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Oases:robustde novoRNA-seq assembly across the dynamic range of expression levels
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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EMBOSS: The European Molecular Biology Open Software Suite
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Alternative isoform regulation in human tissue transcriptomes
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Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Mapping and quantifying mammalian transcriptomes by RNA-Seq
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Comprehensive comparative analysis of strand-specific RNA sequencing methods
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De novo assembly and analysis of RNA-seq data
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RNA-Seq: a revolutionary tool for transcriptomics
inferredcites →https://doi.org/10.1073/pnas.0812841106openalex-snapshot
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s181openalex-snapshot
Splicing graphs and EST assembly problem
inferredcites →https://doi.org/10.1093/bioinformatics/btg109openalex-snapshot
Generating consensus sequences from partial order multiple sequence alignment graphs
inferredcites →https://doi.org/10.1093/bioinformatics/bti1114openalex-snapshot
The fragment assembly string graph
inferredcites →https://doi.org/10.1093/bioinformatics/btp113openalex-snapshot
Statistical inferences for isoform expression in RNA-Seq
inferredcites →https://doi.org/10.1093/bioinformatics/btp367openalex-snapshot
De novo transcriptome assembly with ABySS
inferredcites →https://doi.org/10.1093/hmg/ddp473openalex-snapshot
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing
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Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
inferredcites →https://doi.org/10.1093/nar/gkq041openalex-snapshot
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
inferredcites →https://doi.org/10.1093/nar/gni170openalex-snapshot
An analysis of the feasibility of short read sequencing
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Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.088823.108openalex-snapshot
RazerS—fast read mapping with sensitivity control
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
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Optimization of de novo transcriptome assembly from next-generation sequencing data
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BLAT —The BLAST -Like Alignment Tool
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ALLPATHS: De novo assembly of whole-genome shotgun microreads
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A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
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AN APPROACH TO TRANSCRIPTOME ANALYSIS OF NON-MODEL ORGANISMS USING SHORT-READ SEQUENCES
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Parallel short sequence assembly of transcriptomes
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Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
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Annotating genomes with massive-scale RNA sequencing
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Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler
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ConDeTri - A Content Dependent Read Trimmer for Illumina Data
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inferred← citeshttps://doi.org/10.1007/s10059-013-0127-5openalex-snapshot
Emerging Tools for Synthetic Genome Design
inferred← citeshttps://doi.org/10.1007/s10126-013-9526-zopenalex-snapshot
Transcriptome Analysis Reveals a Rich Gene Set Related to Innate Immunity in the Eastern Oyster (Crassostrea virginica)
inferred← citeshttps://doi.org/10.1007/s10126-014-9595-7openalex-snapshot
High Conopeptide Diversity in Conus tribblei Revealed Through Analysis of Venom Duct Transcriptome Using Two High-Throughput Sequencing Platforms
inferred← citeshttps://doi.org/10.1007/s10126-020-09945-8openalex-snapshot
Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure
inferred← citeshttps://doi.org/10.1007/s10142-018-0647-3openalex-snapshot
A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference
inferred← citeshttps://doi.org/10.1007/s10529-020-03022-9openalex-snapshot
Comprehensive transcriptome profiling of Caragana microphylla in response to salt condition using de novo assembly
inferred← citeshttps://doi.org/10.1007/s10646-016-1748-1openalex-snapshot
De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam
inferred← citeshttps://doi.org/10.1007/s10658-016-1119-zopenalex-snapshot
Analysis of the apple rubbery wood disease by next generation sequencing of total RNA
inferred← citeshttps://doi.org/10.1007/s10681-017-1979-0openalex-snapshot
Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis)
inferred← citeshttps://doi.org/10.1007/s10709-014-9790-5openalex-snapshot
De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease
inferred← citeshttps://doi.org/10.1007/s10750-018-3682-0openalex-snapshot
Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species
inferred← citeshttps://doi.org/10.1007/s10898-025-01556-8openalex-snapshot
Minimum flow decomposition in graphs with cycles using integer linear programming
inferred← citeshttps://doi.org/10.1007/s11032-017-0711-zopenalex-snapshot
Comprehensive transcriptome analysis of Lactuca indica, a traditional medicinal wild plant
inferred← citeshttps://doi.org/10.1007/s11032-018-0782-5openalex-snapshot
De novo transcriptome analysis of abiotic stress-responsive transcripts of Hevea brasiliensis
inferred← citeshttps://doi.org/10.1007/s11033-021-06639-9openalex-snapshot
Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla
inferred← citeshttps://doi.org/10.1007/s11101-015-9451-zopenalex-snapshot
The Amaryllidaceae alkaloids: biosynthesis and methods for enzyme discovery
inferred← citeshttps://doi.org/10.1007/s11103-013-0025-4openalex-snapshot
Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research
inferred← citeshttps://doi.org/10.1007/s11103-013-0125-1openalex-snapshot
De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers
inferred← citeshttps://doi.org/10.1007/s11103-016-0553-9openalex-snapshot
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification
inferred← citeshttps://doi.org/10.1007/s11274-018-2459-yopenalex-snapshot
Comparative transcriptome analysis of Haematococcus pluvialis on astaxanthin biosynthesis in response to irradiation with red or blue LED wavelength
inferred← citeshttps://doi.org/10.1007/s11295-014-0765-6openalex-snapshot
Transcriptome of tung tree mature seeds with an emphasis on lipid metabolism genes
inferred← citeshttps://doi.org/10.1007/s11295-016-0995-xopenalex-snapshot
RNA-seq analysis in forest tree species: bioinformatic problems and solutions
inferred← citeshttps://doi.org/10.1007/s11295-018-1248-yopenalex-snapshot
An annotated transcriptome of highly inbred Thuja plicata (Cupressaceae) and its utility for gene discovery of terpenoid biosynthesis and conifer defense
inferred← citeshttps://doi.org/10.1007/s11427-013-4442-zopenalex-snapshot
Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq
inferred← citeshttps://doi.org/10.1007/s11427-013-4444-xopenalex-snapshot
Comparative analysis of de novo transcriptome assembly
inferred← citeshttps://doi.org/10.1007/s11427-015-0349-4openalex-snapshot
Characterizing and annotating the genome using RNA-seq data
inferred← citeshttps://doi.org/10.1007/s11626-017-0140-7openalex-snapshot
Relevant principal factors affecting the reproducibility of insect primary culture
inferred← citeshttps://doi.org/10.1007/s11816-016-0421-8openalex-snapshot
Comparative transcriptome profiling and SSR marker identification in three Jerusalem artichoke (Helianthus tuberosus L.) cultivars exhibiting phenotypic variation
inferred← citeshttps://doi.org/10.1007/s11816-022-00800-xopenalex-snapshot
De novo transcriptome analysis for exploration of genes responding to salinity in a halophyte New Zealand spinach (Tetragonia tetragonioides)
inferred← citeshttps://doi.org/10.1007/s12033-017-0015-xopenalex-snapshot
Cloning, Production and Characterization of a Glycoside Hydrolase Family 7 Enzyme from the Gut Microbiota of the Termite Coptotermes curvignathus
inferred← citeshttps://doi.org/10.1007/s12041-018-1051-4openalex-snapshot
The complete chloroplast genome of the threatened Dipentodon sinicus (Dipentodontaceae)
inferred← citeshttps://doi.org/10.1007/s12041-019-1064-7openalex-snapshot
Transcriptome profiling of coriander: a dual purpose crop unravels stem gall resistance genes
inferred← citeshttps://doi.org/10.1007/s12298-018-0525-4openalex-snapshot
Identification of genes associated with stress tolerance in moth bean [Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop
inferred← citeshttps://doi.org/10.1007/s12355-021-01098-9openalex-snapshot
Sugarcane Transcriptomics in Response to Abiotic and Biotic Stresses: A Review
inferred← citeshttps://doi.org/10.1007/s12561-012-9064-7openalex-snapshot
Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing
inferred← citeshttps://doi.org/10.1007/s12601-019-0011-0openalex-snapshot
De novo Assembly and Annotation of the Blood Transcriptome of the Southern Elephant Seal Mirounga leonina from the South Shetland Islands, Antarctica
inferred← citeshttps://doi.org/10.1007/s13205-016-0563-yopenalex-snapshot
De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value
inferred← citeshttps://doi.org/10.1007/s13205-018-1162-xopenalex-snapshot
Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata
inferred← citeshttps://doi.org/10.1007/s13258-018-0750-9openalex-snapshot
Transcriptome profiling suggests roles of innate immunity and digestion metabolism in purplish Washington clam
inferred← citeshttps://doi.org/10.1007/s13258-020-00927-7openalex-snapshot
Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation
inferred← citeshttps://doi.org/10.1007/s13258-023-01458-7openalex-snapshot
StringFix: an annotation-guided transcriptome assembler improves the recovery of amino acid sequences from RNA-Seq reads
inferred← citeshttps://doi.org/10.1007/s13562-021-00668-yopenalex-snapshot
De novo assembly, differential gene expression and pathway analyses for anthracnose resistance in chilli (Capsicum annuum L.)
inferred← citeshttps://doi.org/10.1007/s13562-023-00871-zopenalex-snapshot
Transcriptomics: illuminating the molecular landscape of vegetable crops: a review
inferred← citeshttps://doi.org/10.1007/s13580-014-1151-xopenalex-snapshot
Identification of three FLOWERING LOCUS C genes responsible for vernalization response in radish (Raphanus sativus L.)
