Parallel evolution of male germline epigenetic poising and somatic development in animals

Detecting signatures of positive selection associated with musical aptitude in the human genome

(2016) Xuanyao Liu et al.   Scientific Reports

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells

(2015) Kazuki Kurimoto et al.   Cell Stem Cell

Tree of Life Reveals Clock-Like Speciation and Diversification

(2015) S. Blair Hedges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mouse genome database 2016

(2015) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(2015) K. Siklenka et al.   SCIENCE

Fractionation of human spermatogenic cells using STA-PUT gravity sedimentation and their miRNA profiling

(2015) Yun Liu et al.   Scientific Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

Poised chromatin in the mammalian germ line

(2014) B. J. Lesch et al.   DEVELOPMENT

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

(2014) R. K. Arthur et al.   GENOME RESEARCH

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

(2014) Joyce van de Leemput et al.   NEURON

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development

(2014) Karl B. Shpargel et al.   PLoS Genetics

Paternal Poly (ADP-ribose) Metabolism Modulates Retention of Inheritable Sperm Histones and Early Embryonic Gene Expression

(2014) Motomasa Ihara et al.   PLoS Genetics

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

(2014) Daan Noordermeer et al.   eLife

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation

(2013) Radhika Das et al.   BMC GENOMICS

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

(2013) Justin Cotney et al.   CELL

Gene Regulatory Networks Governing Pancreas Development

(2013) H. Efsun Arda et al.   DEVELOPMENTAL CELL

DOCK8 Immune Deficiency as a Model for Primary Cytoskeletal Dysfunction

(2013) Sean A. McGhee et al.   DISEASE MARKERS

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

(2013) Serap Erkek et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

EMAGE mouse embryo spatial gene expression database: 2014 update

(2013) Lorna Richardson et al.   NUCLEIC ACIDS RESEARCH

The mouse Gene Expression Database (GXD): 2014 update

(2013) Constance M. Smith et al.   NUCLEIC ACIDS RESEARCH

Many human accelerated regions are developmental enhancers

(2013) J. A. Capra et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis

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

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline In Vivo

(2013) Michael Sachs et al.   Cell Reports

Genome-Wide and Cell-Specific Epigenetic Analysis Challenges the Role of Polycomb in Drosophila Spermatogenesis

(2013) Sherif El-Sharnouby et al.   PLoS Genetics

Diversification and conservation of the extraembryonic tissues in mediating nutrient uptake during amniote development

(2012) Guojun Sheng et al.   Annals of the New York Academy of Sciences

Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst

(2012) Manabu Ozawa et al.   BMC DEVELOPMENTAL BIOLOGY

Marek’s disease virus infection induces widespread differential chromatin marks in inbred chicken lines

(2012) Apratim Mitra et al.   BMC GENOMICS

Elephant Transcriptome Provides Insights into the Evolution of Eutherian Placentation

(2012) Zhuo-Cheng Hou et al.   Genome Biology and Evolution

TFClass: an expandable hierarchical classification of human transcription factors

(2012) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

A Snapshot of Histone Modifications within Transposable Elements in Drosophila Wild Type Strains

(2012) Rita Rebollo et al.   PLoS One

Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns

(2012) Sofia Fortunato et al.   EvoDevo

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Evolutionary plasticity of segmentation clock networks

(2011) A. J. Krol et al.   DEVELOPMENT

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

(2011) S.-F. Wu et al.   GENOME RESEARCH

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Epigenetic Patterns Maintained in Early Caenorhabditis elegans Embryos Can Be Established by Gene Activity in the Parental Germ Cells

(2011) Jackelyn K. Arico et al.   PLoS Genetics

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

An assessment of histone-modification antibody quality

(2010) Thea A Egelhofer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa

(2010) Urszula Brykczynska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq

(2010) Yi Liu et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Epigenetic Temporal Control of Mouse Hox Genes in Vivo

(2009) N. Soshnikova et al.   SCIENCE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Complementary striped expression patterns of NK homeobox genes during segment formation in the annelid Platynereis

(2008) Alexandra Saudemont et al.   DEVELOPMENTAL BIOLOGY

Genesis and Expansion of Metazoan Transcription Factor Gene Classes

(2008) Claire Larroux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals

(2008) V. J. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY