Publications

• A ventilated perfused lung model platform to dissect the response of the lungs to viral infection.Derman ID, Alioglu MA, Moses JC, Chroneos ZC, Yilmaz YO, Banerjee D, Koff J, Rizvi SHA, Klunk DN, Celik N, Pochareddy S, Umstead TM, Namli I, Holton SE, Mikacenic C, Thompson JL, Castaneda DC, Hickey DR, Nagamine M, Warang P, Schotsaert M, Chen P, Peeples ME, Palucka K, Ozbolat IT. Trends Biotechnol. 2025 Apr 24; 2025 Apr 24. PMID: 40280814.
• Changing Epidemiology of Pediatric Pulmonary Exacerbations in Cystic Fibrosis.Fireizen Y, Ahmed M, Vigers T, Akong K, Ryu J, Hahn A, Fanous H, Koumbourlis A, Tirakitsoontorn P, Arrieta A, Burgener EB, Koff J, Cogen JD, Bouzek DC, Hanley E, Keck A, Stout D, Bradley J, Sagel SD. Pediatr Pulmonol. 2025 Mar. PMID: 40018992.
• Particle size distribution of viable nebulized bacteriophage for the treatment of multi-drug resistant Pseudomonas aeruginosa.Thompson DL, Semersky Z, Feinn R, Huang P, Turner PE, Chan BK, Koff JL, Murray TS. Respir Med Res. 2024 Nov; 2024 Jul 25. PMID: 39121591.
• Phage Therapy for Respiratory Infections: Opportunities and Challenges.Khosravi A, Chen Q, Echterhof A, Koff JL, Bollyky PL. Lung. 2024 Jun; 2024 May 21. PMID: 38772946.
• Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells.Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. PLoS Biol. 2024 Apr; 2024 Apr 23. PMID: 38652717.
• Evaluation of a Virtual Reality-Based Open Educational Resource Software.Würstle S, Spanke LM, Mehlhase N, Stanley G, Koff J, Dimitriadis S, König S, Hann A. J Med Educ Curric Dev. 2024 Jan-Dec; 2024 Apr 2. PMID: 38572090.
• Human iPSC-Based Model of COPD to Investigate Disease Mechanisms, Predict SARS-COV-2 Outcome, and Test Preventive Immunotherapy.Dagher R, Moldobaeva A, Gubbins E, Clark S, Madel Alfajaro M, Wilen CB, Hawkins F, Qu X, Chien Chiang C, Li Y, Clarke L, Ikeda Y, Brown C, Kolbeck R, Ma Q, Rojas M, Koff JL, Ghaedi M. Stem Cells. 2024 Mar 14. PMID: 38183264.
• Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis.Murray TS, Stanley G, Koff JL. Infect Dis Clin North Am. 2024 Mar. PMID: 38280761.
• Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines.Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. bioRxiv. 2024 Feb 6; 2024 Feb 6. PMID: 38370761.
• Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University.Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Sci Rep. 2024 Feb 1; 2024 Feb 1. PMID: 38302552.
• Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia.Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, García-Bernalt Diego J, Lin J, Wu TC, Marches F, Chaussabel D, Yu P, Salner A, Aucello G, Koff J, Hudson B, Church SE, Gorman K, Anguiano E, García-Sastre A, Williams A, Schotsaert M, Palucka K. iScience. 2023 Aug 18; 2023 Jul 13. PMID: 37520727.
• A Novel Zinc (II) Porphyrin Is Synergistic with PEV2 Bacteriophage against Pseudomonas aeruginosa Infections.Geyer J, Krupa KA, Harris ZM, Sun Y, Sharma L, Würstle S, Hu B, Stanley G, Rajagopalan G, Pellot E, Koff JL, Robinson JB. Antibiotics (Basel). 2023 Apr 10; 2023 Apr 10. PMID: 37107097.
• Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia.Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, Diego JG, Lin J, Wu TC, Marches F, Chaussabel D, Yu P, Salner A, Aucello G, Koff J, Hudson B, Church SE, Gorman K, Anguiano E, García-Sastre A, Williams A, Schotsaert M, Palucka K. bioRxiv. 2023 Mar 31; 2023 Mar 31. PMID: 37034597.
• COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation.Patton MJ, Orihuela CJ, Harrod KS, Bhuiyan MAN, Dominic P, Kevil CG, Fort D, Liu VX, Farhat M, Koff JL, Lal CV, Gaggar A, Richter RP, Erdmann N, Might M, Gaggar A. Crit Care. 2023 Jan 23; 2023 Jan 23. PMID: 36691080.
