Publications

* first author if not listed first
† corresponding author if not listed last

In preparation

  1. Gaberino C*, Segnitz RM*, Dill-McFarland KA, Bacharier LB, Calatroni A, Gill MA, Stokes J, Liu AH, Cohen RT, Kumar R, Lang A, Khurana Hershey GK, Sherenian M, Zoratti EM, Teach SJ, Kattan M, Becker PM, Togias A, Busse WW, Jackson DJ, Altman MC. XXXX. Mepolizumab alters gene regulatory networks of airway type-2 and epithelial inflammation in urban children with asthma. In prep.

  2. Dill-McFarland KA†, Simmons JD, Peterson GJ, Nguyen FK, Campo M, Penchek P, Stein CM, Vaisar T, Mayanja-Kizza H, Boom WH, Hawn TR. XXXX. Epigenetic programming of host lipid metabolism associates with resistance to TST/IGRA conversion after exposure to Mycobacterium tuberculosis. Submitted. bioRvix doi: 2024.02.27.582348 — GitHub

  3. Duncombe CJ, Watson FN, Layton ED, Boey K, Conrad EN, Kalata AC, Mariko Seilie A, Dill-McFarland KA, Seshadri C, Shears MJ, Murphy SC. XXXX. Androgens inhibit protective CD8+ T cell responses against pre-erythrocytic malaria parasites. Submitted.

  4. Ivie JJ, Dill-McFarland KA, Simmons JD, Peterson GJ, Benchek PH, Mayanja-Kizza H, Veith LE, Boom WH, Stein CM, Thwaites GE, Thanh HH, Thuong NTT, Chang X, Dunstan S, Hawn TR. XXXX. Genome-wide screen identifies variants associated with Mycobacterium tuberculosis-induced myeloid cell cytokine response. Submitted.

  5. Altman MC, Murphy RS, Janczyk T, Jayavelu ND, Calatroni A, Kattan M, Gill MA, Stokes J, Liu AH, Khurana Hershey GK, Sherenian M, Kumar R, Robison RG, Gruchalla RS, O’Connor GT, Zoratti EM, Teach SJ, Lynch SV, Dill-McFarland KA, Becker PM, Togias A, Gern JE, Bacharier LB, Busse WW, Jackson DJ. XXXX. Inflammatory epithelial and macrophage associated pathways underlie residual asthma exacerbations in urban children treated with mepolizumab therapy. Submitted.

  6. Anterasian C, Gela A, Mwambene D, Shah JA, Ivie J, Dill-McFarland KA, Hanekom WA, Musvosvi M, Hatherill M, Scriba TJ, Hawn TR. XXXX. BCG induced innate immune response heterogeneity and susceptibility to pediatric tuberculosis. Submitted.

  7. Campo M†, Dill-McFarland KA, Peterson GJ, Benson B, Skerrett SJ, Hawn TR. XXXX. Human aveolar and monocyte-derived macrophage responses to Mycobacterium tuberculosis. Submitted. bioRvix doi: 2024.02.20.581265 — GitHub

Software

  1. Dill-McFarland KA, Mitchell K, Batchu S, Segnitz RM, Benson B, Janczyk T, Cox MS, Mayanja-Kizza HA, Boom WH, Benchek P, Stein C, Hawn TR, Altman MC. 2023. kimma: Flexible linear mixed effects modeling with kinship for RNA-seq data. Bioinformatics. 39(5): btad279. doi: 10.1093/bioinformatics/btad279 — GitHub

  2. Dill-McFarland KA, Segnitz RM, Benson B. SEAsnake: A snakemake pipeline for RNA-seq fastq to counts. doi: 10.5281/zenodo.6471546

Human health and disease

  1. Venkatasubramanian S, Plumlee C, Dill-McFarland KA, Cohen SB, Gern B, Rane DA, Meyer MK, Saha A, Pearson GL, Lietzke A, Pacheco A, Chow Y, Hung CF, Soleimanpour SA, Altman MC, Urdahl KB, Shah JA. 2024. Tollip inhibits lipid accumulation and the integrated stress response in alveolar macrophages to control Mycobacterium tuberculosis infection. Nat Microbiol. In press. — GitHub

  2. Hong H, Dill-McFarland KA, Simmons JD, Peterson GJ, Benchek P, Mayanja-Kizza H, Boom WH, Stein CM, Hawn TR. 2024. Mycobacterium tuberculosis-dependent monocyte expression quantitative trait loci and tuberculosis pathogenesis. Front Immunol. In press. medRxiv. doi: 10.1101/2023.08.28.23294698 — GitHub

  3. Dill-McFarland KA, Altman MC, Esnault S, Jarjour NN, Busse W, Rosenkranz M. 2024. Molecular pathways underlying lung-brain axis signaling in asthma: relevance for psychopathology and neuroinflammation. J Allergy Clin Immunol. S53(1): 111-121. doi: 10.1016/j.jaci.2023.07.025 — GitHub

  4. Hong H, Dill-McFarland KA, Benson B, Simmons JD, Peterson GJ, Bencheck P, Stein CM, Boom WH, Mayanja-Kizza M, Hawn TR. 2023. Mycobacterium tuberculosis-induced monocyte transcriptional responses associated with resistance to tuberculin skin test/interferon-γ release assay conversion in people with HIV. AIDS. 37(15): 2287-2296. doi: 10.1097/QAD.0000000000003716

  5. Simmons JD, Segnitz RM, Dill-McFarland KA, Stein CM, Peterson GJ, Mayanja-Kizza H, Boom WH, Hawn TR. 2023. Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. PLoS One. 18(4): e0284498. doi: 10.1371/journal.pone.0284498 — GitHub

  6. Phelan KJ, Dill-McFarland KA, Kothari A, Segnitz RM, Burkle J, Grashel B, Jenkins S, Spagna D, Martin LJ, Haslam DB, Biagini JM, Kalra M, McCoy KS, Ross K, Jackson DJ, Mersha T, Altman MC, Khurana Hershey GK. 2023. Airway transcriptome networks identify susceptibility to frequent asthma exacerbations in children. J Allergy Clin Immunol. 152(1): 73-83. doi: 10.1016/j.jaci.2023.02.031

  7. Murphy RC, Lai Y, Altman MC, Barrow KA, Dill-McFarland KA, Liu M, Hamerman JA, Lacy-Hulbert A, Piliponsky AM, Ziegler SF, Altemeier WA, Debley JS, Gharib SA, Hallstrand TS. 2023. Rhinovirus infection of the airway epithelium enhances mast cell immune responses via epithelial-derived interferons. J Allergy Clin Immunol. 151(6): 1484-1493. doi: 10.1016/j.jaci.2022.12.825

  8. Lindestam Arlehamn CS, Benson B, Kuan R, Dill-McFarland KA, Peterson GJ, Paul S, Nguyen FK, Gilman RH, Saito M, Taplitz R, Arentz M, Goss CH, Aitken ML, Horne DJ, Shah JA, Sette A, Hawn TR. 2022. T-cell deficiency and hyperinflammatory monocyte responses associate with Mycobacterium avium complex lung disease. Front Immunol 13: 1016038 doi: 10.3389/fimmu.2022.1016038

  9. Jackson DJ, Bacharier LB, Gergen PJ, Gagalis L, Calatroni A, Wellford S, Gill MA, Stokes J, Liu AH, Gruchalla RS, Cohen RT, Makhija M, Khurana Hershey GK, O’Connor GT, Pongracic JA, Sherenian MG, Rivera-Spoljaric K, Zoratti EM, Teach SJ, Kattan M, Dutmer CM, Kim H, Lamm C, Sheehan WJ, Segnitz RM, Dill-McFarland KA, Visness CM, Becker PM, Gern JE, Sorkness CA, Busse WW, Altman MC, US NIAID Inner City Asthma Consortium. 2022. Mepolizumab for urban children with exacerbation-prone eosinophilic asthma in the USA (MUPPITS-2): a randomised, double-blind, placebo-controlled, parallel-group trial. Lancet 400(10351): 502-511 doi: 10.1016/S0140-6736(22)01198-9

  10. Simmons JD, Dill-McFarland KA, Stein CM, Van PT, Chihota V, Ntshiqa T, Maenetje P, Peterson GJ, Benchek P, Nsereko M, Velen K, Fielding KL, Grant AD, Gottardo R, Mayanja-Kizza H, Wallis RS, Churchyard G, Boom WH, Hawn TR. 2022. Monocyte transcriptional responses to Mycobacterium tuberculosis associate with resistance to tuberculin skin test and interferon gamma release assay conversion. mSphere 7(3): e0015922. doi: 10.1128/msphere.00159-22 — GitHub

  11. Dill-McFarland KA, Schwartz JT, Zhao H, Shao B, Fulkerson PC, Altman MC, Gill MA. 2022. Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma. J Allergy Clin Immunol. 150(3):666-675. doi: 10.1016/j.jaci.2022.03.025 — GitHub

  12. Dill-McFarland KA*, Tang Z*, Kemis JH, Kerby RL, Chen G, Palloni A, Sorenson T, Rey FE†, Herd P†. 2019. Close social relationships correlate with human gut microbiota composition. Sci Rep 9: 703. doi: 10.1038/s41598-018-37298-9 — GitHub

  13. De Wolfe TJ, Eggers S, Barker AK, Kates A, Dill-McFarland KA, Suen G, Safdar N. 2018. Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection. PLoS One 13(9): e0204253. doi: 10.1371/journal.pone.0204253 — GitHub

  14. Romano KA, Dill-McFarland KA, Kasahara K, Kerby RL, Vivas EI, Amador-Noguez D, Herd P, Rey FE. 2018. Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: Assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation. Microbiome 6(1): 91. doi: 10.1186/s40168-018-0458-8 — GitHub

  15. Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, Carlsson CM, Asthana S, Zetterberg H, Blennow K, Bendlina BB†, Rey FE†. 2017. Gut microbiome alterations in Alzheimer’s disease. Sci Rep 7(1): 13537. doi: 10.1038/s41598-017-13601-y

  16. Jetté ME, Dill-McFarland KA, Hanshew AS, Suen G, Thibeault SL. 2016. The human laryngeal microbiome: effects of cigarette smoke and reflux. Sci Rep 6: 35882. doi: 10.1038/srep35882

Education

  1. Dill-McFarland KA, König SG, Mazel F, Oliver DC, McEwen LM, Hong KY, Hallam SJ. 2021. An integrated, modular approach to data science education in microbiology. PLoS Comput Biol 17(2): e1008661. doi: 10.1371/journal.pcbi.1008661 — GitHub

Animal microbiomes

  1. Kehoe SI†, Dill-McFarland KA, Breaker JD, Suen G. 2019. Effects of corn silage inclusion in preweaning calf diets. J Dairy Sci 102(5): 4131-37. doi: 10.3168/jds.2018-15799

  2. Carroll C, Olsen KD, Ricks NJ, Dill-McFarland KA, Suen G, Robinson TF, Chaston JM. 2019. Bacterial communities in the alpaca gastrointestinal tract vary with diet and body site. Front Microbiol 9: 3334. doi: 10.3389/fmicb.2018.03334

  3. Dill-McFarland KA, Weimer PJ, Breaker JD, Suen G. 2019. Diet influences early microbiota development in dairy calves without long-term impacts on milk production. Appl Environ Microbiol 85(2): e02141-18. doi: 10.1128/AEM.02141-18 — GitHub

  4. Cunha CS, Marcondes MI, Veloso CM, Mantovani HC, Pereira LGR, Tomich TR, Dill-McFarland KA†, Suen G†. 2018. Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production. J Sci Food Agric 99(1): 210-18. doi: 10.1002/jsfa.9162

  5. Dias J, Marcondes MI, de Souza SM, da Mata BC, Noronha MF, Resende RT, Machado FS, Mantovani HC, Dill-McFarland KA†, Suen G†. 2018. Bacterial community dynamics across the gastrointestinal tracts of dairy calves during preweaning development. Appl Environ Microbiol 84(9): e02675-17. doi: 10.1128/AEM.02675-17

  6. Williams CL, Dill-McFarland KA, Sparks DL, Kouba AJ, Willard ST, Suen G, Brown AE. 2018. Dietary changes during weaning shape the gut microbiota of red pandas (Ailurus fulgens). Conserv Physiol 6(1): cox075. doi: 10.1093/conphys/cox075

  7. Cunha CS, Veloso CM, Marcondes MI, Mantovani HC, Tomich TR, Periera LGR, Ferreira MF, Dill-McFarland KA†, Suen G†. 2017. Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate. Syst Appl Microbiol 40(8): 492-99. doi: 10.1016/j.syapm.2017.07.008

  8. Dai X, Weimer PJ, Dill-McFarland KA, Brandao VL, Suen G, Faciola AP. 2017. Camelina seed supplementation at two dietary fat levels changes ruminal bacterial community composition in a dual-flow continuous culture system. Front Microbiol 8: 2147. doi: 10.3389/fmicb.2017.02147

  9. Dias J, Marcondes MI, Noronha MF, Resende RT, Machado FS, Mantovani HC, Dill-McFarland KA†, Suen G†. 2017. Effect of pre-weaning diet on the ruminal archaeal, bacterial, and fungal diversity of dairy calves. Front Microbiol 8: 1553. doi: 10.3389/fmicb.2017.01553

  10. Dill-McFarland KA, Breaker JD, Suen G. 2017. Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation. Sci Rep 7: 40864. doi: 10.1038/srep40864

  11. Williams CL*, Dill-McFarland KA*, Vandewege MW, Sparks DL, Willard ST, Kouba AJ, Suen G†, Brown AE†. 2016. Dietary shifts may trigger dysbiosis and mucous stools in giant pandas (Ailuropoda melanoleuca). Front Microbiol 7: 661. doi: 10.3389/fmicb.2016.00661 — Microbiome Digest’s Best Microbiome Paper 2016

  12. Dill-McFarland KA, Weimer PJ, Pauli JN, Peery MZ, and Suen G. 2016. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environ Microbiol 18(5): 1391-402. doi: 10.1111/1462-2920.13022

  13. Dill-McFarland KA, Suen G, Carey HV. 2016. Spotlight: Bears arouse interest in microbiota’s role in health. Trends Microbiol 24(4): 245-6. doi: 10.1016/j.tim.2016.01.011

  14. Dill-McFarland KA, Neil KL, Zeng A, Sprenger RJ, Kurtz CC, Suen G†, Carey HV†. 2014. Hibernation alters diversity & composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol Ecol 23(18): 4658-69. doi: 10.1111/mec.12884