1,721,003 research outputs found
CONDOP: An R package for CONdition-Dependent Operon Predictions
No full textSummary: The use of high-throughput RNA sequencing to predict dynamic operon structures in prokaryotic genomes has recently gained popularity in bioinformatics. We provide the R implementation of a novel method that uses transcriptomic features extracted from RNA-seq transcriptome profiles to develop ensemble classifiers for condition-dependent operon predictions. The CONDOP package provides a deeper insight into RNA-seq data analysis and allows scientists to highlight the operon organization in the context of transcriptional regulation with a few lines of code
RankFrag: A machine learning-based technique for finding corners in hand-drawn digital curves
No full textWe describe RankFrag: a technique which uses machine learning to detect corner points in hand-drawn digital curves. RankFrag classifies the stroke points by iteratively extracting them from a list of corner candidates. The points extracted in the last iterations are said to have a higher rank and are more likely to be corners. The technique has been tested on three different datasets described in the literature. We observed that, considering both accuracy and efficiency, RankFrag performs better than other state-of-art techniques
Cloning and characterization of a Δ(9)-desaturase gene of the Antarctic fish Chionodraco hamatus and Trematomus bernacchii.
No full textChionodraco hamatus and Trematomus ber- nacchii are perciforms, members of the fish suborder Notothenioidei that live in the Antarctic Ocean and expe- rience very cold and persistent environmental temperature. These fish have biochemical and molecular features that allow them to live at these extreme cold temperatures. Fine tuning of the level of unsaturated fatty acids content in membrane is a key mechanism of living organisms to adapt to cold and high temperatures. Desaturases are key enzymes that synthesize unsaturated fatty acyl-CoAs from saturated fatty acids. We cloned and sequenced a D9-desaturase gene and its cDNA of C. hamatus, and the cDNA of T. bernacchii. The coded proteins are virtually identical and share homology to other D9-desaturase fish sequences. These proteins contain, in the first trans- membrane domain, two cysteine residues that may form a disulfur bond present in the corresponding membrane region of D9-desaturase proteins of other Antarctic fish but not in Eleginops maclovinus that experiences higher envi- ronmental temperatures and in all other D9-desaturase genes of mammals present in data bases. C. hamatus D9-desaturase gene complements a Saccharomyces cere- visiae mutant lacking D9-desaturase (Ole1) gene. Analysis of sequence homology of the trans-membrane domains ofD9-desaturase and the cytoplasmic region of the same proteins of Antarctic fish, non-Antarctic fish and mammals suggest that the significant differences found in the homologous sequences of the first trans-membrane domain may be due to the specific lipid content of their membrane
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Sequence analysis in bioinformatics: methodological and practical aspects
Full text link2011 - 2012My PhD research activities has focused on the development of new
computational methods for biological sequence analyses.
To overcome an intrinsic problem to protein sequence analysis, whose aim was
to infer homologies in large biological protein databases with short queries, I
developed a statistical framework BLAST-based to detect distant homologies
conserved in transmembrane domains of different bacterial membrane proteins.
Using this framework, transmembrane protein domains of all Salmonella spp. have
been screened and more than five thousands of significant homologies have been
identified. My results show that the proposed framework detects distant homologies
that, because of their conservation in distinct bacterial membrane proteins, could
represent ancient signatures about the existence of primeval genetic elements (or
mini-genes) coding for short polypeptides that formed, through a primitive assembly
process, more complex genes. Further, my statistical framework lays the foundation
for new bioinformatics tools to detect homologies domain-oriented, or in other words,
the ability to find statistically significant homologies in specific target-domains.
The second problem that I faced deals with the analysis of transcripts obtained
with RNA-Seq data. I developed a novel computational method that combines
transcript borders, obtained from mapped RNA-Seq reads, with sequence features
based operon predictions to accurately infer operons in prokaryotic genomes. Since
the transcriptome of an organism is dynamic and condition dependent, the RNA-Seq
mapped reads are used to determine a set of confirmed or predicted operons and
from it specific transcriptomic features are extracted and combined with standard
genomic features to train and validate three operon classification models (Random
Forests - RFs, Neural Networks – NNs, and Support Vector Machines - SVMs).
These classifiers have been exploited to refine the operon map annotated by DOOR,
one of the most used database of prokaryotic operons. This method proved that the
integration of genomic and transcriptomic features improve the accuracy of operon
predictions, and that it is possible to predict the existence of potential new operons.
An inherent limitation of using RNA-Seq to improve operon structure predictions is
that it can be not applied to genes not expressed under the condition studied. I
evaluated my approach on different RNA-Seq based transcriptome profiles of
Histophilus somni and Porphyromonas gingivalis. These transcriptome profiles were
obtained using the standard RNA-Seq or the strand-specific RNA-Seq method. My
experimental results demonstrate that the three classifiers achieved accurate operon
maps including reliable predictions of new operons. [edited by author]XI n.s
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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