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Development of machine learning classifiers for blood-based diagnosis and prognosis of suspected acute infections and sepsis

Development of machine learning classifiers for blood-based diagnosis and prognosis of suspected acute infections and sepsis

Buturovic, L. et al. arXiv. Jul 2024.
A 29-mRNA host-response classifier identifies bacterial infections following liver transplantation – a pilot study

A 29-mRNA host-response classifier identifies bacterial infections following liver transplantation – a pilot study

Halder, A. et al. National Library of Medicine. Jun 2024.
A standardized protocol using clinical adjudication to define true infection status in patients presenting to the emergency department with suspected infections and/or sepsis

A standardized protocol using clinical adjudication to define true infection status in patients presenting to the emergency department with suspected infections and/or sepsis

Whitfield, N. et al. Science Direct. May 2024.
A transcriptomic severity classifier IMX-SEV-3b to predict mortality in ICU patients with COVID-19

A transcriptomic severity classifier IMX-SEV-3b to predict mortality in ICU patients with COVID-19

Daenen, K. et al. Genome Medicine. Sep 2023.
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

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

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 TriVerity, Endotypes, Bioinformatics, COVID-19, Machine Learning

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.
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Selected abstracts

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Accuracy of a 29-gene host response test for diagnosis of bacterial and viral infections and prediction of illness severity

Whitfield N. et al. 2024 ECCMID.
April 27-30, 2024

A Transcriptomic Severity Classifier IMX SEV 3b to Predict Mortality in Intensive Care Unit Patients with COVID 19: A Prospective Observational Pilot Study

Daenen, K. et al. ESICEM.
September, 2023

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

Isothermal amplification of host immune mRNAs for rapid bacterial/viral discrimination

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