Baumgartner, A., Robinson, M., Ertekin-Taner, N., Golde, T. E., Jaydev, S., Huang, S., Hadlock, J., & Funk, C. (2025). Fokker-Planck diffusion maps of microglial transcriptomes reveal radial differentiation into substates associated with Alzheimer’s pathology. Communications Biology, 8(1), 279. https://doi.org/10.1038/s42003-025-07594-y Cite

Alipour, E., Gratzl, S., Algohary, A., Lin, H., Bapat, M., Do, D., Baker, C., Rodriguez, T., Cartwright, B., Hadlock, J., Tarczy-Hornoch, P., Oka, A., & Stucky, N. (2025). Multimodal Deep Learning Model to Estimate CT-based Body Composition Measures Using Chest radiographs and Clinical Data. medRxiv. https://doi.org/10.1101/2025.01.16.25320684 Cite Download

Swank, Z., Borberg, E., Chen, Y., Senussi, Y., Chalise, S., Manickas-Hill, Z., Yu, X. G., Alicic, R., Baxter, J., Brennan, C., Caudill, A., Chen, P., Chopra, T., Chu, H. Y., Del Alcazar, J., Duven, A. M., Edmark, R., Emerson, S., Goldman, J. D., … RECOVER Consortium. (2024). Measurement of circulating viral antigens post-SARS-CoV-2 infection in a multicohort study. Clinical Microbiology and Infection. https://doi.org/10.1016/j.cmi.2024.09.001 Cite

Wei, Q., Mease, P. J., Chiorean, M., Iles-Shih, L., Matos, W. F., Baumgartner, A., Molani, S., Hwang, Y. M., Belhu, B., Ralevski, A., & Hadlock, J. (2024). Machine learning to understand risks for severe COVID-19 outcomes: a retrospective cohort study of immune-mediated inflammatory diseases, immunomodulatory medications, and comorbidities in a large US health-care system. The Lancet Digital Health, 6(5), e309–e322. https://doi.org/10.1016/S2589-7500(24)00021-9 Cite Download

Ralevski, A., Taiyab, N., Nossal, M., Mico, L., Piekos, S., & Hadlock, J. (2024). Using Large Language Models to Abstract Complex Social Determinants of Health From Original and Deidentified Medical Notes: Development and Validation Study. Journal of Medical Internet Research, 26, e63445. https://doi.org/10.2196/63445 Cite

Baumgartner, A., Robinson, M., Golde, T., Jaydev, S., Huang, S., Hadlock, J., & Funk, C. (2024). Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer’s pathology. BioRxiv: The Preprint Server for Biology, 2024.06.21.599924. https://doi.org/10.1101/2024.06.21.599924 Cite

Hwang, Y. M., Wei, Q., Piekos, S. N., Vemuri, B., Molani, S., Mease, P., Hood, L., & Hadlock, J. (2024). Maternal-fetal outcomes in patients with immune-mediated inflammatory diseases, with consideration of comorbidities: a retrospective cohort study in a large U.S. healthcare system. EClinicalMedicine, 68, 102435. https://doi.org/10.1016/j.eclinm.2024.102435 Cite Download

Piekos, S. N., Barak, O., Baumgartner, A., Chu, T., Parks, W. T., Hadlock, J., Hood, L., Price, N. D., & Sadovsky, Y. (2024). Placental Network Differences Among Obstetric Syndromes Identified With An Integrated Multiomics Approach. bioRxiv. https://doi.org/10.1101/2024.09.03.611067 Cite Download

Hwang, Y. M., Piekos, S. N., Wei, Q., Price, N. D., Hood, L., & Hadlock, J. J. (2024). Detection of Drug Effect Signals Associated with Adverse Pregnancy Outcomes Using Propensity Score Matching at Scale. medRxiv. https://doi.org/10.1101/2024.03.21.24304579 Cite Download

Ellis, D., Watanabe, K., Wilmanski, T., Lustgarten, M. S., Korat, A. V. A., Glusman, G., Hadlock, J. J., Fiehn, O., Sebastiani, P., Price, N. D., Hood, L., Magis, A. T., Evans, S. J., Pflieger, L., Lovejoy, J. C., Gibbons, S. M., Funk, C. C., Baloni, P., & Rappaport, N. (2024). APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics. bioRxiv. https://doi.org/10.1101/2024.10.17.618322 Cite Download

Qin, G., Narsinh, K., Wei, Q., Roach, J. C., Joshi, A., Goetz, S. L., Moxon, S. T., Brush, M. H., Xu, C., Yao, Y., Glen, A. K., Morris, E. D., Ralevski, A., Roper, R., Belhu, B., Zhang, Y., Shmulevich, I., Hadlock, J., & Glusman, G. (2024). Generating Biomedical Knowledge Graphs from Knowledge Bases, Registries, and Multiomic Data. bioRxiv. https://doi.org/10.1101/2024.11.14.623648 Cite Download

Hwang, Y. M., Piekos, S. N., Paquette, A. G., Wei, Q., Price, N. D., Hood, L., & Hadlock, J. J. (2024). Accelerating adverse pregnancy outcomes research amidst rising medication use: parallel retrospective cohort analyses for signal prioritization. BMC Medicine, 22(1), 495. https://doi.org/10.1186/s12916-024-03717-0 Cite Download

Ralevski, A., Taiyab, N., Nossal, M., Mico, L., Piekos, S. N., & Hadlock, J. (2024). Using Large Language Models to Annotate Complex Cases of Social Determinants of Health in Longitudinal Clinical Records. medRxiv. https://doi.org/10.1101/2024.04.25.24306380 Cite Download

Johnson-Martínez, J. P., Diener, C., Levine, A. E., Wilmanski, T., Suskind, D. L., Ralevski, A., Hadlock, J., Magis, A. T., Hood, L., Rappaport, N., & Gibbons, S. M. (2024). Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function. Cell Reports. Medicine, 5(7), 101646. https://doi.org/10.1016/j.xcrm.2024.101646 Cite

Metz, T. D., Reeder, H. T., Clifton, R. G., Flaherman, V., Aragon, L. V., Baucom, L. C., Beamon, C. J., Braverman, A., Brown, J., Cao, T., Chang, A., Costantine, M. M., Dionne, J. A., Gibson, K. S., Gross, R. S., Guerreros, E., Habli, M., Hadlock, J., Han, J., … NIH Researching COVID to Enhance Recovery (RECOVER) Consortium*. (2024). Post-Acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) After Infection During Pregnancy. Obstetrics and Gynecology. https://doi.org/10.1097/AOG.0000000000005670 Cite

Chang, S.-C., Grunkemeier, G. L., Goldman, J. D., Wang, M., McKelvey, P. A., Hadlock, J., Wei, Q., & Diaz, G. A. (2024). A simplified pneumonia severity index (PSI) for clinical outcome prediction in COVID-19. PloS One, 19(5), e0303899. https://doi.org/10.1371/journal.pone.0303899 Cite Download

Baumgartner, A., Huang, S., Hadlock, J., & Funk, C. (2024). Dimensional reduction of gradient-like stochastic systems with multiplicative noise via Fokker-Planck diffusion maps (No. arXiv:2401.03095). arXiv. https://doi.org/10.48550/arXiv.2401.03095 Cite Download

Hwang, Y. M., Roper, R. T., Piekos, S. N., Enquobahrie, D. A., Hebert, M. F., Paquette, A. G., Baloni, P., Price, N. D., Hood, L., & Hadlock, J. J. (2024). Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events: with a consideration of the COVID-19 pandemic period. The Journal of Maternal-Fetal & Neonatal Medicine, 37(1), 2313364. https://doi.org/10.1080/14767058.2024.2313364 Cite Download

Fecho, K., Bizon, C., Issabekova, T., Moxon, S., Thessen, A. E., Abdollahi, S., Baranzini, S. E., Belhu, B., Byrd, W. E., Chung, L., Crouse, A., Duby, M. P., Ferguson, S., Foksinska, A., Forero, L., Friedman, J., Gardner, V., Glusman, G., Hadlock, J., … Biomedical Data Translator Consortium. (2023). An approach for collaborative development of a federated biomedical knowledge graph-based question-answering system: Question-of-the-Month challenges. Journal of Clinical and Translational Science, 7(1), e214. https://doi.org/10.1017/cts.2023.619 Cite Download

Hwang, Y.-M., Piekos, S., Sorensen, T., Hood, L., & Hadlock, J. (2023). Adoption of a National Prophylactic Anticoagulation Guideline for Hospitalized Pregnant Women With COVID-19: Retrospective Cohort Study. JMIR Public Health and Surveillance, 9, e45586. https://doi.org/10.2196/45586 Cite

Baumgartner, A., Robinson, M., Huang, S., Hadlock, J., & Funk, C. (2023). Integration of multiple single cell microglial datasets reveals radial differentiation into long‐lived substates associated with Alzheimer’s pathology. Alzheimer’s & Dementia, 19. https://doi.org/10.1002/alz.080693 Cite

