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We describe a simple parallel-friendly lightweight graph reordering algorithm for COO graphs (edge lists). Our ``Batched Order By Attachment'' (BOBA) algorithm is linear in the number of edges in terms of reads and linear in the number of…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Biological network alignment is currently in a state of disarray, with more than two dozen network alignment tools having been introduced in the past decade, with no clear winner, and other new tools being published almost quarterly. Part…
The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…
We present a novel multivariate classification technique based on Genetic Programming. The technique is distinct from Genetic Algorithms and offers several advantages compared to Neural Networks and Support Vector Machines. The technique…
Diagnosis of breast cancer has been well studied in the past. Multiple linear programming models have been devised to approximate the relationship between cell features and tumour malignancy. However, these models are less capable in…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
The Extended Burrows Wheeler transform (EBWT) helps to find the distance between two sequences. Implementation of an existing algorithm takes considerable amount of time for small size sequences. In this paper, we give a parallel…
Cancer is one of the most feared diseases in the world it has increased disturbingly and breast cancer occurs in one out of eight women, the prediction of malignancies plays essential roles not only in revealing human genome, but also in…
In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a…
Quantum Genetic Algorithms (QGAs) are an emerging field of multivariate quantum optimization that emulate Darwinian evolution and natural selection, with vast applications in chemistry and engineering. The appropriate application of fitness…
Large language models (LLMs) have made significant advancements in natural language processing (NLP). Broad corpora capture diverse patterns but can introduce irrelevance, while focused corpora enhance reliability by reducing misleading…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
Currently, lightweight hybrid backbone networks have partially alleviated the issue of computational saturation, but the imbalance in computational efficiencys between convolutional neural networks (CNNs) and attention mechanisms is…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
Pancreatic cancer (PC) is the fourth leading cause of cancer death in the United States due to its five-year survival rate of 10%. Late diagnosis, affiliated with the asymptomatic nature in early stages and the location of the cancer with…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…