Publications

A common task in analyzing metatranscriptomics data is to identify microbial metabolic pathways with differential RNA abundances across multiple sample groups. With information from paired metagenomics data, some differential methods control for either DNA or taxa abundances to address their strong correlation with RNA abundance. However, it remains unknown if both factors need to be controlled for simultaneously. We discovered that when either DNA or taxa abundance is controlled for, RNA abundance still has a strong partial correlation with the other factor.

Abstract

Background: COVID-19 causes hypercoagulability, but the association between coagulopathy and hypoxemia in critically ill patients has not been thoroughly explored. This study hypothesized that severity of coagulopathy would be associated with acute respiratory distress syndrome severity, major thrombotic events, and mortality in patients requiring intensive care unit-level care.

Abstract

HIV-1 therapy with single or dual broadly neutralizing antibodies (bNAbs) has shown viral escape, indicating that at least a triple bNAb therapy may be needed for robust suppression of viremia.

Abstract

Background

The ALVAC/gp120 + MF59 vaccines in the HVTN 702 efficacy trial did not prevent HIV-1 acquisition. Vaccine-matched immunological endpoints that were correlates of HIV-1 acquisition risk in RV144 were measured in HVTN 702 and evaluated as correlates of HIV-1 acquisition.

Methods

Abstract

Previous reports demonstrated that SARS-CoV-2 binding IgG did not increase significantly between first and second doses of the BNT162b2 vaccine in previously-infected individuals. We tested neutralizing antibodies (nAb) against SARS-CoV-2 Delta and Omicron variants post first and second doses of BNT162b2 in infection-naïve and previously-infected individuals. Delta, but not Omicron, nAb significantly increased from first to second dose in both groups of individuals.

Abstract

Although hematopoietic stem cell transplantation (HCT) is the only curative treatment for acute myeloid leukemia (AML), it is associated with significant treatment related morbidity and mortality. There is great need for predictive biomarkers associated with overall survival (OS) and clinical outcomes. We hypothesized that circulating metabolic, inflammatory, and immune molecules have potential as predictive biomarkers for AML patients who receive HCT treatment.

In the exploratory data analysis of single-cell or spatial genomic data, single cells or spatial spots are often visualized using a two-dimensional plot where cell clusters or spot clusters are marked with different colors. With tens of clusters, current visualization methods often assigns visually similar colors to spatially neighboring clusters, making it hard to identify the distinction between clusters.

Abstract

For decades, studies of natural killer (NK) cells have focused on those found in peripheral blood (PBNK cells) as the prototype for NK cell biology. Only recently have researchers begun to explore the diversity of tissue-resident NK (tr-NK) cells. While tr-NK cells were initially identified from mice parabiosis and intravascular staining experiments, they can also be identified by tissue retention markers such as CD69, CD103, and others. More importantly, tr-NK cells have distinct functions compared to PBNK cells.