Dr. Kai Tan Uses Systems Biology to Identify Targets for Combination Therapies
Kai Tan, Ph.D., a CSBC investigator at Children’s Hospital of Philadelphia, has always been fascinated by things that are complicated. This led him from graduate studies of genetic networks in bacteria to his current work using systems approaches to understand complex biological interactions during development and disease.
In this interview, Dr. Tan shares his views on systems biology, his advice for students and trainees, and his CSBC research to identify targets for combination therapy based on gene regulatory networks in a high-risk pediatric cancer.
Dr. Trachette Jackson Uses Mathematical Modeling to Improve Treatment Strategies for Cancer
Dr. Trachette Jackson, a CSBC investigator at the University of Michigan, uses data-driven mathematical modeling to identify the best cancer treatment strategies to translate into the clinic.
During her undergraduate training in math, she heard a talk about mathematical biology by a pioneer in the field. This lecture helped her realize that she wanted to pursue a career combining math and the life sciences.
This led her to graduate school in applied math where she started to venture into mathematical oncology. During one of her courses, she ended up meeting some chemists who worked at Bristol Myers Squibb on drug targeting and cancer. They became her mentors and experimental collaborators as she started developing mathematical models to figure out the best ways to deliver cancer drugs for her dissertation.
Now, as a professor and researcher, she constructs models using differential equations to improve the dosing schedule of combination cancer treatments.
Portia Thomas Advocates for Black Lives and Uses Systems Biology to Study Cancer in Diverse Patient Populations
Portia Thomas, an M.D./Ph.D. student and CSBC junior investigator at Meharry Medical College, loves working with children. Even though she is busy with medical school and her thesis research, she makes time to mentor and teach young students. Based on this passion, Portia wants to be a pediatric oncologist and research therapies for pediatric brain tumors as a physician-scientist.
Dr. Kevin Janes Uses Systems Biology to Answer Questions About Breast Cancer
Kevin Janes, Ph.D., is a CSBC investigator at the University of Virginia who enjoys skiing with his wife and two daughters. He’s hoping for a snowy winter, so he can apply his engineering knowledge to speeding down the slopes. As an undergraduate, he studied biomedical engineering and Spanish. This led him to a Fulbright Scholarship research experience in Spain, where he showed that a biopolymer could be used to deliver chemotherapeutics. Now, he uses systems approaches to study breast cancer.
Dr. Stacey Finley Builds Computational Models to Understand and Exploit Metabolic Dependencies in Cancer
Stacey Finley, Ph.D., a CSBC Investigator at the University of Southern California (USC), is working to identify new drug targets for cancer by studying the disease as a system of biochemical reactions. She trained in chemical engineering, since she was excited by the application of math, physics, and chemistry to solve problems. As an undergraduate, she applied her knowledge to manufacturing processes at Procter & Gamble through three summer internships. She worked to optimize refining processes for a product additive, maximize the efficiency of bar soap production, and designed experiments to understand which factors in a system contribute to the physical characteristics of dry laundry detergent particles. Now, Dr. Finley uses engineering tools to answer biological questions about human health.
Dr. Arjun Raj Uses Single-Cell Systems Approaches to Understand Melanoma
Arjun Raj, Ph.D., a CSBC investigator at the University of Pennsylvania, uses systems biology approaches to study therapeutic resistance in melanoma. With a background in mathematics and physics, he pursued a Ph.D. focused on mathematical biology at the Courant Institute of New York University. After his first year as a graduate student, Arjun told his advisor, Charlie Peskin, that he wanted to see what it was really like in a molecular biology lab. Charlie introduced him to Sanjay Tyagi (via Fred Kramer), who was developing molecular beacons for RNA detection at the Public Health Research Institute. Arjun worked in Sanjay’s laboratory every day that summer which ignited his interest in biological research.
