scholarly journals GPPS: an ILP-based approach for inferring cancer progression with mutation losses from single cell data

2018 ◽  
Author(s):  
Simone Ciccolella ◽  
Mauricio Soto Gomez ◽  
Murray Patterson ◽  
Gianluca Della Vedova ◽  
Iman Hajirasouliha ◽  
...  
Keyword(s):  
Single Cell ◽  
Cancer Progression ◽  
Cell Data

scholarly journals gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data

2020 ◽  
Vol 21 (S1) ◽  
Author(s):  
Simone Ciccolella ◽  
Mauricio Soto Gomez ◽  
Murray D. Patterson ◽  
Gianluca Della Vedova ◽  
Iman Hajirasouliha ◽  
...  
Keyword(s):  
Single Cell ◽  
Cancer Progression ◽  
False Negative ◽  
Fixed Number ◽  
Phylogeny Reconstruction ◽  
Sequencing Data ◽  
Progression Model ◽  
Great Specificity ◽  
Cell Data ◽  
Tumor Phylogeny

Abstract Background Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates. Moreover, there has been some recent evidence of back mutations in cancer: this phenomenon is currently widely ignored. Results We present a new tool, , that reconstructs a tumor phylogeny from Single Cell Sequencing data, allowing each mutation to be lost at most a fixed number of times. The General Parsimony Phylogeny from Single cell () tool is open source and available at https://github.com/AlgoLab/gpps. Conclusions provides new insights to the analysis of intra-tumor heterogeneity by proposing a new progression model to the field of cancer phylogeny reconstruction on Single Cell data.

scholarly journals gpps: An ILP-based approach for inferring cancer progression with mutation losses from single cell data

2018 ◽  
Author(s):  
Simone Ciccolella ◽  
Mauricio Soto Gomez ◽  
Murray Patterson ◽  
Gianluca Della Vedova ◽  
Iman Hajirasouliha ◽  
...  
Keyword(s):  
Single Cell ◽  
Open Source ◽  
Computational Methods ◽  
Cancer Progression ◽  
Fixed Number ◽  
Inference Problem ◽  
Fundamental Feature ◽  
Single Cell Sequencing ◽  
Cell Data ◽  
Tumor Phylogeny

AbstractMotivationIn recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progression where mutations are accumulated through histories. However, some recent studies leveraging Single Cell Sequencing (SCS) techniques have shown evidence of mutation losses in several tumor samples [19], making the inference problem harder.ResultsWe present a new tool, gpps, that reconstructs a tumor phylogeny from single cell data, allowing each mutation to be lost at most a fixed number of times.AvailabilityThe General Parsimony Phylogeny from Single cell (gpps) tool is open source and available at https://github.com/AlgoLab/gppf.

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

2021 ◽  
Author(s):  
Jordan W. Squair ◽  
Michael A. Skinnider ◽  
Matthieu Gautier ◽  
Leonard J. Foster ◽  
Grégoire Courtine
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Cell Data

scholarly journals Identifying cell types from single-cell data based on similarities and dissimilarities between cells

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Yuanyuan Li ◽  
Ping Luo ◽  
Yi Lu ◽  
Fang-Xiang Wu
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Spectral Clustering ◽  
Incidence Matrix ◽  
Expression Patterns ◽  
Cell Types ◽  
Clustering Method ◽  
Different Types ◽  
Cell Data ◽  
Spectral Clustering Method

Abstract Background With the development of the technology of single-cell sequence, revealing homogeneity and heterogeneity between cells has become a new area of computational systems biology research. However, the clustering of cell types becomes more complex with the mutual penetration between different types of cells and the instability of gene expression. One way of overcoming this problem is to group similar, related single cells together by the means of various clustering analysis methods. Although some methods such as spectral clustering can do well in the identification of cell types, they only consider the similarities between cells and ignore the influence of dissimilarities on clustering results. This methodology may limit the performance of most of the conventional clustering algorithms for the identification of clusters, it needs to develop special methods for high-dimensional sparse categorical data. Results Inspired by the phenomenon that same type cells have similar gene expression patterns, but different types of cells evoke dissimilar gene expression patterns, we improve the existing spectral clustering method for clustering single-cell data that is based on both similarities and dissimilarities between cells. The method first measures the similarity/dissimilarity among cells, then constructs the incidence matrix by fusing similarity matrix with dissimilarity matrix, and, finally, uses the eigenvalues of the incidence matrix to perform dimensionality reduction and employs the K-means algorithm in the low dimensional space to achieve clustering. The proposed improved spectral clustering method is compared with the conventional spectral clustering method in recognizing cell types on several real single-cell RNA-seq datasets. Conclusions In summary, we show that adding intercellular dissimilarity can effectively improve accuracy and achieve robustness and that improved spectral clustering method outperforms the traditional spectral clustering method in grouping cells.

scholarly journals Integrated analysis of multimodal single-cell data

Cell ◽  
2021 ◽  
Author(s):  
Yuhan Hao ◽  
Stephanie Hao ◽  
Erica Andersen-Nissen ◽  
William M. Mauck ◽  
Shiwei Zheng ◽  
...  
Keyword(s):  
Single Cell ◽  
Integrated Analysis ◽  
Cell Data

Multi-omics integration in the age of million single-cell data

2021 ◽  
Author(s):  
Zhen Miao ◽  
Benjamin D. Humphreys ◽  
Andrew P. McMahon ◽  
Junhyong Kim
Keyword(s):  
Single Cell ◽  
Omics Integration ◽  
Cell Data

scholarly journals High-throughput single cell data analysis – A tutorial

2021 ◽  
pp. 338872
Author(s):  
Gerjen H. Tinnevelt ◽  
Kristiaan Wouters ◽  
Geert J. Postma ◽  
Rita Folcarelli ◽  
Jeroen J. Jansen
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
High Throughput ◽  
Cell Data

484 Bioturing browser: interactively explore public single cell sequencing data

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A520-A520
Author(s):  
Son Pham ◽  
Tri Le ◽  
Tan Phan ◽  
Minh Pham ◽  
Huy Nguyen ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Cell Types ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Data Formats ◽  
Cancer Types ◽  
Cell Data

BackgroundSingle-cell sequencing technology has opened an unprecedented ability to interrogate cancer. It reveals significant insights into the intratumoral heterogeneity, metastasis, therapeutic resistance, which facilitates target discovery and validation in cancer treatment. With rapid advancements in throughput and strategies, a particular immuno-oncology study can produce multi-omics profiles for several thousands of individual cells. This overflow of single-cell data poses formidable challenges, including standardizing data formats across studies, performing reanalysis for individual datasets and meta-analysis.MethodsN/AResultsWe present BioTuring Browser, an interactive platform for accessing and reanalyzing published single-cell omics data. The platform is currently hosting a curated database of more than 10 million cells from 247 projects, covering more than 120 immune cell types and subtypes, and 15 different cancer types. All data are processed and annotated with standardized labels of cell types, diseases, therapeutic responses, etc. to be instantly accessed and explored in a uniform visualization and analytics interface. Based on this massive curated database, BioTuring Browser supports searching similar expression profiles, querying a target across datasets and automatic cell type annotation. The platform supports single-cell RNA-seq, CITE-seq and TCR-seq data. BioTuring Browser is now available for download at www.bioturing.com.ConclusionsN/A

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