Hwang, Y. M., Wei, Q., Piekos, S. N., Vemuri, B., Molani, S., Mease, P., Hood, L., & Hadlock, J. J. (2023). Maternal-fetal outcomes in patients with immune mediated inflammatory diseases, with consideration of comorbidities: a retrospective cohort study in a large U.S. healthcare system. MedRxiv: The Preprint Server for Health Sciences, 2023.08.07.23293726. https://doi.org/10.1101/2023.08.07.23293726 Cite Download

Piekos, S. N., Hwang, Y. M., Roper, R. T., Sorensen, T., Price, N. D., Hood, L., & Hadlock, J. J. (2023). Effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective cohort study. The Lancet. Digital Health, 5(9), e594–e606. https://doi.org/10.1016/S2589-7500(23)00093-6 Cite Download

Wei, Q., Mease, P. J., Chiorean, M., Iles-Shih, L., Matos, W. F., Baumgartner, A., Molani, S., Hwang, Y. M., Belhu, B., Ralevski, A., & Hadlock, J. (2023). Risk factors for severe COVID-19 outcomes: a study of immune-mediated inflammatory diseases, immunomodulatory medications, and comorbidities in a large US healthcare system. MedRxiv: The Preprint Server for Health Sciences, 2023.06.26.23291904. https://doi.org/10.1101/2023.06.26.23291904 Cite Download

Watanabe, K., Wilmanski, T., Diener, C., Earls, J. C., Zimmer, A., Lincoln, B., Hadlock, J. J., Lovejoy, J. C., Gibbons, S. M., Magis, A. T., Hood, L., Price, N. D., & Rappaport, N. (2023). Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention. Nature Medicine, 29(4), 996–1008. https://doi.org/10.1038/s41591-023-02248-0 Cite Download

Hwang, Y. M., Roper, R. T., Piekos, S. N., Enquobahrie, D. A., Hebert, M. F., Paquette, A. G., Baloni, P., Price, N. D., Hood, L., & Hadlock, J. J. (2023). Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events. medRxiv. https://doi.org/10.1101/2023.03.03.23286717 Cite Download

Johnson, J. P., Diener, C., Levine, A. E., Wilmanski, T., Suskind, D. L., Ralevski, A., Hadlock, J., Magis, A. T., Hood, L., Rappaport, N., & Gibbons, S. M. (2023). Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function. bioRxiv. https://doi.org/10.1101/2023.03.04.531100 Cite Download

Molani, S., Hernandez, P. V., Roper, R. T., Duvvuri, V. R., Baumgartner, A. M., Goldman, J. D., Ertekin-Taner, N., Funk, C. C., Price, N. D., Rappaport, N., & Hadlock, J. J. (2022). Risk factors for severe COVID-19 differ by age for hospitalized adults. Scientific Reports, 12(1), 6568. https://doi.org/10.1038/s41598-022-10344-3 Cite Download Download

Piekos, S. N., Price, N. D., Hood, L., & Hadlock, J. J. (2022). The impact of maternal SARS-CoV-2 infection and COVID-19 vaccination on maternal-fetal outcomes. Reproductive Toxicology (Elmsford, N.Y.), S0890-6238(22)00153-8. https://doi.org/10.1016/j.reprotox.2022.10.003 Cite Download

Kwasniewski, M., Korotko, U., Chwialkowska, K., Niemira, M., Jaroszewicz, J., Sobala-Szczygiel, B., Puzanowska, B., Moniuszko-Malinowska, A., Pancewicz, S., Parfieniuk-Kowerda, A., Martonik, D., Zarebska-Michaluk, D., Simon, K., Pazgan-Simon, M., Mozer-Lisewska, I., Bura, M., Adamek, A., Tomasiewicz, K., Pawłowska, M., … Moniuszko, M. (2022). Implementation of the web-based calculator estimating odds ratio of severe COVID-19 for unvaccinated individuals in a country with high coronavirus-related death toll. Allergy. https://doi.org/10.1111/all.15524 Cite Download

Molani, S., Hernandez, P. V., Roper, R. T., Duvvuri, V. R., Baumgartner, A. M., Goldman, J. D., Ertekin-Taner, N., Funk, C. C., Price, N. D., Rappaport, N., & Hadlock, J. J. (2022). Risk factors for severe COVID-19 differ by age: a retrospective study of hospitalized adults [Preprint]. Public and Global Health. https://doi.org/10.1101/2022.02.02.22270287 Cite Download

