Inference of isoforms from short sequence reads

scientific article published on March 2011

Inference of isoforms from short sequence reads is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/jcb/FengLJ11
P356DOI10.1089/CMB.2010.0243
P932PMC publication ID3123862
P698PubMed publication ID21385036
P5875ResearchGate publication ID50347201

P2093author name stringWei Li
Jianxing Feng
Tao Jiang
P2860cites workIdentification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectQ21061203
Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeQ21183894
A general definition and nomenclature for alternative splicing eventsQ21563499
Mapping and quantifying mammalian transcriptomes by RNA-SeqQ22122035
RNA-Seq: a revolutionary tool for transcriptomicsQ24596169
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usageQ24616834
The transcriptional landscape of the yeast genome defined by RNA sequencingQ24633693
Mapping short DNA sequencing reads and calling variants using mapping quality scoresQ24644612
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing dataQ24646450
TopHat: discovering splice junctions with RNA-SeqQ24655505
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arraysQ24655562
Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatmentQ24795297
Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behaviorQ27438170
Serial analysis of gene expressionQ27860777
The transcriptional landscape of the mammalian genomeQ27861110
Alternative isoform regulation in human tissue transcriptomesQ27861118
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarraysQ28235146
Tag-based approaches for transcriptome research and genome annotationQ28258011
SOAP: short oligonucleotide alignment programQ28266228
Stem cell transcriptome profiling via massive-scale mRNA sequencingQ28282295
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing dataQ28752684
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencingQ29547470
RNA maps reveal new RNA classes and a possible function for pervasive transcriptionQ29614334
Global identification of human transcribed sequences with genome tiling arraysQ29614335
The UCSC Genome Browser Database: 2008 updateQ29614575
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptomeQ29615877
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arraysQ29615937
CAGE: cap analysis of gene expressionQ33234345
Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathyQ33287095
Efficient targeted transcript discovery via array-based normalization of RACE librariesQ33337384
MetaSim: a sequencing simulator for genomics and metagenomicsQ33374533
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencingQ33408115
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLiteQ33482616
Personalized copy number and segmental duplication maps using next-generation sequencing.Q33498358
Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genesQ34173384
Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organismsQ34333110
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotationQ34556124
ENCODE: more genomic empowermentQ34637323
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolutionQ34779368
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analysesQ34973377
Genomic variants in exons and introns: identifying the splicing spoilersQ35787564
The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixturesQ36494102
The connection between splicing and cancer.Q36513592
The turning point in genome researchQ36693819
Statistical inferences for isoform expression in RNA-SeqQ37153258
Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.Q37346803
Molecular biology: power sequencing.Q43218943
Detecting alternative gene structures from spliced ESTs: a computational approachQ43766582
Splicing graphs and EST assembly problemQ44095761
Genome-wide analysis of transcript isoform variation in humansQ46809730
Gene discovery in dbEST.Q48078968
P433issue3
P1104number of pages17
P304page(s)305-321
P577publication date2011-03-01
P1433published inJournal of Computational BiologyQ6295003
P1476titleInference of isoforms from short sequence reads
P478volume18

Reverse relations

cites work (P2860)
Q39850400A Network of Splice Isoforms for the Mouse
Q30596722A robust method for transcript quantification with RNA-seq data.
Q30898472Accurate inference of isoforms from multiple sample RNA-Seq data.
Q34406095Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders
Q34355270Application of next generation qPCR and sequencing platforms to mRNA biomarker analysis
Q36525979CIDANE: comprehensive isoform discovery and abundance estimation
Q37172278Cardiovascular transcriptomics and epigenomics using next-generation sequencing: challenges, progress, and opportunities
Q34091481Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.
Q35970681Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements
Q37194744Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.
Q34761600IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference
Q36740961Modeling RNA degradation for RNA-Seq with applications
Q30690326Modeling alternative splicing variants from RNA-Seq data with isoform graphs
Q33565443Next-generation sequencing: from understanding biology to personalized medicine
Q34121449Overview of available methods for diverse RNA-Seq data analyses
Q30870540RNA-Seq Data: A Complexity Journey
Q34018852RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders
Q29547458RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Q61446149Reconstruction of full-length circular RNAs enables isoform-level quantification
Q31121567SDEAP: a splice graph based differential transcript expression analysis tool for population data
Q34463372StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Q21145302Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
Q28728363The human transcriptome: an unfinished story
Q58765268TraRECo: a greedy approach based de novo transcriptome assembler with read error correction using consensus matrix
Q37349453TransComb: genome-guided transcriptome assembly via combing junctions in splicing graphs
Q36901962Transcriptomics analysis of iPSC-derived neurons and modeling of neuropsychiatric disorders.
Q30579842iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data

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