MP faculty publications: August 2021

1. Comprehensive Characterization of COVID-19 Patients with Repeatedly Positive SARS-CoV-2 Tests Using a Large U.S. Electronic Health Record Database

   Dong X, Zhou Y, Shu XO, Bernstam EV, Stern R, Aronoff DM, Xu H, Lipworth L
   Microbiol Spectr. 2021 Aug 18:e0032721

2. Human and Machine Intelligence Together Drive Drug Repurposing in Rare Diseases

   Challa AP, Zaleski NM, Jerome RN, Lavieri RR, Shirey-Rice JK, Barnado A, Lindsell CJ, Aronoff DM, Crofford LJ, Harris RC, Alp Ikizler T, Mayer IA, Holroyd KJ, Pulley JM
   Front Genet. 2021 Jul 28;12:707836

3. Framework for Implementing and Tracking A Molecular Tumor Board at an NCI-Designated Comprehensive Cancer Center

   Jain NM, Schmalz L, Cann C, Adara Holland MBA, Travis Osterman DO, Lang K, Wiesner GL, Pal T, Lovly C, Stricker T, Micheel C, Balko JM, Johnson DB, Park BH, Iams W
   Oncologist. 2021 Aug 14

4. Multi-omic Characterization of Intraspecies Variation in Laboratory and Natural Environments

   Behringer MG
   mSystems. 2021 Aug 24:e0076421

5. CD19 + CD21 lo/neg cells are increased in systemic sclerosis-associated interstitial lung disease

   Wilfong EM, Vowell KN, Bunn KE, Rizzi E, Annapureddy N, Dudenhofer RB, Barnado A, Bonami RH, Johnson JE, Crofford LJ, Kendall PL
   Clin Exp Med. 2021 Aug 10

6. High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide

   Yoo W, Zieba JK, Foegeding NJ, Torres TP, Shelton CD, Shealy NG, Byndloss AJ, Cevallos SA, Gertz E, Tiffany CR, Thomas JD, Litvak Y, Nguyen H, Olsan EE, Bennett BJ, Rathmell JC, Major AS, Bäumler AJ, Byndloss MX
   Science. 2021 Aug 13;373(6556):813-818

7. Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine

   Kramer KJ, Wilfong EM, Voss K, Barone SM, Shiakolas AR, Raju N, Roe CE, Suryadevara N, Walker L, Wall SC, Paulo A, Schaefer S, Dahunsi D, Westlake CS, Crowe JE, Carnahan RH, Rathmell JC, Bonami RH, Georgiev IS, Irish JM
   bioRxiv [Preprint]. 2021 Jul 28:2021.07.28.453981

8. Amelioration of post-traumatic osteoarthritis via nanoparticle depots delivering small interfering RNA to damaged cartilage

   Bedingfield SK, Colazo JM, Yu F, Liu DD, Jackson MA, Himmel LE, Cho H, Crofford LJ, Hasty KA, Duvall CL
   Nat Biomed Eng. 2021 Aug 19

9. Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals

   Chen EC, Gilchuk P, Zost SJ, Suryadevara N, Winkler ES, Cabel CR, Binshtein E, Chen RE, Sutton RE, Rodriguez J, Day S, Myers L, Trivette A, Williams JK, Davidson E, Li S, Doranz BJ, Campos SK, Carnahan RH, Thorne CA, Diamond MS, Crowe JE Jr
   Cell Rep. 2021 Aug 10;36(8):109604

10. Human antibody recognition of H7N9 influenza virus hemagglutinin following natural infection

    Gilchuk IM, Bangaru S, Kose N, Bombardi RG, Trivette A, Li S, Turner HL, Carnahan RH, Ward AB, Crowe JE Jr
    JCI Insight. 2021 Aug 26:152403

11. Pan-protective anti-alphavirus human antibodies target a conserved E1 protein epitope

    Kim AS, Kafai NM, Winkler ES, Gilliland TC Jr, Cottle EL, Earnest JT, Jethva PN, Kaplonek P, Shah AP, Fong RH, Davidson E, Malonis RJ, Quiroz JA, Williamson LE, Vang L, Mack M, Crowe JE Jr, Doranz BJ, Lai JR, Alter G, Gross ML, Klimstra WB, Fremont DH, Diamond MS
    Cell. 2021 Aug 19;184(17):4414-4429.e19

12. Therapeutic alphavirus cross-reactive E1 human antibodies inhibit viral egress

    Williamson LE, Reeder KM, Bailey K, Tran MH, Roy V, Fouch ME, Kose N, Trivette A, Nargi RS, Winkler ES, Kim AS, Gainza C, Rodriguez J, Armstrong E, Sutton RE, Reidy J, Carnahan RH, McDonald WH, Schoeder CT, Klimstra WB, Davidson E, Doranz BJ, Alter G, Meiler J, Schey KL, Julander JG, Diamond MS, Crowe JE Jr
    Cell. 2021 Aug 19;184(17):4430-4446.e22

13. Elicitation of Neutralizing Antibody Responses to HIV-1 Immunization with Nanoparticle Vaccine Platforms

    Murji AA, Qin JS, Hermanus T, Morris L, Georgiev IS
    Viruses. 2021 Jul 2;13(7):1296

