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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...or deletion mutation frequency in aged male rats: a short report. PLoS One 17: e0271850. doi:10.1371/journal.pone.0271850 ↵Herbst A, Aiken JM, Kim C, Gushue D, McKenzie D, Moore TM, Zhou J, Hoang AN, Choi S, Wanagat J. 2023. Age- and time-dependent mitochondrial genotoxic and myopathic effects of beta...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
..., wave peaks identified in DRB/TTchem-seq for the same gene at different DRB release times did not consistently progress in a clear, time-dependent manner (Supplemental Fig. S1D), which limited the number of genes that could be measured.With the combined experimental and computational improvements...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...are typically based on correlation, meaning that they do not necessarily indicate gene regulation. Other methods define neighboring cells along a developmental timeline, which can be inferred through pseudotime analysis (Wang et al. 2023; Zhang and Stumpf 2023). In this approach, coexpression measures are time-dependent...
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Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
- Raunak Shrestha,
- Ermin Hodzic,
- Thomas Sauerwald,
- Phuong Dao,
- Kendric Wang,
- Jake Yeung,
- Shawn Anderson,
- Fabio Vandin,
- Gholamreza Haffari,
- Colin C. Collins,
- and S. Cenk Sahinalp
Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
..., patient-specific driver events based on a time-dependent notion of influence. Finally, none of the available techniques aim to simultaneously consider different types of genomic alterations as potential drivers. To address the above challenges, we have developed a novel combinatorial method, HIT’nDRIVE (a...
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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...-unspliced” fraction, which diminished over 554 time. One interpretation of this increase in splicing index is that these transcripts are 555 spliced post-transcriptionally. Alternatively, all splicing may occur co-transcriptionally, 556 while transcripts that remain unspliced undergo a time-dependent purging...
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Research: Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
...of the impact on the gene function, since alternatively spliced mRNAs may have different functional implications. Alternative splicing is a major source of proteome diversity (Nilsen and Graveley 2010), with important consequences in processes such as development (Kalsotra and Cooper 2011) and disease (Cooper...
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Research: Adaptive selection of an incretin gene in Eurasian populations
- Chia Lin Chang,
- James J. Cai,
- Chiening Lo,
- Jorge Amigo,
- Jae-Il Park,
- and Sheau Yu Teddy Hsu
Genome Res. January 2011 21: 21-32; Published in Advance October 26, 2010, doi:10.1101/gr.110593.110
...their bioactivity. Indeed, functional testing of the synthetic GIP isoforms (GIP, GIP55G, and GIP55S) in vivo showed that similar to conventional GIP, the extended GIP55G and GIP55S suppress hyperglycemia to similar extents in a time-dependent manner in fasting rats (Fig. 3C). The ancestral GIP55S and the derived...
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Method: Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation
- Pengfei Yu,
- Shu Xiao,
- Xiaoyun Xin,
- Chun-Xiao Song,
- Wei Huang,
- Darina McDee,
- Tetsuya Tanaka,
- Ting Wang,
- Chuan He,
- and Sheng Zhong
Genome Res. February 2013 23: 352-364; Published in Advance October 2, 2012, doi:10.1101/gr.144949.112
...time point (Fig. 1B). The sequencing reads from chromatin immunoprecipitation followed by sequencing (ChIPseq) experiments for each epigenetic modification on a genomic segment aremodeled with a Poisson distribution, with the Poisson parameter reflecting the cluster and time-dependent epigenomic state...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
.... pacificus strains. We used these data to study the evolutionary dynamics of different age classes and categories of origin at a population level. Contrasting de novo candidates with new families that arose by duplication and divergence from known genes, we find that de novo candidates are typically shorter...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...of the genes observed to be adjacent to these active enhancer marks were found to be implicated in SCN-enriched functions, including circadian entrainment, calcium signaling, and GABAergic synaptic function (Fig. 1F; Koronowski and Sassone-Corsi 2021; Morris et al. 2021). Furthermore, motif analysis on H3K27ac...
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