Published in Proc Natl Acad Sci U S A on March 01, 2010
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci (2014) 5.52
Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. Proc Natl Acad Sci U S A (2012) 3.52
Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet (2011) 3.27
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
Pax6 is a human neuroectoderm cell fate determinant. Cell Stem Cell (2010) 2.46
Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq. Genome Res (2010) 2.34
Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol (2010) 1.88
High-throughput sequencing for biology and medicine. Mol Syst Biol (2013) 1.75
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome Res (2013) 1.64
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One (2011) 1.60
AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res (2011) 1.59
Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science (2014) 1.54
Promise of personalized omics to precision medicine. Wiley Interdiscip Rev Syst Biol Med (2012) 1.53
A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells (2012) 1.48
Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol (2012) 1.31
Defective photoreceptor phagocytosis in a mouse model of enhanced S-cone syndrome causes progressive retinal degeneration. FASEB J (2011) 1.29
HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology (2012) 1.27
Dynamic association of NUP98 with the human genome. PLoS Genet (2013) 1.16
Alternative splicing produces Nanog protein variants with different capacities for self-renewal and pluripotency in embryonic stem cells. J Biol Chem (2011) 1.15
Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. PLoS Genet (2012) 1.14
RNA-seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. PLoS One (2013) 1.03
Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda) (2013) 1.03
Comprehensive gene expression analysis of human embryonic stem cells during differentiation into neural cells. PLoS One (2011) 1.02
Differentially expressed, variant U1 snRNAs regulate gene expression in human cells. Genome Res (2012) 1.02
Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell (2014) 1.01
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq. PLoS One (2012) 1.00
Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet (2014) 0.99
Transcriptome analysis of microRNAs in developing cerebral cortex of rat. BMC Genomics (2012) 0.96
Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev (2015) 0.95
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics (2011) 0.95
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Res (2013) 0.94
Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. J Biol Chem (2011) 0.92
Repair at single targeted DNA double-strand breaks in pluripotent and differentiated human cells. PLoS One (2011) 0.91
Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery. DNA Res (2011) 0.89
IQdb: an intelligence quotient score-associated gene resource for human intelligence. Database (Oxford) (2013) 0.89
Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells. Genome Res (2011) 0.86
Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes. PLoS One (2014) 0.86
Thyroid hormone signaling and adult neurogenesis in mammals. Front Endocrinol (Lausanne) (2014) 0.86
Building an RNA Sequencing Transcriptome of the Central Nervous System. Neuroscientist (2015) 0.85
Identification and characterisation of the early differentiating cells in neural differentiation of human embryonic stem cells. PLoS One (2012) 0.84
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nat Neurosci (2014) 0.83
Investigating the utility of human embryonic stem cell-derived neurons to model ageing and neurodegenerative disease using whole-genome gene expression and splicing analysis. J Neurochem (2012) 0.83
Transcriptome dynamics during human erythroid differentiation and development. Genomics (2013) 0.83
Alternative splicing switching in stem cell lineages. Front Biol (Beijing) (2013) 0.82
Discovery of novel isoforms of huntingtin reveals a new hominid-specific exon. PLoS One (2015) 0.81
Alternative splicing: An important mechanism in stem cell biology. World J Stem Cells (2015) 0.81
Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo. Development (2014) 0.81
Neural Progenitor Cells Derived from Human Embryonic Stem Cells as an Origin of Dopaminergic Neurons. Stem Cells Int (2015) 0.80
Biomedical and clinical promises of human pluripotent stem cells for neurological disorders. Biomed Res Int (2013) 0.80
Non-coding RNAs in pluripotency and neural differentiation of human pluripotent stem cells. Front Genet (2014) 0.80
Suppression of histone deacetylation promotes the differentiation of human pluripotent stem cells towards neural progenitor cells. BMC Biol (2014) 0.79
Transcriptomic analysis of pluripotent stem cells: insights into health and disease. Genome Med (2011) 0.78
RNA-binding proteins in pluripotency, differentiation, and reprogramming. Front Biol (Beijing) (2014) 0.78
mRNA-Seq and microRNA-Seq whole-transcriptome analyses of rhesus monkey embryonic stem cell neural differentiation revealed the potential regulators of rosette neural stem cells. DNA Res (2014) 0.78
Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration. Proc Natl Acad Sci U S A (2013) 0.77
Recent advances in the involvement of long non-coding RNAs in neural stem cell biology and brain pathophysiology. Front Physiol (2014) 0.77
Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease. Nucleic Acids Res (2016) 0.76
Isoform diversity and its importance for axon regeneration. Neuropathology (2011) 0.76
Noncoding RNA in the transcriptional landscape of human neural progenitor cell differentiation. Front Neurosci (2015) 0.76
Stem cell pluripotency: alternative modes of transcription regulation. Cell Cycle (2010) 0.76
Transcriptional and Genomic Targets of Neural Stem Cells for Functional Recovery after Hemorrhagic Stroke. Stem Cells Int (2017) 0.75
Transcriptome analysis of Rpl11-deficient zebrafish model of Diamond-Blackfan Anemia. Genom Data (2014) 0.75
