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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
....korbie@uq.edu.au or d.korbie@garvan.org.auAbstractBRCA1 and BRCA2 germline variant classification is vital for clinical management of families with hereditary breast and ovarian cancer. However, clinical classification of rare variants outside of the splice donor/acceptor ±1,2-dinucleotides remains challenging...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
.... 2018). Unlike engineered or mutation accumulation strains, these evolved strains are part of the adaptive process of evolutionary changes that includes CNVs as well as single-nucleotide variants (SNVs). The CNVs in this study are extremely young and lack the signatures of paralog divergence that typify...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...that shape miRNA output during development are still to be clarified. Here, we address this question on a -wide scale, using the maize shoot apex as a model. We show that patterns and levels of miRNA accumulation are largely determined at the transcriptional level, but are finessed post...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...degenerative retinopathies, but most are variants of uncertain significance. We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitutions in CRX using a cell-based transcriptional reporter assay, curating a high-confidence list of nearly 2000 variants with altered...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...Disorders Study 2017), and a stringent confidence threshold (posterior probability greater than 0.8) was applied. We used triplet-based mutation rates (Samocha et al. 2014) for each potential single-nucleotide change across our splicing regions of interest to calculate the expected number of DNMs across...
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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
...hotspots collected in this study. (Mis) Missense, (Nons) nonsense, (Syn) synonymous, (Splice) splice site. (C) Fraction of missense mutations affecting protein interactions from published experiments. The error bars indicate standard error of the fraction. (D) Distribution of hotspots and nonrecurrent...
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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
...established from cross-species comparisons that the rate of nucleotide substitution mutations fluctuates at the multimegabase (>106 bp) scale across the (Wolfe et al. 1989; Hodgkinson and Eyre-Walker 2011), with early replicating regions subject to reduced rates of mutation. These patterns similarly manifest...
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Research: Exonic splice regulation imposes strong selection at synonymous sites
- Rosina Savisaar and
- Laurence D. Hurst
Genome Res. October 2018 28: 1442-1454; Published in Advance August 24, 2018, doi:10.1101/gr.233999.117
...Rosina Savisaar and Laurence D. Hurst The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom Corresponding author: r.savisaar@bath.ac.ukAbstractWhat proportion of coding sequence nucleotides have roles in splicing, and how strong...
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Method: ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
- Riccardo Sangermano,
- Mubeen Khan,
- Stéphanie S. Cornelis,
- Valerie Richelle,
- Silvia Albert,
- Alejandro Garanto,
- Duaa Elmelik,
- Raheel Qamar,
- Dorien Lugtenberg,
- L. Ingeborgh van den Born,
- Rob W.J. Collin,
- and Frans P.M. Cremers
Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
...the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.Technological advancements have...
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Method: The dynamic landscape of fission yeast meiosis alternative-splice isoforms
- Zheng Kuang,
- Jef D. Boeke,
- and Stefan Canzar
Genome Res. January 2017 27: 145-156; Published in Advance November 17, 2016, doi:10.1101/gr.208041.116
...at Chicago, Chicago, Illinois 60637, USA; 4Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less...

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