Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

(2016) Eric T Domyan et al.   eLife

Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight

(2015) T. J. Feo et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Function of the Alula in Avian Flight

(2015) Sang-im Lee et al.   Scientific Reports

New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers

(2014) Christian Foth et al.   NATURE

An integrative approach to understanding bird origins

(2014) X. Xu et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

A novel regulatory element for Shh expression in the lung and gut of mouse embryos

(2013) Nagaharu Tsukiji et al.   MECHANISMS OF DEVELOPMENT

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

(2013) Zhuo Wang et al.   NATURE GENETICS

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Evolutionary and Developmental Aspects of Avian-Specific Traits in Limb Skeletal Pattern

(2012) Ryohei Seki et al.   ZOOLOGICAL SCIENCE

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Embryological Evidence Identifies Wing Digits in Birds as Digits 1, 2, and 3

(2011) K. Tamura et al.   SCIENCE

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Exceptional dinosaur fossils show ontogenetic development of early feathers

(2010) Xing Xu et al.   NATURE

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Narrow Primary Feather Rachises in Confuciusornis and Archaeopteryx Suggest Poor Flight Ability

(2010) R. L. Nudds et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Sim1 and Sim2 expression during chick and mouse limb development

(2009) Pascal Coumailleau et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus

(2009) Dongyu Hu et al.   NATURE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Normal developmental stages of the Madagascar ground geckoParoedura pictuswith special reference to limb morphogenesis

(2008) Miyuki Noro et al.   DEVELOPMENTAL DYNAMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY