Searching journal content for articles similar to Azizpour et al. 34 (9): 1468.

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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
...how our method is computationally efficient and scalable in terms of memory and time, and we provide open-source software implemented in Python.ResultsOverview of Proust to detect spatial domains integrating multiple data modalitiesProust is a graph-based contrastive self-supervised learning framework...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...the complex sources of variability inherent to this problem domain (e.g., the nonuniformity of read coverage and variant density within the and across different populations or read length and error profiles of different sequencing platforms).Learning-based approaches, on the other hand, can detect complex...
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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
.... To improve performance when detecting novel serotypes, we develop a graph-based bioinformatic method for NAS, named GNASTy (Graph-based Nanopore Adaptive Sampling Typing, pronounced “nasty”), and benchmark it against the current NAS implementation, which uses linear alignment. Overall, we demonstrate...
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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 sequence correlations among these s, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pan graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pan graphs possess the capability to depict the full range...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
...with lengths that greatly exceed typical sequencing fragment sizes. When applied to data from the 1000 Genomes Project, ScatTR detects potential large TR expansions that other methods missed, highlighting its ability to better characterize -wide TR variation.Tandem repeats (TRs) are consecutively repeated...
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Research: Optical genome mapping enables accurate testing of large repeat expansions
- Bart van der Sanden,
- Kornelia Neveling,
- Syukri Shukor,
- Michael D. Gallagher,
- Joyce Lee,
- Stephanie L. Burke,
- Maartje Pennings,
- Ronald van Beek,
- Michiel Oorsprong,
- Ellen Kater-Baats,
- Eveline Kamping,
- Alide A. Tieleman,
- Nicol C. Voermans,
- Ingrid E. Scheffer,
- Jozef Gecz,
- Mark A. Corbett,
- Lisenka E.L.M. Vissers,
- Andy Wing Chun Pang,
- Alex Hastie,
- Erik-Jan Kamsteeg,
- and Alexander Hoischen
Genome Res. April 2025 35: 810-823; Published in Advance March 20, 2025, doi:10.1101/gr.279491.124
..., with greater accuracy than standard of care (SOC) for long repeats and no apparent upper size limit. Notably, OGM detected somatic instability in a subset of DMPK, CNBP, and RFC1 samples. These findings suggest OGM could advance diagnostic accuracy for large repeat expansions, providing a more comprehensive...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...Accurate and fast graph-based pan annotation and clustering with ggCaller Samuel T. Horsfield1,2, Gerry Tonkin-Hill3, Nicholas J. Croucher1,4 and John A. Lees1,2,4 1MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W12...
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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
...and estimate the distribution of strains based on SNP profiles. We defined detection as an estimated depth of ≥0.1×, a threshold chosen to balance false positives with the sensitivity of strain tracking. All species combined, a median of 59 strains were detected in each metagenomic sample and 191.5 across all...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., et al. 2019. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics 35: 4754–4756. doi:10.1093/bioinformatics/btz431 ↵Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. 2022. DeepRepeat: direct quantification of short tandem...
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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
...and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.Metagenomics...
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