Skip to main content
Table of Contents

June 2014

For the marine invertebrate Ciona intestinalis, the patterning of developing sensory neurons along the tail midlines (demarcated using a midline reporter, green) is irregular, with spacings ranging from one cell (cell nuclei in blue) to thirteen cells between consecutive neurons (double red dots), which are specified through a feedback loop involving Notch-Delta signaling and the microRNA miR-124. Building upon classical Notch-Delta models, this experimental data led to the formulation of an expanded mathematical model that explains this irregular patterning. Experimental and computational evidence from other organisms suggests that this expanded model may also explain Notch-Delta-mediated neuronal patterning in other animals. See Chen et al.

Image Credit: Jerry S. Chen and Robert W. Zeller


Ten Simple Rules for Approaching a New Job

Philip E. Bourne


A New Online Computational Biology Curriculum

David B. Searls

Related Articles

Research Articles

Unsupervised Learning of Cone Spectral Classes from Natural Images

Noah C. Benson, Jeremy R. Manning, David H. Brainard

Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics

Jake M. Ferguson, Jessica B. Langebrake, Vincent L. Cannataro, Andres J. Garcia, Elizabeth A. Hamman, Maia Martcheva, Craig W. Osenberg

Related Articles

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra

Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes

Jaime Iranzo, Manuel J. Gómez, Francisco J. López de Saro, Susanna Manrubia

Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant

Sergei V. Krivov, Hayley Fenton, Paul J. Goldsmith, Rajendra K. Prasad, Julie Fisher, Emanuele Paci

Yeast Mating and Image-Based Quantification of Spatial Pattern Formation

Christian Diener, Gabriele Schreiber, Wolfgang Giese, Gabriel del Rio, Andreas Schröder, Edda Klipp

Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins

Joe DeBartolo, Mikko Taipale, Amy E. Keating

Limits of Feedback Control in Bacterial Chemotaxis

Yann S. Dufour, Xiongfei Fu, Luis Hernandez-Nunez, Thierry Emonet

Related Articles

Pierced Lasso Bundles Are a New Class of Knot-like Motifs

Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings

Quantification of HTLV-1 Clonality and TCR Diversity

Daniel J. Laydon, Anat Melamed, Aaron Sim, Nicolas A. Gillet, Kathleen Sim, Sam Darko, J. Simon Kroll, Daniel C. Douek, David A. Price, Charles R. M. Bangham, Becca Asquith

An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation

Jerry S. Chen, Abygail M. Gumbayan, Robert W. Zeller, Joseph M. Mahaffy

Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses

Nadine Töpfer, Federico Scossa, Alisdair Fernie, Zoran Nikoloski

On the Origins of Suboptimality in Human Probabilistic Inference

Luigi Acerbi, Sethu Vijayakumar, Daniel M. Wolpert

A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

Carlos Castro-González, Miguel A. Luengo-Oroz, Louise Duloquin, Thierry Savy, Barbara Rizzi, Sophie Desnoulez, René Doursat, Yannick L. Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, Andrés Santos

Related Articles

An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load

Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, James I. Mullins

Identifying Crucial Parameter Correlations Maintaining Bursting Activity

Anca Doloc-Mihu, Ronald L. Calabrese

A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells

Borislav Savkovic, James Nichols, Donald Birkett, Tanya Applegate, Scott Ledger, Geoff Symonds, John M. Murray

A Unifying Mechanistic Model of Selective Attention in Spiking Neurons

Bruce Bobier, Terrence C. Stewart, Chris Eliasmith

Spatial Transmission of 2009 Pandemic Influenza in the US

Julia R. Gog, Sébastien Ballesteros, Cécile Viboud, Lone Simonsen, Ottar N. Bjornstad, Jeffrey Shaman, Dennis L. Chao, Farid Khan, Bryan T. Grenfell

Negative Example Selection for Protein Function Prediction: The NoGO Database

Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis Shasha

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh

Model Selection in Systems Biology Depends on Experimental Design

Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni, Michael P. H. Stumpf

Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways

Martin H. Schaefer, Jae-Seong Yang, Luis Serrano, Christina Kiel

Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference

Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch

A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction

Patricia Garcia-Canadilla, Paula A. Rudenick, Fatima Crispi, Monica Cruz-Lemini, Georgina Palau, Oscar Camara, Eduard Gratacos, Bart H. Bijens

Related Articles

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions

Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng

CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data

Michael J. McGeachie, Hsun-Hsien Chang, Scott T. Weiss

Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells

Ondrej Podlaha, Subhajyoti De, Mithat Gonen, Franziska Michor

Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient

Lorena Sigaut, John E. Pearson, Alejandro Colman-Lerner, Silvina Ponce Dawson

A Novel Cell Traction Force Microscopy to Study Multi-Cellular System

Xin Tang, Alireza Tofangchi, Sandeep V. Anand, Taher A. Saif

A Normative Theory of Forgetting: Lessons from the Fruit Fly

Johanni Brea, Robert Urbanczik, Walter Senn

Place Cell Rate Remapping by CA3 Recurrent Collaterals

Trygve Solstad, Hosam N. Yousif, Terrence J. Sejnowski

Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome

Michael Kuhn, Anthony A. Hyman, Andreas Beyer

Optimizing Metabolite Production Using Periodic Oscillations

Steven W. Sowa, Michael Baldea, Lydia M. Contreras

Poisson-Like Spiking in Circuits with Probabilistic Synapses

Rubén Moreno-Bote