Searching journal content for articles similar to Jordan et al. 12 (6): 962.

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  1. LETTER: Mutational and Selective Pressures on Codon and Amino Acid Usage in Buchnera, Endosymbiotic Bacteria of Aphids
    • Claude Rispe,
    • François Delmotte,
    • Roeland C.H.J. van Ham,
    • and Andres Moya
    Genome Res. January 2004 14: 44-53; Published in Advance December 12, 2003, doi:10.1101/gr.1358104
    ...Mutational and Selective Pressures on Codon and Amino Acid Usage in Buchnera , Endosymbiotic Bacteria of Aphids Claude Rispe 1 , 6 , François Delmotte 2 , 3 , Roeland C.H.J. van Ham 4 , 5 , and Andres Moya 2 1 UMR BIO3P...
  2. Research: A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
    • Adam J. Litterman,
    • Robin Kageyama,
    • Olivier Le Tonqueze,
    • Wenxue Zhao,
    • John D. Gagnon,
    • Hani Goodarzi,
    • David J. Erle,
    • and K. Mark Ansel
    Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
    ...selected to create a large amount of protein per transcript, and that these genes tend to be involved in core developmental processes. Consistent with this idea, cell-essential genes exhibit lower 3′ UTR GC content than nonessential genes independently of their sequence conservation. Other classes of genes...
  3. Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
    • Yi Liao,
    • Xinwen Zhang,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
    ...breakpoints coincide with Drosophila TAD boundariesConservation of a considerable fraction of TADs between two distantly related Drosophila species prompted us to investigate whether TADs are evolutionarily constrained. To this end, we identified 1061 rearrangement breakpoints between D. melanogaster and D...
  4. Research: The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease
    • Piaopiao Chen,
    • Dandan Wang,
    • Han Chen,
    • Zhenzhen Zhou,
    • and Xionglei He
    Genome Res. October 2016 26: 1355-1362; Published in Advance July 20, 2016, doi:10.1101/gr.205955.116
    ...biosynthesis pathway is evolutionarily conserved among various lineages including yeast, nematodes, and mammals (Fig. 4A; Kanehisa and Goto 2000). Importantly, partial loss-of-function mutations on the human gene encoding the enzyme ADSL cause ADSL deficiency, a rare Mendelian disease with mental retardation...
  5. Research: Trans-splicing enhances translational efficiency in C. elegans
    • Yu-Fei Yang,
    • Xiaoqing Zhang,
    • Xuehua Ma,
    • Taolan Zhao,
    • Qiushi Sun,
    • Qing Huan,
    • Shaohuan Wu,
    • Zhuo Du,
    • and Wenfeng Qian
    Genome Res. September 2017 27: 1525-1535; Published in Advance July 6, 2017, doi:10.1101/gr.202150.115
    ...of years ago (Stein et al. 2003; Cho et al. 2004; Hillier et al. 2007; Cutter 2008). We repeated the analysis in these species and observed similar phenomena (Fig. 1B–D). This indicates that the enhanced translational efficiencies in SL1 trans-spliced genes are evolutionarily conserved. We further...
  6. LETTER: Evolution and Topology in the Yeast Protein Interaction Network
    • Stefan Wuchty
    Genome Res. July 2004 14: 1310-1314; doi:10.1101/gr.2300204
    ...by a considerable probability of simultaneously being evolutionarily conserved and essential, an observation that does not have an equivalent for nonessential proteins. Providing a thorough assessment of the impact noisy and incomplete data have on our findings, we conclude that our results are largely insensitive...
  7. Method: A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
    • Panagiotis Katsonis and
    • Olivier Lichtarge
    Genome Res. December 2014 24: 2050-2058; Published in Advance September 12, 2014, doi:10.1101/gr.176214.114
    ...reflect fitness (Coyne and Orr 1998), in effect ET and evolutionary gradient are equivalent concepts and we may choose ET ranks to approximate @f/@ri (Fig. 1B). A frequent and simpler measure of evolutionary importance is residue conservation (Livingstone and Barton 1993; Pei and Grishin 2001; Valdar 2002...
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  8. LETTER: Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
    • Dmitri M. Krylov,
    • Yuri I. Wolf,
    • Igor B. Rogozin,
    • and Eugene V. Koonin
    Genome Res. October 2003 13: 2229-2235; doi:10.1101/gr.1589103
    ...from protein sequences. Comput. Appl. Biosci. 8 : 275 -282. ↵ Jordan, I.K., Rogozin, I.B., Wolf, Y.I., and Koonin, E.V. 2002 . Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12 : 962 -968. ↵ Jordan, I.K., Wolf, Y.I., and Koonin, E.V. 2003...
  9. LETTER: Origins and impact of constraints in evolution of gene families
    • Boris E. Shakhnovich and
    • Eugene V. Koonin
    Genome Res. December 2006 16: 1529-1536; Published in Advance October 19, 2006, doi:10.1101/gr.5346206
    ...and rate of evolution . Nature 411 : 1046 – 1049 . ↵ Hurst, L.D. , Smith, N.G. ( 1999 ) Do essential genes evolve slowly? Curr. Biol. 9 : 747 – 750 . ↵ Jordan, I.K. , Rogozin, I.B. , Wolf, Y.I. , Koonin, E.V. ( 2002 ) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria...
  10. Methods: Predicting essential genes in fungal genomes
    • Michael Seringhaus,
    • Alberto Paccanaro,
    • Anthony Borneman,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2006 16: 1126-1135; Published in Advance August 9, 2006, doi:10.1101/gr.5144106
    ...essential genes in the vast majority of pathogens, we must look beyond direct experimental methods. Early comparative genomics approaches involved comparing multiple s to find a core conserved minimal and labeling its component genes essential ( Mushegian and Koonin 1996 ; Arigoni et al. 1998 ; Bruccoleri...
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