Direct Objective Quantification of Corneal Haze after Excimer Laser Photorefractive Keratectomy for High Myopia
Purpose: The purpose of the study is to measure regional distribution differences in corneal haze after excimer laser photorefractive keratectomy for high myopia. Methods: The authors developed computerized gradient edge detectors with which were analyzed digitized anterior slit-lamp photographs of 40 eyes, an average of 21.0 plus or minus 14.5 weeks after photorefractive keratectomy for high myopia (−6 to −22 diopters). A treated area and an adjacent untreated area on the anterior corneal surface, each containing six regions, were quantified, and the difference was correlated with various parameters. Results: Mean differences between scarred and clear areas for haze grade 0.5, 1.0, 2.0, 3.…
Iterative Cluster Analysis of Protein Interaction Data
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The an…
An application of neural networks to natural scene segmentation
This paper introduces a method for low level image segmentation. Pixels of the image are classified corresponding to their chromatic features.
A new method for the optimum generation of real colours on CRT monitors
The use of computers for colour generation is widely extended in colour research. Sometimes the reproduction of colours whose chromaticity coordinates correspond to a specific real standard is fundamental. In this paper we present a review of the capabilities and limitations of CRT monitors to generate colours. Finally, we propose a method for the optimum generation of real colours based on visual perception.
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org . Because it uses novel mapping algorithms VISMapper is remarkably faster t…
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection
AbstractThe olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consort…
Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism.
The human gene parkin, known to cause familial Parkinson disease, as well as several other genes, likely involved in other neurodegenerative diseases or in cancer, encode proteins of the RBR family of ubiquitin ligases. Here, we describe the structural diversity of the RBR family in order to infer their functional roles. Of particular interest is a relationship detected between RBR-mediated ubiquitination and RNA metabolism: a few RBR proteins contain RNA binding domains and DEAH-box RNA helicase domains. Global protein domain graph analyses demonstrate that this connection is not RBR-specific, but instead many other proteins contain both ubiquitination and RNA-related domains. These protei…
A hierarchical clustering strategy and its application to proteomic interaction data
We describe a novel strategy of hierarchical clustering analysis, particularly useful to analyze proteomic interaction data. The logic behind this method is to use the information for all interactions among the elements of a set to evaluate the strength of the interaction of each pair of elements. Our procedure allows the characterization of protein complexes starting with partial data and the detection of "promiscuous" proteins that bias the results, generating false positive data. We demonstrate the usefulness of our strategy by analyzing a real case that involves 137 Saccharomyces cerevisiae proteins. Because most functional studies require the evaluation of similar data sets, our method…
A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics
We have developed a new algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences. It is fast enough as to be used at a genomic scale running on a standard personal computer. As an example, we apply the algorithm to compare the number of all 12-nucleotide long words in human chromosomes 21 and 22, each of them more than 33 million nucleotides long. Sequences that are chromosome specific are detected in less than 2 minutes, being analyzed any pair of chromosomes at a rate of 45 millions of nucleotides (45 Mb) per minute. The size of the words is long enough as to allow further analyses of all significant sequences using conventional database searche…
Reproducibility of digital image analysis for measuring corneal haze after myopic photorefractive keratectomy.
Purpose To evaluate the usefulness of digital image analysis for quantifying corneal haze by determining the reproducibility of its measurements at the corneal plane. Methods In a prospective study, 20 randomly selected eyes that had undergone myopic photorefractive keratectomy were photographed focusing the slit beam on their anterior corneal surface. Each photograph was examined using computer image analysis techniques that detect the edge of the reticular pattern of the image. Quantification of the difference between two areas, treated and adjacent untreated cornea, each containing 3,750 pixels with a resolution of 256 gray levels, was performed. Intra-analyzer variation was determined b…
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Serv…
Reactome pathway analysis: a high-performance in-memory approach
Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data st…
A Clustering Approach for Improving Network Performance in Heterogeneous Systems
A lot of research has focused on solving the problem of computation-aware task scheduling on heterogeneous systems. In this paper, we propose a clustering algorithm that, given a network topology, provides a network partition adapted to the communication requirements of the applications running on the machine. Also, we propose a criterion to measure the quality of each one of the possible mappings of processes to processors based on that network partition. Evaluation results show that these proposals can greatly improve network performance, providing a basis of a communication-aware scheduling technique.
Fast comparison of DNA sequences by oligonucleotide profiling
Provisional abstact and full-text PDF files correspond to the article as it appeared upon acceptance. Fully formatted PDF and final abstract will be made available soon.
Uterine disorders affecting female fertility: what are the molecular functions altered in endometrium?
[EN]: Objective:To determine the molecular functions of genes exhibiting altered expression in the endometrium of women with uterine disorders affecting fertility. Design: Retrospective analysis integrating case and control data from multiple cohorts with endometrium gene expression in women with uterine disorders. Setting: Infertility research department affiliated with a university hospital. Patient(s): Two hundred and forty women, 121 of whom were controls, 119 of whom had endometrial adenocarcinoma (ADC), recurrent implantation failure (RIF), recurrent pregnancy loss (RPL), or stage II–IV endometriosis. Intervention(s): None. Main Outcome Measure(s): Genomewide gene expression and alter…
A feedback mechanism controls rDNA copy number evolution in yeast independently of natural selection.
Ribosomal DNA (rDNA) is the genetic loci that encodes rRNA in eukaryotes. It is typically arranged as tandem repeats that vary in copy number within the same species. We have recently shown that rDNA repeats copy number in the yeast Saccharomyces cerevisiae is controlled by cell volume via a feedback circuit that senses cell volume by means of the concentration of the free upstream activator factor (UAF). The UAF strongly binds the rDNA gene promoter, but is also able to repress SIR2 deacetylase gene transcription that, in turn, represses rDNA amplification. In this way, the cells with a smaller DNA copy number than what is optimal evolve to increase that copy number until they reach a numb…
Reverse-transcribing viruses (Belpaoviridae, Metaviridae, and Pseudoviridae)
Fourth Edition.
HPG pore: an efficient and scalable framework for nanopore sequencing data.
The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer available, the MinION™ from Oxford Nanopore Technologies, is a USB-connected, portable device that allows real-time DNA analysis. In addition, other new instruments are expected to be released soon, which promise to outperform the current short-read technologies in terms of throughput. Despite the flood of data expected from this technology, the data analysis solutions currently available are only designed to manage small projects and are not scalable. Here we present HPG Pore, a toolkit for …
mRNAStab—a web application for mRNA stability analysis
Abstract Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at h…
Soil Bacterial Community Along an Altitudinal Gradient in the Sumaco, a Stratovolcano in the Amazon Region
Our study is a pioneering exploration of the microbiome in the soil of the Sumaco stratovolcano and an assessment of the effects of an elevational gradient and related physicochemical soil parameters on richness and community structure. The Sumaco, as an isolated Amazonian stratovolcano, may be among one of the least studied ecosystems in Ecuador and perhaps the Amazon region. Universal patterns remain unresolved or available information inconclusive to establish a supported consensus on general governing processes by which elevation and its associated environmental gradients may determine the microbial richness and community structure. We tested a recent proposal on how microbial diversity…
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
Transcriptional changes through menstrual cycle reveal a global transcriptional derepression underlying the molecular mechanism involved in the window of implantation
The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brief time in the middle secretory phase, called the window of implantation (WOI). Despite its importance, regulation of the menstrual cycle remains incompletely understood. The aim of this study was to characterize the gene cooperation and regulation of menstrual cycle progression, to dissect the molecular complexity underlying acquisition of endometrial receptivity for a successful pregnancy, and to provide the scientific community with detailed gene co-expression information throughout the menstrual cycle on a user-friendly web-tool database. A retrospective gene co-expression analysis was perfor…
A sequence motif enriched in regions bound by the Drosophila dosage compensation complex
Abstract Background In Drosophila melanogaster, dosage compensation is mediated by the action of the dosage compensation complex (DCC). How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found. Results In this study, we compare the known binding sites of the DCC with oligonucleotide profiles that measure the specificity of the sequences of the D. melanogaster X chromosome. We show that the X chromosome regions bound by the DCC are enriched for a particular type of short, repetitive sequences. Their distribution suggests that these sequences contribute to chromosome recognition, the genera…
Genomic Signature in Evolutionary Biology: A Review
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene …
Global patterns of sequence evolution in Drosophila.
This article is available from: http://www.biomedcentral.com/1471-2164/8/408
UVPAR: fast detection of functional shifts in duplicate genes.
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…
Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria
AbstractProgressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridg…