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


Techniques

Research Areas


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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. Kindt, A, Kraus, Y, Rasp, D, Foerster, KM, Ahmidi, N, Flemmer, AW et al.. Improved Macro- and Micronutrient Supply for Favorable Growth and Metabolomic Profile with Standardized Parenteral Nutrition Solutions for Very Preterm Infants. Nutrients. 2022;14 (19):. doi: 10.3390/nu14193912. PubMed PMID:36235563 PubMed Central PMC9572167.
  16. Baloni, P, Arnold, M, Buitrago, L, Nho, K, Moreno, H, Huynh, K et al.. Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease. Commun Biol. 2022;5 (1):1074. doi: 10.1038/s42003-022-04011-6. PubMed PMID:36209301 PubMed Central PMC9547905.
  17. Batra, R, Whalen, W, Alvarez-Mulett, S, Gomez-Escobar, LG, Hoffman, KL, Simmons, W et al.. Multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. PLoS Pathog. 2022;18 (9):e1010819. doi: 10.1371/journal.ppat.1010819. PubMed PMID:36121875 PubMed Central PMC9484674.
  18. Price, DR, Benedetti, E, Krumsiek, J. Authors' Reply. Am J Pathol. 2022;192 (9):1337-1338. doi: 10.1016/j.ajpath.2022.06.014. PubMed PMID:36064256 PubMed Central PMC9439708.
  19. Ferrara, CR, Bai, JDK, McNally, EM, Putzel, GG, Zhou, XK, Wang, H et al.. Microbes Contribute to Chemopreventive Efficacy, Intestinal Tumorigenesis, and the Metabolome. Cancer Prev Res (Phila). 2022;15 (12):803-814. doi: 10.1158/1940-6207.CAPR-22-0244. PubMed PMID:36049217 .
  20. 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. medRxiv. 2022; :. doi: 10.1101/2022.08.10.22277939. PubMed PMID:35982662 PubMed Central PMC9387152.
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