Searching journal content for articles similar to Stewart 10 (1): 1.

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  1. Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
    • Yi Qiao,
    • Xiaomeng Huang,
    • Philip J. Moos,
    • Jonathan M. Ahmann,
    • Anthony D. Pomicter,
    • Michael W. Deininger,
    • John C. Byrd,
    • Jennifer A. Woyach,
    • Deborah M. Stephens,
    • and Gabor T. Marth
    Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
    ...A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data Yi Qiao1,6, Xiaomeng Huang1,6, Philip J. Moos2, Jonathan M. Ahmann3, Anthony D. Pomicter3, Michael W. Deininger3,4, John C. Byrd5, Jennifer A. Woyach5, Deborah M. Stephens3...
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  2. Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
    • Andrew Ying-Fei Chang and
    • Ben-Yang Liao
    Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
    ...methyltransferase, and its function is Corresponding author: liaoby@nhri.org.tw Article published online before print. Article, supplemental material, and publication date are at http://www..org/cgi/doi/10.1101/gr.221739.117. © 2017 Chang and Liao This article is distributed exclusively by Cold Spring Harbor...
  3. METHODS: High-Throughput Variation Detection and Genotyping Using Microarrays
    • David J. Cutler,
    • Michael E. Zwick,
    • Minerva M. Carrasquillo,
    • Christopher T. Yohn,
    • Katherine P. Tobin,
    • Carl Kashuk,
    • Debra J. Mathews,
    • Nila A. Shah,
    • Evan E. Eichler,
    • Janet A. Warrington,
    • and Aravinda Chakravarti
    Genome Res. November 1, 2001 11: 1913-1925; Published in Advance October 15, 2001, doi:10.1101/gr.197201
    ...-7544. Article published on-line before print: Genome Res., 10.1101/gr.197201. Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.197201. Received May 17, 2001. Accepted August 23, 2001. Cold Spring Harbor Laboratory Press David J, Cutler M Zwick...
  4. METHODS: Phenotype MicroArrays for High-Throughput Phenotypic Testing and Assay of Gene Function
    • Barry R. Bochner,
    • Peter Gadzinski,
    • and Eugenia Panomitros
    Genome Res. July 1, 2001 11: 1246-1255; doi:10.1101/gr.186501
    ...@biolog.com ; FAX (510) 782-4639. Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.186501. Received February 23, 2001. Accepted May 1, 2001. Cold Spring Harbor Laboratory Press B Bochner Bochner, B.R Peter Gadzinski, P Gadzinski, Peter Barry R Bochner...
  5. Method: Discriminative prediction of mammalian enhancers from DNA sequence
    • Dongwon Lee,
    • Rachel Karchin,
    • and Michael A. Beer
    Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
    ..., 2011. Accepted August 23, 2011. Copyright © 2011 by Cold Spring Harbor Laboratory Press Michael A Karchin Rachel, Karchin Rachel Karchin M.A. Beer Dongwon, Lee M Beer Lee, D MA Beer MichaelA Beer Dongwon R Karchin Beer Michael A. Beer, M.A Beer, M Beer Beer, MA Lee, Dongwon...
  6. Method: True single-molecule DNA sequencing of a pleistocene horse bone
    • Ludovic Orlando,
    • Aurelien Ginolhac,
    • Maanasa Raghavan,
    • Julia Vilstrup,
    • Morten Rasmussen,
    • Kim Magnussen,
    • Kathleen E. Steinmann,
    • Philipp Kapranov,
    • John F. Thompson,
    • Grant Zazula,
    • Duane Froese,
    • Ida Moltke,
    • Beth Shapiro,
    • Michael Hofreiter,
    • Khaled A.S. Al-Rasheid,
    • M. Thomas P. Gilbert,
    • and Eske Willerslev
    Genome Res. October 2011 21: 1705-1719; Published in Advance July 29, 2011, doi:10.1101/gr.122747.111
    ...7, 2011. Copyright © 2011 by Cold Spring Harbor Laboratory Press Eske Beth Shapiro Grant, Zazula Froese, Duane Duane, Froese Hofreiter Hofreiter Michael Moltke Ida JF Thompson Khaled Julia, Vilstrup Khaled AS M Thomas P, Gilbert Beth, Shapiro Moltke, Ida Shapiro, Beth Kim Magnussen...
  7. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...of functional binding. Binding affinity is usually degenerate, with multiple sequence variations binding equally well (Stormo and Zhao 2010). Many TFs, especially in eukaryotes with larger s, have low specificity, leading to high false positives in binding site predictions. Short, degenerate DNA sequences...
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  8. Method: Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Roger Pique-Regi,
    • Jacob F. Degner,
    • Athma A. Pai,
    • Daniel J. Gaffney,
    • Yoav Gilad,
    • and Jonathan K. Pritchard
    Genome Res. March 2011 21: 447-455; Published in Advance November 24, 2010, doi:10.1101/gr.112623.110
    ...material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.112623.110 . Received July 7, 2010. Accepted November 1, 2010. Copyright © 2011 by Cold Spring Harbor Laboratory Press Freely available online through the Genome Research Open Access option...
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  9. Dog Special/Letters: Short interspersed elements (SINEs) are a major source of canine genomic diversity
    • Wei Wang and
    • Ewen F. Kirkness
    Genome Res. December 2005 15: 1798-1808; doi:10.1101/gr.3765505
    ...author. E-mail ekirknes@tigr.org ; fax (301) 294-3142. Accepted August 3, 2005. Received January 31, 2005. Cold Spring Harbor Laboratory Press E Kirkness Kirkness EF Kirkness Kirkness, E Kirkness Ewen F. EwenF Kirkness Wang Wei Ewen Kirkness Kirkness, Ewen F Wang...
  10. Research: MRC1-dependent scaling of the budding yeast DNA replication timing program
    • Amnon Koren,
    • Ilya Soifer,
    • and Naama Barkai
    Genome Res. June 2010 20: 781-790; Published in Advance March 10, 2010, doi:10.1101/gr.102764.109
    ...://www.ncbi.nlm.nih.gov/geo ) under accession no. GSE17120.] Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.102764.109 . Received November 2, 2009. Accepted March 3, 2010. Copyright © 2010 by Cold Spring Harbor...
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