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检索条件"主题词=Programming language"

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Molecular Descriptors for Structure–Activity Applications: A Hands-On Approach

Molecular Descriptors for Structure–Activity Applications: ...

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作者： Francesca Grisoni Davide Ballabio Roberto Todeschini Viviana Consonni

Molecular descriptors capture diverse parts of the structural information of molecules and they are the support of many contemporary computer-assisted toxicological and chemical applications. After briefly introducing some fundamental concepts of structure–activity applications (e.g., molecular descriptor dimensionality, classical vs. fingerprint description, and activity landscapes), this chapter guides the readers through a step-by-step explanation of molecular descriptors rationale and application. To this end, the chapter illustrates a case study of a recently published application of molecular descriptors for modeling the activity on cytochrome P450. less

关键词： Database Search Dissection Statistical Calculation MATLAB Principal Component Analysis Machine Learning Decision Tree programming language Python Molecular similarity QSAR Molecular descriptors Chemical space Mathematical chemistry

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Identification of Disease-Related Genes Using a Genome-Wide Association Study Approach

Identification of Disease-Related Genes Using a Genome-Wide ...

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作者： Tobias Wohland Dorit Schleinitz

Genome-wide association studies (GWAS) provide a hypothesis-free approach to discover genetic variants contributing to the risk of a certain disease or disease-related trait. Ongoing efforts to annotate the human genome have helped to localize disease-causing variants and point to mechanisms by which genetic variants might exert functional effects. By integrating bioinformatics approaches with in vivo and in vitro genomic strategies to predict and subsequently validate the functional roles of GWAS-identified variants, disease-related pathways can be characterized, providing new possibilities for therapeutic intervention. Here, we describe a basic workflow, from sample preparation to data analysis, for performing a GWAS to identify disease genes. We also discuss resources for the annotation and interpretation of GWAS results. less

关键词： SNP Annotation Genome-Wide Association Study DNA Extraction Spectroscopy Genotyping Statistical Calculation ANNOVAR Genome Visualization Data analysis Python programming language Ensembl R Affymetrix Illumina GWAS GenABEL

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Quantitative Prioritization of Tool Compounds for Phenotypic Screening

Quantitative Prioritization of Tool Compounds for Phenotypic...

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作者： Yuan Wang Jeremy L. Jenkins

Phenotypic screens are increasingly utilized in drug discovery for multiple purposes such as lead and/or tool compound finding, and target discovery. Using potent and selective chemical tool compounds against well-defined targets in phenotypic screens can help elucidate biological processes modulating assay phenotypes. Unfortunately the identification of such tools from large heterogeneous bioactivity databases is nontrivial and there is repeated use of published unselective compounds as phenotypic tools. Here we describe a computational model, the compound-target tool score (TS), which is an evidence-based quantitative confidence metric that can be used to systematically rank tool compounds for targets. The identified selective and nonselective tool compounds have applications in phenotypic assays for target hypothesis validation as well as assay development. less

关键词： Statistical Calculation Reporter Assay programming language Phenotypic screen Selectivity Chemical probe Tool compound Target hypothesis validation Bioactivity data integration

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BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing

BLASTmap: A Shiny-Based Application to Visualize BLAST Resul...

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作者： Katie Baker Gordon Stephen Shona Strachan Miles Armstrong Ingo Hein

Numerous genes that determine the outcome of plant–pathogen interactions are currently being discovered and include, for example, immune receptors, susceptibility factors and pathogen effectors and their host targets. Target enrichment sequencing provides a means to preferentially resequence these genes of interest without the need to first generate a genotype-specific genome assembly. The Basic Local Alignment Search Tool (BLAST), in combination with the here developed BLASTmap, can be used to design probes that specifically target such gene(s), either by using the target species or the closest related genus as a reference. BLAST is a ubiquitous tool in biological sequence analysis and a multitude of programs are available for the visualization of BLAST alignments. However, there are currently no dedicated programs for visual comparison of large-scale BLAST output attributes such as bit score. The need to quickly and efficiently compare many thousands of BLAST results led to the development of BLASTmap, an interactive web application created using the Shiny R package, customized for clustering and viewing BLAST results as an interactive heat map. Here we show an example of how BLASTmap was successfully applied to analyze custom DNA/RNA probe sequences and to visually determine that four probes are sufficient for the specific yet inclusive enrichment of the potato R2 disease resistance gene family. less

关键词： Genome Assembly Sequence Analysis programming language Enrichment Protein sequence BLAST DNA sequence Interactive map Bait design

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Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage

Tissue Multiplatform-Based Metabolomics/Metabonomics for Enh...

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作者： Panagiotis A. Vorkas M. R. Abellona U Jia V. Li

The use of tissue as a matrix to elucidate disease pathology or explore intervention comes with several advantages. It allows investigation of the target alteration directly at the focal location and facilitates the detection of molecules that could become elusive after secretion into biofluids. However, tissue metabolomics/metabonomics comes with challenges not encountered in biofluid analyses. Furthermore, tissue heterogeneity does not allow for tissue aliquoting. Here we describe a multiplatform, multi-method workflow which enables metabolic profiling analysis of tissue samples, while it can deliver enhanced metabolome coverage. After applying a dual consecutive extraction (organic followed by aqueous), tissue extracts are analyzed by reversed-phase (RP-) and hydrophilic interaction liquid chromatography (HILIC-) ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy. This pipeline incorporates the required quality control features, enhances versatility, allows provisional aliquoting of tissue extracts for future guided analyses, expands the range of metabolites robustly detected, and supports data integration. It has been successfully employed for the analysis of a wide range of tissue types. less

关键词： Metabolomics Metabolic Phenotyping Lipidomics NMR Tissue Extraction Dissection Ultra-performance Liquid Chromatography Mass Spectrometry Liquid Chromatography (LC) Liquid Chromatography-mass Spectrometry Capillary Electrophoresis (CE) Tandem Mass Spectrometry Statistical Calculation Principal Component Analysis Database Search Collision-induced Dissociation Sonication 1D NMR Spectroscopy MATLAB Statistical Total Correlation Spectroscopy 2D NMR Spectroscopy 1H--1H Correlation Spectroscopy 1H-13C Heteronuclear Single Quantum Coherence 13C-1H HMBC Liquid Chromatography-NMR Cytoscape Electrospray Ionization (ESI) programming language Extraction Tissue Metabolome HILIC Lipidome Metabolic profiling UPLC-MS MSE Coverage Multiplatform

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Development and Multiparametric Evaluation of Experimental Atherosclerosis in Rabbits

Development and Multiparametric Evaluation of Experimental A...

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作者： Max L. Senders Mark E. Lobatto Raphael Soler Olivier Lairez Carlos Pérez-Medina Claudia Calcagno Zahi A. Fayad Willem J. Mulder Francois Fay

Several animal models have been developed to study atherosclerosis. Here we present a rabbit atherosclerosis model generated by surgical denudation of the aortic endothelium in combination with a high-fat and cholesterol-enriched diet. This model is characterized by the formation of vascular lesions that exhibit several hallmarks of human atherosclerosis. Due to the rabbit’s relative large size, as compared to rodents, this model is suited for the imaging-guided evaluation of novel therapeutic strategies using clinical scanners. In this chapter, we present an extensive outline of the procedures to induce aortic atherosclerotic lesions in rabbits as well as methods to evaluate the disease, including noninvasive in vivo multiparametric imaging and histopathology. less

关键词： Intramuscular Injection Surgery Fluoroscopy Tomography MRI Intravenous Injection Hematoxylin And Eosin Staining Sterilization Dissection DNA Ligation programming language Oryctolagus cuniculus Translational Imaging model PET/MRI Anti-rabbit

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A reassessment of DNA-immunoprecipitation-based genomic profiling

A reassessment of DNA-immunoprecipitation-based genomic prof...

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作者： Antonio Lentini Cathrine Lagerwall Svante Vikingsson Heidi K. Mjoseng Karolos Douvlataniotis Hartmut Vogt Henrik Green Richard R. Meehan Mikael Benson Colm E. Nestor

DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, the results of independent DIP-seq studies often show considerable variation between profiles of the same genome and between profiles obtained by alternative methods. Here we show that these differences are primarily due to the intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50–99% of regions identified as ‘enriched’ for DNA modifications in DIP-seq data. Correction of this error profoundly altered DNA-modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently revealed novel associations among DNA modifications, chromatin modifications and biological processes. We conclude that both matched input and IgG controls are essential in order for the results of DIP-based assays to be interpreted correctly, and that complementary, non-antibody-based techniques should be used to validate DIP-based findings to avoid further misinterpretation of genome-wide profiling data. less

关键词： DNA Sequencing Methylation Analysis Cell And Tissue Culture DNA Extraction ELISA Mass Spectrometry PCR Statistical Calculation Immunoprecipitation Real-time PCR Gradient Elution Dot Blot Cross-linking Bowtie Bisulfite Sequencing ChIP-seq Metagenomics Genome Visualization bedtools programming language Epigenomics Epigenetics Anti-5-hmC Anti-rabbit Anti-mouse

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From RNA-seq to Biological Inference: Using Compositional Data Analysis in Meta-Transcriptomics

From RNA-seq to Biological Inference: Using Compositional Da...

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作者： Jean M. Macklaim Gregory B. Gloor

The proper analysis of high-throughput sequencing datasets of mixed microbial communities (meta-transcriptomics) is substantially more complex than for datasets composed of single organisms. Adapting commonly used RNA-seq methods to the analysis of meta-transcriptome datasets can be misleading and not use all the available information in a consistent manner. However, meta-transcriptomic experiments can be investigated in a principled manner using Bayesian probabilistic modeling of the data at a functional level coupled with analysis under a compositional data analysis paradigm. We present a worked example for the differential functional evaluation of mixed-species microbial communities obtained from human clinical samples that were sequenced on an Illumina platform. We demonstrate methods to functionally map reads directly, conduct a compositionally appropriate exploratory data analysis, evaluate differential relative abundance, and finally identify compositionally associated (constant ratio) functions. Using these approaches we have found that meta-transcriptomic functional analyses are highly reproducible and convey significant information regarding the ecosystem. less

关键词： Transcriptomics RNA-seq High-Throughput Sequencing RNA Extraction Library Preparation Bowtie DNA Translation Statistical Calculation Real-time PCR Data analysis programming language Microbiome Bayesian inference Compositional data Probability distribution Standardized effect Meta-transcriptome

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Selection of Informative Examples in Chemogenomic Datasets

Selection of Informative Examples in Chemogenomic Datasets

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作者： Daniel Reker J. B. Brown

High-throughput and high-content screening campaigns have resulted in the creation of large chemogenomic matrices. These matrices form the training data which is used to build ligand–target interaction models for pharmacological and chemical biology research. While academic, government, and industrial efforts continuously add to the ligand–target data pairs available for modeling, major research efforts are devoted to improving machine learning techniques to cope with the sparseness, heterogeneity, and size of available datasets as well as inherent noise and bias. This “race of arms” has led to the creation of algorithms to generate highly complex models with high prediction performance at the cost of training efficiency as well as interpretability. In contrast, recent studies have challenged the necessity for “big data” in chemogenomic modeling and found that models built on larger numbers of examples do not necessarily result in better predictive abilities. Automated adaptive selection of the training data (ligand–target instances) used for model creation can result in considerably smaller training sets that retain prediction performance on par with training using hundreds of thousands of data points. In this chapter, we describe the protocols used for one such iterative chemogenomic selection technique, including model construction and update as well as possible techniques for evaluations of constructed models and analysis of the iterative model construction. less

关键词： Data Mining Machine Learning MACCS Key Decision Tree Artificial Intelligence Phylogenetic Tree Generation Statistical Calculation Python programming language Data analysis Sampling Active learning Subset selection Model complexity

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Evaluation of variability in human kidney organoids

Evaluation of variability in human kidney organoids

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作者： Belinda Phipson Pei X. Er Alexander N. Combes Thomas A. Forbes Sara E. Howden Luke Zappia Hsan-Jan Yen Kynan T. Lawlor Lorna J. Hale Jane Sun Ernst Wolvetang Minoru Takasato Alicia Oshlack Melissa H. Little

The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although individual organoids within a differentiation batch showed strong transcriptional correlation, we noted significant variation between experimental batches, particularly in genes associated with temporal maturation. Single-cell profiling revealed shifts in nephron patterning and proportions of component cells. Distinct induced pluripotent stem cell clones showed congruent transcriptional programs, with interexperimental and interclonal variation also strongly associated with nephron patterning. Epithelial cells isolated from organoids aligned with total organoids at the same day of differentiation, again implicating relative maturation as a confounder. This understanding of experimental variation facilitated an optimized analysis of organoid-based disease modeling, thereby increasing the utility of kidney organoids for personalized medicine and functional genomics. less

关键词： Statistical Calculation Immunofluorescence RNA-seq Functional Genomics Confocal Microscopy Surface Rendering Image Processing Fiji Immunofluorescence Microscopy Quantitative Reverse Transcription PCR Real-time PCR Cell And Tissue Culture RNA Extraction Genomics Differential Expression Analysis Single-cell RNA-seq Data analysis Organoid Culture programming language Seurat Homo sapiens Computational models Induced pluripotent stem cells Stem-cell research Anti-E-cadherin

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