Searching journal content for articles similar to Elkon et al. 13 (5): 773.

Displaying results 1-10 of 290
For checked items
  1. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...for five repeat motifs (Q-value < 0.1). Then, using SpliceAid and ATtRACT, we predicted which RBPs bind to the motifs (Fig. 3B; Supplemental Table S5; Piva et al. 2009; Giudice et al. 2016). These experimental and in silico analyses pointed out the several common RBPs. Next, we sought to identify examples...
  2. Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
    • Chenxin Li,
    • Hengping Xu,
    • Fang-Fang Fu,
    • Scott D. Russell,
    • Venkatesan Sundaresan,
    • and Jonathan I. Gent
    Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
    ...cell could be explained by simple loss of 24-nt siRNAs from canonical RdDM loci because 24-nt siRNAs remained abundant relative to other siRNA lengths and even increased in abundance relative to miRNAs. In addition, removal of 24-nt siRNAs from canonical RdDM loci in silico and analysis of the residual...
  3. 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
    ...be in silico separated from pre-existing RNA (Herzog et al. 2017; Baptista and Dölken 2018; Jürges et al. 2018; Schofield et al. 2018). A number of methods were developed for the quantification of RNA dynamics via metabolic labeling, including INSPEcT (de Pretis et al. 2015), DRUID (Lugowski et al. 2018), c...
    OPEN ACCESS ARTICLE
  4. Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
    • Charles E. Vejnar,
    • Mario Abdel Messih,
    • Carter M. Takacs,
    • Valeria Yartseva,
    • Panos Oikonomou,
    • Romain Christiano,
    • Marlon Stoeckius,
    • Stephanie Lau,
    • Miler T. Lee,
    • Jean-Denis Beaudoin,
    • Damir Musaev,
    • Hiba Darwich-Codore,
    • Tobias C. Walther,
    • Saeed Tavazoie,
    • Daniel Cifuentes,
    • and Antonio J. Giraldez
    Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
    ...-coding transcripts. The UTRs and CDS of each transcript were split into 50 bins to normalize their length. Metaplots averaged over each RBP were clustered to group similar binding profiles. (G) Heatmap representing in silico binding profiles obtained by scanning for RBP binding motifs within protein...
  5. Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
    • Ruben Boers,
    • Joachim Boers,
    • Bas de Hoon,
    • Christel Kockx,
    • Zeliha Ozgur,
    • Anco Molijn,
    • Wilfred van IJcken,
    • Joop Laven,
    • and Joost Gribnau
    Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
    ...encompasses restriction enzyme digestion and adaptor ligation, size selection, PCR amplification, and sequencing (Fig. 1A), followed by in silico analysis involving a CG filter, to retrieve the correct fragments and reduce noise, subsequent alignment, and DMR calling (Fig. 1B).View larger version...
  6. Resource: Genome-wide discovery of human splicing branchpoints
    • Tim R. Mercer,
    • Michael B. Clark,
    • Stacey B. Andersen,
    • Marion E. Brunck,
    • Wilfried Haerty,
    • Joanna Crawford,
    • Ryan J. Taft,
    • Lars K. Nielsen,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
    ...Genome-wide discovery of human splicing branchpoints Tim R. Mercer 1 , 2 , 8 , Michael B. Clark 1 , 3 , 8 , Stacey B. Andersen 4 , Marion E. Brunck 4 , Wilfried Haerty 3 , Joanna Crawford 5 , Ryan J...
  7. Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
    • Arkarachai Fungtammasan,
    • Guruprasad Ananda,
    • Suzanne E. Hile,
    • Marcia Shu-Wei Su,
    • Chen Sun,
    • Robert Harris,
    • Paul Medvedev,
    • Kristin Eckert,
    • and Kateryna D. Makova
    Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
    ...Accurate typing of short tandem repeats from genome-wide sequencing data and its applications Arkarachai Fungtammasan 1 , 2 , 3 , 4 , 8 , Guruprasad Ananda 1 , 3 , 4 , 5 , 8 , 9 , Suzanne E. Hile 3 , 6 , Marcia Shu-Wei Su 2 , 3...
  8. Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
    • Huan Wang,
    • Pil Joong Chung,
    • Jun Liu,
    • In-Cheol Jang,
    • Michelle J. Kean,
    • Jun Xu,
    • and Nam-Hai Chua
    Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
    ...Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Huan Wang 1 , 4 , Pil Joong Chung 1 , 2 , 4 , Jun Liu 1 , In-Cheol Jang 1 , 3 , Michelle J. Kean 1 , Jun Xu...
  9. Resource: Modeling transcriptional regulation of model species with deep learning
    • Evan M. Cofer,
    • João Raimundo,
    • Alicja Tadych,
    • Yuji Yamazaki,
    • Aaron K. Wong,
    • Chandra L. Theesfeld,
    • Michael S. Levine,
    • and Olga G. Troyanskaya
    Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
    ...Ark,” modeling the cis-regulatory activities of four of the most widely studied model organisms: C. elegans, D. rerio, D. melanogaster, and M. musculus (Fig. 1A). To the best of our knowledge, DeepArk is the first such resource for these model organisms. DeepArk provides an in silico ChIP-seq capability: Given...
    OPEN ACCESS ARTICLE
  10. Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
    • Alexandra Dallaire,
    • Bethan F. Manley,
    • Maya Wilkens,
    • Iliana Bista,
    • Clement Quan,
    • Edouard Evangelisti,
    • Charles R. Bradshaw,
    • Navin B. Ramakrishna,
    • Sebastian Schornack,
    • Falk Butter,
    • Uta Paszkowski,
    • and Eric A. Miska
    Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
    ...that a well-controlled TE activity directly contributes to evolution in AM fungi.The arbuscular mycorrhizal (AM) symbiosis is hundreds of millions of years old and a majority of the world's plant species are hosts to AM fungi (AMF) (Lutzoni et al. 2018). As such, these fungi exist in a wide range...
    OPEN ACCESS ARTICLE
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research