Publications

Recent News

Clinical and Single-Cell Transcriptomics for Pneumonia Codeathon

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DMID System Biology Consortium for Infectious Disease

Talk by Dr. Misharin at DMID SysBio Consortium for Infectious Disease held by NIAID

Recording with access code: C7njd%K6

Exploring the origins of autoimmunity to find new therapies

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Study Explores How Pneumonia Strains Compete

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All project publications

Publication	PMID	PMCID
Agard MJ, Ozer EA, Morris AR, Piseaux R, Hauser AR. A genomic approach to identify Klebsiella pneumoniae and Acinetobacter baumannii strains with enhanced competitive fitness in the lungs during multistrain pneumonia. Infect Immun. 2019 May 21;87(6):e00871-18. doi: 10.1128/IAI.00871-18. PMID: 30936161; PMCID: PMC6529660.	PMID: 30936161	PMCID: PMC6529660
Alexander MJ, Budinger GRS, Reyfman PA. Breathing fresh air into respiratory research with single-cell RNA sequencing. Eur Respir Rev. 2020 Jul 3;29(156):200060. doi: 10.1183/16000617.0060-2020. PMID: 32620586; PMCID: PMC7719403.	PMID: 32620586	PMCID: PMC7719403
Allen JP, Hauser AR. Diversity of contact-dependent growth inhibition systems of Pseudomonas aeruginosa. J Bacteriol. 2019 Jun 21;201(14):e00776-18. doi: 10.1128/JB.00776-18. PMID: 31036723; PMCID: PMC6597396.	PMID: 31036723	PMCID: PMC6597396
Allen JP, Ozer EA, Minasov G, Shuvalova L, Kiryukhina O, Satchell KJF, Hauser AR. A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant. Proc Natl Acad Sci U S A. 2020;117(12):6811-21. doi: 10.1073/pnas.1919198117. PMID: 32156726; PMCID: PMC7104216.	PMID: 32156726	PMCID: PMC7104216
Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and trees: exploring bacterial virulence with genome-wide association studies and machine learning. Trends Microbiol. 2021;29(7):621-33. doi: 10.1016/j.tim.2020.12.002. PMID: 33455849; PMCID: PMC8187264.	PMID: 33455849	PMCID: PMC8187264
Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Technology dictates algorithms: recent developments in read alignment. Genome Biol. 2021 Aug 26;22(1):249. doi: 10.1186/s13059-021-02443-7. PMID: 34446078; PMCID: PMC8390189.	PMID: 34446078	PMCID: PMC8390189
Arnold J, Gao CA, Malsin E, Todd K, Argento AC, Cuttica M, Coleman JM, Wunderink RG, Smith SB, The NU COVID Investigators. Outcomes of percutaneous tracheostomy for patients with SARS-CoV-2 respiratory failure. J Bronchology Interv Pulmonol. 2022 Apr 5. doi: 10.1097/LBR.0000000000000854. Online ahead of print.
Arnold J, Gao CA, Malsin E, Todd K, Argento AC, Cuttica M, Coleman JM, Wunderink RG, Smith SB. Outcomes of percutaneous tracheostomy for patients with SARS-CoV-2 respiratory failure. medRxiv [Preprint]. 2021 Feb 25:2021.02.23.21252231. doi: 10.1101/2021.02.23.21252231. PMID: 33655275; PMCID: PMC7924300.	PMID: 33655275	PMCID: PMC7924300
Avedissian SN, Liu J, Rhodes NJ, Lee A, Pais GM, Hauser AR, Scheetz MH. A review of the clinical pharmacokinetics of Polymyxin B. antibiotics (Basel). 2019 Mar 22;8(1):31. doi: 10.3390/antibiotics8010031. PMID: 30909507; PMCID: PMC6466567.	PMID: 30909507	PMCID: PMC6466567
Bachta KER, Allen JP, Cheung BH, Chiu CH, Hauser AR. Systemic infection facilitates transmission of Pseudomonas aeruginosa in mice. Nat Commun. 2020 Jan 28;11(1):543. doi: 10.1038/s41467-020-14363-4. PMID: 31992714; PMCID: PMC6987207.	PMID: 31992714	PMCID: PMC6987207
Bachta KER, Ozer EA, Pandit A, Marty FM, Mekalanos JJ, Hauser AR. Draft genome sequence of Pseudomonas aeruginosa strain BWH047, a sequence type 235 multidrug-resistant clinical isolate expressing high levels of colistin resistance. Microbiol Resour Announc. 2019;8(29):e00623-19. doi: 10.1128/mra.00623-19. PMID: 31320415; PMCID: PMC6639617.	PMID: 31320415	PMCID: PMC6639617
Barengolts E, Green SJ, Chlipala GE, Layden BT, Eisenberg Y, Priyadarshini M, Dugas LR. Predictors of obesity among gut microbiota biomarkers in African American men with and without diabetes. Microorganisms. 2019 Sep 5;7(9):320. doi: 10.3390/microorganisms7090320. PMID: 31491976; PMCID: PMC6780321.	PMID: 31491976	PMCID: PMC6780321
Bassetti M, Echols R, Matsunaga Y, Ariyasu M, Doi Y, Ferrer R, Lodise TP, Naas T, Niki Y, Paterson DL, Portsmouth S, Torre-Cisneros J, Toyoizumi K, Wunderink RG, Nagata TD. Efficacy and safety of cefiderocol or best available therapy for the treatment of serious infections caused by carbapenem-resistant gram-negative bacteria (CREDIBLE-CR): a randomised, open-label, multicentre, pathogen-focused, descriptive, phase 3 trial. Lancet Infect Dis. 2021 Feb;21(2):226-240. doi: 10.1016/S1473-3099(20)30796-9. PMID: 33058795.	PMID: 33058795
Bavishi AA, Mylvaganam RJ, Agarwal R, Avery RJ, Cuttica MJ. Timing of intubation in coronavirus disease 2019: a study of ventilator mechanics, imaging, findings, and outcomes. Crit Care Explor. 2021 May 12;3(5):e0415. doi: 10.1097/CCE.0000000000000415. PMID: 34079946; PMCID: PMC8162516.	PMID: 34079946	PMCID: PMC8162516
Bechel MA, Pah AR, Shi H, Mehrotra S, Persell SD, Weiner S, Wunderink RG, Nunes Amaral LA, Weiss CH. A quantitative approach for the analysis of clinician recognition of acute respiratory distress syndrome using electronic health record data. PLoS One. 2019 Sep 20;14(9):e0222826. doi: 10.1371/journal.pone.0222826. PMID: 31539417; PMCID: PMC6754155.	PMID: 31539417	PMCID: PMC6754155
Bellew S, Grijalva CG, Williams DJ, Anderson EJ, Wunderink RG, Zhu Y, Waterer GW, Bramley AM, Jain S, Edwards KM, Self WH. Pneumococcal and legionella urinary antigen tests in community-acquired pneumonia: prospective evaluation of indications for testing. Clin Infect Dis. 2019 May 30;68(12):2026-2033. doi: 10.1093/cid/ciy826. PMID: 30265290; PMCID: PMC7182343.	PMID: 30265290	PMCID: PMC7182343
Bellingan G, Jacono F, Bannard-Smith J, Brealey D, Meyer N, Thickett D, Young D, Bentley A, McVerry BJ, Wunderink RG, Doerschug KC, Summers C, Rojas M, Ting A, Jenkins ED. Safety and efficacy of multipotent adult progenitor cells in acute respiratory distress syndrome (MUST-ARDS): a multicentre, randomised, double-blind, placebo-controlled phase 1/2 trial. Intensive Care Med. 2022;48:36-44. PMCID: PMC8608557.	PMID: 34811567	PMCID: PMC8608557
Bellomo R, Wunderink RG, Szerlip H, English SW, Busse LW, Deane AM, Khanna AK, McCurdy MT, Ostermann M, Young PJ, Handisides DR, Chawla LS, Tidmarsh GF, Albertson TE. Angiotensin I and angiotensin II concentrations and their ratio in catecholamine-resistant vasodilatory shock. Crit Care. 2020 Feb 6;24(1):43. doi: 10.1186/s13054-020-2733-x. PMID: 32028998; PMCID: PMC7006163.	PMID: 32028998	PMCID: PMC7006163
Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, Huttenhower C, Hartmann EM. Mobilizable antibiotic resistance genes are present in dust microbial communities. PLoS Pathog. 2020 Jan 23;16(1):e1008211. doi: 10.1371/journal.ppat.1008211. PMID: 31971995; PMCID: PMC6977718.	PMID: 31971995	PMCID: PMC6977718
Bharat A, Machuca TN, Querrey M, Kurihara C, Garza-Castillon R Jr, Kim S, Manerikar A, Pelaez A, Pipkin M, Shahmohammadi A, Rackauskas M, Kg SR, Balakrishnan KR, Jindal A, Schaheen L, Hashimi S, Buddhdev B, Arjuna A, Rosso L, Palleschi A, Lang C, Jaksch P, Budinger GRS, Nosotti M, Hoetzenecker K. Early outcomes after lung transplantation for severe COVID-19: a series of the first consecutive cases from four countries. Lancet Respir Med. 2021 May;9(5):487-497. doi: 10.1016/S2213-2600(21)00077-1. PMID: 33811829; PMCID: PMC8012035.	PMID: 33811829	PMCID: PMC8012035
Bharat A, Querrey M, Markov NS, Kim S, Kurihara C, Garza-Castillon R, Manerikar A, Shilatifard A, Tomic R, Politanska Y, Abdala-Valencia H, Yeldandi AV, Lomasney JW, Misharin AV, Budinger GRS. Lung transplantation for patients with severe COVID-19. Sci Transl Med. 2020 Dec 16;12(574):eabe4282. doi: 10.1126/scitranslmed.abe4282. PMID: 33257409; PMCID: PMC8050952.	PMID: 33257409	PMCID: PMC8050952
Brazee PL, Morales-Nebreda L, Magnani ND, Garcia JG, Misharin AV, Ridge KM, Budinger GRS, Iwai K, Dada LA, Sznajder JI. Linear ubiquitin assembly complex regulates lung epithelial-driven responses during influenza infection. J Clin Invest. 2020 Mar 2;130(3):1301-1314. doi: 10.1172/JCI128368. PMID: 31714898; PMCID: PMC7269564.	PMID: 31714898	PMCID: PMC7269564
Budinger GRS, Misharin AV, Ridge KM, Singer BD, Wunderink RG. Distinctive features of severe SARS-CoV-2 pneumonia. J Clin Invest. 2021;131(14):e149412. doi: 10.1172/jci149412. PMID: 34263736; PMCID: PMC8279580.	PMID: 34263736	PMCID: PMC8279580
Bulman ZP, Krapp F, Pincus NB, Wenzler E, Murphy KR, Qi C, Ozer EA, Hauser AR. Genomic features associated with the degree of phenotypic resistance to Carbapenems in Carbapenem-Resistant Klebsiella pneumoniae. mSystems. 2021 Oct 26;6(5):e0019421. doi: 10.1128/mSystems.00194-21. PMID: 34519526; PMCID: PMC8547452.	PMID: 34519526	PMCID: PMC8547452
Butler DA, Rana AP, Krapp F, Patel SR, Huang Y, Ozer EA, et al. Optimizing aminoglycoside selection for KPC-producing Klebsiella pneumoniae with the aminoglycoside-modifying enzyme (AME) gene aac(6')-Ib. J Antimicrob Chemother. 2021;76(3):671-9. doi: 10.1093/jac/dkaa480. PMID: 33326561; PMCID: PMC7879147.	PMID: 33326561	PMCID: PMC7879147
Cavallazzi R, Furmanek S, Arnold FW, Beavin LA, Wunderink RG, Niederman MS, Ramirez JA. The burden of community-acquired pneumonia requiring admission to ICU in the United States. Chest. 2020 Sep;158(3):1008-1016. doi: 10.1016/j.chest.2020.03.051. PMID: 32298730.	PMID: 32298730
Chotirmall SH, Leither LM, Çoruh B, Chan LLY, Joudi AM, Brown SM, Singer BD, Seam N. Update in COVID-19 2020. Am J Respir Crit Care Med. 2021 Jun 15;203(12):1462-1471. doi: 10.1164/rccm.202102-0415UP. PMID: 33835905; PMCID: PMC8483226.	PMID: 33835905	PMCID: PMC8483226
Crofts TS, McFarland AG, Hartmann EM. Mosaic ends tagmentation (METa) assembly for highly efficient construction of functional metagenomic libraries. mSystems. 2021 Jun 29;6(3):e0052421. doi: 10.1128/mSystems.00524-21. Epub ahead of print. PMID: 34184912; PMCID: PMC8269240.	PMID: 34184912	PMCID: PMC8269240
Dela Cruz CS, Wunderink RG, Christiani DC, Cormier SA, Crothers K, Doerschuk CM, Evans SE, Goldstein DR, Khatri P, Kobzik L, Kolls JK, Levy BD, Metersky ML, Niederman MS, Nusrat R, Orihuela CJ, Peyrani P, Prince AS, Ramírez JA, Ridge KM, Sethi S, Suratt BT, Sznajder JI, Tsalik EL, Walkey AJ, Yende S, Aggarwal NR, Caler EV, Mizgerd JP. Future research directions in pneumonia. NHLBI Working Group Report. Am J Respir Crit Care Med. 2018 Jul 15;198(2):256-263. doi: 10.1164/rccm.201801-0139WS. PMID: 29546996; PMCID: PMC6058989.	PMID: 29546996	PMCID: PMC6058989
Dilger AE, Peters AT, Wunderink RG, Tan BK, Kern RC, Conley DB, Welch KC, Holl JL, Smith SS. Procalcitonin as a biomarker in rhinosinusitis: a systematic review. Am J Rhinol Allergy. 2019 Mar;33(2):103-112. doi: 10.1177/1945892418810293. PMID: 30871341; PMCID: PMC6421617.	PMID: 30871341	PMCID: PMC6421617
Do-Umehara HC, Chen C, Zhang Q, Misharin AV, Abdala-Valencia H, Casalino-Matsuda SM, Reyfman PA, Anekalla KR, Gonzalez-Gonzalez FJ, Sala MA, Peng C, Wu P, Wong CCL, Kalhan R, Bharat A, Perlman H, Ridge KM, Sznajder JI, Sporn PHS, Chandel NS, Yu J, Fu X, Petrache I, Tuder R, Budinger GRS, Liu J. Epithelial cell-specific loss of function of Miz1 causes a spontaneous COPD-like phenotype and up-regulates Ace2 expression in mice. Sci Adv. 2020 Aug 14;6(33):eabb7238. doi: 10.1126/sciadv.abb7238. PMID: 32851183; PMCID: PMC7428331.	PMID: 32851183	PMCID: PMC7428331
Edward PR, Lorenzo-Redondo R, Reyna ME, Simons LM, Hultquist JF, Patel AB, Ozer EA, Muller WJ, Heald-Sargent T, McHugh M, Dean TJ, Dalal RM, John J, Manz SC, Kociolek LK. Severity of illness caused by severe acute respiratory syndrome coronavirus 2 variants of concern in children: a single-center retrospective cohort study. medRxiv [Preprint]. 2021 Oct 26:2021.10.23.21265402. doi: 10.1101/2021.10.23.21265402. PMID: 34729568; PMCID: PMC8562552.	PMID: 34729568	PMCID: PMC8562552
Edward PR, Reyna ME, Daly MK, Hultquist JF, Muller WJ, Ozer EA, Lorenzo-Redondo R, Seed PC, Simons LM, Sheehan K, Staples J, Kociolek L. Screening students and staff for asymptomatic coronavirus disease 2019 in Chicago schools. J Pediatr. 2021 Dec;239:74-80.e1. doi: 10.1016/j.jpeds.2021.08.017. PMID: 34416262; PMCID: PMC8372436.	PMID: 34416262	PMCID: PMC8372436
Eickelberg O, Misharin AV, Sime PJ. Reproducible single-cell genomic research in pulmonary and critical care medicine. Am J Respir Crit Care Med. 2020;202(11):1495-7. doi: 10.1164/rccm.202008-3073ED. PMID: 32916059; PMCID: PMC7706163.	PMID: 32916059	PMCID: PMC7706163
Evans SE, Jennerich AL, Azar MM, Cao B, Crothers K, Dickson RP, Herold S, Jain S, Madhavan A, Metersky ML, Myers LC, Oren E, Restrepo MI, Semret M, Sheshadri A, Wunderink RG, Dela Cruz CS. Nucleic acid-based testing for noninfluenza viral pathogens in adults with suspected community-acquired pneumonia. an official American Thoracic Society clinical practice guideline. Am J Respir Crit Care Med. 2021 May 1;203(9):1070-1087. doi: 10.1164/rccm.202102-0498ST. PMID: 33929301; PMCID: PMC8314899.	PMID: 33929301	PMCID: PMC8314899
Fahimipour AK, Ben Mamaar S, McFarland AG, Blaustein RA, Chen J, Glawe AJ, Kline J, Green JL, Halden RU, Van Den Wymelenberg K, Huttenhower C, Hartmann EM. Antimicrobial chemicals associate with microbial function and antibiotic resistance indoors. mSystems. 2018 Dec 11;3(6):e00200-18. doi: 10.1128/mSystems.00200-18. PMID: 30574558; PMCID: PMC6290264.	PMID: 30574558	PMCID: PMC6290264
Gao CA, Bailey JI, Walter JM, Coleman JM, Malsin ES, Argento AC, Prickett MH, Wunderink RG, Smith SB. Bronchoscopy on intubated patients with COVID-19 is associated with low infectious risk to operators. Ann Am Thorac Soc. 2021 Jul;18(7):1243-1246. doi: 10.1513/AnnalsATS.202009-1225RL. PMID: 33448892; PMCID: PMC8328373.	PMID: 33448892	PMCID: PMC8328373
Gao CA, Cuttica MJ, Malsin ES, Argento AC, Wunderink RG, Smith SB. Comparing nasopharyngeal and BAL SARS-CoV-2 assays in respiratory failure. Am J Respir Crit Care Med. 2021;203(1):127-9. doi: 10.1164/rccm.202008-3137LE. PMID: 33125256; PMCID: PMC7781122.	PMID: 33125256	PMCID: PMC7781122
