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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
...for ancestry classificationIndividuals that are more closely related in ancestry have spatial autocorrelations in their genomic sequences. This phenomenon is translated into population clusters using dimensionality reduction techniques (Fig. 4). The most common approaches to address ancestry classification...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...as one of the genetic modifiers that influence the penetrance of pathogenic variants (Castel et al. 2018). These common variants, which modify gene expression in specific haplotype combinations with rare pathogenic alleles, “interact” with the latter, thereby modulating their penetrance (Emison et al...
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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
...and gene conversion (Liao 1999). However, the extent of homogenization and variation in observed copy numbers may vary across tandem arrays and may be shaped by various factors (such as natural selection, drift, mutation, drive, age, size, and relative rates of different kinds of recombination) acting...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...and the most recent common ancestor of L. osseus and L. oculatus (Fig. 1A; Supplemental Table S5). Comparative genomic analysis revealed distinctive characteristics of macrochromosomes and microchromosomes in A. spatula, L. osseus, and L. oculatus. Macrochromosomes contain a higher total number of genes...
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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
...alleles based on SNV haplotype groups, or uses a mix of both information sources. STRkit can also genotype haploid alleles for, for example, loci on the sex chromosomes of human XY or XO individuals. If two STRs have common SNV haplotype groups, they will be locally phased. If a phased alignment file...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...number alterations are common driver events in tumors, and copy number losses can contribute to the inactivation of tumor-suppressor genes (Davoli et al. 2013) by creating haploid regions through loss of heterozygosity (LOH) in specific alleles. Although LOH can be advantageous to a tumor, these haploid...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...is well established that miRNAs can repress the expression of their targets, at both the RNA and the protein level (Baek et al. 2008; Selbach et al. 2008). However, alternative functions for miRNAs have also been proposed, including buffering of gene expression variation (noise) (Hornstein and Shomron...
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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
...in a microbial community, but they often fall short in characterizing variation in gene content between strains (Plaza Oñate et al. 2019). As a result, it is challenging to study the functional consequences of strain-level variation in the gut microbiome.The most common way to study microbial gene content...
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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
...on the “literature” page. (G) Entrance to different non-human species on the “species” page.Diverse query strategySynMall features three primary search modes. First is single query (Supplemental Fig. S9A): SynMall supports four common query options by default, including Ensembl transcript ID, genomic region, genomic...
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Method: Pangenome-based genome inference using integer programming
- Ghanshyam Chandra,
- Md Helal Hossen,
- Stephan Scholz,
- Alexander T. Dilthey,
- Daniel Gibney,
- and Chirag Jain
Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
..., gene absence/presence, etc. (Computational Pan-Genomics Consortium 2018).Recent works propose the use of pan references to improve genotyping accuracy from short-read sequencing data (Eggertsson et al. 2017; Sibbesen et al. 2018; Hickey et al. 2020; Letcher et al. 2021; Bradbury et al. 2022; Ebler et...

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