4.7 Article

Targeted search for scaling genes reveals matrix metalloproteinase 3 as a scaler of the dorsal-ventral pattern in Xenopus laevis embryos

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

The BMP signaling gradient is interpreted through concentration thresholds in dorsal-ventral axial patterning

Hannah Greenfeld et al.

Summary: This study identified 57 genes directly activated by BMP signaling and revealed their expression in at least 3 distinct DV domains of the zebrafish embryo using Seurat analysis of single-cell RNA sequencing data. The research demonstrated that cells respond to 3 distinct levels of BMP signaling activity to activate and position target gene expression, instead of relying on BMP signaling gradient slope or exposure duration to account for differential gene expression domains along the DV axis.

PLOS BIOLOGY (2021)

Article Biology

Optogenetic investigation of BMP target gene expression diversity

Katherine W. Rogers et al.

Article Mathematics, Applied

Existence of Pulses for the System of Competition of Species

Martine Marion et al.

JOURNAL OF DYNAMICS AND DIFFERENTIAL EQUATIONS (2019)

Article Biochemistry & Molecular Biology

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

Kornel Labun et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

ilastik: interactive machine learning for (bio) image analysis

Stuart Berg et al.

NATURE METHODS (2019)

Review Developmental Biology

Positional information and tissue scaling during development and regeneration

Daniel Capek et al.

DEVELOPMENT (2019)

Article Developmental Biology

Transcriptome analysis of regeneration during Xenopus laevis experimental twinning

Eric A. Sosa et al.

INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY (2019)

Article Multidisciplinary Sciences

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

James A. Briggs et al.

SCIENCE (2018)

Article Cell Biology

Scale-invariant patterning by size-dependent inhibition of Nodal signalling

Maria Almuedo-Castillo et al.

NATURE CELL BIOLOGY (2018)

Article Multidisciplinary Sciences

Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis

Yi Ding et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Biochemistry & Molecular Biology

Combinatorial Signal Perception in the BMP Pathway

Yaron E. Antebi et al.

Review Cell Biology

Scaling of pattern formations and morphogen gradients

Hidehiko Inomata

DEVELOPMENT GROWTH & DIFFERENTIATION (2017)

Article Multidisciplinary Sciences

Genome evolution in the allotetraploid frog Xenopus laevis

Adam M. Session et al.

NATURE (2016)

Article Multidisciplinary Sciences

Noggin4 is a long-range inhibitor of Wnt8 signalling that regulates head development in Xenopus laevis

Fedor M. Eroshkin et al.

SCIENTIFIC REPORTS (2016)

Article Biochemistry & Molecular Biology

Affinity of the heparin binding motif of Noggin1 to heparan sulfate and its visualization in the embryonic tissues

Alexey M. Nesterenko et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2015)

Article Cell Biology

Axis Patterning by BMPs: Cnidarian Network Reveals Evolutionary Constraints

Grigory Genikhovich et al.

CELL REPORTS (2015)

Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Multidisciplinary Sciences

scikit-image: image processing in Python

Stefan van der Walt et al.

Article Cardiac & Cardiovascular Systems

Proteomic Identification of Matrix Metalloproteinase Substrates in the Human Vasculature

Christin Stegemann et al.

CIRCULATION-CARDIOVASCULAR GENETICS (2013)

Review Developmental Biology

Mechanisms of scaling in pattern formation

David M. Umulis et al.

DEVELOPMENT (2013)

Article Developmental Biology

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

Mayra Garcia et al.

DEVELOPMENTAL BIOLOGY (2013)

Article Multidisciplinary Sciences

Chordin forms a self-organizing morphogen gradient in the extracellular space between ectoderm and mesoderm in the Xenopus embryo

Jean-Louis Plouhinec et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Agr genes, missing in amniotes, are involved in the body appendages regeneration in frog tadpoles

Anastasiya S. Ivanova et al.

SCIENTIFIC REPORTS (2013)

Article Biotechnology & Applied Microbiology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Detecting differential usage of exons from RNA-seq data

Simon Anders et al.

GENOME RESEARCH (2012)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Article Developmental Biology

Novel functions of Noggin proteins: inhibition of Activin/Nodal and Wnt signaling

Andrey V. Bayramov et al.

DEVELOPMENT (2011)

Article Computer Science, Interdisciplinary Applications

Variance based sensitivity analysis of model output. Design and estimator for the total sensitivity index

Andrea Saltelli et al.

COMPUTER PHYSICS COMMUNICATIONS (2010)

Article Multidisciplinary Sciences

Scaling of morphogen gradients by an expansion-repression integral feedback control

Danny Ben-Zvi et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Computer Science, Interdisciplinary Applications

FiPy: Partial Differential Equations with Python

Jonathan E. Guyer et al.

COMPUTING IN SCIENCE & ENGINEERING (2009)

Letter Multidisciplinary Sciences

Scaling of BMP gradients in Xenopus embryos

Paul Francois et al.

NATURE (2009)

Article Cell Biology

Systems Biology of the Self-regulating Morphogenetic Gradient of the Xenopus Gastrula

Jean-Louis Plouhinec et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2009)

Editorial Material Developmental Biology

Induction into the Hall of Fame: tracing the lineage of Spemann's organizer

Richard Harland

DEVELOPMENT (2008)

Article Multidisciplinary Sciences

Scaling of the BMP activation gradient in Xenopus embryos

Danny Ben-Zvi et al.

NATURE (2008)

Article Biochemistry & Molecular Biology

KAAS: an automatic genome annotation and pathway reconstruction server

Yuki Moriya et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Kinetics of morphogen gradient formation

Anna Kicheva et al.

SCIENCE (2007)

Review Cell Biology

Spemann's organizer and self-regulation in amphibian embryos

EM De Robertis

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2006)

Article Developmental Biology

Multiple noggins in vertebrate genome: cloning and expression of noggin2 and noggin4 in Xenopus laevis

FM Eroshkin et al.

GENE EXPRESSION PATTERNS (2006)

Article Developmental Biology

Morphogens, their identification and regulation

T Tabata et al.

DEVELOPMENT (2004)

Article Multidisciplinary Sciences

Robustness of the BMP morphogen gradient in Drosophila embryonic patterning

A Eldar et al.

NATURE (2002)

Article Biochemistry & Molecular Biology

Osteopontin, a novel substrate for matrix metalloproteinase-3 (stromelysin-1) and matrix metalloproteinase-7 (matrilysin)

R Agnihotri et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2001)