Search · four archives
Search · four archives
14 papers · ranked by Valyu relevance
Sidong Qin, Zhihao Xu, Yongqiang Wang, Ziqi Wang + 8 more
C-to-U RNA editing is a pervasive phenomenon in crop mitochondria, playing a pivotal role in the processing of functional proteins encoded by mitochondrial genes and serving as a crucial regulatory mechanism for nuclear control over mitochondrial gene expression. However, identifying editing sites across the…
Anja Adamov, Christian L. Müller, Nicholas A. Bokulich
Microbiome sequencing datasets are sparse, high-dimensional, compositional, and hierarchically structured. Predictive modelling from these data typically relies on ad hoc choices of feature representation, obscuring their impact on performance and biological interpretation. A standardized, compute-efficient framework…
Rajarshi SinhaRoy, Christian Clauß, Ivan Ivanikov, Georg Künze
Enzyme activity and stability are strongly modulated by pH, making the catalytic pH optimum (pH _opt_) a key parameter in enzyme development and biotechnological applications. Experimental determination of pH _opt_ is, however, labor-intensive and time-consuming, motivating the development of accurate computational…
Xuelei Wang, Jana Zweerings, Michael Lührs, Fengyu Cong + 5 more
Identifying informative voxels is a critical, yet challenging step in functional magnetic resonance imaging (fMRI), particularly for multivariate analyses involving multiple related conditions. Existing approaches often rely on predefined regions of interest (ROIs) or activation-based criteria, which may be…
Zhiqian Zhai, Changhu Wang, Chengfeng Jiang, Ziqi Rong + 1 more
Integrating single-cell and spatial transcriptomics data across batches is essential for recovering comparable cell identities—including cell types, subtypes, and states—as a prerequisite for downstream analyses in multi-condition and large-scale studies. This task remains challenging because between-batch variation…
Sumedh S Nagrale, Alik S Widge
The use of Deep Brain Stimulation (DBS) on the ventral capsule/ventral striatum (VCVS) has therapeutic potential for patients with refractory psychiatric disorders, but clinical success is impeded by the need for a time-consuming and trial-and-error process when setting the parameters, this process relying on…
Muhammad Muneeb, David B. Ascher
Polygenic risk score (PRS) tools differ substantially in statistical assumptions, input requirements, and implementation complexity, making direct comparison difficult. We developed a harmonized, implementation-aware benchmarking framework to evaluate 46 PRS tools across seven binary UK Biobank phenotypes and one…
Arif Yelği, Shirmohammad Tavangari, Zahra Shakarami, Sajjad Janfaza
Accurate epigenetic age prediction from DNA methylation profiles is intrinsically high-dimensional, creating a need for parsimonious models that preserve predictive performance while reducing the number of assayed cytosine-phosphate-guanine (CpG) loci. This study introduces MOSurvivor, a population-based…
Edward Ma, James Morrissey, Shutong Duan, Ziqi Lu + 10 more
Process optimization for Chinese hamster ovary (CHO) cell culture remains a challenge in biopharmaceutical development because multiple interacting parameters jointly influence productivity and product quality attributes. Traditional design-of-experiments (DoE) methods, while systematic, become impractically expensive…
Andrea Polo-Rodríguez, David R. Penas, Julio R. Banga
Parameter estimation is a central challenge in systems biology, particularly for large dynamic models described by nonlinear ordinary differential equations (ODEs). These global optimization problems exhibit landscapes which are topologically heterogeneous, often exhibiting a pathological mixture of stiff, smooth…
Viraj Doshi, Malhar Bhide, Akshat Singh, Yash Rathod + 1 more
Gene-therapy design depends on identifying regulatory sequences that drive the right level, timing, and cell-type specificity of expression. Regulatory DNA models offer a way to prioritize such sequences computationally before committing candidates to biological testing. Biological validation involves DNA synthesis…
Stephan Grein, David R. Penas, Daniel Weindl, Polina Lakrisenko + 2 more
Dynamic models are central to the computational life sciences but typically contain unknown parameters that must be inferred from experimental data. High-throughput measurements have made this task increasingly challenging, yielding high-dimensional search spaces and non-convex objectives with many local optima. This…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…
Carlos Martínez, Facundo Rocha Calvette, Marielle Péré, Mauricio Barrientos + 1 more
A hybrid model combines a mechanistic model, described by ordinary differential equations, with a data-driven component, such as neural networks. This strategy leverages both the physical knowledge of the system and the predictive power of machine learning methods, and it has been applied to a variety of bioprocesses.…