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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol (2014) 3.99

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell (2014) 3.70

Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods (2013) 3.59

Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers. Nature (2016) 3.18

Organoid cultures derived from patients with advanced prostate cancer. Cell (2014) 3.12

Assessment of transcript reconstruction methods for RNA-seq. Nat Methods (2013) 3.11

Therapy-induced tumour secretomes promote resistance and tumour progression. Nature (2015) 3.07

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Genomic analyses identify molecular subtypes of pancreatic cancer. Nature (2016) 2.70

Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell (2014) 2.60

Astrocyte scar formation aids central nervous system axon regeneration. Nature (2016) 2.51

Plasmodium Infection Promotes Genomic Instability and AID-Dependent B Cell Lymphoma. Cell (2015) 2.51

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Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition. Nat Med (2016) 2.46

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Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients. Nat Med (2016) 2.36

Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat Biotechnol (2015) 2.30

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Differential L1 regulation in pluripotent stem cells of humans and apes. Nature (2013) 2.29

Unexpected role of interferon-γ in regulating neuronal connectivity and social behaviour. Nature (2016) 2.21

Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression. Nature (2014) 2.20

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Macrophages Facilitate Electrical Conduction in the Heart. Cell (2017) 2.10

Interferon-γ Drives Treg Fragility to Promote Anti-tumor Immunity. Cell (2017) 2.06

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat Med (2016) 2.04

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Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice. Nat Med (2017) 2.02

Transcriptional diversity during lineage commitment of human blood progenitors. Science (2014) 1.93

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature (2015) 1.91

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature (2014) 1.89

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature (2014) 1.84

Multicilin drives centriole biogenesis via E2f proteins. Genes Dev (2014) 1.82

The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Nat Immunol (2015) 1.82

Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. Science (2015) 1.82

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The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat Immunol (2016) 1.74

Targeting renal cell carcinoma with a HIF-2 antagonist. Nature (2016) 1.68

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol (2014) 1.68

Depletion of fat-resident Treg cells prevents age-associated insulin resistance. Nature (2015) 1.68

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell (2016) 1.67

The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat Struct Mol Biol (2013) 1.67

Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Rep (2014) 1.66

High-throughput determination of RNA structure by proximity ligation. Nat Biotechnol (2015) 1.66

Combined inhibition of MAP kinase and KIT signaling synergistically destabilizes ETV1 and suppresses GIST tumor growth. Cancer Discov (2015) 1.65

Reversible methylation of m(6)Am in the 5' cap controls mRNA stability. Nature (2016) 1.63

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol (2015) 1.62

A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature (2015) 1.62

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell (2015) 1.60

Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes. J Am Soc Nephrol (2015) 1.59

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med (2016) 1.59

Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling. Science (2015) 1.59

The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol (2016) 1.53

Designer matrices for intestinal stem cell and organoid culture. Nature (2016) 1.51

L1-associated genomic regions are deleted in somatic cells of the healthy human brain. Nat Neurosci (2016) 1.51

BRD4 is a novel therapeutic target for liver fibrosis. Proc Natl Acad Sci U S A (2015) 1.51

Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science (2016) 1.49

An Immune Atlas of Clear Cell Renal Cell Carcinoma. Cell (2017) 1.49

m(6)A modulates neuronal functions and sex determination in Drosophila. Nature (2016) 1.49

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature (2014) 1.47

Transcriptome analysis reveals differential splicing events in IPF lung tissue. PLoS One (2014) 1.45

GDF10 is a signal for axonal sprouting and functional recovery after stroke. Nat Neurosci (2015) 1.45

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature (2017) 1.44

Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes. Nat Immunol (2017) 1.43

DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling. Nat Med (2016) 1.42

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events. BMC Bioinformatics (2016) 1.41

Loss of Cardio-Protective Effects at the ADAMTS7 Locus Due to Gene-Smoking Interactions. Circulation (2017) 1.41

Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol (2016) 1.41

The genetic basis of parental care evolution in monogamous mice. Nature (2017) 1.40

Loss of maternal Trim28 causes male-predominant early embryonic lethality. Genes Dev (2017) 1.40

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos. Dev Cell (2017) 1.40

Mono-unsaturated fatty acids link H3K4me3 modifiers to C. elegans lifespan. Nature (2017) 1.40

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40

A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biol Evol (2014) 1.40

Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev (2017) 1.39

Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas. Nat Commun (2017) 1.39

Binary gene expression patterning of the molt cycle: the case of chitin metabolism. PLoS One (2015) 1.39

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer. PLoS Genet (2016) 1.39

The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell (2017) 1.39

Necroptosis activation in Alzheimer's disease. Nat Neurosci (2017) 1.38

Increased Vascular Permeability in the Bone Marrow Microenvironment Contributes to Disease Progression and Drug Response in Acute Myeloid Leukemia. Cancer Cell (2017) 1.38

Population differences in olfaction accompany host shift in Drosophila mojavensis. Proc Biol Sci (2016) 1.38

A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nat Genet (2017) 1.38

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med (2017) 1.37

Altered regulation and expression of genes by BET family of proteins in COPD patients. PLoS One (2017) 1.36

PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors. Nat Genet (2014) 1.34

An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res (2014) 1.34

Detecting and correcting systematic variation in large-scale RNA sequencing data. Nat Biotechnol (2014) 1.33

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell (2016) 1.30

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13

Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45

Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res (2004) 28.63

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An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85

Landscape of transcription in human cells. Nature (2012) 20.18

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GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19

Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics (2010) 17.53

Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80

Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods (2010) 9.75

Optimal spliced alignments of short sequence reads. Bioinformatics (2008) 9.45

Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res (2009) 9.40

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13

Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res (2010) 6.95

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics (2011) 6.20

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Pre-mRNA splicing: where and when in the nucleus. Trends Cell Biol (2011) 2.54

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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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Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96

Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63

RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41

CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med (2006) 14.33

Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01

Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39

The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85

Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35

EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06

A promoter-level mammalian expression atlas. Nature (2014) 6.25

Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet (2006) 6.20

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res (2005) 6.08

Global transcription in pluripotent embryonic stem cells. Cell Stem Cell (2008) 5.81

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33

An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82

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Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2004) 2.94

Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A (2005) 2.85

Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76

Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69

Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66

Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res (2014) 2.63

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res (2008) 2.62

TUF love for "junk" DNA. Cell (2006) 2.59

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J Comput Biol (2011) 2.47

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Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 2.18

MyD88 primes macrophages for full-scale activation by interferon-gamma yet mediates few responses to Mycobacterium tuberculosis. J Exp Med (2003) 2.10

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet (2011) 2.07

Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A (2011) 1.89

Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol (2009) 1.36

Molecular biology: RNA discrimination. Nature (2012) 1.28

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics (2006) 1.20

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RNA reference materials for gene expression studies. Difficult first steps. Clin Chem (2004) 1.08

An effort to make sense of antisense transcription in bacteria. RNA Biol (2012) 1.04

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome Res (2013) 1.00

Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief Funct Genomic Proteomic (2003) 1.00

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo. PLoS One (2010) 0.98

The multitasking genome. Nat Genet (2006) 0.94

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Res (2013) 0.94

Differential analysis for high density tiling microarray data. BMC Bioinformatics (2007) 0.87

Microarrays and genetic epidemiology: a multipurpose tool for a multifaceted field. Genet Epidemiol (2002) 0.87

HIV regulation of the IL-7R: a viral mechanism for enhancing HIV-1 replication in human macrophages in vitro. J Leukoc Biol (2006) 0.81

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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

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