Mease, P. J., Wei, Q., Chiorean, M., Iles-Shih, L., & Hadlock, J. (2022). Op0247 Risk Factors for Severe Covid-19 Outcomes: A Study of Immune-Mediated Inflammatory Diseases, Therapies and Comorbidities in a Large Us Healthcare System. Annals of the Rheumatic Diseases, 81(Suppl 1), 161–162. https://doi.org/10.1136/annrheumdis-2022-eular.2163 Cite Download

Watanabe, K., Wilmanski, T., Diener, C., Zimmer, A., Lincoln, B., Hadlock, J. J., Lovejoy, J. C., Magis, A. T., Hood, L., Price, N. D., & Rappaport, N. (2022). Multiomic investigations of Body Mass Index reveal heterogeneous trajectories in response to a lifestyle intervention. medRxiv. https://doi.org/10.1101/2022.01.20.22269601 Cite Download

Goldman, J. D., Wang, K., Röltgen, K., Nielsen, S. C. A., Roach, J. C., Naccache, S. N., Yang, F., Wirz, O. F., Yost, K. E., Lee, J.-Y., Chun, K., Wrin, T., Petropoulos, C. J., Lee, I., Fallen, S., Manner, P. M., Wallick, J. A., Algren, H. A., Murray, K. M., … Heath, J. R. (2022). Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines, 11(1), 5. https://doi.org/10.3390/vaccines11010005 Cite Download

Duvvuri, V. R., Baumgartner, A., Molani, S., Hernandez, P. V., Yuan, D., Roper, R. T., Matos, W. F., Robinson, M., Su, Y., Subramanian, N., Goldman, J. D., Heath, J. R., & Hadlock, J. J. (2022). Angiotensin-Converting Enzyme (ACE) Inhibitors May Moderate COVID-19 Hyperinflammatory Response: An Observational Study with Deep Immunophenotyping. Health Data Science, 2022, 0002. https://doi.org/10.34133/hds.0002 Cite Download

Unni, D. R., Moxon, S. A. T., Bada, M., Brush, M., Bruskiewich, R., Caufield, J. H., Clemons, P. A., Dancik, V., Dumontier, M., Fecho, K., Glusman, G., Hadlock, J. J., Harris, N. L., Joshi, A., Putman, T., Qin, G., Ramsey, S. A., Shefchek, K. A., Solbrig, H., … Biomedical Data Translator Consortium. (2022). Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clinical and Translational Science, 15(8), 1848–1855. https://doi.org/10.1111/cts.13302 Cite Download

Fecho, K., Thessen, A. E., Baranzini, S. E., Bizon, C., Hadlock, J. J., Huang, S., Roper, R. T., Southall, N., Ta, C., Watkins, P. B., Williams, M. D., Xu, H., Byrd, W., Dančík, V., Duby, M. P., Dumontier, M., Glusman, G., Harris, N. L., Hinderer, E. W., … Biomedical Data Translator Consortium. (2022). Progress toward a universal biomedical data translator. Clinical and Translational Science. https://doi.org/10.1111/cts.13301 Cite

Molani, S., Baumgartner, A. M., Hwang, Y. M., Duvvuri, V. R., Goldman, J. D., & Hadlock, J. J. (2022). Time to reinfection and vaccine breakthrough SARS-CoV-2 infections: a retrospective cohort study. 2022.02.07.22270613. https://www.medrxiv.org/content/10.1101/2022.02.07.22270613v1 Cite Download

Baumgartner, A., Molani, S., Wei, Q., & Hadlock, J. (2022). Imputing Missing Observations with Time Sliced Synthetic Minority Oversampling Technique. ArXiv:2201.05634 [Physics, q-Bio, Stat]. http://arxiv.org/abs/2201.05634 Cite Download

Piekos, S. N., Roper, R. T., Hwang, Y. M., Sorensen, T., Price, N. D., Hood, L., & Hadlock, J. J. (2022). The effect of maternal SARS-CoV-2 infection timing on birth outcomes: a retrospective multicentre cohort study. The Lancet. Digital Health, 4(2), e95–e104. https://doi.org/10.1016/S2589-7500(21)00250-8 Cite Download

Su, Y., Yuan, D., Chen, D. G., Ng, R. H., Wang, K., Choi, J., Li, S., Hong, S., Zhang, R., Xie, J., Kornilov, S. A., Scherler, K., Pavlovitch-Bedzyk, A. J., Dong, S., Lausted, C., Lee, I., Fallen, S., Dai, C. L., Baloni, P., … Heath, J. R. (2022). Multiple Early Factors Anticipate Post-Acute COVID-19 Sequelae. Cell, 0(0). https://doi.org/10.1016/j.cell.2022.01.014 Cite Download

