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Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Dynamic tetrahedral simulation pipelines rebuild topology-dependent solver state after every fracture, refinement, or merge event - discarding structural continuity that survives each edit and spending global work on what are often local…
In computer vision, traditional ensemble learning methods exhibit either a low training efficiency or the limited performance to enhance the reliability of deep neural networks. In this paper, we propose a lightweight, loss-function-free,…
Although recent years have witnessed significant advancements in medical image segmentation, the pervasive issue of domain shift among medical images from diverse centres hinders the effective deployment of pre-trained models. Many…
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…
Freely available and easy-to-use audio editing tools make it straightforward to perform audio splicing. Convincing forgeries can be created by combining various speech samples from the same person. Detection of such splices is important…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
We study the oritatami model for molecular co-transcriptional folding. In oritatami systems, the transcript (the "molecule") folds as it is synthesized (transcribed), according to a local energy optimisation process, which is similar to how…
DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…
Single-cell RNA-sequencing (scRNA-seq) stands as a powerful tool for deciphering cellular heterogeneity and exploring gene expression profiles at high resolution. However, its high cost renders it impractical for extensive sample cohorts…
Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules…
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Diffusion models have achieved remarkable success in generative tasks but suffer from high computational costs due to their iterative sampling process and quadratic attention costs. Existing training-free acceleration strategies that reduce…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and Eosin (H&E) stained histology images to spatially resolved gene…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Hyperspectral imaging (HSI) provides rich spectral information for medical imaging, yet encounters significant challenges due to data limitations and hardware variations. We introduce SAMSA, a novel interactive segmentation framework that…