Searching journal content for articles similar to Petrany et al. 34 (10): 1636.

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  1. Method: Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    • Wei-Hao Lee,
    • Lechuan Li,
    • Ruth Dannenfelser,
    • and Vicky Yao
    Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
    ...indicating various categories. Post-ALPINE application, batch effects from sequencing technologies are removed, resulting in aligned clusters of similar cell types across species, although adipocytes remain distinct due to biological differences. (B) Condition embeddings reveal associations between cell...
  2. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...counts, diverging from the uniform distributions typically expected in theoretical modeling count, highlighting inherent biases in RNA-seq. In the experimental setup, the pool of spike-in RNAs used as a sequencing substrate ensures that each spike-in type is present at equimolar concentrations...
  3. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...with MeRIP-seq. (A) SNP distribution in Group 1 ASM. (B) Motif frequencies and modification ratios of motif sequences. The top bar plot illustrates motif sequence frequencies in all m6A instances, while the bottom heatmap indicates modification ratios. The first row presents the modification ratio of all...
  4. 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
    ...of differences in effect size, sequence determinants, and on- versus off-target effects (Li et al. 2014). MAGeCK was the first tool specifically developed to analyze CRISPR/Cas9 pooled screening data, and it combines a negative-binomial distribution model with a modified robust ranking aggregation (α...
    OPEN ACCESS ARTICLE
  5. Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
    • Yehuda Brody,
    • Robert J. Kimmerling,
    • Yosef E. Maruvka,
    • David Benjamin,
    • Juniper J. Elacqua,
    • Nicholas J. Haradhvala,
    • Jaegil Kim,
    • Kent W. Mouw,
    • Kristjana Frangaj,
    • Amnon Koren,
    • Gad Getz,
    • Scott R. Manalis,
    • and Paul C. Blainey
    Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
    ...accuracy and sensitivity for -wide somatic SNV detection, and (3) minimal positive and negative mutation selection biases.Here, we introduce lineage sequencing (Fig. 1) and its application to clonal cell populations cultured in vitro. In lineage sequencing, one collects specific cells representing...
    OPEN ACCESS ARTICLE
  6. Research: Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data
    • Aaron T.L. Lun,
    • Fernando J. Calero-Nieto,
    • Liora Haim-Vilmovsky,
    • Berthold Göttgens,
    • and John C. Marioni
    Genome Res. November 2017 27: 1795-1806; Published in Advance October 13, 2017, doi:10.1101/gr.222877.117
    ...proportional to its theoretical concentration in the spike-in mixture (Supplemental Fig. 11), and the distribution of average read counts across spike-in transcripts or endogenous genes was consistent across plates (Supplemental Fig. 12). These diagnostics indicate that the spike-in transcripts were...
    OPEN ACCESS ARTICLE
  7. Research: Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer
    • Marco L. Leung,
    • Alexander Davis,
    • Ruli Gao,
    • Anna Casasent,
    • Yong Wang,
    • Emi Sei,
    • Eduardo Vilar,
    • Dipen Maru,
    • Scott Kopetz,
    • and Nicholas E. Navin
    Genome Res. August 2017 27: 1287-1299; Published in Advance May 25, 2017, doi:10.1101/gr.209973.116
    ...variantsThe significance of differences in amplicon deep-sequencing of the normal and primary was determined using Bayesian hypothesis testing. Variant read counts were modeled using the beta-binomial distribution: where i is the index of a mutation, VN,i and VP,i are the number of variant reads observed...
  8. Method: metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
    • Frank Jühling,
    • Helene Kretzmer,
    • Stephan H. Bernhart,
    • Christian Otto,
    • Peter F. Stadler,
    • and Steve Hoffmann
    Genome Res. February 2016 26: 256-262; Published in Advance December 2, 2015, doi:10.1101/gr.196394.115
    ...distributions of DMR classes 1–4 are visualized in Supplemental Figure S1B. Again, the number of reads without conversion was drawn from a binomial distribution. Reduced representation bisulfite sequencing data were simulated in a similar fashion as the WGBS data. To make our simulation more realistic, we used...
  9. Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
    • Cheng-Lin Frank Li,
    • Balaji Santhanam,
    • Amanda Nicole Webb,
    • Blaž Zupan,
    • and Gad Shaulsky
    Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
    ...Ljubljana, Slovenia Corresponding author: gadi@bcm.edu Abstract Whole-genome sequencing is a useful approach for identification of chemical-induced lesions, but previous applications involved tedious genetic mapping to pinpoint the causative mutations. We propose that saturation...
  10. Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
    • Daniela Nachmanson,
    • Shenyi Lian,
    • Elizabeth K. Schmidt,
    • Michael J. Hipp,
    • Kathryn T. Baker,
    • Yuezheng Zhang,
    • Maria Tretiakova,
    • Kaitlyn Loubet-Senear,
    • Brendan F. Kohrn,
    • Jesse J. Salk,
    • Scott R. Kennedy,
    • and Rosa Ana Risques
    Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
    ...offers a simple solution for fast and efficient small target enrichment.In the last decade, next-generation sequencing (NGS) has revolutionized the fields of biology and medicine. However, standard NGS suffers from two major problems that negatively impact multiple applications: the limited efficiency...
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