Bio

Jennifer Sequoia, MD, PhD is an Instructor in Neonatology at Stanford University. She completed her Neonatology Fellowship and Pediatrics Residency (Research Track) at Stanford. Prior to coming to Stanford she received her undergraduate and master's degrees from University of California, San Diego and her MD and PhD degrees from The University of Chicago. As faculty at Stanford, she is developing a research program to understand how endogenous cannabinoids impact preeclampsia and other perinatal diseases. She is broadly interested in how lipids mediate inflammatory programs and is working to develop new molecular tools to study lipids in their native environments.

Clinical Focus

  • Neonatology
  • Neonatal-Perinatal Medicine

Academic Appointments

Professional Education

  • Fellowship: Stanford University Neonatology Fellowship (2025) CA
  • Board Certification: American Board of Pediatrics, Pediatrics (2023)
  • Residency: Stanford University Pediatric Residency at Lucile Packard Children's Hospital (2022) CA
  • Medical Education: The University of Chicago Pritzker School of Medicine (2019) IL
  • MD, The University of Chicago - Pritzker School of Medicine (2019)
  • PhD, The University of Chicago, Immunology (2017)
  • MS, University of California, San Diego, Chemistry (2010)
  • BS, University of California, San Diego, Microbiology (2008)

Contact

  • Academic
    j3jacobs@stanford.edu
    University - Other Teaching/Research Department: Pediatrics - Neonatology Position: Instructor
  • Clinical (Primary)  Pediatric Neonatology 725 Welch Rd MC 5804 Palo Alto, CA 94304 (650) 725-8351 (fax)

Additional Clinical Info

Additional Info

  • Mail Code: 5660

All Publications

  • Identification of bacteriophage DNA in human umbilical cord blood. JCI insight Sequoia, J. A., Haddock, N. L., Gay, P. M., Barkal, L. J., Narasimhan, P., Martinez, N., Winn, V. D., Bollyky, P. L. 2025; 10 (13)

    Abstract

    Bacteriophages, viruses that parasitize bacteria, are abundant in the human microbiome and may influence human health, in part, through their interactions with bacterial hosts. Whether endogenous bacteriophages or their products are vertically transmitted from mother to fetus during human pregnancy is not known. Here, we searched for bacteriophage sequences from five bacteriophage databases (474,031 total sequences) in cell-free DNA (cfDNA) of paired maternal and umbilical cord blood samples from two independent cohorts. First, we sequenced cfDNA from 10 pairs of maternal and cord blood samples, including four pairs affected by preeclampsia. We validated our findings in a previously published dataset of 62 paired maternal and cord blood samples, including 43 pairs from preterm or chorioamnionitis-affected deliveries. We identified 94 and 596 bacteriophage sequences in maternal and cord blood cfDNA samples from the first and second cohort, respectively. We identified 58 phage sequences across maternal-infant dyads and 581 phage sequences that were unique to a single sample. We did not identify any phage sequences consistently associated with preeclampsia, preterm, or chorioamnionitis-affected samples. This study demonstrated the presence of bacteriophage DNA in human cord blood at birth, providing evidence that the human fetus is exposed to bacteriophage DNA in utero.

    View details for DOI 10.1172/jci.insight.183123

    View details for PubMedID 40626364

  • Author Correction: AI-guided precision parenteral nutrition for neonatal intensive care units. Nature medicine Phongpreecha, T., Ghanem, M., Reiss, J. D., Oskotsky, T. T., Mataraso, S. J., De Francesco, D., Reincke, S. M., Espinosa, C., Chung, P., Ng, T., Costello, J. M., Sequoia, J. A., Razdan, S., Xie, F., Berson, E., Kim, Y., Seong, D., Szeto, M. Y., Myers, F., Gu, H., Feister, J., Verscaj, C. P., Rose, L. A., Sin, L. W., Oskotsky, B., Roger, J., Shu, C. H., Shome, S., Yang, L. K., Tan, Y., Levitte, S., Wong, R. J., Gaudillière, B., Angst, M. S., Montine, T. J., Kerner, J. A., Keller, R. L., Shaw, G. M., Sylvester, K. G., Fuerch, J., Chock, V., Gaskari, S., Stevenson, D. K., Sirota, M., Prince, L. S., Aghaeepour, N. 2025

