Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

What Does It Take to Evolve an Enhancer? A Simulation-Based Study of Factors Influencing the Emergence of Combinatorial Regulation

(2015) T. Duque et al.   Genome Biology and Evolution

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Automated adaptive inference of phenomenological dynamical models

(2015) Bryan C. Daniels et al.   Nature Communications

Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

(2015) Karl R Wotton et al.   eLife

Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects

(2014) Majid Kazemian et al.   Genome Biology and Evolution

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Morphogenesis at criticality

(2014) D. Krotov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolving phenotypic networks in silico

(2014) Paul François   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A quantitative atlas of Even-skipped and Hunchback expression in Clogmia albipunctata (Diptera: Psychodidae) blastoderm embryos

(2014) Hilde Janssens et al.   EvoDevo

Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes

(2014) Miriam I Rosenberg et al.   eLife

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

(2014) Sarah K Bowman et al.   eLife

An analysis of segmentation dynamics throughout embryogenesis in the centipede Strigamia maritima

(2013) Carlo Brena et al.   BMC BIOLOGY

Evolution of the pair rule gene network: Insights from a centipede

(2013) Jack Green et al.   DEVELOPMENTAL BIOLOGY

Positional information, in bits

(2013) J. O. Dubuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The edges of understanding

(2012) Arthur D Lander   BMC BIOLOGY

Phenotypic models of evolution and development: geometry as destiny

(2012) Paul François et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A segmentation clock operating in blastoderm and germband stages of Tribolium development

(2012) E. El-Sherif et al.   DEVELOPMENT

Efficient Reverse-Engineering of a Developmental Gene Regulatory Network

(2012) Anton Crombach et al.   PLoS Computational Biology

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

(2011) P. Struffi et al.   DEVELOPMENT

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

(2011) M. D. Schroeder et al.   DEVELOPMENT

The Drosophila Gap Gene Network Is Composed of Two Parallel Toggle Switches

(2011) Dmitri Papatsenko et al.   PLoS One

Expression of myriapod pair rule gene orthologs

(2011) Ralf Janssen et al.   EvoDevo

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Comparisons of the embryonic development of Drosophila , Nasonia , and Tribolium

(2011) Jeremy A. Lynch et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Predicting embryonic patterning using mutual entropy fitness and in silico evolution

(2010) P. Francois et al.   DEVELOPMENT

A systematic analysis of the gap gene system in the moth midge Clogmia albipunctata

(2010) Mónica García-Solache et al.   DEVELOPMENTAL BIOLOGY

Parallelism as the pattern and process of mesoevolution

(2010) Ehab Abouheif   EVOLUTION & DEVELOPMENT

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Conservation of enhancer location in divergent insects

(2009) J. Cande et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics