Related papers: BGT: efficient and flexible genotype query across …
Pedigree GWAS (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large scale genome-wide QTL analysis. This analysis (a) works for random sample data, pedigree data, or a mix of both, (b) is…
Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex…
Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time…
Motivation: Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of disparate bioinformatics tools. Results: To provide an…
Genome wide association studies directly assay 10^6 single nucleotide polymorphisms (SNPs) across a study cohort. Probabilistic estimation of additional sites by genotype imputation can increase this set of variants by 10- to 40-fold. Even…
RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology. Despite this importance, RNA research is often hindered by the vast literature available on the…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
Blini is a tool for quick lookup of nucleotide sequences in databases, and for quick dereplication of sequence collections. It is meant to help clean and characterize large collections of assembled contigs or long sequences that would…
Motivation: FASTQ is a standard file format for DNA sequencing data which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gigabytes of FASTQ files, while public archives such as ENA and…
Because of the recent advances of genome sequences, a large number of human genome sequences are available for the study of human genetics. Genome-wide association studies typically focus on associations between single-nucleotide…
The 1000 Genomes Project provides sequencing data on 3,202 samples from 26 populations spanning five continental regions with no access or use restrictions. The kgp R package provides consistent and comprehensive metadata about samples and…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
We present the HPLT (High Performance Language Technologies) language resources, a new massive multilingual dataset including both monolingual and bilingual corpora extracted from CommonCrawl and previously unused web crawls from the…
The Quantitative Group Testing (QGT) is about learning a (hidden) subset $K$ of some large domain $N$ using a sequence of queries, where a result of a query provides information about the size of the intersection of the query with the…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…