Searching journal content for articles similar to Collins 11 (5): 641.

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  1. 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
    ...immunoprecipitation (ChIP) in 1984 followed by ChIP-qPCR and ChIP-seq, which allowed scientists to probe the full palette of DNA molecules bound by proteins of interest. A ChIP experiment begins by using formaldehyde to chemically cross-link DNA and protein molecules (Das et al. 2004). Nuclei are isolated...
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  2. Research: Ultra-long-range interactions between active regulatory elements
    • Elias T. Friman,
    • Ilya M. Flyamer,
    • Davide Marenduzzo,
    • Shelagh Boyle,
    • and Wendy A. Bickmore
    Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
    ...with lipopolysaccharide (LPS) and interferon (IFNG) (Fig. 4B; Reed et al. 2022). Regions that gained H3K27ac upon stimulation also gained ULIs, and regions losing H3K27ac, although relatively lowly enriched to begin with, lost ULIs over the time course. Although the small number of regions affected and the time...
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  3. Commentary: One hundred fifty years without Darwin are enough!
    • Francisco J. Ayala
    Genome Res. May 2009 19: 693-699; doi:10.1101/gr.084285.108
    ...‘‘is not even master in his own house.’’ What the standard version of the Copernican and Darwinian version of the two revolutions says is correct but inadequate, because it misses what is most important about these two intellectual revolutions, namely that they ushered in the beginning of science...
  4. RESOURCE: MEGAN analysis of metagenomic data
    • Daniel H. Huson,
    • Alexander F. Auch,
    • Ji Qi,
    • and Stephan C. Schuster
    Genome Res. March 2007 17: 377-386; Published in Advance January 25, 2007, doi:10.1101/gr.5969107
    ...with regard to the computational cost of an analysis. As sequence databases continue to grow and metagenomic projects increase in size, the computational cost will also increase. However, as databases begin to provide a better coverage of the diversity of life, the computational cost of performing...
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  5. Next-Generation DNA Sequencing/Review: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
    • Micah Hamady and
    • Rob Knight
    Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108
    ...beginning to be applied to human-associated microbial communities (Verberkmoes et al. 2008). Through the use of metagenomic and rRNA-based techniques, much progress has been made in characterizing the human microbiome and its role in health and disease in the past few years, especially with the advent...
  6. COMMENTARY: The Human Genome Sequence Expedition: Views from the “Base Camp”
    • Eric D. Green and
    • Aravinda Chakravarti
    Genome Res. May 1, 2001 11: 645-651; doi:10.1101/gr.188701
    ...—yet exciting—genomic terrain ahead. Indeed, the Human Genome Project is now firmly at the “base camp” of the expedition to elucidate the human genetic blueprint and to begin to understand its content. Nevertheless, this is a milestone of tremendous significance and excitement. Here we outline some of the key...
  7. PERSPECTIVE: Human Whole-Genome Shotgun Sequencing
    • James L. Weber and
    • Eugene W. Myers
    Genome Res. May 1, 1997 7: 401-409; doi:10.1101/gr.7.5.401
    ...54449; 2Department of Computer Science, University of Arizona, Tucson, Arizona 85721 Large-scale sequencing of the human is now under way ( Boguski et al. 1996 ; Marshall and Pennisi 1996 ). Although at the beginning of the Genome Project, many doubted the scientific value of sequencing the entire human...
  8. Insight/Outlook: Academia-Industry Collaboration: An Integral Element for Building “Omic” Resources
    • David E. Hill,
    • Michael A. Brasch,
    • Anthony A. del Campo,
    • Lynn Doucette-Stamm,
    • James I. Garrels,
    • Judith Glaven,
    • James L. Hartley,
    • James R. Hudson, Jr.,
    • Troy Moore,
    • and Marc Vidal
    Genome Res. October 15, 2004 14: 2010-2014; doi:10.1101/gr.2771404
    ...of being ORF-specific and containing the necessary elements for recombinational cloning ( Hartley et al. 2000 ; Walhout et al. 2000b ; Marsischky and LaBaer 2004 ), synthesized and delivered in 96-well format at a time when few groups were even contemplating high-throughput synthesis of thousands...
  9. LETTER: Characterizing Embryonic Gene Expression Patterns in the Mouse Using Nonredundant Sequence-Based Selection
    • Rita Sousa-Nunes,
    • Amer Ahmed Rana,
    • Ross Kettleborough,
    • Joshua M. Brickman,
    • Melanie Clements,
    • Alistair Forrest,
    • Sean Grimmond,
    • Philip Avner,
    • James C. Smith,
    • Sally L. Dunwoodie,
    • and Rosa S.P. Beddington
    Genome Res. December 2003 13: 2609-2620; Published in Advance January 1, 2003, doi:10.1101/gr.1362303
    ...feasible, however, to contemplate targeting the entire proteome in this way, so it is necessary to decide which genes to target first. Work from several species indicates that one criterion might be based on gene expression patterns. In situ hybridization analyses of random clones from unmodified...
  10. LETTER: An intermediate grade of finished genomic sequence suitable for comparative analyses
    • Robert W. Blakesley,
    • Nancy F. Hansen,
    • James C. Mullikin,
    • Pamela J. Thomas,
    • Jennifer C. McDowell,
    • Baishali Maskeri,
    • Alice C. Young,
    • Beatrice Benjamin,
    • Shelise Y. Brooks,
    • Bradley I. Coleman,
    • Jyoti Gupta,
    • Shi-Ling Ho,
    • Eric M. Karlins,
    • Quino L. Maduro,
    • Sirintorn Stantripop,
    • Cyrus Tsurgeon,
    • Jennifer L. Vogt,
    • Michelle A. Walker,
    • Catherine A. Masiello,
    • Xiaobin Guan,
    • NISC Comparative Sequencing Program,
    • Gerard G. Bouffard,
    • and Eric D. Green
    Genome Res. November 2004 14: 2235-2244; Published in Advance October 12, 2004, doi:10.1101/gr.2648404
    ..., significant gains in quality can be achieved with even small amounts of additional effort ( Wilson and Mardis 1997b ; Gordon et al. 2001 ), whereas in later stages, large amounts of effort are often required to accomplish even small quality improvements. In contemplating the sequencing of additional...
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