Results 131 to 140 of about 334,258 (285)

Roast: a tool for reference-free optimization of supertranscriptome assemblies

BMC Bioinformatics
Background Transcriptomic studies involving organisms for which reference genomes are not available typically start by generating de novo transcriptome or supertranscriptome assembly from the raw RNA-seq reads. Assembling a supertranscriptome is, however,
Madiha Shabbir, Aziz Mithani
doaj   +1 more source

Genetic Control of Tissue Remodeling by a Non‐Coding SNP in ITGA8 Explains Carotenoid‐Based Color Polymorphism in Marine Mollusks

Advanced Science, EarlyView.
In this study, the orange‐muscle giant abalone (Haliotis gigantea) is used as a model to identify a non‐coding SNP that disrupts the interaction between ITGA8 pre‐mRNA and the splicing factor ILF2, leading to altered ITGA8 splicing. These splicing changes promote carotenoid accumulation in abalone muscle through the regulation of tissue remodeling ...
Xiaohui Wei, Wenzhu Peng, Zekun Huang, Bingye Yang, Yiyu Wu, Minzhen Han, Yi Wang, Bingling Peng, Guosheng Hu, Jiawei Hong, Guijia Liu, Linwei Nie, Yang Gan, Miaoqin Huang, Xuan Luo, Weiwei You, Wen Liu, Caihuan Ke   +17 more
wiley   +1 more source

Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation

eLife
Styxl2, a poorly characterized pseudophosphatase, was identified as a transcriptional target of the Jak1-Stat1 pathway during myoblast differentiation in culture. Styxl2 is specifically expressed in vertebrate striated muscles.
Xianwei Chen, Yanfeng Li, Jin Xu, Yong Cui, Qian Wu, Haidi Yin, Yuying Li, Chuan Gao, Liwen Jiang, Huating Wang, Zilong Wen, Zhongping Yao, Zhenguo Wu   +12 more
doaj   +1 more source

Integrating Spatial Proteogenomics in Cancer Research

Advanced Science, EarlyView.
Xx xx. ABSTRACT Background: Spatial proteogenomics marks a paradigm shift in oncology by integrating molecular analysis with spatial information from both spatial proteomics and other data modalities (e.g., spatial transcriptomics), thereby unveiling tumor heterogeneity and dynamic changes in the microenvironment.
Yida Wang, Yang Wu, Feng Zhang, Parthiban Periasamy, Haiyue You, Denise Goh, Rachel Elizabeth Ann Fincham, Xin Ning, Danping Wu, Lu Liu, Ying Jiang, Zhiwen Qian, Joe Yeong, Yan Zhang   +13 more
wiley   +1 more source

Plant Genetic Engineering: Technological Pathways, Application Scenarios, and Future Directions

Advanced Science, EarlyView.
This review maps the fast‐evolving landscape of plant genetic engineering, linking enabling platforms with trait‐focused applications in architecture optimization, stress resilience, yield improvement, and quality enhancement. It highlights how genome editing, transgenic strategies, and emerging multi‐gene approaches reshape breeding pipelines, while ...
Peilin Wang, Wenzhi Wang, Dongjiao Wang, Qibin Wu, Youxiong Que   +4 more
wiley   +1 more source

Ammonia Detoxification Inhibits Liver Metastasis by Reshaping Hepatic Microenvironment

Advanced Science, EarlyView.
Liver metastasis diverts aspartate into hyperactive pyrimidine synthesis, disrupting urea cycling and causing pathogenic ammonia accumulation. Ammonia dually reprograms the microenvironment by: (1) activating hepatic stellate cells (HSCs) into pro‐fibrotic metastasis‐associated fibroblasts (MAFs), and (2) suppressing anti‐tumor monocytes/macrophages ...
Sumin Sun, Haili Hu, Long Chen, Yuan Gao, Peng Sun, Liming Chen   +5 more
wiley   +1 more source

Endoplasmic Reticulum Geometry Dictates Neuronal Bursting via Calcium Store Refill Rates and Exposes Selective Neuronal Vulnerability

Advanced Science, EarlyView.
The ER's continuous tubular network is maintained by ER‐shaping proteins whose mutation or dysregulation contributes to neurodegenerative diseases. Here, we show that ER morphology sets the speed of Ca2+ store replenishment between firing events. Disrupting ER continuity slows intra‐ER Ca2+ redistribution from extracellular refill (SOCE) sites, driving
Valentina Davi, Pierre Parutto, Yuyi Zhang, Tasuku Konno, Cecile Crapart, Raquel Pereira, John P. Franklin, Mosab Ali Awadelkareem, Daniel C Maddison, Michael J. Devine, Edgar R. Gomes, Joseph Chambers, Elena Koslover, Edward Avezov   +13 more
wiley   +1 more source

Chemically Engineered L. reuteri Delivering αPD‐L1 and Gallium Ions via Metal‐Phenolic Networks Potentiate Anti‐Tumor Immunity and Ferroptosis

Advanced Science, EarlyView.
A multifaceted chemical strategy, integrating bacterial tropism, metal‐ion interference therapy, and immunotherapy, resulted in significant tumor regression in murine models. A pioneering paradigm for the design of biohybrid materials was established, highlighting how sophisticated chemical engineering of living systems can unlock new avenues for ...
Tingting Zhang, Mengyi Xu, Yan Zhang, Zhiwen Li, Danqing Song, Jing Pang, Ke Li, Yanxiang Wang   +7 more
wiley   +1 more source

De novo transcriptome assembly

, 2015
In this thesis, a de novo transcriptome assembler was implemented based on the overlap-layout-consensus paradigm. It was written in the C++ programming language and was named Ra which is short for RNA assembler. Its overlap phase relies on the enhanced suffix arrays and reproduces exact overlaps between input reads.
openaire   +1 more source

Dose‐Dependent Reprogramming of Chromatin Accessibility by SOX4 Drives the Transcriptional Response to Iron Overload

Advanced Science, EarlyView.
This study demonstrates that iron overload triggers widespread chromatin compaction and transcriptional repression in human granulosa cells, recapitulating features of endometriosis. The epigenetic reprogramming is orchestrated by a TFEB‐SOX4‐SWI/SNF axis, with SOX4 acting as a central, dosage‐sensitive regulator.
Feifei Li, Yaoqiu Wu, Guangyu Yang, Jingyi Lai, Xiaoyue Sun, Liyan Wang, Xiaoli Li, Jing Zhang, Qingxue Zhang, Hui Chen, Haiyan Lin, Bingxiang Xu, Junfeng Zhang, Hailong Wang, Anming Meng, Chunwei Cao   +15 more
wiley   +1 more source