Publications

Lemke, M. M., McLean, M. R., Lee, C. Y., Lopez, E., Bozich, E. R., Rerks-Ngarm, S., Pitisuttithum, P., Nitayaphan, S., Kratochvil, S., Wines, B. D., Hogarth, P. M., Kent, S. J., Chung, A. W., & Arnold, K. B. (2021). A systems approach to elucidate personalized mechanistic complexities of antibody-Fc receptor activation post-vaccination. Cell Reports Medicine, 0(0). https://doi.org/10.1016/j.xcrm.2021.100386

K.J. Selva*C.E. van de Sandt*M.M. Lemke*, C.Y. Lee*S.K. Shoffner*B.Y. ChuaT.H.O. NguyenL.C. RowntreeL. Hensen, M. KoutsakosC.Y. WongD.C. JacksonK.L. FlanaganJ. CroweA.C. ChengD.L. DoolanF. AmanatF. KrammerK. Chappell, N. ModhiranD. WattersonP. YoungB. WinesP.M. HogarthR. Esterbauer,  H.G. Kelly,  H.X. TanJ.A. JunoA.K. WheatleyS.J. KentKelly B. Arnold,  K. Kedzierska,  A.W. Chung. . Systems serology detects functionally distinct coronavirus antibody features in children and elderly. Nat Commun 12, 2037 (2021). https://doi-org/10.1038/s41467-021-22236-7

C.E. Tomaszewski, K.M. DiLillo, B.M. Baker, K.B. Arnold, A. Shikanov. Sequestered cell-secreted extracellular matrix proteins improve murine folliculogenesis and oocyte maturation for fertility preservation. Acta Biomaterialia. ISSN 1742-706 (2021). https://doi.org/10.1016/j.actbio.2021.03.041.

Cheu, R.K., Gustin, A.T., Lee, C.Y., Schifanella, L., Miller, C.J., Ha, A., Kim, C., Rodriguez, V.J., Fischt, M., Burgener, A.D., Arnold, K.B., Alcaide, M.L., Klatt, N.R. Impact of vaginal microbiome communities on HIV antiretroviral-based pre-exposure prophylaxis (PrEP) drug metabolism. PLOS Pathogens  16, 12 (2020).

Lee, C.Y.*, Cheu, R.K.*, Lemke, M.M., Gustin, A.T., France, M.T., Hampel, B., Thurman, A.R., Doncel, G.F., Ravel, J., Klatt, N.R., and Arnold, K.B. Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. Nat Commun 11, 6147 (2020). DOI: 10.1038/s41467-020-19880-w

Tosif, S., Neeland, M.R., Sutton, P., Licciardi S.S., Selva, K.J., Anh Ha Do, L., Denato, C., Zheng, Q.T., Higgins, R., Van de Sandt, C., Lemke, M.M., Lee, C.Y., Suzanne, S.K., Flanagan, K.L.,  Arnold, K.B., et al. Immune responses to SARS-CoV-2 in three children of parents with symptomatic COVID-19. Nat Commun 11, 5703 (2020). DOI: 10.1038/s41467-020-19545-8.

Matera, D.L., DiLillo, K.M., Smith, M.R., Davidson, D.D., Parikh, R., Said, M., Wilk, C.A., Lombaert, I.S., Arnold, K.B., Moore, B.B., Baker, B.M. 2020, “Microengineered 3D pulmonary interstitial mimetics highlight a critical role for matrix degradation in myofibroblast differentiation”, Science Advances 6(37), eabb5069.
DOI: 10.1126/sciadv.abb5069

K.C. Norman, D.N. O’Dwyer, M.L. Salisbury, K.M. DiLillo, V.N. Lama, M Xia, S.J. Gurczynski, E.S. White, K.R. Flaherty, F.J. Martinez, S. Murray, B.B. Moore, K.B. Arnold. Identification of a unique temporal signature in blood and BAL associated with IPF progression. Sci Rep 10, 12049 (2020). https://doi.org/10.1038/s41598-020-67956-w

K.C. Norman, C.M. Freeman, N.S. Bidthanapally, M.K. Han, F.J. Martinez, J.L. Curtis, K.B. Arnold. Inference of Cellular Immune Environments in Sputum and Peripheral Blood Associated with Acute Exacerbations of COPD. Cellular and Molecular Bioengineering (2019) 12:165.

