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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future...
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Methods: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
- Vardges Ter-Hovhannisyan,
- Alexandre Lomsadze,
- Yury O. Chernoff,
- and Mark Borodovsky
Genome Res. December 2008 18: 1979-1990; Published in Advance August 29, 2008, doi:10.1101/gr.081612.108
...on the prediction stage of the gene identification problem (i.e., how to find genes given a training sequence) evolved into automatic self-training systems capable of adjusting to -specific properties in the process of estimating algorithm parameters from anonymous sequence ( Audic and Claverie 1998 ; Hayes...
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METHODS: Detecting and Analyzing DNA Sequencing Errors: Toward a Higher Quality of the Bacillus subtilis Genome Sequence
- Claudine Médigue,
- Matthias Rose,
- Alain Viari,
- and Antoine Danchin
Genome Res. November 1, 1999 9: 1116-1127; doi:10.1101/gr.9.11.1116
.... Biosci. 12 : 31 – 40 . ↵ Gribskov M. , Devereux J. , Burgess R.R. ( 1984 ) The codon preference plot : Graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res. 12 : 539 – 549 . ↵ Hayes S.H. , Borodovsky M. ( 1998 ) How to interpret an anonymous bacterial...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
...in different reading frame from the same mRNA. PhyloP scores can be computed from the UCSC Genome Browser, and noise filtration (by Haar direct wavelet) allows for the identification of distinct purifying selection signals in each reading frames. Here, the example of the dual coding MIEF1 gene is represented...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...for all the HMP sequencer runs. Horizontal transfer and replicate sequencing complicate interpretation of plasmid and gene profiles, particularly when the same plasmid or gene is sequenced multiple times but differently named. Since LMAT takes a “best first match” approach, the reported plasmid or gene...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
...178 . ↵ Birch-Machin, I., Gao, S., Huen, D., McGirr, R., White, R.A., and Russell, S. 2005 . Genomic analysis of heat-shock factor targets in Drosophila. Genome Biol. 6 : R63 . ↵ Boutanaev, A.M., Kalmykova, A.I., Shevelyov, Y.Y., and Nurminsky, D.I. 2002 . Large clusters of co-expressed genes...
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ARTICLE: Generation and analysis of 280,000 human expressed sequence tags.
- L D Hillier,
- G Lennon,
- M Becker,
- M F Bonaldo,
- B Chiapelli,
- S Chissoe,
- N Dietrich,
- T DuBuque,
- A Favello,
- W Gish,
- M Hawkins,
- M Hultman,
- T Kucaba,
- M Lacy,
- M Le,
- N Le,
- E Mardis,
- B Moore,
- M Morris,
- J Parsons,
- C Prange,
- L Rifkin,
- T Rohlfing,
- K Schellenberg,
- and M Marra
Genome Res. September 1996 6: 807-828; doi:10.1101/gr.6.9.807
...role in enhancing the interpretation and annotation of the genomic sequence. ESTs will also contribute to the development of sequence- ready maps. The potential for early gene discovery com- bined with the long-term value of ESTs for analy- sis of the human prompted us, in coop- eration with Merck...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...’ mutation frequencies. However, the gene shown in Figure 5 (middle) offers a less clear interpretation: There exist three main groups of positions with high mutation frequencies (with frequencies ∼1%–2%, 4%–5%, and 6%–7%) covering this gene, as well as a group of mostly unmutated positions. The Supplemental...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
.... Contractions of the human subtelomeric satellite D4Z4 cause facioscapulohumeral muscular dystrophy by altering the chromatin state of nearby genes (Zeng et al. 2009). Sequence variation in a human centromeric satellite is associated with aneuploidy (Aldrup-MacDonald et al. 2016). Variants of the mostly...
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ARTICLE: Dichotomous splicing signals in exon flanks
- Xiang H-F. Zhang,
- Christina S. Leslie,
- and Lawrence A. Chasin
Genome Res. June 2005 15: 768-779; doi:10.1101/gr.3217705
...distribution reflecting an exaggeration of this base composition in flanks relative to the gene as a whole. We divided all exons into two classes according to their flank G+C content and used computational and statistical methods to define pentamers of high relative abundance and phylogenetic conservation...

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