inferred← citeshttps://doi.org/10.1007/s13721-025-00558-6openalex-snapshot
A systematic review on revolutionizing veterinary drug discovery: harnessing omics data to combat complex diseases in domestic animals
inferred← citeshttps://doi.org/10.1007/s40484-016-0069-yopenalex-snapshot
De novo assembly of transcriptome from next‐generation sequencing data
inferred← citeshttps://doi.org/10.1007/s40484-017-0109-2openalex-snapshot
Transcriptome assembly strategies for precision medicine
inferred← citeshttps://doi.org/10.1007/s42464-019-00026-7openalex-snapshot
Utility of PacBio Iso-Seq for transcript and gene discovery in Hevea latex
inferred← citeshttps://doi.org/10.1016/b978-0-08-100596-5.03005-5openalex-snapshot
Food Microbial Ecology in the ‘Omics’ Era
inferred← citeshttps://doi.org/10.1016/b978-0-08-100596-5.22739-xopenalex-snapshot
Mushroom Transcriptome
inferred← citeshttps://doi.org/10.1016/b978-0-12-386882-4.00008-6openalex-snapshot
Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1016/b978-0-12-404634-4.00007-3openalex-snapshot
Genomic Approaches for Interrogating the Biochemistry of Medicinal Plant Species
inferred← citeshttps://doi.org/10.1016/b978-0-12-404748-8.00006-xopenalex-snapshot
RNA-Sequencing and Methylome Analysis
inferred← citeshttps://doi.org/10.1016/b978-0-12-405945-0.00002-8openalex-snapshot
Applications of Deep Sequencing to Developmental Systems
inferred← citeshttps://doi.org/10.1016/b978-0-12-799958-6.00001-9openalex-snapshot
Epigenetic gene expression—an introduction
inferred← citeshttps://doi.org/10.1016/b978-0-12-801105-8.00002-3openalex-snapshot
Analysis Considerations for Utilizing RNA-Seq to Characterize the Brain Transcriptome
inferred← citeshttps://doi.org/10.1016/b978-0-12-805388-1.00011-0openalex-snapshot
Techniques for Genome-Wide Expression Analysis of Noncoding RNA
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20161-1openalex-snapshot
Transcriptome Analysis
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20206-9openalex-snapshot
Next Generation Sequence Analysis
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20211-2openalex-snapshot
Differential Expression From Microarray and RNA-seq Experiments
inferred← citeshttps://doi.org/10.1016/b978-0-12-814513-5.00019-2openalex-snapshot
Integrative Omic Analysis of Neuroblastoma
inferred← citeshttps://doi.org/10.1016/b978-0-12-817109-7.00006-7openalex-snapshot
Sustainable engineering technologies to promote activities of beneficial microbiome
inferred← citeshttps://doi.org/10.1016/b978-0-12-817495-1.00005-0openalex-snapshot
Metagenomic insights into the diversity and functions of microbial assemblages in lakes
inferred← citeshttps://doi.org/10.1016/b978-0-12-819990-9.00012-3openalex-snapshot
Bioinformatics Approaches for Fungal Biotechnology
inferred← citeshttps://doi.org/10.1016/b978-0-12-819990-9.00030-5openalex-snapshot
Next Generation Sequencing: Transcriptomics
inferred← citeshttps://doi.org/10.1016/b978-0-323-89775-4.00002-xopenalex-snapshot
RNA-seq for revealing the function of the transcriptome
inferred← citeshttps://doi.org/10.1016/b978-0-323-89778-5.00011-8openalex-snapshot
Genome informatics: present status and future prospects in agriculture
inferred← citeshttps://doi.org/10.1016/b978-0-323-89778-5.00019-2openalex-snapshot
Computational approaches toward single-nucleotide polymorphism discovery and its applications in plant breeding
inferred← citeshttps://doi.org/10.1016/b978-0-323-91909-8.00039-6openalex-snapshot
Techniques for Analyzing Genome-wide Expression of Non-coding RNA
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00250-5openalex-snapshot
Identification of Novel RNAs
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00292-xopenalex-snapshot
Transcriptome Analysis
inferred← citeshttps://doi.org/10.1016/b978-0-443-16092-9.00012-6openalex-snapshot
Role of bioinformatics in genome analysis
inferred← citeshttps://doi.org/10.1016/b978-0-443-19110-7.00021-5openalex-snapshot
Detection of fusion transcripts by RNA-sequencing data
inferred← citeshttps://doi.org/10.1016/b978-0-443-29281-1.00002-2openalex-snapshot
NGS analysis: Variant calling and genome assembly
inferred← citeshttps://doi.org/10.1016/b978-0-443-31550-3.00008-1openalex-snapshot
Decoding the blueprint: an overview of genome sequencing, assembly, and annotation
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