Division of Mathematical Oncology and Computational Systems Biology

Russell Rockne, Ph.D., is an Associate Professor in the Department of Computational and Quantitative Medicine within Beckman Research Institute of City of Hope. He also serves as director of the Division of Mathematical Oncology and Computational Systems Biology, with the goal of translating mathematics, physics and evolution-based research to clinical care.

Full Bio

Full Bio

Full Bio

Vikram Adhikarla is an Assistant Research Professor in the Division of Mathematical Oncology and Computational Systems Biology at City of Hope. He has a Ph.D. in Physics from the University of Wisconsin – Madison with specialized focus in Medical Physics. His interests lie in the domain of computational modeling and analysis of both pre-clinical and clinical imaging data. He has experience in modeling tumor-vasculature system based on hypoxia and proliferation positron emission tomography (PET) imaging data and has worked on modeling the response of tumor-vasculature system to anti-angiogenic therapy.

He has further trained in the kinetic analysis of PET imaging data in the Department of Radiology at Emory University in Atlanta. His focus in particular has been on the evaluation of novel radiotracers used for imaging neurological disorders.

As a scientist at City of Hope, he uses his skills to analyze the migration of stem cells in immunohistological and three-dimensional cleared images of the mice brain. This data analysis feeds into his work on the prediction of stem cell migration paths for the translational purpose of optimizing the clinical delivery of stem cell therapeutics. Concurrently, he is also involved in analysis of clinical molecular imaging data for evaluation of novel radiotracers poised to deliver clinical impact.

David Frankhouser is an Assistant Research Professor in the Division of Mathematical Oncology and Computational Systems Biology at City of Hope. 

Denis O'Meally is an Assistant Research Professor in the Department of Diabetes & Cancer Discovery Science (DMRI) and the Division of Mathematical Oncology & Computational Systems Biology at City of Hope. His research interests lie understanding genome structure, function and evolution. He holds a PhD from the Australian National University and his post-doctoral studies focused on gene-environment interactions and sequencing the genomes of strange Australian vertebrates. His interests span molecular biology to bioinformatics with a keen focus on reproducibility. At City of Hope, Dr. O’Meally collaborates with faculty across a number of departments to develop new insights and treatments into cancers, diabetes, HIV and other diseases.

Ryan Woodall is an Assistant Research Professor in the Division of Mathematical Oncology and Computational Systems Biology, working with Dr. Rockne on modeling the transport of interstitial fluid within brain tumors using computational fluid dynamics. He utilizes his experience in both computational fluid dynamics and medical image processing to create patient-specific models of fluid transport within the brain and tumor tissue. Ryan is interested in model discovery, and physics-interpretable machine learning, and it's applications to precision medicine. He completed his doctoral training at the University of Texas at Austin, where he worked closely with Dr. Tom Yankeelov on models of fluid flow within tumors and earned an NIH coursework portfolio in Imaging Science and Informatics. Ryan's background consists of developing contrast agent, nano-particle, and fluid delivery models for individual patients at the tissue and cellular scale. He is also interested in standardizing advanced MR acquisition methods across the healthcare industry, for better patient outcomes through applying modern data-driven techniques which require high-quality data. 

Adina Matache is a part-time Senior Research Associate in the Division of Mathematical Oncology and Computational Systems Biology at City of Hope. She received her Ph.D. in Electrical Engineering from University of California, Los Angeles (UCLA) and her B.S. and M.S. degrees, both in Electrical Engineering from University of Washington. 

Adina has extensive research experience with theoretical analysis and modeling and simulation of digital communication systems, including terrestrial and satellite communication systems. She gained her expertise in digital communications and information theory while working for commercial companies and Federally Funded R&D Centers. At City of Hope, she applies her knowledge in communication and information theory to research immune cell signaling in breast cancer. She hopes this research can lead to new insights into how immune cells are signaling and processing molecular information in healthy donors and how the intracellular signaling pathways may be impaired in breast cancer patients.

Martina Conte is a GSP-Visiting Scholar in the Division of Mathematical Oncology and Computational Systems Biology, working with Dr. Rockne on data-driven and data-integrated models for studying Car T-cell based therapy within brain tumors. She has a position as a Postdoctoral Fellow at the Politecnico of Torino (Italy), while she carried on her doctoral research projects at the Basque Center for Applied Mathematics (BCAM - Bilbao) receiving her PhD at the University of Basque Country (Spain). Her Ph.D. research projects collect the development and analysis of several multiscale mathematical models analyzing various aspects of brain tumor growth and migration into the brain. 
 
Currently, her main research lines focus on (i) describing the process of cell migration in the ECM, with a special attention to the case of tumor invasion, (ii) studying tumor-endothelial cells interactions and specific aspects related to the tumor angiogenesis process (e.g. hypoxia, treatment resistance), and (iii) analyzing signal propagation in the brain (through network analysis) and its relationship with physiological and pathological conditions. In the different project, great attention is paid to the integration of biological data into the mathematical models, that is one of the main goals of her Visiting Programme at City of Hope.
 

Yu-Hsuan is currently a graduate student in the Ph.D. in biological sciences program at Irell & Manella Graduate School of Biological Sciences in City of Hope. Yu-Hsuan received his bachelor’s and master’s degrees in clinical laboratory sciences and medical biotechnology from National Taiwan University in Taiwan, where he started his research focused on targeted therapy resistance and drug repositioning in leukemia.

With his enthusiasm for combining his previous training in hematology and cancer research with bioinformatics and mathematical modeling, he is currently working with Dr. Ya-Huei Kuo (Department of Hematologic Malignancies Translational Science, Beckman Research Institute) and Dr. Russell Rockne (Department of Computational and Quantitative Medicine, Beckman Research Institute) to uncover the molecular basis of leukemia stem cells and to develop novel therapeutic strategies.

Babgen Manookian, Ph.D. is a postdoctoral fellow in the Department of Computational and Quantitative Medicine in the Division of Mathematical Oncology and Computational Systems Biology at City of Hope. He works on developing and applying dynamic Bayesian probabilistic algorithms to investigate allosteric mechanisms and causal relationships in transmembrane proteins.

Prior to his fellowship at City of Hope, Babgen completed his doctorate studies at the University of Massachusetts Amherst where he received a Ph.D. in computational chemistry. His thesis focused on investigating the kinetics and thermodynamics of biofuel chemistry within the confined pores of zeolite acid catalysts. Specifically, he tackled the question of how confinement plays a role in key reactions related to the production of biofuels and other energy products. In his research projects he worked with advanced chemistry software in both the static (quantum chemistry) and dynamic (molecular dynamics) realms of modeling. In the latter years of his doctoral work, he developed a microkinetic model of biofuel reactions in zeolites and investigated the concurrence of kinetic and thermodynamic control of product formation. He is currently shifting his focus to a data science approach to study biochemical systems relevant to the field of drug discovery. Babgen also works as a professor of chemistry and has experience teaching at local community colleges in Massachusetts as well as in Los Angeles.

Talant Ruzmetov, Ph.D., is a computational physicist dedicated to advancing our understanding of living organisms, from molecular components-proteins, ligands, DNA, and RNA-to cellular systems. His research integrates deep learning and computational modeling to investigate complex phenomena, including molecular interactions at the atomistic scale, protein conformational dynamics, and the mechanisms driving stem cell differentiation.

Outside the lab, he enjoys playing table tennis on weekends.

Konstancja Urbaniak is a postdoctoral fellow in Dr. Sergio Branciamore's group. She embarked on her Ph.D. journey through an A*STAR program, a joint venture between the University of Manchester in the UK and the A*STAR Bioinformatics Institute in Singapore. Her research focused on combining two fields biochemistry and bioinformatics to decipher the code for SUMO reader: substrate interactions. As a postdoctoral fellow, she has been working on employing causal probabilistic models - Bayesian networks to variety omics datasets, including scRNAseq, spatial RNAseq, and FACS to reveal complex and non-linear relationships in biological systems.

Jennifer Rangel Ambriz, Ph.D., is a Postdoctoral Fellow in the Department of Computational and Quantitative Medicine within Beckman Research Institute of City of Hope working with Dr. Russell Rockne. She has a Ph.D. in Mathematics from the University of California, Riverside with a research focus in Mathematical Biology. During her Ph.D., she worked on interdisciplinary projects in developmental biology, bridging experiments and mathematical models to study epithelial tissue development. More specifically, she developed stochastic and multi-scale mechanistic models for studying mechanisms of development of the Drosophilia (fruit fly) wing imaginal disc, the precursor of the wing.

At City of Hope, Dr. Rangel Ambriz is leveraging her background in mathematical and computational modeling to develop mathematical models that help predict Acute Myeloid Leukemai (AML) development, outcome and response to treatment. She hope this research can lead to novel insights that can be used to identify new therapeutic approaches and better patient outcomes.

Daniel Abler is a PhD physicist with research experience in applied physics, software- and computational bio-engineering. He has been actively involved in multidisciplinary research for 10 years, collaborating with engineers, computer scientists, biologists and clinicians.

At the European Organization for Nuclear Research (CERN), Daniel studied technical feasibility of a new accelerator-based research infrastructure for ion-beam radiobiology. He also investigated model-driven data collection approaches to address semantic interoperability challenges in the context of ion-beam radiotherapy.

Over the past 4 years, Daniel has been working on image-based computational models for various body-sites and medical conditions. His current research focuses on the effect of biomechanical forces on the formation and development of brain tumors and possible implications for treatment; he develops mathematical models to investigate this question.

Daniel is interested in model-based computational approaches for integrating clinical and pre-clinical information into decision processes. He hopes that these efforts will ultimately improve the treatment of individual patients and facilitate the quantitative assessment of therapeutic approaches. Daniel has strong experience in the implementation of image-based finite-element models, related image and data processing, and analysis. His current research appointment as Marie Skłodowska-Curie Fellow was shared between City of Hope and the University of Bern, Switzerland.

C. Laurel Anderson is currently a Data Scientist in the Department of Data Science and Artificial Intelligence at Integra Connect, which is a value-based, precision medicine company. Her educational background includes a BSc in Neuroscience from the University of Miami and an MSc in Human Genetics and Genomic Data Analytics from the Keck Graduate Institute.

Before joining Integra Connect, she interned under Dr. Russell C. Rockne at City of Hope (Department of Computational and Quantitative Medicine, Division of Mathematical Oncology and Computational Systems Biology). After her internship, she transferred to the Department of Applied AI and Data Science for a Data Science Fellowship.

During her time at City of Hope, she utilized mathematical and machine learning models to investigate the disease progression of Acute Myeloid Leukemia in human and mice data. Her fondest memories at City Hope were spent with Dr. Rockne’s team, where she learned invaluable skills and life lessons that she will always cherish for the rest of her life.

Laurel was, and still is, a social butterfly. So if you would like to chat with her about her amazing mathematical oncology internship experience or if you just want to expand your professional network, then please feel free to connect with her on LinkedIn!

Soham Bose is a rising senior at Troy High School fascinated by the intersection of mathematics, computer science, and biology. At school, he is the president of Math Club, captain of the Science Bowl team, and on the varsity tennis team. Some of his hobbies include reading and playing piano, basketball, and video games. Previously, he has worked on research to create ODE models of the reverse Warburg effect and explore the effects of different agents on specific gene expression in mouse fibroblasts. Currently, he was a participant in City of Hope’s Eugene and Ruth Roberts Summer Academy working under Dr. Rockne in the Division of Mathematical Oncology and Computational Systems Biology. Later, as an undergrad and in his career, he hopes to pursue computational biology and applied math.

Alex Brummer is a PhD physicist with research experience in mathematical biology and ecology and evolutionary biology.  His research aims to develop and test mathematical models of cancer growth and treatment response.  He worked jointly with Dr. Russell Rockne (Division of Mathematical Oncology and Computational Systems Biology, Beckman Research Institute) examining cancer treatment response in glioblastoma, breast cancer, and leukemia; and with Dr. Van Savage (Computational Medicine, UCLA) studying imaging biomarkers of lung cancer derived from pulmonary vasculature.
 
Alex is interested in understanding and predicting large scale phenomena from small scale interactions and optimizations.  His research leverages elements from non-linear dynamics, population ecology, fluid mechanics, fractal geometry, spatial networks, shape analysis, computer vision, and allometric scaling theory.  His work with Dr. Rockne is currently focused on (i) studying how different nonlinear model interactions between glioblastoma and CAR T-cells give way to various growth trajectories, and (ii) using data-driven, sparse identification techniques to discover underlying interactions.

Alex is currently tenure-track faculty  in Physics at the College of Charleston in Charleston, South Carolina. 

Michael Cork is a recent graduate of Pomona College, where he received his B.A. in Mathematics with a minor in Biology and Spanish. During his time at Pomona, Michael explored how mathematical models can further our understanding of how cancer oversteps and rewires certain checkpoints in the immune system. Originally from Minneapolis, Minnesota, he has also conducted clinical research at Hennepin County Medical Center, as well as participated in various summer research programs aimed at modeling different biological and physical systems. When he is not investigating the interplay of math and biology, Michael enjoys reading, hiking, discovering new craft breweries and supporting Manchester United.

Jennifer Gutierrez has returned to Roberts Summer Academy after working with Dr. Russell Rockne in the Division of Mathematical Oncology. She participated in the summer academy last year with Dr. Tijana Talisman in the Department of Cancer Biology and Molecular Medicine where she studied the quantification of super-resolution data. She graduated from Mount Saint Mary's University (Los Angeles) in May 2016 where she obtained her baccalaureate degree in Mathematics. In her last year as an undergraduate, she was recognized with an Excellence in Mathematics Award as well as the Courage Award.

She is interested in incorporating the language of mathematics in real-world applications and hence plans to pursue higher education in Biostatistics, Computational Biology, or Applied Mathematics.

While some of her hobbies include, but are not limited to, running, water-coloring, biking, and learning new languages, her ultimate goal is to give back to her alma mater by teaching and providing mentorship to young women pursuing STEM degrees.

Amy Jang is a rising sophomore at Columbia University, majoring in biomedical engineering. Amy has previously done research at USC Information Science Institute where she published her work on “Designing an Ontology for the ENIGMA Neuroscience Collaboration” and on the “Automatic Generation of Portions of Scientific Papers for Large Multi-Institutional Collaborations Based on Semantic Metadata.” Additionally, she won the Best Interdisciplinary Collaboration award at IKCAP and the Best Poster Award at the INCF Neuroinformatics Congress. Amy also collaborated with Edwards Lifesciences to create a prototype version of an automated heart valve sewing machine. During the school year, she is working on identifying neuro-biomarkers for Huntington’s and Parkinson’s Disease patients at the Neurorehabilitation Research Lab and on identifying the relationship between speakers’ gestures and audience comprehension at the Columbia Engineering Laboratory for Intelligent Imaging and Neural Computing.

Outside of biology and computer science, Amy loves to play piano and being up in the sky, whether that be ziplining or parasailing, and she hopes to skydive and bungee jump sometime in the future!

Aleksandra (Ola) Karolak is an Assistant Professor in the Department of Machine Learning at Moffitt Cancer Center. Previously, she was an Assistant Research Professor in Population Sciences at City of Hope, working jointly with Dr. Jeannine McCune (Population Sciences and Hematology & HCT) and Dr. Russell Rockne (Mathematical Oncology) on improvements of outcomes of the patients with hematopoietic stem cell transplants. 

