Searching journal content for articles similar to Sasuga et al. 16 (1): 132.

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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
...sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point...
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Method: Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time
- Andreas Reicher,
- Anna Koren,
- and Stefan Kubicek
Genome Res. December 2020 30: 1846-1855; Published in Advance November 17, 2020, doi:10.1101/gr.261503.120
...on the localization and levels of hundreds of proteins in real time in a pooled format, followed by identification of responding clones by in situ sequencing of the expressed intron-targeting sgRNA that corresponds to the tagged protein (Fig. 1A).View larger version: In this window In a new window Figure 1. Pooled...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...genetic interactions. As sequencing is applied to more families and other disorders, GCOD will enable detection of increasingly large, novel gene combinations, shedding light on combinatorial causes of genetic diseases.Many diseases are genetically heterogeneous such that damaging variants at different...
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Method: Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
- Shijia Zhu,
- John Beaulaurier,
- Gintaras Deikus,
- Tao P. Wu,
- Maya Strahl,
- Ziyang Hao,
- Guanzheng Luo,
- James A. Gregory,
- Andrew Chess,
- Chuan He,
- Andrew Xiao,
- Robert Sebra,
- Eric E. Schadt,
- and Gang Fang
Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
...Mapping and characterizing N6-methyladenine in eukaryotic s using single-molecule real-time sequencing Shijia Zhu1, John Beaulaurier1, Gintaras Deikus1, Tao P. Wu2, Maya Strahl1, Ziyang Hao3, Guanzheng Luo3, James A. Gregory4, Andrew Chess1, Chuan He3, Andrew Xiao2, Robert Sebra1, Eric E. Schadt1...
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Method: Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
- Vishvak Raghavan,
- Yumin Zheng,
- Yue Li,
- and Jun Ding
Genome Res. July 2025 35: 1646-1663; Published in Advance May 2, 2025, doi:10.1101/gr.279771.124
...introduces distinct functionalities not available in other tools (Table 1). Unique to CellAgentChat is its integrated ABM animation platform, which facilitates the visualization of individual-level cellular interactions and supports dynamic simulations. Additionally, through easy and flexible adjustment...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale data sets requires specialized computational tools to organize and analyze the extensive data. Genotypes and Phenotypes in Families (GPF) is an open-source platform that manages...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
...predictions.The omics era has greatly increased the number of sequenced s (Hotaling et al. 2021). With this influx of information, network and system biologists have developed approaches to study gene and protein interactions from a broader perspective and at a much larger scale. Networks of such interactions...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
..., and the biomolecules and pathways related to the individual's immune system, kidney, and liver were highly associated with the personal external exposome. Overall, this data-driven longitudinal monitoring study shows the potential dynamic interactions between the personal exposome and internal multi-omics, as well...
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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...and tracking its variability over time are crucial for understanding the coordination of biological processes mediating normal development, disease progression, and responses to perturbations such as therapies. Existing tools fail to capture time-dependent intercellular interactions and primarily rely...
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Resource: LEMMI: a continuous benchmarking platform for metagenomics classifiers
- Mathieu Seppey,
- Mosè Manni,
- and Evgeny M. Zdobnov
Genome Res. August 2020 30: 1208-1216; Published in Advance July 2, 2020, doi:10.1101/gr.260398.119
...in microbiome analyses. The LEMMI platform offers a novel approach for benchmarking software dedicated to meta composition assessments based on read classification. It enables the integration of newly published methods in an independent and centralized benchmark designed to be continuously open to new...
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