Searching journal content for articles similar to Faux et al. 17 (7): 000.

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  1. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...scenarios in which d can be 10,000 or more. For example, the SILVA NR99 SSU reference database (510,508 sequences, 1.2 GB) spans 9118 distinct genera, which would require a document array profile structure >2 TB.Here, we develop new methods that drastically reduce the space usage. In so doing, we sacrifice...
  2. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
  3. Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    ...TSS with another annotated isoform (Supplemental Fig. S5A). Additionally, TSS signals were detected in this region in the CAGE database (FANTOM6) (Supplemental Fig. S5B).View larger version: In this window In a new window Figure 3. scRaCH-seq reveals different SF3B1 isoform usage by CLL cells from...
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  4. Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    • Jung-Wan Mok,
    • Shelley B. Gibson,
    • Haley A. Dostalik,
    • and Shinya Yamamoto
    Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
    ...the effect of overexpressing human proteins, and testing functional consequences of rare variants of interest by generating analogous fly mutants to contribute to rare disease diagnosis. We argue that data obtained using Drosophila can be leveraged to design effective multiplexed assays for variant effects...
  5. Resource: MPRAbase a Massively Parallel Reporter Assay database
    • Jingjing Zhao,
    • Fotis A Baltoumas,
    • Maxwell A Konnaris,
    • Ioannis Mouratidis,
    • Zhe Liu,
    • Jasmine Sims,
    • Vikram Agarwal,
    • Georgios A Pavlopoulos,
    • Ilias Georgakopoulos-Soares,
    • and Nadav Ahituv
    Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
    ...-side operations are mainly handled by R. Data visualization and graphs are generated using the R/DT and R/plotly packages (Sievert 2020). MPRAbase is available online without fees for academic usage. The database is updated in regular 6-month intervals, as new MPRA studies become available, and have provided...
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  6. Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
    • Aditi Singh,
    • Lilia Häußermann,
    • Christiane Emmerich,
    • Emily Nischwitz,
    • Brandon K.B. Seah,
    • Falk Butter,
    • Mariusz Nowacki,
    • and Estienne C. Swart
    Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
    ...Complex Protein a (ICOPa; PTET.51.1.P0440186) and its closely related ohnolog ISWI1 Complex Protein b (ICOPb; PTET.51.1.P0180124), respectively.We checked if the candidate proteins have homologs that form ISWI complexes in other organisms (Dirscherl and Krebs 2004). Because HMMER3 Pfam database searches...
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  7. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...memory requirements.DiscussionThe increasing size of public reference databases such as NCBI RefSeq makes metagenomic profiling and read classification a computationally challenging task. In particular, reducing memory usage has become an objective of many studies during the past few years. However...
  8. Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
    • Jonas de Tribolet-Hardy,
    • Christian W. Thorball,
    • Romain Forey,
    • Evarist Planet,
    • Julien Duc,
    • Alexandre Coudray,
    • Bara Khubieh,
    • Sandra Offner,
    • Cyril Pulver,
    • Jacques Fellay,
    • Michael Imbeault,
    • Priscilla Turelli,
    • and Didier Trono
    Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
    ...get lost over time because of genetic drift. Most human TEs are retrotransposons spreading by a copy-and-paste mechanism, be they LTR (long terminal repeat)-containing endogenous retroviruses (ERVs), long and short interspersed nuclear elements (LINEs and SINEs), or the composite SINE-variable number...
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  9. Resource: Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
    • Honglan Zheng,
    • Xinhao Yan,
    • Guanluan Li,
    • Hengwei Lin,
    • Siqi Deng,
    • Wenhui Zhuang,
    • Fuqiang Yao,
    • Yu Lu,
    • Xin Xia,
    • Huijun Yuan,
    • Li Jin,
    • and Zhiqiang Yan
    Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
    ...the heterozygous condition in Deafness nonsyndromic autosomal dominant 2 (DFNA2) patients caused by KCNQ4 variants, we coexpressed loss-of-function variants with wild-type KCNQ4 and found 516 variants showed impaired or only partially rescued heterogeneous channel function. Overall, our functional classification...
  10. Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    • Jonathan Cahn,
    • James P.B. Lloyd,
    • Ino D. Karemaker,
    • Pascal W.T.C. Jansen,
    • Jahnvi Pflueger,
    • Owen Duncan,
    • Jakob Petereit,
    • Ozren Bogdanovic,
    • A. Harvey Millar,
    • Michiel Vermeulen,
    • and Ryan Lister
    Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
    ...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
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