Related papers: Indexing arbitrary-length $k$-mers in sequencing r…
In 5G Ultra-Dense Networks, a distributed wireless backhaul is an attractive solution for forwarding traffic to the core. The macro-cell coverage area is divided into many small cells. A few of these cells are designated as gateways and are…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
In bioinformatics, minimizers have become an inescapable method for handling $k$-mers (words of fixed size $k$) extracted from DNA or RNA sequencing, whether for sampling, storage, querying or partitioning. According to some fixed order on…
Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…
Let S be a finite, ordered alphabet, and let x = x_1 x_2 ... x_n be a string over S. A "secondary index" for x answers alphabet range queries of the form: Given a range [a_l,a_r] over S, return the set I_{[a_l;a_r]} = {i |x_i \in [a_l;…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
Sparse linear algebra is a cornerstone of many scientific computing and machine learning applications. Python has become a popular choice for these applications due to its simplicity and ease of use. Yet high performance sparse kernels in…
Probe-level microarray data are usually stored in matrices, where the row and column correspond to array and probe, respectively. Scientists routinely summarize each array by a single index as the expression level of each probe set (gene).…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
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…
We propose a method to reconstruct and cluster incomplete high-dimensional data lying in a union of low-dimensional subspaces. Exploring the sparse representation model, we jointly estimate the missing data while imposing the intrinsic…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
k-mers (nucleotide strings of length k) form the basis of several algorithms in computational genomics. In particular, k-mer abundance information in sequence data is useful in read error correction, parameter estimation for genome…