Shanrong Zhao
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View article: A protein kinase C α and β inhibitor blunts hyperphagia to halt renal function decline and reduces adiposity in a rat model of obesity-driven type 2 diabetes
A protein kinase C α and β inhibitor blunts hyperphagia to halt renal function decline and reduces adiposity in a rat model of obesity-driven type 2 diabetes Open
Type 2 diabetes (T2D) and its complications can have debilitating, sometimes fatal consequences for afflicted individuals. The disease can be difficult to control, and therapeutic strategies to prevent T2D-induced tissue and organ damage a…
View article: The Type I Interferon Signature Reflects Multiple Phenotypic and Activity Measures in Dermatomyositis
The Type I Interferon Signature Reflects Multiple Phenotypic and Activity Measures in Dermatomyositis Open
Objective The type 1 interferon (IFN) pathway is up‐regulated in dermatomyositis (DM). We sought to define how organ‐specific disease activity as well as autoantibodies and other clinical factors are independently associated with systemic …
View article: Single-cell analyses of Crohn’s disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions
Single-cell analyses of Crohn’s disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions Open
View article: AB015. Skin disease activity and autoantibody phenotype are major determinants of blood interferon signatures in dermatomyositis
AB015. Skin disease activity and autoantibody phenotype are major determinants of blood interferon signatures in dermatomyositis Open
Interferon signaling is upregulated in dermatomyositis and thought to play a role in pathogenesis. An interferon gene signature in peripheral blood of dermatomyositis patients correlates with skin disease. However, studies have not analyze…
View article: RNA Sequencing to Explore Dominant Isoform Switch During CCR6+ Memory T Cell Activation
RNA Sequencing to Explore Dominant Isoform Switch During CCR6+ Memory T Cell Activation Open
Alternative splicing (AS) is an essential, but under-investigated component of T-cell function during immune responses. Recent developments in RNA sequencing (RNA-seq) technologies, combined with the advent of computational tools, have ena…
View article: QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing
QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing Open
View article: Pharmacologic inhibition of Protein Kinase C α and Protein Kinase C β halts renal function decline indirectly, by blunting hyperphagia, and directly reduces adiposity in the ZSF1 rat model of type 2 diabetes
Pharmacologic inhibition of Protein Kinase C α and Protein Kinase C β halts renal function decline indirectly, by blunting hyperphagia, and directly reduces adiposity in the ZSF1 rat model of type 2 diabetes Open
Type 2 diabetes (T2D) and its complications can have debilitating, sometimes fatal consequences. Despite advances that address some of the metabolic aspects of T2D, for many patients these approaches do not sufficiently control the disease…
View article: Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols Open
In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for transcriptome profiling. For a given gene, the number of mapped reads is not only dependent on its expression level and gene length, but also the sequencing…
View article: Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data Open
Background The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes s…
View article: Publisher Correction: Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues
Publisher Correction: Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues Open
View article: Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues
Subsets of ILC3−ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues Open
View article: THU0033 RNA PROFILING OF HEALTHY AND RHEUMATOID ARTHRITIS SUBJECTS TREATED WITH TOFACITINIB MONOTHERAPY
THU0033 RNA PROFILING OF HEALTHY AND RHEUMATOID ARTHRITIS SUBJECTS TREATED WITH TOFACITINIB MONOTHERAPY Open
View article: Applications of machine learning in drug discovery and development
Applications of machine learning in drug discovery and development Open
View article: Deep learning of representations for transcriptomics-based phenotype prediction
Deep learning of representations for transcriptomics-based phenotype prediction Open
The ability to predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. This task is complicated because expression data are high dimensional whereas each experiment is usually small (e.g., ∼ 20,00…
View article: Molecular Profiling of Ulcerative Colitis Subjects from the TURANDOT Trial Reveals Novel Pharmacodynamic/Efficacy Biomarkers
Molecular Profiling of Ulcerative Colitis Subjects from the TURANDOT Trial Reveals Novel Pharmacodynamic/Efficacy Biomarkers Open