    View details for DOI 10.1038/s41591-025-03691-x

    View details for PubMedID 40205201

  • AI-guided precision parenteral nutrition for neonatal intensive care units. Nature medicine Phongpreecha, T., Ghanem, M., Reiss, J. D., Oskotsky, T., Mataraso, S. J., De Francesco, D., Reincke, S. M., Espinosa, C., Chung, P., Ng, T., Costello, J. M., Sequoia, J. A., Razdan, S., Xie, F., Berson, E., Kim, Y., Seong, D., Szeto, M. Y., Myers, F., Gu, H., Feister, J., Verscaj, C. P., Rose, L. A., Sin, L. W., Oskotsky, B., Roger, J., Shu, C. H., Shome, S., Yang, L. K., Tan, Y., Levitte, S., Wong, R. J., Gaudillière, B., Angst, M. S., Montine, T. J., Kerner, J. A., Keller, R. L., Shaw, G. M., Sylvester, K. G., Fuerch, J., Chock, V., Gaskari, S., Stevenson, D. K., Sirota, M., Prince, L. S., Aghaeepour, N. 2025

    Abstract

    One in ten neonates are admitted to neonatal intensive care units, highlighting the need for precise interventions. However, the application of artificial intelligence (AI) in guiding neonatal care remains underexplored. Total parenteral nutrition (TPN) is a life-saving treatment for preterm neonates; however, implementation of the therapy in its current form is subjective, error-prone and resource-consuming. Here, we developed TPN2.0-a data-driven approach that optimizes and standardizes TPN using information collected routinely in electronic health records. We assembled a decade of TPN compositions (79,790 orders; 5,913 patients) at Stanford to train TPN2.0. In addition to internal validation, we also validated our model in an external cohort (63,273 orders; 3,417 patients) from a second hospital. Our algorithm identified 15 TPN formulas that can enable a precision-medicine approach (Pearson's R = 0.94 compared to experts), increasing safety and potentially reducing cost. A blinded study (n = 192) revealed that physicians rated TPN2.0 higher than current best practice. In patients with high disagreement between the actual prescriptions and TPN2.0, standard prescriptions were associated with increased morbidities (for example, odds ratio = 3.33; P value = 0.0007 for necrotizing enterocolitis), while TPN2.0 recommendations were linked to reduced risk. Finally, we demonstrated that TPN2.0 employing a transformer architecture enabled guideline-adhering, physician-in-the-loop recommendations that allow collaboration between the care team and AI.

    View details for DOI 10.1038/s41591-025-03601-1

    View details for PubMedID 40133525

    View details for PubMedCentralID 10593864

  • Identification of bacteriophage DNA in human umbilical cord blood Sequoia, J., Haddock, N., Gay, P., Barkal, L., Winn, V., Bollyky, P. AMER ASSOC IMMUNOLOGISTS. 2024

    View details for DOI 10.4049/jimmunol.212.supp.0757.6681

    View details for Web of Science ID 001369592500011

  • Ezh2 Represses Transcription of Innate Lymphoid Genes in B Lymphocyte Progenitors and Maintains the B-2 Cell Fate JOURNAL OF IMMUNOLOGY Jacobsen, J. A., Bartom, E. T., Sigvardsson, M., Kee, B. L. 2020; 204 (7): 1760-1769

    Abstract

    Lymphocyte lineage specification and commitment requires the activation of lineage-specific genes and repression of alternative lineage genes, respectively. The mechanisms governing alternative lineage gene repression and commitment in lymphocytes are largely unknown. In this study, we demonstrate that Ezh2, which represses gene expression through methylation of histone 3 lysine 27, was essential for repression of numerous genes, including genes encoding innate lymphocyte transcription factors, specifically in murine B lymphocyte progenitors, but these cells maintained their B lymphocyte identity. However, adult Ezh2-deficient B lymphocytes expressed Lin28b, which encodes an RNA-binding protein associated with fetal hematopoietic gene expression programs, and these cells acquired a fetal B-1 lymphocyte phenotype in vitro and in vivo. Therefore, Ezh2 coordinates the repression of multiple gene programs in B lymphocytes and maintains the adult B-2 cell fate.