• Bacteriophage Therapy for Pan-Drug-Resistant Pseudomonas aeruginosa in Two Persons With Cystic Fibrosis.Hahn A, Sami I, Chaney H, Koumbourlis AC, Del Valle Mojica C, Cochrane C, Chan BK, Koff JL. J Investig Med High Impact Case Rep. 2023 Jan-Dec. PMID: 37515541.
• IFN-γ Is Protective in Cytokine Release Syndrome-associated Extrapulmonary Acute Lung Injury.Sun Y, Hu B, Stanley G, Harris ZM, Gautam S, Homer R, Koff JL, Rajagopalan G. Am J Respir Cell Mol Biol. 2023 Jan. PMID: 36125351.
• Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter.Winzig F, Gandhi S, Lee A, Würstle S, Stanley GL, Capuano I, Neuringer I, Koff JL, Turner PE, Chan BK. Yale J Biol Med. 2022 Dec; 2022 Dec 22. PMID: 36568830.
• Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis.Murray TS, Stanley G, Koff JL. Clin Chest Med. 2022 Dec. PMID: 36344073.
• Epidermal Growth Factor Receptor Inhibition Is Protective in Hyperoxia-Induced Lung Injury.Harris ZM, Sun Y, Joerns J, Clark B, Hu B, Korde A, Sharma L, Shin HJ, Manning EP, Placek L, Unutmaz D, Stanley G, Chun H, Sauler M, Rajagopalan G, Zhang X, Kang MJ, Koff JL. Oxid Med Cell Longev. 2022; 2022 Sep 20. PMID: 36193076.
• I-SPY COVID adaptive platform trial for COVID-19 acute respiratory failure: rationale, design and operations.Files DC, Matthay MA, Calfee CS, Aggarwal NR, Asare AL, Beitler JR, Berger PA, Burnham EL, Cimino G, Coleman MH, Crippa A, Discacciati A, Gandotra S, Gibbs KW, Henderson PT, Ittner CAG, Jauregui A, Khan KT, Koff JL, Lang J, LaRose M, Levitt J, Lu R, McKeehan JD, Meyer NJ, Russell DW, Thomas KW, Eklund M, Esserman LJ, Liu KD. BMJ Open. 2022 Jun 6; 2022 Jun 6. PMID: 35667714.
• Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro.Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Am J Physiol Lung Cell Mol Physiol. 2022 Jun 1; 2022 Apr 19. PMID: 35438006.
• A neutrophil activation signature predicts critical illness and mortality in COVID-19.Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun HJ. Blood Adv. 2021 Mar 9. PMID: 33635335.
• A Clinic Blueprint for Post-Coronavirus Disease 2019 RECOVERY: Learning From the Past, Looking to the Future.Lutchmansingh DD, Knauert MP, Antin-Ozerkis DE, Chupp G, Cohn L, Dela Cruz CS, Ferrante LE, Herzog EL, Koff J, Rochester CL, Ryu C, Singh I, Tickoo M, Winks V, Gulati M, Possick JD. Chest. 2021 Mar; 2020 Nov 4. PMID: 33159907.
• Multi-dimensional clinical phenotyping of a national cohort of adult cystic fibrosis patients.Conrad DJ, Billings J, Teneback C, Koff J, Rosenbluth D, Bailey BA, Jain R. J Cyst Fibros. 2021 Jan; 2020 Sep 15. PMID: 32948498.
• A neutrophil activation signature predicts critical illness and mortality in COVID-19.Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun H. medRxiv. 2020 Sep 2; 2020 Sep 2. PMID: 32908988.
• Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study.Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI. Lancet Haematol. 2020 Aug; 2020 Jun 30. PMID: 32619411.
• "Small" Intestinal Immunopathology Plays a "Big" Role in Lethal Cytokine Release Syndrome, and Its Modulation by Interferon-γ, IL-17A, and a Janus Kinase Inhibitor.Kale SD, Mehrkens BN, Stegman MM, Kastelberg B, Carnes H, McNeill RJ, Rizzo A, Karyala SV, Coutermarsh-Ott S, Fretz JA, Sun Y, Koff JL, Rajagopalan G. Front Immunol. 2020; 2020 Jun 26. PMID: 32676080.
• Metabolic Adaptation in Methicillin-Resistant Staphylococcus aureus Pneumonia.Gabryszewski SJ, Wong Fok Lung T, Annavajhala MK, Tomlinson KL, Riquelme SA, Khan IN, Noguera LP, Wickersham M, Zhao A, Mulenos AM, Peaper D, Koff JL, Uhlemann AC, Prince A. Am J Respir Cell Mol Biol. 2019 Aug. PMID: 30742488.
• Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria.Kortright KE, Chan BK, Koff JL, Turner PE. Cell Host Microbe. 2019 Feb 13. PMID: 30763536.
• Ezrin links CFTR to TLR4 signaling to orchestrate anti-bacterial immune response in macrophages.Di Pietro C, Zhang PX, O'Rourke TK, Murray TS, Wang L, Britto CJ, Koff JL, Krause DS, Egan ME, Bruscia EM. Sci Rep. 2017 Sep 7; 2017 Sep 7. PMID: 28883468.
• Correction: DNA Repair Interacts with Autophagy To Regulate Inflammatory Responses to Pulmonary Hyperoxia.Ye Y, Lin P, Zhang W, Tan S, Zhou X, Li R, Pu Q, Koff JL, Dhasarathy A, Ma F, Deng X, Jiang J, Wu M. J Immunol. 2017 Aug 1. PMID: 28739596.
• Aging Impairs Alveolar Macrophage Phagocytosis and Increases Influenza-Induced Mortality in Mice.Wong CK, Smith CA, Sakamoto K, Kaminski N, Koff JL, Goldstein DR. J Immunol. 2017 Aug 1; 2017 Jun 23. PMID: 28646038.
• Response to Comment on "DNA Repair Interacts with Autophagy To Regulate Inflammatory Responses to Pulmonary Hyperoxia".Ye Y, Lin P, Zhang W, Tan S, Zhou X, Li R, Pu Q, Koff JL, Dhasarathy A, Ma F, Deng X, Jiang J, Wu M. J Immunol. 2017 Jul 15. PMID: 28696327.
• Cystic Fibrosis Transmembrane Regulator Modulators: Implications for the Management of Depression and Anxiety in Cystic Fibrosis.Talwalkar JS, Koff JL, Lee HB, Britto CJ, Mulenos AM, Georgiopoulos AM. Psychosomatics. 2017 Jul-Aug; 2017 Apr 5. PMID: 28576305.
• DNA Repair Interacts with Autophagy To Regulate Inflammatory Responses to Pulmonary Hyperoxia.Ye Y, Lin P, Zhang W, Tan S, Zhou X, Li R, Pu Q, Koff JL, Dhasarathy A, Ma F, Deng X, Jiang J, Wu M. J Immunol. 2017 Apr 1; 2017 Feb 15. PMID: 28202616.
• Cystic Fibrosis.Koff JL. Clin Chest Med. 2016 Mar; 2015 Dec 24. PMID: 26857777.
• Pharmacological modulation of the AKT/microRNA-199a-5p/CAV1 pathway ameliorates cystic fibrosis lung hyper-inflammation.Zhang PX, Cheng J, Zou S, D'Souza AD, Koff JL, Lu J, Lee PJ, Krause DS, Egan ME, Bruscia EM. Nat Commun. 2015 Feb 10; 2015 Feb 10. PMID: 25665524.
• EGFR activation suppresses respiratory virus-induced IRF1-dependent CXCL10 production.Kalinowski A, Ueki I, Min-Oo G, Ballon-Landa E, Knoff D, Galen B, Lanier LL, Nadel JA, Koff JL. Am J Physiol Lung Cell Mol Physiol. 2014 Jul 15; 2014 May 16. PMID: 24838750.
• Respiratory virus-induced EGFR activation suppresses IRF1-dependent interferon λ and antiviral defense in airway epithelium.Ueki IF, Min-Oo G, Kalinowski A, Ballon-Landa E, Lanier LL, Nadel JA, Koff JL. J Exp Med. 2013 Sep 23; 2013 Sep 2. PMID: 23999497.
• Rhinovirus and other respiratory viruses exert different effects on lung allograft function that are not mediated through acute rejection.Sayah DM, Koff JL, Leard LE, Hays SR, Golden JA, Singer JP. Clin Transplant. 2013 Jan-Feb; 2012 Dec 30. PMID: 23278569.
