Research graph
References from Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis. Local targets link to admitted publications; unresolved targets remain external evidence.
CRISPR–Cas9: a history of its discovery and ethical considerations of its use in genome Editing
2022 · External reference
10.1038/nrd.2017.243
10.1038/nrd.2017.243 · External reference
10.1038/s41587-022-01294-2
10.1038/s41587-022-01294-2 · External reference
A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
2021 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
Ligandability and druggability assessment via machine learning
10.1002/wcms.1676 · 2023 · External reference
Machine learning approaches for predicting protein-ligand binding sites from sequence data
10.3389/fbinf.2025.1520382 · 2025 · External reference
To metabolomics and beyond: a technological portfolio to investigate cancer metabolism
2023 · External reference
10.1038/s41374-022-00830-7
10.1038/s41374-022-00830-7 · External reference
High-Throughput Metabolomics for Identification of Metabolic Pathways and Deciphering the Effect Mechanism of Dioscin on Rectal Cancer From Cell Metabolic Profiles Coupled With Chemometrics Analysis
2020 · External reference
10.1038/s41385-022-00553-4
10.1038/s41385-022-00553-4 · External reference
Hill Catherine Prediction of cancer outcome with microarrays: a multiple random validation strategy
10.1016/s0140-6736(05)17866-0 · 2005 · External reference
More is better: Recent progress in multi-omics data integration methods
10.3389/fgene.2017.00084 · 2017 · External reference
10.1007/s00204-021-03031-1
10.1007/s00204-021-03031-1 · External reference
10.1038/s41576-019-0150-2
10.1038/s41576-019-0150-2 · External reference
Snyder Michael RNA-Seq: a revolutionary tool for transcriptomics
10.1038/nrg2484 · 2009 · External reference
10.1038/nbt.1621
10.1038/nbt.1621 · External reference
A survey of best practices for RNA-seq data analysis
2016 · External reference
Opportunities and challenges in long-read sequencing data analysis
10.1186/s13059-020-1935-5 · 2020 · External reference
Highly parallel direct RN A sequencing on an array of nanopores
10.1038/nmeth.4577 · 2018 · External reference
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
10.1186/s13073-017-0467-4 · 2017 · External reference
Unresolved reference
External reference
Predictive biomarkers for embryotoxicity: a machine learning approach to mitigating multicollinearity in RNA-Seq
10.1007/s00204-024-03852-w · 2024 · External reference
Evaluating the performance of multi-omics integration: a thyroid toxicity case study
10.1007/s00204-024-03876-2 · 2025 · External reference
10.1007/s00204-020-02656-y
10.1007/s00204-020-02656-y · External reference
10.1111/mec.15797
10.1111/mec.15797 · External reference
Whole genome re-sequencing in 437 tobacco germplasms identifies plant height candidate genes
2025 · External reference
RNA sequencing reveals transcriptomic changes in tobacco (Nicotiana tabacum) following NtCPS2 knockdown
2021 · External reference
RNA-seq data science: From raw data to effective interpretation
10.3389/fgene.2023.997383 · 2023 · External reference
RNA-seq and microarray complement each other in transcriptome profiling
10.1186/1471-2164-13-629 · 2012 · External reference
10.1016/j.cmet.2016.08.018
10.1016/j.cmet.2016.08.018 · External reference
mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues
2018 · External reference
Ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
10.1186/s13059-019-1671-x · 2019 · External reference
10.1016/j.cell.2015.05.002
10.1016/j.cell.2015.05.002 · External reference
10.1038/nmeth.1315
10.1038/nmeth.1315 · External reference
10.1038/nbt.2859
10.1038/nbt.2859 · External reference
Single-cell RNA sequencing technologies and applications: A brief overview
10.1002/ctm2.694 · 2022 · External reference
10.1038/nmeth.4220
10.1038/nmeth.4220 · External reference
10.1126/science.aaf2403
10.1126/science.aaf2403 · External reference
10.1038/s41592-020-01033-y
10.1038/s41592-020-01033-y · External reference
10.1038/s41586-021-03634-9
10.1038/s41586-021-03634-9 · External reference
