Search results for " bioinformatics"

Molecular analysis of the fungal community associated with phyllosphere and carposphere of fruit crops

Live genomics for pathogen monitoring in public health.

2014

Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in a short lapse of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the “local” level, such as in the event of a recurrent …

String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.

2011

The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …

Studying Nucleosomes Positioning by a Multi-Layer Model

2007

Eukaryotic DNA is packaged into a highly compact and dynamic structure called chromatin. While this packaging allows the cell to organize a large and complex genome in the nucleus, it can also block the access of transcription factors and other proteins to DNA. Nucleosomes are the fundamental repeating units of eukaryotic chromatin. Nucleosome position can be regulated in vivo by multi-subunit chromatin remodeling complexes, and their position can influence gene expression in eukaryotic cells. Alterations in chromatin structure, and hence in nucleosome organization, can result in a variety of diseases, including cancer, highlighting the need to achieve a better understanding of the molecula…

The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia

2020

Abstract Background Cognitive impairment is a clinically important feature of schizophrenia. Polygenic risk score (PRS) methods have demonstrated genetic overlap between schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), educational attainment (EA), and IQ, but very few studies have examined associations between these PRS and cognitive phenotypes within schizophrenia cases. Methods We combined genetic and cognitive data in 3034 schizophrenia cases from 11 samples using the general intelligence factor g as the primary measure of cognition. We used linear regression to examine the association between cognition and PRS for EA, IQ, schizophrenia, BD, and MDD. The results wer…

Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era-Editorial.

2021

With the advent of high-throughput and next-generation sequencing (NGS) technologies [1], huge amounts of ‘omics’ data (i.e. data from genomics, proteomics, pharmacogenomics, metagenomics, etc.) are continuously produced. Combining and integrating diverse omics data types is important in order to investigate the molecular machinery of complex diseases, with the hope for better disease prevention and treatment [2]. Experimental data repositories of omics data are publicly available, with the main aim of fostering the cooperation among research groups and laboratories all over the world. However, despite their openness, the effective integrated use of available public sources is hampered by t…

Toward completion of the Earth’s proteome: an update a decade later

2017

Protein databases are steadily growing driven by the spread of new more efficient sequencing techniques. This growth is dominated by an increase in redundancy (homologous proteins with various degrees of sequence similarity) and by the incapability to process and curate sequence entries as fast as they are created. To understand these trends and aid bioinformatic resources that might be compromised by the increasing size of the protein sequence databases, we have created a less-redundant protein data set. In parallel, we analyzed the evolution of protein sequence databases in terms of size and redundancy. While the SwissProt database has decelerated its growth mostly because of a focus on i…

On Obtaining Classification Confidence, Ranked Predictions and AUC with Tsetlin Machines

2020

Tsetlin machines (TMs) are a promising approach to machine learning that uses Tsetlin Automata to produce patterns in propositional logic, leading to binary (hard) classifications. In many applications, however, one needs to know the confidence of classifications, e.g. to facilitate risk management. In this paper, we propose a novel scheme for measuring TM confidence based on the logistic function, calculated from the propositional logic patterns that match the input. We then use this scheme to trade off precision against recall, producing area under receiver operating characteristic curves (AUC) for TMs. Empirically, using four real-world datasets, we show that AUC is a more sensitive meas…

Ad-Hoc Segmentation Pipeline for Microarray Image Analysis

2006

Microarray is a new class of biotechnologies able to help biologist researches to extrapolate new knowledge from biological experiments. Image Analysis is devoted to extrapolate, process and visualize image information. For this reason it has found application also in Microarray, where it is a crucial step of this technology (e.g. segmentation). In this paper we describe MISP (Microarray Image Segmentation Pipeline), a new segmentation pipeline for Microarray Image Analysis. The pipeline uses a recent segmentation algorithm based on statistical analysis coupled with K-Means algorithm. The Spot masks produced by MISP are used to determinate spots information and quality measures. A software …

INVESTIGATION OF BIOTIC STRESS RESPONSES IN FRUIT TREE CROPS USING META-ANALYTICAL TECHNIQUES.

2020

In recent years, RNA sequencing and analysis using Next Generation Sequencing (NGS) methods have enabled to understand the gene expression pertaining to plant biotic and abiotic stress conditions in both quantitative and qualitative manner. The large number of transcriptomic works published in plants requires more meta-analysis studies that would identify common and specific features in relation of the high number of objective studies performed at different developmental and environmental conditions. Meta-analysis of transcriptomic data will identify commonalities and differences between differentially regulated gene lists and will allow screen which genes are key players in gene-gene and p…