Research graph
References from Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. Local targets link to admitted publications; unresolved targets remain external evidence.
Gene expression in differentiated cells
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RNA-Seq methods for transcriptome analysis
10.1002/wrna.1364 · 2017 · External reference
RNA sequencing and analysis
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Advanced applications of RNA sequencing and challenges
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10.1038/nmeth.1417 · External reference
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation
10.1038/nbt.3682 · 2016 · External reference
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GC-content normalization for RNA-Seq data
10.1186/1471-2105-12-480 · 2011 · External reference
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10.1093/nar/gkt1021 · External reference
The impact of amplification on differential expression analyses by RNA-seq
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Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA
2011 · External reference
A low-cost library construction protocol and data analysis pipeline for Illumina-based Strand-specific multiplex RNA-Seq
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A high-throughput method for Illumina RNA-Seq library preparation
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Protocol for miRNA isolation from biofluids
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Comprehensive comparison of Pacific biosciences and Oxford Nanopore technologies and their applications to transcriptome analysis
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A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
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Characterization of the human ESC transcriptome by hybrid sequencing
2013 · External reference
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10.1186/1471-2164-13-341 · External reference
Improving PacBio long read accuracy by short read alignment
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Evaluation of tools for long read RNA-seq splice-aware alignment
10.1093/bioinformatics/btx668 · 2018 · External reference
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10.1093/bioinformatics/btu538
10.1093/bioinformatics/btu538 · External reference
Accurate self-correction of errors in long reads using de Bruijn graphs
2016 · External reference
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10.1186/1471-2105-12-323
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10.1038/sdata.2018.61
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10.1038/nmeth.2251
10.1038/nmeth.2251 · External reference
10.1038/nprot.2012.016
10.1038/nprot.2012.016 · External reference
rQuant.web: a tool for RNA-Seq-based transcript quantitation
10.1093/nar/gkq448 · 2010 · External reference
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
10.1186/gb-2011-12-2-r13 · 2011 · External reference
10.1038/nbt.4020
10.1038/nbt.4020 · External reference
10.1093/bioinformatics/btp120
10.1093/bioinformatics/btp120 · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
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10.1038/nmeth.3317
10.1038/nmeth.3317 · External reference
10.1093/bioinformatics/btq057
10.1093/bioinformatics/btq057 · External reference
Limitations of alignment-free tools in total RNA-seq quantification
10.1186/s12864-018-4869-5 · 2018 · External reference
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10.1038/nbt.1621
10.1038/nbt.1621 · External reference
Bias detection and correction in RNA-sequencing data
10.1186/1471-2105-12-290 · 2011 · External reference
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10.1007/s12064-012-0162-3 · External reference
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10.1016/j.cell.2012.08.026
10.1016/j.cell.2012.08.026 · External reference
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10.1038/ng.3988 · External reference
10.1038/nprot.2016.095
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10.1186/gb-2013-14-4-r36
10.1186/gb-2013-14-4-r36 · External reference
10.1261/rna.046037.114
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Sequencing, De novo assembly, and annotation of the Transcriptome of the endangered freshwater pearl bivalve, Cristaria plicata, provides novel insights into functional genes and marker discovery
10.1371/journal.pone.0148622 · 2016 · External reference
10.1186/s13059-014-0572-2
10.1186/s13059-014-0572-2 · External reference
10.1371/journal.pone.0122170
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De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways
10.1007/s11418-016-1041-x · 2017 · External reference
Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis
2016 · External reference
10.1038/nbt.1883
10.1038/nbt.1883 · External reference
10.1016/j.cell.2014.09.029
10.1016/j.cell.2014.09.029 · External reference
10.1038/nature14136
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A promoter-level mammalian expression atlas
10.1038/nature13182 · 2014 · External reference
Linking FANTOM5 CAGE peaks to annotations with CAGEscan
10.1038/sdata.2017.147 · 2017 · External reference
10.1038/nmeth.1517
10.1038/nmeth.1517 · External reference
10.1093/bioinformatics/bts094
10.1093/bioinformatics/bts094 · External reference
SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads
10.1016/j.ygeno.2013.10.003 · 2013 · External reference
10.1093/bioinformatics/btt219
10.1093/bioinformatics/btt219 · External reference
BinPacker: packing-based De novo Transcriptome assembly from RNA-seq data
10.1371/journal.pcbi.1004772 · 2016 · External reference
Simulation-based comprehensive benchmarking of RNA-seq aligners
10.1038/nmeth.4106 · 2017 · External reference
Using synthetic mouse spike-in transcripts to evaluate RNA-Seq analysis tools
10.1371/journal.pone.0153782 · 2016 · External reference
10.1038/nmeth.3958
10.1038/nmeth.3958 · External reference
Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella
10.1038/s41598-017-16057-2 · 2017 · External reference
Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations
10.1038/srep31602 · 2016 · External reference
Different next generation sequencing platforms produce different microbial profiles and diversity in cystic fibrosis sputum
10.1016/j.mimet.2016.09.002 · 2016 · External reference
10.1038/ncomms11706
10.1038/ncomms11706 · External reference
A single-molecule long-read survey of human Transcriptomes using LoopSeq synthetic long read sequencing
2019 · External reference
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BLAT--theBLAST-like alignment tool
2002 · External reference
10.1093/bioinformatics/bts635
10.1093/bioinformatics/bts635 · External reference
10.1093/bioinformatics/bti310
10.1093/bioinformatics/bti310 · External reference
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
10.1186/1471-2105-13-238 · 2012 · External reference
10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
10.3390/ncrna5010017
10.3390/ncrna5010017 · External reference
10.1101/gad.1800909
10.1101/gad.1800909 · External reference
10.3390/ncrna4020012
10.3390/ncrna4020012 · External reference
Regulatory RNAs discovered in unexpected places
10.1002/wrna.1309 · 2015 · External reference
10.1186/gb-2012-13-11-r107
10.1186/gb-2012-13-11-r107 · External reference
10.1093/nar/gky587
10.1093/nar/gky587 · External reference
Identifying protein-coding genes in genomic sequences
10.1186/gb-2009-10-1-201 · 2009 · External reference
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10.1073/pnas.0709013104 · External reference
Tunable protein synthesis by transcript isoforms in human cells
10.7554/elife.10921 · 2016 · External reference
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes
10.1186/s13059-017-1293-0 · 2017 · External reference
Identification of transcribed protein coding sequence remnants within lincRNAs
10.1093/nar/gky608 · 2018 · External reference
Nearly all new protein-coding predictions in the CHESS database are not protein-coding
2018 · External reference
10.1186/s13059-018-1590-2
10.1186/s13059-018-1590-2 · External reference
10.1093/bioinformatics/btq033
10.1093/bioinformatics/btq033 · External reference
Glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data
10.1186/2045-9769-3-1 · 2014 · External reference
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10.1093/nar/gkh379 · External reference
10.1093/nar/gkt006
10.1093/nar/gkt006 · External reference
FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome
2017 · External reference
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NRC: non-coding RNA classifier based on structural features
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Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs
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Revealing the complexity of retroviral repression
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Regulation of mouse Retroelement MuERV-L/MERVL expression by REX1 and epigenetic control of stem cell potency
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Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
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Conserved expression of transposon-derived non-coding transcripts in primate stem cells
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hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
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Unresolved reference
2018 · External reference
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