Jan Krumsiek, Ph.D.

Assistant Professor of Physiology and Biophysics

  • Assistant Professor of Computational Genomics in Computational Biomedicine in the Institute for Computational Biomedicine

646-962-4152

1305 York Avenue, Room Y-13.15A
New York, NY 10021

Lab website: https://krumsieklab.org

Techniques

Research Areas

Member of:

Research Summary:

Dr. Krumsiek develops and applies novel methods for the analysis of metabolomics and multi-omics data. This includes pathway-based methods, computational simulations, and machine learning techniques. As special focus of his work is the inference of metabolic networks from data, providing a condition-specific, unbiased in vivo view on metabolism. He has mainly published on etiology and risk prediction in the field of diabetes and obesity research, and is now transitioning to novel projects in the cancer research. The lab elucidates metabolic associations of drug treatment and clinical parameters in different types of cancer.

https://pubs.acs.org/doi/abs/10.1021/pr501130a

Recent Publications:

  1. Schweickart, A, Batra, R, Neth, BJ, Martino, C, Shenhav, L, Zhang, AR et al.. Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease. NPJ Metab Health Dis. 2024;2 (1):15. doi: 10.1038/s44324-024-00016-3. PubMed PMID:38962750 PubMed Central PMC11216994.
  2. Harada, M, Adam, J, Covic, M, Ge, J, Brandmaier, S, Muschet, C et al.. Bidirectional modulation of TCA cycle metabolites and anaplerosis by metformin and its combination with SGLT2i. Cardiovasc Diabetol. 2024;23 (1):199. doi: 10.1186/s12933-024-02288-x. PubMed PMID:38867314 PubMed Central PMC11170891.
  3. Houerbi, N, Kim, J, Overbey, EG, Batra, R, Schweickart, A, Patras, L et al.. Secretome profiling reveals acute changes in oxidative stress, brain homeostasis, and coagulation following short-duration spaceflight. Nat Commun. 2024;15 (1):4862. doi: 10.1038/s41467-024-48841-w. PubMed PMID:38862464 PubMed Central PMC11166969.
  4. Overbey, EG, Kim, J, Tierney, BT, Park, J, Houerbi, N, Lucaci, AG et al.. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank. Nature. 2024; :. doi: 10.1038/s41586-024-07639-y. PubMed PMID:38862028 .
  5. Pandey, RS, Arnold, M, Batra, R, Krumsiek, J, Kotredes, KP, Garceau, D et al.. Metabolomics profiling reveals distinct, sex-specific signatures in serum and brain metabolomes in mouse models of Alzheimer's disease. Alzheimers Dement. 2024;20 (6):3987-4001. doi: 10.1002/alz.13851. PubMed PMID:38676929 PubMed Central PMC11180854.
  6. Sanidad, KZ, Rager, SL, Carrow, HC, Ananthanarayanan, A, Callaghan, R, Hart, LR et al.. Gut bacteria-derived serotonin promotes immune tolerance in early life. Sci Immunol. 2024;9 (93):eadj4775. doi: 10.1126/sciimmunol.adj4775. PubMed PMID:38489352 .
  7. Noch, EK, Palma, L, Yim, I, Bullen, N, Barnett, D, Walsh, A et al.. Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production. Proc Natl Acad Sci U S A. 2024;121 (8):e2317343121. doi: 10.1073/pnas.2317343121. PubMed PMID:38359293 PubMed Central PMC10895255.
  8. Arnold, M, Buyukozkan, M, Doraiswamy, PM, Nho, K, Wu, T, Gudnason, V et al.. Individual bioenergetic capacity as a potential source of resilience to Alzheimer's disease. medRxiv. 2024; :. doi: 10.1101/2024.01.23.23297820. PubMed PMID:38313266 PubMed Central PMC10836119.
