Publications

Complete publication list

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Highlights

  • Phongpreecha T, Ghanem M, Reiss JD, Oskotsky T, Mataraso SJ, De Francesco D, Reincke SM, Espinosa C, Chung P, Ng T, Costello JM, Sequoia JA, Razdan S, Xie F, Berson E, Kim Y, Seong D, Szeto MY, Myers F, Gu H, Feister J, Verscaj CP, Rose LA, Sin LWY, Oskotsky B, Roger J, Shu CH, Shome S, Yang LK, Tan Y, Levitte S, Wong RJ, Gaudillière B, Angst MS, Montine TJ, Kerner JA, Keller RL, Shaw GM, Sylvester KG, Fuerch J, Chock V, Gaskari S, Stevenson DK, Sirota M, Prince LS, Aghaeepour N. AI-driven Precision Total Parenteral Nutrition in Neonatal Intensive Care Units with TPN2.0. Nature Medicine (in press), 2025.
  • Mataraso SJ, Espinosa CA, Seong D, Reincke SM, Berson E, Reiss JD, Kim Y, Ghanem M, Shu CH, James T, Tan Y, Shome S, Stelzer IA, Feyaerts D, Wong RJ, Shaw GM, Angst MS, Gaudilliere B, Stevenson DK, Aghaeepour N. A machine learning approach to leveraging electronic health records for enhanced omics analysis. Nature Machine Intelligence, 2025.
  • Seong D, Mataraso S, Espinosa C, Berson E, Reincke SM, Xue L, Kashiwagi C, Kim Y, Shu CH, Chung P, Ghanem M, Xie F, Wong RJ, Angst MS, Gaudilliere B, Shaw GM, Stevenson DK, Aghaeepour N. Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models. Briefings in Bioinformatics, 2024.
  • De Francesco D, Reiss J, Roger J, Tang A, Chang A, Becker M, Phongpreecha T, Espinosa C, Morin S, Berson E, Thuraiappah M, Le B, Ravindra N, Payrovnaziri SN, Mataraso S, Kim Y, Xue L, Rosenstein M, Oskotsky T,  Maric I, Gaudilliere B, Carvalho B, Bateman B, Angst M, Prince L, Blumenfeld Y, Benitz W, Fuerch J, Shaw G, Sylvester K, Stevenson D, Sirota M, Nima Aghaeepour. Data-Driven Longitudinal Characterization of Neonatal Health and Morbidity. Science Translational Medicine, 2023.
  • Ravindra NG, Espinosa C, Berson E, Phongpreecha T, Zhao P, Becker M, Chang AL, Shome S, Marić I, De Francesco D, Mataraso S, Saarunya G, Thuraiappah M, Xue L, Gaudillière B, Angst MS, Shaw GM, Herzog ED, Stevenson DK, England SK, Aghaeepour N. Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity. npj Digital Medicine, 2023.
  • Espinosa CA, Khan W, Khanam R, Das S, Khalid J, Pervin J, Kasaro MP, Contrepois K, Chang AL, Phongpreecha T, Michael B, Ellenberger M, Mehmood U, Hotwani A, Nizar A, Kabir F, Wong RJ, Becker M, Berson E, Culos A, De Francesco D, Mataraso S, Ravindra N, Thuraiappah M, Xenochristou M, Stelzer IA, Marić I, Dutta A, Raqib R, Ahmed S, Rahman S, Hasan ASMT, Ali SM, Juma MH, Rahman M, Aktar S, Deb S, Price JT, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Stringer JSA, Gaudilliere B, Snyder MP, Angst MS, Rahman A, Baqui AH, Jehan F, Nisar MI, Vwalika B, Sazawal S, Shaw GM, Stevenson DK, Aghaeepour N. Multiomic signals associated with maternal epidemiological factors contributing to preterm birth in low- and middle-income countries. Science Advances, 2023.
  • Becker M, Nassar H, Espinosa C, Stelzer IA, Feyaerts D, Berson E, Bidoki NH, Chang AL, Saarunya G, Culos A, De Francesco D, Fallahzadeh R, Liu Q, Kim Y, Marić I, Mataraso SJ, Payrovnaziri SN, Phongpreecha T, Ravindra NG, Stanley N, Shome S, Tan Y, Thuraiappah M, Xenochristou M, Xue L, Shaw G, Stevenson D, Angst MS, Gaudilliere B, Aghaeepour N. Large-scale correlation network construction for unraveling the coordination of complex biological systems. Nature Computational Sciences, 2023.
