Team

Principal Investigator

Ludmil B. Alexandrov, Ph.D.

I am a 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 & Research Associates

Christopher Steele, Ph.D.

I am a research associate specializing in applying signature methodologies to copy number and structural data in cancer genomes. I have an interest in understanding some of the most complex cancers at a structural level, and this approach has proved fruitful in delineating some of the processes leading to structural alterations across cancer. This approach has promise to aid in patient stratification for therapy and to enhance prognostication for patients, and to aid the wider research community in better understanding their cancers of interest.

Shuvro Prakash Nandi, Ph.D.

I am an Assistant Project Scientist in the Alexandrov Lab at UC San Diego. My research focuses on cancer genomics, mutational signatures, and the biological processes that shape somatic mutations. I develop advanced sequencing technologies—including duplex sequencing approaches—for ultra-sensitive detection of rare mutations and their applications in cancer risk, environmental mutagenesis, and precision oncology. My work spans both experimental and computational genomics across diverse biological systems and patient-derived datasets. I integrate assay development, large-scale sequencing analysis, and translational collaboration to uncover mutational processes and enable biomarker discovery. I have extensive experience leading multidisciplinary collaborations and mentoring trainees at all levels, with a continued focus on driving advances in translational cancer genomics and genomic technologies.

June-Young Koh, M.D., Ph.D.

I am a pediatrician with a Ph.D. in medical science, dedicated to understanding how genomic alterations—particularly mutational signatures—drive disease onset and progression. With a background in immunology and genetics, I investigate the interplay between genome instability and immune dysregulation, focusing on their roles in pediatric cancers and chronic inflammatory diseases. By integrating next-generation sequencing, computational analysis, and clinical insights, I aim to uncover the molecular mechanisms that shape disease phenotypes. Additionally, I study how these mechanisms evolve with age, contributing to mutational processes that predispose individuals to malignancies and immune-related disorders. My work aligns with ongoing efforts to systematically map cancer- and aging-associated mutational signatures, with the goal of advancing targeted therapies and precision medicine.

Ammal Abbasi, Ph.D.

I am a Postdoct in the Alexandrov Lab. 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.

Yuhe Cheng, Ph.D.

I am a Postdoc in the Alexandrov Lab. 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.

Graduate Students

Ting Yang, B.S.

I am a Ph.D. student in the Bioengineering department. Before starting my graduate journey at UCSD, my undergrad research mainly focused on developing paper-based point-of-care diagnostic tools. In the Alexandrov Lab, I am interested in applying computational and biological tools to study the underlying mechanism that drives tumorigensis and rapid cancer progression. In my spare time, I enjoy reading, surfing, and swimming.

Jessica Au, B.S.

I am a Ph.D. student in the Bioinformatics and Systems Biology program. I graduated from UC Davis with a degree in computational mathematics. Prior to UCSD, I conducted research in a variety of fields like theoretical cardiology & developmental biology, as well as helped manage the ENCODE database as part of the Data Coordination Center at Stanford University. My research interests involve cancer genomics and the underlying mechanisms that drive tumor evolution and development. More recently, I've become interested in investigating how specific genomic alterations can be used as biomarkers in a clinical setting, while utilizing computational tools to make the study of personalized medicine all possible. When I'm not busy being a workaholic, I enjoy staying active and being a plant mom.

Douglas Meyer, B.S.

I am a Ph.D. student in the Bioinformatics and Systems Biology program (2022 cohort). Prior to starting graduate school I worked as an ORISE fellow at the FDA where my research focused on understanding the role of synonymous variants in human disease. My current research aims to develop new methods to detect germline-somatic interactions affecting oncogenic pathways. I am co-advised with the Hannah Carter Lab.

Rongjie Wu, B.S.

