Searching journal content for articles similar to Kwasnieski et al. 24 (10): 1595.

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  1. Method: High-throughput characterization of genetic effects on DNA–protein binding and gene transcription
    • Cynthia A. Kalita,
    • Christopher D. Brown,
    • Andrew Freiman,
    • Jenna Isherwood,
    • Xiaoquan Wen,
    • Roger Pique-Regi,
    • and Francesca Luca
    Genome Res. November 2018 28: 1701-1708; Published in Advance September 25, 2018, doi:10.1101/gr.237354.118
    ...Natl Acad Sci 109: 19498–19503. ↵Kwasnieski J, Fiore C, Chaudhari H, Cohen B. 2014. High-throughput functional testing of ENCODE segmentation predictions. Genome Res 24: 1595–1602. ↵Lee YJ, Kim KM, Jang JY, Song K. 2015. Association of TNFSF15 polymorphisms in Korean children with Crohn's disease...
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  2. Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
    • Wenli Xu,
    • Chang Liu,
    • Bing Deng,
    • Penghui Lin,
    • Zhenghua Sun,
    • Anrui Liu,
    • Jiajia Xuan,
    • Yuying Li,
    • Keren Zhou,
    • Xiaoqin Zhang,
    • Qiaojuan Huang,
    • Hui Zhou,
    • Qingyu He,
    • Bin Li,
    • Lianghu Qu,
    • and Jianhua Yang
    Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
    ...) Distribution of reads for two lncRNA ORFs reported to encode peptides.We next identified the candidate ORFs according to the selected RPF reads using the RiboCode software (Xiao et al. 2018). The types of predicted ORFs (P < 0.05) were composed of seven parts: (1) 37,031 (59.89%) annotated protein-coding ORFs...
  3. Method: SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    • Zhengqing Ouyang,
    • Michael P. Snyder,
    • and Howard Y. Chang
    Genome Res. February 2013 23: 377-387; Published in Advance October 11, 2012, doi:10.1101/gr.138545.112
    ..., SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure...
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  4. Method: nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    • Andrew McPherson,
    • Chunxiao Wu,
    • Alexander W. Wyatt,
    • Sohrab Shah,
    • Colin Collins,
    • and S. Cenk Sahinalp
    Genome Res. November 2012 22: 2250-2261; Published in Advance June 28, 2012, doi:10.1101/gr.136572.111
    ...predicted from matched high-throughput cDNA sequencing (RNA-seq). We have applied our method, nFuse, to the discovery of CGRs in publicly available data from the well-studied breast cancer cell line HCC1954 and primary prostate tumor sample 963. We first establish the sensitivity and specificity of the n...
  5. 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
    ...approaches preceding the availability of structural data. PWM-based predictions depend on databases like TRANSFAC (Matys et al. 2006) and JASPAR (Khan et al. 2018). Modern high-throughput techniques that experimentally identify protein–DNA binding, such as ChIP-seq, SELEX, and protein-binding microarrays...
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  6. Methods: Comprehensive high-throughput arrays for relative methylation (CHARM)
    • Rafael A. Irizarry,
    • Christine Ladd-Acosta,
    • Benilton Carvalho,
    • Hao Wu,
    • Sheri A. Brandenburg,
    • Jeffrey A. Jeddeloh,
    • Bo Wen,
    • and Andrew P. Feinberg
    Genome Res. May 2008 18: 780-790; Published in Advance March 3, 2008, doi:10.1101/gr.7301508
    ...the HELP segments are small for the region shown in Figure 4 , this result was expected, as Figure 3 demonstrates that the HELP method is not sensitive for small fragments. Supplemental Figure 5 shows several other examples. CHARM, comprehensive high-throughput arrays for relative methylation Based...
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  7. Perspective: What does our genome encode?
    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    ...will be required. Presently, few appreciate the depth of this problem, and thus little systematic effort is being devoted to visualization apart from first-generation utilities developed by the leading data producers (Lajoie et al. 2009). Signal and noise Virtually all data resulting from high-throughput assays...
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  8. Research: Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing
    • Florian Caiment,
    • Carole Charlier,
    • Tracy Hadfield,
    • Noelle Cockett,
    • Michel Georges,
    • and Denis Baurain
    Genome Res. December 2010 20: 1651-1662; Published in Advance October 13, 2010, doi:10.1101/gr.108787.110
    ...Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing Florian Caiment 1 , Carole Charlier 1 , Tracy Hadfield 2 , Noelle Cockett 2 , Michel Georges 1 , 3 and Denis...
  9. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    ...corresponding to the input DNA segment. Subsequently, Basenji (Kelley et al. 2018) and Enformer (Avsec et al. 2021a) showed that it was possible to predict the intensity of the chromatin accessibility signal corresponding to the input DNA sequence with a relatively lower resolution (128bp) by binning the signal...
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  10. Method: High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
    • Adam D. Ewing and
    • Haig H. Kazazian, Jr
    Genome Res. September 2010 20: 1262-1270; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
    ...High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes Adam D. Ewing and Haig H. Kazazian Jr 1 University of Pennsylvania Department of Genetics, Philadelphia, Pennsylvania 19104, USA...
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