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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...blocks in other retinal disease-associated genes.Another notable instance of intron retention was observed in WHRN transcripts, where nearly half of the sequenced transcripts exhibited retention of intron 4. While intron retention is generally thought to disrupt protein production due to the introduction...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...Chromosome-scale assemblies of Acanthamoeba castellanii s provide insights into Legionella pneumophila infection–related chromatin reorganization Cyril Matthey-Doret1,2,6, Morgan J. Colp3,6, Pedro Escoll4, Agnès Thierry1, Pierrick Moreau1, Bruce Curtis3, Tobias Sahr4, Matt Sarrasin5, Michael W...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...Table 1).View this table: In this window In a new window Table 1. Disease-associated repeat discovery by yearRecent repeat mutation identifications also highlight the importance of functional and clinical aspects of TR expansions in the discovery process. Expansions of TRs of the same repeat unit motifs...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
....2 deletion syndrome (22q11.2DS, MIM 188400) is the most common microdeletion in humans with an estimated incidence of 1 in 2148 live births (Blagojevic et al. 2021). 22q11.2DS has a heterogeneous presentation, including multiple congenital and later-onset features, such as cardiac, palatal, metabolic...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...resources for discovering distinct genomic features of PAS variants and also develop a credible and convenient experimental tool to validate the effect of PAS variants on expression of disease-associated genes. This approach will greatly accelerate the deciphering of PAS variation-related human diseases...
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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...@cau.edu.cnAbstractAlthough CRISPR-Cas-based editing has made significant strides over the past decade, achieving simultaneous homozygous gene editing of multiple targets in primary cells remains a significant challenge. In this study, we optimized a coselection strategy to enhance homozygous gene editing rates in the s of primary...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...; Iossifov et al. 2014; Satterstrom et al. 2020). This genetic heterogeneity provides a substantial challenge to the development of broadly useful therapeutics. If, at an extreme, each disease-associated gene follows a separate mechanistic route, then each will require the development of an independent...
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Method: Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's disease
- Jielin Xu,
- Pengyue Zhang,
- Yin Huang,
- Yadi Zhou,
- Yuan Hou,
- Lynn M. Bekris,
- Justin Lathia,
- Chien-Wei Chiang,
- Lang Li,
- Andrew A. Pieper,
- James B. Leverenz,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. October 2021 31: 1900-1912; Published in Advance February 24, 2021, doi:10.1101/gr.272484.120
...Sciences, University of Nevada Las Vegas, Las Vegas, Nevada 89154, USA ↵15 These authors contributed equally to this work. Corresponding author: chengf@ccf.orgAbstractBecause disease-associated microglia (DAM) and disease-associated astrocytes (DAA) are involved in the pathophysiology of Alzheimer...
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Research: Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland
- Danesh Moradigaravand,
- Christine J. Boinett,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2016 26: 1101-1109; Published in Advance July 18, 2016, doi:10.1101/gr.205245.116
...Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland Danesh Moradigaravand 1 , Christine J. Boinett 1 , Veronique Martin 2 , Sharon J. Peacock 1 , 3 , 4 and Julian...
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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
...@princeton.edu, mona@cs.princeton.eduAbstractMultiple sequence alignment (MSA) is a critical step in the study of protein sequence and function. Typically, MSA algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment algorithms use scoring systems...
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