Now showing items 1-20 of 28

    • A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. 

      McClain, Micah T; Constantine, Florica J; Nicholson, Bradly P; Nichols, Marshall; Burke, Thomas W; Henao, Ricardo; Jones, Daphne C; ... (16 authors) (The Lancet. Infectious diseases, 2020-09-24)
      BACKGROUND:Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify ...
    • A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. 

      Fourati, Slim; Talla, Aarthi; Mahmoudian, Mehrad; Burkhart, Joshua G; Klén, Riku; Henao, Ricardo; Yu, Thomas; ... (27 authors) (Nature communications, 2018-10-24)
      The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine ...
    • A Decade On: Systematic Review of ClinicalTrials.gov Infectious Disease Trials, 2007-2017. 

      Jaffe, Ian S; Chiswell, Karen; Tsalik, Ephraim L (Open forum infectious diseases, 2019-06)
      Background:Registration of interventional trials of Food and Drug Administration-regulated drug and biological products and devices became a legal requirement in 2007; the vast majority of these trials are registered in ...
    • A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses. 

      McClain, Micah T; Nicholson, Bradly P; Park, Lawrence P; Liu, Tzu-Yu; Hero, Alfred O; Tsalik, Ephraim L; Zaas, Aimee K; ... (15 authors) (Open Forum Infect Dis, 2016-01)
      Early, presymptomatic intervention with oseltamivir (corresponding to the onset of a published host-based genomic signature of influenza infection) resulted in decreased overall influenza symptoms (aggregate symptom scores ...
    • A host gene expression approach for identifying triggers of asthma exacerbations. 

      Lydon, Emily C; Bullard, Charles; Aydin, Mert; Better, Olga M; Mazur, Anna; Nicholson, Bradly P; Ko, Emily R; ... (13 authors) (PloS one, 2019-01)
      RATIONALE:Asthma exacerbations often occur due to infectious triggers, but determining whether infection is present and whether it is bacterial or viral remains clinically challenging. A diagnostic strategy that clarifies ...
    • A miRNA Host Response Signature Accurately Discriminates Acute Respiratory Infection Etiologies. 

      Poore, Gregory D; Ko, Emily R; Valente, Ashlee; Henao, Ricardo; Sumner, Kelsey; Hong, Christopher; Burke, Thomas W; ... (13 authors) (Frontiers in microbiology, 2018-01)
      Background: Acute respiratory infections (ARIs) are the leading indication for antibacterial prescriptions despite a viral etiology in the majority of cases. The lack of available diagnostics to discriminate viral and bacterial ...
    • An integrated transcriptome and expressed variant analysis of sepsis survival and death. 

      Tsalik, Ephraim L; Langley, Raymond J; Dinwiddie, Darrell L; Miller, Neil A; Yoo, Byunggil; van Velkinburgh, Jennifer C; Smith, Laurie D; ... (24 authors) (Genome Med, 2014)
      BACKGROUND: Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor ...
    • Analytical Evaluation of the Abbott RealTime CT/NG Assay for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Rectal and Pharyngeal Swabs. 

      Adamson, Paul C; Pandori, Mark W; Doernberg, Sarah B; Komarow, Lauren; Sund, Zoe; Tran, Thuy Tien T; Jensen, David; ... (15 authors) (The Journal of molecular diagnostics : JMD, 2020-06)
      Chlamydia trachomatis and Neisseria gonorrhoeae infections in the rectum and pharynx are important extragenital reservoirs of infection. Few assays approved by the US Food and Drug Administration are commercially available ...
    • Average Weighted Accuracy: Pragmatic Analysis for a Rapid Diagnostics in Categorizing Acute Lung Infections (RADICAL) Study. 

      Liu, Ying; Tsalik, Ephraim L; Jiang, Yunyun; Ko, Emily R; Woods, Christopher W; Henao, Ricardo; Evans, Scott R (Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2020-06)
      Patient management relies on diagnostic information to identify appropriate treatment. Standard evaluations of diagnostic tests consist of estimating sensitivity, specificity, positive/negative predictive values, likelihood ...
    • Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity. 

      Giroux, Nicholas S; Ding, Shengli; McClain, Micah T; Burke, Thomas W; Petzold, Elizabeth; Chung, Hong A; Palomino, Grecia R; ... (22 authors) (bioRxiv, 2020-12-05)
      SARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide ...
    • Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever. 

      Ko, Emily R; Philipson, Casandra W; Burke, Thomas W; Cer, Regina Z; Bishop-Lilly, Kimberly A; Voegtly, Logan J; Tsalik, Ephraim L; ... (10 authors) (BMC infectious diseases, 2019-10-28)
      BACKGROUND:Antibiotic resistance is rising at disturbing rates and contributes to the deaths of millions of people yearly. Antibiotic resistant infections disproportionately affect those with immunocompromising conditions, ...
    • Dusp3 and Psme3 are associated with murine susceptibility to Staphylococcus aureus infection and human sepsis. 

      Yan, Qin; Sharma-Kuinkel, Batu K; Deshmukh, Hitesh; Tsalik, Ephraim L; Cyr, Derek D; Lucas, Joseph; Woods, Christopher W; ... (13 authors) (PLoS Pathog, 2014-06)
      Using A/J mice, which are susceptible to Staphylococcus aureus, we sought to identify genetic determinants of susceptibility to S. aureus, and evaluate their function with regard to S. aureus infection. One QTL region on ...
    • Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches. 

      McClain, Micah T; Constantine, Florica J; Henao, Ricardo; Liu, Yiling; Tsalik, Ephraim L; Burke, Thomas W; Steinbrink, Julie M; ... (16 authors) (medRxiv, 2020-07-26)
      In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on peripheral blood samples across 77 timepoints from 46 subjects with COVID-19 and compared them to subjects with seasonal ...
    • Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. 

      McClain, Micah T; Constantine, Florica J; Henao, Ricardo; Liu, Yiling; Tsalik, Ephraim L; Burke, Thomas W; Steinbrink, Julie M; ... (20 authors) (Nature communications, 2021-02-17)
      SARS-CoV-2 infection has been shown to trigger a wide spectrum of immune responses and clinical manifestations in human hosts. Here, we sought to elucidate novel aspects of the host response to SARS-CoV-2 infection through ...
    • Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. 

      Ahn, Sun Hee; Tsalik, Ephraim L; Cyr, Derek D; Zhang, Yurong; van Velkinburgh, Jennifer C; Langley, Raymond J; Glickman, Seth W; ... (18 authors) (PLoS One, 2013)
      Staphylococcus aureus causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. A growing literature suggests the host's inflammatory response to the ...
    • Host gene expression classifiers diagnose acute respiratory illness etiology. 

      Tsalik, Ephraim L; Henao, Ricardo; Nichols, Marshall; Burke, Thomas; Ko, Emily R; McClain, Micah T; Hudson, Lori L; ... (24 authors) (Sci Transl Med, 2016-01-20)
      Acute respiratory infections caused by bacterial or viral pathogens are among the most common reasons for seeking medical care. Despite improvements in pathogen-based diagnostics, most patients receive inappropriate antibiotics. ...
    • Host-Based Diagnostics for Acute Respiratory Infections. 

      Ross, Melissa H; Zick, Brittany L; Tsalik, Ephraim L (Clinical therapeutics, 2019-10)
      PURPOSE:The inappropriate use of antimicrobials, especially in acute respiratory infections (ARIs), is largely driven by difficulty distinguishing bacterial, viral, and noninfectious etiologies of illness. A new frontier ...
    • Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis 

      Wang, Liuyang; Ko, Emily R; Gilchrist, James J; Pittman, Kelly J; Rautanen, Anna; Pirinen, Matti; Thompson, J Will; ... (25 authors) (Science Advances, 2017-03-08)
      Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine ...
    • MASTERMIND: Bringing Microbial Diagnostics to the Clinic. 

      Patel, Robin; Tsalik, Ephraim L; Petzold, Elizabeth; Fowler, Vance G; Klausner, Jeffrey D; Evans, Scott; Antibacterial Resistance Leadership Group (ARLG) (Clin Infect Dis, 2017-02-01)
      New diagnostics are urgently needed to address emerging antimicrobial resistance. The Antibacterial Resistance Leadership Group proposes a strategy called MASTERMIND (Master Protocol for Evaluating Multiple Infection Diagnostics) ...
    • Pediatric Antibacterial and Antifungal Trials From 2007 to 2017. 

      Thaden, Joshua T; Chiswell, Karen; Jaffe, Ian; Bergin, Stephen P; Yang, William E; Romaine, Andrew; Roberts, Jamie; ... (12 authors) (Pediatrics, 2018-09)
      BACKGROUND AND OBJECTIVES:The impact of the Best Pharmaceuticals for Children Act (BPCA) and the Pediatric Research Equity Act (PREA) on pediatric antibacterial or antifungal drug trials is unknown. Our objective was to ...