ArticlePLoS computational biology2006
A third approach to gene prediction suggests thousands of additional human transcribed regions.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Host genetics predominates over gut microbiota in serum copper levels in boars.Journal of animal science · 2025Article
- Downregulation of long noncoding RNA CASC15 inhibits progression, migration and invasion of papillary thyroid cancer.Archives of medical science : AMS · 2023Article
- LncRNA CASC15, MiR-23b Cluster and SMAD3 form a Novel Positive Feedback Loop to promote Epithelial-Mesenchymal Transition and Metastasis in Ovarian Cancer.International journal of biological sciences · 2022Article
- CASC15 polymorphisms are correlated with cervical cancer susceptibility in Chinese women.Molecular genetics & genomic medicine · 2020Article
- The Regulatory Role of Non-coding RNAs on Programmed Cell Death Four in Inflammation and Cancer.Frontiers in oncology · 2019Review
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Long non-coding RNA CASC15 promotes melanoma progression by epigenetically regulating PDCD4.Cell & bioscience · 2018Article
- Article
- The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching.The Journal of investigative dermatology · 2015Article
- Realistic artificial DNA sequences as negative controls for computational genomics.Nucleic acids research · 2014Article
- DNA-energetics-based analyses suggest additional genes in prokaryotes.Journal of biosciences · 2012Article
- Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes.Current genomics · 2012Article
- Genomic signatures of germline gene expression.Genome research · 2010Article
- Transposon identification using profile HMMs.BMC genomics · 2010Article
- The completion of the Mammalian Gene Collection (MGC).Genome research · 2009Article
- Conserved introns reveal novel transcripts in Drosophila melanogaster.Genome research · 2009Article
- Small molecule activators of pre-mRNA 3' cleavage.RNA (New York, N.Y.) · 2009Article
- Transcription induces strand-specific mutations at the 5' end of human genes.Genome research · 2008Article
- Genomic DNA from animals shows contrasting strand bias in large and small subsequences.BMC genomics · 2008Article
- Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression.BMC genomics · 2008Article
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Authors and funding
7 authors.
Funding
Abstract
The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome. Many algorithms for computational gene prediction have been described, ultimately derived from two basic concepts: (1) modeling gene structure and (2) recognizing sequence similarity. Successful hybrid methods combining these two concepts have also been developed. We present a third orthogonal approach to gene prediction, based on detecting the genomic signatures of transcription, accumulated over evolutionary time. We discuss four algorithms based on this third concept: Greens and CHOWDER, which quantify mutational strand biases caused by transcription-coupled DNA repair, and ROAST and PASTA, which are based on strand-specific selection against polyadenylation signals. We combined these algorithms into an integrated method called FEAST, which we used to predict the location and orientation of thousands of putative transcription units not overlapping known genes. Many of the newly predicted transcriptional units do not appear to code for proteins. The new algorithms are particularly apt at detecting genes with long introns and lacking sequence conservation. They therefore complement existing gene prediction methods and will help identify functional transcripts within many apparent "genomic deserts."
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