Searching journal content for articles similar to Rasmussen and Kellis 17 (12): 1932.

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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
    ...to the proteotranscriptomics-validated ORFs, that is, those supported by peptide evidence. Thus, we used 1516 orthology protein groups that only have one-to-one orthologs across all species. By multiple alignment of these protein sequences, we reconstructed individual gene trees for each orthology group with three different...
  2. Method: Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
    • Yi-Chieh Wu,
    • Matthew D. Rasmussen,
    • Mukul S. Bansal,
    • and Manolis Kellis
    Genome Res. March 2014 24: 475-486; Published in Advance December 5, 2013, doi:10.1101/gr.161968.113
    ...of the loci at the speciationnodeswould allowus to infer evolution within each species tree branch independently of one another. Therefore, rather than inferring the locus map and order for the entire gene tree at once, we consider the subproblem of determining species-specific locus maps and orders...
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  3. Method: Unified modeling of gene duplication, loss, and coalescence using a locus tree
    • Matthew D. Rasmussen and
    • Manolis Kellis
    Genome Res. April 2012 22: 755-765; Published in Advance January 23, 2012, doi:10.1101/gr.123901.111
    ...and drifts until it fixes or goes extinct. Duplications, losses, and coalescence Genome Research 757 www..org that the blue tree in Figure 2A is not a species tree (e.g., species B and C are represented multiple times), and yet it is distinct from the gene tree. Therefore, it is a third kind of tree, which...
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  4. Research: The genomic basis of evolutionary differentiation among honey bees
    • Bertrand Fouks,
    • Philipp Brand,
    • Hung N. Nguyen,
    • Jacob Herman,
    • Francisco Camara,
    • Daniel Ence,
    • Darren E. Hagen,
    • Katharina J. Hoff,
    • Stefanie Nachweide,
    • Lars Romoth,
    • Kimberly K.O. Walden,
    • Roderic Guigo,
    • Mario Stanke,
    • Giuseppe Narzisi,
    • Mark Yandell,
    • Hugh M. Robertson,
    • Nikolaus Koeniger,
    • Panuwan Chantawannakul,
    • Michael C. Schatz,
    • Kim C. Worley,
    • Gene E. Robinson,
    • Christine G. Elsik,
    • and Olav Rueppell
    Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
    ...et al. 2021).The evolution of complex insect societies represents one of the major evolutionary transitions (Maynard Smith and Szathmáry 1995). Genomic signatures of this transition share few commonalities across taxa, except for an increase in gene regulatory capacity (Gadau et al. 2012; Simola et...
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  5. Resource: The genomic architecture and molecular evolution of ant odorant receptors
    • Sean K. McKenzie and
    • Daniel J.C. Kronauer
    Genome Res. November 2018 28: 1757-1765; Published in Advance September 24, 2018, doi:10.1101/gr.237123.118
    ...tandem duplications as the predominant drivers of gene expansion in these gene clades. The many short species-specific tandem arrays in the bottom half of A and C and throughout D indicate that genomic transpositions followed by tandem duplications drove expansions in these clades.To examine the genomic...
  6. Resource: Global networks of functional coupling in eukaryotes from comprehensive data integration
    • Andrey Alexeyenko and
    • Erik L.L. Sonnhammer
    Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108
    ...to be most accurate for identifying functional counterparts ( Hulsen et al. 2006 ). Nonetheless, the transfer can be done in many ways in case of multiple co-orthologs (inparalogs) stemming from species-specific gene duplication, which is commonplace in eukaryotes. As shown in Figure 4 , the FC may evolve...
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