Introduction to sequencing the brain transcriptome.

[1]  Sarah E. London,et al.  Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior , 2014, PeerJ.

[2]  R. Harris,et al.  Altered Gamma-Aminobutyric Acid Type B Receptor Subunit 1 Splicing In Alcoholics , 2014, Biological Psychiatry.

[3]  Roland Eils,et al.  SplicingCompass: differential splicing detection using RNA-Seq data , 2013, Bioinform..

[4]  S. Grant,et al.  Discovering Genes Involved in Alcohol Dependence and Other Alcohol Responses , 2012, Alcohol research : current reviews.

[5]  Juan Liu,et al.  Integrating many co-splicing networks to reconstruct splicing regulatory modules , 2012, BMC Systems Biology.

[6]  R. Mains,et al.  Global Approaches to the Role of miRNAs in Drug-Induced Changes in Gene Expression , 2012, Front. Gene..

[7]  Daniel Bottomly,et al.  Utilizing RNA-Seq data for de novo coexpression network inference , 2012, Bioinform..

[8]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[9]  M. Miles,et al.  Ethanol modulation of gene networks: Implications for alcoholism , 2012, Neurobiology of Disease.

[10]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[11]  Athanasia C. Tzika,et al.  Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles , 2011, EvoDevo.

[12]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[13]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[14]  Alvaro G. Hernandez,et al.  Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns , 2011, PloS one.

[15]  Robert W. Williams,et al.  Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing , 2011, Front. Neurosci..

[16]  B. Graveley,et al.  microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. , 2011, RNA.

[17]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[18]  H. Steven Wiley,et al.  Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling , 2011, Bioinform..

[19]  J. Mattick.  The central role of RNA in human development and cognition , 2011, FEBS letters.

[20]  B. Tabakoff,et al.  A systems genetic analysis of alcohol drinking by mice, rats and men: Influence of brain GABAergic transmission , 2011, Neuropharmacology.

[21]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[22]  S. Horvath,et al.  Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology , 2011, Nature.

[23]  C. Harrington,et al.  Computational Detection of Alternative Exon Usage , 2011, Front. Neurosci..

[24]  J. Eberwine,et al.  Transcriptome Analysis of Single Cells , 2011, Journal of visualized experiments : JoVE.

[25]  K. Hughes,et al.  Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome , 2011, BMC Genomics.

[26]  Daniel Bottomly,et al.  Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays , 2011, PloS one.

[27]  Elaine R. Mardis,et al.  A decade’s perspective on DNA sequencing technology , 2011, Nature.

[28]  Fatih Ozsolak,et al.  RNA sequencing: advances, challenges and opportunities , 2011, Nature Reviews Genetics.

[29]  Shuli Kang,et al.  Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network , 2011, Nucleic acids research.

[30]  Songnian Hu,et al.  A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. , 2010, Genomics.

[31]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[32]  Shannon McWeeney,et al.  Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse , 2010, BMC Genomics.

[33]  A. Ciccodicola,et al.  Uncovering the Complexity of Transcriptomes with RNA-Seq , 2010, Journal of biomedicine & biotechnology.

[34]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[35]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.

[36]  Li Zhang,et al.  Large scale analysis of positional effects of single-base mismatches on microarray gene expression data , 2010, BioData Mining.

[37]  J. Rinn,et al.  Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.

[38]  Wei Zhao,et al.  Weighted Gene Coexpression Network Analysis: State of the Art , 2010, Journal of biopharmaceutical statistics.

[39]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[40]  Peter A. Noble,et al.  Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities , 2009, Nucleic acids research.

[41]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[42]  G. Koob,et al.  Genetical genomic determinants of alcohol consumption in rats and humans , 2009, BMC Biology.

[43]  N. Walter,et al.  Mapping a Barbiturate Withdrawal Locus to a 0.44 Mb Interval and Analysis of a Novel Null Mutant Identify a Role for Kcnj9 (GIRK3) in Withdrawal from Pentobarbital, Zolpidem, and Ethanol , 2009, The Journal of Neuroscience.

[44]  C. Harrington,et al.  High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs , 2009, BMC Genomics.

[45]  T. Borodina,et al.  Transcriptome analysis by strand-specific sequencing of complementary DNA , 2009, Nucleic acids research.

[46]  D. Geschwind,et al.  Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis , 2009, Neuron.

[47]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[48]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[49]  Gene W. Yeo,et al.  Determination of tag density required for digital transcriptome analysis: Application to an androgen-sensitive prostate cancer model , 2008, Proceedings of the National Academy of Sciences.

[50]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[51]  Mikkel H. Schierup,et al.  RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters , 2008, Science.