Gelarden I, Nguyen J, Gao J, Chen Q, Morales-Nebreda L, Wunderink R, Li L, Chmiel JS, Hrisinko M, Marszalek L, Momnani S, Patel P, Sumugod R, Chao Q, Jennings LJ, Zembower TR, Ji P, Chen YH. Comprehensive evaluation of bronchoalveolar lavage from patients with severe COVID-19 and correlation with clinical outcomes. Hum Pathol. 2021 Jul;113:92-103. doi: 10.1016/j.humpath.2021.04.010. PMID: 33905777; PMCID: PMC8159767.	PMID: 33905777	PMCID: PMC8159767
Grant RA, Morales-Nebreda L, Markov NS, Swaminathan S, Querrey M, Guzman ER, Abbott DA, Donnelly HK, Donayre A, Goldberg IA, Klug ZM, Borkowski N, Lu Z, Kihshen H, Politanska Y, Sichizya L, Kang M, Shilatifard A, Qi C, Lomasney JW, Argento AC, Kruser JM, Malsin ES, Pickens CO, Smith SB, Walter JM, Pawlowski AE, Schneider D, Nannapaneni P, Abdala-Valencia H, Bharat A, Gottardi CJ, Budinger GRS, Misharin AV, Singer BD, Wunderink RG; NU SCRIPT Study Investigators. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature. 2021 Feb;590(7847):635-641. doi: 10.1038/s41586-020-03148-w. PMID: 33429418; PMCID: PMC7987233.	PMID: 33429418	PMCID: PMC7987233
Helmin KA, Morales-Nebreda L, Torres Acosta MA, Anekalla KR, Chen SY, Abdala-Valencia H, Politanska Y, Cheresh P, Akbarpour M, Steinert EM, Weinberg SE, Singer BD. Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function. J Clin Invest. 2020 Dec 1;130(12):6571-6587. doi: 10.1172/JCI137712. PMID: 32897881; PMCID: PMC7710299.	PMID: 32897881	PMCID: PMC7710299
Hoste E, Bihorac A, Al-Khafaji A, Ortega LM, Ostermann M, Haase M, Zacharowski K, Wunderink R, Heung M, Lissauer M, Self WH, Koyner JL, Honore PM, Prowle JR, Joannidis M, Forni LG, Kampf JP, McPherson P, Kellum JA, Chawla LS; RUBY Investigators. Identification and validation of biomarkers of persistent acute kidney injury: the RUBY study. Intensive Care Med. 2020 May;46(5):943-953. doi: 10.1007/s00134-019-05919-0. PMID: 32025755; PMCID: PMC7210248.	PMID: 32025755	PMCID: PMC7210248
Hsu CM, Gupta S, Tighiouart H, Goyal N, Faugno AJ, Tariq A, Raichoudhury R, Sharma JH, Meyer L, Kshirsagar RK, Jose A, Leaf DE, Weiner DE; STOP-COVID Investigators. Kidney recovery and death in critically ill patients with COVID-19-associated acute kidney injury treated with dialysis: The STOP-COVID Cohort Study. Am J Kidney Dis. 2022 Mar;79(3):404-416.e1. doi: 10.1053/j.ajkd.2021.11.004. PMID: 34871701; PMCID: PMC8641974.	PMID: 34871701	PMCID: PMC8641974
Hu J, Ben Maamar S, Glawe AJ, Gottel N, Gilbert JA, Hartmann EM. Impacts of indoor surface finishes on bacterial viability. Indoor Air. 2019 Jul;29(4):551-562. doi: 10.1111/ina.12558. PMID: 30980566; PMCID: PMC6851865.	PMID: 30980566	PMCID: PMC6851865
Huang Y, Rana AP, Wenzler E, Ozer EA, Krapp F, Bulitta JB, Hauser AR, Bulman ZP. Aminoglycoside-resistance gene signatures are predictive of aminoglycoside MICs for carbapenem-resistant Klebsiella pneumoniae. J Antimicrob Chemother. 2021 Oct 20:dkab381. doi: 10.1093/jac/dkab381. Epub ahead of print. PMID: 34668007.	PMID: 34668007	PMCID: PMC9097246
Huang Y, Sokolowski K, Rana A, Singh N, Wang J, Chen K, Lang Y, Zhou J, Kadiyala N, Krapp F, Ozer EA, Hauser AR, Li J, Bulitta JB, Bulman ZP. Generating genotype-specific aminoglycoside combinations with ceftazidime/avibactam for kpc-producing Klebsiella pneumoniae. Antimicrob Agents Chemother. 2021 Aug 17;65(9):e0069221. doi: 10.1128/AAC.00692-21. PMID: 34152820; PMCID: PMC8370209.	PMID: 34152820	PMCID: PMC8370209
I-SPY COVID Consortium. Clinical trial design during and beyond the pandemic: the I-SPY COVID trial. Nat Med. 2022 Jan;28(1):9-11. doi: 10.1038/s41591-021-01617-x. PMID: 35058620; PMCID: PMC8922451.	PMID: 35058620	PMCID: PMC8922451
Isturiz R, Grant L, Gray S, Alexander-Parrish R, Jiang Q, Jodar L, Peyrani P, Ford KD, Pride MW, Self WH, Counselman F, Volturo G, Ostrosky-Zeichner L, Wunderink RG, Sherwin R, Overcash JS, File T, Ramirez J. Expanded analysis of 20 pneumococcal serotypes associated with radiographically confirmed community-acquired pneumonia in hospitalized US adults. Clin Infect Dis. 2021 Oct 5;73(7):1216-1222. doi: 10.1093/cid/ciab375. PMID: 33982098; PMCID: PMC8492118.	PMID: 33982098	PMCID: PMC8492118
Isturiz RE, Ramirez J, Self WH, Grijalva CG, Counselman FL, Volturo G, Ostrosky-Zeichner L, Peyrani P, Wunderink RG, Sherwin R, Overcash JS, Oliva SP, File T, Wiemken TL, McLaughlin JM, Pride MW, Gray S, Alexander R, Ford KD, Jiang Q, Jodar L. Pneumococcal epidemiology among us adults hospitalized for community-acquired pneumonia. Vaccine. 2019 May 31;37(25):3352-3361. doi: 10.1016/j.vaccine.2019.04.087. PMID: 31072732.	PMID: 31072732
Johnson CR, Tran MN, Michelitsch LM, Abraham S, Hu J, Gray KA, Hartmann EM. Nano-enabled, antimicrobial toothbrushes - How physical and chemical properties relate to antibacterial capabilities. J Hazard Mater. 2020 Sep 5;396:122445. doi: 10.1016/j.jhazmat.2020.122445. PMID: 32298860.	PMID: 32298860
Joshi N, Watanabe S, Verma R, Jablonski RP, Chen CI, Cheresh P, Markov NS, Reyfman PA, McQuattie-Pimentel AC, Sichizya L, Lu Z, Piseaux-Aillon R, Kirchenbuechler D, Flozak AS, Gottardi CJ, Cuda CM, Perlman H, Jain M, Kamp DW, Budinger GRS, Misharin AV. A spatially restricted fibrotic niche in pulmonary fibrosis is sustained by M-CSF/M-CSFR signalling in monocyte-derived alveolar macrophages. Eur Respir J. 2020 Jan 16;55(1):1900646. doi: 10.1183/13993003.00646-2019. PMID: 31601718; PMCID: PMC6962769.	PMID: 31601718	PMCID: PMC6962769
Joudi AM, Reyes Flores CP, Singer BD. Epigenetic control of regulatory T cell stability and function: implications for translation. Front Immunol. 2022 Mar 2;13:861607. doi: 10.3389/fimmu.2022.861607. PMID: 35309306; PMCID: PMC8924620.	PMID: 35309306	PMCID: PMC8924620
Katsube T, Nicolau DP, Rodvold KA, Wunderink RG, Echols R, Matsunaga Y, Menon A, Portsmouth S, Wajima T. Intrapulmonary pharmacokinetic profile of cefiderocol in mechanically ventilated patients with pneumonia. J Antimicrob Chemother. 2021 Oct 11;76(11):2902-2905. doi: 10.1093/jac/dkab280. Erratum in: J Antimicrob Chemother. 2021 Sep 17;: PMID: 34383901; PMCID: PMC8521398.	PMID: 34383901	PMCID: PMC8521398
Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, Goldfarb DM, Pernica JM, Arscott-Mills T, Boiditswe S, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Feemster KA, Seed PC. Pneumococcal colonization and the nasopharyngeal microbiota of children in Botswana. Pediatr Infect Dis J. 2018 Nov;37(11):1176-1183. doi: 10.1097/INF.0000000000002174. PMID: 30153231; PMCID: PMC6181769.	PMID: 30153231	PMCID: PMC6181769
Kelly MS, Ward DV, Severyn CJ, Arshad M, Heston SM, Jenkins K, Martin PL, McGill L, Stokhuyzen A, Bhattarai SK, Bucci V, Seed PC. Gut colonization preceding mucosal barrier injury bloodstream infection in pediatric hematopoietic stem cell transplantation recipients. Biol Blood Marrow Transplant. 2019 Nov;25(11):2274-2280. doi: 10.1016/j.bbmt.2019.07.019. PMID: 31326608; PMCID: PMC6861666.	PMID: 31326608	PMCID: PMC6861666
