Core and region-enriched networks of behaviorally regulated genes and the singing genome

Npas4 Regulates Excitatory-Inhibitory Balance within Neural Circuits through Cell-Type-Specific Gene Programs

(2014) Ivo Spiegel et al.   CELL

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Convergent transcriptional specializations in the brains of humans and song-learning birds

(2014) A. R. Pfenning et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Global view of the functional molecular organization of the avian cerebrum: Mirror images and functional columns

(2013) Erich D. Jarvis et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

Calbindin expression in developing striatum of zebra finches and its relation to the formation of area X

(2012) Elena Garcia-Calero et al.   JOURNAL OF COMPARATIVE NEUROLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Molecular Microcircuitry Underlies Functional Specification in a Basal Ganglia Circuit Dedicated to Vocal Learning

(2012) Austin T. Hilliard et al.   NEURON

Specialized Motor-Driven dusp1 Expression in the Song Systems of Multiple Lineages of Vocal Learning Birds

(2012) Haruhito Horita et al.   PLoS One

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

(2011) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

Evo-devo, deep homology and FoxP2: implications for the evolution of speech and language

(2011) C. Scharff et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mechanisms of specificity in neuronal activity-regulated gene transcription

(2011) Michelle R. Lyons et al.   PROGRESS IN NEUROBIOLOGY

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

(2011) A. E. West et al.   Cold Spring Harbor Perspectives in Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The dusp1 immediate early gene is regulated by natural stimuli predominantly in sensory input neurons

(2010) Haruhito Horita et al.   JOURNAL OF COMPARATIVE NEUROLOGY

CREB: a multifaceted regulator of neuronal plasticity and protection

(2010) Kensuke Sakamoto et al.   JOURNAL OF NEUROCHEMISTRY

Reduced Cortical BDNF Expression and Aberrant Memory in Carf Knock-Out Mice

(2010) K. A. McDowell et al.   JOURNAL OF NEUROSCIENCE

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways

(2010) Andreas R. Pfenning et al.   PLoS One

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

(2010) Jaebum Kim et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Integrative analysis of RUNX1 downstream pathways and target genes

(2009) Joëlle Michaud et al.   BMC GENOMICS

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation

(2009) Tamara Aid-Pavlidis et al.   BMC GENOMICS

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

(2009) J. Boros et al.   GENOME RESEARCH

Dopamine receptors in a songbird brain

(2009) Lubica Kubikova et al.   JOURNAL OF COMPARATIVE NEUROLOGY

The Function of Activity-Regulated Genes in the Nervous System

(2009) Sven Loebrich et al.   PHYSIOLOGICAL REVIEWS

Honey bee aggression supports a link between gene regulation and behavioral evolution

(2009) C. Alaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discrete molecular states in the brain accompany changing responses to a vocal signal

(2009) S. Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signaling Mechanisms Linking Neuronal Activity to Gene Expression and Plasticity of the Nervous System

(2008) Steven W. Flavell et al.   Annual Review of Neuroscience

The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution

(2008) Kirstin L Replogle et al.   BMC GENOMICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Developmental and activity-dependent genomic occupancy profiles of CREB in monkey area V1

(2008) J. Lalonde et al.   GENES BRAIN AND BEHAVIOR

Systematic functional characterization of cis-regulatory motifs in human core promoters

(2008) S. Sinha et al.   GENOME RESEARCH

Birdsong Decreases Protein Levels of FoxP2, a Molecule Required for Human Speech

(2008) Julie E. Miller et al.   JOURNAL OF NEUROPHYSIOLOGY

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection

(2008) Steven W. Flavell et al.   NEURON

G2Cdb: the Genes to Cognition database

(2008) M. D. R. Croning et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2008) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Molecular Mapping of Movement-Associated Areas in the Avian Brain: A Motor Theory for Vocal Learning Origin

(2008) Gesa Feenders et al.   PLoS One

Birdsong “Transcriptomics”: Neurochemical Specializations of the Oscine Song System

(2008) Peter V. Lovell et al.   PLoS One

Rapid encoding of new information alters the profile of plasticity-related mRNA transcripts in the hippocampal CA3 region

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

A Specialized Forebrain Circuit for Vocal Babbling in the Juvenile Songbird

(2008) D. Aronov et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY