Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration

Notum deacylates Wnt proteins to suppress signalling activity

(2015) Satoshi Kakugawa et al.   NATURE

Limbform: a functional ontology-based database of limb regeneration experiments

(2014) D. Lobo et al.   BIOINFORMATICS

Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search

(2014) Marianna Budnikova et al.   BMC BIOINFORMATICS

The origin and loss of periodic patterning in the turtle shell

(2014) J. E. Moustakas-Verho et al.   DEVELOPMENT

A linear-encoding model explains the variability of the target morphology in regeneration

(2014) D. Lobo et al.   Journal of the Royal Society Interface

A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut

(2014) Daniel Botman et al.   PLoS One

Amplify scientific discovery with artificial intelligence

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Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients

(2014) J. Raspopovic et al.   SCIENCE

Bioelectrical Mechanisms for Programming Growth and Form: Taming Physiological Networks for Soft Body Robotics

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Planform: an application and database of graph-encoded planarian regenerative experiments

(2013) D. Lobo et al.   BIOINFORMATICS

A review of morphogenetic engineering

(2013) René Doursat et al.   Natural Computing

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster

(2013) Kolja Becker et al.   PLoS Computational Biology

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

(2013) Evan J. Molinelli et al.   PLoS Computational Biology

Thick and thin fingers point out Turing waves

(2013) Andrew D Economou et al.   GENOME BIOLOGY

Making sense—data-based simulations of vertebrate limb development

(2012) Dagmar Iber et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Stem cell systems and regeneration in planaria

(2012) Jochen C. Rink   DEVELOPMENT GENES AND EVOLUTION

Normalized shape and location of perturbed craniofacial structures in the Xenopus tadpole reveal an innate ability to achieve correct morphology

(2012) Laura N. Vandenberg et al.   DEVELOPMENTAL DYNAMICS

The cell biology of regeneration

(2012) Ryan S. King et al.   JOURNAL OF CELL BIOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Developmental Pattern Formation: Insights from Physics and Biology

(2012) A. Kicheva et al.   SCIENCE

Hox Genes Regulate Digit Patterning by Controlling the Wavelength of a Turing-Type Mechanism

(2012) R. Sheth et al.   SCIENCE

Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm

(2012) Daniel Lobo et al.   PLoS Computational Biology

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

(2012) Anton Crombach et al.   PLoS Computational Biology

Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis

(2012) D. Lobo et al.   Biology Open

Quantitative Variation in Autocrine Signaling and Pathway Crosstalk in the Caenorhabditis Vulval Network

(2011) Erika Hoyos et al.   CURRENT BIOLOGY

Noggin and Noggin-Like Genes Control Dorsoventral Axis Regeneration in Planarians

(2011) M. Dolores Molina et al.   CURRENT BIOLOGY

A Bmp/Admp Regulatory Circuit Controls Maintenance and Regeneration of Dorsal-Ventral Polarity in Planarians

(2011) Michael A. Gaviño et al.   CURRENT BIOLOGY

Clonogenic Neoblasts Are Pluripotent Adult Stem Cells That Underlie Planarian Regeneration

(2011) D. E. Wagner et al.   SCIENCE

Polarized notum Activation at Wounds Inhibits Wnt Function to Promote Planarian Head Regeneration

(2011) C. P. Petersen et al.   SCIENCE

Comparison of evolutionary algorithms in gene regulatory network model inference

(2010) Alina Sîrbu et al.   BMC BIOINFORMATICS

On growth and form: a Cartesian coordinate system of Wnt and BMP signaling specifies bilaterian body axes

(2010) C. Niehrs   DEVELOPMENT

Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response

(2010) Kyle A. Gurley et al.   DEVELOPMENTAL BIOLOGY

Chiral Forces Organize Left-Right Patterning in C. elegans by Uncoupling Midline and Anteroposterior Axis

(2010) Christian Pohl et al.   DEVELOPMENTAL CELL

A computational model of teeth and the developmental origins of morphological variation

(2010) Isaac Salazar-Ciudad et al.   NATURE

Genotype to Phenotype: A Complex Problem

(2010) R. D. Dowell et al.   SCIENCE

Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation

(2010) S. Kondo et al.   SCIENCE

Predictive Mesoscale Network Model of Cell Fate Decisions during C. elegans Embryogenesis

(2009) David A. Winkler et al.   ARTIFICIAL LIFE

Beta-catenin and axis formation in planarians

(2009) Hans Meinhardt   BIOESSAYS

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration

(2009) Néstor J. Oviedo et al.   DEVELOPMENTAL BIOLOGY

Planarian regeneration: achievements and future directions after 20 years of research

(2009) Emili Salo et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Quantitative approaches in developmental biology

(2009) Andrew C. Oates et al.   NATURE REVIEWS GENETICS

A wound-induced Wnt expression program controls planarian regeneration polarity

(2009) C. P. Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Planarian Hh Signaling Regulates Regeneration Polarity and Links Hh Pathway Evolution to Cilia

(2009) J. C. Rink et al.   SCIENCE

The Automation of Science

(2009) Ross D. King et al.   SCIENCE

Gradients in Planarian Regeneration and Homeostasis

(2009) T. Adell et al.   Cold Spring Harbor Perspectives in Biology

Models for the Generation and Interpretation of Gradients

(2009) H. Meinhardt   Cold Spring Harbor Perspectives in Biology

Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation

(2009) Manu et al.   PLOS BIOLOGY

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

(2009) Manu et al.   PLoS Computational Biology

Comparative Aspects of Animal Regeneration

(2008) Jeremy P. Brockes et al.   Annual Review of Cell and Developmental Biology

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

Silencing of Smed- catenin1 generates radial-like hypercephalized planarians

(2008) M. Iglesias et al.   DEVELOPMENT

Michigan molecular interactions r2: from interacting proteins to pathways

(2008) V. G. Tarcea et al.   NUCLEIC ACIDS RESEARCH

 -Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis

(2007) K. A. Gurley et al.   SCIENCE

Smed- catenin-1 Is Required for Anteroposterior Blastema Polarity in Planarian Regeneration

(2007) C. P. Petersen et al.   SCIENCE