Dr. Juan Fuxman Bass uses systems biology to understand cancer-specific molecular interactions
Juan Fuxman Bass, a CSBC investigator at Boston University, studied biology as an undergraduate and graduate student at the University of Buenos Aires in Argentina. Now, he uses systems approaches to investigate the role of gene regulatory networks in cancer.
Dr. Darryl Shibata is Investigating the Evolution of Cancer at Multiple Scales
Darryl Shibata, M.D., is a CSBC investigator at the University of Southern California (USC) who uses evolutionary models to advance cancer systems biology. According to him, “the principles of evolution fit naturally into systems biology, since biology is basically built by evolution.”
Dr. Marian Waterman: Investigating Non-Genetic Heterogeneity in Colon Cancer
Marian Waterman, Ph.D., a CSBC investigator at the University of California, Irvine (UC Irvine), began her career as a biochemist using reductionist approaches to investigate gene transcription. As a young investigator, she moved into cancer biology and studied the role of a transcription factor family in colon cancer. Later, the focus in her lab shifted as she realized that a systems biology approach could take data from reductionist experiments and place it in a larger context. Now, Marian integrates mathematical modeling with experimentation to study tumor heterogeneity.
Dr. Peter Sorger Constructs Models of Responsiveness and Resistance to Cancer Therapies
Peter Sorger, Ph.D., a CSBC investigator at Harvard Medical School, constructs and validates network-level models of pharmacological actions. As a graduate student in England, he characterized one of the first eukaryotic transcription factors involved in stress responses. Later, he used his critical thinking and analytical skills to investigate chromosome segregation as a postdoc in the lab of Dr. Harold Varmus. This eventually led him to studies of cell transformation, cell death, and signal transduction. Now, he uses systems approaches to understand the mechanisms of response and resistance to cancer treatments. In this interview he discusses his views on cancer systems biology, shares his perspective on collaboration, and describes his CSBC research.
Dr. Vito Quaranta Uses Computational Models to Study the Complexities of Tumor Heterogeneity
Vito Quaranta, M.D., a CSBC Investigator at Vanderbilt University, uses systems approaches to study heterogeneity and treatment responses in cancer. As a young investigator, he created antibodies that could target tumor-specific antigens in pancreatic tumors. One of these antigens turned out to be a cell adhesion protein and led him into the field of cell adhesion and migration. In the early 2000s, he started using systems biology approaches in his cell adhesion research and built cellular-level models integrating cancer cell interactions with the extracellular matrix. Now, he is investigating how lung cancer cells adapt to different microenvironments and cancer treatments.
Dr. Melissa Kemp Uses Computational Models to Understand Redox Metabolism in Cancer
Melissa Kemp, Ph.D., a CSBC investigator at the Georgia Institute of Technology, studies the metabolic state of cells and how it affects cell signaling pathways. During her postdoc, she trained with several current CSBC members, including Doug Lauffenburger, Peter Sorger, and Forest White, at the Massachusetts Institute of Technology (MIT) Cell Decision Process Center. Now, she uses systems biology approaches to understand redox metabolism in tumors.
Dr. Aaron Meyer Identifies Combination Therapies for Lung Cancer
Aaron Meyer, Ph.D., a CSBC investigator at the University of California, Los Angeles (UCLA), uses systems approaches to improve the development of new drugs for cancer patients. His lab combines biological experiments with data-driven models to identify effective drug combinations for lung cancer. Models allow him to think about biology in an innovative way, define hypotheses, and communicate his findings.
Dr. Andrea Califano Investigates Regulatory Mechanisms in Cancer Using Computational Algorithms and Biological Experiments
Columbia University CSBC Investigator Andrea Califano, Ph.D., studies proteins that control cellular networks, known as master regulators, and their role in cancer progression.
As a post-doc in physics at MIT, he was excited by the emerging areas of artificial intelligence and machine vision. Then, he worked for IBM, first developing algorithms for pattern discovery and then applying mathematical models to biological data. However, according to him, he transitioned to academic systems biology research because, “I wanted to put my money where my mouth was and have a chance to experimentally validate my computational predictions.”