CCR9 and OSM are implicated as novel pharmacodynamic and efficacy biomarkers. These findings occur amid coordinated transcriptional changes that enable the definition of surrogate efficacy biomarkers based on inflamed biopsy or blood trans…
View article: Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy
Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy Open
Obese ZSF1 rats exhibit spontaneous time-dependent diabetic nephropathy and are considered to be a highly relevant animal model of progressive human diabetic kidney disease. We previously identified gene expression changes between disease …
View article: canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit
canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit Open
Summary We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel and producing multi-panel publication-ready figure…
View article: Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion
Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion Open
View article: canvasXpress: A versatile interactive high-resolution scientific multi-panel visualization toolkit
canvasXpress: A versatile interactive high-resolution scientific multi-panel visualization toolkit Open
To the Editor: CanvasXpress ( https://canvasxpress.org ) was developed as the core visualization component for bioinformatics and systems biology analysis at Bristol-Myers Squibb and further enhanced by scientists around the world and serv…
View article: Evaluation and comparison of computational tools for RNA-seq isoform quantification
Evaluation and comparison of computational tools for RNA-seq isoform quantification Open
View article: RORγt and RORα signature genes in human Th17 cells
RORγt and RORα signature genes in human Th17 cells Open
RORγt and RORα are transcription factors of the RAR-related orphan nuclear receptor (ROR) family. They are expressed in Th17 cells and have been suggested to play a role in Th17 differentiation. Although RORγt signature genes have been cha…
View article: High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy
High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy Open
ZSF1 rats exhibit spontaneous nephropathy secondary to obesity, hypertension, and diabetes, and have gained interest as a model system with potentially high translational value to progressive human disease. To thoroughly characterize this …
View article: Cloud Computing - Architecture and Applications
Cloud Computing - Architecture and Applications Open
In the era of Internet of Things and with the explosive worldwide growth of\nelectronic data volume, and associated need of processing, analysis, and\nstorage of such humongous volume of data, it has now become mandatory to\nexploit the po…
View article: Cloud Computing for Next-Generation Sequencing Data Analysis
Cloud Computing for Next-Generation Sequencing Data Analysis Open
High-throughput next-generation sequencing (NGS) technologies have evolved rapidly and are reshaping the scope of genomics research. The substantial decrease in the cost of NGS techniques in the past decade has led to its rapid adoption in…
View article: QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization
QuickRNASeq: Guide for Pipeline Implementation and for Interactive Results Visualization Open
i. Summary/Abstract Sequencing of transcribed RNA molecules (RNA-seq) has been used wildly for studying cell transcriptomes in bulk or at the single-cell level (1, 2, 3) and is becoming the de facto technology for investigating gene expres…
View article: QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing Open
The rich visualization features implemented allow end users to interactively explore the results and gain more insights into miRNA-seq data analyses. The high degree of automation and interactivity in QuickMIRSeq leads to a substantial red…
View article: Bioinformatics for RNA‐Seq Data Analysis
Bioinformatics for RNA‐Seq Data Analysis Open
While RNA sequencing (RNA‐seq) has become increasingly popular for transcriptome profiling, the analysis of the massive amount of data generated by large‐scale RNA‐seq still remains a challenge. RNA‐seq data analyses typically consist of (…
View article: Impact of Gene Annotation on RNA-seq Data Analysis
Impact of Gene Annotation on RNA-seq Data Analysis Open
RNA-seq has become increasingly popular in transcriptome profiling. One of the major challenges in RNA-seq data analysis is the accurate mapping of junction reads to their genomic origins. To detect splicing sites in short reads, many RNA-…
View article: QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization
QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization Open
View article: Bioinformatics Tools for RNA-seq Gene and Isoform Quantification
Bioinformatics Tools for RNA-seq Gene and Isoform Quantification Open
In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression.'Union-exon' and transcript based approaches are widely used in gene quantification.The 'Union-exon' based approach is simple, but…