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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...between ETV6 and FLI1. Moreover, KMAP identifies four prevalent patterns in gene editing data of the AAVS1 locus, aligning with findings reported in the literature. These applications underscore that KMAP can be a valuable tool across various biological contexts.DNA sequence serve as the primary carrier...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...sample. Reads and/or haplotype data (e.g., alternate reference assemblies) are then aligned to the graph (once per color) by trivial lookups of shared k-mers. Discrepancies between the sequence and the graph manifest as missing k-mers, correctable by traversing the graph between the gap boundaries...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
.... S1F). As shown in Figure 3F, the sequence-only model identified several annotated PASs from gene DKK1 that are not expressed/used at all, whereas when adding RNA-seq coverage features, the integrated model successfully discarded those unused PASs. Another example was shown in Supplemental Figure S1G...
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Method: Localizing unmapped sequences with families to validate the Telomere-to-Telomere assembly and identify new hotspots for genetic diversity
- Brianna Chrisman,
- Chloe He,
- Jae-Yoon Jung,
- Nate Stockham,
- Kelley Paskov,
- Peter Washington,
- Juli Petereit,
- and Dennis P. Wall
Genome Res. October 2023 33: 1734-1746; Published in Advance October 25, 2023, doi:10.1101/gr.277175.122
...in our original alignment, as this is the standard in alignment pipelines. Often fix patches indicate a more complicated change than a simple inserted or alternate sequence, such as a change in coordinate system.Additionally, several of these regions are well-cataloged hotspots for genetic diversity...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...we leverage Oxford Nanopore Technologies native RNA sequencing (dRNA), as well as ribosome profiling data, to uncover the full range of polyadenylated transcripts and translated open reading frames. We identify 332 alternative isoforms affecting the coding sequences of 262 different genes, 97...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
..., alignment of all the cattle assemblies mentioned above identified an additional 70 Mb of sequence not present in the Hereford reference (Crysnanto et al. 2021), with between 3.3 and 4.4 Mb unique to each taurine assembly. The pan representation created from this small sample of breeds showed that variant...
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Method: Direct determination of diploid genome sequences
- Neil I. Weisenfeld,
- Vijay Kumar,
- Preyas Shah,
- Deanna M. Church,
- and David B. Jaffe
Genome Res. May 2017 27: 757-767; Published in Advance April 5, 2017, doi:10.1101/gr.214874.116
...in the , then with high probability, multiple molecules (in the partitions) bridge the gap between the two lines. Therefore for any line, we may find candidate lines in its neighborhood by looking for other lines sharing many of the same barcodes. By scoring alternative orders and orientations (O&Os) of these lines, we...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...in specific genes or genetic pathways. One unanticipated finding of this study is the evidence that recombination rates per megabase of autosomal sequence are significantly lower in rhesus macaques relative to humans. Prior studies of pedigree-based recombination had suggested the potential for reduced...
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Research: Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
...in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple...

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