Searching journal content for articles similar to Teh et al. 24 (7): 1064.

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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...“logistic mixing,” a neural network without hidden layers that uses a simple update rule to adjust the output probabilities for better bitstream coding. This idea has been brought to genomic compression of sequencing reads with GeCo3 (Silva et al. 2020). Another recent use of neural networks for DNA...
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Research: T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population
- Daniel Schmitz,
- Adam Ameur,
- and Åsa Johansson
Genome Res. November 2025 35: 2377-2388; Published in Advance September 16, 2025, doi:10.1101/gr.279320.124
...(NGI) in Stockholm (NGI-S) and Uppsala (NGI-U). After fragmenting to 350-bp inserts and library preparation, DNA samples underwent WGS on the Illumina HiSeq X platform using v2.5 chemistry (Ameur et al. 2017). The 1000 individuals included in the data set all passed QC. The original mappings were...
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Method: ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
- Haotian Zhang,
- Yiming Zhang,
- Teng Gao,
- and Yufeng Wu
Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
...that improves the original ScisTree. The input for running ScisTree2 is generated by processing single-cell DNA-seq or other types of single-cell sequencing data with genetic variants. Given single-cell sequencing data (reads), the first step is using a genotype caller (e.g., GATK [McKenna et al. 2010]) to call...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...Methods 7: 461–472. doi:10.1038/nmeth.1459 ↵Galeone V, Dabernig-Heinz J, Lohde M, Brandt C, Kohler C, Wagner GE, Hölzer M. 2025. Decoding bacterial methylomes in four public health-relevant microbial species: nanopore sequencing enables reproducible analysis of DNA modifications. BMC Genomics 26: 394. doi...
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Method: Secure phasing of private genomes in a trusted execution environment with TX-Phase
- Natnatee Dokmai,
- Kaiyuan Zhu,
- S. Cenk Sahinalp,
- and Hyunghoon Cho
Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
...the secure processing of users’ data, without requiring complete trust in the SP and their security precautions. For example, recent work (Dokmai et al. 2021) has shown that genotype imputation can be securely and accurately performed within trusted execution environments (TEEs) (Sabt et al. 2015). TEEs...
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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...: a program to analyze DNA sequences. Nucleic Acids Res 27: 573–580. doi:10.1093/nar/27.2.573 ↵Blauw HM, van Rheenen W, Koppers M, Van Damme P, Waibel S, Lemmens R, van Vught PWJ, Meyer T, Schulte C, Gasser T, et al. 2012. NIPA1 polyalanine repeat expansions are associated with amyotrophic lateral sclerosis...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...non-human species. For each human sSNV, SynMall provides multilevel annotations that combine American College of Medical Genetics and Genomics (ACMG)–aligned variant interpretation information, such as allele frequencies and functional effects, with more than 100 descriptors at the DNA, RNA...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...accuracy can offer opportunities to reuse large volumes of already generated data. Here, we explore the prospects to leverage hundreds of thousands of LPS s, generated from cell-free DNA (cfDNA) during noninvasive prenatal screening (NIPS) (Wang et al. 2021; Van Riel et al. 2023), for the study of maternal...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...the depth in this region. Dramatic variation in depth plots may indicate errors in the assemblies, such as putative misassemblies, collapsed or expanded duplications, etc. The depth plot (Supplemental Fig. 8) for iso-1 indicates that a region of ∼250 kb immediately distal to the rDNA exhibits twice...
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Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
- Degui Zhi,
- Xiaoqian Jiang,
- and Arif Harmanci
Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
...decrease in imputation accuracy for variants in a wide range of allele frequencies.Decreasing costs of DNA sequencing and genotyping brought about a massive increase in the number of personal s (Muir et al. 2016). Starting with the small-scale population-wide sequencing (Chen et al. 2022) efforts...
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