Klein M, Bacher J, Barth S, Atrzadeh F, Siebenhaller K, Ferreira I, Beisken S, Posch AE, Carroll KC, Wunderink RG, Qi C, Wu F, Hardy DJ, Patel R, Sims MD. Multicenter evaluation of the unyvero platform for testing bronchoalveolar lavage fluid. J Clin Microbiol. 2021 Feb 18;59(3):e02497-20. doi: 10.1128/JCM.02497-20. PMID: 33328178; PMCID: PMC8106704.	PMID: 33328178	PMCID: PMC8106704
Koch CM, Prigge AD, Anekalla KR, Shukla A, Do Umehara HC, Setar L, Chavez J, Abdala-Valencia H, Politanska Y, Markov NS, Hahn GR, Heald-Sargent T, Sanchez-Pinto LN, Muller WJ, Singer BD, Misharin AV, Ridge KM, Coates BM. Age-related differences in the nasal mucosal immune response to SARS-CoV-2. Am J Respir Cell Mol Biol. 2021 Nov 3. doi: 10.1165/rcmb.2021-0292OC. Epub ahead of print. PMID: 34731594.	PMID: 34731594	PMC8845137
Kochan TJ, Ozer EA, Pincus NB, Fitzpatrick MA, Hauser AR. Complete genome sequence of Klebsiella pneumoniae Strain TK421, a conjugative hypervirulent isolate. Microbiol Resour Announc. 2020;9(3):e01408-19. doi: 10.1128/mra.01408-19. PMID: 31948967; PMCID: PMC6965585.	PMID: 31948967	PMCID: PMC6965585
Kociolek LK, Patel AB, Hultquist JF, Ozer EA, Simons LM, McHugh M, Muller WJ, Lorenzo-Redondo R. Viral whole-genome sequencing to assess impact of universal masking on SARS-CoV-2 transmission among pediatric healthcare workers. Infect Control Hosp Epidemiol. 2021 Oct 1:1-5. doi: 10.1017/ice.2021.415. Epub ahead of print. PMID: 34593066.	PMID: 34593066
Kollef MH, Nováček M, Kivistik Ü, Réa-Neto Á, Shime N, Martin-Loeches I, Timsit JF, Wunderink RG, Bruno CJ, Huntington JA, Lin G, Yu B, Butterton JR, Rhee EG. Ceftolozane-tazobactam versus meropenem for treatment of nosocomial pneumonia (ASPECT-NP): a randomised, controlled, double-blind, phase 3, non-inferiority trial. Lancet Infect Dis. 2019 Dec;19(12):1299-1311. doi: 10.1016/S1473-3099(19)30403-7. PMID: 31563344.	PMID: 31563344
Krapp F, Ozer EA, Qi C, Hauser AR. Case report of an extensively drug-resistant Klebsiella pneumoniae infection with genomic characterization of the strain and review of similar cases in the United States. Open Forum Infect Dis. 2018 Apr 6;5(5):ofy074. doi: 10.1093/ofid/ofy074. PMID: 29876363; PMCID: PMC5961207.	PMID: 29876363	PMCID: PMC5961207
Kruser JM, Benjamin BT, Gordon EJ, Michelson KN, Wunderink RG, Holl JL, Schwarze ML. Patient and family engagement during treatment decisions in an ICU: a discourse analysis of the electronic health record. Crit Care Med. 2019 Jun;47(6):784-791. doi: 10.1097/CCM.0000000000003711. PMID: 30896465; PMCID: PMC6522290.	PMID: 30896465	PMCID: PMC6522290
Kurihara C, Manerikar A, Gao CA, Watanabe S, Kandula V, Klonis A, Hoppner V, Karim A, Saine M, Odell DD, Lung K, Garza-Castillon R, Kim SS, Walter JM, Wunderink RG, Budinger GRS, Bharat A. Outcomes after extracorporeal membrane oxygenation support in COVID-19 and non-COVID-19 patients. Artif Organs. 2022 Apr;46(4):688-696. doi: 10.1111/aor.14090. PMID: 34694655; PMCID: PMC8653196.	PMID: 34694655	PMCID: PMC8653196
Kurihara C, Manerikar A, Querrey M, Felicelli C, Yeldandi A, Garza-Castillon Jr R, Lung K, Kim S, Ho B, Tomic R, Arunachalam A, Budinger GRS, Pesce L, Bharat A. Clinical characteristics and outcomes of patients with COVID-19-associated ARDS who underwent lung transplantation at an academic medical center in the US. JAMA. Forthcoming, 2022.	PMID: 35085383	PMCID: PMC8796055
Kurihara C, Walter JM, Karim A, Thakkar S, Saine M, Odell DD, Kim S, Tomic R, Wunderink RG, Budinger GRS, Bharat A. Feasibility of venovenous extracorporeal membrane oxygenation without systemic anticoagulation. Ann Thorac Surg. 2020 Oct;110(4):1209-1215. doi: 10.1016/j.athoracsur.2020.02.011.: 32173339; PMCID: PMC7486253.	PMID: 32173339	PMCID: PMC7486253
Kurihara C, Walter JM, Singer BD, Cajigas H, Shayan S, Al-Qamari A, DeCamp MM, Wunderink R, Budinger GRS, Bharat A. Extracorporeal membrane oxygenation can successfully support patients with severe acute respiratory distress syndrome in lieu of mechanical ventilation. Crit Care Med. 2018 Nov;46(11):e1070-e1073. doi: 10.1097/CCM.0000000000003354. PMID: 30095500; PMCID: PMC6185806.	PMID: 30095500	PMCID: PMC6185806
Lax S, Cardona C, Zhao D, Winton VJ, Goodney G, Gao P, Gottel N, Hartmann EM, Henry C, Thomas PM, Kelley ST, Stephens B, Gilbert JA. Microbial and metabolic succession on common building materials under high humidity conditions. Nat Commun. 2019 Apr 16;10(1):1767. doi: 10.1038/s41467-019-09764-z. PMID: 30992445; PMCID: PMC6467912.	PMID: 30992445	PMCID: PMC6467912
Lodise TP, Rosenkranz SL, Finnemeyer M, Evans S, Sims M, Zervos MJ, Creech CB, Patel PC, Keefer M, Riska P, Silveira FP, Scheetz M, Wunderink RG, Rodriguez M, Schrank J, Bleasdale SC, Schultz S, Barron M, Stapleton A, Wray D, Chambers H, Fowler VG, Holland TL. The emperor's new clothes: Prospective observational evaluation of the association between initial vancomycin exposure and failure rates among adult hospitalized patients with methicillin-resistant Staphylococcus aureus bloodstream infections (PROVIDE). Clin Infect Dis. 2020 Apr 10;70(8):1536-1545. doi: 10.1093/cid/ciz460. PMID: 31157370; PMCID: PMC7145993.	PMID: 31157370	PMCID: PMC7145993
Lodise TP, Van Wart S, Sund ZM, Bressler AM, Khan A, Makley AT, Hamad Y, Salata RA, Silveira FP, Sims MD, Kabchi BA, Saad MA, Brown C, Oler RE Jr, Fowler V Jr, Wunderink RG. Pharmacokinetic and pharmacodynamic profiling of minocycline for injection following a single infusion in critically ill adults in a phase iv open-label multicenter study (ACUMIN). Antimicrob Agents Chemother. 2021 Feb 17;65(3):e01809-20. doi: 10.1128/AAC.01809-20. PMID: 33168615; PMCID: PMC8092545.	PMID: 33168615	PMCID: PMC8092545
Lorenzo-Redondo R, Nam HH, Roberts SC, Simons LM, Jennings LJ, Qi C, Achenbach CJ, Hauser AR, Ison MG, Hultquist JF, Ozer EA. A unique clade of SARS-CoV-2 viruses is associated with lower viral loads in patient upper airways. medRxiv [Preprint]. 2020 Jun 21:2020.05.19.20107144. doi: 10.1101/2020.05.19.20107144. Update in: EBioMedicine. 2020 Dec;62:103112. PMID: 32511558; PMCID: PMC7274239.	PMID: 32511558	PMCID: PMC7274239
Lotfollahi M, Naghipourfar M, Luecken MD, Khajavi M, Büttner M, Wagenstetter M, Avsec Ž, Gayoso A, Yosef N, Interlandi M, Rybakov S, Misharin AV, Theis FJ. Mapping single-cell data to reference atlases by transfer learning. Nat Biotechnol. 2021 Aug 30. doi: 10.1038/s41587-021-01001-7. Epub ahead of print. PMID: 34462589.	PMID: 34462589
Luo Y, Wunderink RG, Lloyd-Jones D. Proactive vs reactive machine learning in health care: lessons from the COVID-19 pandemic. JAMA. 2022 ;327(7):623-624. doi: 10.1001/jama.2021.24935. PMID: 35085382.	PMID: 35085382
Madden P, Thomas Y, Blair R, Samer S, Doyle M, Midkiff C, Doyle-Meyers L, Becker M, Arif S, McRaven M, Simons L, Carias A, Martinelli E, Lorenzo-Redondo R, Hultquist J, Villinger F, Veazey R, Hope T. An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques. Res Sq [Preprint]. 2022 Apr 8:rs.3.rs-1479315. PMID: 35411346; PMCID: PMC8996619.	PMID: 35411346	PMCID: PMC8996619
