About Dr. Karabacak

Dr. Uyugun

Brief Biography

N. Murat Karabacak, PhD, received his BS in Chemistry from Bilkent University and his PhD in Chemistry with Specialization in Quantitative Biology from Brandeis University. He joined the Center as a postdoctoral fellow in 2011 and was promoted to Instructor in Surgery at Harvard Medical School in 2016.

Dr. Karabacek is the recipient of Tosteson Postdoctoral Fellowship in 2015 for his work regarding circulating tumor cells, and Brandeis University Provost’s Research Award in 2009 for his work on post-translational modifications of Superoxide Dismutase-1 in Amyotrophic Lateral Sclerosis patients.

During his postdoctoral work, Dr. Karabacak developed approaches to isolate and analyze extremely rare cells from blood and bone marrow for understanding their biology and for their use in the clinic.

Circulating tumor cells (CTCs) have eluded researchers for decades because they are so rare—as few as one CTC may be present in one milliliter of blood containing billions of blood cells.

Dr. Karabacak specifically focused on developing marker-free methods of rare cell isolation that is applicable to CTC isolation for all cancers, regardless of the tissue of origin and epithelial character.

This technique allowed performing unbiased CTC isolation from patients with prostate, skin, brain, pancreas, lung and breast tumors and application of variety of methods including single cell DNA and RNA sequencing, immunological and cytopathological analyses to patient CTCs.

Research Summary

Dr. Karabacak’s work is at the interface of mass spectrometry, microfluidics and medicine. Current topics include:

1. Defining tumor-stromal cell interactions across metastatic cascade. Cancer originally confined to the primary site eventually disseminates through the blood to distal sites including the bone, lung, liver and brain and continues to evolve, leading to cellular and molecular heterogeneity between tumor cells.

This heterogeneity causes pharmaceutical treatments to be less effective and consequently tumors to recur. Working closely with researchers at the Cancer Center, Dr. Karabacak's research aims to better understand this dynamic biological adaptation during metastatic cascade and resulting heterogeneity via single-cell proteomic analysis.

2. Deconvoluting rare bone marrow stromal progenitor cell subsets. The tissue microenvironment surrounding hematopoietic stem/progenitor cells is complex, containing various cell types that support bone marrow function and bone maintenance.

In many studies, these stromal cells are poorly defined, since they are rare and heterogeneous. Dr. Karabacak is working closely with researchers at the Center for Regenerative Medicine to help define these populations and decipher their behavior in steady-state and in functionally-relevant stress conditions.


  • BS, Chemistry, Bilkent University, 2005
  • PhD, Chemistry and Quantitative Biology, Brandeis University, 2010

Research Thrusts