[52]  Ryan W. Kim,et al.  Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum , 2008, PloS one.

[53]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[54]  S. Horvath,et al.  Functional organization of the transcriptome in human brain , 2008, Nature Neuroscience.

[55]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[56]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[57]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[58]  Neil A. Miller,et al.  Transcriptome sequencing of malignant pleural mesothelioma tumors , 2008, Proceedings of the National Academy of Sciences.

[59]  N. Walter,et al.  Characterization of the quantitative trait locus for haloperidol‐induced catalepsy on distal mouse chromosome 1 , 2008, Genes, brain, and behavior.

[60]  E. Mardis.  The impact of next-generation sequencing technology on genetics. , 2008, Trends in genetics : TIG.

[61]  Christian Schlötterer,et al.  Gene expression profiling by massively parallel sequencing. , 2007, Genome research.

[62]  Douglas L. Black,et al.  Neuronal regulation of alternative pre-mRNA splicing , 2007, Nature Reviews Neuroscience.

[63]  Jiong Yang,et al.  PathFinder: mining signal transduction pathway segments from protein-protein interaction networks , 2007, BMC Bioinformatics.

[64]  M. Salit,et al.  Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays , 2007, BMC Bioinformatics.

[65]  J. Ohlrogge,et al.  Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.

[66]  Margit Burmeister,et al.  SNPs on Chips: The Hidden Genetic Code in Expression Arrays , 2007, Biological Psychiatry.

[67]  S. Horvath,et al.  Conservation and evolution of gene coexpression networks in human and chimpanzee brains , 2006, Proceedings of the National Academy of Sciences.

[68]  Donny D. Licatalosi,et al.  Splicing Regulation in Neurologic Disease , 2006, Neuron.

[69]  Thomas R. Sutter,et al.  How replicable are mRNA expression QTL? , 2006, Mammalian Genome.

[70]  Megan K. Mulligan,et al.  Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Sikela,et al.  DNA microarray and proteomic strategies for understanding alcohol action. , 2006, Alcoholism, clinical and experimental research.

[72]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[73]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[74]  Robert W. Williams,et al.  Complex genetics of interactions of alcohol and CNS function and behavior. , 2005, Alcoholism, clinical and experimental research.

[75]  S. Horvath,et al.  A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.

[76]  Kerrie H. Lodowski,et al.  Expression Profiling in Alcoholism Research. , 2005, Alcoholism, clinical and experimental research.

[77]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[78]  W. Mcbride,et al.  Alcohol effects on central nervous system gene expression in genetic animal models. , 2005, Alcoholism, clinical and experimental research.

[79]  Nengjun Yi,et al.  The Collaborative Cross, a community resource for the genetic analysis of complex traits , 2004, Nature Genetics.

[80]  C. Harrington,et al.  On the integration of alcohol-related quantitative trait loci and gene expression analyses. , 2004, Alcoholism, clinical and experimental research.

[81]  V. Arango,et al.  Using the Gene Ontology for Microarray Data Mining: A Comparison of Methods and Application to Age Effects in Human Prefrontal Cortex , 2004, Neurochemical Research.

[82]  J. Wehner,et al.  Gene expression in brain: a window on ethanol dependence, neuroadaptation, and preference. , 2003, Alcoholism, clinical and experimental research.

[83]  R. Harris,et al.  Gene expression in human alcoholism: microarray analysis of frontal cortex. , 2000, Alcoholism, clinical and experimental research.

[84]  L. Wodicka,et al.  Regional and strain-specific gene expression mapping in the adult mouse brain. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[85]  G. Tononi,et al.  Differences in brain gene expression between sleep and waking as revealed by mRNA differential display and cDNA microarray technology , 1999, Journal of sleep research.

[86]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[87]  H. Loh,et al.  High-affinity GABA and glutamate transport in developing nerve ending particles , 1978, Brain Research.

[88]  N. Smalheiser,et al.  Preparing synaptoneurosomes from adult mouse forebrain. , 2013, Methods in molecular biology.

[89]  Gang Feng,et al.  Using the bioconductor GeneAnswers package to interpret gene lists. , 2012, Methods in molecular biology.

[90]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[91]  W. Telford,et al.  SNPs matter: impact on detection of differential expression , 2007 .

[92]  D. Allison,et al.  Microarray data analysis: from disarray to consolidation and consensus , 2006, Nature Reviews Genetics.

[93]  Y. Leea,et al.  Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target , 2006 .

[94]  Daniel E. Zak,et al.  PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. , 2003, Omics : a journal of integrative biology.

[95]  E. Lander.  Array of hope , 1999, Nature Genetics.