Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Identification of the macrophage-specific promoter signature in FANTOM5 mouse embryo developmental time course data

(2017) Kim M. Summers et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Gene editing in birds takes flight

(2017) Mark E. Woodcock et al.   MAMMALIAN GENOME

Genes and molecular pathways underpinning ciliopathies

(2017) Jeremy F. Reiter et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease

(2017) Sarah M Carpanini et al.   NEUROGENETICS

Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat

(2017) Angelica Van Goor et al.   PLoS One

Systematic analysis of transcription start sites in avian development

(2017) Marina Lizio et al.   PLOS BIOLOGY

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

(2017) Emily L. Clark et al.   PLoS Genetics

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples

(2017) Anna Esteve-Codina et al.   PLoS One

Transcriptome analyses of differential gene expression in the bursa of Fabricius between Silky Fowl and White Leghorn

(2017) Deping Han et al.   Scientific Reports

Rab32 and Rab38 genes in chordate pigmentation: an evolutionary perspective

(2016) Ugo Coppola et al.   BMC EVOLUTIONARY BIOLOGY

The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens

(2016) A. Psifidi et al.   BMC GENOMICS

Genetic Basis for Red Coloration in Birds

(2016) Ricardo J. Lopes et al.   CURRENT BIOLOGY

Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas

(2016) Else Eising et al.   HUMAN GENETICS

Mutations inCEP120cause Joubert syndrome as well as complex ciliopathy phenotypes

(2016) Susanne Roosing et al.   JOURNAL OF MEDICAL GENETICS

Transcriptomic changes throughout post-hatch development inGallus galluspituitary

(2016) Elizabeth M Pritchett et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Transcriptome sequencing reveals genetic mechanisms underlying the transition between the laying and brooding phases and gene expression changes associated with divergent reproductive phenotypes in chickens

(2016) Xu Shen et al.   MOLECULAR BIOLOGY REPORTS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis

(2016) Fei He et al.   PLANT JOURNAL

mRNA expression in different developmental stages of the chicken bursa of Fabricius

(2016) Xiao-dong Liu et al.   POULTRY SCIENCE

Specification of tissue-resident macrophages during organogenesis

(2016) E. Mass et al.   SCIENCE

RNA sequencing analysis of the developing chicken retina

(2016) Christophe J. Langouet-Astrie et al.   Scientific Data

Immunolocalization of a Histidine-Rich Epidermal Differentiation Protein in the Chicken Supports the Hypothesis of an Evolutionary Developmental Link between the Embryonic Subperiderm and Feather Barbs and Barbules

(2016) Lorenzo Alibardi et al.   PLoS One

Transcriptome analysis of Streptococcus pneumoniae treated with the designed antimicrobial peptides, DM3

(2016) Cheng-Foh Le et al.   Scientific Reports

Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force

(2015) K. Piórkowska et al.   ANIMAL GENETICS

The development and maintenance of the mononuclear phagocyte system of the chick is controlled by signals from the macrophage colony-stimulating factor receptor

(2015) Valerie Garceau et al.   BMC BIOLOGY

Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

(2015) Shanrong Zhao et al.   BMC GENOMICS

Third Report on Chicken Genes and Chromosomes 2015

(2015) Michael Schmid et al.   CYTOGENETIC AND GENOME RESEARCH

Cell-Autonomous Sex Differences in Gene Expression in Chicken Bone Marrow–Derived Macrophages

(2015) Carla Garcia-Morales et al.   JOURNAL OF IMMUNOLOGY

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

(2015) Anagha Joshi et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation

(2015) Xiaodi Su et al.   NATURE IMMUNOLOGY

Integrated interactions database: tissue-specific view of the human and model organism interactomes

(2015) Max Kotlyar et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

BioGPS: building your own mash-up of gene annotations and expression profiles

(2015) Chunlei Wu et al.   NUCLEIC ACIDS RESEARCH

ERK Signaling Is Essential for Macrophage Development

(2015) Edward T. Richardson et al.   PLoS One

Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

(2015) Ping Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The Extent of mRNA Editing Is Limited in Chicken Liver and Adipose, but Impacted by Tissular Context, Genotype, Age, and Feeding as Exemplified with a Conserved Edited Site in COG3

(2015) Pierre-François Roux et al.   G3-Genes Genomes Genetics

RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

(2015) Christopher W. Resnyk et al.   PLoS One

Dynamic Changes in the Follicular Transcriptome and Promoter DNA Methylation Pattern of Steroidogenic Genes in Chicken Follicles throughout the Ovulation Cycle

