Searching journal content for articles similar to Casey et al..

Displaying results 1-10 of 6109

For checked items

view abstracts
download to citation manager

Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
OPEN ACCESS ARTICLE
Select this article
Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...Science and Technology of China, Quzhou 324000, Zhejiang, China; 3College of Biomedical Engineering, Sichuan University, Chengdu 610041, Sichuan, China Corresponding author: luoximei@uestc.edu.cnAbstractDNA N4-methylcytosine (4mC), a key epigenetic modification regulating DNA repair and replication...
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
...of the complex relationship between chromatin organization and transcription.Every eukaryotic encodes the information necessary for cellular viability and growth. Although the underlying instructions embedded in the DNA are identical among the cells of an organism, complex regulatory mechanisms transform...
Select this article
Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
...of genetic information. In diverse research contexts, investigators aim to uncover patterns within DNA sequences, a pursuit central to various applications. Among the most prominent of these is the study of transcription factor (TF) DNA-binding specificity. Researchers employ methods like SELEX-seq (Kinzler...
OPEN ACCESS ARTICLE
Select this article
Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...functional domains: the N-terminal DNA-binding domain (HD) and the C-terminal transcription effector domain. Disease-associated mutations are distributed across both domains, with amino acid substitutions primarily observed in the CRX HD (Tran and Chen 2014; Zheng and Chen 2024). To understand how HD...
OPEN ACCESS ARTICLE
Select this article
Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...integrated analyses of single-cell RNA-seq data from multiple human tissues and organs. Single-cell epigenomic data further indicate that the expression is likely driven by an alternative promoter at the end of the first exon, resulting in at least one shorter transcript (referred to as sXIST) that is active...
OPEN ACCESS ARTICLE
Select this article
Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...24 0 to 8 hours) integrates over 250 paired transcriptome and proteome measurements. We 25 observe upregulation of known DNA repair proteins as well as a global dynamic response of 26 not yet characterized transcripts and proteins. Using artificial neural networks, we classify 27 different expression...
- Abstract
- Full Text (PDF)
ACCEPTED MANUSCRIPT
Select this article
LETTER: The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis
- Valérie Ledent and
- Michel Vervoort
Genome Res. May 1, 2001 11: 754-770; doi:10.1101/gr.177001
..., determination, and differentiation ( Jan and Jan 1993 ; Weintraub 1993 ; Hassan and Bellen 2000 ). The bHLH domain is ∼60 amino acids long and comprises a DNA-binding basic region (b) followed by two α-helices separated by a variable loop region (HLH) ( Ferre-D'Amar et al. 1993 ). The HLH domain promotes...
Select this article
Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...) and thyroid hormone receptor (THR) proteins directly compete for binding to response elements involved in regulating lipid metabolism, cell growth, and differentiation (Miyamoto et al. 1997). In fungi, a well-known example of competitive TF-DNA binding is that of Saccharomyces cerevisiae basic helix-loop-helix...
OPEN ACCESS ARTICLE
Select this article
Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...for their ability to integrate high-dimensional features have recently been applied to the field of liquid biopsy. In this review, we highlight various AI and ML approaches in cfDNA-based diagnostics. We first introduce the biology of cell-free DNA and basic concepts of ML and AI technologies. We then discuss...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Casey et al..

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: