Searching journal content for articles similar to Biezuner et al. 26 (11): 1588.

Displaying results 1-10 of 22
For checked items
  1. Review: Advancements in prospective single-cell lineage barcoding and their applications in research
    • Xiaoli Zhang,
    • Yirui Huang,
    • Yajing Yang,
    • Qi-En Wang,
    • and Lang Li
    Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
    ...of these sites. (D) CRISPR–Cas9-based barcoding: During cell differentiation, Cas9 induces double-strand breaks, and incomplete nonhomologous end joining (NHEJ) repair leads to the generation of barcode insertions and deletions over time, serving as a valuable tool for lineage tracing.In response...
    OPEN ACCESS ARTICLE
  2. Method: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells
    • Christopher Jen-Yue Wei and
    • Kun Zhang
    Genome Res. April 2020 30: 602-610; Published in Advance March 3, 2020, doi:10.1101/gr.255851.119
    ..., is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Biezuner T, Spiro A, Raz O, Amir S, Milo L, Adar R, Chapal-Ilani N, Berman V, Fried Y, Ainbinder E, et al. 2016. A generic, cost-effective...
    OPEN ACCESS ARTICLE
  3. Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
    • Yuwei Cao,
    • Lauren Patel,
    • Lauren Alcoser,
    • Eric Mendenhall,
    • Christopher Benner,
    • Sven Heinz,
    • and Alon Goren
    Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
    ...the genomic localization of DNA-associated proteins. However, conventional protocols include multiple manual steps that can introduce inconsistency and limit scalability, thereby restricting the inclusion of appropriate replicates and controls. Although the introduction of liquid handling platforms has...
  4. Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    • Inswasti Cahyani,
    • John Tyson,
    • Nadine Holmes,
    • Josh Quick,
    • Chris Moore,
    • Nick Loman,
    • and Matthew Loose
    Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
    ...for sequencing scalability.Here, we describe the FindingNemo protocol (named after the characteristic orange color of the CoHex buffer) for the generation of high-occupancy UL reads on nanopore platforms. This protocol can generate equivalent or more throughputs to disc-based methods and may have additional...
    OPEN ACCESS ARTICLE
  5. Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
    • Samuel T. Horsfield,
    • Basil C.T. Fok,
    • Yuhan Fu,
    • Paul Turner,
    • John A. Lees,
    • and Nicholas J. Croucher
    Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
    ...@ebi.ac.ukAbstractSerotype surveillance of Streptococcus pneumoniae (the pneumococcus) is critical for understanding the effectiveness of current vaccination strategies. However, existing methods for serotyping are limited in their ability to identify co-carriage of multiple pneumococci and detect novel serotypes. To develop a scalable...
    OPEN ACCESS ARTICLE
  6. 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
    ...of microsatellites incur significant “stutter” artifacts that interfere with accurate genotyping, and sequencing costs preclude whole- microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of more than 150,000 microsatellites...
  7. Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
    • Yuelin Liu,
    • Xuan Cindy Li,
    • Farid Rashidi Mehrabadi,
    • Alejandro A. Schäffer,
    • Drew Pratt,
    • David R. Crawford,
    • Salem Malikić,
    • Erin K. Molloy,
    • Vishaka Gopalan,
    • Stephen M. Mount,
    • Eytan Ruppin,
    • Kenneth D. Aldape,
    • and S. Cenk Sahinalp
    Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
    ...of information from the parental generation is the necessary condition for the infinite sites assumption (Kimura 1969; Ma et al. 2008) and Dollo parsimony (Dollo 1893), which form the basis for tumor lineage inference tools based on mutation profiles. However, as of now, there is no known set of CpG sites...
  8. Method: Parallel analysis of replication timing, gene expression and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. March 19, 2026 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...to detect CNVs with this 263 sequencing depth makes this approach cost-effective and scalable for clonal tracking, 264 integrity screenings, and cancer alterations studies, with the addition of joint profiling of RT and gene 265 regulation. 266 For Repli-seq analysis in PARTAGE, we took advantage of our...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  9. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    ...technologies, long-read sequencing (PacBio and ONT) avoids the generation of PCR duplicates common to short-read sequencing, which avoids the corresponding biases during taxonomic profiling. Third, portable long-read sequencing sequencers, such as ONT Flongle and MinION, enable cost-effective, in...
    OPEN ACCESS ARTICLE
  10. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    ...abundant, cost-effective, bias-reduced cell type annotations as well as a reproducible reference framework. When integrated with CAMUS, these AI-generated reference atlases should markedly enhance the robustness and cross-study comparability.One potential limitation of CAMUS is that it does not consider...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research