Published in Nat Methods on May 30, 2008
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
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
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
An integrated genomic analysis of human glioblastoma multiforme. Science (2008) 51.36
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science (2008) 36.02
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics (2008) 24.32
A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol (2010) 22.10
Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature (2010) 22.04
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol (2011) 16.53
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012) 14.76
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell (2013) 13.43
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc (2013) 13.33
Statistical inferences for isoform expression in RNA-Seq. Bioinformatics (2009) 12.50
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71
Genome regulation by long noncoding RNAs. Annu Rev Biochem (2012) 11.70
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (2009) 10.74
Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32
Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods (2010) 10.13
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res (2008) 10.10
Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol (2010) 10.05
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68
The origin and evolution of mutations in acute myeloid leukemia. Cell (2012) 9.66
Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res (2009) 9.42
Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40
Initial impact of the sequencing of the human genome. Nature (2011) 9.18
Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol (2010) 9.15
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics (2009) 8.69
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol (2014) 8.13
Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res (2012) 7.52
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol (2009) 7.47
An anatomically comprehensive atlas of the adult human brain transcriptome. Nature (2012) 7.46
Modular regulatory principles of large non-coding RNAs. Nature (2012) 7.42
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res (2011) 6.90
Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell (2010) 6.88
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet (2011) 6.52
A unifying model for mTORC1-mediated regulation of mRNA translation. Nature (2012) 6.44
Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics (2009) 6.41
The antisense transcriptomes of human cells. Science (2008) 6.29
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol (2010) 6.10
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci (2011) 6.01
Next-generation transcriptome assembly. Nat Rev Genet (2011) 5.89
Next-generation genomics: an integrative approach. Nat Rev Genet (2010) 5.88
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci (2014) 5.52
Determinants of nucleosome organization in primary human cells. Nature (2011) 5.50
Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet (2013) 5.48
Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol (2011) 5.48
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res (2009) 5.24
CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics (2009) 5.14
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
Stacks: building and genotyping Loci de novo from short-read sequences. G3 (Bethesda) (2011) 4.99
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res (2012) 4.81
Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol (2014) 4.74
The genetic landscape of high-risk neuroblastoma. Nat Genet (2013) 4.71
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods (2009) 4.69
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Landscape of transcription in human cells. Nature (2012) 20.18
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res (2013) 3.61
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res (2006) 3.23
For outpatient rotator cuff surgery, nerve block anesthesia provides superior same-day recovery over general anesthesia. Anesthesiology (2005) 3.13
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell (2012) 2.38
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99
Significance and statistical errors in the analysis of DNA microarray data. Proc Natl Acad Sci U S A (2002) 1.92
Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res (2010) 1.73
Adverse outcomes associated with stimulator-based peripheral nerve blocks with versus without ultrasound visualization. Reg Anesth Pain Med (2009) 1.68
Adverse outcomes associated with nerve stimulator-guided and ultrasound-guided peripheral nerve blocks by supervised trainees: update of a single-site database. Reg Anesth Pain Med (2012) 1.50
Effect of adjuvant drugs on the action of local anesthetics in isolated rat sciatic nerves. Reg Anesth Pain Med (2012) 1.49
Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A (2013) 1.48
Retrospective evaluation of unanticipated admissions and readmissions after same day surgery and associated costs. J Clin Anesth (2002) 1.44
The up-down methodology and practical peripheral nerve blockade. Reg Anesth Pain Med (2010) 1.42
Post-operative nausea and vomiting prevention with perphenazine: long overdue. Eur J Anaesthesiol (2011) 1.38
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biol (2013) 1.37
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Res (2011) 1.24
Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects. Plant Cell (2012) 1.17
Transient heat hyperalgesia during resolution of ropivacaine sciatic nerve block in the rat. Reg Anesth Pain Med (2011) 1.15
Brachial plexus anatomy: normal and variant. ScientificWorldJournal (2009) 1.15
Femoral nerve block for anterior cruciate ligament reconstruction--do we have the information we need? Letter to the editor. Am J Sports Med (2015) 1.08
Ultrasound guidance with nerve stimulation reduces the time necessary for resident peripheral nerve blockade. Reg Anesth Pain Med (2007) 1.04
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A (2012) 1.04
