Statistical and Computational Methods for Analysis of Spatial Transcriptomics Data

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ISBN 13 :
Total Pages : 39 pages
Book Rating : 4.:/5 (119 download)

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Book Synopsis Statistical and Computational Methods for Analysis of Spatial Transcriptomics Data by : Dylan Maxwell Cable

Download or read book Statistical and Computational Methods for Analysis of Spatial Transcriptomics Data written by Dylan Maxwell Cable and published by . This book was released on 2020 with total page 39 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spatial transcriptomic technologies measure gene expression at increasing spatial resolution, approaching individual cells. One limitation of current technologies is that spatial measurements may contain contributions from multiple cells, hindering the discovery of cell type-specific spatial patterns of localization and expression. In this thesis, I will explore the development of Robust Cell Type Decomposition (RCTD), a computational method that leverages cell type profiles learned from single-cell RNA sequencing data to decompose mixtures, such as those observed in spatial transcriptomic technologies. Our RCTD approach accounts for platform effects introduced by systematic technical variability inherent to different sequencing modalities. We demonstrate RCTD provides substantial improvement in cell type assignment in Slide-seq data by accurately reproducing known cell type and subtype localization patterns in the cerebellum and hippocampus. We further show the advantages of RCTD by its ability to detect mixtures and identify cell types on an assessment dataset. Finally, we show how RCTD’s recovery of cell type localization uniquely enables the discovery of genes within a cell type whose expression depends on spatial environment. Spatial mapping of cell types with RCTD has the potential to enable the definition of spatial components of cellular identity, uncovering new principles of cellular organization in biological tissue.

Computational Methods for Single-Cell Data Analysis

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Publisher : Humana Press
ISBN 13 : 9781493990566
Total Pages : 271 pages
Book Rating : 4.9/5 (95 download)

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Book Synopsis Computational Methods for Single-Cell Data Analysis by : Guo-Cheng Yuan

Download or read book Computational Methods for Single-Cell Data Analysis written by Guo-Cheng Yuan and published by Humana Press. This book was released on 2019-02-14 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.

Computational Methods for Analysis of Spatial Trancsriptomics Data

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Publisher :
ISBN 13 : 9789180401425
Total Pages : pages
Book Rating : 4.4/5 (14 download)

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Book Synopsis Computational Methods for Analysis of Spatial Trancsriptomics Data by : Alma Andersson

Download or read book Computational Methods for Analysis of Spatial Trancsriptomics Data written by Alma Andersson and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Methods for Analysis and Modeling of Time-course Gene Expression Data

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (654 download)

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Book Synopsis Computational Methods for Analysis and Modeling of Time-course Gene Expression Data by :

Download or read book Computational Methods for Analysis and Modeling of Time-course Gene Expression Data written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genes encode proteins, some of which in turn regulate other genes. Such interactions make up gene regulatory relationships or (dynamic) gene regulatory networks. With advances in the measurement technology for gene expression and in genome sequencing, it has become possible to measure the expression level of thousands of genes simultaneously in a cell at a series of time points over a specific biological process. Such time-course gene expression data may provide a snapshot of most (if not all) of the interesting genes and may lead to a better understanding gene regulatory relationships and networks. However, inferring either gene regulatory relationships or networks puts a high demand on powerful computational methods that are capable of sufficiently mining the large quantities of time-course gene expression data, while reducing the complexity of the data to make them comprehensible. This dissertation presents several computational methods for inferring gene regulatory relationships and gene regulatory networks from time-course gene expression. These methods are the result of the authors doctoral study. Cluster analysis plays an important role for inferring gene regulatory relationships, for example, uncovering new regulons (sets of co-regulated genes) and their putative cis-regulatory elements. Two dynamic model-based clustering methods, namely the Markov chain model (MCM)-based clustering and the autoregressive model (ARM)-based clustering, are developed for time-course gene expression data. However, gene regulatory relationships based on cluster analysis are static and thus do not describe the dynamic evolution of gene expression over an observation period. The gene regulatory network is believed to be a time-varying system. Consequently, a state-space model for dynamic gene regulatory networks from time-course gene expression data is developed. To account for the complex time-delayed relationships in gene regulatory networks, the state space model is extended to.

