Dylan Kotliar
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View article: An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans
An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans Open
Aging of the blood system impacts systemic health and can be traced to hematopoietic stem cells (HSCs). Despite multiple reports on human HSC aging, a unified map detailing their molecular age-related changes is lacking. We developed a con…
View article: Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions Open
View article: A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease Open
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti…
View article: Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions
Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions Open
T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclus…
View article: Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever Open
View article: Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses Open
View article: Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression
Three linked variants have opposing regulatory effects on isovaleryl-CoA dehydrogenase gene expression Open
While genome-wide association studies (GWAS) and positive selection scans identify genomic loci driving human phenotypic diversity, functional validation is required to discover the variant(s) responsible. We dissected the IVD gene locus—w…
View article: A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease Open
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires an understanding of how cellular networks change following therapy. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following…
View article: Three linked opposing regulatory variants under selection associate with<i>IVD</i>
Three linked opposing regulatory variants under selection associate with<i>IVD</i> Open
While genome-wide association studies (GWAS) and selection scans identify genomic loci driving human phenotypic diversity, functional validation is required to discover the variant(s) responsible. We dissected the IVD locus, implicated by …
View article: Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment Open
Motivation Visualizing two-dimensional embeddings (such as UMAP or tSNE) is a useful step in interrogating single-cell RNA sequencing (scRNA-Seq) data. Subsequently, users typically iterate between programmatic analyses (including clusteri…
View article: Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment Open
Summary Visualizing two-dimensional (2D) embeddings (e.g. UMAP or tSNE) is a key step in interrogating single-cell RNA sequencing (scRNA-Seq) data. Subsequently, users typically iterate between programmatic analyses (e.g. clustering and di…
View article: The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response
The Origins and Future of Sentinel: An Early-Warning System for Pandemic Preemption and Response Open
While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work …
View article: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics Open
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell prote…
View article: Single-cell profiling of Ebola virus infection<i>in vivo</i>reveals viral and host transcriptional dynamics
Single-cell profiling of Ebola virus infection<i>in vivo</i>reveals viral and host transcriptional dynamics Open
Summary Ebola virus (EBOV) causes epidemics with high case fatality rates, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. To better understand EBOV infection in vivo , we used si…
View article: Identification of Common CD8<sup>+</sup>T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone
Identification of Common CD8<sup>+</sup>T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone Open
The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regio…
View article: High crossreactivity of human T cell responses between Lassa virus lineages
High crossreactivity of human T cell responses between Lassa virus lineages Open
Lassa virus infects hundreds of thousands of people each year across rural West Africa, resulting in a high number of cases of Lassa fever (LF), a febrile disease associated with high morbidity and significant mortality. The lack of approv…
View article: Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq
Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq Open
Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although singl…
View article: Author response: Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq
Author response: Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Identifying gene expression programs under…
View article: Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018
Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018 Open
During 2018, an unusual increase in Lassa fever cases occurred in Nigeria, raising concern among national and international public health agencies. We analyzed 220 Lassa virus genomes from infected patients, including 129 from the 2017-201…
View article: Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk Open
View article: Analysis of CD8 <sup>+</sup> T cell response during the 2013–2016 Ebola epidemic in West Africa
Analysis of CD8 <sup>+</sup> T cell response during the 2013–2016 Ebola epidemic in West Africa Open
Significance Zaire ebolavirus (EBOV) is a viral pathogen of significant global health concern best exemplified by more than 28,000 human infections during the recent West African epidemic. Examining immunity in EBOV disease survivors has b…
View article: Identifying Gene Expression Programs of Cell-type Identity and Cellular Activity with Single-Cell RNA-Seq
Identifying Gene Expression Programs of Cell-type Identity and Cellular Activity with Single-Cell RNA-Seq Open
Identifying gene expression programs underlying both cell-type identity and cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although singl…
View article: Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever
Field validation of recombinant antigen immunoassays for diagnosis of Lassa fever Open
View article: Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk Open
Biological interpretation of GWAS data frequently involves analyzing unsigned genomic annotations comprising SNPs involved in a biological process and assessing enrichment for disease signal. However, it is often possible to generate signe…
View article: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia Open
Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships,…
View article: Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia
Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia Open
View article: Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay Open
View article: Medical education in the United States: do residents feel prepared?
Medical education in the United States: do residents feel prepared? Open
Background Medical schools face a growing challenge in providing a comprehensive educational experience. Students must graduate with not only the medical knowledge but also the requisite skills to care for patients and serve as physicians-…