Published in Nucleic Acids Res on September 07, 2012
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
RNA-Seq gene profiling--a systematic empirical comparison. PLoS One (2014) 3.03
HISAT: a fast spliced aligner with low memory requirements. Nat Methods (2015) 2.83
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat Biotechnol (2014) 2.65
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol (2015) 2.09
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol (2016) 1.99
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol (2013) 1.75
NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genomics (2016) 1.39
A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol (2014) 1.37
TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Res (2016) 1.27
CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biol (2013) 1.26
Accurate detection of differential RNA processing. Nucleic Acids Res (2013) 1.18
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol (2015) 1.17
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics (2013) 1.16
Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun (2014) 1.10
RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. Genetics (2014) 1.01
Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics (2015) 0.99
JAGuaR: junction alignments to genome for RNA-seq reads. PLoS One (2014) 0.98
Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Med (2015) 0.98
PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Res (2013) 0.97
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. Bioinformatics (2014) 0.96
TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics (2014) 0.94
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics (2015) 0.94
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems. BMC Bioinformatics (2014) 0.93
Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching. BMC Bioinformatics (2013) 0.92
Bayesian transcriptome assembly. Genome Biol (2014) 0.92
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki). BMC Bioinformatics (2013) 0.92
RNA Sequencing and Analysis. Cold Spring Harb Protoc (2015) 0.90
Reducing bias in RNA sequencing data: a novel approach to compute counts. BMC Bioinformatics (2014) 0.90
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Nucleic Acids Res (2014) 0.89
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. BMC Bioinformatics (2013) 0.89
CLASS: constrained transcript assembly of RNA-seq reads. BMC Bioinformatics (2013) 0.87
EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering. BMC Bioinformatics (2015) 0.87
Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA (2015) 0.87
Computational approaches for isoform detection and estimation: good and bad news. BMC Bioinformatics (2014) 0.85
SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. Bioinformatics (2015) 0.85
Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ (2013) 0.84
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level. Bioinformatics (2014) 0.84
RNA sequencing: from tag-based profiling to resolving complete transcript structure. Cell Mol Life Sci (2014) 0.83
Genetic data simulators and their applications: an overview. Genet Epidemiol (2014) 0.83
miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. BMC Bioinformatics (2015) 0.82
Alternative Splicing QTLs in European and African Populations. Am J Hum Genet (2015) 0.82
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. Microbiome (2014) 0.82
A comparative study of RNA-seq analysis strategies. Brief Bioinform (2015) 0.82
A novel statistical approach for jointly analyzing RNA-Seq data from F1 reciprocal crosses and inbred lines. Genetics (2014) 0.82
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience (2015) 0.82
Augmenting transcriptome assembly by combining de novo and genome-guided tools. PeerJ (2013) 0.81
Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics (2015) 0.81
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. Bioinformatics (2016) 0.81
An Approach for Assessing RNA-seq Quantification Algorithms in Replication Studies. IEEE Int Workshop Genomic Signal Process Stat (2013) 0.80
The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data. Nucleic Acids Res (2016) 0.78
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. PLoS Comput Biol (2016) 0.78
MetaDiff: differential isoform expression analysis using random-effects meta-regression. BMC Bioinformatics (2015) 0.78
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. Bioinformatics (2016) 0.78
MMR: a tool for read multi-mapper resolution. Bioinformatics (2015) 0.78
On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs. BioData Min (2016) 0.78
CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biol (2016) 0.77
WemIQ: an accurate and robust isoform quantification method for RNA-seq data. Bioinformatics (2014) 0.77
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PLoS Comput Biol (2015) 0.77
Estimation of data-specific constitutive exons with RNA-Seq data. BMC Bioinformatics (2013) 0.77
Prediction and Quantification of Splice Events from RNA-Seq Data. PLoS One (2016) 0.76
Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics (2014) 0.76
A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biol (2016) 0.76
Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform (2014) 0.76
Designing alternative splicing RNA-seq studies. Beyond generic guidelines. Bioinformatics (2015) 0.76
A fast and robust protocol for metataxonomic analysis using RNAseq data. Microbiome (2017) 0.75
Mapping Splicing Quantitative Trait Loci in RNA-Seq. Cancer Inform (2015) 0.75
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biol (2016) 0.75
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. BMC Bioinformatics (2014) 0.75
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. Algorithms Mol Biol (2017) 0.75
A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples. BMC Bioinformatics (2015) 0.75
TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs. Genome Biol (2016) 0.75
Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms. BMC Bioinformatics (2016) 0.75
Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways. Cell Syst (2016) 0.75
Boiler: lossy compression of RNA-seq alignments using coverage vectors. Nucleic Acids Res (2016) 0.75
CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Res (2016) 0.75
Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates. PLoS Comput Biol (2017) 0.75
Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma. Cancer Cell (2017) 0.75
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. BMC Bioinformatics (2017) 0.75
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. BMC Bioinformatics (2017) 0.75
Evaluation and comparison of computational tools for RNA-seq isoform quantification. BMC Genomics (2017) 0.75
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (2009) 20.75
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
The UCSC Known Genes. Bioinformatics (2006) 14.67
