Related papers: Which is faster: Bowtie2GP > Bowtie > Bowtie2 > BW…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
Designing novel proteins with desired characteristics remains a significant challenge due to the large sequence space and the complexity of sequence-function relationships. Efficient exploration of this space to identify sequences that meet…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…
DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies. Although the standard Transformer…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…
Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…
In this paper we discuss a genetic version (GWA) of the Whitehead's algorithm, which is one of the basic algorithms in combinatorial group theory. It turns out that GWA is surprisingly fast and outperforms the standard Whitehead's algorithm…
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…
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…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…