Related papers: The Updated Genome Warehouse: Enhancing Data Value…
An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers a highly interactive visualization and…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Centralized electronic health record repositories are critical for advancing disease surveillance, public health research, and evidence-based policymaking. However, developing countries face persistent challenges in achieving this due to…
Numerous studies have utilized NCBI data for genomic analysis, gene annotation, and identifying disease-associated variants, yet NCBI's epidemiological potential remains underexplored. This study demonstrates how NCBI datasets can be…
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection,…
Background. Clinical data warehouses (CDWs) are essential in the reuse of hospital data in observational studies or predictive modeling. However, state of-the-art CDW systems present two drawbacks. First, they do not support the management…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach…
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome…
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing…
Artificial Intelligence (AI) incorporating genetic and medical information have been applied in disease risk prediction, unveiling disease mechanism, and advancing therapeutics. However, AI training relies on highly sensitive and private…
Stanford Medicine is building a new data platform for our academic research community to do better clinical data science. Hospitals have a large amount of patient data and researchers have demonstrated the ability to reuse that data and AI…
Message passing is a core mechanism in Graph Neural Networks (GNNs), enabling the iterative update of node embeddings by aggregating information from neighboring nodes. Graph Convolutional Networks (GCNs) exemplify this approach by adapting…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run…
The House of Graphs is an online database of graphs which can be accessed at https://houseofgraphs.org/. It serves as a central repository for complete lists of graphs for various graph classes. However, its main feature is a searchable…
Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of crucial details and…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…