The incidence of falls at home in patients with perineural femoral catheters: a retrospective summary of a randomized clinical trial. Anesth Analg (2007) 1.03
Hospitalization costs of total knee arthroplasty with a continuous femoral nerve block provided only in the hospital versus on an ambulatory basis: a retrospective, case-control, cost-minimization analysis. Reg Anesth Pain Med (2007) 1.02
Additives to local anesthetics for peripheral nerve blockade. Int Anesthesiol Clin (2011) 1.02
Anesthesia and postoperative analgesia: outcomes following orthopedic surgery. Orthopedics (2003) 0.99
Microglia in the cerebral cortex in autism. J Autism Dev Disord (2012) 0.95
Diplopia: a complication of dural puncture. Anesthesiology (2004) 0.95
Loss of extension following anterior cruciate ligament reconstruction: analysis of incidence and etiology using IKDC criteria. Arthroscopy (2007) 0.94
Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing. Angew Chem Int Ed Engl (2006) 0.94
Aprepitant plus ondansetron compared with ondansetron alone in reducing postoperative nausea and vomiting in ambulatory patients undergoing plastic surgery. Plast Reconstr Surg (2012) 0.94
Case report: postoperative analgesia and preserved motor function with clonidine and buprenorphine via a sciatic perineural catheter. J Clin Anesth (2009) 0.91
Diabetes mellitus, independent of body mass index, is associated with a "higher success" rate for supraclavicular brachial plexus blocks. Reg Anesth Pain Med (2009) 0.91
Antiemetics in outpatient regional anesthesia for invasive orthopedic surgery. Int Anesthesiol Clin (2005) 0.85
Post-anesthesia vomiting: impact of isoflurane and morphine on ferrets and musk shrews. Physiol Behav (2012) 0.84
Updating RNA-Seq analyses after re-annotation. Bioinformatics (2013) 0.84
Transcriptional regulation by nicotine in dopaminergic neurons. Biochem Pharmacol (2013) 0.83
Fast-track ambulatory anesthesia: impact on nursing workload when analgesia and antiemetic prophylaxis are near-optimal. Can J Anaesth (2007) 0.82
For outpatients, does regional anesthesia truly shorten the hospital stay, and how should we define postanesthesia care unit bypass eligibility? Anesthesiology (2004) 0.82
Mechanisms underlying midazolam-induced peripheral nerve block and neurotoxicity. Reg Anesth Pain Med (2014) 0.81
Diabetes mellitus and subclinical neuropathy: a call for new paths in peripheral nerve block research. Anesthesiology (2008) 0.80
Potential economic benefits of regional anesthesia for acute pain management: the need to study both inputs and outcomes. Reg Anesth Pain Med (2006) 0.79
Postoperative nausea and vomiting in ambulatory regional anesthesia. Int Anesthesiol Clin (2011) 0.79
Eliminating postoperative nausea and vomiting in outpatient surgery with multimodal strategies including low doses of nonsedating, off-patent antiemetics: is "zero tolerance" achievable? ScientificWorldJournal (2007) 0.79
Self-assembling peptide assemblies bound to ZnS nanoparticles and their interactions with mammalian cells. Colloids Surf B Biointerfaces (2012) 0.78
Transcription factor redundancy and tissue-specific regulation: evidence from functional and physical network connectivity. Genome Res (2012) 0.78
Skin reactions at the femoral perineural catheter insertion site: retrospective summary of a randomized clinical trial. Anesth Analg (2007) 0.78
Neurotoxicity of common peripheral nerve block adjuvants. Curr Opin Anaesthesiol (2015) 0.77
Aprepitant in a multimodal approach for prevention of postoperative nausea and vomiting in high-risk patients: is there such a thing as "too many modalities"? ScientificWorldJournal (2009) 0.77
Continuous perineural infusions at home: narrowing the focus. Reg Anesth Pain Med (2004) 0.77
Local anesthetics in diabetic rats (and patients): shifting from a known slippery slope toward a potentially better multimodal perineural paradigm? Reg Anesth Pain Med (2012) 0.77
Economics and practice management issues associated with acute pain management. Anesthesiol Clin (2011) 0.77
A ratiometric-based measure of gene co-expression. BMC Bioinformatics (2014) 0.76
Extrapyramidal symptoms following administration of oral perphenazine 4 or 8 mg: an 11-year retrospective analysis. Eur J Anaesthesiol (2014) 0.76
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A (2014) 0.76
Regional anesthesia and ambulatory surgery. Curr Opin Anaesthesiol (2013) 0.76
A scalable and integrative system for pathway bioinformatics and systems biology. Adv Exp Med Biol (2010) 0.75
In response. Anesth Analg (2015) 0.75
A post hoc analysis of research study staffing: budgetary effects of the Health Insurance Portability and Accountability Act on research staff work hours during a prospective, randomized clinical trial. Anesthesiology (2007) 0.75
Toward a potential paradigm shift for the clinical care of diabetic patients requiring perineural analgesia: strategies for using the diabetic rodent model. Reg Anesth Pain Med (2010) 0.75
Development of a standardized peripheral nerve block procedure note form. Reg Anesth Pain Med (2005) 0.75
Electrical stimulation: an important force behind the growth of regional anesthesia. Can J Anaesth (2007) 0.75
Seeds, trees, and shade-personal experience in research career development. Reg Anesth Pain Med (2007) 0.75
No Surprise-For Long-term Opioid Avoidance, Do We Reap What We Sow? Anesth Analg (2017) 0.75
The role of diagnostic ultrasound-guided selective common peroneal nerve block in a patient with negative imaging but with classic neuropathic pain after below knee amputation. A A Case Rep (2014) 0.75
Diphenyleneiodonium Mitigates Bupivacaine-Induced Sciatic Nerve Damage in a Diabetic Neuropathy Rat Model by Attenuating Oxidative Stress. Anesth Analg (2017) 0.75
Economics: projecting costs and revenue for an interventional pain service in the ambulatory setting. Int Anesthesiol Clin (2011) 0.75
Billing for outpatient regional anesthesia services in the United States. Int Anesthesiol Clin (2005) 0.75
Regional anesthesia procedures for outpatient shoulder surgery. Int Anesthesiol Clin (2005) 0.75