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. 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; :. doi: 10.1001/jamapsychiatry.2023.0685. PubMed PMID:37074710 PubMed Central PMC10116384.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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 .
  11. 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.
  12. Batra, R, Whalen, W, Alvarez-Mulett, S, Gómez-Escobar, LG, Hoffman, KL, Simmons, W et al.. Multi-omic comparative analysis of COVID-19 and bacterial sepsis-induced ARDS. medRxiv. 2022; :. doi: 10.1101/2022.05.16.22274587. PubMed PMID:35982655 PubMed Central PMC9387161.
  13. Batra, R, Arnold, M, Wörheide, MA, Allen, M, Wang, X, Blach, C et al.. The landscape of metabolic brain alterations in Alzheimer's disease. Alzheimers Dement. 2022; :. doi: 10.1002/alz.12714. PubMed PMID:35829654 PubMed Central PMC9837312.
  14. Gomari, DP, Schweickart, A, Cerchietti, L, Paietta, E, Fernandez, H, Al-Amin, H et al.. Variational autoencoders learn transferrable representations of metabolomics data. Commun Biol. 2022;5 (1):645. doi: 10.1038/s42003-022-03579-3. PubMed PMID:35773471 PubMed Central PMC9246987.
  15. Buyukozkan, M, Alvarez-Mulett, S, Racanelli, AC, Schmidt, F, Batra, R, Hoffman, KL et al.. Integrative metabolomic and proteomic signatures define clinical outcomes in severe COVID-19. iScience. 2022;25 (7):104612. doi: 10.1016/j.isci.2022.104612. PubMed PMID:35756895 PubMed Central PMC9212983.
  16. Ganly, I, Liu, EM, Kuo, F, Makarov, V, Dong, Y, Park, J et al.. Mitonuclear genotype remodels the metabolic and microenvironmental landscape of Hürthle cell carcinoma. Sci Adv. 2022;8 (25):eabn9699. doi: 10.1126/sciadv.abn9699. PubMed PMID:35731870 PubMed Central PMC9216518.
  17. Kindt, ASD, Förster, KM, Cochius-den Otter, SCM, Flemmer, AW, Hauck, SM, Flatley, A et al.. Validation of disease-specific biomarkers for the early detection of bronchopulmonary dysplasia. Pediatr Res. 2023;93 (3):625-632. doi: 10.1038/s41390-022-02093-w. PubMed PMID:35595912 PubMed Central PMC9988689.
  18. Price, DR, Benedetti, E, Hoffman, KL, Gomez-Escobar, L, Alvarez-Mulett, S, Capili, A et al.. Angiopoietin 2 Is Associated with Vascular Necroptosis Induction in Coronavirus Disease 2019 Acute Respiratory Distress Syndrome. Am J Pathol. 2022;192 (7):1001-1015. doi: 10.1016/j.ajpath.2022.04.002. PubMed PMID:35469796 PubMed Central PMC9027298.
  19. Suhre, K, Sarwath, H, Engelke, R, Sohail, MU, Cho, SJ, Whalen, W et al.. Identification of Robust Protein Associations With COVID-19 Disease Based on Five Clinical Studies. Front Immunol. 2021;12 :781100. doi: 10.3389/fimmu.2021.781100. PubMed PMID:35145507 PubMed Central PMC8821526.
  20. Rendeiro, AF, Vorkas, CK, Krumsiek, J, Singh, HK, Kapadia, SN, Cappelli, LV et al.. Metabolic and Immune Markers for Precise Monitoring of COVID-19 Severity and Treatment. Front Immunol. 2021;12 :809937. doi: 10.3389/fimmu.2021.809937. PubMed PMID:35095900 PubMed Central PMC8790058.
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