Related papers: EGC: a format for expressing prokaryotic genomes c…
Despite recent advancement in 3D molecule conformation generation driven by diffusion models, its high computational cost in iterative diffusion/denoising process limits its application. In this paper, an equivariant consistency model…
By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…
Omics data, such as transcriptomics, proteomics, and metabolomics, provide critical insights into disease mechanisms and clinical outcomes. However, their high dimensionality, small sample sizes, and intricate biological networks pose major…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Electrocardiogram (ECG) biometrics have emerged as a promising modality for continuous, liveness-aware authentication in wearable systems. However, many prior studies report overly optimistic results due to data leakage (e.g., random splits…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Electrocardiograms (ECG) are electrical recordings of the heart that are critical for diagnosing cardiovascular conditions. ECG language models (ELMs) have recently emerged as a promising framework for ECG classification accompanied by…
In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure,…
The cost of DNA sequencing has resulted in a surge of genetic data being utilised to improve scientific research, clinical procedures, and healthcare delivery in recent years. Since the human genome can uniquely identify an individual, this…
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
Electronic health records (EHR) contain extensive structured and unstructured data, including tabular information and free-text clinical notes. Querying relevant patient information often requires complex database operations, increasing the…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
Electroencephalography-based Emotion Recognition (EEG-ER) has become a growing research area in recent years. Analyzing 216 papers published between 2018 and 2023, we uncover that the field lacks a unified evaluation protocol, which is…
Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical…
This paper describes the software implementation of genetic algorithm for identifying and selecting most relevant results received during sequentially executed subject search operations. Simulated evolutionary process generates sustainable…
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
Grammar-Guided Genetic Programming (GGGP) employs a variety of insights from evolutionary theory to autonomously design solutions for a given task. Recent insights from evolutionary biology can lead to further improvements in GGGP…
Single-cell gene expression data are often characterized by large matrices, where the number of cells may be lower than the number of genes of interest. Factorization models have emerged as powerful tools to condense the available…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…