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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
...and the International Cancer Research Consortium (ICGC), have facilitated the development of clinical-grade classifiers that leverage machine-learning episignatures for diagnosing brain tumors (Wu et al. 2022) and certain Mendelian disorders (Sadikovic et al. 2020). While clinical implementation requires careful...
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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
...length as a function of the location of the midpoint of each fragment and colored the points based on their local density. The result is a near-nucleotide-resolution -wide view of chromatin occupancy for each deletion strain (Fig. 1D–F).View larger version: In this window In a new window Figure 1. Genome-wide...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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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
...ancestry from the 1000 Genomes Project data set (Phase 3) (The 1000 Genomes Project Consortium 2015), assuming a scaled mutation rate of θ = 0.00075 and scaled recombination rate of ρ = 0.0006, corresponding to an unscaled mutation rate μ = 1.25 × 10−8, an unscaled recombination rate r = 10...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...result in strong genetic drift with long-lasting -wide consequences on genetic diversity and allele frequencies (Ellegren et al. 2012; The 1000 Genomes Project Consortium 2015; Friis et al. 2018). The genomic background patterns caused by genetic drift make it challenging to identify the typical “genomic...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...Castel et al. 2010; Pinto et al. 2013). Further, -wide association studies (GWASs) for the age of onset and progression of Huntington's disease have identified mutations in MLH1 (Genetic Modifiers of Huntington's Disease (GeM-HD) Consortium 2015) and MSH3 (Moss et al. 2017) that lead to increased somatic...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...cell lines of The ENCODE Project Consortium (The ENCODE Project Consortium 2012, The ENCODE Project Consortium et al. 2020) and as a wealth of other functional genomic data exists for them. Because we expected to recover less DNA than for regular ATAC libraries given that KAS-ATAC captures only...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...-TRs in GTEx v8 data, consisting of WGS of 838 donors and RNA-seq of 15,253 samples from 49 tissues, by using FastQTL (Fig. 1; Supplemental Table S1; Ongen et al. 2016; The GTEx Consortium 2020). TRs were sized using GangSTR, which handles TRs with motifs of up to 20 bp (n = 40,598 after quality control...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...regulatory roles in DNA methylation (Fig. 1), we first performed a -wide QTL analysis between STR genotypes and DNA methylation levels of nearby CpGs in a discovery cohort of 245 samples collected by the Pediatric Cardiac Genomics Consortium (PCGC). This analysis identified a total of 19,129 pairwise...

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