Searching journal content for articles similar to Sanderson 18 (4): 517.

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  1. Method: A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes
    • Andy Lin,
    • Richard T. Wang,
    • Sangtae Ahn,
    • Christopher C. Park,
    • and Desmond J. Smith
    Genome Res. August 2010 20: 1122-1132; Published in Advance May 27, 2010, doi:10.1101/gr.104216.109
    ...protein–protein interaction networks is limited (Gandhi et al. 2006). Therefore it is necessary to explore mammalian genetic interactions in the mammalian setting. An additional problem for mammalian cells is the apparent lack of a simple and cheap method for combining alleles of distinct genes...
  2. Letter: The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host–pathogen interactions
    • Eric E. Smith and
    • Harmit S. Malik
    Genome Res. May 2009 19: 850-858; Published in Advance March 19, 2009, doi:10.1101/gr.085647.108
    ...APOL6 function by interacting at the base of the MAD hinge—a region under strong positive selection (shown in dark gray). By recognizing this critical region, antagonists may be able to manipulate APOL6 in different ways. One possibility is that antagonists promote infections by preventing APOL6...
  3. Method: Spatial Cellular Networks from omics data with SpaCeNet
    • Stefan Schrod,
    • Niklas Lück,
    • Robert Lohmayer,
    • Stefan Solbrig,
    • Dennis Völkl,
    • Tina Wipfler,
    • Katherine H. Shutta,
    • Marouen Ben Guebila,
    • Andreas Schäfer,
    • Tim Beißbarth,
    • Helena U. Zacharias,
    • Peter J. Oefner,
    • John Quackenbush,
    • and Michael Altenbuchinger
    Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124
    ...estimates of spatial gene–gene dependencies between gene i and j. (C) A sketch of the more complex scenario of a set of interacting cells. Here, the expression of the cell a is affected by all surrounding cells in a distance-dependent way, as illustrated by thin and bold dotted lines for long- and short...
  4. Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
    • Dhanur P. Iyer,
    • Lambert Moyon,
    • Lars Wittler,
    • Chieh-Yu Cheng,
    • Francisca R. Ringeling,
    • Stefan Canzar,
    • Annalisa Marsico,
    • and Aydan Bulut-Karslioğlu
    Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
    ..., the pluripotent epiblast depends on miRNA activity, the absence of which results in the loss of pluripotent cells. Through the integration of high-sensitivity small RNA expression profiling of individual embryos and protein expression of miRNA targets with public data of protein–protein interactions, we...
  5. Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
    • Stephania Contreras Castillo,
    • Bertille Montibus,
    • Azucena Rocha,
    • Will Duke,
    • Ferdinand von Meyenn,
    • Donal McLornan,
    • Claire Harrison,
    • Ann Mullally,
    • Reiner Schulz,
    • and Rebecca J. Oakey
    Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
    ...of myeloproliferative neoplasms (MPNs), for which HC is the first-line treatment, will provide a better understanding of its molecular effects. To explore the effects of HC -wide, transcriptomic analyses were performed on two clinically relevant cell types at different stages of differentiation treated with HC...
  6. Resource: Transcriptional milestones in Dictyostelium development
    • Mariko Katoh-Kurasawa,
    • Karin Hrovatin,
    • Shigenori Hirose,
    • Amanda Webb,
    • Hsing-I Ho,
    • Blaž Zupan,
    • and Gad Shaulsky
    Genome Res. August 2021 31: 1498-1511; Published in Advance June 28, 2021, doi:10.1101/gr.275496.121
    ...performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological...
  7. Research: Human-specific features of spatial gene expression and regulation in eight brain regions
    • Chuan Xu,
    • Qian Li,
    • Olga Efimova,
    • Liu He,
    • Shoji Tatsumoto,
    • Vita Stepanova,
    • Takao Oishi,
    • Toshifumi Udono,
    • Katsushi Yamaguchi,
    • Shuji Shigenobu,
    • Akiyoshi Kakita,
    • Hiroyuki Nawa,
    • Philipp Khaitovich,
    • and Yasuhiro Go
    Genome Res. August 2018 28: 1097-1110; Published in Advance June 13, 2018, doi:10.1101/gr.231357.117
    ...cortical regions and the cerebellum. An analysis of the predicted regulatory interactions driving these differences revealed the role of transcription factors in species-specific transcriptome changes, and epigenetic modifications were linked to spatial expression differences conserved across species...
    OPEN ACCESS ARTICLE
  8. Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    • Daniel Marbach,
    • Sushmita Roy,
    • Ferhat Ay,
    • Patrick E. Meyer,
    • Rogerio Candeias,
    • Tamer Kahveci,
    • Christopher A. Bristow,
    • and Manolis Kellis
    Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
    ...motifs, gene expression, and chromatin modification data sets as input features. Applying these methods to Drosophila melanogaster, we predict ∼300,000 regulatory edges in a network of ∼600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional...
  9. PERSPECTIVE: Comparing the human and chimpanzee genomes: Searching for needles in a haystack
    • Ajit Varki and
    • Tasha K. Altheide
    Genome Res. December 2005 15: 1746-1758; doi:10.1101/gr.3737405
    ...Diego, La Jolla, California 92093, USA Abstract The chimpanzee genome sequence is a long-awaited milestone, providing opportunities to explore primate evolution and genetic contributions to human physiology and disease. Humans and chimpanzees shared a common ancestor ∼5-7 million years ago...
  10. PERSPECTIVE: Xenomics
    • Enrique Amaya
    Genome Res. December 2005 15: 1683-1691; doi:10.1101/gr.3801805
    .... The transmembrane protein XFLRT3 forms a complex with FGF receptors and promotes FGF signalling. Nat. Cell Biol. 6 : 38 -44. ↵ Bronchain, O.J., Hartley, K.O., and Amaya, E. 1999 . A gene trap approach in Xenopus . Curr. Biol. 9 : 1195 -1198. ↵ Brown, P.O. and Botstein, D. 1999 . Exploring the new world...
    OPEN ACCESS ARTICLE
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