I am a Ph.D. student in Shu Chien - Gene Lay Department of Bioengineering. Prior to my graduate study, I obtained my Bachelor’s degree from UCSD in Bioengineering: Bioinformatics. My academic interest is to develop engineering approaches and computational tools on cancer omics dataset. In the Alexandrov Lab, I am mainly interested in disentangling APOBEC mutagenesis and clonal hematopoiesis in tumor development. Besides research, I also enjoy listening to classical music, practicing the piano and the violin, and learning new languages.

Zichen Jiang, B.S.

I am a Ph.D. student in the Bioengineering department (2023 cohort). Before starting graduate school, I received my undergraduate degree with honors in bioinformatics from the Biological Sciences department at UCSD. I am passionate about understanding the genetic characteristics of tumorigenesis. My current research focuses on the automation and analysis of highly accurate DNA sequencing of normal tissues to understand healthy longevity and cancer predisposition. Outside of research, I enjoy singing, surfing, and savoring good coffee.

Haoran Zhang, B.S.

I am a Ph.D. student in the Bioinformatics and Systems Biology program at the University of California, San Diego. I earned my B.S. from UC San Diego, with double majors in Biology with specializations in Bioinformatics and Biochemistry/Chemistry. My research interests lie in developing novel computational methods and algorithms for analyzing mutational signatures in cancer genomics. I am also interested in integrating machine learning approaches to my computational framework. Through my work, I aim to contribute to the discovery of novel biomarkers in cancer genetics and deepen our understanding of cancer mutagenesis.

Banghua Xu, B.S.

I am a Ph.D. student in the Bioinformatics and Systems Biology program at UCSD (2023 cohort). Prior to my graduate studies, I obtained my Bachelor's degree in Biology and Computer Science from UBC where I conducted machine learning and deep learning research in metabolomics and transcriptomics. In the Alexandrov Lab, I focus on developing efficient and accessible bioinformatics tools and apply deep learning techniques to analyze histopathological slides from cancer patients, aiming to democratize these computational approaches for clinical implementation and improve personalized treatment outcomes.

Gabi Yung, B.S.

I am a Ph.D. student in the Bioengineering department at UC San Diego. After obtaining my B.S. in Biomedical Engineering from UC Davis, I worked in drug discovery and stem cell biology at biotech startups in San Francisco before joining the Alexandrov Lab. My research integrates next-generation sequencing, bioinformatics, and statistical genomics to understand how environmental exposures leave mutational footprints in healthy tissues and contribute to cancer risk. Outside of research, I enjoy discovering great coffee, baking, and being a dog mom.

Staff

Mousumy Kundu, M.S.

I am a Bioinformatics Programmer at the Alexandrov Lab, UC San Diego Health, where I develop and maintain computational pipelines for large-scale cancer genomics data analysis, contribute to the SigProfiler suite of bioinformatics tools, and manage the lab's HPC and data storage infrastructure. I recently completed a Master's in Data Science and Engineering at UC San Diego, with a growing focus on machine learning and AI approaches applied to genomic and biomedical data.

Agnieszka D'Antonio-Chronowska, Ph.D.

I am the Director of Strategy and Operations for the Cancer Grand Challenges CAUSE project in the Alexandrov Lab at the University of California San Diego. I oversee strategic planning, international collaborations, operational management, and program execution for one of the world's largest multidisciplinary cancer research initiatives. With more than 20 years of experience in molecular and cellular biology, human genetics, epigenomics, and single-cell genomics, I combine scientific expertise with strategic leadership to enable collaborative, data-driven research that advances our understanding of cancer etiology and accelerates discoveries in cancer prevention and treatment.

Janelle Duong, B.S.

I recently graduated from UC San Diego with a Bachelor’s in Molecular and Cell Biology. I am working as a Research Assistant in the Alexandrov Lab where I contribute to understanding the mutational profiles of tumor and healthy samples using novel sequencing approaches. When I am not in the lab, I enjoy reading, baking, and trying new matcha places!

Undergraduate Students

Leo Joseph Bioengineering

Vikas Murali Bioengineering

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