Searching journal content for articles similar to Bernhardt et al. 13 (2): 224.

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  1. Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
    • Ned Peel,
    • Samuel Martin,
    • Darren Heavens,
    • Douglas W. Yu,
    • Matthew D. Clark,
    • and Richard M. Leggett
    Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
    ...under their earlier taxonomic names in the original study (Lactobacillus fermentum and Bacillus subtilis, respectively) but were reported by MARTi using current nomenclature.DiscussionONT's long-read sequencing platforms are the first to enable progressive real-time data analysis, with the potential...
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  2. Research: Proteome-wide structural analysis quantifies structural conservation across distant species
    • Shijie Zhang,
    • Teng Zhang,
    • and Yuan Fu
    Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
    ...relies on sequence information to infer evolutionary relationships between genes or proteins. In contrast, protein structural information has long been overlooked, although structures are more conserved and closely linked to the functions than the sequences. To address this gap, we conducted a proteome...
  3. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for the characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established...
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  4. Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    ...simplification or node scaling was applied in VRPG for this visualization. All other options were left with defaults.The DOG2 deletionThe yeast paralog gene pairs DOG1 and DOG2 encode 2-deoxyglucose-6-phosphate phosphatase involved in glucose metabolism. They are homologous to the human PUDP (previously known...
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  5. Resource: Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR
    • Wouter De Coster,
    • Ida Höijer,
    • Inge Bruggeman,
    • Svenn D'Hert,
    • Malin Melin,
    • Adam Ameur,
    • and Rosa Rademakers
    Genome Res. November 2024 34: 2074-2080; Published in Advance August 15, 2024, doi:10.1101/gr.279265.124
    ...STR provides rich visualizations of this data set and the feature to upload one's data for comparison along the control cohort. We demonstrate the implementation of this application using data from targeted nanopore sequencing of a patient with myotonic dystrophy type 1. This resource will empower the genetics...
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  6. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...of the method was very high, the restrained proteome coverage of the mass spectrometry measurements poses a certain limit to the comprehensiveness of our annotation. In principle, the overall range of detected proteins could be extended by applying technological and methodological adjustments (Levin and Butter...
  7. Research: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins
    • Rosario Avolio,
    • Ilenia Agliarulo,
    • Daniela Criscuolo,
    • Daniela Sarnataro,
    • Margherita Auriemma,
    • Sabrina De Lella,
    • Sara Pennacchio,
    • Giovanni Calice,
    • Martin Y. Ng,
    • Carlotta Giorgi,
    • Paolo Pinton,
    • Barry S. Cooperman,
    • Matteo Landriscina,
    • Franca Esposito,
    • and Danilo Swann Matassa
    Genome Res. August 2023 33: 1242-1257; Published in Advance July 24, 2023, doi:10.1101/gr.277755.123
    ..., the nuclear coordinates mitochondrial and cytosolic translations to orchestrate the timely synthesis of oxidative phosphorylation complexes, representing a previously underestimated regulatory layer shaping the mitochondrial proteome (Couvillion et al. 2016). Accordingly, the mitochondrial protein import...
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  8. Resource: The developmental proteome of Drosophila melanogaster
    • Nuria Casas-Vila,
    • Alina Bluhm,
    • Sergi Sayols,
    • Nadja Dinges,
    • Mario Dejung,
    • Tina Altenhein,
    • Dennis Kappei,
    • Benjamin Altenhein,
    • Jean-Yves Roignant,
    • and Falk Butter
    Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
    ...RNA and protein, underscoring the importance of proteomics to study developmental progression. Data integration of our embryogenesis proteome with tissue-specific data revealed spatial and temporal information for further functional studies of yet uncharacterized proteins. Overall, our high resolution proteomes...
  9. Research: Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism
    • Daniel R. Reuß,
    • Josef Altenbuchner,
    • Ulrike Mäder,
    • Hermann Rath,
    • Till Ischebeck,
    • Praveen Kumar Sappa,
    • Andrea Thürmer,
    • Cyprien Guérin,
    • Pierre Nicolas,
    • Leif Steil,
    • Bingyao Zhu,
    • Ivo Feussner,
    • Stefan Klumpp,
    • Rolf Daniel,
    • Fabian M. Commichau,
    • Uwe Völker,
    • and Jörg Stülke
    Genome Res. February 2017 27: 289-299; Published in Advance December 13, 2016, doi:10.1101/gr.215293.116
    ...Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism Daniel R. Reuß 1 , 9 , Josef Altenbuchner 2 , 9 , Ulrike Mäder 3 , 9 , Hermann Rath 3 , Till Ischebeck...
  10. Method: Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore
    • Narendra Chaudhary,
    • Si-Hyeong Nho,
    • Hayoon Cho,
    • Narangerel Gantumur,
    • Jae Sun Ra,
    • Kyungjae Myung,
    • and Hajin Kim
    Genome Res. September 2020 30: 1306-1316; Published in Advance September 4, 2020, doi:10.1101/gr.260018.119
    ..., Ulsan 44919, Republic of Korea Corresponding author: hajinkim@unist.ac.krAbstractThe higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure–function relationship, it is necessary to directly visualize genomic elements...
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