Achromatium spp. are giant bacteria harboring hundreds of non-clonal chromosomes per cell. The allelic divergence they exhibit could be a mechanism to enable fine-tuned responses to environmental changes, enabling this organism to broaden its ecological range. However, while ubiquitous in freshwater and marine environm...
Sophie-Luise Heidig, Sunu Lama, Jeewan Babu Rijal et al.· Zenodo (CERN European Organi...· 0 citations
The escalating crisis of multi-drug resistant (MDR) Klebsiella pneumoniae (KP) renders standard antibiotic treatments increasingly ineffective, necessitating a shift toward alternative approaches like vaccination. However, the development of a broadly protective vaccine remains hindered by the pathogen's extensive sero...
Shuangjun He, Yang Zhang, Ahui Song et al.· Emerging Microbes and Infect...· 0 citations
This record contains the data and analysis code underlying the figures of the study Folding without glutamine: proteome-scale removal of a canonical amino acid. Using the Escherichia coli reference proteome as a test case, the work asks whether an entire canonical amino acid can be removed from every protein in a prote...
Alejandro Garcíarrubio, Blanca Ramos-Cerrillo, Enrique Morett et al.· Zenodo (CERN European Organi...· 0 citations
This work provides a conceptual and practical framework for targeting recoding-dependent gene products such as PEG10 in disease and suggests broader applicability of structure-directed ASOs to viral and cellular frameshifting elements.
Ondrej Kostov, Myriam Moreno Swanton, Katie R. Waldon et al.· bioRxiv· 0 citations
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Dynamic Topology Optimization (DTO) is a powerful technique for designing complex systems, particularly those exhibiting dynamic behavior, such as protein folding and cellular automata. Traditional topology optimization methods often rely on manually crafted constraints and iterative refinement, limiting their adaptabi...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
Protein folding prediction is a critical challenge in bioinformatics, demanding significant computational resources. This research explores the potential of quantum computing to accelerate and enhance this process. We formulate the protein folding problem as a quantum optimization problem, employing quantum simulation...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
The development of simple, bio-friendly strategies to engineer bright fluorescent proteins (FPs) is crucial for biosensing and bioimaging. Conventional synthesis of FPs requires time-consuming chromophore maturation and tedious preparation, while covalent conjugation methods often involve long reactions and risk loss...
Yi-Hui Lai, Gan Zhang, Zhen-Zhen Chen et al.· Analytical Chemistry· 0 citations
This paper presents a novel geometric simulation method, termed Wave Function Collapse (WFC), designed to model complex biological processes. Traditional computational methods often struggle to effectively represent the intricate dynamics of biological systems due to their inherent complexity. WFC utilizes quantum-insp...
Jincheng Zhang· Zenodo (CERN European Organi...· 0 citations
Overview This dataset contains residue-level biophysical measurements, translational kinetics profiles, and downstream mRNA thermodynamic stability metrics across 1,270 non-redundant human proteins (410,151 total residue observations). The dataset is designed to benchmark whether co-translational protein folding is pac...
Muhammad Saad Ul Hassan· Zenodo (CERN European Organi...· 0 citations
Overview This dataset contains residue-level biophysical measurements, translational kinetics profiles, and downstream mRNA thermodynamic stability metrics across 1,270 non-redundant human proteins (410,151 total residue observations). The dataset is designed to benchmark whether co-translational protein folding is pac...
Muhammad Saad Ul Hassan· Zenodo (CERN European Organi...· 0 citations
Achromatium spp. are giant bacteria harboring hundreds of non-clonal chromosomes per cell. The allelic divergence they exhibit could be a mechanism to enable fine-tuned responses to environmental changes, enabling this organism to broaden its ecological range. However, while ubiquitous in freshwater and marine environm...
Sophie-Luise Heidig, Sunu Lama, Jeewan Babu Rijal et al.· Zenodo (CERN European Organi...· 0 citations
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The contemporary definition of hydrocephalus is a disorder of cerebrospinal fluid (CSF) physiology producing active ventricular distension and neurological dysfunction, which is distinct from radiological ventriculomegaly alone. Once post-hemorrhagic ventriculomegaly (PHV) is established, the clinically decis...
Y. Lee, Solji Jung, K. Lee et al.· Journal of Korean Neurosurgi...· 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.
