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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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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...regulatory genes (Narang et al. 2015), determine changes in regulatory mechanisms that are key to cellular identity (Wang et al. 2021), and prioritize genes that drive phenotypic variability (van Dam et al. 2017).Despite the utility of GCNs in understanding biological systems, network inference is still...
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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
...al. 2024). However, whether genomic mechanisms govern these slow rates of molecular evolution, and whether they are restricted to a subset of the , such as protein-coding genes (Takezaki 2018; Brownstein et al. 2024) and fourfold degenerate sites (Venkatesh et al. 2014; Gemmell et al. 2020), remain...
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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
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Method: Ultrafast genome-wide inference of pairwise coalescence times
- Regev Schweiger and
- Richard Durbin
Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
....1111/1755-0998.12968 ↵Harris K, Sheehan S, Kamm JA, Song YS. 2014. Decoding coalescent hidden Markov models in linear time. Res Comput Mol Biol 8394: 100–114. doi:10.1007/978-3-319-05269-4_8 ↵Hein J, Schierup M, Wiuf C. 2004. Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford University Press...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulatory events occur at TF binding sites some distance from the TSS, and predicting these is crucial in computational genetics. TF binding operates within a topologically associating domain typically upstream of the TSS but sometimes within the gene. However, predicting the boundaries of this domain...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
....Cytosine methylation plays a critical role in genomic imprinting, gene regulation, X-Chromosome inactivation (XCI), cellular differentiation, aging, and tumorigenesis. Cells have an extensive system of proteins that establish these methylation patterns through de novo methylation or demethylation, copy methylation...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...editing produces a Euclidean graph, and reconstructed paths are extracted using Eulerian tour and decomposition methods. (D) Interpretation and visualization. Structural variations are annotated using ISCN nomenclature; disrupted genes are identified; and results are compiled into an interactive HTML...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...alterations in nucleosome occupancy toward the 3′ end of gene bodies. Specifically, we computed occupancy changes surrounding the polyadenylation site (PAS) and observed a negative correlation (R = –0.44, P = 1.8 × 10–12) between PAS nucleosome occupancy changes and gene expression changes (Fig. 5E...

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