Zhou, Dan Udpa, Nitin Gersten, Merril Visk, DeeAnn W Bashir, Ali Xue, Jin Frazer, Kelly A Posakony, James W Subramaniam, Shankar Bafna, Vineet
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Published in
Proceedings of the National Academy of Sciences of the United States of America
Through long-term laboratory selection (over 200 generations), we have generated Drosophila melanogaster populations that tolerate severe, normally lethal, levels of hypoxia. Because of initial experiments suspecting genetic mechanisms underlying this adaptation, we compared the genomes of the hypoxia-selected flies with those of controls using dee...
Holm, F Hellqvist, E Mason, Cn Ali, Sa Delos-Santos, N Christian Barrett Chun, Hj Minden, Md Moore, Ra Marra, Ma
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Published in
Proceedings of the National Academy of Sciences
Formative research suggests that a human embryonic stem cell-specific alternative splicing gene regulatory network, which is repressed by Muscleblind-like (MBNL) RNA binding proteins, is involved in cell reprogramming. In this study, RNA sequencing, splice isoform-specific quantitative RT-PCR, lentiviral transduction, and in vivo humanized mouse mo...
Kl, Mcnally Kl, Childs R, Bohnert Rm, Davidson K, Zhao Vj, Ulat G, Zeller Rm, Clark Dr, Hoen Te, Bureau
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Published in
Proceedings of the National Academy of Sciences
Rice, the primary source of dietary calories for half of humanity, is the first crop plant for which a high-quality reference genome sequence from a single variety was produced. We used resequencing microarrays to interrogate 100 Mb of the unique fraction of the reference genome for 20 diverse varieties and landraces that capture the impressive gen...
Christian Barrett Deboever, C Jepsen, K Saenz, Cc Carson, Da Kelly A. Frazer
Published in
Proceedings of the National Academy of Sciences
Tumor-specific molecules are needed across diverse areas of oncology for use in early detection, diagnosis, prognosis and therapy. Large and growing public databases of transcriptome sequencing data (RNA-seq) derived from tumors and normal tissues hold the potential of yielding tumor-specific molecules, but because the data are new they have not be...
Zhu, Y Jong, Mc Kelly A. Frazer Gong, E Krauss, Rm Cheng, Jf Boffelli, D Rubin, Em
Published in
Proceedings of the National Academy of Sciences
To accelerate the biological annotation of novel genes discovered in sequenced regions of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such genes. Here we describe the targeted deletion of a 450-kb region on mouse chromosome 11, which, based on computational analysis of the deleted murine se...
Jiang, Qingfei Crews, Leslie A Barrett, Christian L Chun, Hye-Jung Court, Angela C Isquith, Jane M Zipeto, Maria A Goff, Daniel J Minden, Mark Sadarangani, Anil
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Published in
Proceedings of the National Academy of Sciences of the United States of America
The molecular etiology of human progenitor reprogramming into self-renewing leukemia stem cells (LSC) has remained elusive. Although DNA sequencing has uncovered spliceosome gene mutations that promote alternative splicing and portend leukemic transformation, isoform diversity also may be generated by RNA editing mediated by adenosine deaminase act...
