Principal Investigator

I am an Assistant Professor in the Department of Cellular and Molecular Medicine and the Department of Bioengineering at the University of California San Diego. I am interested in disentangling the enigmatic secrets hidden in large omics datasets. My research is focused on developing novel machine-learning approaches and in leveraging these approaches to elucidate the basic molecular mechanism underlying cancer development and cancer progression. My hope is that this understanding will allow us to improve cancer treatment and cancer prevention.

Postdoctoral Fellows

Burcak Otlu, Ph.D.

I am a computer scientist specialized in bioinformatics. My research mainly focuses on the development of algorithmic solutions to emerging problems in genomics. I work on genome analysis with an emphasis on annotation and enrichment analysis of genomic loci. I am also interested in genomic variations, specifically, integrative analysis of variations in various cancer types. In this lab, my aim is to apply machine learning and data science techniques in cancer genomics and develop bioinformatics software pipelines. When I am not working, I enjoy spending time with my daughter and son that always keep me on my toes!

S. M. Ashiqul Islam (Mishu), Ph.D.

I am an intent data analyst and always enjoy discovering hidden patterns form an array of information. Originally being a molecular biologist, I gathered skill in developing various machine-learning-assisted algorithms during my Ph.D. In future, I want to make myself engaged in genomic data analysis where I will be able to dig out new information on the mystery of our life which we do not know yet.

Maria Zhivagui, Ph.D.

Specialized in cancer research, I chose this field given its enigmatic aspect inciting the need for discovery. I am a post-doc, interested in cancer biology and phenomena. Contributing to cancer genomics, including genetics and epigenetics, is a privilege for me that may allow unraveling mysteries of carcinogenesis. Given that the realm of science is broad and interconnected, one of the aspects that interests me is bioinformatics. Therefore, I would like to expand my knowledge on complex data analysis and programming.

Graduate Students

Erik Bergstrom, B.S.

I am a PhD student in the Bioengineering department. I am interested in exploring the underlying characteristics of mutational signatures found in various cancer types. I would like to explore the biological implications and affected mechanisms correlated with these mutational signatures, while developing bioinformatics software to aid in the downstream data analysis.

Phoebe He, B.S.

I am a PhD student in the Biomedical Sciences Program. Prior to starting my graduate studies, I worked for a pharmaceutical company developing biological and chemical treatments for cancer. In the Alexandrov Lab, I study the the genetic alterations in benign and early stage tumors to bring understanding to the causes and the early molecular events of this disease.

Ashrith Reddy, B.Tech.

I am a PhD student in the Bioengineering department. Prior to starting graduate school, I worked for two years at an analytics advisory firm focusing on healthcare analytics. My primary research interest lies in understanding cancer through a combination of machine learning and complex systems modeling. I would like to uncover fundamental laws that govern the genotypic and phenotypic evolution of the system combined with their underlying genomics.

Visiting Scholars

Chrsitopher Steele, Ph.D.

I am a statistical geneticist working primarily on the genomics and biology of soft tissue sarcomas. In the course of my work I have become particularly interested in understanding highly rearranged and complex genomes, and have developed a copy number signature framework to do just that in undifferentiated sarcoma. I will be spending two months in the Alexandrov lab to learn from their expertise in mutational signatures, and to apply the copy number signature method to a pan-cancer dataset.

Marcos Diaz-Gay, M.S.

I am a PhD student in the August Pi i Sunyer Biomedical Research Institute (IDIBAPS) of Barcelona. Originally trained in engineering, I have focused my career in biomedical research, with a strong interest in genomic data analysis. My project focuses on the integration of germline and somatic sequencing data to better understand the inherited predisposition to colorectal cancer. I will benefit from my stay in the Alexandrov lab to gain knowledge into new computational methodologies in somatic characterization, such as mutational signatures, and to incorporate them into our research.

Undergraduate Students

Noelia Valenzuela

Biochemistry and Cell Biology

Arielle Soomi Yoo

Bioengineering: Bioinformatics

Yi- Yu (Yoyo) Yeh

Bioengineering: Biosystems

Evelyn Yuzhou Tong

Bioengineering: Biotechnology

Frances Keer

Bioengineering: Biotechnology


Willie Chao

Bioinformatics Staff2018

Melissa Yakuta

Visiting Scholar2018