14. Intestinal Regulatory T Cells as Specialized Tissue-Restricted Immune Cells in Intestinal Immune Homeostasis and Disease

    Jacobse J, Li J, Rings EHHM, Samsom JN, Goettel JA
    Front Immunol. 2021 Aug 4;12:716499

15. Pharmacogenetics of interaction between depot medroxyprogesterone acetate and efavirenz, rifampicin, and isoniazid during treatment of HIV and tuberculosis

    Haas DW, Mngqibisa R, Francis J, McIlleron H, Robinson JA, Kendall MA, Baker P, Mawlana S, Badal-Faesen S, Angira F, Omoz-Oarhe A, Samaneka WP, Denti P, Cohn SE; AIDS Clinical Trials Group A5338 Study Team
    Pharmacogenet Genomics. 2021 Aug 6

16. Sequence-dependent mechanics of collagen reflect its structural and functional organization

    Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR
    Biophys J. 2021 Aug 11:S0006-3495(21)00659-7

17. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy

    Barone SM, Paul AG, Muehling LM, Lannigan JA, Kwok WW, Turner RB, Woodfolk JA, Irish JM
    Elife. 2021 Aug 5;10:e64653

18. Identifying requirements for RSK2 specific inhibitors

    Wright EB, Fukuda S, Li M, Li Y, O'Doherty GA, Lannigan DA
    J Enzyme Inhib Med Chem. 2021 Dec;36(1):1798-1809

19. Metabolic pre-conditioning in CD4 T cells restores inducible immune tolerance in lupus prone mice

    Wilson CS, Stocks BT, Hoopes EM, Rhoads JP, McNew KL, Major AS, Moore DJ
    JCI Insight. 2021 Aug 17:143245

20. Development of a standardized MRI protocol for pancreas assessment in humans

    Virostko J, Craddock RC, Williams JM, Triolo TM, Hilmes MA, Kang H, Du L, Wright JJ, Kinney M, Maki JH, Medved M, Waibel M, Kay TWH, Thomas HE, Greeley SAW, Steck AK, Moore DJ, Powers AC
    PLoS One. 2021 Aug 24;16(8):e0256029

21. Host genetic determinants associated with Helicobacter pylori eradication treatment failure: A systematic review and meta-analysis

    Shah SC, Tepler A, Chung CP, Suarez G, Peek RM Jr, Hung A, Roumie C, Narula N
    Gastroenterology. 2021 Aug 3:S0016-5085(21)03338-2

22. LTB 4-Driven Inflammation and Increased Expression of ALOX5/ ACE2 During Severe COVID-19 in Individuals With Diabetes

    Bonyek-Silva I, Machado AFA, Cerqueira-Silva T, Nunes S, Silva Cruz MR, Silva J, Santos RL, Barral A, Oliveira PRS, Khouri R, Serezani CH, Brodskyn C, Caldas JR, Barral-Netto M, Boaventura V, Tavares NM
    Diabetes. 2021 Jun 15:db201260

23. Imaging Infection Across Scales of Size: From Whole Animals to Single Molecules

    Skaar EP
    Annu Rev Microbiol. 2021 Aug 3

24. The zinc transporter ZnuABC is critical for the virulence of Chromobacterium violaceum and contributes to diverse zinc-dependent physiological processes

    Santos RERS, da Silva Júnior WP, Harrison S, Skaar EP, Chazin WJ, da Silva Neto JF
    Infect Immun. 2021 Aug 2:IAI0031121

25. Ornithine decarboxylase (ODC1) gene variant (rs2302615) is associated with gastric cancer independently of Helicobacter pylori CagA serostatus

    Miller AK, Tavera G, Dominguez RL, Camargo MC, Waterboer T, Wilson KT, Williams SM, Morgan DR
    Oncogene. 2021 Aug 10

26. Adapting decarbonylation chemistry for the development of prodrugs capable of in vivo delivery of carbon monoxide utilizing sweeteners as carrier molecules

    De La Cruz LK, Yang X, Menshikh A, Brewer M, Lu W, Wang M, Wang S, Ji X, Cachuela A, Yang H, Gallo D, Tan C, Otterbein L, de Caestecker M, Wang B
    Chem Sci. 2021 Jul 1;12(31):10649-10654

27. CircleNet: Anchor-free Glomerulus Detection with Circle Representation

    Yang H, Deng R, Lu Y, Zhu Z, Chen Y, Roland JT, Lu L, Landman BA, Fogo AB, Huo Y
    Med Image Comput Comput Assist Interv. 2020;2020:35-44

28. High-Density Lipoproteins in Kidney Disease

    Kon V, Yang HC, Smith LE, Vickers KC, Linton MF
    Int J Mol Sci. 2021 Jul 30;22(15):8201

29. Protocol for multimodal analysis of human kidney tissue by imaging mass spectrometry and CODEX multiplexed immunofluorescence

    Neumann EK, Patterson NH, Allen JL, Migas LG, Yang H, Brewer M, Anderson DM, Harvey J, Gutierrez DB, Harris RC, deCaestecker MP, Fogo AB, Van de Plas R, Caprioli RM, Spraggins JM
    STAR Protoc. 2021 Aug 13;2(3):100747.