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Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…
In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
We explored an uncharted part of the solution space for sorting algorithms: the role of symmetry in divide&conquer algorithms. We found/designed novel simple binary Quicksort and Mergesort algorithms operating in contiguous space which…
Screening mammograms are a routine imaging exam performed to detect breast cancer in its early stages to reduce morbidity and mortality attributed to this disease. In order to maximize the efficacy of breast cancer screening programs,…
Matching local features across images is a fundamental problem in computer vision. Targeting towards high accuracy and efficiency, we propose Seeded Graph Matching Network, a graph neural network with sparse structure to reduce redundant…
Genome engineering is undergoing unprecedented development and is now becoming widely available. To ensure responsible biotechnology innovation and to reduce misuse of engineered DNA sequences, it is vital to develop tools to identify the…
Neural network models of real-world systems, such as industrial processes, made from sensor data must often rely on incomplete data. System states may not all be known, sensor data may be biased or noisy, and it is not often known which…
Memristive in-memory sorting has been proposed recently to improve hardware sorting efficiency. Using iterative in-memory min computations, data movements between memory and external processing units can be eliminated for improved latency…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…
Simultaneous localization and mapping (SLAM) based on laser sensors has been widely adopted by mobile robots and autonomous vehicles. These SLAM systems are required to support accurate localization with limited computational resources. In…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Bloom filters are a fundamental data structure for approximate membership queries, with applications ranging from data analytics to databases and genomics. Several variants have been proposed to accommodate parallel architectures. GPUs,…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
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…
Computing-in-memory (CIM) has attracted significant attentions in recent years due to its massive parallelism and low power consumption. However, current CIM designs suffer from large area overhead of small CIM macros and bad programmablity…