Search results for " BioInformatics."

Overload breakdown in models for photosynthesis

2015

In many models of the Calvin cycle of photosynthesis it is observed that there are solutions where concentrations of key substances belonging to the cycle tend to zero at late times, a phenomenon known as overload breakdown. In this paper we prove theorems about the existence and non-existence of solutions of this type and obtain information on which concentrations tend to zero when overload breakdown occurs. As a starting point we take a model of Pettersson and Ryde-Pettersson which seems to be prone to overload breakdown and a modification of it due to Poolman which was intended to avoid this effect.

Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning

2014

Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms of k-mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k-mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open. Results: We present the first analysis on the role of k-mers in the composition of nucleosome enriched and depleted genomic regions (NER and NDR for short) that is: (i) exhau…

Antimicrobial Activity, in silico Molecular Docking, ADMET and DFT Analysis of Secondary Metabolites from Roots of Three Ethiopian Medicinal Plants

2021

Mathewos Anza,1 Milkyas Endale,1 Luz Cardona,2 Diego Cortes,3 Rajalakshmanan Eswaramoorthy,1 Jesus Zueco,4 Hortensia Rico,4 Maria Trelis,5 Belen Abarca2 1Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia; 2Department of Organic Chemistry, Faculty of Chemistry, University of Valencia, Burjassot, Spain; 3Department of Pharmacology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain; 4Department of Microbiology and Ecology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain; 5Parasites and Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy…

AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation

2020

Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not only makes them challenging to understand and extend, but also difficult to port to other platforms. We present AnySeq - a novel library for computing different types of pairwise alignments of DNA sequences. Our approach combines high performance with an intuitively understandable implementation, which is achieved through the concept of partial evaluation. Using the AnyDSL compiler framework, AnySeq enables the compilation of algorithmic variants that ar…

Extending the Tsetlin Machine With Integer-Weighted Clauses for Increased Interpretability

2020

Despite significant effort, building models that are both interpretable and accurate is an unresolved challenge for many pattern recognition problems. In general, rule-based and linear models lack accuracy, while deep learning interpretability is based on rough approximations of the underlying inference. Using a linear combination of conjunctive clauses in propositional logic, Tsetlin Machines (TMs) have shown competitive performance on diverse benchmarks. However, to do so, many clauses are needed, which impacts interpretability. Here, we address the accuracy-interpretability challenge in machine learning by equipping the TM clauses with integer weights. The resulting Integer Weighted TM (…

Interval Length Analysis in Multi Layer Model

2009

In this paper we present an hypothesis test of randomness based on the probability density function of the symmetrized Kulback-Leibler distance estimated, via a Monte Carlo simulation, by the distributions of the interval lengths detected using the Multi-Layer Model (MLM). The $MLM$ is based on the generation of several sub-samples of an input signal; in particular a set of optimal cut-set thresholds are applied to the data to detect signal properties. In this sense MLM is a general pattern detection method and it can be considered a preprocessing tool for pattern discovery. At the present the test has been evaluated on simulated signals which respect a particular tiled microarray approach …

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…