K.C. Norman, B.B. Moore, K.B. Arnold, D.N. O’Dwyer. Proteomics: Clinical and research applications in respiratory diseasesRespirology (2018) Aug 13; 1–11. 

H. Zhou, J.T. Decker, M.M. Lemke, C. Tomaszweski, L. Shea, K.B. Arnold, A. Shikanov. Synergy of Paracrine Signaling During Early-Stage Mouse Ovarian Follicle Development In Vitro. Cellular and Molecular Bioengineering (2018) Aug 9; 1-16.

D.N. O’Dwyer, X. Zhou, C.A. Wilke, M. Xia, N.R. Falkowski, K.C. Norman, K.B. Arnold, G.B. Huffnagle, S. Murray, J.R. Erb-Downward, G.A. Yanik, B.B. Moore, R.P. Dickson. Lung Dysbiosis, Inflammation, and Injury in Hematopoietic Cell Transplantation. Am J Respir Crit Care Med. (2018) Jun 7; [Epub ahead of print].

K.B. Arnold* and A.W. Chung*.  Prospects from Systems Serology Research.  Immunology (2017) Nov 15; [Epub ahead of print].

D.N. O’Dwyer*, K.C. Norman*, M. Xia, Y.  Huang, S.J. Gurczynski, S.L. Ashley, E.S. White, K.R. Flaherty, F.J. Martinez, S. Murray, I. Noth, K.B. Arnold#, and B.B. Moore#. The peripheral blood proteome signature of idiopathic pulmonary fibrosis is distinct from normal and is associated with novel immunological processes. Scientific Reports (2017) Apr 25;7:46560.

J.T. Decker, E.C. Hobson, Y. Zhang, S. Shin, A.L. Thomas, J.S. Jeruss, K.B. Arnold, and L.D. Shea.  Systems analysis of dynamic transcription factor activity identifies targets for treatment in olaparib resistant cancer cells. Biotechnology and Bioengineering (2017) Mar 21; [Epub ahead of print].

S.N. Byrareddy*, J. Arthos*, C. Cicala*, F. Villinger, K.T. Ortiz, D. Little, N. Sidell, M.A. Kane, J. Yu, J.W. Jones, P.J. Santangelo, C. Zurla, L.R. McKinnon, K.B. Arnold, C.E. Woody, L. Walter, C. Roos, A. Noll, D. Van Ryk, K. Jelicic, R. Cimbro, S. Gumber, M.D. Reid, V. Adsay, P.K. Amancha, Ann E. Mayne,T.G. Parslow, A.S. Fauci, A.A. Ansari. Sustained virologic control in SIV+ macaques after antiretroviral and α4β7 antibody therapy. Science (2016) Oct 14; 354(3609): 197-202.

A.W. Chung*, M.P. Kumar*, K.B. Arnold*, W.H. Yu*, M.K. Schoen, L.J. Dunphy, T.J. Suscovich, N. Frahm, C. Linde, A.E. Mahan, M. Hoffner, H. Streeck, M.E. Ackerman, J. McElrath, H. Schuitemaker, M.G. Pau, L.R. Baden, J.H. Kim, N.L. Michael, D.H. Barouch, D.A. Lauffenburger, and G. Alter.  Dissecting the polyclonal nature of vaccine-induced humoral immunity using Systems Serology.  Cell (2015) Nov 5;163(4):988-98.

L. Masson, K.B. Arnold, F. Little, K. Mlisana, D.A. Lewis, N. Mkhize, H. Gamieldien, S. Ngcapu, L. Johnson, D.A. Lauffenburger, Q. Abdool Karim, S.S. Abdool Karim, J.S. Passmore. Inflammatory cytokine biomarkers to identify women with asymptomatic sexually transmitted infections and bacterial vaginosis who are at high risk of HIV infection. Sexually Transmitted Infections (2015).  Oct 28 [Epub ahead of print].

K.B. Arnold*, G.S. Szeto*, G. Alter, D.J. Irvine, and D.A. Lauffenburger.  CD4+ T cell-dependent and -independent cytokine/chemokine network changes in immune responses of HIV-infected individuals.  Science Signaling (2015) Oct 20;8(399):ra104.

