Results 131 to 140 of about 2,360,372 (228)

SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data. [PDF]

BMC Bioinformatics
Zhu H, Liu T, Shrestha B, Wang Z.
europepmc   +1 more source

Haplotype‐Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine

Advanced Science, EarlyView.
This study presents a haplotype‐resolved 3D genomic landscape of grapevine, revealing that structural variations (SVs) are closely associated with phased topologically associating domain (TAD) boundary transitions. These rearrangements coordinate with allele‐specific DNA methylation (ASM) and allele‐biased gene expression (ASE) to shape key agronomic ...
Yanling Peng, Lianzhu Zhou, Xinyue Fang, Ruoyan Zhao, Qi Xu, Mengrui Du, Ting Hou, Guizhou Huang, Yingchun Zhang, Sheng Yan, Ruo Yang, Zhongxin Jin, Yang Dong, Yanshuai Xu, Hua Xiao, Xiaodong Xu, Yi Liao, Xiping Wang, Yongfeng Zhou   +18 more
wiley   +1 more source

SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing. [PDF]

Bioinformatics
Huang J, Ma R, Strobel M, Hu Y, Ye T, Jiang T, Ma W.   +6 more
europepmc   +1 more source

Stress History Establishes a Transient Tolerant State That Shapes Antibiotic Survival Upon Resuscitation

Advanced Science, EarlyView.
High‐throughput single‐cell analysis of resuscitating bacteria reveals a starvation‐history‐dependent transiently tolerant subpopulation that survives β$\beta$‐lactam exposure by temporarily reducing growth. Distinct from classical persisters, these actively growing yet dynamically modulated cells dominate survival across clinically relevant antibiotic
Kieran Abbott, Georgeos Hardo, Ruizhe Li, Jack Bradley, Ashraf Zarkan, Somenath Bakshi   +5 more
wiley   +1 more source

Integrating Hi-C data and RNA-seq data to reveal the 3D genome in sheep. [PDF]

BMC Genomics
Xu Q, Zhang X, Li F, Tian H, Zhang D, Huang K, Zhang Y, Zhao Y, Li X, Zhao L, Cheng J, Xu D, Ma Z, Yang X, Weng X, Wang W.   +15 more
europepmc   +1 more source

Two Routes to Land: Genomic Underpinnings of Parallel Aerial Egg Deposition in Aquatic Old‐World Pila and New‐World Pomacea (Ampullariidae)

Advanced Science, EarlyView.
Comparative genomics of Gondwana‐diverged Pila and Pomacea reveals parallel evolution of aerial oviposition. Convergent chromosomal rearrangements reshape regulatory landscapes within topologically associating domains. Lineage‐specific gene family expansions and viral‐derived perivitelline proteins (PV1) underpin desiccation resistance.
Yufei Zhou, Huawei Mu, Xueying Nie, Yue Gao, Hui Wang, Ling Fang, Tiangang Luan, Monthon Ganmanee, Jian‐Wen Qiu, Jin Sun, Jack Chi‐Ho Ip   +10 more
wiley   +1 more source

EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data. [PDF]

Commun Biol
Chowdhury HMAM, Oluwadare O.
europepmc   +1 more source

The BnTFL1‐BnJAM3‐BnSWEETs Module Orchestrates Seed Storage Reserve Accumulation in Brassica napus

Advanced Science, EarlyView.
BnaC03.TFL1 and BnaA01.JAM3 form a complex that facilitates the transport of soluble sugars from the seed coat to the embryo by directly activating the expression of BnSWEETs. Furthermore, BnaC03.TFL1 and BnaA01.JAM3 work cooperatively to promote soluble sugar and oil production while suppressing protein deposition.
Jianjun Wang, Zijin Liu, Minshan Jin, Junting Liu, Shihao Wei, Dengmao Yang, Saiqi Yang, Yuan Guo, Mingxun Chen   +8 more
wiley   +1 more source

HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data. [PDF]

Brief Bioinform
Shrestha B, Wang Z.
europepmc   +1 more source

The Trichinella Super‐Pangenome Reveals the Evolution of Encapsulation and Predicted Host–Parasite Protein Interactions

Advanced Science, EarlyView.
ABSTRACT The muscle capsule of Trichinella is a critical structure that impedes immune attacks and drug penetration, yet the molecular mechanisms underlying its formation remain poorly understood. Using a high‐quality super‐pangenome comprising 12 Trichinella species, we compared extensive genomic variations between encapsulating and non‐encapsulating ...
Qingbo Lv, Yi Liu, Ning Xu, Xiao Zhang, Yaming Yang, Chengyao Li, Hanhai Mao, Mingyuan Liu, Xiaolei Liu   +8 more
wiley   +1 more source