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Abstract Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 9...

Motivation: Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment pro...

MOTIVATION: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate thes...

SUMMARY: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized ben...

Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses ...

MOTIVATION: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene ...

MOTIVATION: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling ...

MOTIVATION: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare...

BACKGROUND: Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns a...

BACKGROUND: Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insuff...

SUMMARY: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alig...

Fil: Garavaglia, Matías Javier. Universidad Nacional de Quilmes. Laboratorio de Ingeniería Genética, Biología Celular y Molecular; Argentina. A lo largo del presente trabajo, se intentaron abordar distintas problemá...

Complementary DNA (cDNA) microarrays are a powerful high throughput technology developed in the last decade allowing researchers to analyze the behaviour and interaction of thousands of genes simultaneously. The large am...

Fil: Monzón, Alexander Miguel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. El concepto de estado nativo ha evolucionado en el tiempo junto a las técnicas de caracterización de pr...

Materias / palabras clave: Angiogenesis; Cancer; Function (biology); Cancer therapy; Clinical trial; Medicine; Computational biology; Biology; Bioinformatics; Cancer research; Internal medicine; Cell biology

Materias / palabras clave: Diabetes mellitus; Blindness; Stroke (engine); Disease; Medicine; Superoxide; Mitochondrion; Myocardial infarction; Vascular disease; Bioinformatics; Biology; Neuroscience

DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to ...

Materias / palabras clave: Biology; Suite; Software; Software suite; Scale (ratio); Software development; Sequence (biology); Computational biology; Data science; Bioinformatics; Computer science; Genetics

Viral hepatitis in all its forms is a major public health problem throughout the world, affecting several hundreds of millions of people.Viral hepatitis is a cause of con- siderable morbidity and mortality both from acut...

BACKGROUND: Protein-protein interaction (PPI) network analyses are highly valuable in deciphering and understanding the intricate organisation of cellular functions. Nevertheless, the majority of available protein-protei...

Materias / palabras clave: Immune system; Inflammation; Biology; Disease; Mechanism (biology); Function (biology); Homeostasis; Metabolic pathway; Bioinformatics; Immunology; Neuroscience; Medicine

Materias / palabras clave: microRNA; Biology; Gene expression profiling; Computational biology; RNA; Messenger RNA; Gene expression; Genetics; Gene; Bioinformatics

Although cancer classification has improved over the past 30 years, there has been no general approach for identifying new cancer classes (class discovery) or for assigning tumors to known classes (class prediction). Her...