Unresolved reference
External reference
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
10.1038/s41467-021-26271-2 · 2021 · External reference
Long Noncoding RNAs in Neurodegenerative Diseases: Pathogenesis and Potential Implications as Clinical Biomarkers
10.3389/fnmol.2021.685143 · 2021 · External reference
Studying the function of tRNA modifications: experimental challenges and opportunities
10.1016/j.jmb.2024.168934 · 2025 · External reference
Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes
10.1038/s41467-025-56348-1 · 2025 · External reference
10.1038/nmeth.3508
10.1038/nmeth.3508 · External reference
10.1016/j.celrep.2017.07.029
10.1016/j.celrep.2017.07.029 · External reference
Small rna-sequencing: Approaches and considerations for mirna analysis
10.3390/diagnostics11060964 · 2021 · External reference
10.1101/2021.09.18.460910
10.1101/2021.09.18.460910 · External reference
HydraPsiSeq: A method for systematic and quantitative mapping of pseudouridines in RNA
10.1093/nar/gkaa769 · 2020 · External reference
Control of translation and mRNA degradation by miRNAs and siRNAs
10.1101/gad.1399806 · 2006 · External reference
Therapeutic siRNA: state of the art
2020 · External reference
Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs
10.1186/s13059-020-02221-x · 2021 · External reference
10.1007/s00018-020-03720-7
10.1007/s00018-020-03720-7 · External reference
The RNA binding protein SORBS2 suppresses metastatic colonization of ovarian cancer by stabilizing tumor-suppressive immunomodulatory transcripts
10.1186/s13059-018-1412-6 · 2018 · External reference
Systematic comparison of small RNA library preparation protocols for next-generation sequencing
10.1186/s12864-018-4491-6 · 2018 · External reference
A low-bias and sensitive small RNA library preparation method using randomized splint ligation
10.1093/nar/gkaa480 · 2020 · External reference
Addressing bias in small RNA library preparation for sequencing: A new protocol recovers microRNAs that evade capture by current methods
10.3389/fgene.2015.00352 · 2015 · External reference
10.1261/rna.036475.112
10.1261/rna.036475.112 · External reference
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
10.1186/s12864-024-10440-w · 2024 · External reference
Biases in Illumina transcriptome sequencing caused by random hexamer priming
10.1093/nar/gkq224 · 2010 · External reference
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
10.1186/s13059-021-02411-1 · 2021 · External reference
10.1038/s41592-019-0617-2
10.1038/s41592-019-0617-2 · External reference
10.1038/s41586-019-1711-4
10.1038/s41586-019-1711-4 · External reference
RNA-seq Data: challenges in and Recommendations for Experimental Design and Analysis
2014 · External reference
10.1093/bib/bbr004
10.1093/bib/bbr004 · External reference
RNA-seq reproducibility of Pseudomonas aeruginosa in laboratory models of cystic fibrosis
10.1128/spectrum.01513-24 · 2025 · External reference
RNA-seq: Technical variability and sampling
10.1186/1471-2164-12-293 · 2011 · External reference
Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software
10.1186/1471-2164-15-1045 · 2014 · External reference
Transcriptome Signatures Predict Phenotypic Variations of Candida auris
10.3389/fcimb.2021.662563 · 2021 · External reference
10.1111/1462-2920.12327
10.1111/1462-2920.12327 · External reference
Replicate sequencing libraries are important for quantification of allelic imbalance
10.1038/s41467-021-23544-8 · 2021 · External reference
10.1261/rna.053959.115
10.1261/rna.053959.115 · External reference
Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
2016 · External reference
PROPER: Comprehensive power evaluation for differential expression using RNA-seq
10.1093/bioinformatics/btu640 · 2015 · External reference
RNA-seq: Basic Bioinformatics Analysis
2018 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Systematic evaluation of differential splicing tools for RNA-seq studies
10.1093/bib/bbz126 · 2020 · External reference
Unresolved reference
2024 · External reference
Unresolved reference
External reference
CAP-miRSeq: A comprehensive analysis pipeline for microRNA sequencing data
