David F Smith

Johns Hopkins Medicine, Baltimore, Maryland, United States

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Publications (96)490.18 Total impact

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    ABSTRACT: Bacteriophage receptor binding proteins (RBPs) confer host specificity. We previously identified a putative RBP (Gp047) from the campylobacter lytic phage NCTC 12673 and demonstrated that Gp047 has a broader host range than its parent phage. While NCTC 12673 recognizes the capsular polysaccharide (CPS) of a limited number of Campylobacter jejuni isolates, Gp047 binds to a majority of C. jejuni and related Campylobacter coli strains. In this study, we demonstrate that Gp047 also binds to acapsular mutants, suggesting that unlike the parent phage, CPS is not the receptor for Gp047. Affinity chromatography and far-western analyses of C. jejuni lysates using Gp047 followed by mass spectrometry indicated that Gp047 binds to the major flagellin protein, FlaA. Since C. jejuni flagellin is extensively glycosylated, we investigated this binding specificity further and demonstrate that Gp047 only recognizes flagellin decorated with acetamidino-modified pseudaminic acid. This binding activity is localized to the C-terminal quarter of the protein and both wild type and coccoid forms of C. jejuni are recognized. In addition, Gp047 treatment agglutinates vegetative cells and reduces their motility. Since Gp047 is highly conserved among all campylobacter phages sequenced to date, it is likely that this protein plays an important role in the phage lifecycle.
    Molecular Microbiology 10/2014; · 5.03 Impact Factor
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    ABSTRACT: Glycan microarrays have become a powerful platform to investigate the interactions of carbohydrates with a variety of biomolecules. However, the number and diversity of glycans available for use in such arrays represents a key bottleneck in glycan array fabrication. To address this challenge, we describe a novel glycan array platform based on surface patterning of engineered glycophages that display unique carbohydrate epitopes. Specifically, we show that glycophages are compatible with surface immobilization procedures and that phage-displayed oligosaccharides retain the ability to be recognized by different glycan-binding proteins (e.g., antibodies, lectins) after immobilization. A key advantage of glycophage arrays is that large quantities of glycophages can be produced biosynthetically from recombinant bacteria and isolated directly from bacterial supernatants without laborious purification steps. Taken together, the glycophage array technology described here should help to expand the diversity of glycan libraries and provide a complement to the existing toolkit for high-throughput analysis of glycan-protein interactions.
    Biotechnology Journal 09/2014; · 3.71 Impact Factor
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    ABSTRACT: GlycoPattern is web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics (CFG). This resource includes algorithms and tools to discover structural motifs, a heatmap visualization to compare multiple experiments, hierarchical clustering of Glycan Binding Proteins with respect to their binding motifs, and a structural search feature on the experimental data. Availability: GlycoPattern is freely available on the web at http://glycopattern.emory.edu with all major browsers supported.
    Bioinformatics (Oxford, England). 08/2014;
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    ABSTRACT: We have shown that recombinant forms of VP8* domains of the human rotavirus outer capsid spike protein VP4 from human neonatal strains N155(G10P[11]) and RV3(G3P[6]) and a bovine strain (B223) recognize unique glycans within the repertoire of human milk glycans (HMG). The accompanying study by Yu et al, describes a HMG shotgun glycan microarray that led to the identification of 32 specific glycans in the human milk tagged glycan library (TGL) that were recognized by these human rotaviruses. These microarray analyses also provided a variety of metadata about the recognized glycan structures compiled from anti-glycan antibody and lectin binding before and after specific glycosidase digestions, along with compositional information from mass analysis by MALDI MS. To deduce glycan sequence and utilize information predicted by analyses of metadata from each glycan, 28 of the glycan targets were retrieved from the TGL for detailed sequencing using sequential disassembly of glycans by ion-trap mass spectrometry. Our aim is to obtain a deeper structural understanding of these key glycans using an orthogonal approach for structural confirmation in a single ion trap mass spectrometer. This sequential ion disassembly strategy details the complexities of linkage and branching in multiple compositions, several of which contained isomeric mixtures including several novel structures. The application of this approach exploits both library matching with standard materials and de novo approaches. This combination together with the metadata generated from lectin and antibody-binding data before and after glycosidase digestions provide a heretofore-unavailable level of analytical detail to glycan structure analysis. The results of these studies showed that among the 28 glycan targets analyzed 27 unique structures were identified, and 23 of the HMGs recognized by human rotaviruses represent novel structures not previously described as glycans in human milk. The functional glycomics analysis of HMG provides significant insight into the repertoire of glycans comprising the human milk metaglycome.
    Molecular & cellular proteomics : MCP. 07/2014;
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    ABSTRACT: Human milk contains a rich set of soluble, reducing glycans whose functions and bioactivities are not well understood. Because human milk glycans (HMGs) have been implicated as receptors for various pathogens, we explored the functional glycome of human milk using shotgun glycomics. The free glycans from pooled milk samples of donors with mixed Lewis and Secretor phenotypes were labeled with a fluorescent tag and separated by multidimensional HPLC to generate a tagged glycan library containing 247 HMG targets that were printed to generate an HMG shotgun glycan microarray (SGM). To investigate the potential role of HMG as decoy receptors for rotavirus (RV), a leading cause of severe gastroenteritis in children, we interrogated the HMG-SGM with recombinant forms of VP8* domains of the RV outer capsid spike protein VP4 from human neonatal strains, N155(G10P[11]) and RV3(G3P[6]), and a bovine strain, B223(G10P[11]). Glycans that were bound by RV attachment proteins were selected for detailed structural analyses using Metadata-Assisted Glycan Sequencing, which compiles data on each glycan based on its binding by antibodies and lectins before and after exo- and endo-glycosidase digestion of the SGM, coupled with independent MSn analyses. These complementary structural approaches resulted in the identification of 32 glycans based on RV VP8*-binding, many of which are novel HMGs, whose detailed structural assignments by MSn are described in the accompanying manuscript by Ashline et al. Although sialic acid has been thought to be important as a surface receptor for RVs, our studies indicated sialic acid is not required for binding of glycans to individual VP8* domains. Remarkably, each VP8* recognized specific glycan determinants within a unique subset of related glycan structures where specificity differences arise from subtle differences in glycan structures.
    Molecular & cellular proteomics : MCP. 07/2014;
  • David F Smith, Richard D Cummings
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    ABSTRACT: While all viruses must transit the plasma membrane of mammalian cells to initiate infection, we know little about the complex processes involved in viral attachment, which commonly involve recognition of glycans by viral proteins. Glycan microarrays derived from both synthetic glycans and natural glycans isolated through shotgun glycomics approaches provide novel platforms for interrogating diverse glycans as potential viral receptors. Recent studies with influenza and rotaviruses using such glycan microarrays provide examples of their utility in exploring the challenging questions raised in efforts to define the complex mechanistic protein-glycan interactions that regulate virus attachment to host cells.
    Current opinion in virology. 07/2014; 7C:79-87.
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    ABSTRACT: IMPORTANCE Reconstruction of oncologic or traumatic head and neck defects often requires complex planning of locoregional, pedicled, or interpolated flaps. In cases with a higher risk of flap failure, vascular delay with staged reconstruction can help improve tissue perfusion and increase chances of flap survival. An objective tool is needed to help guide reconstructive surgeons with the intraoperative decision to pursue vascular delay. OBJECTIVES To describe a pilot study using a novel application of a technique that quantifies and validates the benefit of the vascular delay procedure in locoregional flaps and to demonstrate a practical and broadly applicable technology that can be easily incorporated into intraoperative decision making and improve outcomes for high-risk flaps. DESIGN, SETTING, AND PARTICIPANTS A pilot study using intraoperative laser-assisted indocyanine green imaging measurements and fluorescence videos to objectively measure the benefit of vascular delay procedures in patients with head and neck defects and wound healing risk factors requiring locoregional flap reconstruction at an academic tertiary care center. MAIN OUTCOMES AND MEASURES Intraoperative laser-assisted indocyanine green imaging with video documentation and quantitative measurements was used to evaluate flap perfusion before a vascular delay procedure. Measurements were repeated after a 3-week vascular delay procedure. RESULTS Two patients were identified based on comorbid conditions that resulted in a higher risk of flap failure, as well as the need for a locoregional flap for reconstruction. At the initial elevation of the flap, quantitative results from flap imaging demonstrated low perfusion numbers and minimal fluorescence, suggesting poor tissue perfusion and increased likelihood of postoperative flap compromise or failure. Following a vascular delay of 3 weeks, repeat measurements were substantially improved. No wound healing issues were observed. CONCLUSIONS AND RELEVANCE This is the first study to date to quantitatively demonstrate the benefit of the vascular delay technique in patients with potential vascular compromise in locoregional head and neck flap reconstruction. Data obtained suggest that this technology can be used to guide intraoperative decision making in complicated reconstructions and help optimize patient outcomes.
