Related papers: metaSPAdes: a new versatile de novo metagenomics a…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Dynamic ensemble selection (DES) techniques work by estimating the level of competence of each classifier from a pool of classifiers. Only the most competent ones are selected to classify a given test sample. Hence, the key issue in DES is…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data typically harbors reads of variable lengths and different…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Meta-analysis is routinely performed in many scientific disciplines. This analysis is attractive since discoveries are possible even when all the individual studies are underpowered. However, the meta-analytic discoveries may be entirely…
International Classification of Diseases (ICD) are the de facto codes used globally for clinical coding. These codes enable healthcare providers to claim reimbursement and facilitate efficient storage and retrieval of diagnostic…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
This paper looks into the problem of handling imbalanced data in a multi-label classification problem. The problem is solved by proposing two novel methods that primarily exploit the geometric relationship between the feature vectors. The…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Subsampling of node sets is useful in contexts such as multilevel methods, computer graphics, and machine learning. On uniform grid-based node sets, the process of subsampling is simple. However, on node sets with high density variation,…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Advances in next-generation metagenome sequencing have the potential to revolutionize the point-of-care diagnosis of novel pathogen infections, which could help prevent potential widespread transmission of diseases. Given the high volume of…
When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…