Computational Methods for Image-Based Spatial Transcriptomics

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Publisher :
ISBN 13 : 9789151320526
Total Pages : 0 pages
Book Rating : 4.3/5 (25 download)

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Book Synopsis Computational Methods for Image-Based Spatial Transcriptomics by : Axel Andersson

Download or read book Computational Methods for Image-Based Spatial Transcriptomics written by Axel Andersson and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Methods for the Analysis of Genomic Data and Biological Processes

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Publisher :
ISBN 13 : 9783039437726
Total Pages : 222 pages
Book Rating : 4.4/5 (377 download)

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Book Synopsis Computational Methods for the Analysis of Genomic Data and Biological Processes by : Francisco A. Gómez Vela

Download or read book Computational Methods for the Analysis of Genomic Data and Biological Processes written by Francisco A. Gómez Vela and published by . This book was released on 2021 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.

Statistical Simulation and Analysis of Single-cell RNA-seq Data

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ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (141 download)

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Book Synopsis Statistical Simulation and Analysis of Single-cell RNA-seq Data by : Tianyi Sun

Download or read book Statistical Simulation and Analysis of Single-cell RNA-seq Data written by Tianyi Sun and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The recent development of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized transcriptomic studies by revealing the genome-wide gene expression levels within individual cells. In contrast to bulk RNA sequencing, scRNA-seq technology captures cell-specific transcriptome landscapes, which can reveal crucial information about cell-to-cell heterogeneity across different tissues, organs, and systems and enable the discovery of novel cell types and new transient cell states. According to search results from PubMed, from 2009-2023, over 5,000 published studies have generated datasets using this technology. Such large volumes of data call for high-quality statistical methods for their analysis. In the three projects of this dissertation, I have explored and developed statistical methods to model the marginal and joint gene expression distributions and determine the latent structure type for scRNA-seq data. In all three projects, synthetic data simulation plays a crucial role. My first project focuses on the exploration of the Beta-Poisson hierarchical model for the marginal gene expression distribution of scRNA-seq data. This model is a simplified mechanistic model with biological interpretations. Through data simulation, I demonstrate three typical behaviors of this model under different parameter combinations, one of which can be interpreted as one source of the sparsity and zero inflation that is often observed in scRNA-seq datasets. Further, I discuss parameter estimation methods of this model and its other applications in the analysis of scRNA-seq data. My second project focuses on the development of a statistical simulator, scDesign2, to generate realistic synthetic scRNA-seq data. Although dozens of simulators have been developed before, they lack the capacity to simultaneously achieve the following three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill in this gap, scDesign2 is developed as a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple scRNA-seq protocols and other single-cell gene expression count-based technologies. Compared with existing simulators, scDesign2 is advantageous in its transparent use of probabilistic models and is unique in its ability to capture gene correlations via copula. We verify that scDesign2 generates more realistic synthetic data for four scRNA-seq protocols (10x Genomics, CEL-Seq2, Fluidigm C1, and Smart-Seq2) and two single-cell spatial transcriptomics protocols (MERFISH and pciSeq) than existing simulators do. Under two typical computational tasks, cell clustering and rare cell type detection, we demonstrate that scDesign2 provides informative guidance on deciding the optimal sequencing depth and cell number in single-cell RNA-seq experimental design, and that scDesign2 can effectively benchmark computational methods under varying sequencing depths and cell numbers. With these advantages, scDesign2 is a powerful tool for single-cell researchers to design experiments, develop computational methods, and choose appropriate methods for specific data analysis needs. My third project focuses on deciding latent structure types for scRNA-seq datasets. Clustering and trajectory inference are two important data analysis tasks that can be performed for scRNA-seq datasets and will lead to different interpretations. However, as of now, there is no principled way to tell which one of these two types of analysis results is more suitable to describe a given dataset. In this project, we propose two computational approaches that aim to distinguish cluster-type vs. trajectory-type scRNA-seq datasets. The first approach is based on building a classifier using eigenvalue features of the gene expression covariance matrix, drawing inspiration from random matrix theory (RMT). The second approach is based on comparing the similarity of real data and simulated data generated by assuming the cell latent structure as clusters or a trajectory. While both approaches have limitations, we show that the second approach gives more promising results and has room for further improvements.

Computational Methods for the Analysis of Single-Cell RNA-Seq Data

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (119 download)

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Book Synopsis Computational Methods for the Analysis of Single-Cell RNA-Seq Data by : Marmar Moussa

Download or read book Computational Methods for the Analysis of Single-Cell RNA-Seq Data written by Marmar Moussa and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Single cell transcriptional profiling is critical for understanding cellular heterogeneity and identification of novel cell types and for studying growth and development of tissues and tumors. Leveraging recent advances in single cell RNA sequencing (scRNA-Seq) technology requires novel methods that are robust to high levels of technical and biological noise and scale to datasets of millions of cells. In this work, we address several challenges in the analysis work-flow of scRNA-Seq data: First, we propose novel computational approaches for unsupervised clustering of scRNA-Seq data based on Term Frequency - Inverse Document Frequency (TF-IDF) transformation that has been successfully used in text analysis. Here, we present empirical experimental results showing that TF-IDF methods consistently outperform commonly used scRNA-Seq clustering approaches. Second, we study the so called 'drop-out' effect that is considered one of the most notable challenges in scRNA-Seq analysis, where only a fraction of the transcriptome of each cell is captured. The random nature of drop-outs, however, makes it possible to consider imputation methods as means of correcting for drop-outs. In this part we study existing scRNA-Seq imputation methods and propose a novel iterative imputation approach based on efficiently computing highly similar cells. We then present results of a comprehensive assessment of existing and proposed methods on real scRNA-Seq datasets with varying per cell sequencing depth. Third, we present a computational method for assigning and/or ordering cells based on their cell-cycle stages from scRNA-Seq. And finally, we present a web-based interactive computational work-flow for analysis and visualization of scRNA-seq data.

Statistical and Computational Methods for Analyzing High-Throughput Genomic Data

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Publisher :
ISBN 13 :
Total Pages : 226 pages
Book Rating : 4.:/5 (858 download)

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Book Synopsis Statistical and Computational Methods for Analyzing High-Throughput Genomic Data by : Jingyi Li

Download or read book Statistical and Computational Methods for Analyzing High-Throughput Genomic Data written by Jingyi Li and published by . This book was released on 2013 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the burgeoning field of genomics, high-throughput technologies (e.g. microarrays, next-generation sequencing and label-free mass spectrometry) have enabled biologists to perform global analysis on thousands of genes, mRNAs and proteins simultaneously. Extracting useful information from enormous amounts of high-throughput genomic data is an increasingly pressing challenge to statistical and computational science. In this thesis, I will address three problems in which statistical and computational methods were used to analyze high-throughput genomic data to answer important biological questions. The first part of this thesis focuses on addressing an important question in genomics: how to identify and quantify mRNA products of gene transcription (i.e., isoforms) from next-generation mRNA sequencing (RNA-Seq) data? We developed a statistical method called Sparse Linear modeling of RNA-Seq data for Isoform Discovery and abundance Estimation (SLIDE) that employs probabilistic modeling and L1 sparse estimation to answer this ques- tion. SLIDE takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with existing deterministic isoform assembly algorithms, SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms. Simulation and real data studies show that SLIDE performs as well as or better than major competitors in both isoform discovery and abundance estimation. The second part of this thesis demonstrates the power of simple statistical analysis in correcting biases of system-wide protein abundance estimates and in understanding the rela- tionship between gene transcription and protein abundances. We found that proteome-wide surveys have significantly underestimated protein abundances, which differ greatly from previously published individual measurements. We corrected proteome-wide protein abundance estimates by using individual measurements of 61 housekeeping proteins, and then found that our corrected protein abundance estimates show a higher correlation and a stronger linear relationship with mRNA abundances than do the uncorrected protein data. To estimate the degree to which mRNA expression levels determine protein levels, it is critical to measure the error in protein and mRNA abundance data and to consider all genes, not only those whose protein expression is readily detected. This is a fact that previous proteome-widely surveys ignored. We took two independent approaches to re-estimate the percentage that mRNA levels explain in the variance of protein abundances. While the percentages estimated from the two approaches vary on different sets of genes, all suggest that previous protein-wide surveys have significantly underestimated the importance of transcription. In the third and final part, I will introduce a modENCODE (the Model Organism ENCyclopedia Of DNA Elements) project in which we compared developmental stages, tis- sues and cells (or cell lines) of Drosophila melanogaster and Caenorhabditis elegans, two well-studied model organisms in developmental biology. To understand the similarity of gene expression patterns throughout their development time courses is an interesting and important question in comparative genomics and evolutionary biology. The availability of modENCODE RNA-Seq data for different developmental stages, tissues and cells of the two organisms enables a transcriptome-wide comparison study to address this question. We undertook a comparison of their developmental time courses and tissues/cells, seeking com- monalities in orthologous gene expression. Our approach centers on using stage/tissue/cell- associated orthologous genes to link the two organisms. For every stage/tissue/cell in each organism, its associated genes are selected as the genes capturing specific transcriptional activities: genes highly expressed in that stage/tissue/cell but lowly expressed in a few other stages/tissues/cells. We aligned a pair of D. melanogaster and C. elegans stages/tissues/cells by a hypergeometric test, where the test statistic is the number of orthologous gene pairs associated with both stages/tissues/cells. The test is against the null hypothesis that the two stages/tissues/cells have independent sets of associated genes. We first carried out the alignment approach on pairs of stages/tissues/cells within D. melanogaster and C. elegans respectively, and the alignment results are consistent with previous findings, supporting the validity of this approach. When comparing fly with worm, we unexpectedly observed two parallel collinear alignment patterns between their developmental timecourses and several interesting alignments between their tissues and cells. Our results are the first findings regarding a comprehensive comparison between D. melanogaster and C. elegans time courses, tissues and cells.

Computational Methods for Multi-Omics Data Analysis in Cancer Precision Medicine

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Publisher : Frontiers Media SA
ISBN 13 : 2832530389
Total Pages : 433 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Computational Methods for Multi-Omics Data Analysis in Cancer Precision Medicine by : Ehsan Nazemalhosseini-Mojarad

Download or read book Computational Methods for Multi-Omics Data Analysis in Cancer Precision Medicine written by Ehsan Nazemalhosseini-Mojarad and published by Frontiers Media SA. This book was released on 2023-08-02 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer is a complex and heterogeneous disease often caused by different alterations. The development of human cancer is due to the accumulation of genetic and epigenetic modifications that could affect the structure and function of the genome. High-throughput methods (e.g., microarray and next-generation sequencing) can investigate a tumor at multiple levels: i) DNA with genome-wide association studies (GWAS), ii) epigenetic modifications such as DNA methylation, histone changes and microRNAs (miRNAs) iii) mRNA. The availability of public datasets from different multi-omics data has been growing rapidly and could facilitate better knowledge of the biological processes of cancer. Computational approaches are essential for the analysis of big data and the identification of potential biomarkers for early and differential diagnosis, and prognosis.

Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (125 download)

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Book Synopsis Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization by : Anastasiya Belyaeva

Download or read book Computational Methods for Analyzing and Modeling Gene Regulation and 3D Genome Organization written by Anastasiya Belyaeva and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological processes from differentiation to disease progression are governed by gene regulatory mechanisms. Currently large-scale omics and imaging data sets are being collected to characterize gene regulation at every level. Such data sets present new opportunities and challenges for extracting biological insights and elucidating the gene regulatory logic of cells. In this thesis, I present computational methods for the analysis and integration of various data types used for cell profiling. Specifically, I focus on analyzing and linking gene expression with the 3D organization of the genome. First, I describe methodologies for elucidating gene regulatory mechanisms by considering multiple data modalities. I design a computational framework for identifying colocalized and coregulated chromosome regions by integrating gene expression and epigenetic marks with 3D interactions using network analysis. Then, I provide a general framework for data integration using autoencoders and apply it for the integration and translation between gene expression and chromatin images of naive T-cells. Second, I describe methods for analyzing single modalities such as contact frequency data, which measures the spatial organization of the genome, and gene expression data. Given the important role of the 3D genome organization in gene regulation, I present a methodology for reconstructing the 3D diploid conformation of the genome from contact frequency data. Given the ubiquity of gene expression data and the recent advances in single-cell RNA-sequencing technologies as well as the need for causal modeling of gene regulatory mechanisms, I then describe an algorithm as well as a software tool, difference causal inference (DCI), for learning causal gene regulatory networks from gene expression data. DCI addresses the problem of directly learning differences between causal gene regulatory networks given gene expression data from two related conditions. Finally, I shift my focus from basic biology to drug discovery. Given the current COVID19 pandemic, I present a computational drug repurposing platform that enables the identification of FDA approved compounds for drug repurposing and investigation of potential causal drug mechanisms. This framework relies on identifying drugs that reverse the signature of the infection in the space learned by an autoencoder and then uses causal inference to identify putative drug mechanisms.

Computational Methods for Analysis and Modeling of Time-course Gene Expression Data

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (654 download)

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Book Synopsis Computational Methods for Analysis and Modeling of Time-course Gene Expression Data by :

Download or read book Computational Methods for Analysis and Modeling of Time-course Gene Expression Data written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genes encode proteins, some of which in turn regulate other genes. Such interactions make up gene regulatory relationships or (dynamic) gene regulatory networks. With advances in the measurement technology for gene expression and in genome sequencing, it has become possible to measure the expression level of thousands of genes simultaneously in a cell at a series of time points over a specific biological process. Such time-course gene expression data may provide a snapshot of most (if not all) of the interesting genes and may lead to a better understanding gene regulatory relationships and networks. However, inferring either gene regulatory relationships or networks puts a high demand on powerful computational methods that are capable of sufficiently mining the large quantities of time-course gene expression data, while reducing the complexity of the data to make them comprehensible. This dissertation presents several computational methods for inferring gene regulatory relationships and gene regulatory networks from time-course gene expression. These methods are the result of the authors doctoral study. Cluster analysis plays an important role for inferring gene regulatory relationships, for example, uncovering new regulons (sets of co-regulated genes) and their putative cis-regulatory elements. Two dynamic model-based clustering methods, namely the Markov chain model (MCM)-based clustering and the autoregressive model (ARM)-based clustering, are developed for time-course gene expression data. However, gene regulatory relationships based on cluster analysis are static and thus do not describe the dynamic evolution of gene expression over an observation period. The gene regulatory network is believed to be a time-varying system. Consequently, a state-space model for dynamic gene regulatory networks from time-course gene expression data is developed. To account for the complex time-delayed relationships in gene regulatory networks, the state space model is extended to.

Computational Methods for the Analysis of Genomic Data and Biological Processes

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Publisher : MDPI
ISBN 13 : 3039437712
Total Pages : 222 pages
Book Rating : 4.0/5 (394 download)

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Book Synopsis Computational Methods for the Analysis of Genomic Data and Biological Processes by : Francisco A. Gómez Vela

Download or read book Computational Methods for the Analysis of Genomic Data and Biological Processes written by Francisco A. Gómez Vela and published by MDPI. This book was released on 2021-02-05 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality.

Bayesian Models for High Throughput Spatial Transcriptomics

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ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (136 download)

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Book Synopsis Bayesian Models for High Throughput Spatial Transcriptomics by : Carter Allen

Download or read book Bayesian Models for High Throughput Spatial Transcriptomics written by Carter Allen and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seek to identify sub-populations of cells within a tissue sample that may inform biological phenomena such as disease status, treatment response, sex bias, et cetera. However, computational approaches for discerning sub-populations in HST data are still limited in that they (i) are unable to directly model normalized gene expression features to achieve more biologically interpretable sub-populations; (ii) fail to accommodate multi-sample experimental designs, thereby precluding the study of group effects such as treatment or disease status; or (iii) consider sub-populations as static entities, thus ignoring the interactive nature of cells within and between sub-populations. This dissertation seeks to address these gaps through development of various Bayesian statistical models and software. In Chapter 1, we introduce HST data and discuss germane features, such as spatial autocorrelation, skewness, and batch effects. In Chapter 2 we develop SPRUCE: a Bayesian spatial mixture model capable of achieving state of the art identification of cell sub-populations relative to manual expert annotations. An R package, spruce, is available through The Comprehensive R Archive Network (CRAN). In Chapter 3, we present MAPLE: the first HST analysis tool capable of differential abundance analysis (DAA) in multi-sample HST data. Further, we introduce uncertainty quantification to HST data analysis to account for the inherent uncertainty in sub-population labels that is ignored by existing computational methods. An R package, maple, is available through CRAN. Finally, in Chapter 4 we introduce analysis of community connectivity (ACC) to HST data. Through ACC, we seek to not only label biologically informative sub-populations in a tissue sample, but describe the similarity among groups of cells within and between sub-populations. We achieve ACC through the development of a novel multi-layer stochastic block model, which jointly models the inter-relationships among cells in terms of spatial information and gene expression patterns. We provide an R package, banyan, for implementation of ACC. Taken together, this dissertation utilizes Bayesian statistical modeling to enhance the available methodology for HST data analysis. In doing so, this work expands the range of biological insights available from HST data.

Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer

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Publisher : Elsevier
ISBN 13 : 0443296510
Total Pages : 376 pages
Book Rating : 4.4/5 (432 download)

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Book Synopsis Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer by :

Download or read book Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer written by and published by Elsevier. This book was released on 2024-09-12 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cutting Edge Artificial Intelligence, Spatial Transcriptomics and Proteomics Approaches to Analyze Cancer, Volume 163 in the Advances in Cancer Research series, highlights new advances in the field, with this new volume presenting interesting topics on the Impact of thermal processing on food flavonoids, Bioinformatics and bioactive peptides from foods: does it work together?, Food off-flavor volatiles generation, characterization and advances in novel strategies for mitigating off-flavor perception, Innovations in Food Packaging for a Sustainable and Circular economy, Upcycling of seafood side streams for circularity, Edible insects in foods, Effect of novel food processing technologies on Bacillus cereus spores, and more. Contains contributions that have been carefully selected based on their vast experience and expertise on the subject Includes updated, in-depth, and critical discussions of available information, giving the reader a unique opportunity to learn Encompasses a broad view of the topics at hand

Novel Computational Methods for Sequencing Data Analysis

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ISBN 13 :
Total Pages : 145 pages
Book Rating : 4.:/5 (15 download)

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Book Synopsis Novel Computational Methods for Sequencing Data Analysis by : Xinan Liu

Download or read book Novel Computational Methods for Sequencing Data Analysis written by Xinan Liu and published by . This book was released on 2018 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Methods for High-Throughput Transcriptomic Data

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (118 download)

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Book Synopsis Computational Methods for High-Throughput Transcriptomic Data by : Florian Battke

Download or read book Computational Methods for High-Throughput Transcriptomic Data written by Florian Battke and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: