Searching journal content for articles similar to Zhang et al. 33 (11): 1975.

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  1. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...and not on experimental evidence (Supplemental Fig. S2), the gene prediction quality cannot be estimated confidently. This represents a bottleneck in the broad-scale understanding of nematode evolution and may lead to misinterpretations (Han et al. 2013). As a result, evolutionary studies across different species have so...
  2. Resource: Building better genome annotations across the tree of life
    • Adam H. Freedman and
    • Timothy B. Sackton
    Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
    ..., for example, among tools that solely produce protein-coding predictions.Proteome: BUSCO recoveryThe ability of a gene prediction method to recover protein-coding genes known to be conserved across a wide array of taxa is a good approximation for its ability to recover at least some subsequence of any gene...
  3. Research: A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
    • Mélisande Blein-Nicolas,
    • Sandra Sylvia Negro,
    • Thierry Balliau,
    • Claude Welcker,
    • Llorenç Cabrera-Bosquet,
    • Stéphane Dimitri Nicolas,
    • Alain Charcosset,
    • and Michel Zivy
    Genome Res. November 2020 30: 1593-1604; Published in Advance October 15, 2020, doi:10.1101/gr.255224.119
    ...coexpression network analysis (WGCNA) of protein coexpression across the 251 genotypes in the two watering conditions separately (Supplemental Table S5). The two resulting networks differed in the presence of condition-specific modules indicating that water deficit has altered the structure of the protein...
  4. ARTICLE: The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
    • Cristian I. Castillo-Davis,
    • Fyodor A. Kondrashov,
    • Daniel L. Hartl,
    • and Rob J. Kulathinal
    Genome Res. May 2004 14: 802-811; doi:10.1101/gr.2195604
    ...and conservative rates of evolution between species? Do similar forces act across diverse lineages as distinct as phyla? From recently completed -sequencing projects, it has been demonstrated that most multi-cellular organisms contain a similar complement of genes and gene families, owing, in part, to a common...
  5. Research: Evolutionary rate covariation reveals shared functionality and coexpression of genes
    • Nathan L. Clark,
    • Eric Alani,
    • and Charles F. Aquadro
    Genome Res. April 2012 22: 714-720; Published in Advance January 27, 2012, doi:10.1101/gr.132647.111
    ...in constraint is the greater contributor to ERC because it acts on all proteins. Indeed, we observe ERC proteome-wide, including between many highly conserved proteins that would only on rare occasion experience positively selected substitutions. In addition, Elyashiv et al. (2010) have used polymorphism data...
  6. Method: System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA–protein complexes
    • Cornelia Kilchert,
    • Tea Kecman,
    • Emily Priest,
    • Svenja Hester,
    • Ebru Aydin,
    • Krzysztof Kus,
    • Oliver Rossbach,
    • Alfredo Castello,
    • Shabaz Mohammed,
    • and Lidia Vasiljeva
    Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
    ...similar to the mammalian module. Moreover, the residues involved in PAS recognition by CPSF30 and the WD40 domain of WDR33 are conserved in the homologous proteins Yth1p and Pfs2p, suggesting structural conservation of RNA binding between distant clades. Other components of the polymerase module, CPSF160...
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