    View details for DOI 10.4049/jimmunol.1901188

    View details for Web of Science ID 000521730100007

    View details for PubMedID 32094206

    View details for PubMedCentralID PMC7344269

  • Peripheral T-Cell Lymphomas are Characterized by Transcriptionally Active FOXO3 Parilla, M., Leukam, M., Kadri, S., Ritterhouse, L., Segal, J., Jacobsen, J., Krunic, M., Gurbuxani, S. NATURE PUBLISHING GROUP. 2020: 1361-1362

    View details for Web of Science ID 000518328803130

  • Peripheral T-Cell Lymphomas are Characterized by Transcriptionally Active FOXO3 Parilla, M., Leukam, M., Kadri, S., Ritterhouse, L., Segal, J., Jacobsen, J., Krunic, M., Gurbuxani, S. SPRINGERNATURE. 2020: 1361-1362

    View details for Web of Science ID 000518328903130

  • EZH2 Regulates the Developmental Timing of Effectors of the Pre-Antigen Receptor Checkpoints JOURNAL OF IMMUNOLOGY Jacobsen, J. A., Woodard, J., Mandal, M., Clark, M. R., Bartom, E. T., Sigvardsson, M., Kee, B. L. 2017; 198 (12): 4682-4691

    Abstract

    The histone methyltransferase EZH2 is required for B and T cell development; however, the molecular mechanisms underlying this requirement remain elusive. In a murine model of lymphoid-specific EZH2 deficiency we found that EZH2 was required for proper development of adaptive, but not innate, lymphoid cells. In adaptive lymphoid cells EZH2 prevented the premature expression of Cdkn2a and the consequent stabilization of p53, an effector of the pre-Ag receptor checkpoints. Deletion of Cdkn2a in EZH2-deficient lymphocytes prevented p53 stabilization, extended lymphocyte survival, and restored differentiation resulting in the generation of mature B and T lymphocytes. Our results uncover a crucial role for EZH2 in adaptive lymphocytes to control the developmental timing of effectors of the pre-Ag receptor checkpoints.

    View details for DOI 10.4049/jimmunol.1700319

    View details for Web of Science ID 000405271300015

    View details for PubMedID 28490575

    View details for PubMedCentralID PMC5527689

  • EZH2 regulates cell cycle and survival in B and T lymphocyte progenitors Jacobsen, J., Woodard, J., Kee, B. L. AMER ASSOC IMMUNOLOGISTS. 2016

    View details for Web of Science ID 000380288300210

  • EZH2 in B lymphocyte commitment Jacobsen, J., Kee, B. AMER ASSOC IMMUNOLOGISTS. 2015

    View details for Web of Science ID 000379404500227

  • Identifying Chelators for Metalloprotein Inhibitors Using a Fragment-Based Approach JOURNAL OF MEDICINAL CHEMISTRY Jacobsen, J. A., Fullagar, J. L., Miller, M. T., Cohen, S. M. 2011; 54 (2): 591-602

    Abstract

    Fragment-based lead design (FBLD) has been used to identify new metal-binding groups for metalloenzyme inhibitors. When screened at 1 mM, a chelator fragment library (CFL-1.1) of 96 compounds produced hit rates ranging from 29% to 43% for five matrix metalloproteases (MMPs), 24% for anthrax lethal factor (LF), 49% for 5-lipoxygenase (5-LO), and 60% for tyrosinase (TY). The ligand efficiencies (LE) of the fragment hits are excellent, in the range of 0.4-0.8 kcal/mol. The MMP enzymes all generally elicit the same chelators as hits from CFL-1.1; however, the chelator fragments that inhibit structurally unrelated metalloenzymes (LF, 5-LO, TY) vary considerably. To develop more advanced hits, one hit from CFL-1.1, 8-hydroxyquinoline, was elaborated at four different positions around the ring system to generate new fragments. 8-Hydroxyquinoline fragments substituted at either the 5- or 7-positions gave potent hits against MMP-2, with IC(50) values in the low micromolar range. The 8-hydroxyquinoline represents a promising new chelator scaffold for the development of MMP inhibitors that was discovered by use of a metalloprotein-focused chelator fragment library.

