Searching journal content for articles similar to Liu et al. 30 (11): 1655.

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  1. Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    • Haotian Zhang,
    • Yiming Zhang,
    • Teng Gao,
    • and Yufeng Wu
    Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
    ..., a recently developed variant caller, SComatic, can detect somatic SNVs from scRNA-seq and scATAC-seq, which typically contain 1000s to 10,000s of cells (Muyas et al. 2024). Currently, no existing probabilistic cell lineage tree inference methods are capable of handling data sets of this size. Thus, a new...
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  2. 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
    ...prediction. We build on these data, implementing further filtering steps to remove families with homology with other species, to identify putative SSOGs in the gut microbiome and to study them systematically. By looking for patterns in large-scale comparisons, we attempt to disentangle the evolutionary...
  3. Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
    • Amy R. Vandiver,
    • Allen Herbst,
    • Paul Stothard,
    • and Jonathan Wanagat
    Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
    ...expression, and, when possible, the underlying mtDNA deletion mutation frequency.ResultsChimeric mtRNA transcripts are observed in patients with mitochondrial myopathy owing to large-scale mtDNA deletion mutationsTo test whether chimeric mitochondrial transcripts corresponding to large deletion events can...
  4. Method: High-fidelity, large-scale targeted profiling of microsatellites
    • Caitlin A. Loh,
    • Danielle A. Shields,
    • Adam Schwing,
    • and Gilad D. Evrony
    Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
    ...tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.Microsatellites, also known as short tandem repeats, are genomic sequences composed of tandem repeats of short (1...
  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
  6. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...to evaluate how high-dimensional structural features captured by the clusters influence local sequencing efficiency.Structure-determined sequencing biases in synthetic RNA librariesThe structural complexity of an RNA transcript can be assessed at three hierarchical levels—primary, secondary, and tertiary...
  7. Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
    • Manuela Baquero Pérez,
    • Gertjan Laenen,
    • Isabelle Loïodice,
    • Mickaël Garnier,
    • Ugo Szachnowski,
    • Antonin Morillon,
    • Myriam Ruault,
    • and Angela Taddei
    Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
    ...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...
  8. Method: Secure discovery of genetic relatives across large-scale and distributed genomic data sets
    • Matthew M. Hong,
    • David Froelicher,
    • Ricky Magner,
    • Victoria Popic,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. September 2024 34: 1312-1323; Published in Advance August 7, 2024, doi:10.1101/gr.279057.124
    ...-Relate on the UK Biobank and All of Us data sets. On a data set of 200,000 individuals split between two parties, SF-Relate detects 97% of third-degree or closer relatives within 15 h of runtime. Our work enables secure identification of relatives across large-scale genomic data sets.Collaborative studies that aim...
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  9. Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
    • Joshua Lee,
    • Elizabeth A. Snell,
    • Joanne Brown,
    • Charlotte E. Booth,
    • Rosamonde E. Banks,
    • Daniel J. Turner,
    • Naveen S. Vasudev,
    • and Dimitris Lagos
    Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
    ...establish transcriptional codependencies, i.e. coexistence of distinct features (e.g. specific splice junctions and untranslated regions—UTRs) on the same transcript. Long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) have emerged as transformative methodological alternatives to overcome...
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  10. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (sRNA...
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