Published in Nat Protoc on March 01, 2012
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Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. Nat Genet (2014) 1.67
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One (2013) 1.66
The transcriptome of equine peripheral blood mononuclear cells. PLoS One (2015) 1.65
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res (2013) 1.64
Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas. Nat Genet (2016) 1.63
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A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat Commun (2014) 1.60
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Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat Neurosci (2014) 1.57
RNA sequencing of cancer reveals novel splicing alterations. Sci Rep (2013) 1.57
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Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol (2014) 1.56
Dynamic changes in histone modifications precede de novo DNA methylation in oocytes. Genes Dev (2015) 1.56
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Skin Adipocyte Stem Cell Self-Renewal Is Regulated by a PDGFA/AKT-Signaling Axis. Cell Stem Cell (2016) 1.54
Silencing of germline-expressed genes by DNA elimination in somatic cells. Dev Cell (2012) 1.54
High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol (2014) 1.53
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Combinatorial gene regulation by modulation of relative pulse timing. Nature (2015) 1.51
Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biol (2013) 1.50
Inferring expressed genes by whole-genome sequencing of plasma DNA. Nat Genet (2016) 1.50
An integrative transcriptomic atlas of organogenesis in human embryos. Elife (2016) 1.50
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The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing. Hum Mutat (2015) 1.46
Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae. Nat Microbiol (2016) 1.46
m(6)A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature (2016) 1.46
The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. Dev Cell (2016) 1.45
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The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS Genet (2016) 1.45
Differentiated human stem cells resemble fetal, not adult, β cells. Proc Natl Acad Sci U S A (2014) 1.44
Germinal centre hypoxia and regulation of antibody qualities by a hypoxia response system. Nature (2016) 1.44
Coupling organelle inheritance with mitosis to balance growth and differentiation. Science (2017) 1.44
Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLoS One (2015) 1.44
Development and Characterization of Bladder Cancer Patient-Derived Xenografts for Molecularly Guided Targeted Therapy. PLoS One (2015) 1.44
Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of Cis- and Trans-Molecular Regulation in Human Fetal and Adult Hearts. Circ Cardiovasc Genet (2016) 1.44
Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown. PLoS One (2015) 1.44
Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans. PLoS Genet (2015) 1.44
RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res (2013) 1.44
Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis. Cell (2017) 1.43
svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res (2014) 1.43
High-resolution transcriptome of human macrophages. PLoS One (2012) 1.42
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS One (2015) 1.42
Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors. Proc Natl Acad Sci U S A (2016) 1.42
Cardiomyocyte-Specific Ablation of Med1 Subunit of the Mediator Complex Causes Lethal Dilated Cardiomyopathy in Mice. PLoS One (2016) 1.41
ROR-γ drives androgen receptor expression and represents a therapeutic target in castration-resistant prostate cancer. Nat Med (2016) 1.41
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
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Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
The impact of next-generation sequencing technology on genetics. Trends Genet (2008) 21.07
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 17.53
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009) 14.83
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature (2011) 13.94
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (2009) 10.74
Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) 10.63
Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods (2010) 10.13
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
Sequence identification of 2,375 human brain genes. Nature (1992) 9.53
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
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Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (2011) 8.05
Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81
Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods (2011) 7.52
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J Am Chem Soc (2007) 4.81
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol Biol (2011) 2.98
Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS One (2011) 2.80
Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.). BMC Genomics (2010) 1.96
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Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
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Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 23.55
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
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Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
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A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) 10.63
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
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Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
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The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61
Modular regulatory principles of large non-coding RNAs. Nature (2012) 7.42
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
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A histone H3 lysine 27 demethylase regulates animal posterior development. Nature (2007) 6.57
Disordered microbial communities in asthmatic airways. PLoS One (2010) 6.35
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Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature (2008) 5.96
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
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A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93
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MAVID: constrained ancestral alignment of multiple sequences. Genome Res (2004) 5.83
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Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol (2005) 5.48
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
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Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet (2010) 5.37
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
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Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28
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Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
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Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80