(2015) Guiyu Zhu et al.   PLoS One

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Influence of RNA extraction methods and library selection schemes on RNA-seq data

(2014) Marc Sultan et al.   BMC GENOMICS

Visualisation of chicken macrophages using transgenic reporter genes: insights into the development of the avian macrophage lineage

(2014) A. Balic et al.   DEVELOPMENT

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Origin and Functions of Tissue Macrophages

(2014) Slava Epelman et al.   IMMUNITY

TIM-4 Expressed on APCs Induces T Cell Expansion and Survival

(2014) R. Rodriguez-Manzanet et al.   JOURNAL OF IMMUNOLOGY

Osteal Tissue Macrophages Are Intercalated throughout Human and Mouse Bone Lining Tissues and Regulate Osteoblast Function In Vitro and In Vivo

(2014) M. K. Chang et al.   JOURNAL OF IMMUNOLOGY

Evolutionary Origin and Diversification of Epidermal Barrier Proteins in Amniotes

(2014) Bettina Strasser et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

In silico prediction of physical protein interactions and characterization of interactome orphans

(2014) Max Kotlyar et al.   NATURE METHODS

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens1

(2014) Y. Wang et al.   POULTRY SCIENCE

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment

(2013) Tamasin N Doig et al.   BMC GENOMICS

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions

(2013) Brian R Johnson et al.   BMC GENOMICS

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

Development of a high density 600K SNP genotyping array for chicken

(2013) Andreas Kranis et al.   BMC GENOMICS

Can DCs be distinguished from macrophages by molecular signatures?

(2013) David A Hume et al.   NATURE IMMUNOLOGY

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Claudins and the Modulation of Tight Junction Permeability

(2013) Dorothee Günzel et al.   PHYSIOLOGICAL REVIEWS

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

(2013) Thomas P. van Gurp et al.   PLoS One

Chick stem cells: Current progress and future prospects

(2013) Sittipon Intarapat et al.   Stem Cell Research

Integrated Genomic Approaches to Enhance Genetic Resistance in Chickens

(2013) Hans H. Cheng et al.   Annual Review of Animal Biosciences

A gene expression atlas of the domestic pig

(2012) Tom C Freeman et al.   BMC BIOLOGY

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Pig Bone Marrow-Derived Macrophages Resemble Human Macrophages in Their Response to Bacterial Lipopolysaccharide

(2012) R. Kapetanovic et al.   JOURNAL OF IMMUNOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

(2012) Emmanuel L Gautier et al.   NATURE IMMUNOLOGY

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Generation of mice with functional inactivation of talpid3, a gene first identified in chicken

(2011) F. Bangs et al.   DEVELOPMENT

From buds to follicles: Matrix metalloproteinases in developmental tissue remodeling during feather morphogenesis

(2011) Ting-Xin Jiang et al.   DIFFERENTIATION

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Large-scaleDe NovoPrediction of Physical Protein-Protein Association

(2011) Antigoni Elefsinioti et al.   MOLECULAR & CELLULAR PROTEOMICS

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

TassDB2 - A comprehensive database of subtle alternative splicing events

(2010) Rileen Sinha et al.   BMC BIOINFORMATICS

The induction of STAT1 gene by activating transcription factor 3 contributes to pancreatic β-cell apoptosis and its dysfunction in streptozotocin-treated mice

(2010) Ji Yeon Kim et al.   CELLULAR SIGNALLING

All-Trans Retinoic Acid Regulates Cx43 Expression, Gap Junction Communication and Differentiation in Primary Lens Epithelial Cells

(2010) Amy C. Long et al.   CURRENT EYE RESEARCH

Functional clustering and lineage markers: Insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations

(2010) David A. Hume et al.   GENOMICS

Uric acid transport and disease

(2010) Alexander So et al.   JOURNAL OF CLINICAL INVESTIGATION

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation

(2009) Y. Yin et al.   DEVELOPMENT

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

MafB/c-Maf Deficiency Enables Self-Renewal of Differentiated Functional Macrophages

(2009) A. Aziz et al.   SCIENCE

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair

(2008) Dong-Dong Wu et al.   BMC EVOLUTIONARY BIOLOGY

Biochemical characterization of human epidermal retinol dehydrogenase 2

(2008) Seung-Ah Lee et al.   CHEMICO-BIOLOGICAL INTERACTIONS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

PU.1 and C/EBP /  convert fibroblasts into macrophage-like cells

(2008) R. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

(2008) Z. Bar-Joseph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA