Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data [0.03%]
Sean K Simmons,Xian Adiconis,Nathan Haywood et al.
Sean K Simmons et al.
Combining allele-specific expression (ASE) analysis with single-cell RNA-seq can elucidate how genomic variation affects RNA expression at the single-cell level. We explore how experimental and computational choices impact the power of ASE-...
DNA damaging properties of G-quadruplex ligand QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC [0.03%]
Garance Psalmon,Angélique Pipier,Manon Barbotte et al.
Garance Psalmon et al.
Background: QN-302 is a tetra-substituted naphthalene diimide (NDI) designed to bind G-quadruplex (G4) DNA and is in a phase 1 clinical trial for pancreatic ductal adenocarcinoma (PDAC) and other solid tumors. The mechani...
Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer [0.03%]
Benjamin P Berman,Sarah A Erdman,Christina Wheeler et al.
Benjamin P Berman et al.
Background: Altered circulating cell-free DNA (cfDNA) fragmentation patterns serve as cancer biomarkers, yet standard short-read sequencing fails to capture the full fragment-length spectrum. Although cancer patients ofte...
Allelic structural variation at the NLR25-1 locus enhances defense against Pseudomonas syringae in kiwifruit [0.03%]
Ying Wu,Yingzhen Wang,Yunzhi Lin et al.
Ying Wu et al.
Background: Canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) poses a major threat to cultivated kiwifruit, and utilization of wild relatives are key to improve resistance. However, comprehensive comparat...
Li-Ting Ku,Vincent Bernard,Jimin Min et al.
Li-Ting Ku et al.
Background: Cell-cell communication via ligand-receptor signaling is a fundamental mechanism shaping multicellular organization and functional heterogeneity within tissue microenvironments. Recent advances in spatial tran...
Transposable element-mediated evolutionary expansion of Sox2- and Brn2-binding regulatory modules for mammalian neural-cell differentiation [0.03%]
Hidenori Nishihara,Atsushi Komiya
Hidenori Nishihara
Background: In mammalian genomes, at least several thousand copies of transposable elements (TEs) may function as enhancers or promoters that regulate gene expression, cellular processes, and development. However, it is s...
Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome [0.03%]
Robert J M Eveleigh,Sarah J Reiling,Jose Hector Galvez et al.
Robert J M Eveleigh et al.
Background: Advances in sequencing technologies continue to improve the resolution and completeness with which human genetic variation can be characterized. Short-read sequencing remains widely used due to its high base a...
Sex and tissue resolved co-expression networks reveal a female placental-brain axis protective against prenatal PCB exposure [0.03%]
Kelly H Chau,Kari Neier,Anthony E Valenzuela et al.
Kelly H Chau et al.
Background: Neurodevelopmental disorders have a strong male bias that is poorly understood. The placenta provides molecular information about environmental interactions with genetics (including biological sex) that shape ...
Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus [0.03%]
Yue Hu,Yupeng Jia,Zhiquan Yang et al.
Yue Hu et al.
Background: Regulatory elements and their interactions underpin transciptional control and are essential for plant growth and development. Yet, in the allopolyploid crop Brassica napus, the global regulatory landscape and...
An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease [0.03%]
William Gao,Peng Hu,Brittney Wick et al.
William Gao et al.
Background: As the first organ to develop in utero, the human heart undergoes extensive molecular, structural and metabolic remodeling during development and must sustain its function throughout life. ...