Research Article

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01/15/2015
Bioinformatics; Ensemble learning; Imbalances; Machine learning; miRNA

Imbalances typically exist in bioinformatics and are also common in other areas. A drawback of traditional machine learning methods is the relatively little attention given to small sample classification. Thus, we developed imDC, which uses an ensemble learning concept in combination with weights and sample misclassification information to effectively classify imbalanced data. Our method ... more

C.Y. Wang; L.L. Hu; M.Z. Guo; X.Y. Liu; Q. Zou
02/17/2012
Animal model; Brain; Energy metabolism; Ethanol; Extended amygdala

We examined a possible relationship between genes responsible for energy metabolism of the brain and addictive behavior in an animal model. We used non-inbred, Swiss mice exposed to a three-bottle free-choice model [water, 5% (v/v) ethanol, and 10% (v/v) ethanol] over a 16-week period, consisting of four phases: acquisition, withdrawal, reexposure, and quinine-adulteration. The mice were ... more

A.F. Ribeiro; D. Correia; R. Boerngen-Lacerda; A.L. Brunialti-Godard
04/13/2015
Brain; Contrast-enhanced ultrasound; Conventional ultrasound; Crossbreed dogs; Gunshot wound

This study aimed to investigate the characteristic features of craniocerebral gunshot wounds by conventional ultrasound (CUS) and evaluate the efficacy of contrast-enhanced ultrasound (CEUS) in differentiation of tissue condition in wounds. Twenty crossbreed dogs (treatment: N = 15; control: N = 5) were used in the study. Pipe-shaped hyperechoes of varying size were found by CUS in most ... more

D. Deng; G. Dan; J. Tao; X.B. Wu; Z. Chen; M. Chang; M.S. Liao; F. He
12/30/2004
Bioinformatics; Genetic determinism; Genomics; Human genome; Public understand of science; Science and technology studies

The literature about genomics and bioinformatics achievements in high-impact journals such as Nature and Science has raised disproportionate expectations amongst the general public about fast and revolutionary drugs and breakthroughs in biomedicine. However, the yield obtained by database mining activities has been modest, as reported in the February 2001 issues of ... more

M. Leite
12/30/2004
Bioinformatics; Computing; Modeling; Physics; Post-genomics

I give here a very personal perspective of Bioinformatics and its future, starting by discussing the origin of the term (and area) of bioinformatics and proceeding by trying to foresee the development of related issues, including pattern recognition/data mining, the need to reintegrate biology, the potential of complex networks as a powerful and flexible framework for bioinformatics ... more

Lda Fontour Costa
12/30/2004
Alternative splicing; Bioinformatics; Exon skipping; Expressed sequences; Extracellular matrix; Human transcriptome

Alternative splicing increases protein diversity through the generation of different mRNA molecules from the same gene. Although alternative splicing seems to be a widespread phenomenon in the human transcriptome, it is possible that different subgroups of genes present different patterns, related to their biological roles. Analysis of a subgroup may enhance common features of its ... more

N.Jo Sakabe; M.Dulcetti Vibranovski; S.José de Souza
12/30/2004
Bioinformatics; DNA sequence analysis software; Perl programming

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by ... more

E. Binneck; J.Flávio V. Silva; N. Neumaier; J.Renato B. Farias; A.L. Nepomuceno
10/04/2007
Bioinformatics; Latent semantic indexing; Molecular comparisons; Sequence alignments

Most molecular analyses, including phylogenetic inference, are based on sequence alignments. We present an algorithm that estimates relatedness between biomolecules without the requirement of sequence alignment by using a protein frequency matrix that is reduced by singular value decomposition (SVD), in a latent semantic index information retrieval system. Two databases were used: one ... more

B.R.G.M. Couto; A.P. Ladeira; M.A. Santos
10/04/2007
Bioinformatics; Flagellar motility; Genome screens; Intraflagellar transport; Intraflagellar transport complex; Leishmania

Flagella are constructed and maintained through the highly conserved process of intraflagellar transport (IFT), which is a rapid movement of particles along the axonemal microtubules of cilia/flagella. Particles that are transported by IFT are composed of several protein subunits comprising two complexes (A and B), which are conserved among green algae, nematodes, and vertebrates. To ... more

J.J.S. Gouveia; E.J.R. Vasconcelos; A.C.L. Pacheco; R. Araújo-Filho; A.R.S. Maia; M.T. Kamimura; M.P. Costa; D.A. Viana; R.B. Costa; R. Maggioni; D.M. Oliveira
10/06/2006
Bioinformatics; Membrane-bound protein; Schistosoma mansoni; Sm29; Transcriptome; Vaccine

Progress in schistosome genome research has enabled investigators to move rapidly from genome sequences to vaccine development. Proteins bound to the surface of parasites are potential vaccine candidates, or they can be used for diagnosis. We analyzed 4342 proteins deduced from the Schistosoma mansoni transcriptome with bioinformatic computer programs. Thirty-four proteins had ... more

F.C. Cardoso; J.M.R. Pinho; V. Azevedo; S.C. Oliveira

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