K.B. Arnold*, A. Burgener*, K. Birse, L. Romas, L.J. Dunphy, K. Shahabi, M. Abou, J. Kwatampora, B. Nyanga, J. Kimani, L. Liebenberg, L. Masson, S.S. Abdool Karim, J.S. Passmore, D.A. Lauffenburger, R. Kaul, and L.R. McKinnon.  Increased levels of inflammatory cytokines in the female reproductive tract are associated with altered expression of proteases, mucosal barrier proteins, and an influx of HIV-susceptible target cells.  Mucosal Immunology (2015) Jun 24 [Epub ahead of print]

K. Birse, K.B. Arnold, R.M. Novak, S. McCorrister, G.R. Westmacott, T.B. Ball, D.A. Lauffenburger, and A. Burgener. Molecular signatures of immune activation and epithelial barrier remodeling are enhanced during the luteal phase of the menstrual cycle: implications for HIV susceptibility. Journal of Virology (2015) Sep 1;89(17):8793-805.

R.P. Madan, J. Tugetman, L. Masson, L. Werner, A. Grobler, K. Mlisana, Y. Lo, D. Che, K.B. Arnold, S.S. Abdool Karim, J.S. Passmore, and B.C. Herold.  Innate antibacterial activity in female genital tract secretions is associated with increased risk of HIV acquisition. AIDS Research and Human Retroviruses (2015) Jul 14.  [Epub ahead of print].

L. Masson*, J.S. Passmore*, L.J. Lienbenberg*, L. Werner, C. Baxter, K.B. Arnold, C. Williamson, F. Little, L.E. Masoor, V. Naranbhai, D.A. Lauffenburger, K. Ronacher, G. Walzl, N.J. Garrett, B.L Williams, M. Couto-Rodriguez, M. Hornig, W.I. Lipkin, A. Grobler, Q. Abdool Karim, and S.S. Abdool Karim. Genital inflammation and the risk of HIV acquisition in women. Clinical Infectious Diseases (2015) Jul 15;61(2):260-9.

J. Z. Li*, K.B. Arnold*, J. Lo, A.-S. Dugast, J. Plants, H.J. Ribaudo, K. Cesa, A. Heisey, D.R. Kuritzkes, D.A. Lauffenburger, G. Alter, A. Landay, S. Grinspoon, and F. Pereyra. Differential levels of soluble inflammatory markers by human immunodeficiency virus controller status and demographics. Open Forums of Infectious Disease (2013) Jan 13;2(1):ofu117.

C. D. Palmer, J. Tomassilli, M. Sirignano, M. Romero Tejeda, K.B. Arnold, D. Che, S. Jost, T. Allen, K. H. Mayer, and M. Altfeld. Enhanced immune activation and transient endotoxemia in HIV-exposed seronegative men who have sex with men. AIDS (2014) Sep 10;28(14):2162-6.

R.P. Simmons, E.P. Scully, E.E. Groden, K.B. Arnold, J.J. Chang, K. Lane, J. Lifson, E. Rosenberg, D.A. Lauffenburger, and M. Altfeld.  HIV infection induces strong production of IP-10 through TLR7/9-dependent pathways.  AIDS (2013) Oct 23;27(16):2505-17.

K.F. Benedict and D.A. Lauffenburger.  Insights into proteomic immune cell signaling and communication via data-driven modeling.  Current Topics in Microbiology and Immunology (2013) 363:201-33.

Y.J. Yamanaka, G.L. Szeto, T.M. Gierahn, T.L. Forcier, K.F. Benedict, M.S. Brefo, D.A. Lauffenburger, D.J. Irvine, and J.C. Love.  Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving.  Analytical Chemistry (2012) Dec 18;84(24):10531-6.

K.F. Benedict, G.S. Coffin, E.J. Barrett and T.C. Skalak.  Hemodynamic systems analysis of capillary network remodeling during the progression of type 2 diabetes.  Microcirculation (2011) Jan;18(1):63-73.  

K.F. Benedict, F. Mac Gabhann*, R.K. Amanfu*, A.K. Chavali*, E.P. Gianchandani*, L.S. Glaw*, M.A. Oberhardt*, B.C. Thorne*, J.H. Yang*, J.A. Papin, S.M. Peirce, J.J. Saucerman, and T.C. Skalak.  Systems analysis of small signaling modules relevant to eight human diseases.  Annals of Biomedical Engineering (2011) Feb; 39(2): 621–635. 

*denotes equal contribution ,#co-corresponding authors