Martin-Loeches I, Timsit JF, Kollef MH, Wunderink RG, Shime N, Nováček M, Kivistik Ü, Réa-Neto Á, Bruno CJ, Huntington JA, Lin G, Jensen EH, Motyl M, Yu B, Gates D, Butterton JR, Rhee EG. Clinical and microbiological outcomes, by causative pathogen, in the ASPECT-NP randomized, controlled, phase 3 trial comparing ceftolozane/tazobactam and meropenem for treatment of hospital-acquired/ventilator-associated bacterial pneumonia. J Antimicrob Chemother. 2022;77:1166-1177. doi: 10.1093/jac/dkab494. PMID: 35022730.	PMID: 35022730
McElroy GS, Chakrabarty RP, D'Alessandro KB, Vasan K, Tan J, Stoolman JS, Weinberg SE, Steinert EM, Reyfman PA, Singer BD, Ladiges WC, Gao L, Lopéz-Barneo J, Budinger GRS, Chandel NS. Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice. Sci Rep. 2022 Mar 25;12(1):5196. doi: 10.1038/s41598-022-09074-3. PMID: 35338200; PMCID: PMC8956724.	PMID: 35338200	PMCID: PMC8956724
McFarland AG, Bertucci HK, Littman E, Shen J, Huttenhower C, Hartmann EM. Triclosan tolerance is driven by a conserved mechanism in diverse pseudomonas species. Appl Environ Microbiol. 2021 Mar 11;87(7):e02924-20. doi: 10.1128/AEM.02924-20. PMID: 33483311; PMCID: PMC8091609.	PMID: 33483311	PMCID: PMC8091609
McGrath-Morrow SA, Ndeh R, Helmin KA, Chen SY, Anekalla KR, Abdala-Valencia H, D'Alessio FR, Collaco JM, Singer BD. DNA methylation regulates the neonatal CD4+ T-cell response to pneumonia in mice. J Biol Chem. 2018 Jul 27;293(30):11772-11783. doi: 10.1074/jbc.RA118.003589. PMID: 29866884; PMCID: PMC6066312.	PMID: 29866884	PMCID: PMC6066312
McQuattie-Pimentel AC, Ren Z, Joshi N, Watanabe S, Stoeger T, Chi M, Lu Z, Sichizya L, Aillon RP, Chen CI, Soberanes S, Chen Z, Reyfman PA, Walter JM, Anekalla KR, Davis JM, Helmin KA, Runyan CE, Abdala-Valencia H, Nam K, Meliton AY, Winter DR, Morimoto RI, Mutlu GM, Bharat A, Perlman H, Gottardi CJ, Ridge KM, Chandel NS, Sznajder JI, Balch WE, Singer BD, Misharin AV, Budinger GRS. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging. J Clin Invest. 2021 Feb 15;131(4):e140299. doi: 10.1172/JCI140299. PMID: 33586677; PMCID: PMC7919859.	PMID: 33586677	PMCID: PMC7919859
Mithal LB, Otero S, Simons LM, Hultquist JF, Miller ES, Ozer EA, Shanes ED, Goldstein JA. Low-level SARS-CoV-2 viremia coincident with COVID placentitis and stillbirth. Placenta. 2022 Apr;121:79-81. doi: 10.1016/j.placenta.2022.03.003. PMID: 35290925; PMCID: PMC8904001.	PMID: 35290925	PMCID: PMC8904001
Morales-Nebreda L, Alakija O, Ferguson KT, Singer BD. Systemic lupus erythematosus-associated diffuse alveolar hemorrhage: a case report and review of the literature. Clin Pulm Med. 2018 Sep;25(5):166-169. PMID: 30220838; PMCID: PMC6136257.	PMID: 30220838	PMCID: PMC6136257
Morales-Nebreda L, Helmin KA, Singer BD. CoRESTed development of regulatory T cells. J Clin Invest. 2020;130(4):1618-21. doi: 10.1172/jci135713. PMID: 32125289; PMCID: PMC7108887.	PMID: 32125289	PMCID: PMC7108887
Morales-Nebreda L, Helmin KA, Torres Acosta MA, Markov NS, Hu JY, Joudi AM, Piseaux-Aillon R, Abdala-Valencia H, Politanska Y, Singer BD. Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia. JCI Insight. 2021 Mar 22;6(6):e141690. doi: 10.1172/jci.insight.141690. PMID: 33600379; PMCID: PMC8026188.	PMID: 33600379	PMCID: PMC8026188
Morales-Nebreda L, McLafferty FS, Singer BD. DNA methylation as a transcriptional regulator of the immune system. Transl Res. 2019;204:1-18. doi: 10.1016/j.trsl.2018.08.001. PMID: 30170004; PMCID: PMC6331288.	PMID: 30170004	PMCID: PMC6331288
Niederman MS, Alder J, Bassetti M, Boateng F, Cao B, Corkery K, Dhand R, Kaye KS, Lawatscheck R, McLeroth P, Nicolau DP, Wang C, Wood GC, Wunderink RG, Chastre J. Inhaled amikacin adjunctive to intravenous standard-of-care antibiotics in mechanically ventilated patients with gram-negative pneumonia (INHALE): a double-blind, randomised, placebo-controlled, phase 3, superiority trial. Lancet Infect Dis. 2020 Mar;20(3):330-340. doi: 10.1016/S1473-3099(19)30574-2. PMID: 31866328.	PMID: 31866328
Ozer EA, Hauser AR, Gerding DN, Espinosa RO, Hecht DW, Kociolek LK. Complete genome sequence of Clostridioides difficile epidemic strain DH/NAP11/106/ST-42, isolated from stool from a pediatric patient with diarrhea. Genome Announc. 2017;5(38):e00923-17. doi: 10.1128/genomeA.00923-17. PMID: 28935729; PMCID: PMC5609408.	PMID: 28935729	PMCID: PMC5609408
Ozer EA, Nnah E, Didelot X, Whitaker RJ, Hauser AR. The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages. Genome Biol Evol. 2019;11(1):1780-96. doi: 10.1093/gbe/evz119. PMID: 31173069; PMCID: PMC6690169.	PMID: 31173069	PMCID: PMC6690169
Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Dean TJ, Zayas J, Bhimalli PP, Ash MK, Godzik A, Schneider JR, Mamede JI, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria. medRxiv [Preprint]. 2021 Jul 2:2021.04.09.21255206. doi: 10.1101/2021.04.09.21255206. PMID: 33880483; PMCID: PMC8057251.	PMID: 33880483	PMCID: PMC8057251
Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Olayinka OA, Dean TJ, Zayas J, Bhimalli PP, Ash MK, Maiga AI, Somboro AM, Maiga M, Godzik A, Schneider JR, Mamede JI, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria. Nat Commun. 2022 Feb 3;13(1):688. doi: 10.1038/s41467-022-28317-5. PMID: 35115515; PMCID: PMC8813984.	PMID: 35115515	PMCID: PMC8813984
Ozer EA. ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements. BMC Bioinformatics. 2018;19(1):150. doi: 10.1186/s12859-018-2154-x. PMID: 29678129; PMCID: PMC5910555.	PMID: 29678129	PMCID: PMC5910555
Park Y, West RA, Pathmendra P, Favier B, Stoeger T, Capes-Davis A, Cabanac G, Labbé C, Byrne JA. Identification of human gene research articles with wrongly identified nucleotide sequences. Life Sci Alliance. 2022 Jan 12;5(4):e202101203. doi: 10.26508/lsa.202101203. PMID: 35022248; PMCID: PMC8807875.	PMID: 35022248	PMCID: PMC8807875
Peters AT, Pickens CI, Postelnick MJ, Zembower TR, Qi C, Wunderink RG. Decreasing incidence of Acinetobacter baumannii pneumonia and trends in antibiotic consumption: a single-center retrospective observational study. Infect Control Hosp Epidemiol. 2021:1-7. doi: 10.1017/ice.2021.348. PMID: 34387183.	PMID: 34387183
Pickens C, Wunderink RG, Qi C, Mopuru H, Donnelly H, Powell K, Sims MD. A multiplex polymerase chain reaction assay for antibiotic stewardship in suspected pneumonia. Diagn Microbiol Infect Dis. 2020 Dec;98(4):115179. doi: 10.1016/j.diagmicrobio.2020.115179. PMID: 32927409; PMCID: PMC7428672.	PMID: 32927409	PMCID: PMC7428672
Pickens CI, Qi C, Postelnick M, Paonessa J, Donnelly HK, Wunderink RG. Association between a rapid diagnostic test to detect methicillin-resistant Staphylococcus Aureus pneumonia and decreased vancomycin use in a medical intensive care unit over a 30-month period. Infect Control Hosp Epidemiol. 2021;42(11):1385-7. doi: 10.1017/ice.2020.1406. PMID: 33517926.	PMID: 33517926
Pickens CI, Wunderink RG. Methicillin-resistant Staphylococcus aureus hospital-acquired pneumonia/ventilator-associated pneumonia. Semin Respir Crit Care Med. 2022;43:304-309. PMID: 35170002.	PMID: 35170002
Pickens CO, Gao CA, Cuttica MJ, Smith SB, Pesce LL, Grant RA, Kang M, Morales-Nebreda L, Bavishi AA, Arnold JM, Pawlowski A, Qi C, Budinger GRS, Singer BD, Wunderink RG; NU COVID Investigators. Bacterial superinfection pneumonia in patients mechanically ventilated for COVID-19 pneumonia. Am J Respir Crit Care Med. 2021 Oct 15;204(8):921-932. doi: 10.1164/rccm.202106-1354OC. PMID: 34409924; PMCID: PMC8534629.	PMID: 34409924	PMCID: PMC8534629
Pincus NB, Bachta KER, Ozer EA, Allen JP, Pura ON, Qi C, Rhodes NJ, Marty FM, Pandit A, Mekalanos JJ, Oliver A, Hauser AR. Long-term persistence of an extensively drug-resistant subclade of globally distributed Pseudomonas aeruginosa clonal complex 446 in an academic medical center. Clin Infect Dis. 2020 Sep 12;71(6):1524-1531. doi: 10.1093/cid/ciz973. PMID: 31583403; PMCID: PMC7486844.	PMID: 31583403	PMCID: PMC7486844
Pincus NB, Ozer EA, Allen JP, Nguyen M, Davis JJ, Winter DR, Chuang CH, Chiu CH, Zamorano L, Oliver A, Hauser AR. A genome-based model to predict the virulence of Pseudomonas aeruginosa isolates. mBio. 2020 Aug 25;11(4):e01527-20. doi: 10.1128/mBio.01527-20. Erratum in: mBio. 2021 Feb 23;12(1): PMID: 32843552; PMCID: PMC7448275.	PMID: 32843552	PMCID: PMC7448275
Pletz MW, Blasi F, Chalmers JD, Dela Cruz CS, Feldman C, Luna CM, Ramirez JA, Shindo Y, Stolz D, Torres A, Webb B, Welte T, Wunderink R, Aliberti S. International perspective on the new 2019 American Thoracic Society/Infectious Diseases Society of America community-acquired pneumonia guideline: a critical appraisal by a global expert panel. Chest. 2020 Nov;158(5):1912-1918. doi: 10.1016/j.chest.2020.07.089. PMID: 32858009; PMCID: PMC7445464.	PMID: 32858009	PMCID: PMC7445464
Pratt CQ, Zhu Y, Grijalva CG, Wunderink RG, Mark Courtney D, Waterer G, Levine MZ, Jefferson S, Self WH, Williams DJ, Finelli L, Bramley AM, Edwards KM, Jain S, Anderson EJ. Serological response to influenza vaccination among adults hospitalized with community-acquired pneumonia. Influenza Other Respir Viruses. 2019 Mar;13(2):208-212. doi: 10.1111/irv.12622. PMID: 30485702; PMCID: PMC6379631.	PMID: 30485702	PMCID: PMC6379631
Prigge AD, Ma R, Coates BM, Singer BD, Ridge KM. Age-dependent differences in T-Cell responses to influenza A virus. Am J Respir Cell Mol Biol. 2020;63(4):415-23. doi: 10.1165/rcmb.2020-0169TR. PMID: 32609537; PMCID: PMC7528914.	PMID: 32609537	PMCID: PMC7528914
Qi C, Hountras P, Pickens CO, Walter JM, Kruser JM, Singer BD, Seed P, Green SJ, Wunderink RG. Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing. J Med Microbiol. 2019 Jul;68(7):996-1002. doi: 10.1099/jmm.0.000968. Erratum in: J Med Microbiol. 2020 Jan;69(1):146. PMID: 31136295; PMCID: PMC6939159.	PMID: 31136295	PMCID: PMC6939159
Rahimi RA, Cho JL, Jakubzick CV, Khader SA, Lambrecht BN, Lloyd CM, Molofsky AB, Talbot S, Bonham CA, Drake WP, Sperling AI, Singer BD. Advancing lung immunology research: a workshop report. Am J Respir Cell Mol Biol. Forthcoming, 2022.
Ramirez JA, Musher DM, Evans SE, Dela Cruz C, Crothers KA, Hage CA, Aliberti S, Anzueto A, Arancibia F, Arnold F, Azoulay E, Blasi F, Bordon J, Burdette S, Cao B, Cavallazzi R, Chalmers J, Charles P, Chastre J, Claessens YE, Dean N, Duval X, Fartoukh M, Feldman C, File T, Froes F, Furmanek S, Gnoni M, Lopardo G, Luna C, Maruyama T, Menendez R, Metersky M, Mildvan D, Mortensen E, Niederman MS, Pletz M, Rello J, Restrepo MI, Shindo Y, Torres A, Waterer G, Webb B, Welte T, Witzenrath M, Wunderink R. Treatment of community-acquired pneumonia in immunocompromised adults: a consensus statement regarding initial strategies. Chest. 2020 Nov;158(5):1896-1911. doi: 10.1016/j.chest.2020.05.598. PMID: 32561442; PMCID: PMC7297164.	PMID: 32561442	PMCID: PMC7297164
Rello J, Kalwaje Eshwara V, Lagunes L, Alves J, Wunderink RG, Conway-Morris A, Rojas JN, Alp E, Zhang Z. A global priority list of the top ten resistant microorganisms (TOTEM) study at intensive care: a prioritization exercise based on multi-criteria decision analysis. Eur J Clin Microbiol Infect Dis. 2019 Feb;38(2):319-323. doi: 10.1007/s10096-018-3428-y. PMID: 30426331.	PMID: 30426331
Ren CY, Wu EL, Hartmann EM, Zhao HP. Biological Mitigation of Antibiotic Resistance Gene Dissemination by Antioxidant-Producing Microorganisms in Activated Sludge Systems. Environ Sci Technol. 2021 Dec 7;55(23):15831-15842. doi: 10.1021/acs.est.1c04641. PMID: 34615350.	PMID: 34615350
Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, Verma R, Abdala-Valencia H, Nam K, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Watanabe S, Williams KJN, Flozak AS, Nicholson TT, Morgan VK, Winter DR, Hinchcliff M, Hrusch CL, Guzy RD, Bonham CA, Sperling AI, Bag R, Hamanaka RB, Mutlu GM, Yeldandi AV, Marshall SA, Shilatifard A, Amaral LAN, Perlman H, Sznajder JI, Argento AC, Gillespie CT, Dematte J, Jain M, Singer BD, Ridge KM, Lam AP, Bharat A, Bhorade SM, Gottardi CJ, Budinger GRS, Misharin AV. Single-cell transcriptomic analysis of human lung provides insights into the pathobiology of pulmonary fibrosis. Am J Respir Crit Care Med. 2019 Jun 15;199(12):1517-1536. doi: 10.1164/rccm.201712-2410OC. PMID: 30554520; PMCID: PMC6580683.	PMID: 30554520	PMCID: PMC6580683
Rhodes NJ, Cruce CE, O'Donnell JN, Wunderink RG, Hauser AR. Resistance trends and treatment options in gram-negative ventilator-associated pneumonia. Curr Infect Dis Rep. 2018 Mar 6;20(2):3. doi: 10.1007/s11908-018-0609-x. PMID: 29511909; PMCID: PMC6319819.	PMID: 29511909	PMCID: PMC6319819
Rhodes NJ, Jozefczyk CC, Moore WJ, Yarnold PR, Harkabuz K, Maxwell R, Sutton SH, Silkaitis C, Qi C, Wunderink RG, Zembower TR. Characterizing risk factors for Clostridioides difficile infection among hospitalized patients with community-acquired pneumonia. Antimicrob Agents Chemother. 2021 Jun 17;65(7):e0041721. doi: 10.1128/AAC.00417-21. PMID: 33875439; PMCID: PMC8373232.	PMID: 33875439	PMCID: PMC8373232
Rutherford V, Yom K, Ozer EA, Pura O, Hughes A, Murphy KR, Cudzilo L, Mitchell D, Hauser AR. Environmental reservoirs for exoS+ and exoU+ strains of Pseudomonas aeruginosa. Environ Microbiol Rep. 2018 Aug;10(4):485-492. doi: 10.1111/1758-2229.12653. PMID: 29687624; PMCID: PMC6108916.	PMID: 29687624	PMCID: PMC6108916
Sala MA, Balderas-Martínez YI, Buendía-Roldan I, Abdala-Valencia H, Nam K, Jain M, Bhorade S, Bharat A, Reyfman PA, Ridge KM, Pardo A, Sznajder JI, Budinger GRS, Misharin AV, Selman M. Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis. Respir Res. 2018 Nov 26;19(1):233. doi: 10.1186/s12931-018-0932-7. PMID: 30477498; PMCID: PMC6257973.	PMID: 30477498	PMCID: PMC6257973
Sala MA, Markov NS, Politanska Y, Abdala-Valencia H, Misharin AV, Jain M. Expression of ACE2 - a key SARS-CoV-2 entry factor - is not increased in the nasal mucosa of people with cystic fibrosis. Am J Respir Cell Mol Biol. 2022 Apr 1. doi: 10.1165/rcmb.2021-0341LE. Epub ahead of print. PMID: 35363994.	PMID: 35363994
Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. The human lung cell atlas: a high-resolution reference map of the human lung in health and disease. Am J Respir Cell Mol Biol. 2019 Jul;61(1):31-41. doi: 10.1165/rcmb.2018-0416TR. PMID: 30995076; PMCID: PMC6604220.	PMID: 30995076	PMCID: PMC6604220
Self WH, Wunderink RG, DiNubile MJ, Stossel TP, Levinson SL, Williams DJ, Anderson EJ, Bramley AM, Jain S, Edwards KM, Grijalva CG. Low admission plasma gelsolin concentrations identify community-acquired pneumonia patients at high risk for severe outcomes. Clin Infect Dis. 2019 Sep 13;69(7):1218-1225. doi: 10.1093/cid/ciy1049. PMID: 30561561; PMCID: PMC6743831.	PMID: 30561561	PMCID: PMC6743831
Semler MW, Bernard GR, Aaron SD, Angus DC, Biros MH, Brower RG, Calfee CS, Colantuoni EA, Ferguson ND, Gong MN, Hopkins RO, Hough CL, Iwashyna TJ, Levy BD, Martin TR, Matthay MA, Mizgerd JP, Moss M, Needham DM, Self WH, Seymour CW, Stapleton RD, Thompson BT, Wunderink RG, Aggarwal NR, Reineck LA. Identifying clinical research priorities in adult pulmonary and critical care: NHLBI working group report. Am J Respir Crit Care Med. 2020 Mar 9;202(4):511–23. doi: 10.1164/rccm.201908-1595WS. Epub ahead of print. PMID: 32150460; PMCID: PMC7427373.	PMID: 32150460	PMCID: PMC7427373
Shen J, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward accurate and robust environmental surveillance using metagenomics. Front Genet. 2021 Mar 5;12:600111. doi: 10.3389/fgene.2021.600111. PMID: 33747038; PMCID: PMC7973286.	PMID: 33747038	PMCID: PMC7973286
Singer BD, Chandel NS. Immunometabolism of pro-repair cells. J Clin Invest. 2019;129(7):2597-607. doi: 10.1172/jci124613. PMID: 31081802; PMCID: PMC6597201.	PMID: 31081802	PMCID: PMC6597201
Singer BD, Chotirmall SH, Leither LM, Meldrum OW, Joudi AM, Seam N, Brown SM, Çoruh B. Update in COVID-19 2021. Am J Respir Crit Care Med. 2022. doi: 10.1164/rccm.202202-0277UP. PMID: 35442171.	PMID: 35442171
Singer BD, Jain M, Budinger GRS, Wunderink RG. A call for rational intensive care in the era of COVID-19. Am J Respir Cell Mol Biol. 2020;63(1):132-3. doi: 10.1165/rcmb.2020-0151LE. PMID: 32315548; PMCID: PMC7328253.	PMID: 32315548	PMCID: PMC7328253
Singer BD. A practical guide to the measurement and analysis of DNA methylation. Am J Respir Cell Mol Biol. 2019;61(4):417-28. doi: 10.1165/rcmb.2019-0150TR. PMID: 31264905; PMCID: PMC6775954.	PMID: 31264905	PMCID: PMC6775954
Singer BD. COVID-19 and the next influenza season. Sci Adv. 2020;6(31):eabd0086. doi: 10.1126/sciadv.abd0086. PMID: 32789184; PMCID: PMC7399656.	PMID: 32789184	PMCID: PMC7399656
Soberanes S, Misharin AV, Jairaman A, Morales-Nebreda L, McQuattie-Pimentel AC, Cho T, Hamanaka RB, Meliton AY, Reyfman PA, Walter JM, Chen CI, Chi M, Chiu S, Gonzalez-Gonzalez FJ, Antalek M, Abdala-Valencia H, Chiarella SE, Sun KA, Woods PS, Ghio AJ, Jain M, Perlman H, Ridge KM, Morimoto RI, Sznajder JI, Balch WE, Bhorade SM, Bharat A, Prakriya M, Chandel NS, Mutlu GM, Budinger GRS. Metformin targets mitochondrial electron transport to reduce air-pollution-induced thrombosis. Cell Metab. 2019 Feb 5;29(2):503. doi: 10.1016/j.cmet.2018.12.001. Erratum for: Cell Metab. 2019 Feb 5;29(2):335-347.e5. PMID: 30726761; PMCID: PMC6377562.	PMID: 30726761	PMCID: PMC6377562
Stoeger T, Gerlach M, Morimoto RI, Nunes Amaral LA. Large-scale investigation of the reasons why potentially important genes are ignored. PLoS Biol. 2018;16(9):e2006643. doi: 10.1371/journal.pbio.2006643. PMID: 30226837; PMCID: PMC6143198.	PMID: 30226837	PMCID: PMC6143198
Stoeger T, Nunes Amaral LA. COVID-19 research risks ignoring important host genes due to pre-established research patterns. eLife. 2020 Nov 24;9:e61981. doi: 10.7554/eLife.61981. PMID: 33231169; PMCID: PMC7685703.	PMID: 33231169	PMCID: PMC7685703
Stoeger T, Nunes Amaral LA. The characteristics of early-stage research into human genes are substantially different from subsequent research. PLoS Biol. 2022 Jan 6;20(1):e3001520. doi: 10.1371/journal.pbio.3001520. PMID: 34990452; PMCID: PMC8769369.	PMID: 34990452	PMCID: PMC8769369
Sun M, Baron J, Dighe A, Szolovits P, Wunderink RG, Isakova T, Luo Y. Early prediction of acute kidney injury in critical care setting using clinical notes and structured multivariate physiological measurements. Stud Health Technol Inform. 2019 Aug 21;264:368-372. doi: 10.3233/SHTI190245. PMID: 31437947.	PMID: 31437947
Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL; HCA Lung Biological Network. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med. 2020 May;26(5):681-687. doi: 10.1038/s41591-020-0868-6. PMID: 32327758; PMCID: PMC8637938.	PMID: 32327758	PMCID: PMC8637938
Taylor SA, Chen SY, Gadhvi G, Feng L, Gromer KD, Abdala-Valencia H, Nam K, Dominguez ST, Montgomery AB, Reyfman PA, Ostilla L, Wechsler JB, Cuda CM, Green RM, Perlman H, Winter DR. Transcriptional profiling of pediatric cholestatic livers identifies three distinct macrophage populations. PLoS One. 2021 Jan 7;16(1):e0244743. doi: 10.1371/journal.pone.0244743. PMID: 33411796; PMCID: PMC7790256.	PMID: 33411796	PMCID: PMC7790256
Tighe RM, Redente EF, Yu YR, Herold S, Sperling AI, Curtis JL, Duggan R, Swaminathan S, Nakano H, Zacharias WJ, Janssen WJ, Freeman CM, Brinkman RR, Singer BD, Jakubzick CV, Misharin AV. Improving the quality and reproducibility of flow cytometry in the lung. an official American Thoracic Society workshop report. Am J Respir Cell Mol Biol. 2019 Aug;61(2):150-161. doi: 10.1165/rcmb.2019-0191ST. PMID: 31368812; PMCID: PMC6670040.	PMID: 31368812	PMCID: PMC6670040
Timsit JF, Huntington JA, Wunderink RG, Shime N, Kollef MH, Kivistik Ü, Nováček M, Réa-Neto Á, Martin-Loeches I, Yu B, Jensen EH, Butterton JR, Wolf DJ, Rhee EG, Bruno CJ. Ceftolozane/tazobactam versus meropenem in patients with ventilated hospital-acquired bacterial pneumonia: subset analysis of the ASPECT-NP randomized, controlled phase 3 trial. Crit Care. 2021 Aug 11;25(1):290. doi: 10.1186/s13054-021-03694-3. PMID: 34380538; PMCID: PMC8356211.	PMID: 34380538	PMCID: PMC8356211
Titov I, Wunderink RG, Roquilly A, Rodríguez Gonzalez D, David-Wang A, Boucher HW, Kaye KS, Losada MC, Du J, Tipping R, Rizk ML, Patel M, Brown ML, Young K, Kartsonis NA, Butterton JR, Paschke A, Chen LF. A randomized, double-blind, multicenter trial comparing efficacy and safety of imipenem/cilastatin/relebactam versus piperacillin/tazobactam in adults with hospital-acquired or ventilator-associated bacterial pneumonia (RESTORE-IMI 2 Study). Clin Infect Dis. 2021 Dec 6;73(11):e4539-e4548. doi: 10.1093/cid/ciaa803. PMID: 32785589; PMCID: PMC8662781.	PMID: 32785589	PMCID: PMC8662781
Torres A, Chalmers JD, Dela Cruz CS, Dominedò C, Kollef M, Martin-Loeches I, Niederman M, Wunderink RG. Challenges in severe community-acquired pneumonia: a point-of-view review. Intensive Care Med. 2019 Feb;45(2):159-171. doi: 10.1007/s00134-019-05519-y. PMID: 30706119; PMCID: PMC7094947.	PMID: 30706119	PMCID: PMC7094947
Torres Acosta MA, Singer BD. Pathogenesis of COVID-19-induced ARDS: implications for an ageing population. Eur Respir J. 2020 Sep 24;56(3):2002049. doi: 10.1183/13993003.02049-2020. PMID: 32747391; PMCID: PMC7397945.	PMID: 32747391	PMCID: PMC7397945
Tsuji BT, Pogue JM, Zavascki AP, Paul M, Daikos GL, Forrest A, Giacobbe DR, Viscoli C, Giamarellou H, Karaiskos I, Kaye D, Mouton JW, Tam VH, Thamlikitkul V, Wunderink RG, Li J, Nation RL, Kaye KS. International consensus guidelines for the optimal use of the polymyxins: endorsed by the American College of Clinical Pharmacy (ACCP), European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Infectious Diseases Society of America (IDSA), International Society for Anti-infective Pharmacology (ISAP), Society of Critical Care Medicine (SCCM), and Society of Infectious Diseases Pharmacists (SIDP). Pharmacotherapy. 2019 Jan;39(1):10-39. doi: 10.1002/phar.2209. PMID: 30710469; PMCID: PMC7437259.	PMID: 30710469	PMCID: PMC7437259
Turner TL, Wunderink R, Ozer E, Hauser A. First report of Pseudomonas nitroreducens cultured from the lungs of a patient with pneumonia. BMJ Case Rep. 2021 May 24;14(5):e241327. doi: 10.1136/bcr-2020-241327. PMID: 34031078; PMCID: PMC8154954.	PMID: 34031078	PMCID: PMC8154954
Villafuerte D, Aliberti S, Soni NJ, Faverio P, Marcos PJ, Wunderink RG, Rodriguez A, Sibila O, Sanz F, Martin-Loeches I, Menzella F, Reyes LF, Jankovic M, Spielmanns M, Restrepo MI; GLIMP investigators. prevalence and risk factors for Enterobacteriaceae in patients hospitalized with community-acquired pneumonia. Respirology. 2020 May;25(5):543-551. doi: 10.1111/resp.13663. PMID: 31385399.	PMID: 31385399
Walter JM, Corbridge TC, Singer BD. Invasive mechanical ventilation. South Med J. 2018 Dec;111(12):746-753. doi: 10.14423/SMJ.0000000000000905. PMID: 30512128; PMCID: PMC6284234.	PMID: 30512128	PMCID: PMC6284234
Walter JM, Helmin KA, Abdala-Valencia H, Wunderink RG, Singer BD. Multidimensional assessment of alveolar T cells in critically ill patients. JCI Insight. 2018 Sep 6;3(17):e123287. doi: 10.1172/jci.insight.123287. PMID: 30185658; PMCID: PMC6171809.	PMID: 30185658	PMCID: PMC6171809
Walter JM, Ren Z, Yacoub T, Reyfman PA, Shah RD, Abdala-Valencia H, Nam K, Morgan VK, Anekalla KR, Joshi N, McQuattie-Pimentel AC, Chen CI, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Aillon RP, Watanabe S, Williams KJN, Lu Z, Paonessa J, Hountras P, Breganio M, Borkowski N, Donnelly HK, Allen JP, Amaral LA, Bharat A, Misharin AV, Bagheri N, Hauser AR, Budinger GRS, Wunderink RG. Multidimensional assessment of the host response in mechanically ventilated patients with suspected pneumonia. Am J Respir Crit Care Med. 2019 May 15;199(10):1225-1237. doi: 10.1164/rccm.201804-0650OC. PMID: 30398927; PMCID: PMC6519857.	PMID: 30398927	PMCID: PMC6519857
Walter JM, Wunderink RG. Testing for respiratory viruses in adults with severe lower respiratory infection. Chest. 2018;154(5):1213-22. doi: 10.1016/j.chest.2018.06.003. PMID: 29908153; PMCID: PMC6224704.	PMID: 29908153	PMCID: PMC6224704
Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome. 2021 Jan 21;9(1):17. doi: 10.1186/s40168-020-00961-3. PMID: 33478576; PMCID: PMC7819323.	PMID: 33478576	PMCID: PMC7819323
Watanabe S, Alexander M, Misharin AV, Budinger GRS. The role of macrophages in the resolution of inflammation. J Clin Invest. 2019;129(7):2619-28. doi: 10.1172/jci124615. PMID: 31107246; PMCID: PMC6597225.	PMID: 31107246	PMCID: PMC6597225
Watanabe S, Markov NS, Lu Z, Piseaux Aillon R, Soberanes S, Runyan CE, Ren Z, Grant RA, Maciel M, Abdala-Valencia H, Politanska Y, Nam K, Sichizya L, Kihshen HG, Joshi N, McQuattie-Pimentel AC, Gruner KA, Jain M, Sznajder JI, Morimoto RI, Reyfman PA, Gottardi CJ, Budinger GRS, Misharin AV. Resetting proteostasis with ISRIB promotes epithelial differentiation to attenuate pulmonary fibrosis. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2101100118. doi: 10.1073/pnas.2101100118. PMID: 33972447; PMCID: PMC8157939.	PMID: 33972447	PMCID: PMC8157939
Waterer GW, Rello J, Wunderink RG. COVID-19: first do no harm. Am J Respir Crit Care Med. 2020;201(11):1324-5. doi: 10.1164/rccm.202004-1153ED. PMID: 32311297; PMCID: PMC7258628.	PMID: 32311297	PMCID: PMC7258628
Weinberg SE, Singer BD. Toward a paradigm to distinguish distinct functions of FOXP3(+) regulatory T cells. Immunohorizons. 2021;5(12):944-52. doi: 10.4049/immunohorizons.2100046. PMID: 34893512; PMCID: PMC8691855.	PMID: 34893512	PMCID: PMC8691855
Weiss E, Zahar JR, Alder J, Asehnoune K, Bassetti M, Bonten MJM, Chastre J, De Waele J, Dimopoulos G, Eggimann P, Engelhardt M, Ewig S, Kollef M, Lipman J, Luna C, Martin-Loeches I, Pagani L, Palmer LB, Papazian L, Poulakou G, Prokocimer P, Rello J, Rex JH, Shorr AF, Talbot GH, Thamlikitkul V, Torres A, Wunderink RG, Timsit JF. Elaboration of consensus clinical endpoints to evaluate antimicrobial treatment efficacy in future hospital-acquired/ventilator-associated bacterial pneumonia clinical trials. Clin Infect Dis. 2019 Nov 13;69(11):1912-1918. doi: 10.1093/cid/ciz093. PMID: 30722013.	PMID: 30722013
Wunderink RG, Giamarellos-Bourboulis EJ, Rahav G, Mathers AJ, Bassetti M, Vazquez J, Cornely OA, Solomkin J, Bhowmick T, Bishara J, Daikos GL, Felton T, Furst MJL, Kwak EJ, Menichetti F, Oren I, Alexander EL, Griffith D, Lomovskaya O, Loutit J, Zhang S, Dudley MN, Kaye KS. Effect and safety of meropenem-vaborbactam versus best-available therapy in patients with carbapenem-resistant Enterobacteriaceae infections: the TANGO II randomized clinical trial. Infect Dis Ther. 2018 Dec;7(4):439-455. doi: 10.1007/s40121-018-0214-1. PMID: 30270406; PMCID: PMC6249182.	PMID: 30270406	PMCID: PMC6249182
Wunderink RG, Roquilly A, Croce M, Rodriguez Gonzalez D, Fujimi S, Butterton JR, Broyde N, Popejoy MW, Kim JY, De Anda C. A Phase 3, randomized, double-blind study comparing tedizolid phosphate and linezolid for treatment of ventilated gram-positive hospital-acquired or ventilator-associated bacterial pneumonia. Clin Infect Dis. 2021 Aug 2;73(3):e710-e718. doi: 10.1093/cid/ciab032. PMID: 33720350; PMCID: PMC8326538.	PMID: 33720350	PMCID: PMC8326538
Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J, Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F, Richardson RAK, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR. Mathematical models to study the biology of pathogens and the infectious diseases they cause. iScience. 2022 Mar 15;25(4):104079. doi: 10.1016/j.isci.2022.104079. PMID: 35359802; PMCID: PMC8961237.	PMID: 35359802	PMCID: PMC8961237
Yoshida M, Worlock KB, Huang N, Lindeboom RGH, Butler CR, Kumasaka N, Conde CD, Mamanova L, Bolt L, Richardson L, Polanski K, Madissoon E, Barnes JL, Allen-Hyttinen J, Kilich E, Jones BC, de Wilton A, Wilbrey-Clark A, Sungnak W, Pett JP, Weller J, Prigmore E, Yung H, Mehta P, Saleh A, Saigal A, Chu V, Cohen JM, Cane C, Iordanidou A, Shibuya S, Reuschl AK, Herczeg IT, Argento AC, Wunderink RG, Smith SB, Poor TA, Gao CA, Dematte JE; NU SCRIPT Study Investigators, Reynolds G, Haniffa M, Bowyer GS, Coates M, Clatworthy MR, Calero-Nieto FJ, Göttgens B, O'Callaghan C, Sebire NJ, Jolly C, de Coppi P, Smith CM, Misharin AV, Janes SM, Teichmann SA, Nikolić MZ, Meyer KB. Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature. 2021 Dec 22. doi: 10.1038/s41586-021-04345-x. Epub ahead of print. PMID: 34937051.	PMID: 34937051	PMCID: PMC8828466