Tomoki is a new postdoctoral fellow in the lab.
Author Archives: Ali Zaib
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Oct
Chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) are clinically and molecularly heterogeneous diseases. We utilized clustering and integrative network analyses to elucidate roles for microRNAs (miRNAs) and miRNA isoforms (isomiRs) in COPD and ILD pathogenesis. Short RNA sequencing was performed on 351 lung tissue samples of COPD (n=145), ILD (n=144) and controls ……
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Oct
Analysis of single-cell RNA-seq (scRNA-seq) data can reveal novel insights into heterogeneity of complex biological systems. Many tools and workflows have been developed to perform different types of analysis. However, these tools are spread across different packages or programming environments, rely on different underlying data structures, and can only be utilized by people with knowledge ……
11
Oct
Oct
To understand functional duality of the complement system in host defense and lung injury, a more comprehensive view of its localized production in the lung, and the impact of age on complement production are essential. Here, we explored the expression of complement genes through computational analysis of preexisting single cell RNA sequencing data from lung ……
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Oct
Oct
Xu, K., Shi, X., Husted, C., Hong, R., Wang, Y., Ning, B., Sullivan, T., Rieger-Christ, K., Duan, F., Marques, H., Gower, A., Xiao, X., Liu, H., Liu, G., Duclos, G., Platt, M., Spira, A., Mazzilli, S., Billatos, E., Lenburg, M., … Beane, J. (accepted by scientific report) Abstract Background: SARS-CoV-2 infection and disease severity are ……
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Oct
Oct
Motivation R Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for storing one or more matrix-like assays along with associated row and column data. These objects have been used to facilitate the storage and analysis of high-throughput genomic data generated from technologies such as single-cell RNA sequencing. One common computational task in many genomics analysis workflows ……
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Oct
Oct
Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, various technical artifacts can be present in scRNA-seq data and should be assessed before performing downstream analyses. While several tools have been developed to perform individual quality control (QC) tasks, they are scattered in different packages across several ……
11
Oct
Oct
The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general “a la carte” workflow gives users the ability access ……