Diaz, G. A., Christensen, A. B., Pusch, T., Goulet, D., Chang, S.-C., Grunkemeier, G. L., McKelvey, P. A., Robicsek, A., French, T., Parsons, G. T., Doherty, G., Laurenson, C., Roper, R., Hadlock, J., Cover, C. J., Footer, B., Robinson, P., Micikas, M., Marfori, J. E., … Goldman, J. D. (2021). Remdesivir and Mortality in Patients With Coronavirus Disease 2019. Clinical Infectious Diseases, ciab698. https://doi.org/10.1093/cid/ciab698 Cite Download

Jiang, Y., Duffy, F., Hadlock, J., Raappana, A., Styrchak, S., Beck, I., Mast, F. D., Miller, L. R., Chour, W., Houck, J., Armistead, B., Duvvuri, V. R., Yeung, W., Haglund, M., Wallner, J., Wallick, J. A., Hardy, S., Oldroyd, A., Ko, D., … Harrington, W. E. (2021). Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection. PloS One, 16(11), e0259902. https://doi.org/10.1371/journal.pone.0259902 Cite Download

Lee, J. W., Su, Y., Baloni, P., Chen, D., Pavlovitch-Bedzyk, A. J., Yuan, D., Duvvuri, V. R., Ng, R. H., Choi, J., Xie, J., Zhang, R., Murray, K., Kornilov, S., Smith, B., Magis, A. T., Hoon, D. S. B., Hadlock, J. J., Goldman, J. D., Price, N. D., … Heath, J. R. (2021). Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19. Nature Biotechnology. https://doi.org/10.1038/s41587-021-01020-4 Cite Download

Lee, J. Y., Molani, S., Fang, C., Jade, K., O’Mahony, D. S., Kornilov, S. A., Mico, L. T., & Hadlock, J. J. (2021). Ambulatory Risk Models for the Long-Term Prevention of Sepsis: Retrospective Study. JMIR Medical Informatics, 9(7), e29986. https://doi.org/10.2196/29986 Cite Download

Su, Y., Yuan, D., Chen, D. G., Wang, K., Choi, J., Dai, C. L., Hong, S., Zhang, R., Xie, J., Li, S., Scherler, K., Pavlovitch-Bedzyk, A. J., Dong, S., Lausted, C., Ng, R. H., Lee, I., Fallen, S., Kornilov, S. A., Baloni, P., … Heath, J. R. (2021). Heterogeneous immunological recovery trajectories revealed in post-acute COVID-19. MedRxiv, 2021.03.19.21254004. https://doi.org/10.1101/2021.03.19.21254004 Cite Download

Dai, C. L., Kornilov, S. A., Roper, R. T., Cohen-Cline, H., Jade, K., Smith, B., Heath, J. R., Diaz, G., Goldman, J. D., Magis, A. T., & Hadlock, J. J. (2021). Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciab154 Cite Download

Goldman, J. D., Wang, K., Röltgen, K., Nielsen, S. C. A., Roach, J. C., Naccache, S. N., Yang, F., Wirz, O. F., Yost, K. E., Lee, J.-Y., Chun, K., Wrin, T., Petropoulos, C. J., Lee, I., Fallen, S., Manner, P. M., Wallick, J. A., Algren, H. A., Murray, K. M., … Heath, J. R. (2020). Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report (p. 2020.09.22.20192443). https://www.medrxiv.org/content/10.1101/2020.09.22.20192443v1 Cite Download

Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C. L., Voillet, V., Duvvuri, V. R., Scherler, K., Troisch, P., Baloni, P., Qin, G., Smith, B., Kornilov, S. A., Rostomily, C., Xu, A., Li, J., Dong, S., Rothchild, A., … Heath, J. R. (2020). Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19. Cell, S0092867420314446. https://doi.org/10.1016/j.cell.2020.10.037 Cite Download

Fecho, K., Ahalt, S. C., Arunachalam, S., Champion, J., Chute, C. G., Davis, S., Gersing, K., Glusman, G., Hadlock, J., Lee, J., Pfaff, E., Robinson, M., Sid, E., Ta, C., Xu, H., Zhu, R., Zhu, Q., Peden, D. B., & Biomedical Data Translator Consortium. (2019). Sex, obesity, diabetes, and exposure to particulate matter among patients with severe asthma: Scientific insights from a comparative analysis of open clinical data sources during a five-day hackathon. Journal of Biomedical Informatics, 100, 103325. https://doi.org/10.1016/j.jbi.2019.103325 Cite