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res (2007) 14.24
Fluorescence detection in automated DNA sequence analysis. Nature (1986) 12.53
Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) 10.63
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res (2004) 10.18
Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol (2007) 9.45
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
Gene expression profiling by massively parallel sequencing. Genome Res (2007) 6.69
MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One (2008) 6.54
Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res (2000) 3.78
FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods (2010) 3.55
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol (2010) 2.79
Assembly of a processive messenger RNA polyadenylation complex. EMBO J (1993) 2.58
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures. Proc Natl Acad Sci U S A (2008) 2.12
Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res (2011) 2.12
Zipf's law in gene expression. Phys Rev Lett (2003) 2.10
Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One (2011) 1.91
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46
A probability concept about size distributions of sonicated lipid vesicles. Biochim Biophys Acta (1985) 1.15
Zipf's law and human transcriptomes: an explanation with an evolutionary model. C R Biol (2004) 0.98
Identifying expressed genes. Proc Natl Acad Sci U S A (2000) 0.97
A computer model for hydrodynamic shearing of DNA. Comput Programs Biomed (1979) 0.92
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
International network of cancer genome projects. Nature (2010) 20.35
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
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Characterization of mammalian selenoproteomes. Science (2003) 9.07
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14
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
Comparative gene prediction in human and mouse. Genome Res (2003) 4.13
The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods (2012) 3.89
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
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
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
A combinatorial code for CPE-mediated translational control. Cell (2008) 3.23
Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature (2002) 3.01
Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Mol Cell (2005) 2.99
Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods (2013) 2.92
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Fast computation and applications of genome mappability. PLoS One (2012) 2.73
ASTD: The Alternative Splicing and Transcript Diversity database. Genomics (2008) 2.72
Improving gene annotation using peptide mass spectrometry. Genome Res (2006) 2.69
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett (2005) 2.68
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
Based Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms. BMC Microbiol (2007) 2.52
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol (2011) 2.37
RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC Infect Dis (2003) 2.33
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A (2012) 2.24
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res (2012) 2.04
Using geneid to identify genes. Curr Protoc Bioinformatics (2007) 2.04
Recent advances in gene structure prediction. Curr Opin Struct Biol (2004) 1.90
The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet (2012) 1.88
Comparative analysis of amino acid repeats in rodents and humans. Genome Res (2004) 1.78
The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat Struct Mol Biol (2009) 1.75
Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform (2009) 1.72
A general definition and nomenclature for alternative splicing events. PLoS Comput Biol (2008) 1.72
Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66
Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep (2004) 1.58
Hnf1alpha (MODY3) controls tissue-specific transcriptional programs and exerts opposed effects on cell growth in pancreatic islets and liver. Mol Cell Biol (2009) 1.58
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res (2007) 1.52
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res (2013) 1.51
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics (2012) 1.42
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Res (2006) 1.40
Comparison of splice sites in mammals and chicken. Genome Res (2004) 1.40
Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach. PLoS One (2012) 1.37
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes. Nat Struct Mol Biol (2011) 1.31
Estimation of alternative splicing variability in human populations. Genome Res (2011) 1.27
Identifying protein-coding genes in genomic sequences. Genome Biol (2009) 1.26
Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res (2005) 1.24
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23
CPEB1 coordinates alternative 3'-UTR formation with translational regulation. Nature (2013) 1.23
Transcription factor map alignment of promoter regions. PLoS Comput Biol (2006) 1.22
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol (2013) 1.18
Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One (2012) 1.16
The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter". Front Genet (2012) 1.15
Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes. PLoS One (2008) 1.15
Modes and cuts in metabolic networks: complexity and algorithms. Biosystems (2008) 1.14
EGASP: Introduction. Genome Biol (2006) 1.13
Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol (2011) 1.12
Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Syst Biol (2007) 1.07
An 18-year review of sports groin injuries in the elite hockey player: clinical presentation, new diagnostic imaging, treatment, and results. Clin J Sport Med (2008) 1.06
The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol (2011) 1.05
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res (2012) 1.03
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Nucleic Acids Res (2005) 1.01
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements. Nucleic Acids Res (2008) 1.00
Splice site identification by idlBNs. Bioinformatics (2004) 1.00
BlastR--fast and accurate database searches for non-coding RNAs. Nucleic Acids Res (2011) 0.98
Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs. BMC Genomics (2013) 0.97
Intron-centric estimation of alternative splicing from RNA-seq data. Bioinformatics (2012) 0.97
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Bioinformatics (2009) 0.97
Grape RNA-Seq analysis pipeline environment. Bioinformatics (2013) 0.96
Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster. Proc Natl Acad Sci U S A (2003) 0.94
Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). Bioinformatics (2012) 0.92