Brad T Sherman

Brad T Sherman
Leidos Biomedical Research, Inc. · Laboratory of Human Retrovirology and Immunoinformatics

Master of Science

About

124
Publications
24,824
Reads
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70,572
Citations
Citations since 2016
71 Research Items
41974 Citations
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201620172018201920202021202201,0002,0003,0004,0005,0006,000
201620172018201920202021202201,0002,0003,0004,0005,0006,000
201620172018201920202021202201,0002,0003,0004,0005,0006,000
Additional affiliations
February 2001 - present
Leidos Biomedical Research, Inc.
Position
  • Analyst

Publications

Publications (124)
Article
Full-text available
Pneumocystis jirovecii is an important opportunistic pathogen associated with AIDS and other immunodeficient conditions. Currently, very little is known about its nuclear and mitochondrial genomes. In this study, we sequenced the complete mitochondrial genome (mtDNA) of this organism and its closely related species Pneumocystis carinii and Pneumocy...
Article
Full-text available
The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes world...
Article
Full-text available
DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experi...
Article
Full-text available
Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging and daunting task. The gene-annotation enrichment analysis is a promising high-throughput strategy that increases the likelihood for investigators to identify biological proce...
Article
Full-text available
Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-base...
Article
Full-text available
Background: Levels of plasma SARS-CoV-2 nucleocapsid (N) antigen may be an important biomarker in patients with COVID-19 and enhance our understanding of the pathogenesis of COVID-19. Objective: To evaluate whether levels of plasma antigen can predict short-term clinical outcomes and identify clinical and viral factors associated with plasma ant...
Article
Full-text available
Motivation: The existence of quasispecies in the viral population causes difficulties for disease prevention and treatment. High-throughput sequencing provides opportunity to determine rare quasispecies and long sequencing reads covering full genomes reduce quasispecies determination to a clustering problem. The challenge is high similarity of qua...
Article
Full-text available
DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms,...
Article
Full-text available
Herpes simplex virus type 2 (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD9...
Article
Background: In a randomized, placebo-controlled, clinical trial, bamlanivimab, a SARS-CoV-2-neutralizing monoclonal antibody, given in combination with remdesivir, did not improve outcomes among hospitalized patients with COVID-19 based on an early futility assessment. Objective: To evaluate the a priori hypothesis that bamlanivimab has greater...
Article
Full-text available
Citation: Yang, J.; Hao, M.; Khan, M.A.; Rehman, M.T.; Highbarger, H.C.; Chen, Q.; Goswami, S.; Sherman, B.T.; Rehm, C.A.; Dewar, R.L.; et al. Abstract: We have recently reported that a recombinant HIV-1NL4.3 containing Met-to-Ile change at codon 50 of integrase (IN) (IN:M50I) exhibits suppression of the virus release below 0.5% of WT HIV, and the...
Preprint
BACKGROUND Bamlanivimab, a neutralizing monoclonal antibody given in combination with remdesivir, did not improve outcomes among hospitalized COVID-19 patients based on an early futility assessment. In this final study report, we evaluate an a priori hypothesis that greater benefit of bamlanivimab would be identified in those without detectable end...
Article
Full-text available
Interleukin-27 (IL-27) is a pleiotropic cytokine that influences the innate and adaptive immune systems. It inhibits viral infection and regulates the expression of microRNAs (miRNAs). We recently reported that macrophages differentiated from human primary monocytes in the presence of IL-27 and human AB serum resisted human immunodeficiency virus (...
Article
Full-text available
Objectives: Interleukin-27 (IL-27) is known as an anti-HIV cytokine. We have recently demonstrated that IL-27-pretreatment promotes phytohaemagglutinin (PHA)-stimulated CD4(+) T cells into HIV-1-resistant cells by inhibiting uncoating step. Purpose: To further characterize the function of the HIV resistant T cells, we investigated profiles of mi...
Article
Full-text available
Objectives: Elevated levels of interleukin-6 (IL-6), D-dimer, and C-reactive protein (hsCRP) are associated with increased incidence of comorbid disease and mortality among people living with HIV (PLWH). Prior studies suggest a genetic basis for these biomarker elevations in the general population. The study objectives are to identify the genetic...
Article
Full-text available
HIV-1 proviruses persist in the CD4 ⁺ T cells of HIV-infected individuals despite years of combination antiretroviral therapy (cART) with suppression of HIV-1 RNA levels <40 copies/mL. Greater than 95% of these proviruses detected in circulating peripheral blood mononuclear cells (PBMCs) are referred to as “defective” by virtue of having large inte...
Article
Full-text available
Macrophages play an essential role in the immune system. Recent studies have shown that long non-coding RNAs (lncRNAs) can regulate genes encoding products involved in the immune response. Interleukin (IL)-27 is a member of the IL-6/IL-12 family of cytokines with broad anti-viral effects that inhibits human immunodeficiency virus (HIV) type-1 and h...
Article
Full-text available
Herpes simplex virus 1 (HSV-1) strain McKrae is highly virulent and relatively neuroinvasive in animal models compared with other wild-type HSV-1 strains. To identify the genetic determinants that lead to the unique phenotypes of the McKrae strain, we sequenced its genome with PacBio single-molecule real-time (SMRT) technology and resolved the comp...
Article
Full-text available
Herpes simplex virus type 1 (HSV-1) strain MacIntyre has a severe defect in the anterograde spread after replication in the nucleus. To better understand and identify the genetic determinants that lead to the unique phenotypes of the MacIntyre strain, we sequenced its genome with PacBio single-molecule real-time sequencing technology and resolved t...
Article