    JAMA facial plastic surgery. 06/2014;
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    ABSTRACT: Genomic approaches continue to provide unprecedented insight into the microbiome, yet host immune interactions with diverse microbiota can be difficult to study. We therefore generated a microbial microarray containing defined antigens isolated from a broad range of microbial flora to examine adaptive and innate immunity. Serological studies with this microarray show that immunoglobulins from multiple mammalian species have unique patterns of reactivity, whereas exposure of animals to distinct microbes induces specific serological recognition. Although adaptive immunity exhibited plasticity toward microbial antigens, immunological tolerance limits reactivity toward self. We discovered that several innate immune galectins show specific recognition of microbes that express self-like antigens, leading to direct killing of a broad range of Gram-negative and Gram-positive microbes. Thus, host protection against microbes seems to represent a balance between adaptive and innate immunity to defend against evolving antigenic determinants while protecting against molecular mimicry.
    Nature Chemical Biology 05/2014; · 12.95 Impact Factor
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    ABSTRACT: Schistosomiasis is a debilitating parasitic disease of humans, endemic in tropical areas, for which no vaccine is available. Evidence points to glycan antigens as being important in immune responses to infection. Here we describe our studies on the comparative humoral immune responses to defined schistosome-type glycan epitopes in Schistosoma mansoni-infected humans, rhesus monkeys, and mice. Rhesus anti-glycan responses over the course of infection were screened on a defined glycan microarray comprised of semi-synthetic glycopeptides terminating with schistosome-associated or control mammalian-type glycan epitopes, as well as a defined glycan microarray of mammalian-type glycans representing over 400 glycan structures. Infected rhesus monkeys generated a high IgG antibody response to the core xylose/core α3 fucose epitope of N-glycans, which peaked at 8-11 weeks post infection, coinciding with maximal ability to kill schistosomula in vitro. By contrast, infected humans generated low antibody levels to this epitope. At 18 months following praziquantel therapy to eliminate the parasite, antibody levels were negligible. Mice chronically infected with S. mansoni generated high levels of anti-LDNF IgM antibodies, but lacked a robust response to the core xylose/core α3 fucose N-glycan antigens compared to other species studied, and their sera demonstrated an intermediate level of schistosomula killing in vitro. These differential responses to parasite glycan antigens may be related to the ability of rhesus monkeys to self-cure in contrast to the chronic infection seen in humans and mice. Our results validate defined glycan microarrays as a useful technology to evaluate diagnostic and vaccine antigens for schistosomiasis and perhaps other infections.
    Glycobiology 04/2014; · 3.54 Impact Factor
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    ABSTRACT: Schistosomiasis caused by infection with parasitic helminthes of Schistosoma spp. is a major global health problem due to inadequate treatment and lack of a vaccine. The immune response to schistosomes includes glycan antigens, which could be valuable diagnostic markers and vaccine targets. However, no precedent exists for how to design vaccines targeting eukaryotic glycoconjugates. The di- and tri-saccharide motifs LacdiNAc (GalNAcβ1,4GlcNAc; LDN) and fucosylated LacdiNAc (GalNAcβ1,4(Fucα1-3)GlcNAc; LDNF), are the basis for several important schistosome glycan antigens. They occur in monomeric form or as repeating units (poly-LDNF) and as part of a variety of different glycoconjugates. Because chemical synthesis and conjugation of such antigens is exceedingly difficult, we sought to develop a recombinant expression system for parasite glycans. We hypothesized that presentation of parasite glycans on the cell surface would induce glycan-specific antibodies. We generated Chinese Hamster Ovary (CHO) Lec8 cell lines expressing poly-LDN (L8-GT) and poly-LDNF (L8-GTFT) abundantly on their membrane glycoproteins. Sera from S. mansoni-infected mice were highly cross-reactive with the cells and with cell-surface N-glycans. Immunizing mice with L8-GT and L8-GTFT cells induced glycan-specific antibodies. The L8-GTFT cells induced a sustained booster response, with antibodies that bound to S. mansoni lysates and recapitulated the exquisite specificity of the anti-parasite response for particular presentations of LDNF antigen. In summary, this recombinant expression system promotes successful generation of antibodies to the glycans of S. mansoni, and it can be adapted to study the role of glycan antigens and anti-glycan immune responses in many other infections and pathologies.
    Glycobiology 04/2014; · 3.54 Impact Factor
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    ABSTRACT: Carbohydrates participate in almost every aspect of biology from protein sorting to modulating cell differentiation and cell-cell interactions. To date, the majority of data gathered on glycan expression has been obtained via analysis with either anti-glycan antibodies or lectins. A detailed understanding of the specificities of these reagents is critical to the analysis of carbohydrates in biological systems. Glycan microarrays are increasingly used to determine the binding specificity of glycan-binding proteins. In this study, six different glycan microarray platforms with different modes of glycan presentation were compared using five well known lectins; Con A, HPA, MAL-I, SNA and WGA. A new method (universal threshold) was developed to facilitate systematic comparisons across distinct array platforms. The strongest binders of each lectin were identified using the universal threshold across all platforms while identification of weaker binders was influenced by platform-specific factors including presentation of determinants, array composition and self-reported thresholding methods. This work compiles a rich dataset for comparative analysis of glycan array platforms and has important implications for the implementation of microarrays in the characterization of glycan binding proteins.
    Glycobiology 03/2014; · 3.54 Impact Factor
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    ABSTRACT: The MIRAGE (Minimum Information Required for A Glycomics Experiment) initiative was founded in 2011 in order to develop guidelines for reporting the qualitative and quantitative results obtained by diverse types of glycomics analyses, including the conditions and techniques that were applied to prepare the glycans for analysis and generate the primary data along with the tools and parameters that were used to process and annotate this data. These guidelines must address a broad range of issues, as glycomics data are inherently complex and are generated using diverse methods, including mass spectrometry, chromatography, glycan array binding assays, nuclear magnetic resonance (NMR) and other rapidly developing technologies. The acceptance of these guidelines by scientists conducting research on biological systems in which glycans have a significant role will facilitate the evaluation and reproduction of glycomics experiments and data that is reported in scientific journals and uploaded to glycomics databases. As a first step, MIRAGE guidelines for glycan analysis by mass spectrometry have been recently published [1], allowing them to be implemented and evaluated in the context of real-world glycobiology research. In this paper we set out the historical context, organization structure and overarching objectives of the MIRAGE initiative.
    Glycobiology 03/2014; · 3.54 Impact Factor
  • Robert S Matson, David F Smith
    Current opinion in chemical biology 02/2014; · 8.30 Impact Factor
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    ABSTRACT: Glycan microarrays have become indispensable tools for studying protein-glycan interactions. Along with chemo-enzymatic synthesis, glycans isolated from natural sources have played important roles in array development and will continue to be a major source of glycans. N-glycans and O-glycans from glycoproteins, and glycans from glycosphingolipids (GSLs) can be released from corresponding glycoconjugates with relatively mature methods, although isolation of large numbers and quantities of glycans is still very challenging. Glycosylphosphatidylinositol (GPI) anchors and glycosaminoglycans (GAGs) are less represented on current glycan microarrays. Glycan microarray development has been greatly facilitated by bifunctional fluorescent linkers, which can be applied in a 'Shotgun Glycomics' approach to incorporate isolated natural glycans. Glycan presentation on microarrays may affect glycan binding by GBPs, often through multivalent recognition by the GBP.
    Current opinion in chemical biology 01/2014; 18C:70-77. · 8.30 Impact Factor
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    ABSTRACT: Objective: Obstructive sleep apnea (OSA) is increasingly recognized as a significant factor in peri-operative and inpatient health. Because of this, hospitalized OSA patients are encouraged to utilize CPAP therapy while inpatient. We investigated the cost difference of patient-owned versus hospital-provided CPAP machine use by admitted adult patients with OSA. Study Design: Prospective cohort study at a tertiary academic center Methods: All new-patient admissions >18 years prescribed CPAP while inpatient over a 2-month period were included. Demographic information was collected, and cost analysis was performed. Results: CPAP was used for 162 (1.2%) admissions. Mean patient age was 59±13 years; the majority was white (56.8%) and male (64.2%). Average CPAP utilization was 5.3±5.5 nights. The differential cost-per-day for patients using hospital-provided CPAP was $416.10 more than for patients using home-CPAP machines. This cost included direct costs of an extended respiratory therapy (RT) initial visit, machine rental fee ($27.50), and additional RT evaluation time (mean 85-145/RVUs). The base initial visit was the same for all patients. Over the 2-month study period, the total cost difference in charges was $195,912; this extrapolates to $1,175,471 yearly. Conclusions: This is the first study to characterize the magnitude of cost savings from utilization of home versus hospital-provided CPAP machines in patients requiring inpatient CPAP machine use. The use of patient-owned CPAP machines may reflect an opportunity to provide cheaper care while maintaining high patient safety and quality care. The actual economic impact to an individual hospital would vary based on the insurance payer mix.
    The Laryngoscope 01/2014; · 1.98 Impact Factor
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    ABSTRACT: Glycan microarrays have become indispensable tools for studying protein–glycan interactions. Along with chemo-enzymatic synthesis, glycans isolated from natural sources have played important roles in array development and will continue to be a major source of glycans. N-glycans and O-glycans from glycoproteins, and glycans from glycosphingolipids (GSLs) can be released from corresponding glycoconjugates with relatively mature methods, although isolation of large numbers and quantities of glycans is still very challenging. Glycosylphosphatidylinositol (GPI) anchors and glycosaminoglycans (GAGs) are less represented on current glycan microarrays. Glycan microarray development has been greatly facilitated by bifunctional fluorescent linkers, which can be applied in a ‘Shotgun Glycomics’ approach to incorporate isolated natural glycans. Glycan presentation on microarrays may affect glycan binding by GBPs, often through multivalent recognition by the GBP.
    Current Opinion in Chemical Biology. 01/2014; 18:70–77.
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    ABSTRACT: Objective A standardized assay to determine the HPV status of head and neck squamous cell carcinoma (HNSCC) specimens has not yet been established, particularly for cytologic samples. The goal of this study was to determine whether the hybrid capture-2 (HC-2) assay, already widely used for the detection of high risk HPV in cervical brushings, is applicable to cytologic specimens obtained from patients with suspected HNSCCs. Materials and methods Fine needle aspirates (FNA) of cervical lymph nodes were pre-operatively obtained from patients with suspected HNSCCs and evaluated for the presence of HPV using the HC-2 assay. HPV analysis was performed on the corresponding resected tissue specimens using p16 immunohistochemistry (IHC) and HR-HPV in situ hybridization (ISH). A cost analysis was performed using the Center for Medicare & Medicaid Services. Results HPV status of the cervical lymph node metastases was correctly classified using the HC-2 assay in 84% (21/25) of cases. Accuracy was improved to 100% when cytologic evaluation confirmed the presence of cancer cells in the test samples. The estimated cost savings to CMS using the HC-2 assay ranged from $113.74 to $364.63 per patient. Conclusions HC-2 is a reliable method for determining the HPV status of HNSCCs. Its application to HNSCCs may reduce costs by helping to localize the primary site during the diagnostic work-up as well as decrease the interval time of determining the HPV status which would be relevant for providing prognostic information to the patient as well as determining eligibility for clinical trials targeting this unique patient population.
    Oral Oncology 01/2014; · 2.70 Impact Factor
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    ABSTRACT: The recognition of sialic acids by two strains of minute virus of mice (MVM), MVMp (prototype) and MVMi (immunosuppressive), is an essential requirement for successful infection. To understand the potential for recognition of different modifications of sialic acid by MVM, three types of capsids, virus-like particles, wild type empty (no DNA) capsids, and DNA packaged virions, were screened on a sialylated glycan microarray (SGM). Both viruses demonstrated a preference for binding to 9-O-methylated sialic acid derivatives, while MVMp showed additional binding to 9-O-acetylated and 9-O-lactoylated sialic acid derivatives, indicating recognition differences. The glycans recognized contained a type-2 Galβ1-4GlcNAc motif (Neu5Acα2-3Galβ1-4GlcNAc or 3'SIA-LN) and were biantennary complex-type N-glycans with the exception of one. To correlate the recognition of the 3'SIA-LN glycan motif as well as the biantennary structures to their natural expression in cell lines permissive for MVMp, MVMi, or both strains, the N- and O-glycans, and polar glycolipids present in three cell lines used for in vitro studies, A9 fibroblasts, EL4 T lymphocytes, and the SV40 transformed NB324K cells, were analyzed by MALDI-TOF/TOF mass spectrometry. The cells showed an abundance of the sialylated glycan motifs recognized by the viruses in the SGM and previous glycan microarrays supporting their role in cellular recognition by MVM. Significantly, the NB324K showed fucosylation at the non-reducing end of their biantennary glycans, suggesting that recognition of these cells is possibly mediated by the Lewis X motif as in 3'SIA-Le(X) identified in a previous glycan microarray screen.
    PLoS ONE 01/2014; 9(1):e86909. · 3.53 Impact Factor
  • David F Smith, Richard D Cummings
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    ABSTRACT: While all viruses must transit the plasma membrane of mammalian cells to initiate infection, we know little about the complex processes involved in viral attachment, which commonly involve recognition of glycans by viral proteins. Glycan microarrays derived from both synthetic glycans and natural glycans isolated through shotgun glycomics approaches provide novel platforms for interrogating diverse glycans as potential viral receptors. Recent studies with influenza and rotaviruses using such glycan microarrays provide examples of their utility in exploring the challenging questions raised in efforts to define the complex mechanistic protein–glycan interactions that regulate virus attachment to host cells.
    Current Opinion in Virology. 01/2014; 7:79–87.
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    ABSTRACT: Influenza viruses initiate infection by attaching to sialic acid receptors on the surface of host cells. It has been recognized for some time that avian influenza viruses usually bind to terminal sialic acid that is linked in the α2-3 configuration to the next sugar while human viruses show preference for α2-6 linked sialic acid. With developments in synthetic chemistry and chemo-enzymatic methods of synthesizing quite complex glycans, it has become clear that the binding specificity extends beyond the sialic acid, and this has led to considerable interest in developing glycan reagents that could be used either as a diagnostic tool for particular influenza viruses, or to identify cells that are susceptible to infection by certain influenza viruses. Here we describe the use of the Consortium for Functional Glycomics Glycan Array to investigate binding specificity of influenza hemagglutinin and cleavage by neuraminidase, using seasonal and pandemic H1N1 influenza viruses as examples, and compare the results with published data using other array methods.
    Cancer biomarkers: section A of Disease markers 01/2014; 14(1):43-53. · 0.97 Impact Factor

Publication Stats

1k Citations
490.18 Total Impact Points

Institutions

  • 2014
    • Johns Hopkins Medicine
      • Department of Otolaryngology - Head and Neck Surgery
      Baltimore, Maryland, United States
  • 2010–2014
    • Johns Hopkins University
      • Department of Otolaryngology - Head and Neck Surgery
      Baltimore, Maryland, United States
  • 2007–2014
    • Emory University
      • Department of Biochemistry
      Atlanta, Georgia, United States
  • 2007–2013
    • University of Oklahoma Health Sciences Center
      • Department of Biochemistry and Molecular Biology
      Oklahoma City, Oklahoma, United States
  • 2012
    • University at Buffalo, The State University of New York
      • Department of Oral Biology
      Buffalo, NY, United States
  • 2009–2012
    • Medical College of Wisconsin
      • Department of Biochemistry
      Milwaukee, WI, United States
  • 2008–2012
    • Ghent University
      • Department of Molecular Biotechnology
      Gent, VLG, Belgium
  • 2011
    • University of California, Davis
      • Department of Chemistry
      Davis, California, United States