  • Marić I, Contrepois K, Moufarrej MN, Stelzer IA, Feyaerts D, Han X, Tang A, Stanley N, Wong RJ, Traber GM, Ellenberger M, Chang AL, Fallahzadeh R, Nassar H, Becker M, Xenochristou M, Espinosa C, De Francesco D, Ghaemi MS, Costello EK, Culos A, Ling XB, Sylvester KG, Darmstadt GL, Winn VD, Shaw GM, Relman DA, Quake SR, Angst MS, Snyder MP, Stevenson DK, Gaudilliere B, Aghaeepour N. Early prediction and longitudinal modeling of preeclampsia from multiomics. Patterns, 2022.
  • Fallahzadeh R, Verdonk F, Ganio E, Culos A, Stanley N, Marić I, Chang AL, Becker M, Phongpreecha T, Xenochristou M, De Francesco D, Espinosa C, Gao X, Tsai A, Sultan P, Tingle M, Amanatullah DF, Huddleston JI, Goodman SB, Gaudilliere B, Angst MS, Aghaeepour N. Objective Activity Parameters Track Patient-Specific Physical Recovery Trajectories After Surgery and Link With Individual Preoperative Immune States. Annals of Surgery, 2021.
  • Jehan F, Sazawal S, Baqui AH, Nisar MI, Dhingra U, Khanam R, Ilyas M, Dutta A, Mitra DK, Mehmood U, Deb S, Mahmud A, Hotwani A, Ali SM, Rahman S, Nizar A, Ame SM, Moin MI, Muhammad S, Chauhan A, Begum N, Khan W, Das S, Ahmed S, Hasan T, Khalid J, Rizvi SJR, Juma MH, Chowdhury NH, Kabir F, Aftab F, Quaiyum A, Manu A, Yoshida S, Bahl R, Rahman A, Pervin J, Winston J, Musonda P, Stringer JSA, Litch JA, Ghaemi MS, Moufarrej MN, Contrepois K, Chen S, Stelzer IA, Stanley N, Chang AL, Hammad GB, Wong RJ, Liu C, Quaintance CC, Culos A, Espinosa C, Xenochristou M, Becker M, Fallahzadeh R, Ganio E, Tsai AS, Gaudilliere D, Tsai ES, Han X, Ando K, Tingle M, Maric I, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Shaw GM, Stevenson DK, Snyder MP, Quake SR, Angst MS, Gaudilliere B, Aghaeepour N; Alliance for Maternal and Newborn Health Improvement, the Global Alliance to Prevent Prematurity and Stillbirth, and the Prematurity Research Center at Stanford University. Multiomics Characterization of Preterm Birth in Low- and Middle-Income Countries. JAMA Network Open, 2020.
  • Culos A, Tsai AS, Stanley N, Becker M, Ghaemi MS, McIlwain DR, Fallahzadeh R, Tanada A, Nassar H, Espinosa C, Xenochristou M, Ganio E, Peterson L, Han X, Stelzer IA, Ando K, Gaudilliere D, Phongpreecha T, Marić I, Chang AL, Shaw GM, Stevenson DK, Bendall S, Davis KL, Fantl W, Nolan GP, Hastie T, Tibshirani R, Angst MS, Gaudilliere B, Aghaeepour N. Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions. Nature Machine Intelligence, 2020.
  • Stanley N, Stelzer IA, Tsai AS, Fallahzadeh R, Ganio E, Becker M, Phongpreecha T, Nassar H, Ghaemi S, Maric I, Culos A, Chang AL, Xenochristou M, Han X, Espinosa C, Rumer K, Peterson L, Verdonk F, Gaudilliere D, Tsai E, Feyaerts D, Einhaus J, Ando K, Wong RJ, Obermoser G, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. VoPo leverages cellular heterogeneity for predictive modeling of single-cell data. Nature Communications, 2020.
  • Tsai AS, Berry K, Beneyto MM, Gaudilliere D, Ganio EA, Culos A, Ghaemi MS, Choisy B, Djebali K, Einhaus JF, Bertrand B, Tanada A, Stanley N, Fallahzadeh R, Baca Q, Quach LN, Osborn E, Drag L, Lansberg MG, Angst MS, Gaudilliere B, Buckwalter MS, Aghaeepour N. A year-long immune profile of the systemic response in acute stroke survivors, Brain. 2019.
  • Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics, 2019.
  • Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B. An immune clock of human pregnancy. Science Immunology, 2017.

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