Searching journal content for articles similar to Moqtaderi et al. 31 (11): 2050.

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  1. Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
    • Etienne Routhier,
    • Edgard Pierre,
    • Ghazaleh Khodabandelou,
    • and Julien Mozziconacci
    Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
    ...method to predict the nucleosome density from the DNA sequence, emphasizing the preferential positioning of nucleosomes on specific DNA statistical motifs. Numerous computational methods (for review, see Teif 2016) were developed afterward to predict the positions of nucleosomes from the DNA sequence...
  2. Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
    • Mattia Furlan,
    • Eugenia Galeota,
    • Nunzio Del Gaudio,
    • Erik Dassi,
    • Michele Caselle,
    • Stefano de Pretis,
    • and Mattia Pelizzola
    Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
    ...modulated by a circadian oscillation of synthesis rates or by a circadian oscillation of both synthesis and degradation rates opportunely out of phase (Fig. 6A). Models returned by both INSPEcT+ and INSPEcT− and obtained by fitting sigmoid or impulse functions had a poor goodness of fit for the oscillating...
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  3. Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • Jakob Skou Pedersen,
    • Eivind Valen,
    • Amhed M. Vargas Velazquez,
    • Brian J. Parker,
    • Morten Rasmussen,
    • Stinus Lindgreen,
    • Berit Lilje,
    • Desmond J. Tobin,
    • Theresa K. Kelly,
    • Søren Vang,
    • Robin Andersson,
    • Peter A. Jones,
    • Cindi A. Hoover,
    • Alexei Tikhonov,
    • Egor Prokhortchouk,
    • Edward M. Rubin,
    • Albin Sandelin,
    • M. Thomas P. Gilbert,
    • Anders Krogh,
    • Eske Willerslev,
    • and Ludovic Orlando
    Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
    ...Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome Jakob Skou Pedersen 1 , 14 , 15 , Eivind Valen 2 , 3 , 14 , Amhed M. Vargas Velazquez 4 , Brian J. Parker 3 , Morten Rasmussen 4 , 5 , Stinus...
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  4. Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Sergei A. Filichkin,
    • Henry D. Priest,
    • Scott A. Givan,
    • Rongkun Shen,
    • Douglas W. Bryant,
    • Samuel E. Fox,
    • Weng-Keen Wong,
    • and Todd C. Mockler
    Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
    ...(RUST) (Lewis et al. 2003; Lareau et al. 2007). Genome-wide studies of alternative pre-mRNA splicing in a variety of organisms have relied on Sanger sequencing of expressed sequence tags (ESTs) and cDNAs, high-density DNA microarrays (for review, see Mockler et al. 2005) and most recently ultrahigh...
  5. ARTICLE: Genome-Wide Epistatic Interaction Analysis Reveals Complex Genetic Determinants of Circadian Behavior in Mice
    • Kazuhiro Shimomura,
    • Sharon S. Low-Zeddies,
    • David P. King,
    • Thomas D.L. Steeves,
    • Andrew Whiteley,
    • Jani Kushla,
    • Peter D. Zemenides,
    • Andrew Lin,
    • Martha Hotz Vitaterna,
    • Gary A. Churchill,
    • and Joseph S. Takahashi
    Genome Res. June 1, 2001 11: 959-980; doi:10.1101/gr.171601
    ...scans using our own analysis tools (based on permutation testing; see Methods) ( Churchill and Doerge 1994 ). View this table: In this window In a new window Table 2. List of Markers Initially Used for Genome-Wide Scan Free-Running Period The period of oscillation is a key factor in describing...
  6. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ....70%). Therefore, the number of chimeric reads at integration loci is not positively associated with host CNV alterations.HBV enhancer I (HBV-Enh I), a highly conserved element, was previously shown to be active in Hep3B and PLC/PRF/5 cell lines, suggesting its potential role in hepatocellular carcinogenesis...
  7. Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
    • Akanksha Bafna,
    • Gareth Banks,
    • Michael H. Hastings,
    • and Patrick M. Nolan
    Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
    ...in the SCN central clock that potentially contributes to maintaining its uniquely stable circadian timekeeping.ResultsGenome-wide promoter and enhancer site mapping in the SCN using histone ChIP-seqTo identify DNA regulatory elements influencing gene transcription in the SCN, we focused on SCN...
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  8. Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
    • Aleix Palahí i Torres,
    • Lars Höök,
    • Karin Näsvall,
    • Daria Shipilina,
    • Christer Wiklund,
    • Roger Vila,
    • Peter Pruisscher,
    • and Niclas Backström
    Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
    ...it is most likely a consequence of founder effects during the recolonization of Scandinavia from glacial refugia.Genome-wide distribution of the recombination rate in wood whitesThe -wide recombination rate varies considerably between different insects, from comparatively low in Diptera (<1 cM/Mb) (Beye et...
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  9. Research: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
    • Laura Wiehle,
    • Graeme J. Thorn,
    • Günter Raddatz,
    • Christopher T. Clarkson,
    • Karsten Rippe,
    • Frank Lyko,
    • Achim Breiling,
    • and Vladimir B. Teif
    Genome Res. May 2019 29: 750-761; Published in Advance April 4, 2019, doi:10.1101/gr.239707.118
    ...of CTCF binding.View larger version: In this window In a new window Figure 3. Genome-wide CTCF rearrangement happens preferentially at CpGs that gain methylation in DKO ESCs. (A) The average CTCF occupancy profiles around commonly methylated CpGs (methylation >0.8 both in WT and DKO cells; N = 10...
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  10. Research: Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
    • Alaaddin Bulak Arpat,
    • Angélica Liechti,
    • Mara De Matos,
    • René Dreos,
    • Peggy Janich,
    • and David Gatfield
    Genome Res. July 2020 30: 985-999; Published in Advance July 23, 2020, doi:10.1101/gr.257741.119
    ...signals. Pause site association with specific amino acids, peptide motifs, and nascent polypeptide structure is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing...
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