The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Open accessAbstract
As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Likelihood Ratio Tests for Model Selection and Non-Nested Hypotheses
Vuong, Q. H. (1989) · Econometrica · doi:10.2307/1912557 · Cited by 5,929
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
Self-citationWooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,032
Improved microbial gene identification with GLIMMER
Delcher, A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.23.4636 · Cited by 2,493
RNA sequencing: advances, challenges and opportunities
Ozsolak, F., & Milos, P. M. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2934 · Cited by 2,135 · cited 2×
“Major challenges remain in integrating these methods into coherent pipelines, harmonizing the results with existing genome annotation databases, and coping with the uneven coverage and relatively high error rate of current high-throughput sequencing technologies (Ozsolak and Milos, 2011).”
BackgroundEvolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Sequencing and comparison of yeast species to identify genes and regulatory elements
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., & Lander, E. S. (2003) · Nature · doi:10.1038/nature01644 · Cited by 1,753
Self-citationAligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Blanchette, M., Kent, W. J., Riemer, C., Elnitski, L., Smit, A. F. A., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., et al. (2004) · Genome Research · doi:10.1101/gr.1933104 · Cited by 1,452
Cited by
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
“Additional data types, including PhyloCSF (20), CpGIslands, RepeatMasker (21) and Cap analysis of gene expression (CAGE) data (22), are sometimes used as additional support.”
MethodGENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Self-citationUtilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
Sun, L., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., & Zhao, Y. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt646 · Cited by 2,099
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
Kang, Y.-J., Yang, D.-C., Kong, L., Hou, M., Meng, Y.-Q., Wei, L., & Gao, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx428 · Cited by 1,637
Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J., Barnes, I., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1087 · Cited by 1,334
Self-citation
Metadata
- Authors
- Lin, M., Jungreis, I., & Kellis, M.
- Venue
- Nature Precedings
- Published
- 2010-08-18
- Volume
- 27
- Issue
- 13
- Pages
- i275-i282
- ISSN
- 1756-0357 (ISSN-L)
- OpenAlex
- W2139658526
- Cited by
- 1,016
- References
- 35
- Type
- posted content
- Language
- en
- Open access
- diamond
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. https://app.cochat.ai/papers/10.1038/npre.2010.4784.1
- The paper
- Lin, M., Jungreis, I., & Kellis, M. (2010). PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Nature Precedings. https://doi.org/10.1038/npre.2010.4784.1
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
