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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...the frequency of optimal codons correlates with gene expression to quantify the intensity of translational selection (S). We observed that few metazoans show clear signs of translational selection. As predicted by the nearly neutral theory, the highest values of S are observed in species with large effective...
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Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
- Yi-Fei Huang and
- Adam Siepel
Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
...protein-coding sequences in the human . This map is generally consistent with previous inferences of the bulk distribution of fitness effects but reveals pervasive weak negative selection against synonymous mutations. In addition, the estimated selection coefficients are highly predictive of inherited...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...of completely sequenced s, the large majority of which (>90%) originate from prokaryotes (Reddy et al. 2015). The accurate annotation of all protein-coding genes (interchangeably used with CDSs from here on) is essential to exploit this genomic information at multiple levels: from small, focused experiments, up...
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Research: Overlapping codes within protein-coding sequences
- Shalev Itzkovitz,
- Eran Hodis,
- and Eran Segal
Genome Res. November 2010 20: 1582-1589; Published in Advance September 14, 2010, doi:10.1101/gr.105072.110
...amino acid sequence can be encoded by many different DNA sequences. A recent study even suggested that the genetic code is nearly optimal for accommodating additional information (Itzkovitz and Alon 2007). Several studies highlighted measures of information content that are unique to the protein-coding...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
..., Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark. Abstract The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under...
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Research: Interplay between coding and exonic splicing regulatory sequences
- Nicolas Fontrodona,
- Fabien Aubé,
- Jean-Baptiste Claude,
- Hélène Polvèche,
- Sébastien Lemaire,
- Léon-Charles Tranchevent,
- Laurent Modolo,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. May 2019 29: 711-722; Published in Advance April 8, 2019, doi:10.1101/gr.241315.118
...regulatory sequences lie within protein-coding sequences, a major challenge is to understand how coding sequences accommodate this overlapping layer of information (Itzkovitz et al. 2010; Lin et al. 2011; Savisaar and Hurst 2017a,b). To date, a general assumption is that protein-coding sequences can...
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Letter: Darwinian and demographic forces affecting human protein coding genes
- Rasmus Nielsen,
- Melissa J. Hubisz,
- Ines Hellmann,
- Dara Torgerson,
- Aida M. Andrés,
- Anders Albrechtsen,
- Ryan Gutenkunst,
- Mark D. Adams,
- Michele Cargill,
- Adam Boyko,
- Amit Indap,
- Carlos D. Bustamante,
- and Andrew G. Clark
Genome Res. May 2009 19: 838-849; Published in Advance March 11, 2009, doi:10.1101/gr.088336.108
...removed. Here we fit a detailed model of human demography that incorporates divergence, migration, admixture, and changes in population size to directly sequenced data from 13,400 protein coding genes from 20 European-American and 19 African-American individuals. Based on this demographic model, we use...
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Method: Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
- David R. Kelley,
- Jasper Snoek,
- and John L. Rinn
Genome Res. July 2016 26: 990-999; Published in Advance May 3, 2016, doi:10.1101/gr.200535.115
...for their motifs along the sequence and output a matrix with a row for every filter and column for every position in the sequence (Fig. 1). Computing nonlinear functions of the information flowing through the network allows for more expressive models. In each convolution layer, we apply a rectifier operation (i...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...selection. ( C ) Nonsense mutation in (the sequenced strain of) D. melanogaster . Reading frame of translation In addition to locating protein-coding regions, the comparative information reveals the reading frame of translation under purifying selection, since the signature of codon substitution frequencies...
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LETTER: Tandem Repeats in Protein Coding Regions of Primate Genes
- Branko Borštnik and
- Danilo Pumpernik
Genome Res. June 1, 2002 12: 909-915; doi:10.1101/gr.138802
...of the standard models adapted for protein coding regions. By comparing the results of the computer simulation with the results of the analyses of natural sequences, one can get useful information about the nature of repeat generation in protein coding regions. The protein coding regions represent an essentially...

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