Team

Principal Investigator

I am an Associate 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 postdoctoral scholar specializing 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!

Maria Zhivagui, Ph.D.

Specialized in cancer research, I chose this field given its enigmatic aspect inciting the need for discovery. I am a postdoctoral scholar, 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.

Marcos Diaz-Gay, Ph.D.

I am a postdoctoral scholar, who was originally trained in engineering. I have focused my career in biomedical research, with a strong interest in bioinformatics, particularly genomic data analysis. I have become fascinated by the development of new computational methodologies in cancer research allowing the discovery of the underlying mechanisms of cancer predisposition and progression. Making this knowledge accessible to the research community is one of my main goals at the Alexandrov lab.

Shuvro Prakash Nandi, Ph.D.

I am a postdoctoral scholar at UC San Diego. Originally being a molecular biologist, I have acquired skills in measuring genome-wide DNA damage, repair, and mutagenesis during my Ph.D. I am interested in understanding the mutational patterns imprinted by the biological processes operative within somatic cells. Specifically, I am going to look at the early-stage events involving DNA damages and repairs that contribute to endpoint mutational signatures observed within cancer genomes. I hope this will have important implications for assessing individual risk of cancer predisposition to inform on lifestyle choice and stratified treatment for cancer therapy.

Raviteja Vangara, Ph.D.

I am currently a postdoctoral scholar in the Department of Cellular and Molecular Medicine at UCSD under the supervision of Dr. Ludmil B. Alexandrov. I am a versatile computational scientist and engineer, interested in developing novel technologies for various scientific applications using data science and Machine learning. I am specialized in unsupervised ML methods, specifically Non Negative Matrix and Tensor Factorization techniques . My current research activities utilize these machine learning approaches for accurate detection of mutational signatures in human cancer.

Graduate Students

Erik Bergstrom, B.S.

I am a Ph.D. 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 Ph.D. 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 Ph.D. 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.

Azhar Khandekar, B.S.

I am a Ph.D. student in the UCSD Bioinformatics and Systems Biology program. I am interested in integrating large-scale omics datasets to elucidate the biological mechanisms that drive cancer formation and progression. Previously, I worked at the NIH on integrating methylation and somatic mutation data to study mechanism of mutagenesis, and currently in the Alexandrov lab I am working on analyzing copy number variation and structural variants in normal and tumor genomes. Coming from a molecular biology background, my goal is to learn how to apply computational techniques to various omics datasets to derive biological insight.

Yuhe Cheng, B.S.

I am a Ph.D. student in the Bioengineering department. I am interested in combining experimental and computation methods to explore the phenotypic profiling of mutational signatures in tumors and normal tissues. My goal is to map the multi-omic landscape of mutations that provides biological insights into the onset of cancer.

Ammal Abbasi, B.S.

I am a Ph.D. student in the Bioinformatics and Systems Biology program. I am primarily interested in cancer genomics and the use of computational tools to uncover genetic driver events responsible for cancer onset and metastasis. More specifically, I am interested in the clinical applicability of mutational signature driven biomarkers for better personalized use of cancer therapies.

Mariya Kazachkova, B.S.

I am a Ph.D. student in the Biomedical Sciences program. I am interested in using omics datasets and computational approaches to better understand cancer and its development. Prior to starting graduate school, I worked with genome-scale CRISPR screening data at the Broad Institute. I aim to continue integrating computational tools and biological knowledge to gain insight into cancer development and progression.

Staff

Mark Barnes, B.S.

I have a degree in Mathematics-Computer Science from UC San Diego and I am interested in the intersection between computer science, mathematics, and biology. I will be working as a bioinformatics programmer and will be developing software to help study mutational signatures and to understand the activity of mutational signatures in different cancer types.

Mousumy Kundu, B.S.

I have completed my graduation in Computer Science and Engineering. I am interested in applying Machine Learning algorithms to biological data for prediction of diseases towards personalized treatment. Within Alexandrov lab, I will be working on benchmarking of SigProfilerHotSpots tool as well as implementing, running, and optimizing the existing computational pipelines for analysis of cancer genomics data.

Undergraduate Students

Mia Jeffris

Bioengineering: Bioinformatics

Matias Lin

Computer Science: Bioinformatics

Zichen Jiang (Cardiff)

Biology: Bioinformatics

Xi Wang (Sam)

Bioengineering: Bioinformatics

Audrey Kristin

Biology: Human Biology

Areebah Hodah

Biology: Human Biology

Alumni

S.M Ashiqul Islam (Mishu)

Postdoctoral Scholar 2018-2021

Jason Dai

Undergraduate Student2019-2021

Yuzhou Tong (Evelyn)

Undergraduate Student 2018-2020

Noelia Valenzuela

Undergraduate Student 2019-2020

Carolina Castañeda

Visiting Scholar2019

Uma Mahto

Undergraduate Researcher2019

Christopher Steele

Visiting Scholar2019

Melissa Yakuta

Visiting Scholar2018

Willie Chao

Bioinformatics Staff2018

Lab Photos

Mishu's going away party. Best wishes Mishu!Jason's graduation celebrationBeach hike with the labLake Hodges hikeRegents pizza