Search results for "Bioinformatics"
showing 10 items of 1632 documents
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
2015
This is a post-peer-review, pre-copyedit version of an article published in IEEE - ACM Transactions on Computational Biology and Bioinformatics. The final authenticated version is available online at: http://dx.doi.org/10.1109/TCBB.2015.2389958 [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. Computational methods to detect epistasis therefore suffer from prohibitively lon…
The ten grand challenges of synthetic life
2011
The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life i…
Protein data condensation for effective quaternary structure classification
2007
Many proteins are composed of two or more subunits, each associated with different polypeptide chains. The number and the arrangement of subunits forming a protein are referred to as quaternary structure. The quaternary structure of a protein is important, since it characterizes the biological function of the protein when it is involved in specific biological processes. Unfortunately, quaternary structures are not trivially deducible from protein amino acid sequences. In this work, we propose a protein quaternary structure classification method exploiting the functional domain composition of proteins. It is based on a nearest neighbor condensation technique in order to reduce both the porti…
Indexing a sequence for mapping reads with a single mismatch
2014
Mapping reads against a genome sequence is an interesting and useful problem in computational molecular biology and bioinformatics. In this paper, we focus on the problem of indexing a sequence for mapping reads with a single mismatch. We first focus on a simpler problem where the length of the pattern is given beforehand during the data structure construction. This version of the problem is interesting in its own right in the context of the next generation sequencing. In the sequel, we show how to solve the more general problem. In both cases, our algorithm can construct an efficient data structure in time and space and can answer subsequent queries in time. Here, n is the length of the s…
An Online Observer for Minimization of Pulsating Torque in SMPM Motors.
2015
A persistent problem of surface mounted permanent magnet (SMPM) motors is the non-uniformity of the developed torque. Either the motor design or the motor control needs to be improved in order to minimize the periodic disturbances. This paper proposes a new control technique for reducing periodic disturbances in permanent magnet (PM) electro-mechanical actuators, by advancing a new observer/estimator paradigm. A recursive estimation algorithm is implemented for online control. The compensating signal is identified and added as feedback to the control signal of the servo motor. Compensation is evaluated for different values of the input signal, to show robustness of the proposed method.
"Nanodentistry": exploring the beauty of miniature
2011
Feynman’s early vision in 1959 gave birth to the concept of nanotechnology. He saw it as an unavoidable development in the progress of science and said that there is plenty of room at the bottom. Since then, nanotechnology has been part of mainstream scientific theory with potential medical and dental applications. Numerous theoretical predictions have been made based on the potential applications of nanotechnology in dentistry, with varying levels of optimism. While a few layers of nanotechnologic capability have become a reality for oral health in the last decade, many of these applications are still in their puerile stage .The most substantial contribution of nanotechnology to dentistry …
CellMap visualizes protein-protein interactions and subcellular localization [version 2; referees: 2 approved]
2018
Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers.
A reliable and unbiased human protein network with the disparity filter
2017
AbstractThe living cell operates thanks to an intricate network of protein interactions. Proteins activate, transport, degrade, stabilise and participate in the production of other proteins. As a result, a reliable and systematically generated protein wiring diagram is crucial for a deeper understanding of cellular functions. Unfortunately, current human protein networks are noisy and incomplete. Also, they suffer from both study and technical biases: heavily studied proteins (e.g. those of pharmaceutical interest) are known to be involved in more interactions than proteins described in only a few publications. Here, we use the experimental evidence supporting the interaction between protei…
Bioinformatics and Computational Biology
2009
Bioinformatics is a new, rapidly expanding field that uses computational approaches to answer biological questions (Baxevanis, 2005). These questions are answered by means of analyzing and mining biological data. The field of bioinformatics or computational biology is a multidisciplinary research and development environment, in which a variety of techniques from computer science, applied mathematics, linguistics, physics, and, statistics are used. The terms bioinformatics and computational biology are often used interchangeably (Baldi, 1998; Pevzner, 2000). This new area of research is driven by the wealth of data from high throughput genome projects, such as the human genome sequencing pro…
Time-resolved imaging of pulse-induced magnetization reversal with a microwave assist field
2015
AbstractThe reversal of the magnetization under the influence of a field pulse has been previously predicted to be an incoherent process with several competing phenomena such as domain wall relaxation, spin wave-mediated instability regions and vortex-core mediated reversal dynamics. However, there has been no study on the direct observation of the switching process with the aid of a microwave signal input. We report a time-resolved imaging study of magnetization reversal in patterned magnetic structures under the influence of a field pulse with microwave assistance. The microwave frequency is varied to demonstrate the effect of resonant microwave-assisted switching. We observe that the swi…