• Amphiregulin, an epidermal growth factor receptor ligand, plays an essential role in the pathogenesis of transforming growth factor-β-induced pulmonary fibrosis.Zhou Y, Lee JY, Lee CM, Cho WK, Kang MJ, Koff JL, Yoon PO, Chae J, Park HO, Elias JA, Lee CG. J Biol Chem. 2012 Dec 7; 2012 Oct 19. PMID: 23086930.
• Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SV. PLoS One. 2010 Jun 23; 2010 Jun 23. PMID: 20585638.
• Neutrophil-derived IL-6 limits alveolar barrier disruption in experimental ventilator-induced lung injury.Wolters PJ, Wray C, Sutherland RE, Kim SS, Koff J, Mao Y, Frank JA. J Immunol. 2009 Jun 15. PMID: 19494331.
• Treatment of recurrent Crohn's uveitis with infliximab.Ally MR, Veerappan GR, Koff JM. Am J Gastroenterol. 2008 Aug. PMID: 18796120.
• Hemodialysis for hyperammonemia associated with ornithine transcarbamylase deficiency.Collen JF, Das NP, Koff JM, Neff RT, Abbott KC. Appl Clin Genet. 2008; 2008 Jul 24. PMID: 23776342.
• Multiple TLRs activate EGFR via a signaling cascade to produce innate immune responses in airway epithelium.Koff JL, Shao MX, Ueki IF, Nadel JA. Am J Physiol Lung Cell Mol Physiol. 2008 Jun; 2008 Mar 28. PMID: 18375743.
• False positive acetaminophen concentrations in patients with liver injury.Polson J, Wians FH Jr, Orsulak P, Fuller D, Murray NG, Koff JM, Khan AI, Balko JA, Hynan LS, Lee WM. Clin Chim Acta. 2008 May; 2008 Jan 26. PMID: 18279672.
• Regulation of interleukin-8 via an airway epithelial signaling cascade.Nakanaga T, Nadel JA, Ueki IF, Koff JL, Shao MX. Am J Physiol Lung Cell Mol Physiol. 2007 May; 2007 Jan 12. PMID: 17220369.
• The cost-effectiveness of CT colonography in screening for colorectal neoplasia.Vijan S, Hwang I, Inadomi J, Wong RK, Choi JR, Napierkowski J, Koff JM, Pickhardt PJ. Am J Gastroenterol. 2007 Feb; 2006 Dec 11. PMID: 17156139.
• Pseudomonas lipopolysaccharide accelerates wound repair via activation of a novel epithelial cell signaling cascade.Koff JL, Shao MX, Kim S, Ueki IF, Nadel JA. J Immunol. 2006 Dec 15. PMID: 17142770.
• Case report: a case of wood-smoke-related pulmonary disease.Diaz JV, Koff J, Gotway MB, Nishimura S, Balmes JR. Environ Health Perspect. 2006 May. PMID: 16675433.
• Inverted appendiceal orifice masquerading as a cecal polyp on virtual colonoscopy.Koff JM, Choi JR, Hwang I. Gastrointest Endosc. 2005 Aug. PMID: 16047004.
• Maintenance immunosuppression use and the associated risk of avascular necrosis after kidney transplantation in the United States.Abbott KC, Koff J, Bohen EM, Oglesby RJ, Agodoa LY, Lentine KL, Schnitzler MA. Transplantation. 2005 Feb 15. PMID: 15699764.
• Retained endoclip.Koff JM, Napierkowski JJ, Smith MT. Gastrointest Endosc. 2005 Feb. PMID: 15729242.
• Impact of diabetes and hepatitis after kidney transplantation on patients who are affected by hepatitis C virus.Abbott KC, Lentine KL, Bucci JR, Agodoa LY, Koff JM, Holtzmuller KC, Schnitzler MA. J Am Soc Nephrol. 2004 Dec. PMID: 15579520.
• Echolalia in a liver transplant recipient.Koff JM, Matsumoto CS, Holtzmuller KC. Transplantation. 2004 Aug 15. PMID: 15316384.
• Hepatitis C with normal liver enzymes: to treat or not to treat. Pro: most patients should be treated.Koff JM, Younossi Z. Am J Gastroenterol. 2004 Jun. PMID: 15180709.
• Obtaining antibiotics without a prescription.Goff BJ, Koff JM, Geiling JA. N Engl J Med. 2002 Jul 18. PMID: 12124419.