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Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

Probabilistic cell-type assignment of single-cell RNA-seq fo...

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作者： Allen W. Zhang Ciara O’Flanagan Elizabeth A. Chavez Jamie L. Lim Nicholas Ceglia Andrew McPherson Matt Wiens Pascale Walters Tim Chan Brittany Hewitson Daniel Lai Anja Mottok Clementine Sarkozy Lauren Chong Tomohiro Aoki Xuehai Wang Andrew P Weng Jessica N. McAlpine Samuel Aparicio Christian Steidl Kieran R. Campbell Sohrab P. Shah

Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via ‘mapping’ to existing data. However, manual interpretation scales poorly to large datasets, mapping approaches require purified or pre-annotated data and both are prone to batch effects. To overcome these issues, we present CellAssign, a probabilistic model that leverages prior knowledge of cell-type marker genes to annotate single-cell RNA sequencing data into predefined or de novo cell types. CellAssign automates the process of assigning cells in a highly scalable manner across large datasets while controlling for batch and sample effects. We demonstrate the advantages of CellAssign through extensive simulations and analysis of tumor microenvironment composition in high-grade serous ovarian cancer and follicular lymphoma.

关键词： Genomics Single-cell RNA-seq Statistical Inference Differential Expression Analysis Cell And Tissue Culture Cell Enrichment Library Preparation Principal Component Analysis Immunohistochemistry Seurat Data analysis programming language Computational models Statistical methods Cancer microenvironment

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XML for Data Representation and Model Specification in Neuroscience

XML for Data Representation and Model Specification in Neuro...

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作者： Sharon M. Crook Fred W. Howell

EXtensible Markup language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) reading and writing XML from applications, (2) exporting XML from databases, (3) using XML standards to represent neuronal morphology data, (4) using XML to represent experimental metadata, and (5) creating new XML specifications for models. less

关键词： Data Mining Electrophysiology programming language Data analysis XML MorphML NeuroML neuronal morphology neuroinformatics

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Understanding language Profile of Open Source Software using Association Rule Mining

Understanding Language Profile of Open Source Software using...

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Future Technologies Conference

作者： Munish Saini Kuljit Kaur Chahal Dept. of Computer Science Guru Nanak Dev University

ISBN: (纸本)9781509041725

The development of open source software has gained popularity. Most of the software projects use diverse sets of programming languages for development. In this work, the Knowledge Discovery in Data (KDD) approach to analyze the data of 30,518 open source projects hosted on SourceForge. The process of knowledge discovery is explored by using the association rule mining algorithm to find the programming languages, which are often used together in combination for the development of software project. The group-matrix based visualization technique is further implied to visualize the generated associated group of languages. The generated knowledge base and visualization of associated languages provide current and future developers with insight knowledge of multiple set of programming languages which are used together frequently for the development of open source software projects.

关键词： Open source software programming language Association rule mining Knowledge discovery in data (KDD) Group-matrix based visualization

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Physiologically Based Pharmacokinetic/Toxicokinetic Modeling

Physiologically Based Pharmacokinetic/Toxicokinetic Modeling

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作者： Jerry L. Campbell Rebecca A. Clewell P. Robinan Gentry Melvin E. Andersen Harvey J. Clewell

Physiologically based pharmacokinetic (PBPK) models differ from conventional compartmental pharmacokinetic models in that they are based to a large extent on the actual physiology of the organism. The application of pharmacokinetics to toxicology or risk assessment requires that the toxic effects in a particular tissue are related in some way to the concentration time course of an active form of the substance in that tissue. The motivation for applying pharmacokinetics is the expectation that the observed effects of a chemical will be more simply and directly related to a measure of target tissue exposure than to a measure of administered dose. The goal of this work is to provide the reader with an understanding of PBPK modeling and its utility as well as the procedures used in the development and implementation of a model to chemical safety assessment using the styrene PBPK model as an example. less

关键词： Tube Feeding Monte Carlo Simulations MATLAB Statistical Calculation programming language Styrene Pharmacokinetics PBPK

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Monitoring early S-phase origin firing and replication fork movement by sequencing nascent DNA from synchronized cells

Monitoring early S-phase origin firing and replication fork ...

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作者： Morgane Macheret Thanos D. Halazonetis

A better understanding of DNA replication initiation in human cells and how this process is altered upon DNA replication stress requires the ability to study origin firing genome wide. Previously described methods of mapping DNA replication origins in higher eukaryotes rely principally on fractionation of DNA fragments based on their size and, optionally, on the presence of ribonucleotides at their 5ʹ end. Here, we describe a protocol for EdUseq-HU, a method for mapping early S-phase replication origins. Cells, synchronized by mitotic shake-off, are released in medium containing 5-ethynyl-2′-deoxyuridine (EdU; to label nascent DNA) and hydroxyurea (HU; to limit fork progression after origin firing). After using click chemistry to tag the EdU label with a biotin conjugate that is cleavable under mild conditions, the nascent DNA is captured on streptavidin beads. One variant of EdUseq-HU allows mapping of DNA replication origins on the genome at a resolution of 10 kb, and a second variant monitors progression of replication forks. Using EdUseq-HU, the spatiotemporal program of DNA replication in human cell lines can be interrogated in <2 weeks. The protocol requires basic cell culture and molecular biology skills, as well as familiarity with the Perl programming language and the Linux operating system. less

关键词： Cell And Tissue Culture Cell Separation And Isolation Cell Fixation Flow Cytometry DNA Extraction Library Preparation Fractionation Click Chemistry Trypsination Sonication ChIP Assay Genome Visualization Electrophoresis programming language TruSeq Mycoplasma U2OS DNA replication Origin firing

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Identification of

Identification of

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作者： Leonardo Mariño-Ramírez Kannan Tharakaraman Olivier Bodenreider John Spouge David Landsman

Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology–derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes. less

关键词： Microarray Simulated Annealing Cytoscape Multiple Sequence Alignment programming language gene ontology networks Promoter sequences co-expression transcription factor–binding sites Gibbs sampling

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3D Printing of Functionally Graded Films by Controlling Process Parameters

3D Printing of Functionally Graded Films by Controlling Proc...

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作者： Alessandra Bonfanti Loris Domenicale Atul Bhaskar

Scaffolds are often used in bioengineering to replace damaged tissues. They promote cell ingrowth and provide mechanical support until cells regenerate. Such scaffolds are often made using the additive manufacturing process, given its ability to create complex shapes, affordability, and the potential for patient-specific solutions. The success of the implant is closely related to the match of the scaffold mechanical properties to those of the host tissue. Many biological tissues show properties that vary in space. Therefore, the aim is to manufacture materials with variable properties, commonly referred to as functionally graded materials. Here we present a novel technique used to manufacture porous films with functionally graded properties using 3D printers. Such an approach exploits the control of a process parameter, without any hardware modification. The mechanical properties of the manufactured films have been experimentally tested and analytically characterized. less

关键词： Extrusion programming language Additive manufacturing Functionally graded material Graded films G-code Process parameter

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Identification of Genomic Alterations Through Multilevel DNA Structural Analysis

Identification of Genomic Alterations Through Multilevel DNA...

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作者： Ryan K. Shultzaberger John Dresios

Current methods to identify genomic alterations using whole-genome sequencing (WGS) data are often limited to single nucleotide polymorphismsSingle nucleotide polymorphism (SNP) and insertions and deletions that are less than 10 bp in length. These limitations are largely due to challenges in accurately mapping short sequencing reads that significantly diverge from the reference genome. Newer sequencing-based methods have been developed to define and characterize larger DNA structural elements. This is achieved by enriching for and sequencing regions of the genome that contain a specific element, followed by identifying genomic regions with high densities of mapped short reads that designate the location of these elements. This process essentially aggregates short read data into larger structural units for further characterization. Here, we describe protocols for identifying various types of genomic alterations using differential analysis of these structural units. We focus on changes in DNA accessibility, protein–DNA interactions, and chromosomal contacts as measured by ATAC-Seq, ChIP-Seq, and Hi-C respectively. As many protocols have been published describing the generation and processing of these data, we focus on simple methods that can be used to identify mutations in these data, and can be executed by someone with limited computational expertise. less

关键词： ChIP-seq ATAC-Seq Whole-genome Sequencing Immunoprecipitation Genetic Engineering Genomics PCR Sanger Sequencing programming language Genome Sequencing Chromatin Hi-C Mutation detection DNA–protein interactions DNA organization DNA accessibility

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Improving miRNA Target Prediction Using CLASH Data

Improving miRNA Target Prediction Using CLASH Data

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作者： Xiaoman Li Haiyan Hu

In this chapter, we present a computational method, TarPmiR, for miRNA target prediction. TarPmiR is based on emerging features of miRNA–target interactions learned from CLASH (crosslinking, ligation and sequencing of hybrids) data. First, we introduce miRNA target prediction, delineate existing methods for miRNA target prediction, and discuss their usage and limitations. Next, we describe available CLASH data, the learning of new miRNA binding features from CLASH data, and the usage of CLASH features in miRNA target prediction. Finally, we detail the computational pipeline of TarPmiR, discuss its performance compared with existing computational methods for miRNA target prediction, and present its installation and usage for miRNA target prediction. This chapter will facilitate the common understanding of CLASH data, new characteristics of miRNA–target interactions, and the use of the CLASH based miRNA target prediction tool TarPmiR. less

关键词： Machine Learning High-Throughput Sequencing CLIP-Seq PAR-CLIP Python programming language miRNA miRNA target prediction CLASH data New features TarPmiR

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Statistical Methods for Identifying Differentially Expressed Gene Combinations

Statistical Methods for Identifying Differentially Expressed...

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作者： Yen-Yi Ho Leslie Cope Marcel Dettling Giovanni Parmigiani

Identification of coordinate gene expression changes across phenotypes or biological conditions is the basis of the ability to decode the role of gene expression regulatory networks. Statistically, the identification of these changes can be viewed as a search for groups (most typically pairs) of genes whose expression provides better phenotype discrimination when considered jointly than when considered individually. Such groups are defined as being jointly differentially expressed. In this chapter several approaches for identifying jointly differentially expressed groups of genes are reviewed of compared on a set of simulations. less

关键词： Microarray Statistical Calculation programming language correlation entropy High-order interactions liquid correlation joint differential expression

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