Related papers: MUSIC: A Hybrid Computing Environment for Burrows-…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
Modeling complex phenomena typically involves the use of both discrete and continuous variables. Such a setting applies across a wide range of problems, from identifying trends in time-series data to performing effective compositional scene…
The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…
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…
Recommender systems serve a dual purpose for users: sifting out inappropriate or mismatched information while accurately identifying items that align with their preferences. Numerous recommendation algorithms are designed to provide users…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…
This article presents new numerical simulation tools, respectively developed in Matlab and Blender softwares. Available in open-source under the GPL 3.0 license, it uses a ray-tracing/image-sources hybrid method to calculate the room…
In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…
Assembling genomes from short-read sequencing data remains difficult in repetitive regions, where reference bias and combinatorial complexity limit existing methods. Pangenome-guided sequence assembly (PGSA) mitigates reference bias by…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Music can be represented in multiple forms, such as in the audio form as a recording of a performance, in the symbolic form as a computer readable score, or in the image form as a scan of the sheet music. Music synchronisation provides a…
In this paper, a novel dual-mode scheduling framework is proposed that jointly performs user applications (UA) selection and scheduling over microwave ($\mu$W) and millimeter wave (mmW) bands. The proposed scheduling framework utilizes a…
Audio-to-score alignment is a long-standing challenge in music information retrieval and arguably the most widely applicable alignment task for music research. Alignment algorithms match two versions of a piece of music, and for this to…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations…
Computational harmony analysis is important for MIR tasks such as automatic segmentation, corpus analysis and automatic chord label estimation. However, recent research into the ambiguous nature of musical harmony, causing limited…
As high-throughput sequencers become standard equipment outside of sequencing centers, there is an increasing need for efficient methods for pre-processing and primary analysis. While a vast literature proposes methods for HTS data…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…