Related papers: COCACOLA: binning metagenomic contigs using sequen…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large…
Metagenomic binning is an essential task in analyzing metagenomic sequence datasets. To analyze structure or function of microbial communities from environmental samples, metagenomic sequence fragments are assigned to their taxonomic…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
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…
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Many modern applications produce massive amounts of data series that need to be analyzed, requiring efficient similarity search operations. However, the state-of-the-art data series indexes that are used for this purpose do not scale well…
Diverse applications - particularly in tumour subtyping - have demonstrated the importance of integrative clustering techniques for combining information from multiple data sources. Cluster-Of-Clusters Analysis (COCA) is one such approach…
Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of…
The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic…
Motivation: The size of available omics datasets is steadily increasing with technological advancement in recent years. While this increase in sample size can be used to improve the performance of relevant prediction tasks in healthcare,…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
We study the oritatami model for molecular co-transcriptional folding. In oritatami systems, the transcript (the "molecule") folds as it is synthesized (transcribed), according to a local energy optimisation process, which is similar to how…
High-throughput sequencing has transformed microbiome research, but it also produces inherently compositional data that challenge standard statistical and machine learning methods. In this work, we propose a multinomial classification…
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
Coflow provides a key application-layer abstraction for capturing communication patterns, enabling the efficient coordination of parallel data flows to reduce job completion times in distributed systems. Modern data center networks (DCNs)…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…