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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
..., this is aided and abetted by new standards of encoding methylation information directly into the alignment files (BAMs) as sequence tags.LRS is changing the landscape of molecular diagnosticsMolecular diagnosis is crucial for managing genetic diseases, offering confirmation, specialized care, risk...
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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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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
...to ABCA7 dysfunction and posed a risk for Alzheimer's disease (De Roeck et al. 2018). Although these scattered studies have reported splicing-associated TRs (spl-TRs) and provided a glance at the potential mechanism and relevance to disease, no large-scale study on this issue has been conducted. Here, we...
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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
...from patients with Parkinson's disease and healthy individuals, in order to investigate whether diagnosis status influenced our findings, we repeated the association analysis separately in patients (n = 362) and controls (n = 117) and observed that 99.9% of the validated STR:CpG associations retained...
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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
...healthy individuals. Identifying these determinants may give insights into disease risk or progression and could improve population-genetic models of mutations. Recombinant inbred strains such as those in the BXD family have accumulated mutations over dozens of generations of inbreeding, offering a unique...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
..., Massachusetts 02115, USA Corresponding author: gary.churchill@jax.orgAbstractInvestigation of the molecular mechanisms of aging in the human heart is challenging because of confounding factors, such as diet and medications, as well as limited access to tissues from healthy aging individuals. The laboratory...
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Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...as those with the highest 5% of PRSs, whereas low-risk individuals were identified as those with the lowest 5% of PRSs. High-risk individuals defined by PRS-Net exhibited an elevated risk of disease throughout their lifetime compared with those predicted by baseline methods, especially for UC, asthma, RA...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...between circRNA expression changes and disease status at the system level, we performed the weighted gene coexpression network analysis (WGCNA) to assign individual circRNAs to coexpression modules according to the 1060 circRNAs identified in the 134 cortex samples. As shown in Figure 2A, we identified 14...
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Research: Genome-wide analysis of differential RNA editing in epilepsy
- Prashant Kumar Srivastava,
- Marta Bagnati,
- Andree Delahaye-Duriez,
- Jeong-Hun Ko,
- Maxime Rotival,
- Sarah R. Langley,
- Kirill Shkura,
- Manuela Mazzuferi,
- Bénédicte Danis,
- Jonathan van Eyll,
- Patrik Foerch,
- Jacques Behmoaras,
- Rafal M. Kaminski,
- Enrico Petretto,
- and Michael R. Johnson
Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
...of genetic information through RNA editing contributes to proteomic diversity, but the extent and significance of RNA editing in disease is poorly understood. In particular, few studies have investigated the relationship between RNA editing and disease at a -wide level. Here, we developed a framework...
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Resource: A genome-wide interactome of DNA-associated proteins in the human liver
- Ryne C. Ramaker,
- Daniel Savic,
- Andrew A. Hardigan,
- Kimberly Newberry,
- Gregory M. Cooper,
- Richard M. Myers,
- and Sara J. Cooper
Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117
...–660. Ingham PW, Nakano Y, Seger C. 2011. Mechanisms and functions of Hedgehog signalling across the metazoa. Nat Rev Genet 12: 393–406. Johnson DS, Mortazavi A, Myers RM. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497–1503. Kaiser VB, Taylor MS, Semple CA. 2016. Mutational...

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