  9. Pandey, RS, Arnold, M, Batra, R, Krumsiek, J, Kotredes, KP, Garceau, D et al.. Metabolomics profiling reveals distinct, sex-specific signatures in the serum and brain metabolomes in the mouse models of Alzheimer's disease. bioRxiv. 2023; :. doi: 10.1101/2023.12.22.573059. PubMed PMID:38187571 PubMed Central PMC10769366.
  10. Schweickart, A, Batra, R, Neth, BJ, Martino, C, Shenhav, L, Zhang, AR et al.. A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis. medRxiv. 2023; :. doi: 10.1101/2023.11.27.23298990. PubMed PMID:38076824 PubMed Central PMC10705656.
  11. Benedetti, E, Chetnik, K, Flynn, T, Barbieri, CE, Scherr, DS, Loda, M et al.. Plasma metabolomics profiling of 580 patients from an Early Detection Research Network prostate cancer cohort. Sci Data. 2023;10 (1):830. doi: 10.1038/s41597-023-02750-7. PubMed PMID:38007532 PubMed Central PMC10676366.
  12. Liu, S, Benito-Martin, A, Pelissier Vatter, FA, Hanif, SZ, Liu, C, Bhardwaj, P et al.. Breast adipose tissue-derived extracellular vesicles from obese women alter tumor cell metabolism. EMBO Rep. 2023;24 (12):e57339. doi: 10.15252/embr.202357339. PubMed PMID:37929643 PubMed Central PMC10702795.
  13. Jo, T, Kim, J, Bice, P, Huynh, K, Wang, T, Arnold, M et al.. Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data. EBioMedicine. 2023;97 :104820. doi: 10.1016/j.ebiom.2023.104820. PubMed PMID:37806288 PubMed Central PMC10579282.
  14. Batra, R, Krumsiek, J, Wang, X, Allen, M, Blach, C, Kastenmüller, G et al.. Comparative brain metabolomics reveals shared and distinct metabolic alterations in Alzheimer's disease and progressive supranuclear palsy. medRxiv. 2023; :. doi: 10.1101/2023.07.25.23293055. PubMed PMID:37546878 PubMed Central PMC10402214.
  15. Benedetti, E, Liu, EM, Tang, C, Kuo, F, Buyukozkan, M, Park, T et al.. A multimodal atlas of tumour metabolism reveals the architecture of gene-metabolite covariation. Nat Metab. 2023;5 (6):1029-1044. doi: 10.1038/s42255-023-00817-8. PubMed PMID:37337120 PubMed Central PMC10290959.
  16. Amin, N, Liu, J, Bonnechere, B, MahmoudianDehkordi, S, Arnold, M, Batra, R et al.. Interplay of Metabolome and Gut Microbiome in Individuals With Major Depressive Disorder vs Control Individuals. JAMA Psychiatry. 2023;80 (6):597-609. doi: 10.1001/jamapsychiatry.2023.0685. PubMed PMID:37074710 PubMed Central PMC10116384.
  17. Gomari, D, Achkar, IW, Benedetti, E, Tabling, J, Halama, A, Krumsiek, J et al.. piTracer - Automatic reconstruction of molecular cascades for the identification of synergistic drug targets. bioRxiv. 2023; :. doi: 10.1101/2023.04.08.535933. PubMed PMID:37066188 PubMed Central PMC10104160.
  18. Liu, S, Benito-Martin, A, Pelissier Vatter, FA, Hanif, SZ, Liu, C, Bhardwaj, P et al.. Breast adipose tissue-derived extracellular vesicles from women with obesity stimulate mitochondrial-induced dysregulated tumor cell metabolism. bioRxiv. 2023; :. doi: 10.1101/2023.02.08.527715. PubMed PMID:36798307 PubMed Central PMC9934680.
  19. Batra, R, Uni, R, Akchurin, OM, Alvarez-Mulett, S, Gómez-Escobar, LG, Patino, E et al.. Urine-based multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. Mol Med. 2023;29 (1):13. doi: 10.1186/s10020-023-00609-6. PubMed PMID:36703108 PubMed Central PMC9879238.
  20. Buyukozkan, M, Benedetti, E, Krumsiek, J. rox: A Statistical Model for Regression with Missing Values. Metabolites. 2023;13 (1):. doi: 10.3390/metabo13010127. PubMed PMID:36677052 PubMed Central PMC9861384.
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