Related papers: BGT: efficient and flexible genotype query across …
Similarity search, the task of identifying objects most similar to a given query object under a specific metric, has gathered significant attention due to its practical applications. However, the absence of coordinate information to…
While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise…
Systematic reviews are comprehensive reviews of the literature for a highly focused research question. These reviews are often treated as the highest form of evidence in evidence-based medicine, and are the key strategy to answer research…
Genetic Programming (GP) is a computationally intensive technique which also has a high degree of natural parallelism. Parallel computing architectures have become commonplace especially with regards Graphics Processing Units (GPU). Hence,…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of…
Gaussian Boson Sampling (GBS) is a recently developed paradigm of quantum computing consisting of sending a Gaussian state through a linear interferometer and then counting the number of photons in each output mode. When the system encodes…
Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
State-of-the-art brain graph analysis methods fail to fully encode the small-world architecture of brain graphs (accompanied by the presence of hubs and functional modules), and therefore lack biological plausibility to some extent. This…
Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in…
Interpreting and communicating electrocardiogram (ECG) findings are crucial yet challenging tasks in cardiovascular diagnosis, traditionally requiring significant expertise and precise clinical communication. This paper introduces…
Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
In this paper, we present BlinkDB, a massively parallel, sampling-based approximate query engine for running ad-hoc, interactive SQL queries on large volumes of data. The key insight that BlinkDB builds on is that one can often make…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…