Related papers: PhenotypeToGeneDownloaderR: automated multi-source…
Data volumes and rates of research infrastructures will continue to increase in the upcoming years and impact how we interact with their final data products. Little of the processed data can be directly investigated and most of it will be…
Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have…
Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
The accelerating pace of research on autoregressive generative models has produced thousands of papers, making manual literature surveys and reproduction studies increasingly impractical. We present a fully open-source, reproducible…
Summary: Genotype networks are a method used in systems biology to study the innovability of a given phenotype, determining whether the phenotype is robust to mutations, and how do the genotypes associated to it are distributed in the…
Python's dynamic typing mechanism, while promoting flexibility, is a significant source of runtime type errors that plague large-scale software, which inspires the automatic type inference techniques. Existing type inference tools have…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
The increased availability of electronic health records (EHRs) have spearheaded the initiative for precision medicine using data driven approaches. Essential to this effort is the ability to identify patients with certain medical conditions…
This work presents a novel four-stage open-domain QA pipeline R2-D2 (Rank twice, reaD twice). The pipeline is composed of a retriever, passage reranker, extractive reader, generative reader and a mechanism that aggregates the final…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
The future of the agriculture industry is intertwined with automation. Accurate fruit detection, yield estimation, and harvest time estimation are crucial for optimizing agricultural practices. These tasks can be carried out by robots to…
An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that…
Rare diseases often manifest with distinctive facial phenotypes in children, offering valuable diagnostic cues for clinicians and AI-assisted screening systems. However, progress in this field is severely limited by the scarcity of curated,…
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their…
Identifying disease genes from human genome is an important and fundamental problem in biomedical research. Despite many publications of machine learning methods applied to discover new disease genes, it still remains a challenge because of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Chart-to-code reconstruction -- the task of recovering executable plotting scripts from chart images -- provides important insights into a model's ability to ground data visualizations in precise, machine-readable form. Yet many existing…