Results 141 to 150 of about 1,301,283 (332)

RiboDiffusion: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models [PDF]

arXiv
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural constraints, known as the inverse folding problem.
arxiv  

Inhibitor of DNA binding‐1 is a key regulator of cancer cell vasculogenic mimicry

Molecular Oncology, EarlyView.
Elevated expression of transcriptional regulator inhibitor of DNA binding 1 (ID1) promoted cancer cell‐mediated vasculogenic mimicry (VM) through regulation of pro‐angiogenic and pro‐cancerous genes (e.g. VE‐cadherin (CDH5), TIE2, MMP9, DKK1). Higher ID1 expression also increased metastases to the lung and the liver.
Emma J. Thompson, Emma L. Dorward, Kristyn Jurrius, Nathalie Nataren, Markus Tondl, Kay K. Myo Min, Michaelia P. Cockshell, Anahita Fouladzadeh, John Toubia, Mark DeNichilo, Delphine Merino, Claudine S. Bonder   +11 more
wiley   +1 more source

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

Genomics, Proteomics & Bioinformatics, 2017
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to
Meiling Piao, Lei Sun, Qiangfeng Cliff Zhang   +2 more
doaj  

RiboFlow: Conditional De Novo RNA Sequence-Structure Co-Design via Synergistic Flow Matching [PDF]

arXiv
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing RNA's conformational flexibility, ensuring structural validity, and overcoming data scarcity.
arxiv  

Detecting homologous recombination deficiency for breast cancer through integrative analysis of genomic data

Molecular Oncology, EarlyView.
This study develops a semi‐supervised classifier integrating multi‐genomic data (1404 training/5893 validation samples) to improve homologous recombination deficiency (HRD) detection in breast cancer. Our method demonstrates prognostic value and predicts chemotherapy/PARP inhibitor sensitivity in HRD+ tumours.
Rong Zhu, Katherine Eason, Suet‐Feung Chin, Paul A. W. Edwards, Raquel Manzano Garcia, Richard Moulange, Jia Wern Pan, Soo Hwang Teo, Sach Mukherjee, Maurizio Callari, Carlos Caldas, Stephen‐John Sammut, Oscar M. Rueda   +12 more
wiley   +1 more source

Regulation of coronavirus nsp15 cleavage specificity by RNA structure. [PDF]

PLoS One, 2023
Salukhe I, Choi R, Van Voorhis W, Barrett L, Hyde J.   +4 more
europepmc   +2 more sources

Understanding and measuring mechanical signals in the tumor stroma

FEBS Open Bio, EarlyView.
This review discusses cancer‐associated fibroblast subtypes and their functions, particularly in relation to extracellular matrix production, as well as the development of 3D models to study tumor stroma mechanics in vitro. Several quantitative techniques to measure tissue mechanical properties are also described, to emphasize the diagnostic and ...
Fàtima de la Jara Ortiz, Chiara Cimmino, Maurizio Ventre, Alessandra Cambi   +3 more
wiley   +1 more source

HDAC4 regulates apoptosis in Acan‐CreERT2;HDAC4d/d mice with osteoarthritis by downregulating ATF4

FEBS Open Bio, EarlyView.
Using the AcanCreERT2;HDAC4fl/fl genetic mouse model, we further investigated the role of histone deacetylase 4 (HDAC4) in chondrocyte apoptosis. We found that knocking down HDAC4 may be associated with chondrocyte apoptosis by upregulating the activating transcription factor 4 (ATF4)/CAAT/enhancer binding protein homologous (CHOP) signaling pathway ...
Jingrui Huang, Yukun Xu, Yujia Li, Yiming Pang, Xueting Ding, Raorao Zhou, Dan Liang, Xianda Che, Yuanyu Zhang, Chunfang Wang, Wenjin Li, Pengcui Li   +11 more
wiley   +1 more source

Prediction of RNA Secondary Structure [PDF]

, 1971
Charles DeLisi, Donald M. Crothers
openalex   +1 more source

Comparative activity of dimethyl fumarate derivative IDMF in three models relevant to multiple sclerosis and psoriasis

FEBS Open Bio, EarlyView.
IDMF is a derivative of dimethyl fumarate (DMF) with a unique therapeutic potential at the intersection of psoriasis and multiple sclerosis. Here, we demonstrate that it compares favorably with DMF and its other derivatives, such as Diroximel, in the zebrafish, microglia, and lymphocyte models.
Yulin He, Guiyi Gong, Geovani Quijas, Simon Ming‐Yuen Lee, Ratan K. Chaudhuri, Krzysztof Bojanowski   +5 more
wiley   +1 more source