Steven J. Clipman

Steven J. Clipman
Johns Hopkins Medicine | JHUSOM · Department of Medicine

Doctor of Philosophy • Master of Science in Public Health

About

24
Publications
1,344
Reads
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106
Citations

Publications

Publications (24)
Article
Full-text available
About 20–30% of people infected with Chagas disease present with chronic Chagas cardiomyopathy (CCC), the most serious and frequent manifestation of the disease, while others remain asymptomatic and often do not experience Chagas-specific mortality. It is not currently well understood what causes these differential disease outcomes, but a genetic p...
Article
Background: Autosomal recessive cerebellar ataxias (ARCA) are a complex group of neurodegenerative disorders with high clinical and genetic heterogeneity. In most cases, the cerebellar ataxia is not pure, and complicating clinical features such as pyramidal signs or extraneurological features are found. Objective: To identify the genetic origin...
Article
Full-text available
The adult Taenia solium, the pork tapeworm, usually lives as a single worm in the small intestine of humans, its only known definitive host. Mechanisms of genetic variation in T. solium are poorly understood. Using three microsatellite markers previously reported [1], this study explored the genetic variability of T. solium from cysts recovered fro...
Article
Full-text available
INTRODUCTION: Trypanosoma cruzi (Tc) infection is usually acquired in childhood in endemic areas, leading to Chagas disease, which progresses to Chagas cardiomyopathy in 20-30% of infected individuals over decades. The pathogenesis of Chagas cardiomyopathy involves the host inflammatory response to T. cruzi, in which upstream caspase-1 activation p...
Article
Full-text available
Soybean production in Pennsylvania has increased substantially over the past 20 years and is a highly valued field crop, together with corn. Soil borne pathogens such as Pythium spp. can contribute to soybean stand establishment issues, particularly under the conservation tillage practices that are common in the state. In this study, we collected s...
Article
Human immune responses to viral infections are highly variable, but the genetic factors that contribute to this variability are not well characterized. We used VirScan, a high-throughput epitope scanning technology, to analyze pan-viral antibody reactivity profiles of twins and SNP-genotyped individuals. Using these data, we determined the heritabi...
Article
Full-text available
Public health officials discouraged travel and non-household gatherings for Thanksgiving, but data suggests that travel increased over the holidays. The objective of this analysis was to assess associations between holiday gatherings and SARS-CoV-2 positivity in the weeks following Thanksgiving. Using an online survey, we sampled 7770 individuals a...
Article
Background: SARS-CoV-2 testing is critical for monitoring case counts, early detection and containment of infection, clinical management, and surveillance of variants. However, community-based data on the access, uptake, and barriers to testing have been lacking. Methods: We conducted serial cross-sectional online surveys covering demographics,...
Article
Full-text available
Background: People who inject drugs (PWID) account for some of the most explosive HIV and hepatitis C virus (HCV) epidemics globally. While individual drivers of infection are well understood, less is known about network factors, with minimal data beyond direct ties. Methods: 2,512 PWID in New Delhi, India were recruited in 2017-19 using a sociomet...
Article
Background and aims: Implementing effective interventions for hepatitis C virus (HCV) requires detailed understanding of local transmission dynamics and geospatial spread. Little is known about HCV phylodynamics, particularly among high-burden populations such as people who inject drugs (PWID). Approach and results: We used 483 HCV sequences and...
Preprint
Full-text available
There is enormous variability in human immune responses to viral infections. However, the genetic factors that underlie this variability are not well characterized. We used VirScan, a high-throughput viral epitope scanning technology, to analyze the antibody binding specificities of twins and SNP-genotyped individuals. These data were used to estim...
Preprint
Full-text available
Masks are effective measures to prevent the transmission of SARS-CoV-2, however, lack of a national mandate coupled with poor adherence has led to suboptimal levels of transmission reduction. Although data has suggested that mask adherence is high, few studies have captured details on how mask wearing changes with activities and how these behaviors...
Preprint
Full-text available
In the US, public health officials discouraged travel and social gatherings for Thanksgiving. Data suggests that many individuals did travel over the holidays, albeit in smaller numbers than previous years. Using an online panel survey of individuals across ten US states, we found that many individuals reported spending Thanksgiving outside of thei...
Preprint
Full-text available
Objective To characterize the SARS-CoV-2 testing cascade and associated barriers in three US states. Methods We recruited participants from Florida, Illinois, and Maryland (∼1000/state) for an online survey September 16 – October 15, 2020. The survey covered demographics, COVID-19 symptoms, and experiences around SARS-CoV-2 PCR testing in the prio...
Article
Full-text available
Background: Current mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Monitoring NPI adoption and their association with SARS-CoV-2 infection history can provide key information for public health. Methods: We sampled 1,030 individual...
Article
Background: Diagnosis of congenital Chagas disease (CChD) in most endemic areas is based on low-sensitive microscopy at birth and 9-month IgG, which has poor adherence. We aim to evaluate the accuracy of the IgM-Shed Acute Phase Antigen (IgM-SAPA) test in the diagnosis of CChD at birth. Methods: Two cohort studies (training and validation cohort...
Article
Background: Data from high-income countries suggest increasing hepatitis C virus (HCV) prevalence/incidence among HIV-infected men who have sex with men (MSM), but limited data derive from low-and-middle-income countries (LMICs). Methods: We recruited 4,994 MSM from 5 states across India using respondent-driven sampling (RDS). Logistic regressio...
Poster
Full-text available
Little data exist on HCV phylodynamics and transmission networks among people who inject drugs (PWID), especially from low- and middle-income countries (LMICs). HCV epidemics in a city can be considered a series of sub-epidemics caused by phylogenetically distinct viral lineages. Mapping these lineages to generate transmission clusters and overlayi...
Data
PED and MAP files of raw minimal anonymized dataset. (ZIP)
Data
List of SNPs tested in association analysis of NLRP1, CARD, and CASP1 genes with CCC. (DOCX)
Data
Expected heterozygosity of microsatellite markers by group of cysts genotyped from each pig in the rural community. (DOCX)
Data
Genotypes of evaluated cysts based on sequencing. (DOCX)
Poster
Next-generation sequencing technologies are revealing a more complete picture of biological diversity within various environments and are posed to fundamentally challenge our current understanding of species interactions. However, in order to maximize the potential of this new resource, appropriate molecular loci need to be chosen and vetted to fac...

Questions

Question (1)
Question
I have a set of HIV pol sequence data, and after alignment it is clear that some sequences are much shorter than others – primarily due to sequencing issues. Because the gaps/missing data are not necessarily meaningful, I consider these a "complete deletion" when doing a maximum likelihood phylogenetic analysis. Doing this, however, reduces the number of positions that could be included in the analysis since only positions where there is data for all sequences can be used. I was wondering what the best approach to handle this would be. Is there a general lower limit for the number of bases that should be included for an informative viral phylogenetic analysis, and is it better to remove samples with shorter sequence lengths? Would a Bayesian approach using programs like BEAST overcome this? Thank you!