Literature DB >> 22007136

A computational statistics approach for estimating the spatial range of morphogen gradients.

Jitendra S Kanodia1, Yoosik Kim, Raju Tomer, Zia Khan, Kwanghun Chung, John D Storey, Hang Lu, Philipp J Keller, Stanislav Y Shvartsman.   

Abstract

A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.

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Year:  2011        PMID: 22007136      PMCID: PMC3201657          DOI: 10.1242/dev.071571

Source DB:  PubMed          Journal:  Development        ISSN: 0950-1991            Impact factor:   6.868


  37 in total

1.  Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.

Authors:  Julia Zeitlinger; Robert P Zinzen; Alexander Stark; Manolis Kellis; Hailan Zhang; Richard A Young; Michael Levine
Journal:  Genes Dev       Date:  2007-02-15       Impact factor: 11.361

2.  dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo.

Authors:  Y T Ip; R E Park; D Kosman; K Yazdanbakhsh; M Levine
Journal:  Genes Dev       Date:  1992-08       Impact factor: 11.361

Review 3.  How the Dorsal gradient works: insights from postgenome technologies.

Authors:  Joung-Woo Hong; David A Hendrix; Dmitri Papatsenko; Michael S Levine
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-22       Impact factor: 11.205

Review 4.  Signaling pathways that establish the dorsal-ventral pattern of the Drosophila embryo.

Authors:  D Morisato; K V Anderson
Journal:  Annu Rev Genet       Date:  1995       Impact factor: 16.830

5.  Organism-scale modeling of early Drosophila patterning via bone morphogenetic proteins.

Authors:  David M Umulis; Osamu Shimmi; Michael B O'Connor; Hans G Othmer
Journal:  Dev Cell       Date:  2010-02-16       Impact factor: 12.270

6.  End-on imaging: a new perspective on dorsoventral development in Drosophila embryos.

Authors:  Melissa M Witzberger; James A J Fitzpatrick; Justin C Crowley; Jonathan S Minden
Journal:  Dev Dyn       Date:  2008-11       Impact factor: 3.780

7.  Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence.

Authors:  Louisa M Liberman; Angelike Stathopoulos
Journal:  Dev Biol       Date:  2008-12-25       Impact factor: 3.582

Review 8.  The interpretation of morphogen gradients.

Authors:  Hilary L Ashe; James Briscoe
Journal:  Development       Date:  2006-02       Impact factor: 6.868

9.  Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy.

Authors:  Philipp J Keller; Annette D Schmidt; Anthony Santella; Khaled Khairy; Zhirong Bao; Joachim Wittbrodt; Ernst H K Stelzer
Journal:  Nat Methods       Date:  2010-07-04       Impact factor: 28.547

10.  The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila.

Authors:  Hsiao-Lan Liang; Chung-Yi Nien; Hsiao-Yun Liu; Mark M Metzstein; Nikolai Kirov; Christine Rushlow
Journal:  Nature       Date:  2008-10-19       Impact factor: 49.962

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  13 in total

1.  Efficient processing and analysis of large-scale light-sheet microscopy data.

Authors:  Fernando Amat; Burkhard Höckendorf; Yinan Wan; William C Lemon; Katie McDole; Philipp J Keller
Journal:  Nat Protoc       Date:  2015-10-01       Impact factor: 13.491

2.  Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data.

Authors:  Theodore Alexandrov; Nina Golyandina; David Holloway; Alex Shlemov; Alexander Spirov
Journal:  J Comput Biol       Date:  2018-08-17       Impact factor: 1.479

3.  Microfluidic trap array for massively parallel imaging of Drosophila embryos.

Authors:  Thomas J Levario; Mei Zhan; Bomyi Lim; Stanislav Y Shvartsman; Hang Lu
Journal:  Nat Protoc       Date:  2013-03-14       Impact factor: 13.491

4.  Size-dependent regulation of dorsal-ventral patterning in the early Drosophila embryo.

Authors:  Mayra Garcia; Marcos Nahmad; Gregory T Reeves; Angelike Stathopoulos
Journal:  Dev Biol       Date:  2013-06-22       Impact factor: 3.582

5.  Zelda potentiates morphogen activity by increasing chromatin accessibility.

Authors:  Sun Melody Foo; Yujia Sun; Bomyi Lim; Ruta Ziukaite; Kevin O'Brien; Chung-Yi Nien; Nikolai Kirov; Stanislav Y Shvartsman; Christine A Rushlow
Journal:  Curr Biol       Date:  2014-06-05       Impact factor: 10.834

6.  Pattern formation by graded and uniform signals in the early Drosophila embryo.

Authors:  Jitendra S Kanodia; Hsiao-Lan Liang; Yoosik Kim; Bomyi Lim; Mei Zhan; Hang Lu; Christine A Rushlow; Stanislav Y Shvartsman
Journal:  Biophys J       Date:  2012-02-07       Impact factor: 4.033

7.  A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila.

Authors:  Claudio D T Barros; Maira A Cardoso; Paulo M Bisch; Helena M Araujo; Francisco J P Lopes
Journal:  PLoS Comput Biol       Date:  2021-05-27       Impact factor: 4.475

8.  Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.

Authors:  Mounia Lagha; Jacques P Bothma; Emilia Esposito; Samuel Ng; Laura Stefanik; Chiahao Tsui; Jeffrey Johnston; Kai Chen; David S Gilmour; Julia Zeitlinger; Michael S Levine
Journal:  Cell       Date:  2013-05-23       Impact factor: 41.582

9.  Kinetics of gene derepression by ERK signaling.

Authors:  Bomyi Lim; Núria Samper; Hang Lu; Christine Rushlow; Gerardo Jiménez; Stanislav Y Shvartsman
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-03       Impact factor: 11.205

10.  RTK signaling modulates the Dorsal gradient.

Authors:  Aharon Helman; Bomyi Lim; María José Andreu; Yoosik Kim; Tatyana Shestkin; Hang Lu; Gerardo Jiménez; Stanislav Y Shvartsman; Ze'ev Paroush
Journal:  Development       Date:  2012-07-12       Impact factor: 6.868

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