    View details for DOI 10.1021/jm101266s

    View details for Web of Science ID 000286306400015

    View details for PubMedID 21189019

    View details for PubMedCentralID PMC3024453

  • Chelator Fragment Libraries for Targeting Metalloproteinases CHEMMEDCHEM Agrawal, A., Johnson, S. L., Jacobsen, J. A., Miller, M. T., Chen, L., Pellecchia, M., Cohen, S. M. 2010; 5 (2): 195-199

    View details for DOI 10.1002/cmdc.200900516

    View details for Web of Science ID 000274538600004

    View details for PubMedID 20058293

    View details for PubMedCentralID PMC2825879

  • To bind zinc or not to bind zinc: An examination of innovative approaches to improved metalloproteinase inhibition BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH Jacobsen, J. A., Jourden, J. L., Miller, M. T., Cohen, S. M. 2010; 1803 (1): 72-94

    Abstract

    This short review highlights some recent advances in matrix metalloproteinase inhibitor (MMPi) design and development. Three distinct approaches to improved MMP inhibition are discussed: (1) the identification and investigation of novel zinc-binding groups (ZBGs), (2) the study of non-zinc-binding MMPi, and (3) mechanism-based MMPi that form covalent adducts with the protein. Each of these strategies is discussed and their respective advantages and remaining challenges are highlighted. The studies discussed here bode well for the development of ever more selective, potent, and well-tolerated MMPi for treating several important disease pathologies.

    View details for DOI 10.1016/j.bbamcr.2009.08.006

    View details for Web of Science ID 000275508500007

    View details for PubMedID 19712708

  • Hydrogen-bond rigidified BODIPY dyes DALTON TRANSACTIONS Jacobsen, J. A., Stork, J. R., Magde, D., Cohen, S. M. 2010; 39 (3): 957-962

    Abstract

    Boron difluoride adducts of diamidodipyrromethenes have been synthesized and characterized. The compounds represent a new group of the BODIPY family of fluorescent dyes. X-ray crystallography and solution (19)F NMR experiments show that a persistent hydrogen bond is formed between the boron-bound fluoride groups and the peripheral amide substituents. The modular synthesis of these compounds and their robust photophysical properties suggest that they may be useful compounds for materials and biological photochemical applications.

    View details for DOI 10.1039/b921772j

    View details for Web of Science ID 000272992500034

    View details for PubMedID 20066240

  • Effects of Novel Semiselective Matrix Metalloproteinase Inhibitors on Ex Vivo Cardiac Structure-Function JOURNAL OF CARDIOVASCULAR PHARMACOLOGY Romero-Perez, D., Agrawal, A., Jacobsen, J., Yan, Y., Thomas, R., Cohen, S., Villarreal, F. 2009; 53 (6): 452-461

    Abstract

    The purpose of this study was to evaluate the ability of novel semiselective matrix metalloproteinase inhibitors (MMPI) to protect myocardial structure-function in the setting of ischemia-reperfusion injury. For this purpose, an isolated rat model of myocardial stunning and infarction was used. Isolated hearts were subjected to 20-30 minutes of global no-flow ischemia and 30-minute reperfusion. Myocardial performance was assessed as the product of the heart rate and left ventricular developed pressure (rate-pressure product, RPP). Coronary flow rates, ventricular weights, indicators of muscle (troponin I), and fibrillar collagen damage (collagen opalation) were measured. Four MMPI were tested: 2 non-hydroxamate, semiselective inhibitors (PY-2 and 1,2-HOPO-2) and 2 broad-spectrum inhibitors (PD166793 and CGS27023A). The non-hydroxamate, semiselective inhibitors were shown to be nontoxic in cocultures of cardiac cells. Results indicate that semiselective inhibitors (in particular 1,2-HOPO-2) yield improved cardiac performance (approximately 23% higher RPP vs. controls) and coronary flow rates (approximately 22%), reducing muscle (approximately 25%) and fibrillar collagen damage (approximately 60%). Evidence suggests the involvement of matrix metalloproteinase-2 in these actions. Interestingly, broad-spectrum inhibitors only show modest improvement (approximately 8% higher RPP vs. controls) without affecting the other measured parameters. In conclusion, semiselective MMPI can act as cardioprotectors in isolated perfused rat hearts. Protection is observed in all structural components of the myocardium translating into improved contractile function. Based on these findings, non-hydroxamate, semiselective MMPI warrant further studies as to their ability to protect ischemic myocardium in the in vivo setting.

