Searching journal content for articles similar to Maier and Sahlin 33 (7): 1162.

Displaying results 1-10 of 5528
For checked items
  1. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...species-specific modeling with ensemble deep learning architectures to systematically optimize feature encoding schemes. Evaluated across six species, EnDeep4mC demonstrates commendable prediction performance and significantly outperforms current state-of-the-art predictors. Cross-species validation...
    OPEN ACCESS ARTICLE
  2. Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
    • Irene Mei,
    • Susanne Nichterwitz,
    • Melanie Leboeuf,
    • Jik Nijssen,
    • Isadora Lenoel,
    • Dirk Repsilber,
    • Christian S. Lobsiger,
    • and Eva Hedlund
    Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
    ...vulnerability code of 39 genes, including Atf4, Nupr1, Ddit3, and Penk, involved in apoptosis, as well as a proregenerative and antiapoptotic signature consisting of Atf3, Vgf, Ina, Sprr1a, Fgf21, Gap43, Adcyap1, and Mt1. Machine learning using genes upregulated in SOD1G93A spinal MN predicts disease in human...
    OPEN ACCESS ARTICLE
  3. Research: Genomic context sensitivity of insulator function
    • André M. Ribeiro-dos-Santos,
    • Megan S. Hogan,
    • Raven D. Luther,
    • Ran Brosh,
    • and Matthew T. Maurano
    Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
    ...distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition...
  4. Research: Enhancer RNA profiling predicts transcription factor activity
    • Joseph G. Azofeifa,
    • Mary A. Allen,
    • Josephina R. Hendrix,
    • Timothy Read,
    • Jonathan D. Rubin,
    • and Robin D. Dowell
    Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
    .... 2014; Danko et al. 2015).eRNA detection requires extremely sensitive methods, both in the laboratory as well as computationally. Because they are unstable, eRNAs are rarely observed via steady-state RNA assays such as RNA-seq. Nascent transcription assays capture transcription throughout...
    OPEN ACCESS ARTICLE
  5. Method: Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
    • Hyun-Hwan Jeong,
    • Seon Young Kim,
    • Maxime W.C. Rousseaux,
    • Huda Y. Zoghbi,
    • and Zhandong Liu
    Genome Res. June 2019 29: 999-1008; Published in Advance April 23, 2019, doi:10.1101/gr.245571.118
    ..., with greater sensitivity and a much lower false discovery rate. It also accommodates staggered sgRNA sequences. In conjunction with CRISPRcloud, CB2 brings CRISPR screen analysis within reach for a wider community of researchers.Genetic screens have become a favored tool for gathering information about disease...
    OPEN ACCESS ARTICLE
  6. Resource: Adaptive seeds tame genomic sequence comparison
    • Szymon M. Kiełbasa,
    • Raymond Wan,
    • Kengo Sato,
    • Paul Horton,
    • and Martin C. Frith
    Genome Res. March 2011 21: 487-493; Published in Advance January 5, 2011, doi:10.1101/gr.113985.110
    ...implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. Footnotes ↵ 4 Corresponding author. E-mail martin@cbrc.jp ; fax 81-3-3599-8081. [Supplemental material is available for this article. LAST software...
    OPEN ACCESS ARTICLE
  7. Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
    • Tatsunori Hashimoto,
    • Richard I. Sherwood,
    • Daniel D. Kang,
    • Nisha Rajagopal,
    • Amira A. Barkal,
    • Haoyang Zeng,
    • Bart J.M. Emons,
    • Sharanya Srinivasan,
    • Tommi Jaakkola,
    • and David K. Gifford
    Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
    ...A synergistic DNA logic predicts genome-wide chromatin accessibility Tatsunori Hashimoto 1 , 3 , Richard I. Sherwood 2 , 3 , Daniel D. Kang 1 , 3 , Nisha Rajagopal 1 , Amira A. Barkal 1 , 2 , Haoyang Zeng 1 , Bart J...
  8. Research: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
    • Lei Zhang,
    • Anshun He,
    • Bohan Chen,
    • Jinfang Bi,
    • Jun Chen,
    • Dianhao Guo,
    • Yuyang Qian,
    • Wenbin Wang,
    • Tengfei Shi,
    • Zhongfang Zhao,
    • Jiandang Shi,
    • Woojin An,
    • Frank Attenello,
    • and Wange Lu
    Genome Res. February 2020 30: 155-163; Published in Advance January 17, 2020, doi:10.1101/gr.251058.119
    ...limiting its effectiveness. Thus, knowledge of mechanisms underlying this outcome could improve patient prognosis. Here, we report that deletion of a regulatory element in the HOTAIR locus increases glioma cell sensitivity to TMZ and alters transcription of multiple genes. Analysis of a combination of RNA...
  9. Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
    • Antonio L.C. Gomes,
    • Thomas Abeel,
    • Matthew Peterson,
    • Elham Azizi,
    • Anna Lyubetskaya,
    • Luís Carvalho,
    • and James Galagan
    Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
    ...the best performance by predicting 21 binding sites. We thus further checked GEM’s performance by running analyses with a range of parameters (e.g., –k_min 8 –k_max 14,–k 14,–seed GGG-C-TT-G-CCC, k_win 40, k_win 50, k_win 60, and combinations) and by following the authors’ recommendations to improve motif...
  10. Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
    • Deborah R. Winter,
    • Lingyun Song,
    • Sayan Mukherjee,
    • Terrence S. Furey,
    • and Gregory E. Crawford
    Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
    ...DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types Deborah R. Winter 1 , 2 , Lingyun Song 1 , Sayan Mukherjee 1 , 3 , Terrence S. Furey 4 , 6 and Gregory E. Crawford 1 , 5 , 6...
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