Selected Publications
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A machine learning classifier using 33 host immune response mRNAs accurately distinguishes viral and non-viral acute respiratory illnesses in nasal swab samples
A machine learning classifier using 33 host immune response mRNAs accurately distinguishes viral and non-viral acute respiratory illnesses in nasal swab samples
Pandya, R. et al. Genome Medicine. Aug 2023.
Prime-time for clinical use of transcriptomics for differentiating viral from bacterial respiratory infection
de la Fuente, A. et al. Wiley Online Library. Feb 2023.
Multisite validation of a host response signature for predicting likelihood of bacterial and viral infections in patients with suspected influenza
Multisite validation of a host response signature for predicting likelihood of bacterial and viral infections in patients with suspected influenza
Shojaei, M. et al. Wiley Online Library. Jan 2023.
Using a 29-mRNA host response classifier to detect bacterial coinfections and predict outcomes in COVID-19 patients presenting to the emergency department
Using a 29-mRNA host response classifier to detect bacterial coinfections and predict outcomes in COVID-19 patients presenting to the emergency department
Ram-Mohan, N. et al. Microbiology Spectrum (asm.org). Oct 2022.
Detection of viral infection and bacterial co- and superinfection in COVID-19 patients presenting to the emergency department using the 29-mRNA host response classifier BVN-3 – a multicenter study
Detection of viral infection and bacterial co- and superinfection in COVID-19 patients presenting to the emergency department using the 29-mRNA host response classifier BVN-3 – a multicenter study
Bauer, W. et al. Open Forum Infectious Diseases. Aug 2022.
Evaluation of a multivalent transcriptomic metric for diagnosing surgical sepsis and estimating mortality among critically ill patients
Brakenridge, S. et al. Critical Care Medicine. July 2022.
Redefining critical illness
Maslove, D. et al. Nature Medicine. June 2022.
Prospective validation of a transcriptomic severity classifier among patients with suspected acute infection and sepsis in the ED
Galtung, N. et al. European Journal of Emergency Medicine. April 2022.
Towards equitable patient subgroup performance by gene-expression-based diagnostic classifiers of acute infection
Mayhew, M. et al. MedRxiv. April 2022.
Diagnostic host gene expression analysis by quantitative reverse transcription loop-mediated isothermal amplification to discriminate between bacterial and viral infections
Diagnostic host gene expression analysis by quantitative reverse transcription loop-mediated isothermal amplification to discriminate between bacterial and viral infections
Remmel M, et al. Clinical Chemistry. Feb 2022.
A robust gene expression signature for NASH in liver expression data
Hasin‑Brumshtein Y, et al. Scientific Reports. Feb 2022.
A 6-mRNA host response using patients with non-COVID-19 infections accurately predicts severity of COVID-19
Buturovic, L. et. al. Nature, Jan 2022.
A transcriptomic severity metric that predicts clinical outcomes in critically ill surgical sepsis patients
Brakenridge, S. et al. Critical Care Explorations. Oct 2021.
A Multi-mRNA Prognostic Signature for Anti-TNFα Therapy Response in Patients with Inflammatory Bowel Disease
Sakaram, S. et.al. Diagnostics. Oct 2021.
The optimization and biological significance of a 29-host-immune-mRNA panel for the diagnosis of acute infections and sepsis
He, Y. et al. J. Pers. Med. June 2021.
Prospective validation of an 11-gene mRNA host response score for mortality risk stratification in the intensive care unit
Moore, A. et al. Nature. June 2021.
A host transcriptomic signature for identification of respiratory viral infections in the community
Almansa, R. et al. Wiley Online Library. June 2021.
A novel 29-messenger RNA host-response assay from whole blood accurately identifies bacterial and viral infections in the ED
Bauer, W. et al. Critical Care Medicine. June 2021.
Gene expression–based diagnosis of infections in critically ill patients: Validation of the SepsisMetaScore
Thair, S. et al. Critical Care Medicine. April 2021.
A 29-mRNA host response test from blood accurately distinguishes bacterial and viral infections among ED patients
Safarika, A. et al. ICMx. June 2021.
Sepsis subclasses: A framework for development and interpretation
DeMerle, K. et al. Critical Care Medicine. Feb 2021.
Validation of inflammopathic, adaptive, and coagulopathic sepsis endotypes in Coronavirus disease 2019
Sweeney, T. et al. Critical Care Medicine. Feb 2021.
A novel method for classification of tabular data using convolutional neural networks
Buturovic, L. and Miljkovic, D. BioRxiv. Jan 2021.
Evaluation of Bayesian optimization to select predictive models of acute infection and in-hospital mortality
Mayhew, M. et al. Pac Symp Biocomput. Jan 2021.
Outcomes of metabolic resuscitation early treatment of sepsis (ORANGES) trial
Iglesias, J. et al. J. Pers. Med. Dec 2020.
Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections
Thair, S. et al. Science Direct. Dec 2020.
A multi-mRNA host-response molecular blood test for the diagnosis and prognosis of acute infections and sepsis
Ducharme, J. et al. J. Pers. Med. Dec 2020.
External corroboration that corticosteroids may be harmful to septic shock endotype A patients
Wong, H. et al. Critical Care Med. Nov 2020.
Hunting for genes linked to risk of, not from, bloodstream infection
Sweeney, T. Critical Care Med. Nov 2020.
Cost impact model of a novel multi-mRNA host response assay for diagnosis and risk assessment of acute infections and sepsis in the ED
Schneider JE, Romanowsky J, et al. JHEOR. 2020.
A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections
Mayhew M, et al. Nature Communications. Mar 2020.
Pilot study of a novel serum mRNA gene panel for diagnosis of acute septic arthritis
Schultz B, et al. World Journal of Orthopedics. Dec 2019.
Pilot study of a novel serum mRNA gene panel for diagnosis of acute septic arthritis
Sweeney TE, Schultz B, et al. World Journal of Orthopedics. Dec 2019.
Diagnosis of bacterial sepsis: Why are tests for bacteremia not sufficient?
Sweeney TE, Liesenfeld O. Expert Review of Molecular Diagnostics. Aug 2019.
Diagnosing and managing sepsis by probing the host response to infection: Advances, opportunities, and challenges
Gunsolus I, Sweeney TE, et al. Journal of Clinical Microbiology. Jul 2019.
A 20-gene set predictive of progression to severe dengue
Robinson M, Sweeney TE, et al. Cell Reports. Jan 2019.
Validity of a blood-based 3-gene signature score for progression and diagnosis of tuberculosis, disease severity and tx response
Warsinke HC, et al. JAMA. Oct 2018.
A machine learning method for subgroup analysis of randomized controlled trials
Buturovic, L. BioRxiv. Jun 2018.
Unsupervised analysis of transcriptomics in bacterial sepsis across multiple datasets reveals three robust clusters
Sweeney, TE, et al. Critical Care Medicine. Mar 2018.
A community approach to mortality prediction in sepsis via gene expression analysis
Sweeney TE, et al. Nature Communications. Feb 2018.
Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival
Azad TD, et al. Journal of Clinical Investigation. Jan 2018.
Generalizable biomarkers in critical care: Toward precision medicine
Sweeney TE, Khatri P. Critical Care Medicine. Jun 2017.
A robust host-based gene expression diagnostic for malaria versus other infectious diseases
Aditya R, et al. 27th ECCMID, Vienna Austria. April 22-25, 2017.
Validation of the sepsis metascore for diagnosis of neonatal sepsis
Sweeney TE, et al. J Ped Infect Dis Soc. Apr 2017.
Methods to increase reproducibility in differential gene expression via meta-analysis
Sweeney TE, et al. Nucleic Acid Research. Jan 2017.
Benchmarking sepsis gene expression diagnostics using public data
Sweeney TE, Khatri P. Critical Care Medicine. Jan 2017.
Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity
Lofgren S, et al. Journal of Clinical Investigation. Dec 2016.
Robust classification of bacterial and viral infections via integrated host gene expression diagnostics
Sweeney TE, Wong HR, Khatri P. Science Translational Medicine. Jul 2016.
Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis
Sweeney TE, et al. Lancet Respiratory Medicine. Feb 2016.
Integrated multicohort analysis identifies conserved transcriptional signatures across multiple respiratory viruses
Andres-Terre M, et al. Immunity. Dec 2015.
A comprehensive time-course-based meta-analysis of sepsis and sterile inflammation reveals a robust discriminatory gene set
Sweeney TE, et al. Science Translational Medicine. May 2015.
A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation
Khatri P, et al. Journal of Experimental Medicine. Oct 2013.
Selected Abstracts
A 29-mRNA host response risk classifier enhances severity prediction in patients with suspected infection in the emergency department – a multicenter, observational study
Giamarellos-Bourboulis, E. et al. ISICEM.
September, 2021
A baseline gene expression-based prognostic for anti-TNFα therapy response in patients with inflammatory bowel disease
Sakaram S, et al. IBD supplement.
January, 2021
Development of a 29-mRNA loop mediated isothermal amplification assay for the rapid diagnosis of acute infection and sepsis
Remmel M, et al. AMP 2020.
November 16-20, 2020
Similarities and differences in the transcriptomic host response between SARS-CoV-2 and other viral infections
Thair S, et al. ID Week 2020.
October 21-25, 2020
A 5-mRNA host response whole-blood classifier trained using patients with non-COVID-19 viral infections accurately predicts severity of COVID-19
Buturovic L, et al. ID Week 2020.
October 21-25, 2020
A 29-mRNA host response signature accurately distinguishes bacterial and viral infections among Emergency Department patients
Safarika A, et al. e-ISICEM 2020.
September 15-19, 2020
Prospective validation of a 29-mRNA host response signature to diagnose suspected acute infections in ED patients
Galtung N, et al. EUSEM Virtual 2020.
September 19-22, 2020
A mRNA host response signature accurately distinguishes bacterial and viral infections among Emergency Department patients
Safarika A, et al. ASM Microbe 2020, Greece BVN-2.
June 22 – August 17, 2020
An ultra-rapid host response assay to discriminate between bacterial and viral infections using quantitative isothermal gene expression analysis
Rawling D, et al. 2019 ECCMID.
April 13-16, 2019
Diagnosis of acute bacterial and viral infections using a 29-mRNA neural network
Mayhew M, et al. 2019 ECCMID.
April 13-16, 2019
Multiplex RT-qPCR for diagnosis and risk stratification of acute infection and sepsis using a 30-mRNA host response signature
Rawling D, et al. 2019 ECCMID.
April 13-16, 2019
Rapid host mRNA-based discrimination between bacterial and viral infection
Rawling D, et al. SAEM Western Regional Meeting.
March 21‐22, 2019
Multiplexing of an 18-host-gene signature using rapid PCR for better antibiotics decision
Nie W, et al. SAEM Western Regional Meeting.
March 21‐22, 2019
An ultra-rapid host response assay to discriminate between bacterial and viral infections using quantitative isothermal gene expression analysis
Rawling D, et al. 2018 IDWeek.
October 3-7, 2018
Rapid multiplex host gene expression profiling to discriminate bacterial from viral infections
Nie W, et al. 2018 IDWeek.
October 3-7, 2018
Cost effectiveness of ED use of a novel multi-mRNA assay for diagnosis and risk assessment of acute respiratory tract infections and sepsis
Stojanovic I, et al. Intnl. Sepsis Forum 2018.
October 1-3, 2018
Dual-cohort independent validation of a novel 12-mRNA score for sepsis prognosis
Sweeney T, et al. International Sepsis Forum 2018.
October 1-3, 2018
Survey-based assessment of emergency room physician practices for patients with suspected infection and sepsis
Schultz, et al. EUSEM 2018.
September 8-12, 2018
A host gene signature for diagnosis and risk stratification of acute infection and sepsis at hospital admission: HostDx™ Sepsis
Liesenfeld O, et al. EUSEM 2018.
September 8-12, 2018
Integration of next-gen sequencing, viral sequencing, and host-response profiling for the diagnosis of acute infections
Cheng H, et al. ID Week 2017.
October 7, 2017
The derivation and validation of three novel sepsis molecular subtypes to help guide precision therapies
Sweeney T, et al. Sepsis 2017.
September 11-13, 2017
Host-response biomarkers for diagnosing acute infections
Sweeney T, Khatri P, MHSRS.
August 28-29, 2017
Prospective validation of the sepsis metascore for diagnosis of infections post traumatic injury
Sweeney T, et al. American Surgical Congress.
February 7-9, 2017
