Searching journal content for articles similar to Bajic and Seah 13 (8): 1923.

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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...region and starts synthesizing RNA. The selection of transcription start sites (TSSs) plays a fundamental role in determining transcript diversity and gene expression patterns. Most gene loci harbor multiple TSSs, which are differentially regulated in response to cellular conditions, developmental cues...
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Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
- Vikram S. Shivakumar and
- Ben Langmead
Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
..., yielding an array called unique_threshold. Each value in unique_threshold is either 0, indicating no UM or MUM starts at that offset, or l > 0, indicating the match occurring at that offset will become nonunique at length l or shorter. Algorithm 1 describes and Figure 1A–D illustrates merging two...
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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
...the PDB helps predict putative rare driver events in lung tumors. By extending the analysis with high-quality structural models from AlphaFold using The Encyclopedia of Domains (TED), we find a significant increase in the diversity of both genes and functional families with postduplication FIEs in lung...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
...by an alternative 5′ transcription start site, the inclusion of previously unannotated exons, or alternative splicing events across the 11 Usher syndrome–associated genes. These findings have significant implications for genetic diagnostics and therapeutic development. The analysis applied here on Usher syndrome...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...primarily employed RNA sequencing(Jin et al. 2025), which, while 63 informative, does not fully elucidate the complex regulatory mechanisms underlying 64 transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a 65 spatiotemporal manner through precise gene regulatory...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...-molecule fluorescent in situ hybridization. We find that resilient ocular MNs regulate few genes in response to disease. Instead, they exhibit high baseline gene expression of neuroprotective factors, including En1, Pvalb, Cd63, and Gal, some of which vulnerable MNs upregulate during disease. Vulnerable MN groups...
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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
...correlated with gene expression, we further explored connections among features to determine any additional relationships (Supplemental Fig. S11). Nucleosome occupancy within the start of the gene body (+1/+2/+3 positions) was correlated with nucleosome occupancy changes near the PAS (R = 0.46), which...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...–10 bp repeat units. Melters et al. (2013) applied tandem repeat finder (TRF; Benson 1999) to Sanger reads and fragmented short-read contigs to find the most common monomer in each species. TAREAN (Novák et al. 2017) does all-versus-all comparison between short reads, clusters the reads...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
....24.0) (Wang et al. 2022) was used to annotate the location of the nested genes inside their host. A custom GTF file containing only the information about the host transcripts involved in host/nested gene pairs was used as a reference and a BED file containing the start and end coordinates of the nested genes...
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