    View details for DOI 10.1097/FJC.0b013e3181a6aa83

    View details for Web of Science ID 000267456500005

    View details for PubMedID 19365278

    View details for PubMedCentralID PMC2835692

  • Thioamide Hydroxypyrothiones Supersede Amide Hydroxypyrothiones in Potency against Anthrax Lethal Factor JOURNAL OF MEDICINAL CHEMISTRY Agrawal, A., de Oliveira, C. A., Cheng, Y., Jacobsen, J. A., McCammon, J. A., Cohen, S. M. 2009; 52 (4): 1063-1074

    Abstract

    Anthrax lethal factor (LF) is a critical virulence factor in the pathogenesis of anthrax. A structure-activity relationship (SAR) of potential lethal factor inhibitors (LFi) is presented in which the zinc-binding group (ZBG), linker, and backbone moieties for a series of hydroxypyrone-based compounds were systematically varied. It was found that hydroxypyrothione ZBGs generate more potent inhibitors than hydroxypyrone ZBGs. Furthermore, coupling the hydroxypyrothione to a backbone group via a thioamide bond improves potency when compared to an amide linker. QM/MM studies show that the thioamide bond in these inhibitors allows for the formation of two additional hydrogen bonds with the protein active site. In both types of hydroxypyrothione compounds, ligand efficiencies of 0.29-0.54 kcal mol(-1) per heavy atom were achieved. The results highlight the need for a better understanding to optimize the interplay between the ZBG, linker, and backbone to get improved LFi.

    View details for DOI 10.1021/jm8013212

    View details for Web of Science ID 000263530200018

    View details for PubMedID 19170530

    View details for PubMedCentralID PMC2698031

  • Zinc-binding groups modulate selective inhibition of MMPs CHEMMEDCHEM Agrawal, A., Romero-Perez, D., Jacobsen, J. A., Villarreal, F. J., Cohen, S. M. 2008; 3 (5): 812-820

    Abstract

    The need for selective matrix metalloproteinase (MMP) inhibition is of interest because of the range of pathologies mediated by different MMP isoforms. The development of more selective MMP inhibitors (MMPi) may help to overcome some of the undesired side effects that have hindered the clinical success of these compounds. In an effort to devise new approaches to selective inhibitors, herein we describe several novel MMPi and show that their selectivity is dependent on the nature of the zinc-binding group (ZBG). This is in contrast to most current MMPi, which obtain isoform selectivity solely from the peptidomimetic backbone portion of the compound. In the present study, six different hydroxypyrone and hydroxypyridinone ZBGs were appended to a common biphenyl backbone and the inhibition efficiency of each inhibitor was determined in vitro (IC(50) values) against MMP-1, -2, -3, -7, -8, -9, -12, and -13. The results show that the selectivity profile of each inhibitor is different as a result of the various ZBGs. Computational modeling studies were used to explain some trends in the observed selectivity profiles. To assess the importance of the ZBG in a biological model, two of the semiselective, potent MMPi (and one control) were evaluated using an isolated perfused rat heart system. Hearts were subjected to ischemia reperfusion injury, and recovery of contractile function was examined. In this model, only one of the two MMPi showed significant and sustained heart recovery, demonstrating that the choice of ZBG can have a significant effect in a relevant pathophysiological endpoint.

    View details for DOI 10.1002/cmdc.200700290

    View details for Web of Science ID 000256183300016

    View details for PubMedID 18181119

    View details for PubMedCentralID PMC2836234