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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...-seq), including short-read RNA sequencing (srRNA-seq) and long-read RNA sequencing (lrRNA-seq), and a sequential window acquisition of all theoretical mass spectra (SWATH-MS)-based proteomic approach (i.e., proteogenomics). Transcriptomic and proteomic analyses have been individually applied in plant research...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...in Figure 5, D and E. The translated sequences can be found in Supplemental Figure S12, together with two additional examples and their translations (selected for visualization based on their short alignment length). In both these cases, based on the multiple stop codons present in the orthologous sequences...
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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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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: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...splicing and polyadenylation sites, including a potential cryptic polyadenylation site in the widely used Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE). Using artificial polyadenylation of the lentiviral RNA, we also identify multiple hairpin-associated truncations in the analyzed...
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Method: OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
...across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete s. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...and to determine loci controlling certain phenotypes. The obtained information can then be used to investigate nearby and distant regulatory sequences of such loci and to forward orthologous sequences for translational studies.In this study, we aimed to establish high-continuity chromosomal assemblies for three...
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Research: Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways
- Blair W. Perry,
- Siddharth S. Gopalan,
- Giulia I.M. Pasquesi,
- Drew R. Schield,
- Aundrea K. Westfall,
- Cara F. Smith,
- Ivan Koludarov,
- Paul T. Chippindale,
- Mark W. Pellegrino,
- Edward B. Chuong,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. June 2022 32: 1058-1073; Published in Advance June 1, 2022, doi:10.1101/gr.276251.121
...venom glands (Schield et al. 2019) and incorporated CTCF ChIP-seq data to investigate the role of CTCF binding and insulation in VG regions (Fig. 8). Only the PLA2 VG cluster falls entirely within a single TAD, with SVMP and SVSP clusters each spanning multiple TADs (Fig. 8A,B). The most highly...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...in regulating chromatin. Specifically, we depleted ASH1L, CHD8, CREBBP, EHMT1, and NSD1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers...

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