Aging is associated with a decline in blood-brain barrier (BBB) integrity. Interestingly, recent reports suggest that females may be more resistant to BBB disruption than males. Using a robust model of hypoxia-induced BBB disruption, we exposed aged (20 months) male and female mice to chronic mild hypoxia (CMH; 8% O 2...
Arjun Sapkota, Sebok K. Halder, Alexis Garduno et al.· Fluids and Barriers of the C...· 0 citations
This paper explores the development of novel algorithmic complexity metrics specifically tailored for analyzing the computational demands of biological systems, including protein folding, gene regulation, and cellular signaling pathways. Traditional complexity measures often lack the nuanced understanding required to e...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
This paper explores the development of novel algorithmic complexity metrics specifically tailored for analyzing the computational demands of biological systems, including protein folding, gene regulation, and cellular signaling pathways. Traditional complexity measures often lack the nuanced understanding required to e...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
The ER-α36 isoform is expressed in both ER-positive and ER-negative breast cancer cell lines. ER-α36 is implicated in promoting the proliferation, invasion, and metastasis of tumor cells. Runt-related transcription factor 2 (RUNX2) is widely recognized as a driver of bone-specific metastasis in breast cancer. The study...
Jia Sun, Xin Guan, Hongyan Li et al.· Steroids· 0 citations
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Protein folding, the process by which a polypeptide chain attains its functional three-dimensional structure, is a fundamental problem in biochemistry and bioinformatics. Traditional approaches to predicting protein folding pathways have faced significant challenges due to the complex, high-dimensional nature of the un...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
“Undruggable” proteins without surface-accessible binding sites pose significant challenges to target-based drug discovery. Innovative approaches are needed to tackle these proteins. One promising strategy is targeting them in their nascent chain form at the ribosome, where they have a different conformation than in th...
P. Fischer, Sebastian Hiller· bioRxiv· 0 citations
Evolution ONE is a standalone, vendor‑neutral platform that models cancer progression through the lens of Self‑Organised Criticality (SOC), duon biology, and physics‑based structural refinement. It ingests genomic mutation data (MAF, VCF) and outputs a complete oncological profile: the evolutionary regime of the tumour...
Mr.PAI And Mrs.Yoon A (Mei Mei) (美美) / Yoon A Limsuwan· Zenodo (CERN European Organi...· 0 citations
It is shown that HSPD1 depletion in MYCN-amplified NB cells led to reduced mitochondrial translation, MYCN expression, and tumorigenesis in vitro and in vivo and establishes HSPD1 as a promising target for the treatment of MYCN-amplified NB.
Shatha S. Alassam, Dinesh Babu Manikandan, Hila Ben-David et al.· bioRxiv· 0 citations
Dynamic Topology Optimization (DTO) is a powerful tool for designing complex systems, such as neural networks and protein folding, by iteratively refining the topology to meet specific requirements. Traditional DTO methods often rely on static parameters, limiting the system's adaptability and potentially hindering the...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
Yarrowia lipolytica is a promising industrial host, yet its metabolic engineering potential remains limited by insufficient genetic tools. Here, we engineered a synthetic Transcription Activation Toolkit (TAT) based on LacI–VPRH, a chimeric protein fusing the prokaryotic DNA-binding domain LacI with the eukaryotic ac...
Yunhe Li, Wen-Ping Wei, Ping Zhang et al.· Journal of Agricultural and...· 0 citations
This paper introduces a novel adaptive multi-dynamics simulation framework designed to model complex biological systems and optimize biological engineering design through automated parameter adjustment based on simulation results. Traditional multi-dynamics simulations often require extensive manual parameter tuning, h...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
First version submitted to Bioconductor. NADIA covers the differential abundance analysis of protein quantification data from the raw report to the figure, treating the missing values that dominate data-independent acquisition as the central problem rather than a nuisance to be filtered away. Reports from Spectronaut,...
Sergio Ciordia· Zenodo (CERN European Organi...· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
