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Diagnosing and Managing Sepsis by Probing the Host Response to Infection: Advances, Opportunities, and Challenges.

Gunsolus IL, Sweeney TE, Liesenfeld O, Ledeboer NA.

J Clin Microbiol. 2019 Jun 25;57(7). pii: e00425-19. doi: 10.1128/JCM.00425-19. Print 2019 Jul. Review.


A 20-Gene Set Predictive of Progression to Severe Dengue.

Robinson M, Sweeney TE, Barouch-Bentov R, Sahoo MK, Kalesinskas L, Vallania F, Sanz AM, Ortiz-Lasso E, Albornoz LL, Rosso F, Montoya JG, Pinsky BA, Khatri P, Einav S.

Cell Rep. 2019 Jan 29;26(5):1104-1111.e4. doi: 10.1016/j.celrep.2019.01.033.


Assessment of Validity of a Blood-Based 3-Gene Signature Score for Progression and Diagnosis of Tuberculosis, Disease Severity, and Treatment Response.

Warsinske HC, Rao AM, Moreira FMF, Santos PCP, Liu AB, Scott M, Malherbe ST, Ronacher K, Walzl G, Winter J, Sweeney TE, Croda J, Andrews JR, Khatri P.

JAMA Netw Open. 2018 Oct 5;1(6):e183779. doi: 10.1001/jamanetworkopen.2018.3779.


Combined resistance and aerobic exercise training reduces insulin resistance and central adiposity in adolescent girls who are obese: randomized clinical trial.

Bharath LP, Choi WW, Cho JM, Skobodzinski AA, Wong A, Sweeney TE, Park SY.

Eur J Appl Physiol. 2018 Aug;118(8):1653-1660. doi: 10.1007/s00421-018-3898-8. Epub 2018 May 30.


Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters.

Sweeney TE, Azad TD, Donato M, Haynes WA, Perumal TM, Henao R, Bermejo-Martin JF, Almansa R, Tamayo E, Howrylak JA, Choi A, Parnell GP, Tang B, Nichols M, Woods CW, Ginsburg GS, Kingsmore SF, Omberg L, Mangravite LM, Wong HR, Tsalik EL, Langley RJ, Khatri P.

Crit Care Med. 2018 Jun;46(6):915-925. doi: 10.1097/CCM.0000000000003084.


A community approach to mortality prediction in sepsis via gene expression analysis.

Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, Burnham KL, Hinds CJ, Knight JC, Woods CW, Kingsmore SF, Ginsburg GS, Wong HR, Parnell GP, Tang B, Moldawer LL, Moore FE, Omberg L, Khatri P, Tsalik EL, Mangravite LM, Langley RJ.

Nat Commun. 2018 Feb 15;9(1):694. doi: 10.1038/s41467-018-03078-2.


Inflammatory macrophage-associated 3-gene signature predicts subclinical allograft injury and graft survival.

Azad TD, Donato M, Heylen L, Liu AB, Shen-Orr SS, Sweeney TE, Maltzman JS, Naesens M, Khatri P.

JCI Insight. 2018 Jan 25;3(2). pii: 95659. doi: 10.1172/jci.insight.95659. eCollection 2018 Jan 25.


Multicohort Analysis of Whole-Blood Gene Expression Data Does Not Form a Robust Diagnostic for Acute Respiratory Distress Syndrome.

Sweeney TE, Thomas NJ, Howrylak JA, Wong HR, Rogers AJ, Khatri P.

Crit Care Med. 2018 Feb;46(2):244-251. doi: 10.1097/CCM.0000000000002839.


Pediatric Sepsis Endotypes Among Adults With Sepsis.

Wong HR, Sweeney TE, Hart KW, Khatri P, Lindsell CJ.

Crit Care Med. 2017 Dec;45(12):e1289-e1291. doi: 10.1097/CCM.0000000000002733.


Unique transcriptomic response to sepsis is observed among patients of different age groups.

Raymond SL, López MC, Baker HV, Larson SD, Efron PA, Sweeney TE, Khatri P, Moldawer LL, Wynn JL.

PLoS One. 2017 Sep 8;12(9):e0184159. doi: 10.1371/journal.pone.0184159. eCollection 2017.


Encouraging Mindfulness in Medical House Staff via Smartphone App: A Pilot Study.

Wen L, Sweeney TE, Welton L, Trockel M, Katznelson L.

Acad Psychiatry. 2017 Oct;41(5):646-650. doi: 10.1007/s40596-017-0768-3. Epub 2017 Aug 9.


Identifying Distinct Subgroups of ICU Patients: A Machine Learning Approach.

Vranas KC, Jopling JK, Sweeney TE, Ramsey MC, Milstein AS, Slatore CG, Escobar GJ, Liu VX.

Crit Care Med. 2017 Oct;45(10):1607-1615. doi: 10.1097/CCM.0000000000002548.


Generalizable Biomarkers in Critical Care: Toward Precision Medicine.

Sweeney TE, Khatri P.

Crit Care Med. 2017 Jun;45(6):934-939. doi: 10.1097/CCM.0000000000002402. No abstract available.


Validation of the Sepsis MetaScore for Diagnosis of Neonatal Sepsis.

Sweeney TE, Wynn JL, Cernada M, Serna E, Wong HR, Baker HV, Vento M, Khatri P.

J Pediatric Infect Dis Soc. 2018 May 15;7(2):129-135. doi: 10.1093/jpids/pix021.


Gene Expression Analysis to Assess the Relevance of Rodent Models to Human Lung Injury.

Sweeney TE, Lofgren S, Khatri P, Rogers AJ.

Am J Respir Cell Mol Biol. 2017 Aug;57(2):184-192. doi: 10.1165/rcmb.2016-0395OC.


The authors reply.

Sweeney TE, Khatri P.

Crit Care Med. 2017 Apr;45(4):e457-e458. doi: 10.1097/CCM.0000000000002269. No abstract available.


The authors reply.

Sweeney TE, Khatri P.

Crit Care Med. 2017 Mar;45(3):e341. doi: 10.1097/CCM.0000000000002219. No abstract available.


Septic Cardiomyopathy: Getting to the Heart of the Matter.

Sweeney TE, Khatri P.

Crit Care Med. 2017 Mar;45(3):556-557. doi: 10.1097/CCM.0000000000002239. No abstract available.


Simplification of a Septic Shock Endotyping Strategy for Clinical Application.

Wong HR, Sweeney TE, Lindsell CJ.

Am J Respir Crit Care Med. 2017 Jan 15;195(2):263-265. doi: 10.1164/rccm.201607-1535LE. No abstract available.


Hospital-acquired Pneumonia: A Host of Factors.

Sweeney TE, Khatri P.

Am J Respir Crit Care Med. 2016 Dec 1;194(11):1309-1311. No abstract available.



Haynes WA, Vallania F, Liu C, Bongen E, Tomczak A, Andres-Terrè M, Lofgren S, Tam A, Deisseroth CA, Li MD, Sweeney TE, Khatri P.

Pac Symp Biocomput. 2017;22:144-153. doi: 10.1142/9789813207813_0015.


Complement pathway amplifies caspase-11-dependent cell death and endotoxin-induced sepsis severity.

Napier BA, Brubaker SW, Sweeney TE, Monette P, Rothmeier GH, Gertsvolf NA, Puschnik A, Carette JE, Khatri P, Monack DM.

J Exp Med. 2016 Oct 17;213(11):2365-2382. Epub 2016 Oct 3.


Benchmarking Sepsis Gene Expression Diagnostics Using Public Data.

Sweeney TE, Khatri P.

Crit Care Med. 2017 Jan;45(1):1-10.


Methods to increase reproducibility in differential gene expression via meta-analysis.

Sweeney TE, Haynes WA, Vallania F, Ioannidis JP, Khatri P.

Nucleic Acids Res. 2017 Jan 9;45(1):e1. doi: 10.1093/nar/gkw797. Epub 2016 Sep 14.


Robust classification of bacterial and viral infections via integrated host gene expression diagnostics.

Sweeney TE, Wong HR, Khatri P.

Sci Transl Med. 2016 Jul 6;8(346):346ra91. doi: 10.1126/scitranslmed.aaf7165.


Blood transcriptional signatures for tuberculosis diagnosis: a glass half-empty perspective - Authors' reply.

Sweeney TE, Khatri P.

Lancet Respir Med. 2016 Jun;4(6):e29. doi: 10.1016/S2213-2600(16)30039-X. No abstract available.


Risk Stratification and Prognosis in Sepsis: What Have We Learned from Microarrays?

Sweeney TE, Wong HR.

Clin Chest Med. 2016 Jun;37(2):209-18. doi: 10.1016/j.ccm.2016.01.003. Epub 2016 Mar 10. Review.


Learning statistical models of phenotypes using noisy labeled training data.

Agarwal V, Podchiyska T, Banda JM, Goel V, Leung TI, Minty EP, Sweeney TE, Gyang E, Shah NH.

J Am Med Inform Assoc. 2016 Nov;23(6):1166-1173. doi: 10.1093/jamia/ocw028. Epub 2016 May 12.


Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis.

Sweeney TE, Braviak L, Tato CM, Khatri P.

Lancet Respir Med. 2016 Mar;4(3):213-24. doi: 10.1016/S2213-2600(16)00048-5. Epub 2016 Feb 20.


Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses.

Andres-Terre M, McGuire HM, Pouliot Y, Bongen E, Sweeney TE, Tato CM, Khatri P.

Immunity. 2015 Dec 15;43(6):1199-211. doi: 10.1016/j.immuni.2015.11.003.


Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.

Sweeney TE, Chen AC, Gevaert O.

Sci Rep. 2015 Nov 19;5:16971. doi: 10.1038/srep16971.


Comprehensive Validation of the FAIM3:PLAC8 Ratio in Time-matched Public Gene Expression Data.

Sweeney TE, Khatri P.

Am J Respir Crit Care Med. 2015 Nov 15;192(10):1260-1. doi: 10.1164/rccm.201507-1321LE. No abstract available.


Prediction of neurosurgical intervention after mild traumatic brain injury using the national trauma data bank.

Sweeney TE, Salles A, Harris OA, Spain DA, Staudenmayer KL.

World J Emerg Surg. 2015 Jun 6;10:23. doi: 10.1186/s13017-015-0017-6. eCollection 2015.


A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set.

Sweeney TE, Shidham A, Wong HR, Khatri P.

Sci Transl Med. 2015 May 13;7(287):287ra71. doi: 10.1126/scitranslmed.aaa5993.


Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT.

Mortensen JM, Minty EP, Januszyk M, Sweeney TE, Rector AL, Noy NF, Musen MA.

J Am Med Inform Assoc. 2015 May;22(3):640-8. doi: 10.1136/amiajnl-2014-002901. Epub 2014 Oct 23.


Metabolic surgery: action via hormonal milieu changes, changes in bile acids or gut microbiota? A summary of the literature.

Sweeney TE, Morton JM.

Best Pract Res Clin Gastroenterol. 2014 Aug;28(4):727-40. doi: 10.1016/j.bpg.2014.07.016. Epub 2014 Aug 12. Review.


The human gut microbiome: a review of the effect of obesity and surgically induced weight loss.

Sweeney TE, Morton JM.

JAMA Surg. 2013 Jun;148(6):563-9. doi: 10.1001/jamasurg.2013.5. Review.


A toll-like receptor 2 pathway regulates the Ppargc1a/b metabolic co-activators in mice with Staphylococcal aureus sepsis.

Sweeney TE, Suliman HB, Hollingsworth JW, Welty-Wolf KE, Piantadosi CA.

PLoS One. 2011;6(9):e25249. doi: 10.1371/journal.pone.0025249. Epub 2011 Sep 26.


Heme oxygenase-1 couples activation of mitochondrial biogenesis to anti-inflammatory cytokine expression.

Piantadosi CA, Withers CM, Bartz RR, MacGarvey NC, Fu P, Sweeney TE, Welty-Wolf KE, Suliman HB.

J Biol Chem. 2011 May 6;286(18):16374-85. doi: 10.1074/jbc.M110.207738. Epub 2011 Mar 18.


Staphylococcus aureus sepsis and mitochondrial accrual of the 8-oxoguanine DNA glycosylase DNA repair enzyme in mice.

Bartz RR, Suliman HB, Fu P, Welty-Wolf K, Carraway MS, MacGarvey NC, Withers CM, Sweeney TE, Piantadosi CA.

Am J Respir Crit Care Med. 2011 Jan 15;183(2):226-33. doi: 10.1164/rccm.200911-1709OC. Epub 2010 Aug 23.


Differential regulation of the PGC family of genes in a mouse model of Staphylococcus aureus sepsis.

Sweeney TE, Suliman HB, Hollingsworth JW, Piantadosi CA.

PLoS One. 2010 Jul 15;5(7):e11606. doi: 10.1371/journal.pone.0011606.


Co-regulation of nuclear respiratory factor-1 by NFkappaB and CREB links LPS-induced inflammation to mitochondrial biogenesis.

Suliman HB, Sweeney TE, Withers CM, Piantadosi CA.

J Cell Sci. 2010 Aug 1;123(Pt 15):2565-75. doi: 10.1242/jcs.064089. Epub 2010 Jun 29.


Nitric oxide synthase-2 regulates mitochondrial Hsp60 chaperone function during bacterial peritonitis in mice.

Suliman HB, Babiker A, Withers CM, Sweeney TE, Carraway MS, Tatro LG, Bartz RR, Welty-Wolf KE, Piantadosi CA.

Free Radic Biol Med. 2010 Mar 1;48(5):736-46. doi: 10.1016/j.freeradbiomed.2009.12.019. Epub 2010 Jan 4.


Intravascular pressure and diameter profile of the utero-ovarian resistance artery network: estrous cycle-dependent modulation of resistance artery tone.

Sweeney TE, Bagher P, Bailey J, Cherra SJ 3rd, Grisafi FN, Pauli EM, Riley K, Soares S.

Am J Physiol Heart Circ Physiol. 2007 Nov;293(5):H2937-44. Epub 2007 Aug 17.


Impaired flow-induced dilation in mesenteric resistance arteries from receptor protein tyrosine phosphatase-mu-deficient mice.

Koop EA, Gebbink MF, Sweeney TE, Mathy MJ, Heijnen HF, Spaan JA, Voest EE, VanBavel E, Peters SL.

Am J Physiol Heart Circ Physiol. 2005 Mar;288(3):H1218-23.


Effect of steady versus oscillating flow on porcine coronary arterioles: involvement of NO and superoxide anion.

Sorop O, Spaan JA, Sweeney TE, VanBavel E.

Circ Res. 2003 Jun 27;92(12):1344-51. Epub 2003 May 22.


A new in vivo microvascular preparation of the hamster ovary.

Sweeney TE, Bonadio JA, Freiman MA, Getts RT, Lloyd BT, McKeown K, Platt MP, Won JH.

Microcirculation. 1999 Dec;6(4):315-20.


Alteration of testicular microvascular pressures during venous pressure elevation.

Sweeney TE, Rozum JS, Gore RW.

Am J Physiol. 1995 Jul;269(1 Pt 2):H37-45.


Limitations of methods of osmometry: measuring the osmolality of biological fluids.

Sweeney TE, Beuchat CA.

Am J Physiol. 1993 Mar;264(3 Pt 2):R469-80. Review.


Regional hydrostatic pressure differences: relation to spatial variations in arteriolar cell flux and tone.

Sweeney TE, Gore RW.

Microvasc Res. 1992 Jan;43(1):112-7. No abstract available.


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