Searching journal content for articles similar to Kumar et al. 26 (5): 612.

Displaying results 1-10 of 5899

For checked items

view abstracts
download to citation manager

Select this article
Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...integrative analysis of publicly available ChIP-seq data reveals distinct cofactor landscapes at ERBS subgroups.ERBS groups are associated with distinct long-range chromatin looping featuresERBS are mostly found at putative enhancer regions rather than promoters (Carroll et al. 2005). As estrogen stimulation...
Select this article
Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...overlapping ranges for signature scores across B cells (Fig. 2A).View larger version: In this window In a new window Figure 2. Comparative analysis of scoring methods for cell-type and cell-state annotation. Only nonoverlapping cell-type- or cell-state-specific signatures were used. (A) Score distributions...
OPEN ACCESS ARTICLE
Select this article
Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...targets and tagmentation (CUT&Tag) to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages, and investigated how SEs influence skeletal muscle development. We identify three SE families with distinct temporal dynamics...
Select this article
Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...at cis-regulatory elements (Lago et al. 2021; Shen et al. 2021; Spiegel et al. 2021; Georgakopoulos-Soares et al. 2022a,d), including in promoters, enhancers, and CTCF binding sites, whereas in higher eukaryotes, they have also emerged in proximity to splice sites to modulate alternative splicing...
OPEN ACCESS ARTICLE
Select this article
Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...analyses of protozoa and fungi within more than 1000 rumen metas, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi...
Select this article
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
...152 in the microglia dataset. We observed a significant enrichment of upregulated DEGs in these 153 signatures (Fig. 2D), and signature scores displayed a clear trend of increasing expression with 154 age (Fig. 2E). 155 Functional enrichment analysis of age-associated DEGs revealed that upregulated...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...other species, enhancers are distinguished from promoters based on enrichment of distinct and conserved histone modifications, including H3K27 acetylation and H3K4 methylation (Evans et al. 2016; Daugherty et al. 2017). Mapping enhancer chromatin features and analyses of individual genes suggest...
Select this article
Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...in Chr 15 that was assigned two distinct SV types (DUP and INS), and thus cataloged as missing according to the benchmark by Valle-Inclan et al. Manual inspection in IGV showed the SV. Notice that these alignments contain mapping artifacts in the ONT samples.We compared these 49 SVs to a previously...
Select this article
Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...for dimensionality reduction to these one-hot encoded spike-in sequences revealed approximately 16 major clusters (Fig. 2C), each with well-defined outlines. This distinct clustering pattern is directly attributable to the inherent design of the spike-ins: each 50-nt spike-in sequence is fixed except for eight...
Select this article
Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...with functional genomics data from human embryonic stem cells 132 (hESCs) that have undergone directed differentiation to represent distinct endoderm cell 133 populations along the anterior-posterior axis. 134 135 7 Results 136 ATAC-seq reveals CRMs functioning in distinct sox17-expressing lineages during...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kumar et al. 26 (5): 612.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: