Search results for "Computation"

Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Ant…

2017

Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a “gold standard” to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species. The proteomic results consist of a dynamic portray of over- and down-represented protein species that…

MicroRNA Interaction Networks

2021

La tesi di Giorgio Bertolazzi è incentrata sullo sviluppo di nuovi algoritmi per la predizione dei legami miRNA-mRNA. In particolare, un algoritmo di machine-learning viene proposto per l'upgrade del web tool ComiR; la versione originale di ComiR considerava soltanto i siti di legame dei miRNA collocati nella regione 3'UTR dell'RNA messaggero. La nuova versione di ComiR include nella ricerca dei legami la regione codificante dell'RNA messaggero. Bertolazzi’s thesis focuses on developing and applying computational methods to predict microRNA binding sites located on messenger RNA molecules. MicroRNAs (miRNAs) regulate gene expression by binding target messenger RNA molecules (mRNAs). Therefo…

Mapreduce in computational biology - A synopsis

2017

In the past 20 years, the Life Sciences have witnessed a paradigm shift in the way research is performed. Indeed, the computational part of biological and clinical studies has become central or is becoming so. Correspondingly, the amount of data that one needs to process, compare and analyze, has experienced an exponential growth. As a consequence, High Performance Computing (HPC, for short) is being used intensively, in particular in terms of multi-core architectures. However, recently and thanks to the advances in the processing of other scientific and commercial data, Distributed Computing is also being considered for Bioinformatics applications. In particular, the MapReduce paradigm, to…

Preface to "Computational Approaches: Drug Discovery and Design in Medicinal Chemistry and Bioinformatics"

2021

Fast comparison of DNA sequences by oligonucleotide profiling

2008

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.

Sparse Manifold Clustering and Embedding to discriminate gene expression profiles of glioblastoma and meningioma tumors.

2013

Sparse Manifold Clustering and Embedding (SMCE) algorithm has been recently proposed for simultaneous clustering and dimensionality reduction of data on nonlinear manifolds using sparse representation techniques. In this work, SMCE algorithm is applied to the differential discrimination of Glioblastoma and Meningioma Tumors by means of their Gene Expression Profiles. Our purpose was to evaluate the robustness of this nonlinear manifold to classify gene expression profiles, characterized by the high-dimensionality of their representations and the low discrimination power of most of the genes. For this objective, we used SMCE to reduce the dimensionality of a preprocessed dataset of 35 single…

Detection of condition-specific marker genes from RNA-seq data with MGFR

2019

The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups s…

Natural Language Parsing

2009

Automatic natural language processing captures a lion’s share of the attention in open information management. In one way or another, many applications have to deal with natural language input. In this chapter the authors investigate the problem of natural language parsing from the perspective of biolinguistics. They argue that the human mind succeeds in the parsing task without the help of languagespecific rules of parsing and language-specific rules of grammar. Instead, there is a universal parser incorporating a universal grammar. The main argument comes from language acquisition: Children cannot learn language specific parsing rules by rule induction due to the complexity of unconstrain…

Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti

2013

Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…

Electronic aspects of the hydride transfer mechanism. Ab initio analytical gradient studies of the cyclopropenyl‐cation/lithium hydride model reactan…

1985

The electronic mechanisms of a model hydride transfer reaction are theoretically studied with ab inito RHF and UHF SCF MO procedures at the 4‐31G basis set level and analytical gradient methods. The model system describes the reduction of cyclopropenyl cation to cyclopropene by the oxidation of lithium hydride to lithium cation. The molecular fragments corresponding to the asymptotic reactive channels characterizing the stepwise mechanisms currently discussed in the literature have been characterized. The binding energy between the fragments is estimated within a simple electrostatic approximate scheme. The results show that a hydride‐ion mechanism is a likely pathway for this particular sy…