Searching journal content for articles similar to Salari et al. 32 (1): 28.

Displaying results 1-10 of 5953

For checked items

view abstracts
download to citation manager

Select this article
Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., modeling 3D chromatin organization, and predicting gene expression (Thibodeau et al. 2021; Karbalayghareh et al. 2022; Tan et al. 2023; Zhang et al. 2023; Grover et al. 2024). Although experimental assays such as FAIRE-seq (Giresi et al. 2007), DNase-seq (Song and Crawford 2010), and ATAC-seq (Buenrostro...
OPEN ACCESS ARTICLE
Select this article
Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
..., coinciding with a loss of spatial compartmentalization and radial positioning of the 3D . Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on Chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on Chromosome 10. This insertion...
Select this article
Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...the accumulation of alleles involved in speciation (Filatov 2018). Finally, fusions could alter the spatial arrangement of chromatin, consequently impacting the gene expression and recombination landscape (Gibcus and Dekker 2013; Vara et al. 2021).Here, we report chromosome-level s of three economically important...
Select this article
Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...(stripe anchor) and a continuum of genomic regions (Banigan et al. 2020). For example, chromatin stripes may be based on CTCF/cohesin loops, in which multiple genomic sites that lie far apart linearly are brought into spatial proximity to a distal single locus by loop extrusion. At the bulk...
OPEN ACCESS ARTICLE
Select this article
Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...using a BD FACS Melody with the following channels: 405 nm laser, 448/45 bandpass filter; 488 nm laser, 488/15 bandpass filter; 561 nm laser, 605LP dichroic mirror, 613/18 filter. After sorting, cells were pelleted by centrifugation, flash-frozen in liquid N2, and stored at −80°C until Hi-C library...
OPEN ACCESS ARTICLE
Select this article
Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
..., yet the chromatin changes driving this decline remain unclear. Polycomb-mediated repression is essential for silencing developmental genes, but this regulatory mechanism becomes dysregulated with age. Although shifts in Polycomb regulation within intestinal stem cells have been linked to gut aging...
OPEN ACCESS ARTICLE
Select this article
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
...owing to low differential expression. Because chromatin features can also highlight the mechanistic context of transcriptional regulation, we extended our chromatin TRN by employing a spatial layout to represent changes in nucleosome (y-axis) and TF (x-axis) occupancy (Fig. 7C). This allows us...
Select this article
Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...on conservation alone is limited. Therefore, we integrated multiple data sets to functionally annotate the top 60 modules of the network by performing enrichment analyses. This included overrepresentation of protein domains (Mistry et al. 2021), regionally enriched genes as identified from spatial transcriptomics...
Select this article
Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...to the DNA repair mechanisms, including base excision repair, which are particularly active in early-replicating regions consisting of open chromatin (Amouroux et al. 2010; Rhind and Gilbert 2013). Further, the A3A-associated mutation rate in the lagging strand of DNA replication was 1.26-fold higher...
OPEN ACCESS ARTICLE
Select this article
Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
..., enabling a detailed analysis of their transcriptome, chromatin landscapes, and replication timing dynamics. This approach uncovered previously unrecognized chromosome-specific differences in chromatin regulation between GSCs and CySCs, shedding new light on the molecular mechanisms regulating stem...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Salari et al. 32 (1): 28.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: