Reference health
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
57/57 checkable references clean · checked 2026-07-24
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
2 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 57 checked references that resolve
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB
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Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
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Long Noncoding RNAs: Cellular Address Codes in Development and Disease
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The long non-coding RNAs, a new cancer diagnostic and therapeutic gold mine
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CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
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PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
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Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
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A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
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The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
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Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery
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De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
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Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
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Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (<i>Coregonus</i> spp. Salmonidae)
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Hybrid error correction and de novo assembly of single-molecule sequencing reads
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Next generation deep sequencing and vaccine design: today and tomorrow
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Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing
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RNA sequencing reveals a diverse and dynamic repertoire of the <i>Xenopus tropicalis</i> transcriptome over development
resolves10.1186/gb-2010-11-8-r86
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
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Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
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A long-term demasculinization of X-linked intergenic noncoding RNAs in <i>Drosophila melanogaster</i>
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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
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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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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
resolves10.1093/gbe/evs020
Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome
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Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs
resolves10.1186/1471-2105-14-S5-S12
Gene prediction in metagenomic fragments based on the SVM algorithm
resolves10.1093/bioinformatics/btr016
A <i>k</i>-mer scheme to predict piRNAs and characterize locust piRNAs
resolves10.1186/1471-2105-12-216
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM
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Mechanism of a genetic glissando*: structural biology of indel mutations
resolves10.1186/gb-2014-15-2-r40
Genome-wide discovery and characterization of maize long non-coding RNAs
The 2 references without a DOI — listed, not checked
no DOI — not checkedFlintoft L: Non-coding RNA: Structure and function for lncRNAs. Nat Rev Genet. 2013, 14 (9): 598-
no DOI — not checkedPacBio blog, data release, human MCF-7 transcriptome. [http://blog.pacificbiosciences.com/2013/12/data-release-human-mcf-7-transcriptome.html]
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