Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

Ecological developmental biology: environmental signals for normal animal development

(2015) Scott F. Gilbert   EVOLUTION & DEVELOPMENT

Common developmental pathways link tooth shape to regeneration

(2013) Gareth J. Fraser et al.   DEVELOPMENTAL BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Mechanical regulation of signaling pathways in bone

(2012) William R. Thompson et al.   GENE

Rising StARs: Behavioral, hormonal, and molecular responses to social challenge and opportunity

(2012) Lin S. Huffman et al.   HORMONES AND BEHAVIOR

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Altered Trabecular Bone Structure and Delayed Cartilage Degeneration in the Knees of Collagen VI Null Mice

(2012) Susan E. Christensen et al.   PLoS One

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation

(2011) Moritz Muschick et al.   BMC EVOLUTIONARY BIOLOGY

Traditional and geometric morphometrics detect morphological variation of lower pharyngeal jaw inCoris julis(Teleostei, Labridae)

(2011) C. Fruciano et al.   ITALIAN JOURNAL OF ZOOLOGY

Type XII collagen regulates osteoblast polarity and communication during bone formation

(2011) Yayoi Izu et al.   JOURNAL OF CELL BIOLOGY

Evolution and molecular mechanisms of adaptive developmental plasticity

(2011) PATRÍCIA BELDADE et al.   MOLECULAR ECOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Genes as leaders and followers in evolution

(2011) Tanja Schwander et al.   TRENDS IN ECOLOGY & EVOLUTION

Metaorganisms as the new frontier

(2011) Thomas C.G. Bosch et al.   ZOOLOGY

Alternative splicing in bone following mechanical loading

(2010) Sara M. Mantila Roosa et al.   BONE

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Gene expression patterns in bone following mechanical loading

(2010) Sara M Mantila Roosa et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The amazing osteocyte

(2010) Lynda F Bonewald   JOURNAL OF BONE AND MINERAL RESEARCH

MorphoJ: an integrated software package for geometric morphometrics

(2010) CHRISTIAN PETER KLINGENBERG   Molecular Ecology Resources

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Dietary shift in benthivorous cichlids after the ecological changes in Lake Victoria

(2009) Mary Kishe-Machumu et al.   ANIMAL BIOLOGY

From mechanotransduction to extracellular matrix gene expression in fibroblasts

(2009) Matthias Chiquet et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

A comparative view on mechanisms and functions of skeletal remodelling in teleost fish, with special emphasis on osteoclasts and their function

(2009) P. Eckhard Witten et al.   BIOLOGICAL REVIEWS

Promiscuous and Depolarization-Induced Immediate-Early Response Genes Are Induced by Mechanical Strain of Osteoblasts

(2009) Claus-Eric Ott et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies

(2009) Fernando Rivadeneira et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes

(2009) K. R. Elmer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

(2009) Eva Jablonka et al.   QUARTERLY REVIEW OF BIOLOGY

An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws

(2009) Gareth J Fraser et al.   PLOS BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A Test of the “Flexible Stem” Model of Evolution: Ancestral Plasticity, Genetic Accommodation, and Morphological Divergence in the Threespine Stickleback Radiation

(2008) Matthew A. Wund et al.   AMERICAN NATURALIST

A periodic pattern generator for dental diversity

(2008) Gareth J Fraser et al.   BMC BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Surface-dependent modulation of proliferation, bone matrix molecules, and inflammatory factors in human osteoblasts

(2008) Beatrice Tonnarelli et al.   JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A

Fish and chips: functional genomics of social plasticity in an African cichlid fish

(2008) S. C. P. Renn et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS