Searching journal content for articles similar to Rocha et al. 16 (12): 1537.

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  1. 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
    ...analysis, providing comprehensive exploration of gene expression across diverse biological contexts. However, RNA-seq data are susceptible to various biases that can significantly compromise the accuracy and reliability of transcript quantification. This study investigates the influence of high...
  2. Method: A full-proteome, interaction-specific characterization of mutational hotspots across human cancers
    • Siwei Chen,
    • Yuan Liu,
    • Yingying Zhang,
    • Shayne D. Wierbowski,
    • Steven M. Lipkin,
    • Xiaomu Wei,
    • and Haiyuan Yu
    Genome Res. January 2022 32: 135-149; Published in Advance December 28, 2021, doi:10.1101/gr.275437.121
    ...of mutations in human diseases.View larger version: In this window In a new window Figure 1. Proteome-wide structural analysis of mutational hotspots. (A) Data resource of mutational hotspots and workflow of our full-proteome interaction-specific characterization framework. (B) Composition of mutational...
  3. Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
    • Vera B. Kaiser,
    • Lana Talmane,
    • Yatendra Kumar,
    • Fiona Semple,
    • Marie MacLennan,
    • Deciphering Developmental Disorders Study,
    • David R. FitzPatrick,
    • Martin S. Taylor,
    • and Colin A. Semple
    Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
    ...of mutations on the X Chromosome is expected for a male-biased mutational process. We find the X Chromosome to be strongly depleted for short singleton gnomAD insertions (5–20 bp), with a ratio of X to autosome variants per uniquely mappable site of 0.78 (Supplemental Table S12). However, we note that, despite...
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  4. Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
    • Zoe June Assaf,
    • Susanne Tilk,
    • Jane Park,
    • Mark L. Siegal,
    • and Dmitri A. Petrov
    Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
    ...biases.Our ability to study mutation, however, is severely limited. This is because mutation rates are extremely low and because a substantial fraction of new mutations are deleterious and so purged from populations by purifying selection. These two problems can, at first glance, be overcome...
  5. Method: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
    • László Halász,
    • Zsolt Karányi,
    • Beáta Boros-Oláh,
    • Tímea Kuik-Rózsa,
    • Éva Sipos,
    • Éva Nagy,
    • Ágnes Mosolygó-L,
    • Anett Mázló,
    • Éva Rajnavölgyi,
    • Gábor Halmos,
    • and Lóránt Székvölgyi
    Genome Res. June 2017 27: 1063-1073; Published in Advance March 24, 2017, doi:10.1101/gr.219394.116
    ...by a few laboratories, without paying attention to the potential caveats that might affect the outcome of RNA-DNA hybrid mapping. To assess the accuracy and utility of this technology, we pursued an analytical approach to estimate inherent biases and errors in the DRIP protocol. By performing DRIP...
  6. Research: Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
    • Peng Mao,
    • Alexander J. Brown,
    • Ewa P. Malc,
    • Piotr A. Mieczkowski,
    • Michael J. Smerdon,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. October 2017 27: 1674-1684; Published in Advance September 14, 2017, doi:10.1101/gr.225771.117
    ...as 7meG and 3meA lesions, strongly correlated with the trinucleotide composition of the yeast (P≤ 0.002; Pearson coefficient > 0.75 for independent comparisons of G-mutation to G bases in WT yeast and A-mutations to A bases in mag1Δ by Pearson correlation tests; P = 0.042; Pearson coefficient = 0...
  7. Research: High mutational rates of large-scale duplication and deletion in Daphnia pulex
    • Nathan Keith,
    • Abraham E. Tucker,
    • Craig E. Jackson,
    • Way Sung,
    • José Ignacio Lucas Lledó,
    • Daniel R. Schrider,
    • Sarah Schaack,
    • Jeffry L. Dudycha,
    • Matthew Ackerman,
    • Andrew J. Younge,
    • Joseph R. Shaw,
    • and Michael Lynch
    Genome Res. January 2016 26: 60-69; Published in Advance October 30, 2015, doi:10.1101/gr.191338.115
    ...of 72%.With an observed A+T composition of 59%, the composition of D. pulex cannot be explained by base-substitution forces alone, and opposing forces such as GC-biased gene conversion may be countering the observed mutational pressure to A+T. Taking into account the GCbias of conversion we report (54...
  8. Research: Intron evolution in Neurospora: the role of mutational bias and selection
    • Yu Sun,
    • Carrie A. Whittle,
    • Pádraic Corcoran,
    • and Hanna Johannesson
    Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
    ...and losses in Neurospora Our data indicate that, in Neurospora, the 59 positional biased intron distribution is influenced by multiple factors, including mutational bias and selection. For intron gains, our data suggest that NHEJ is involved as a mechanism, but this process is unlikely to be biased...
  9. Research: Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation
    • Carlo G. Artieri and
    • Hunter B. Fraser
    Genome Res. December 2014 24: 2011-2021; Published in Advance October 7, 2014, doi:10.1101/gr.175893.114
    ..., where local base composition of RNAs can produce undesirable secondary structure, bias reverse transcription priming, and interfere with enzymatic steps such as ligation (Zheng et al. 2011). Such effects manifest themselves as protocol-specific biases in read coverage along transcripts, leading to over...
  10. Resource: MuSiC: Identifying mutational significance in cancer genomes
    • Nathan D. Dees,
    • Qunyuan Zhang,
    • Cyriac Kandoth,
    • Michael C. Wendl,
    • William Schierding,
    • Daniel C. Koboldt,
    • Thomas B. Mooney,
    • Matthew B. Callaway,
    • David Dooling,
    • Elaine R. Mardis,
    • Richard K. Wilson,
    • and Li Ding
    Genome Res. August 2012 22: 1589-1598; Published in Advance July 3, 2012, doi:10.1101/gr.134635.111
    ...whether specific mutations/genes are associated with a particular clinical feature. As these associations can sometimes be biased by covariate clinical features, MuSiC also offers a generalized linear model (GLM) analysis option within the CCT. This tool allows users to define any number of clinical...
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