Dr. Karolak obtained a MSc in metal-organic chemistry of bio-inorganic polymers and transition metals complexes from the Adam Mickiewicz University in Poland. During PhD at the University of South Florida in Tampa, she studied computational and biophysical chemistry. While at USF, she applied and developed computational methods for the conformational studies of biomolecules on various levels of resolution including ab initio, atomistic and coarse- grained models of small molecules, proteins and DNA. Her first postdoctoral training in the Mathematical Oncology Department at Moffitt Cancer Center in Tampa focused on applications of theoretical and computational methods in clinically relevant settings. At Moffitt, she worked on 2D models of imaging agents penetration through the tumor tissue, and 3D models of tumor organoids growth. Her desire to more completely contribute to the field of precision medicine led her to the Institute for Research in Biomedicine in Barcelona, Spain where her postdoctoral training was jointly funded by MSCA actions and BIST. At IRB, she applied multi-omics and machine learning approaches to uncover the structural signatures of cancer mutations in individual or subgroups of patients.
 
In her research she combines approaches from computational and biophysical chemistry, structural biology, mathematical oncology and biostatistics to elucidate the role of heterogeneity in cancer progression and response to treatment. She seeks to understand variations in disease evolution, variability in the response to treatment and development of resistance, and how this knowledge, explored on the multi-scaled resolution levels using highly interdisciplinary approach, can be utilized to improve the outcomes of individual patients. 

Maxim Kuznetsov, Ph.D., is a Postdoctoral Fellow in the Division of Mathematical Oncology and Computational Systems Biology within Beckman Research Institute of City of Hope. He focuses on mathematical modeling of various types of antitumor treatment with the key goal of suggesting the ways to improve their efficacy in clinical setting.

Dr. Kuznetsov received his doctorate in Physics and Mathematics with dissertation on the topic “Mathematical modeling of tumor growth under the influence of antiangiogenic therapy and radiotherapy”. In the last years he was working in P.N. Lebedev Physical Institute, where his main research interest was spatiotemporal optimization of external beam radiotherapy. Another direction of his research was the investigation of formation and evolution of spatiotemporal structures in general nonlinear systems. In City of Hope he applies his expertise in particular to the task of optimization of targeted radionuclide therapy and immunotherapy.

David Khachatrian is a rising senior at UCLA, studying bioengineering. In addition to his studies, David spends his time tutoring and leading review sessions for core undergraduate STEM courses as Academic Outreach officer for the UCLA chapter of Tau Beta Pi. When he gets the chance to relax, you will likely find him bouldering or playing his accordion.

David previously conducted research in Dr. Karen Aboody's lab profiling a novel neural stem cell line, and gained a more quantitative understanding on biological phenomena during his time in the Division of Mathematical Oncology and Computational Systems Biology to supplement his academic studies and for a more broad appreciation of biological processes. In the future, David hopes to use this background to develop a functional method of using computer-aided protein engineering to treat a variety of diseases.

Alexandra Levy is a graduate student intern, pursuing her M.S. in Human Genetics and Genomic Data Analytics from Keck Graduate Institute in Claremont, California. Her interests center around glioblastoma research, specifically the immune response to angiogenesis in glioblastoma models, and polyclonal tumor evolution. 

She is currently working on her capstone project alongside Dr. Russell Rockne (Mathematical Oncology, Beckman Research Institute), Dr. Sergio Branciamore (Computational and Quantitative Medicine, Beckman Research Institute), and Dr. Floris Barthel (TGen, Computational and Quantitative Medicine, Beckman Research Institute).

Davide joined the Division of Mathematical Oncology and Computational Systems Biology in March 2017. He obtained a Master Degree in Theoretical Physics in 2011 at Univerista`degli Studi di Torino (Italy) with a final project on the study of Bose-Einstein Condensates (BECs). He then moved to the University of East Anglia (UK) where in 2016 he obtained a Ph.D. in Applied Mathematics focusing on the study of quantized vortices in BECs in confined geometries by using a statistical mechanical approach.

