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Parallel biological computing
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CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis and visualization of the resulting datasets, we develop CRISPRO, a computational pipeline that maps functional scores associated with guide RNAs to genomes, transcripts, and protein coordinates and structures.
19p
vigalileogalilei
27-02-2022
16
1
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High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the different types of NGS data, there are certain common challenging steps involved in analysing those data.
13p
vikentucky2711
26-11-2020
21
0
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Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators.
13p
vioklahoma2711
19-11-2020
14
1
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A gene regulatory network (GRN) represents interactions of genes inside a cell or tissue, in which vertexes and edges stand for genes and their regulatory interactions respectively. Reconstruction of gene regulatory networks, in particular, genome-scale networks, is essential for comparative exploration of different species and mechanistic investigation of biological processes.
8p
vioklahoma2711
19-11-2020
7
1
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Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging.
13p
vioklahoma2711
19-11-2020
7
1
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The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models.
24p
vioklahoma2711
19-11-2020
13
1
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RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maximization, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model.
10p
viflorida2711
30-10-2020
19
2
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The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level.
10p
viflorida2711
30-10-2020
11
2
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Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration.
18p
viflorida2711
30-10-2020
43
2
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RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology.
12p
viconnecticut2711
29-10-2020
7
1
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Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used for gene regulatory network inference, with both successes and limitations.
19p
vijisoo2711
27-10-2020
13
1
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Genome-scale metabolic models are increasingly employed to predict the phenotype of various biological systems pertaining to healthcare and bioengineering. To characterize the full metabolic spectrum of such systems, Fast Flux Variability Analysis (FFVA) is commonly used in parallel with static load balancing.
13p
vicolorado2711
22-10-2020
19
2
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Massively parallel genetic sequencing allows rapid testing of known intellectual disability (ID) genes. However, the discovery of novel syndromic ID genes requires molecular confirmation in at least a second or a cluster of individuals with an overlapping phenotype or similar facial gestalt.
9p
vihamax2711
21-04-2020
16
0
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Bioinformatics is a growing multidisciplinary field of science comprising biology, computer science, and mathematics. It is the theoretical and computational arm of modern biology. In other words, bioinformatics is a tool in the hands of biologists for analyzing huge amount of biological data available on mainstream public databases. Currently, bioinformatics has gained variety of applications in agriculture, medicine, engineering, and natural science. This book discusses a small portion of these applications along with basic concepts and fundamental techniques in bioinformatics....
736p
greengrass304
15-09-2012
91
15
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In the fourth chapter of this section, the authors present a modification of the Crank- Nicholson scheme for two-dimensional fluid mechanical, heat and mass transfer problems. The modification divides the nodal points into groups of four. The method is applicable to parallel computing, which is increasing in importance as problems become more computationally intensive. Computational experiments demonstrate improved convergence rates over previous methods.
0p
contentnew
12-04-2012
99
13
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Artificial neural network (ANN) models have been extensively studied with the aim of achieving human-like performance, especially in the field of pattern recognition. These networks are composed of a number of nonlinear computational elements which operate in parallel and are arranged in a manner reminiscent of biological neural interconnections. ANNs are known by many names such as connectionist models, parallel distributed processing models and neuromorphic systems (Lippmann 1987).
8p
doroxon
12-08-2010
115
23
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