Background: HIV-infected patients with poor virologic control and multi-drug resistant virus have limited therapeutic options. The current study was undertaken to evaluate the safety, immunologic effects, and antiviral activity of peripheral lymphocytes transferred from an elite controller, whose immune system is able to control viral replication...
Article
Full-text available
The impact of variation in host genetics on replication of HIV-1 in demographically diverse populations remains uncertain. Here, we perform a genome-wide screen for associations of single nucleotide polymorphisms (SNP) to viral load (VL) in antiretroviral therapy-naïve participants (n=2,440) with varying demographics from the Strategic Timing of An...
Article
Full-text available
After initiating antiretroviral therapy (ART), a rapid decline in HIV viral load is followed by a long period of undetectable viremia. Viral outgrowth assay suggests the reservoir continues to decline slowly. Here, we use full-length sequencing to longitudinally study the proviral landscape of four subjects on ART to investigate the selective press...
Article
Full-text available
Background HIV-1 set-point viral load (SPVL) is predictive of disease progression and shows variability across HIV-1-positive (HIV+) persons. Various factors may influence SPVL including viral features, environmental exposure and host genetics. To identify single nucleotide polymorphisms (SNPs) associated with SPVL, we performed a genome-wide assoc...
Preprint
After initiating antiretroviral therapy (ART), a rapid decline in plasma viremia is followed by reservoir stabilization. Viral outgrowth assay suggests the reservoir continues to decline slowly, but variation over time and among individuals complicates our understanding of selective pressures during ART. We used full-length sequencing to study more...
Article
Full-text available
We have previously demonstrated that Interleukin-27 differentially regulates the expression of seven novel microRNAs. Here we elucidate the functional significance of these novel microRNAs. Of the seven microRNAs, over expression of miRNA-6852 (miR-SX4) mimic induces cell cycle arrest at G2/M phase and induces necrosis in HEK293 and panel of cervic...
Conference Paper
Full-text available
Many of the infectious diseases which have jeopardized and still are a threat to public health are caused by RNA viruses, including HIV, HCV, Influenza virus, Ebola virus and Zika virus. Because of a high rate of mutations and recombination events, rapidly evolving RNA viruses prevail within a host as a collection of closely related variants, refer...
Article
Full-text available
We previously identified Ku70, a subunit of a DNA repair protein complex, as a cytosolic DNA sensor that induces the production of interferon-λ1 (IFN-λ1) by human primary cells and cell lines. IFN-λ1 is a type III IFN and has similar antiviral activity to that of the type I IFNs (IFN-α and IFN-β). We observed that human embryonic kidney (HEK) 293T...
Article
Full-text available
MicroRNAs (miRNAs) regulate gene expression and thereby influence cell fate and function. Recent studies suggest that an abundant class of miRNAs play important roles in immune cells, such as T cells, natural killer (NK) cells, B cells, and dendritic cells (DCs). Interleukin (IL)-27 is a member of the IL-12 family of cytokines with broad anti-viral...
Article
Full-text available
Objective IL-15 has been postulated to play an important role in HIV-1 infection, yet there are conflicting reports regarding its expression levels in these patients. We sought to measure the level of IL-15 in a large, well characterised cohort of HIV-1 infected patients and correlate this with well known markers of inflammation, including CRP, D-d...
Data
Correlation between IL-15 level and HIV viral load in patients treated with ART. HIV-1 infected patients with ART were divided into 4 groups based on viral load and comparisons were made with IL-15 level using the Mann-Whitney test. (TIFF)
Data
Information of each patient’s viral load, CD4 counts and AIDS defining illness. (XLSX)
Data
ART treatment regimen for each patient. PO: oral administration, SQ: subcutaneous injection, QID: once a day, TID: three times a day, BID: twice a day, QHS: at every bed time. (XLSX)
Data
The multivariate analysis for those who were on ART. (DOCX)
Data
The multivariate analysis for those who were ART naïve. (DOCX)
Article
β-glucans, which can activate innate immune responses, are a major component in the cell wall of the cyst form of Pneumocystis. In the current study we examined whether β-1,3 glucans are masked by surface proteins in Pneumocystis, and what role β-glucans play in Pneumocystis-associated inflammation. For 3 species, including P. jirovecii, which caus...
Article
Full-text available
Background Gene isoforms are commonly found in both prokaryotes and eukaryotes. Since each isoform may perform a specific function in response to changing environmental conditions, studying the dynamics of gene isoforms is important in understanding biological processes and disease conditions. However, genome-wide identification of gene isoforms is...
Article
Full-text available
Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneum...
Data
Supplementary Figures 1-15, Supplementary Tables 1-5, Supplementary Notes 1-7, Supplementary Methods and Supplementary References
Data
Pneumocystis genes involved in DNA recombination.
Data
Pneumocystis genes encoding ATPase.
Data
Pneumocystis genes involved in carbohydrate metabolism.
Data
Pneumocystis genes involved in lipid metabolism.
Data
Pneumocystis genes involved in proteasome.
Data
Pneumocystis genes involved in glucan metabolism.
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Pneumocystis genes involved in spliceosome.
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Pneumocystis genes with alternative splicing.
Data
Pneumocystis genes involved in mating and meiosis.
Data
Pneumocystis genes involved in cell signaling and stress responses.
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Pneumocystis genes encoding histone deacetylase.
Data
Transcription factors in Pneumocystis and other fungi.
Data
Pneumocystis genes involved in nucleotide metabolism.
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Pneumocystis genes involved in cofactor metabolism.
Data
Pneumocystis genes involved in oxidative phophorylation.
Data
Members of the msg superfamily in three Pneumocystis species.
Data
Pneumocystis genes involved in amino acid metabolism.
Data
Pneumocystis genes involved in clathrin-dependent endocytosis.
Data
Glycopeptide mapping of P. carinii Msg protein digests.