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Liquid-handling Lego robots and experiments for STEM education and research.

PLoS biology Mar 21, 2017
Liquid-handling robots have many applications for biotechnology and the life sciences, with increasing impact on everyday life. While playful robotics such as Lego Mindstorms significantly support education initiatives in mechatronics and programming...
Schools Biotechnology Science Software Automation, Laboratory Robotics
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An empirical fuzzy multifactor dimensionality reduction method for detecting gene-gene interactions.

BMC genomics Mar 14, 2017
BACKGROUND: Detection of gene-gene interaction (GGI) is a key challenge towards solving the problem of missing heritability in genetics. The multifactor dimensionality reduction (MDR) method has been widely studied for detecting GGIs. MDR reduces the...
Fuzzy Logic Polymorphism, Single Nucleotide Datasets as Topic Humans Internet Genotype Epistasis, Genetic Crohn Disease Models, Genetic Software Multifactor Dimensionality Reduction Bipolar Disorder
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Artificial Neural Network System to Predict the Postoperative Outcome of Percutaneous Nephrolithotomy.

Journal of endourology Mar 13, 2017
PURPOSE: To construct, train, and apply an artificial neural network (ANN) system for prediction of different outcome variables of percutaneous nephrolithotomy (PCNL). We calculated predictive accuracy, sensitivity, and precision for each outcome var...
Tomography, X-Ray Computed Female Reproducibility of Results Adult Male Middle Aged Machine Learning Software Prospective Studies Humans Neural Networks, Computer Nephrolithotomy, Percutaneous Nephrostomy, Percutaneous Data Mining Lithotripsy Treatment Outcome Postoperative Period Blood Transfusion Kidney Calculi Models, Statistical
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Reproducibility of computational workflows is automated using continuous analysis.

Nature biotechnology Mar 13, 2017
Replication, validation and extension of experiments are crucial for scientific progress. Computational experiments are scriptable and should be easy to reproduce. However, computational analyses are designed and run in a specific computing environme...
Workflow Sensitivity and Specificity Gene Expression Profiling User-Computer Interface Computational Biology Machine Learning Software Reproducibility of Results
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predCar-site: Carbonylation sites prediction in proteins using support vector machine with resolving data imbalanced issue.

Analytical biochemistry Mar 9, 2017
The carbonylation is found as an irreversible post-translational modification and considered a biomarker of oxidative stress. It plays major role not only in orchestrating various biological processes but also associated with some diseases such as Al...
Models, Biological Protein Carbonylation Sequence Analysis, Protein Support Vector Machine Protein Processing, Post-Translational Proteins Algorithms Humans Computational Biology Software
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Bayesian molecular design with a chemical language model.

Journal of computer-aided molecular design Mar 9, 2017
The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techni...
Monte Carlo Method Small Molecule Libraries Bayes Theorem Models, Chemical Pharmaceutical Preparations Machine Learning Software Computer Simulation Computer-Aided Design Drug Design Molecular Structure
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Crystal Structure Representation for Neural Networks using Topological Approach.

Molecular informatics Mar 7, 2017
In the present work we describe a new approach, which uses topology of crystals for physicochemical properties prediction using artificial neural networks (ANN). The topologies of 268 crystal structures were determined using ToposPro software. Quotie...
Humans Models, Molecular Molecular Structure Entropy Neural Networks, Computer Software Algorithms
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GuideScan software for improved single and paired CRISPR guide RNA design.

Nature biotechnology Mar 6, 2017
We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. We a...
Machine Learning Chromosome Mapping Gene Silencing CRISPR-Cas Systems RNA, Small Interfering Clustered Regularly Interspaced Short Palindromic Repeats Software Algorithms Sequence Analysis, RNA
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Prediction of potent shRNAs with a sequential classification algorithm.

Nature biotechnology Mar 6, 2017
We present SplashRNA, a sequential classifier to predict potent microRNA-based short hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms previous algorithms and reliably predicts the most efficient shRNAs for a give...
Chromosome Mapping Gene Silencing CRISPR-Cas Systems RNA, Small Interfering Machine Learning Clustered Regularly Interspaced Short Palindromic Repeats Software Algorithms Sequence Analysis, RNA
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Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request.

Journal of biomedical semantics Mar 3, 2017
BACKGROUND: The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effectiveness research, primarily to...
Humans Analgesics, Opioid Software Data Mining Antimalarials Antihypertensive Agents Biological Ontologies Drug Monitoring
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