7: e33843. Published online 2018 Apr 6. doi: 10.7554/eLife.33843