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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. May 24, 2022 ; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
    .....org candidates, whichwere predicted to encode a total of 404 peptides. Among these lncRNA-encoded peptides, 80.44% (325 out of 404) were sORF-encodedpolypeptides (SEPs, fewer than100aminoacids [aa]) (Fig. 2D; Supplemental Table S5). Therewere up to 79peptides and 24 peptides longer than or equal to 100 aa...
  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. Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...:10.1186/1471-2105-14-128 ↵Chen S, Lake BB, Zhang K. 2019. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat Biotechnol 37: 1452–1457. doi:10.1038/s41587-019-0290-0 ↵Cooper S. 2003. Rethinking synchronization of mammalian cells for cell cycle analysis...
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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. 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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  9. 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...
  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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