Publications

See an up-to-date list of Lee Lab publications on Google Scholar.

Selected Publications

  • Nickerson R, Thornton CS, Johnston B, Lee AHY, Cheng Z. Pseudomonas aeruginosa in chronic lung disease: untangling the dysregulated host immune response. Front Immunol. 2024 Jun 28;15:1405376. doi: 10.3389/fimmu.2024.1405376. PMID: 39015565; PMCID: PMC11250099.


  • Fidanza M, Hibbert J, Acton E, Harbeson D, Schoeman E, Skut P, Woodman T, Eynaud A, Hartnell L, Brook B, Cai B, Lo M, Falsafi R, Hancock REW, Chiume-Kayuni M, Lufesi N, Popescu CR, Lavoie PM, Strunk T, Currie AJ, Kollmann TR, Amenyogbe N, Lee AH. Angiogenesis-associated pathways play critical roles in neonatal sepsis outcomes. Sci Rep. 2024 May 20;14(1):11444. doi: 10.1038/s41598-024-62195-9. PMID: 38769383; PMCID: PMC11106288.


  • Shannon CP, Lee AH, Tebbutt SJ, Singh A. A Commentary on Multi-omics Data Integration in Systems Vaccinology. J Mol Biol. 2024 Apr 15;436(8):168522. doi: 10.1016/j.jmb.2024.168522. Epub 2024 Mar 7. PMID: 38458605.


  • Dhillon BK, Kortbeek S, Baghela A, Brindle M, Martin DA, Jenne CN, Vogel HJ, Lee AHY, Thompson GC, Hancock REW. Gene Expression Profiling in Pediatric Appendicitis. JAMA Pediatr. 2024 Feb 19:e236721. doi: 10.1001/jamapediatrics.2023.6721. Epub ahead of print. PMID: 38372989; PMCID: PMC10877506.


  • An AY, Baghela A, Zhang PGY, Blimkie TM, Gauthier J, Kaufmann DE, Acton E, Lee AHY, Levesque RC, Hancock REW. Post-COVID symptoms are associated with endotypes reflecting poor inflammatory and hemostatic modulation. Front Immunol. 2023 Aug 23;14:1243689. doi: 10.3389/fimmu.2023.1243689. PMID: 37680625; PMCID: PMC10482103.


  • Lau WYV, Taylor PK, Brinkman FSL, Lee AHY. Pathogen-associated gene discovery workflows for novel antivirulence therapeutic development. EBioMedicine. 2023 Feb;88;104429. doi:10.1016/j.ebiom.2022.104429. PMID: 36628845; PMCID: PMC9843249.


  • Baghela A, An A, Zhang P, Acton E, Gauthier J, Brunet-Ratnasingham E, Blimkie T, Freue GC, Kaufmann D, Lee AHY, Levesque RC, Hancock REW. Predicting severity in COVID-19 disease using sepsis blood gene expression signatures. Sci Rep. 2023 Jan 23;13(1):1247. doi: 10.1038/s41598-023-28259-y. PMID: 36690713; PMCID: PMC9868505.


  • Baghela A, Pena OM, Lee AH, Baquir B, Falsafi R, An A, Farmer SW, Hurlburt A, Mondragon-Cardona A, Rivera JD, Baker A, Trahtemberg U, Shojaei M, Jimenez-Canizales CE, Dos Santos CC, Tang B, Bouma HR, Cohen Freue GV, Hancock REW. Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures. EBioMedicine. 2022 Jan;75:103776. doi: 10.1016/j.ebiom.2021.103776. Epub 2022 Jan 10. PMID: 35027333; PMCID: PMC8808161.


  • Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock REW, Koff WC, Kollmann TR, Sadarangani M, Lee AH. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front Immunol. 2020 Nov 30;11:578801. doi: 10.3389/fimmu.2020.578801. PMID: 33329547; PMCID: PMC7734088.