Transcriptional Regulation of Human NANOG by Alternate Promoters in Embryonic Stem Cells. J Stem Cell Res Ther (2012) 0.75
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. Nucleic Acids Res (2016) 0.75
Human Embryonic Stem Cells: A Model for the Study of Neural Development and Neurological Diseases. Stem Cells Int (2016) 0.75
EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression. Mol Cancer (2017) 0.75
Morphogenesis of human embryonic stem cells into mature neurons under in vitro culture conditions. World J Exp Med (2016) 0.75
Comparative analysis of neural transcriptomes and functional implication of unannotated intronic expression. BMC Genomics (2011) 0.75
Transcriptomics analysis of iPSC-derived neurons and modeling of neuropsychiatric disorders. Mol Cell Neurosci (2015) 0.75
HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells. PLoS One (2015) 0.75
Laser capture microdissection in Ectocarpus siliculosus: the pathway to cell-specific transcriptomics in brown algae. Front Plant Sci (2015) 0.75
Identification of key factors regulating self-renewal and differentiation in EML hematopoietic precursor cells by RNA-sequencing analysis. J Vis Exp (2014) 0.75
Human neural progenitors derived from integration-free iPSCs for SCI therapy. Stem Cell Res (2017) 0.75
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
Feeder-free growth of undifferentiated human embryonic stem cells. Nat Biotechnol (2001) 11.53
Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell (2008) 10.34
Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat Biotechnol (2003) 9.41
Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res (2006) 7.10
Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81
The development of neural stem cells. Nature (2001) 5.54
Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci U S A (2008) 4.75
Neural progenitors from human embryonic stem cells. Nat Biotechnol (2001) 4.48
Long-term self-renewal and directed differentiation of human embryonic stem cells in chemically defined conditions. Proc Natl Acad Sci U S A (2006) 3.90
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
Differentiation of human embryonic stem cells to neural lineages in adherent culture by blocking bone morphogenetic protein signaling. Stem Cells (2005) 2.36
The completion of the Mammalian Gene Collection (MGC). Genome Res (2009) 2.21
The problem of neuronal cell types: a physiological genomics approach. Trends Neurosci (2006) 2.06
Concise review: Pax6 transcription factor contributes to both embryonic and adult neurogenesis as a multifunctional regulator. Stem Cells (2008) 1.99
A Sox1 to Pax6 switch drives neuroectoderm to radial glia progression during differentiation of mouse embryonic stem cells. Stem Cells (2009) 1.71
The novel roles of glial cells revisited: the contribution of radial glia and astrocytes to neurogenesis. Curr Top Dev Biol (2005) 1.47
Sox1 acts through multiple independent pathways to promote neurogenesis. Dev Biol (2004) 1.44
SoxB transcription factors specify neuroectodermal lineage choice in ES cells. Mol Cell Neurosci (2004) 1.38
Large-scale RT-PCR recovery of full-length cDNA clones. Biotechniques (2004) 1.37
Human ESC-derived neural rosettes and neural stem cell progression. Cold Spring Harb Symp Quant Biol (2009) 1.28
Differentiation of neural lineage cells from human pluripotent stem cells. Methods (2008) 1.13
Neural differentiation of human ES cells. Curr Protoc Cell Biol (2007) 1.09
Neural commitment of embryonic stem cells: molecules, pathways and potential for cell therapy. J Pathol (2008) 0.96
Gene expression profiling of primate neocortex: molecular neuroanatomy of cortical areas. Genes Brain Behav (2006) 0.94
Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol (2006) 0.91
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science (2009) 16.35
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A (2002) 13.58
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Unlocking the secrets of the genome. Nature (2009) 11.80
A metagenomic survey of microbes in honey bee colony collapse disorder. Science (2007) 11.72
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
High-quality binary protein interaction map of the yeast interactome network. Science (2008) 10.65
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Variation in transcription factor binding among humans. Science (2010) 9.33
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation. Mol Cell Biol (2007) 7.97
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med (2008) 7.73
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
HTRA1 promoter polymorphism in wet age-related macular degeneration. Science (2006) 7.12
Performance comparison of exome DNA sequencing technologies. Nat Biotechnol (2011) 7.11
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med (2006) 6.96
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet (2004) 6.33
Unbiased whole-genome amplification directly from clinical samples. Genome Res (2003) 6.29
Analysis of one million base pairs of Neanderthal DNA. Nature (2006) 6.17
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
A novel class of small RNAs in mouse spermatogenic cells. Genes Dev (2006) 5.85
miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev Cell (2002) 5.85
Performance comparison of whole-genome sequencing platforms. Nat Biotechnol (2011) 5.79
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development (2004) 5.47
Linking disease associations with regulatory information in the human genome. Genome Res (2012) 5.47
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol (2009) 5.13
What is a gene, post-ENCODE? History and updated definition. Genome Res (2007) 4.96
Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PLoS Pathog (2009) 4.88
High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A (2006) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med (2009) 4.71
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol (2009) 4.64
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62