Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

(2020) M. M. Halstead et al.   Scientific Reports

Perspectives on ENCODE

(2020) Michael P. Snyder et al.   NATURE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

(2020) Michelle M. Halstead et al.   BMC GENOMICS

Analysis of the wnt1 regulatory chromosomal landscape

(2019) Arne C. Lekven et al.   DEVELOPMENT GENES AND EVOLUTION

Convergent regulatory evolution and loss of flight in paleognathous birds

(2019) Timothy B. Sackton et al.   SCIENCE

Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits

(2019) Ruidong Xiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animal source foods: Sustainability problem or malnutrition and sustainability solution? Perspective matters

(2019) Adegbola T. Adesogan et al.   Global Food Security-Agriculture Policy Economics and Environment

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

(2019) Sylvain Foissac et al.   BMC BIOLOGY

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq

(2019) N. B. Kingsley et al.   Genes

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

(2018) Min Wang et al.   BMC GENOMICS

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

(2018) Ruidong Xiang et al.   BMC GENOMICS

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

(2018) Colin Kern et al.   BMC GENOMICS

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

(2018) E. N. Burns et al.   ANIMAL GENETICS

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

(2018) Elisabetta Giuffra et al.   Annual Review of Animal Biosciences

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

(2017) Fidel Botero-Castro et al.   MOLECULAR BIOLOGY AND EVOLUTION

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions

(2017) Artem V. Artemov et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2017) Ryohei Seki et al.   Nature Communications

GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

(2016) Christopher K. Tuggle et al.   ANIMAL GENETICS

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Structure, function and evolution of topologically associating domains (TADs) atHOXloci

(2015) Nicolas Lonfat et al.   FEBS LETTERS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

The Role of Six1 in the Genesis of Muscle Cell and Skeletal Muscle Development

(2014) Wangjun Wu et al.   International Journal of Biological Sciences

Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria

(2014) Craig B. Lowe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Genetic adaptation to high altitude in the Ethiopian highlands

(2012) Laura B Scheinfeldt et al.   GENOME BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

(2011) Zhihua Zhang et al.   BMC BIOINFORMATICS

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor

(2010) D.E. Janes et al.   Genome Biology and Evolution

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

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

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(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

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

(2009) Da Wei Huang et al.   Nature Protocols

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY