Searching journal content for articles similar to Williams and Bowles 14 (6): 1060.

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  1. 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
    ...), presumably because deleting boundaries might destroy the insulating effect separating neighboring TADs. Thus, TAD boundaries share hallmarks of other functional genomic regions, like strong evolutionary constraints (Fudenberg and Pollard 2019). However, other than the dearth of deletions at TAD boundaries...
  2. Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
    • Itai Yanai and
    • Craig P. Hunter
    Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
    ...examined gene neighbors without setting a threshold for genomic distance. However, when restricting to only those gene neighbors within 1 kb, we found a greater divergence between orthologs of coexpressed neighbors relative to the divergence observed in more distant genes (Supplemental Fig. S8). Second, we...
  3. LETTER: An Arabidopsis gene network based on the graphical Gaussian model
    • Shisong Ma,
    • Qingqiu Gong,
    • and Hans J. Bohnert
    Genome Res. November 2007 17: 1614-1625; Published in Advance October 5, 2007, doi:10.1101/gr.6911207
    ...network for the Arabidopsis thaliana transcriptome based on a modified graphical Gaussian model (GGM). Through partial correlation (pcor), GGM infers coregulation patterns between gene pairs conditional on the behavior of other genes. Regularized GGM calculated pcor between gene pairs among ∼2000 input...
  4. LETTER: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
    • Besma Ben Amor,
    • Sonia Wirth,
    • Francisco Merchan,
    • Philippe Laporte,
    • Yves d’Aubenton-Carafa,
    • Judith Hirsch,
    • Alexis Maizel,
    • Allison Mallory,
    • Antoine Lucas,
    • Jean Marc Deragon,
    • Herve Vaucheret,
    • Claude Thermes,
    • and Martin Crespi
    Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
    ...of significant BLAST hits against NCBI nr protein databank. Mapping of other ESTs and cDNAs on these genomic regions did not bridge the gap with already annotated neighboring genes. Mapping of short RNAs (sRNAs) on the total set of 76 npcRNA was performed using a large data set of massively sequenced A. thaliana...
  5. Method: Prioritizing candidate disease genes by network-based boosting of genome-wide association data
    • Insuk Lee,
    • U. Martin Blom,
    • Peggy I. Wang,
    • Jung Eun Shim,
    • and Edward M. Marcotte
    Genome Res. July 2011 21: 1109-1121; Published in Advance May 2, 2011, doi:10.1101/gr.118992.110
    ...–protein interactions, protein complex, and comparative genomics data sets, in combinationwith similar lines of evidence fromorthologs inyeast, fly, andworm,were analyzed using an approach previously developed and validated for yeast (Lee et al. 2004, 2007a),C. elegans (Lee et al. 2008, 2010b), and Arabidopsis (Lee et...
  6. LETTER: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
    • Ligeng Ma,
    • Chen Chen,
    • Xigang Liu,
    • Yuling Jiao,
    • Ning Su,
    • Lin Li,
    • Xiangfeng Wang,
    • Mengliang Cao,
    • Ning Sun,
    • Xiuqing Zhang,
    • Jingyue Bao,
    • Jian Li,
    • Soren Pedersen,
    • Lars Bolund,
    • Hongyu Zhao,
    • Longping Yuan,
    • Gane Ka-Shu Wong,
    • Jun Wang,
    • Xing Wang Deng,
    • and Jian Wang
    Genome Res. September 2005 15: 1274-1283; doi:10.1101/gr.3657405
    ...gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar...
  7. Research: Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
    • Takashi Makino and
    • Aoife McLysaght
    Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111
    ...distribution using singletons with trans-PPIs (Table 4). The estimated P-values were adjusted by Bonferroni correction. Acknowledgments This work is supported by Science Foundation Ireland. References The Arabidopsis Genome Initiative. 2000. Analysis of the sequence of the flowering plant Arabidopsis thaliana...
  8. Research: The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species
    • Jingping Yang,
    • Edward Ramos,
    • and Victor G. Corces
    Genome Res. November 2012 22: 2199-2207; Published in Advance August 15, 2012, doi:10.1101/gr.142125.112
    ...Research www..org Dhadi SR, Krom N, Ramakrishna W. 2009. Genome-wide comparative analysis of putative bidirectional promoters from rice, Arabidopsis and Populus. Gene 429: 65–73. Drosophila 12 Genomes Consortium. 2007. Evolution of genes and s on the Drosophila phylogeny. Nature 450: 203–218. Handoko L, Xu...
  9. Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat Biotechnol 37: 133–138. doi:10 .1038/s41587-019-0013-6 Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD. 2004. Analysis of the transcriptional complexity of Arabidopsis thaliana by massively...
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  10. LETTER: Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
    • Brian C. Thomas,
    • Brent Pedersen,
    • and Michael Freeling
    Genome Res. July 2006 16: 934-946; Published in Advance June 7, 2006, doi:10.1101/gr.4708406
    ...the typical fate of any gene duplicate is loss ( Haldane 1933 ; Lynch and Force 2000 ). Arabidopsis thaliana, a dicot flowering plant (125-Mb with ∼26,000 annotated genes) ( The Arabidopsis Genome Initiative 2000 ), has retained duplicates in overlapping syntenous blocks that have been explained by multiple...
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