Our lab is located at the Department of Medical Biosciences, Umeå University and is affiliated with SciLifeLab. We are part of the national program for data-driven life science (DDLS), funded generously by the Knut and Alice Wallenberg Foundation. Our lab aims to merge machine learning and mechanistic computational models with patient data to create clinically predictive computational models for cancer. We are a computational biology lab with a foot in the wet-lab.

Current Team

C_Erdem Cemal Erdem
Role: PI
Education:
PhD, University of Pittsburgh & Carnegie Mellon University
MSc, Koc University
BSc, Middle East Technical University
Links: LinkedIn / Google Scholar / Lab GitHub


bogus This could be "You"
Role: PhD student
Education:
Any university in the universe
Links:
You should at least have google scholar!

Check University careers page for the appplication!




Lab Alumni

...

Cemal Erdem
Assistant Professor and DDLS Fellow
Department of Medical Biosciences, Umeå University
SciLifeLab and Wallenberg National Program for Data-Driven Life Science

Mailing address:
By 6M, Sjukhusområdet
Umeå Universitet, 901 85 Umeå

Email: cemal.erdem@umu.se

Peer-reviewed Publications

* denotes corresponding authorship

  1. (Preprint) Mutsuddy A, Huggins JR, Amrit A, Erdem C, Calhoun JC, Birtwistle MR* (2024). Mechanistic modeling of cell viability assays with in silico lineage tracing. bioRxiv. 2024--08. doi.org/10.1101/2024.08.23.609433

  2. Erdem C, Gross SM, Heiser LM*, Birtwistle MR* (2023). MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms. Nature Communications. 14, 3991.

  3. Erdem C*, Birtwistle MR* (2023). MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets. Frontiers in Systems Biology. 3. Invited special issue paper.

  4. Erdem C, Mutsuddy A, Salim M, Cook D, Hobbs N, Birtwistle MR* (2023). Computational speed-up of large-scale, single-cell model simulations via a fully-integrated SBML-based format. Bioinformatics Advances. 3 (1).

  5. Erdem C*, Mutsuddy A, Bensman EM, Dodd W, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR* (2022). A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications. 13, 3555.

  6. Gross SM, Dane MA, Smith RL, Devlin K, McLean I, Derrick D, Mills C, Subramanian K, London AB, Torre D, Evangelista J, Clarke D, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn D, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe J, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM* (2022). A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Communications Biology (Nature). 5, 1066.

  7. Zadeh CO, Huggins JR, Sarmah D, Westbury BC, Interiano WR, Jordan MC, Phillips SA, Dodd WB, Meredith WO, Harold NJ, Erdem C, and Birtwistle MR* (2022). Mesowestern Blot: Simultaneous Quantitative Analysis for Hundreds of Sub-Microliter Lysates. ACS Omega. 7 (33), 28912-28923.

  8. Erdem C, Lee AV, Taylor DL, Lezon TR* (2021). Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells. PLOS Computational Biology. 17 (6), e1009125.

  9. Erdem C, Nagle AM, Casa AJ, Litzenburger B, Wang Y, Taylor DL, Lee AV, Lezon TR* (2016). Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. Molecular & Cellular Proteomics. 15 (9), 3045-3057.

  10. Erdem C, Bozkurt Y, Erman B, Gul A, Demir A* (2015). Mathematical Modeling of Behcet's Disease: A dynamical systems approach. Journal of Biological Systems. 23 (02), 231-57.

Projects

!!! Coming soon !!!

Open positions

We have PhD and postdoc positions available. If you like to join our team to be at the forefront of data-driven life sciences, please email.

Current opennings: Two PhD positions! Application deadline: 2024-01-14