定量生物学
Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…
The neural coding is yet to be discovered. The neuronal operational modes that arise with fixed inputs but with varying degrees of stimulation help to elucidate their coding properties. In neurons receiving {\it in vivo} stimulation, we…
Transformers have revolutionized nucleotide sequence analysis, yet capturing long-range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length…
Template-based molecular generation offers a promising avenue for drug design by ensuring generated compounds are synthetically accessible through predefined reaction templates and building blocks. In this work, we tackle three core…
Identifying evolutionary correspondences between cell types across species is a fundamental challenge in comparative genomics and evolutionary biology. Existing approaches often rely on either reference-based matching, which imposes…
Molecular discovery has brought great benefits to the chemical industry. Various molecule design techniques are developed to identify molecules with desirable properties. Traditional optimization methods, such as genetic algorithms,…
In this methods article, we provide a flexible but easy-to-use implementation of Direct Coupling Analysis (DCA) based on Boltzmann machine learning, together with a tutorial on how to use it. The package \texttt{adabmDCA 2.0} is available…
Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research…
Past work has reported inverted-U relationships between arousal and auditory task performance, but the underlying neural network mechanisms remain unclear. To make progress, we recorded auditory cortex activity from behaving mice during…
DNA methylation can be associated with phenotypic plasticity, yet how temperature shapes DNA methylation diversity in natural populations is unclear. Analyzing whole-genome bisulfite sequencing from 1075 Arabidopsis thaliana accessions…
This paper introduces variational representational similarity analysis RSA (vRSA) for electromagnetic recordings of neural responses (e.g., EEG, MEG, ECoG or LFP). Variational RSA is a Bayesian approach for testing whether the similarity of…
Introduction: Epigenomic datasets from high-throughput sequencing experiments are commonly summarized as genomic intervals. As the volume of this data grows, so does interest in analyzing it through deep learning. However, the heterogeneity…
The key to successful drug design lies in the correct comprehension of protein-ligand interactions. Within the current knowledge paragm, these interactions can be described from both thermodynamic and kinetic perspectives. In recent years,…
In this paper we use Species Distribution Models (SDMs) to forecast the future diversity and distribution of orchids in Great Britain and Ireland under scenarios of climate and land-use change. The study analyzes occurrence data for native…
Summary: We present AmpliconHunter2 (AHv2), a highly scalable in silico PCR engine written in C that can handle degenerate primers and uses a highly accurate melting temperature model. AHv2 implements a bit-mask IUPAC matcher with AVX2 SIMD…
Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to…
This study aimed to systematically identify and quantify risks for drug-induced rhabdomyolysis (DIR) using real-world data and to propose an evidence-based risk mitigation framework. We conducted a retrospective pharmacovigilance study…
Geographic atrophy (GA) is a key biomarker of dry age-related macular degeneration (AMD) traditionally identified through color fundus photography. Hyper-transmission defects (hyperTDs), a feature highly correlated with GA, have recently…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
In control problems and basic scientific modeling, it is important to compare observations with dynamical simulations. For example, comparing two neural systems can shed light on the nature of emergent computations in the brain and deep…