Search results for " BioInformatics."

Discovering discriminative graph patterns from gene expression data

2016

We consider the problem of mining gene expression data in order to single out interesting features characterizing healthy/unhealthy samples of an input dataset. We present an approach based on a network model of the input gene expression data, where there is a labelled graph for each sample. To the best of our knowledge, this is the first attempt to build a different graph for each sample and, then, to have a database of graphs for representing a sample set. Our main goal is that of singling out interesting differences between healthy and unhealthy samples, through the extraction of "discriminative patterns" among graphs belonging to the two different sample sets. Differently from the other…

SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments

2017

Abstract Motivation Due to their universal applicability, global stochastic optimization methods are popular for designing improvements of biochemical networks. The drawbacks of global stochastic optimization methods are: (i) no guarantee of finding global optima, (ii) no clear optimization run termination criteria and (iii) no criteria to detect stagnation of an optimization run. The impact of these drawbacks can be partly compensated by manual work that becomes inefficient when the solution space is large due to combinatorial explosion of adjustable parameters or for other reasons. Results SpaceScanner uses parallel optimization runs for automatic termination of optimization tasks in case…

Biomolecular computers with multiple restriction enzymes

2017

Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…

How to deal with Haplotype data: An Extension to the Conceptual Schema of the Human Genome

2016

[EN] The goal of this work is to describe the advantages of the application of Conceptual Modeling (CM) in complex domains, such as genomics. Nowadays, the study and comprehension of the human genome is a major challenge due to its high level of complexity. The constant evolution in the genomic domain contributes to the generation of ever larger amounts of new data, which means that if we do not manage it correctly data quality could be compromised (i.e., problems related with heterogeneity and inconsistent data). In this paper, we propose the use of a Conceptual Schema of the Human Genome (CSHG), designed to understand and improve our ontological commitment to the domain and also extend (e…

Molecular Pathways Mediating Immunosuppression in Response to Prolonged Intensive Physical Training, Low-Energy Availability, and Intensive Weight Lo…

2019

Exercise and exercise-induced weight loss have a beneficial effect on overall health, including positive effects on molecular pathways associated with immune function, especially in overweight individuals. The main aim of our study was to assess how energy deprivation (i.e., "semi-starvation") leading to substantial fat mass loss affects the immune system and immunosuppression in previously normal weight individuals. Thus, to address this hypothesis, we applied a high-throughput systems biology approach to better characterize potential key pathways associated with immune system modulation during intensive weight loss and subsequent weight regain. We examined 42 healthy female physique athle…

Paving the way for synthetic biology-based bioremediation in Europe

2009

Synthetic biology (SB) has a dual definition. It is both the design and construction of new biological parts, devices and systems, and also the re‐design of existing, natural systems for useful purposes. The latter field is maybe one of the major challenges within this discipline, since the promising prospect that biological systems may be used as biomachines will certainly be exploited in the near future. Synthetic biology has challenging conceptual possibilities (Moya et al., 2009a) and impressive progress has already been made in biotechnology following SB approaches (de Lorenzo and Danchin, 2008). Much more is expected in the near future from current efforts aiming to make synthetic gen…

MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments

2020

Multiple sequence alignments are usually phylogenetically driven. They are studied in the framework of evolution. But sometimes, it is interesting to study residue conservation at positions unconstrained by evolutionary rules. We present a supervised method to access a layer of information difficult to appreciate visually when many protein sequences are aligned. This new tool (MAGA; http://cbdm-01.zdv.uni-mainz.de/~munoz/maga/ ) locates positions in multiple sequence alignments differentially conserved in manually defined groups of sequences.

Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts

2019

Abstract In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pe…

DNA MICROARRAY AND BIOINFORMATICS AS TOOLS TO IDENTIFY A COMMON MOLECULAR SIGNATURE SHARED BY HUMAN ANEUPLOID CELLS

Genomic instability is a hallmark of the majority of human tumors explaining the heterogeneity shown by tumor cells. This phenomenon is often associated with chromosomal instability (CIN) and aneuploidy, a condition in which tumor cells lose or gain chromosomes. Previously, we showed that posttranscriptional silencing by RNAi of pRb(1), DNMT1(2) and MAD2(3) is associated with aneuploidy in cultured human cells reinforcing the idea that there are several roads leading to aneuploidy. In the attempt to understand if a common molecular signature exists that underlies aneuploidy and its tolerance in tumor cells, we did post transcriptional silencing of Rb, MAD2 and DNMT1 in human fibroblasts (IM…

Intrusion Detection with Interpretable Rules Generated Using the Tsetlin Machine

2020

The rapid deployment in information and communication technologies and internet-based services have made anomaly based network intrusion detection ever so important for safeguarding systems from novel attack vectors. To this date, various machine learning mechanisms have been considered to build intrusion detection systems. However, achieving an acceptable level of classification accuracy while preserving the interpretability of the classification has always been a challenge. In this paper, we propose an efficient anomaly based intrusion detection mechanism based on the Tsetlin Machine (TM). We have evaluated the proposed mechanism over the Knowledge Discovery and Data Mining 1999 (KDD’99) …