2014 · External reference
10.1038/nrg3642
10.1038/nrg3642 · External reference
The impact of read length on quantification of differentially expressed genes and splice junction detection
10.1186/s13059-015-0697-y · 2015 · External reference
10.1038/s41592-024-02298-3
10.1038/s41592-024-02298-3 · External reference
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
10.1186/s13059-019-1910-1 · 2019 · External reference
10.1038/nrg3117
10.1038/nrg3117 · External reference
Complete genomic and transcriptional landscape analysis using third-generation sequencing: A case study of Saccharomyces cerevisiae CEN.PK113-7D
10.1093/nar/gky014 · 2018 · External reference
Origins of the Large Differences in Stability of DNA and RNA Helices: C-5 Methyl and 2’-Hydroxyl Effects
10.1021/bi00012a031 · 1995 · External reference
The RIN: An RNA integrity number for assigning integrity values to RNA measurements
10.1186/1471-2199-7-3 · 2006 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
External reference
N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease
10.1186/s13059-020-02249-z · 2021 · External reference
Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae
10.3389/fbioe.2022.842299 · 2022 · External reference
10.1261/rna.078937.121
10.1261/rna.078937.121 · External reference
Long-read assembly of the Brassica napus reference genome Darmor-bzh
2021 · External reference
Advances in nanopore direct RNA sequencing Access options
10.1038/s41592-022-01633-w · 2022 · External reference
Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities
10.1038/s41598-025-18768-3 · 2025 · External reference
NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs
10.15252/rc.2024646146 · 2024 · External reference
RNA-seq: Impact of RNA degradation on transcript quantification
10.1186/1741-7007-12-42 · 2014 · External reference
A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
10.1186/s12864-017-3827-y · 2017 · External reference
DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing
10.1155/2020/9349132 · 2020 · External reference
Impact of RNA degradation on next-generation sequencing transcriptome data
2022 · External reference
10.1038/nrg3074
10.1038/nrg3074 · External reference
Small rna-sequencing: Approaches and considerations for mirna analysis
10.3390/diagnostics11060964 · 2021 · External reference
10.1101/2024.03.28.587190
10.1101/2024.03.28.587190 · External reference
tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease
2024 · External reference
Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation
10.3390/genes15030374 · 2024 · External reference
NcRNAseq: Simple modifications to RNA-seq library preparation allow recovery and analysis of mid-sized non-coding RNAs
10.2144/btn-2021-0035 · 2022 · External reference
RNA sequencing and analysis
10.1101/pdb.top084970 · 2015 · External reference
10.1196/annals.1310.010
10.1196/annals.1310.010 · External reference
Unresolved reference
External reference
10.1038/s41598-018-23226-4
10.1038/s41598-018-23226-4 · External reference
Unresolved reference
2014 · External reference
Unresolved reference
2017 · External reference
Short paired-end reads trump long single-end reads for expression analysis
10.1186/s12859-020-3484-z · 2020 · External reference
Unresolved reference
2014 · External reference
Multi-pass, single-molecule nanopore reading of long protein strands
2024 · External reference
10.1038/s41576-020-0236-x
10.1038/s41576-020-0236-x · External reference
10.1038/s41587-020-00746-x
10.1038/s41587-020-00746-x · External reference
Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies
2022 · External reference
10.12688/f1000research.9005.1
10.12688/f1000research.9005.1 · External reference
10.1038/nrg2825
10.1038/nrg2825 · External reference
Unresolved reference
2009 · External reference
Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality
10.1186/s12859-022-04775-y · 2022 · External reference
10.1038/nbt.2931
10.1038/nbt.2931 · External reference
10.1093/biostatistics/kxj037
10.1093/biostatistics/kxj037 · External reference
10.1093/nar/gkv007
10.1093/nar/gkv007 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
variancePartition: Interpreting drivers of variation in complex gene expression studies
10.1186/s12859-016-1323-z · 2016 · External reference
International cancer genome consortium data portal-a one-stop shop for cancer genomics data
10.1093/database/bar026 · 2011 · External reference
A Quick Introduction to Version Control with Git and GitHub
10.1371/journal.pcbi.1004668 · 2016 · External reference
NGSQC: Cross-platform quality analysis pipeline for deep sequencing data
2010 · External reference
Unresolved reference
External reference
Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp
10.1002/imt2.107 · 2023 · External reference
Unresolved reference
2018 · External reference
Flexbar 3.0 - SIMD and multicore parallelization
10.1093/bioinformatics/btx330 · 2017 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/btr026
10.1093/bioinformatics/btr026 · External reference
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
2010 · External reference
Unresolved reference
External reference
10.1093/bioinformatics/bts635
10.1093/bioinformatics/bts635 · External reference
10.1093/bioinformatics/btw354
10.1093/bioinformatics/btw354 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Genome tools: A comprehensive software library for efficient processing of structured genome annotations
10.1109/tcbb.2013.68 · 2013 · External reference
10.1038/s41587-019-0201-4
10.1038/s41587-019-0201-4 · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
2013 · External reference
10.1038/nmeth.4197
10.1038/nmeth.4197 · External reference
10.1038/nbt.3519
10.1038/nbt.3519 · External reference
Impact of gene annotation choice on the quantification of RNA-seq data
10.1186/s12859-022-04644-8 · 2022 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
10.1038/nprot.2013.084
10.1038/nprot.2013.084 · External reference
Unresolved reference
External reference
SOAPsplice: Genome-wide ab initio detection of splice junctions from RNA-Seq data
10.3389/fgene.2011.00046 · 2011 · External reference
10.1093/bioinformatics/btq057
10.1093/bioinformatics/btq057 · External reference
10.1093/bioinformatics/bti610
10.1093/bioinformatics/bti610 · External reference
10.1093/bioinformatics/btu077
10.1093/bioinformatics/btu077 · External reference
10.1093/bioinformatics/bts094
10.1093/bioinformatics/bts094 · External reference
10.1038/nbt.1883
10.1038/nbt.1883 · External reference
10.1038/nbt.3122
10.1038/nbt.3122 · External reference
10.1101/2025.05.21.655404
10.1101/2025.05.21.655404 · External reference
10.1093/bioinformatics/btt656
10.1093/bioinformatics/btt656 · External reference
10.1038/nmeth.4197
10.1038/nmeth.4197 · External reference
Integrative genomics viewer
10.1038/nbt.1754 · 2011 · External reference
Detecting and correcting systematic variation in large-scale RNA sequencing data
10.1038/nbt.3000 · 2014 · External reference
NCBI GEO: Archive for functional genomics data sets - Update
2013 · External reference
10.1093/nar/30.1.207
10.1093/nar/30.1.207 · External reference
10.1093/nar/gkad965
10.1093/nar/gkad965 · External reference
The BioStudies database
10.15252/msb.20156658 · 2015 · External reference
10.1093/nar/gkx965
10.1093/nar/gkx965 · External reference
Unresolved reference
External reference
10.1093/nar/gky964
10.1093/nar/gky964 · External reference
Expression Atlas update: From tissues to single cells
2020 · External reference
From ArrayExpress to BioStudies
10.1093/nar/gkaa1062 · 2021 · External reference
Expression Atlas update: Gene and protein expression in multiple species
10.1093/nar/gkab1030 · 2022 · External reference
Unresolved reference
External reference
10.1093/nar/gkab1053
10.1093/nar/gkab1053 · External reference
The sequence read archive: Explosive growth of sequencing data
10.1093/nar/gkr854 · 2012 · External reference
A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)
2024 · External reference
Unresolved reference
External reference
recount3: summaries and queries for large-scale RNA-seq expression and splicing
10.1186/s13059-021-02533-6 · 2021 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
Unresolved reference
External reference