Davide's research covers non-linear physics, non-equilibrium statistical mechanics, dynamical systems and mathematical modeling of cancer dynamics. In particular, he is currently working on the developing of a mathematical model of Acute Myeloid Leukemia.

Dhanya Mahesh is a twelfth grader at Monta Vista High School in Cupertino, CA. She is particularly interested in the field of Neuroscience and has ranked in the top 25 nationally at the Brain Bee, a neuroscience competition. She is a proud member of the Girls Who Code organization and has designed a novel headphone alert system which is currently patent pending. She has pursued research projects involving Alzheimer's disease as well as water pollution which have placed at both the Synopsys Science Fair and the Bay Area Research Exposition. Currently she is interested in computational diagnostics.

Manohara is a rising senior at Glendora High School. His favorite subjects are mathematics and science. He has been an active member of the GHS Academic Decathlon Club, and currently serves as its president. In his spare time he likes to play tennis, video games, read books, and play piano. During his internship at City of Hope he learned how mathematics is applied in real-life situations. He hopes to continue his passion for math by pursuing a career in engineering.

Jan Pineda is going into her senior year at UC Santa Barbara as a chemistry major. She was a participant in City of Hope's Eugene and Ruth Roberts Summer Student Academy working under Dr. Lusine Tumyan in collaboration with Dr. Rockne to study the influence of pharmacokinetics in breast cancer research. After undergrad, she is interested in obtaining her masters in medicinal chemistry or pursuing a career in water chemistry. In her free time, she likes to spend time with her friends, family and her dog, Lucy.

Prativa Sahoo has 10 years of experience (including a Ph.D.) in the field of magnetic resonance imaging post-processing. She has been actively involved in the detailed study of MRI, perfusion imaging (DCE), diffusion imaging (DWI, DTI), mathematical modeling and algorithm development and implementation. She has extensive experience in Java and Matlab. In her four-year industry experience, she has worked closely with clinicians and radiologists to understand clinical needs and problems, and has designed and developed a DCE-MRI post-processing tool and validated it for 500 brain tumor patients. Currently, it is being used in multiple centers in India and abroad (Italy, Korea, Thailand and Nepal).

She has developed a new three-compartmental kinetic model for DCE-MRI post-processing and the work has been selected for coverpage publication in the Journal of Magnetic Resonance Imaging (JMRI). Over the years she has published 7 journal papers published and 26 ISMRM conference proceedings. She is interested in developing new algorithms and MR methodologies to answer various clinical questions and also to explore new areas like rs-fMRI and CEST imaging.

Ryan Sun is a rising senior at Temple City High School with a tremendous interest in Mathematics and Biology. He is also an active member of his school's Science Olympiad and Science Bowl teams. Aside from being a student, he is also a golfer and car enthusiast. As an intern at City of Hope, Ryan Sun was a member of the Eugene and Ruth Roberts Summer Student Academy working under Dr. Russell Rockne in the Division of Mathematical Oncology and Computational Systems Biology. He wishes to explore career opportunities in the fields of mathematics and biology as well as apply his  mathematical and scientific skills in a real world environment.

Lisa Uechi received her Ph.D. and M.Sc. in Informatics (Computer Science) from the Department of Intelligence Science and Technology, Kyoto University, Japan. The research subjects of her graduate program included computational biology and applied mathematics for the prediction of economic activities. In her research projects, she developed mathematical models for analyzing the dynamical pattern changes of population density and evaluating the damage expansion rate via a metabolic networks. She also proposed a novel method that could predict significant financial sectors along with the changes in economic trends by collaborating economists at Boston University.

After her graduate programs, she focused on information theory-based methods for data mining and applications for genetic data.  She proposed mathematical models and algorithms based on information theory to analyze the dependencies among the observed phenotypes and genetic variants. She created a model for evaluating the reliability of multi-variable interaction analysis based on the concept of communication channels for data with noise and missing values. She is currently working on the development of mathematical models based on thermodynamics and information theory for Acute Myeloid Leukemia.