Searching journal content for articles similar to Chen et al. 30 (3): 315.

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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
.... The fundamental tasks are to classify or group sequencing reads into distinct genomic bins, each representing a different taxon (e.g., species or strain) within a metagenomic sample (taxonomic binning), and to identify the taxa present while estimating their relative abundances in the sample (taxonomic profiling...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
..., can further improve assembly by correcting misassemblies and scaffolding contigs (Šimková et al. 2024). By combining these technologies with metagenomic assembly techniques, we were able to generate nearly complete Blastocystis s without the need for axenic culturing. This approach allows us...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...-specific impacts on human health, and methods that accurately determine gene content from metagenomic data can greatly improve our understanding of the extent and importance of this intraspecific diversity. Widely used tools for analyzing metagenomic data can accurately quantify the abundance of species present...
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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
..., Gainesville, Florida 32611, USA Corresponding author: langmea@cs.jhu.eduAbstractTaxonomic sequence classification is a computational problem central to the study of metagenomics and evolution. Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...with spike-in metaWe extended the previous AMR haplotyping experiment to a metagenomics setting. In metagenomics, the input is a mixture of microbial genomic reads and reads from AMR genes. Thus, we mixed the previously simulated AMR reads into a simulated long-read mouse gut meta from CAMI2 (labeled...
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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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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...elements using the former (Supplemental Fig. S4A,B). Additionally, the curation process yielded significantly longer consensus sequences compared with the uncurated ones (Supplemental Fig. S4C), suggesting a more accurate reconstruction of their complete structure (Peona et al. 2024). Finally, we managed...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...–resolved population metagenomic data sets to track 18 MGEs for which structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...a genomic basis to study host-microbe interactions, and we demonstrate its utility in identifying candidate pathways in the bacteria affecting chemotaxis behavior and survival in the nematodes. Second, we generate nematode transcriptomes of P. pacificus nematodes on 38 bacterial diets and characterize 60...
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Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
- Taishan Hu,
- Timothy L. Mosbruger,
- Nikolaos G. Tairis,
- Amalia Dinou,
- Pushkala Jayaraman,
- Mahdi Sarmady,
- Kingham Brewster,
- Yang Li,
- Tristan J. Hayeck,
- Jamie L. Duke,
- and Dimitri S. Monos
Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
..., characterizing the MHC beyond exons is critical to resolve disease-associated variants accurately.Acknowledging the importance of complete genomic characterization of the MHC early on, two homozygous B lymphoblastoid cell lines (BLCLs), PGF and COX, were fully sequenced for their MHC (Stewart et al. 2004). Later...
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