A5003081455- Machine Learning in Materials Science
- Computational Drug Discovery Methods
- Atherosclerosis and Cardiovascular Diseases
- Single-cell and spatial transcriptomics
- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- HIV-related health complications and treatments
- Gene Regulatory Network Analysis
- Chronic Obstructive Pulmonary Disease (COPD) Research
- HIV Research and Treatment
- Cytomegalovirus and herpesvirus research
- S100 Proteins and Annexins
- Phonocardiography and Auscultation Techniques
- Telemedicine and Telehealth Implementation
- NMR spectroscopy and applications
- Hepatitis C virus research
- Healthcare Policy and Management
- Respiratory Support and Mechanisms
- Pneumocystis jirovecii pneumonia detection and treatment
- Breastfeeding Practices and Influences
- Microbial Metabolic Engineering and Bioproduction
- Heparin-Induced Thrombocytopenia and Thrombosis
- Drug-Induced Adverse Reactions
- Transplantation: Methods and Outcomes
- Urticaria and Related Conditions
University of Rochester
2018-2023
University of Rochester Medical Center
2021-2022
University of Pittsburgh
2012-2019
Pathway analysis is widely used to gain mechanistic insights from high-throughput omics data. However, most existing methods do not consider signal integration represented by pathway topology, resulting in enrichment of convergent pathways when downstream genes are modulated. Incorporation flow and could rank the based on modulation key regulatory genes. This implementation can be facilitated for large-scale data discrete state network modeling due simplicity parameterization. Here, we model...
Background In addition to farming exposures in childhood, maternal provide strong protection against allergic disease their children; however, the effect of lifestyle on human milk (HM) composition is unknown. Objective This study aims characterize immune effects Old Order Mennonite (OOM) traditional when compared with Rochester (ROC) families at higher risk for asthma and diseases using HM as a proxy. Methods samples collected median 2 months lactation from 52 OOM 29 ROC mothers were...
Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation LBMC, protein side chain configurations are pre-calculated stored in libraries, while bonded interactions along backbone treated explicitly. Because AA coordinates maintained at minimal run-time cost, arbitrary sites interaction terms can be turned to create mixed-resolution...
Efficacious HIV-1 vaccination requires elicitation of long-lived antibody responses. However, our understanding how different vaccine types elicit durable responses is lacking. To assess the impact type on responses, we measured IgG isotypes against four consensus HIV antigens from 2 weeks to 10 years post and used mixed effects models estimate half-life in human clinical trials. Compared protein-boosted regimens, half-lives gp120-specific antibodies were longer but peak magnitudes lower...
Atherosclerosis (AS)-associated cardiovascular disease is an important cause of mortality in aging population people living with HIV (PLWH). This elevated risk has been attributed to viral infection, anti-retroviral therapy, chronic inflammation, and lifestyle factors. However, the rates at which PLWH develop AS vary even after controlling for length treatment duration, To investigate molecular signaling underlying this variation, we sequenced 9368 peripheral blood mononuclear cells (PBMCs)...
There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed docking approach geared especially highly poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which intended offer...
Abstract People living with HIV are at higher risk of atherosclerosis (AS). The pathogenesis this is not fully understood. To assess the regulatory networks involved in AS we sequenced mRNA peripheral blood mononuclear cells (PBMCs) and measured cytokine chemokine levels plasma 13 persons 12 matched HIV-negative without AS. microRNAs (miRNAs) known to play a role infection may modulate gene regulation drive Hence, further assessed miRNA expression PBMCs subset HIV+ people atherosclerosis. We...
Overdose prevention health centers (OPHCs), also known as overdose or safe injection centers, are an evidence-based strategy for people to use drugs in environment monitored by care professionals with access drug education, sterile supplies, and referral infrastructure higher levels of medical behavioral resources. Though still illegal under federal law throughout the United States, many legal quasi-legal (including some States) have operated since 1980s (Beletsky, Baker et al. 2018). Using...
Abstract Atherosclerosis (AS)-associated cardiovascular disease is an important cause of mortality in aging population people living with HIV (PLWH). This elevated risk has been attributed to viral infection, anti-retroviral therapy, chronic inflammation, and lifestyle factors. However, rates at which PLWH develop AS vary even after controlling for length treatment duration, To investigate the molecular signaling underlying this variation, we sequenced 9368 peripheral blood mononuclear cells...
Abstract Background Access to infectious disease (ID) providers has been heavily impacted by COVID-19. Telemedicine (TM) viewed as a promising solution the challenges in care delivery posed this pandemic. However, perceptions of TM among ID remain unclear. This study investigated impact on outpatient during COVID-19 pandemic, efficacy clinics, which clinical conditions within that may be best suited for, and influences provider attitudes toward TM. Methods We conducted online surveys via...
Abstract There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed docking approach geared especially highly poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which...
Abstract Background Many tools exist to perform a rigorous pathway analysis, though traditional gene set enrichment analysis remains among the most common. While useful for many applications, one common situation where it is less so metabolic profiling of bulk omics datasets. Rate limiting steps in more linear pathways are main determinant flux through these pathways, but differential expression enzymes that catalyze usually not differentially weighted analysis. Fluximplied was built with...
Abstract Transcriptional changes involved in neuronal recovery after sports-related concussion (SRC) may be obscured by inter-individual variation mRNA expression and nonspecific related to physical exertion. Using a co-twin study, the objective of this study was identify important differences among single pair monozygotic (MZ) twins discordant for concussion. A MZ were enrolled as part larger biomarkers collegiate athletes. During Twin sustained SRC, allowing comparison nonconcussed B....
Abstract Background Despite the use of antimicrobial prophylaxis in liver transplant recipients (LTR), infection remains most likely cause death (18.94%) first year. There is limited data describing characteristics, & infections LTR while hospitalized year post-transplantation. We aimed to review incidence and outcomes post-transplant during hospitalization or re-hospitalization. Graph 1.Y-axis; Number cultures collected, X-axis; type organism dived over time. Site bacterial Table...
Introduction: Immunosuppression of heart transplant (txp) recipients increases risk infection. This study will identify the most common pathogens and characterize at-risk patients. Methods: We performed a single center retrospective cohort at University Rochester. Demographics, pretransplant characteristics, infections requiring rehospitalization were obtained (table 1) from electronic records patients who received txp January 1, 2011 through July 2020. Chi-square, t-test, Wilcoxon rank-sum...