Related papers: Highly Scalable Algorithms for Robust String Barco…

Given the vast reservoirs of data stored worldwide, efficient mining of data from a large information store has emerged as a great challenge. Many databases like that of intrusion detection systems, web-click records, player statistics,…

Ongoing progress in computational intelligence (CI) has led to an increased desire to apply CI techniques for the purpose of improving software engineering processes, particularly software testing. Existing state-of-the-art automated…

A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…

High performance packet classification is a key component to support scalable network applications like firewalls, intrusion detection, and differentiated services. With ever increasing in the line-rate in core networks, it becomes a great…

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…

Scalable packet classification is a key requirement to support scalable network applications like firewalls, intrusion detection, and differentiated services. With ever increasing in the line-rate in core networks, it becomes a great…

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…

Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…

mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…

The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…

Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…

To accommodate the needs of large-scale distributed P2P systems, scalable data management strategies are required, allowing applications to efficiently cope with continuously growing, highly dis tributed data. This paper addresses the…

We present a novel technique for encoding and decoding constant weight binary codes that uses a geometric interpretation of the codebook. Our technique is based on embedding the codebook in a Euclidean space of dimension equal to the weight…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…

Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…

Kernel approximation methods create explicit, low-dimensional kernel feature maps to deal with the high computational and memory complexity of standard techniques. This work studies a supervised kernel learning methodology to optimize such…

Strings form a fundamental data type in computer systems. String searching has been extensively studied since the inception of computer science. Increasingly many applications have to deal with imprecise strings or strings with fuzzy…

There is a tension between robustness and efficiency when designing Markov chain Monte Carlo (MCMC) sampling algorithms. Here we focus on robustness with respect to tuning parameters, showing that more sophisticated algorithms tend to be…

Processing large complex networks recently attracted considerable interest. Complex graphs are useful in a wide range of applications from technological networks to biological systems like the human brain. Sometimes these networks are…

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…