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. 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.
  2. 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.
  3. 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; :. doi: 10.1158/1940-6207.CAPR-22-0244. PubMed PMID:36049217 .
  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. medRxiv. 2022; :. doi: 10.1101/2022.08.10.22277939. PubMed PMID:35982662 PubMed Central PMC9387152.
  5. 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.
  6. 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 .
  7. 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.
  8. 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.
  9. 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.
  10. 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. 2022; :. doi: 10.1038/s41390-022-02093-w. PubMed PMID:35595912 .
  11. 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.
  12. 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.
  13. 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.
  14. Horgusluoglu, E, Neff, R, Song, WM, Wang, M, Wang, Q, Arnold, M et al.. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer's disease. Alzheimers Dement. 2022;18 (6):1260-1278. doi: 10.1002/alz.12468. PubMed PMID:34757660 PubMed Central PMC9085975.
  15. Marullo, R, Castro, M, Yomtoubian, S, Calvo-Vidal, MN, Revuelta, MV, Krumsiek, J et al.. The metabolic adaptation evoked by arginine enhances the effect of radiation in brain metastases. Sci Adv. 2021;7 (45):eabg1964. doi: 10.1126/sciadv.abg1964. PubMed PMID:34739311 PubMed Central PMC8570607.
  16. Chetnik, K, Benedetti, E, Gomari, DP, Schweickart, A, Batra, R, Buyukozkan, M et al.. maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines. Bioinformatics. 2021; :. doi: 10.1093/bioinformatics/btab741. PubMed PMID:34694386 PubMed Central PMC8796365.
  17. Aliluev, A, Tritschler, S, Sterr, M, Oppenländer, L, Hinterdobler, J, Greisle, T et al.. Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice. Nat Metab. 2021;3 (9):1202-1216. doi: 10.1038/s42255-021-00458-9. PubMed PMID:34552271 PubMed Central PMC8458097.
  18. Buyukozkan, M, Suhre, K, Krumsiek, J. SGI: Automatic clinical subgroup identification in omics datasets. Bioinformatics. 2021; :. doi: 10.1093/bioinformatics/btab656. PubMed PMID:34529048 PubMed Central PMC8723155.
  19. Whalen, W, Buyukozkan, M, Moore, B, Moon, JS, Dela Cruz, CS, Martinez, FJ et al.. Association of circulating cell-free double-stranded DNA and metabolic derangements in idiopathic pulmonary fibrosis. Thorax. 2022;77 (2):186-190. doi: 10.1136/thoraxjnl-2021-217315. PubMed PMID:34521729 PubMed Central PMC8758529.
  20. Calvo-Vidal, MN, Zamponi, N, Krumsiek, J, Stockslager, MA, Revuelta, MV, Phillip, JM et al.. Oncogenic HSP90 Facilitates Metabolic Alterations in Aggressive B-cell Lymphomas. Cancer Res. 2021;81 (20):5202-5216. doi: 10.1158/0008-5472.CAN-21-2734. PubMed PMID:34479963 PubMed Central PMC8530929.
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