Searching journal content for articles similar to Torkamani and Schork 19 (9): 1570.

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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...repeats.Identification of de novo SNMs and indelsWe used DeepVariant 1.4.0 (Poplin et al. 2018) to call SNMs and indels from PacBio read alignments enabling the option “‐‐model_type=PACBIO.” A combined VCF containing mutation calls from all the samples was then generated with GLnexus 1.3.1 (Yun et al...
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Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
...humans and animal models.Advances in -scale measurement and mathematical modeling herald opportunities for high-quality reconstruction of transcriptional regulatory networks (TRNs). TRNs describe the control of gene expression patterns by transcription factors (TFs) (Hecker et al. 2009; Chai et al. 2014...
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Method: Mutual exclusivity analysis identifies oncogenic network modules
- Giovanni Ciriello,
- Ethan Cerami,
- Chris Sander,
- and Nikolaus Schultz
Genome Res. February 2012 22: 398-406; Published in Advance September 9, 2011, doi:10.1101/gr.125567.111
...and identified network modules enriched for mutations and potential rare cancer driver mutations (Torkamani and Schork 2009). Vandin and colleagues have used a network diffusion algorithm to identify subnetworks enriched for mutations within a large gene interaction network (Vandin et al. 2010). Vaske...
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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
..., and the acquisition of drug resistance. However, available -wide methods have a limited ability to resolve rare somatic variants and the relationships between these variants. Here, we present lineage sequencing, a new sequencing approach that enables somatic event reconstruction by providing quality somatic mutation...
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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
...and their biological and clinical significance in human cancers.Through DNA sequencing of tumor mutations, precision oncology has enabled the identification of cancer drivers, therapy targets, and prognostic mutations that can guide individualized therapies for many cancer patients. For example, what was once defined...
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Method: Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
...of microbial communities. Their circular s correspond to circular walks in meta graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular s. We present DomCycle, an algorithm that reconstructs likely...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes. Footnotes...
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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...published proximity ligation data sets, we show that RNA:RNA homodimers mediated by direct base-pairing are rare across the human transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA, and a subset of tRNAs. Mutations in the homodimerization domain of U8 snoRNA impede...
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Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...be an ancestral gain-of-function mutation. In conclusion, our reconstruction is able to generate a subfamily ancestor similar to the Repbase consensus and reveals evolutionary events that would otherwise be missed.Identification of important TFBS motifs in LTR18A enhancersWe designed our LTR18A MPRA library...
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Method: De novo individualized disease modules reveal the synthetic penetrance of genes and inform personalized treatment regimens
- Taylor M. Weiskittel,
- Choong Y. Ung,
- Cristina Correia,
- Cheng Zhang,
- and Hu Li
Genome Res. January 2022 32: 124-134; Published in Advance December 7, 2021, doi:10.1101/gr.275889.121
...the pipeline's ability to recover known disease drivers, and thus, it is an imperfect test of our pipeline because we seek to identify rare and frequent drivers in an individualized manner. We retained the individualized omic features of fold change and mutation status because of this in our final pipeline...
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