Daniel Bunis
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View article: Differential Assembly of Mouse and Human Tumor Microenvironments
Differential Assembly of Mouse and Human Tumor Microenvironments Open
Summary Mouse models are frequently used to develop treatments for human cancer. Yet, we lack a comprehensive understanding of the comparative organization of mouse and human tumor microenvironments (mu/huTMEs). Through immunoprofiling of …
View article: A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain
A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain Open
Introduction and Methods Endometriosis has limited treatment options, prompting the search for novel therapeutics. We previously used a transcriptomics-based computational drug repositioning pipeline to analyze public bulk transcriptomic d…
View article: Searching for influencers among placental immune cells in preeclampsia
Searching for influencers among placental immune cells in preeclampsia Open
Cells in maternal and fetal immune systems may communicate, leading to immune tolerance during pregnancy; however, this hypothesis remains controversial. Here, we profiled single-cell transcriptional signatures in placental layers comprisi…
View article: Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach
Identifying therapeutic candidates for endometriosis through a transcriptomics-based drug repositioning approach Open
Existing medical treatments for endometriosis-related pain are often ineffective, underscoring the need for new therapeutic strategies. In this study, we applied a computational drug repurposing pipeline to stratified and unstratified dise…
View article: Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data
Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data Open
In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the …
View article: Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data
Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data Open
In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the …
View article: HIV silencing and cell survival signatures in infected T cell reservoirs
HIV silencing and cell survival signatures in infected T cell reservoirs Open
View article: Applying a computational transcriptomics-based drug repositioning pipeline to identify therapeutic candidates for endometriosis
Applying a computational transcriptomics-based drug repositioning pipeline to identify therapeutic candidates for endometriosis Open
Endometriosis is a common, inflammatory pain disorder comprised of disease in the pelvis and abnormal uterine lining and ovarian function that affects ∼200 million women of reproductive age worldwide and up to 50% of those with pelvic pain…
View article: Decision letter: Generating colorblind-friendly scatter plots for single-cell data
Decision letter: Generating colorblind-friendly scatter plots for single-cell data Open
View article: Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans
Homeostatic cytokines reciprocally modulate the emergence of prenatal effector PLZF+CD4+ T cells in humans Open
The development of human adaptive immunity progresses faster than previously appreciated, with the emergence of memory CD4 + T cells alongside regulatory T (Treg) cells by the second trimester of pregnancy. We previously identified a prena…
View article: Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis
Whole-Tissue Deconvolution and scRNAseq Analysis Identify Altered Endometrial Cellular Compositions and Functionality Associated With Endometriosis Open
The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be…
View article: xCell signature gene sets
xCell signature gene sets Open
Lists of genes used for each of the 64 cell type signatures used by xCell
View article: Signature-Cell Type Target Map
Signature-Cell Type Target Map Open
Targeting relationship between xCell cell type signatures and cell types identified in healthy human endometrium scRNAseq dataset, used in Fig.2B
View article: Normalized signature scores of xCell signatures
Normalized signature scores of xCell signatures Open
Medium normalized signature score between each xCell cell type signature and each cell type identified in healthy human endometrium scRNAseq dataset, as shown in Fig.2B
View article: Cell Type names
Cell Type names Open
Names for the 64 cell types in xCell signature for Fig.3.
View article: ratioNext Scores
ratioNext Scores Open
Final 'ratioNext' scores of xCell signatures, as shown in Fig.2B and elsewhere
View article: Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer’s Disease Across Two Brain Regions
Sex-Stratified Single-Cell RNA-Seq Analysis Identifies Sex-Specific and Cell Type-Specific Transcriptional Responses in Alzheimer’s Disease Across Two Brain Regions Open
Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can infor…
View article: Multi-modal single-cell sequencing identifies cellular immunophenotypes associated with juvenile dermatomyositis disease activity
Multi-modal single-cell sequencing identifies cellular immunophenotypes associated with juvenile dermatomyositis disease activity Open
Juvenile dermatomyositis (JDM) is a rare autoimmune condition with insufficient biomarkers and treatments, in part, due to incomplete knowledge of the cell types mediating disease. We investigated immunophenotypes and cell-specific genes a…
View article: Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and functionality associated with endometriosis
Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and functionality associated with endometriosis Open
The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be…
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in Alzheimer’s disease across two brain regions.
Sex-stratified single-cell RNA-Seq analysis identifies sex-specific and cell type-specific transcriptional responses in Alzheimer’s disease across two brain regions. Open
Alzheimer’s disease (AD) is a pervasive neurodegenerative disorder that disproportionately affects women. Since neural anatomy and disease pathophysiology differ by sex, investigating sex-specific mechanisms in AD pathophysiology can infor…
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: Single-cell transcriptomic analysis elucidates APOE genotype specific changes across cell types in two brain regions in Alzheimer’s disease
Single-cell transcriptomic analysis elucidates APOE genotype specific changes across cell types in two brain regions in Alzheimer’s disease Open
Alzheimer’s Disease (AD) is a complex neurodegenerative disease that gravely affects patients and imposes an immense burden on caregivers. Apolipoprotein E4 (APOE4) has been identified as the most common genetic risk factor for AD, yet the…
View article: Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells
Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells Open
Whereas the human fetal immune system is poised to generate immune tolerance and suppress inflammation in utero, an adult-like immune system emerges to orchestrate anti-pathogen immune responses in post-natal life. It has been posited that…
View article: naive T cell single-cell RNA-seq, raw counts and annotation
naive T cell single-cell RNA-seq, raw counts and annotation Open
naive CD4 and CD8 T cell single-cell RNA-sequencing data from human samples, both raw counts, generated by cellranger, and cell's sample annotations, generated with Demuxlet.
View article: Immune Cell scRNAseq
Immune Cell scRNAseq Open
Seurat object for all immune cells from healthy human endometrium analyzed in this study, containing cell type annotation and signature score calculated using method by F. Pont, M. Tosolini, J. J. Fournié, Nucleic Acids Res. 47, e133 (2019…
View article: dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit Open
Summary A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use and allows highly customizable generation of both daily-use a…
View article: Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19 Open
The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We uti…
View article: Data Integration for Immunology
Data Integration for Immunology Open
Over the last several years, next-generation sequencing and its recent push toward single-cell resolution have transformed the landscape of immunology research by revealing novel complexities about all components of the immune system. With…
View article: Microarray data, annotated
Microarray data, annotated Open
Microarray transcriptome data from naive CD4 T cells and classical monocytes of human samples.