  • Lee AH, Shannon CP, Amenyogbe N, Bennike TB, Diray-Arce J, Idoko OT, Gill EE, Ben-Othman R, Pomat WS, van Haren SD, Cao KL, Cox M, Darboe A, Falsafi R, Ferrari D, Harbeson DJ, He D, Bing C, Hinshaw SJ, Ndure J, Njie-Jobe J, Pettengill MA, Richmond PC, Ford R, Saleu G, Masiria G, Matlam JP, Kirarock W, Roberts E, Malek M, Sanchez-Schmitz G, Singh A, Angelidou A, Smolen KK; EPIC Consortium, Brinkman RR, Ozonoff A, Hancock REW, van den Biggelaar AHJ, Steen H, Tebbutt SJ, Kampmann B, Levy O, Kollmann TR. Dynamic molecular changes during the first week of human life follow a robust developmental trajectory. Nat Commun. 2019 Mar 12;10(1):1092. doi: 10.1038/s41467-019-08794-x. PMID: 30862783; PMCID: PMC6414553.


  • Ng S, Strunk T, Lee AH, Gill EE, Falsafi R, Woodman T, Hibbert J, Hancock REW, Currie A. Whole blood transcriptional responses of very preterm infants during late-onset sepsis. PLoS One. 2020 Jun 1;15(6):e0233841. doi: 10.1371/journal.pone.0233841. PMID: 32479514; PMCID: PMC7263612.


  • Belanger CR, Lee AH, Pletzer D, Dhillon BK, Falsafi R, Hancock REW. Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media. Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33519-33529. doi: 10.1073/pnas.2007626117. Epub 2020 Dec 14. PMID: 33318204; PMCID: PMC7777150.


  • Facciuolo A, Lee AH, Trimble MJ, Rawlyk N, Townsend HGG, Bains M, Arsic N, Mutharia LM, Potter A, Gerdts V, Napper S, Hancock REW, Griebel PJ. A Bovine Enteric Mycobacterium Infection Model to Analyze Parenteral Vaccine-Induced Mucosal Immunity and Accelerate Vaccine Discovery. Front Immunol. 2020 Nov 23;11:586659. doi: 10.3389/fimmu.2020.586659. PMID: 33329565; PMCID: PMC7719698.


  • Facciuolo A, Lee AH, Gonzalez Cano P, Townsend HGG, Falsafi R, Gerdts V, Potter A, Napper S, Hancock REW, Mutharia LM, Griebel PJ. Regional Dichotomy in Enteric Mucosal Immune Responses to a Persistent Mycobacterium avium ssp. paratuberculosis Infection. Front Immunol. 2020 May 29;11:1020. doi: 10.3389/fimmu.2020.01020. PMID: 32547548; PMCID: PMC7272674.


  • Yeung ATY, Choi YH, Lee AHY, Hale C, Ponstingl H, Pickard D, Goulding D, Thomas M, Gill E, Kim JK, Bradley A, Hancock REW, Dougan G. A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Salmonella Infection. mBio. 2019 Oct 8;10(5):e02169-19. doi: 10.1128/mBio.02169-19. PMID: 31594818; PMCID: PMC6786873.


  • Hinshaw SJ, Lee AHY, Gill EE, Hancock REW. MetaBridge: enabling network-based integrative analysis via direct protein interactors of metabolites. Bioinformatics. 2018 Sep 15;34(18):3225-3227. doi: 10.1093/bioinformatics/bty331. PMID: 29688253.


  • Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W, Parry-Smith D, Goulding D, Pickard D, Roumeliotis T, Choudhary J, Thomson N, Skarnes WC, Dougan G, Hancock REW. Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis. Nat Commun. 2017 Apr 25;8:15013. doi: 10.1038/ncomms15013. PMID: 28440293; PMCID: PMC5414054.


  • Lee AH, Flibotte S, Sinha S, Paiero A, Ehrlich RL, Balashov S, Ehrlich GD, Zlosnik JE, Mell JC, Nislow C. Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs. Genome Res. 2017 Apr;27(4):650-662. doi: 10.1101/gr.213363.116. Epub 2017 Mar 21. PMID: 28325850; PMCID: PMC5378182.