Dr. Diana Murray Encourages Students to Consider Careers in Cancer Systems Biology
Diana Murray, Ph.D., is a CSBC Investigator and the Outreach Core Leader at the Center for Cancer Systems Therapeutics (CaST) of Columbia University.
Along with computational biology investigations, Dr. Murray helps public school and post-baccalaureate students learn about career paths in basic research. She wants to give young people the chance to experience scientific studies in a multi-disciplinary field that integrates diverse interests.
She likes studying science and riding a motorcycle for similar reasons: “Both tasks are challenging and require deep concentration.”
Dr. Joe Gray: A Nuclear Physicist Who Studies Tumor Heterogeneity
Joe Gray, Ph.D., a CSBC Investigator at Oregon Health and Science University (OHSU), views systems biology as the application of experimental and computational tools to understand and predict the behavior of biological systems.
His lab is developing tools, including molecular profiling and multiscale imaging technologies, to explore the components and multiscale organization of cancer systems. Using these approaches, he wants to find better ways to control and treat cancer.
Dr. Douglas Lauffenburger Investigates Cancer Biology from an Engineering Perspective
Doug Lauffenburger, Ph.D., a CSBC Investigator at the Massachusetts Institute of Technology (MIT), has been integrating engineering and computation with biology throughout his long career. When describing his research journey, he said, “Systems biology was established and coined around 2000, but I didn’t see it as anything different from what I had already been doing for 20 years.”
Dr. Nevan Krogan: Generating a Map of Biological Networks in a Cancer Cell
Dr. Nevan Krogan, a CSBC Investigator and Director of the Quantitative Biosciences Institute at the University of California, San Francisco (UCSF), develops tools to study quantitative changes in biomolecules.
Dr. Trey Ideker: Mapping the Circuitry of a Cancer Cell
Trey Ideker, Ph.D., a CSBC Investigator at the University of California, San Diego (UCSD), is working to map the circuits of a cancer cell.
After training in electrical engineering, he found himself, like many other engineering and computer science graduates, working in the defense sector. However, according to Dr. Ideker, “the fact that I was facilitating mass destruction didn’t sit well on my conscience, so I knew that I needed to find a different career.”
Dr. Sylvia Plevritis Engineers Analytical Approaches to Understand Cancer Metastasis
Sylvia Plevritis, Ph.D., a CSBC Investigator at Stanford University, develops computational tools to analyze genomic and imaging data related to cancer metastasis, the progressive spread of cancer cells from an initial tumor to another part of the body.
Dr. Mark Lemmon Brings Biochemistry Expertise to Cancer Systems Biology
Mark Lemmon, Ph.D., a CSBC Investigator at Yale University, is a biochemist who examines molecular mechanisms and integrated networks in cancer. In this interview, he discusses research collaborations, the application of systems approaches for cancer research, and emerging areas for cancer systems biology.
Dr. Andrea Bild Enjoys the Challenging Terrain of Cancer Systems Biology
CSBC Investigator Andrea Bild, Ph.D., is a Professor in the Division of Molecular Pharmacology at City of Hope Medical Center in Duarte, CA. She is an avid hiker who has trekked up mountains in Utah and Colorado to admire the beauty of nature. Similarly, as a scientist and cancer researcher, she has set out on a journey to understand the complex landscape of cancer.
Dr. Ellen Langer Differentiated from a Cell Biologist to an Expert in Tumor Heterogeneity
Ellen Langer, Ph.D., a CSBC junior investigator at Oregon Health and Science University (OHSU), trained as a cell biologist and studied cellular plasticity at Washington University in St. Louis and the University of Utah. This work led to her current studies examining breast cancer cell phenotypes using systems biology approaches.
Dr. Nathan Reticker-Flynn Follows the Beat of Biological Systems in Cancer
There are many similarities between science and music, including quantitative patterns within elaborate compositions. In this interview, Nathan discusses his views on systems biology and its application to understanding cancer metastasis and immunotherapy.
Dr. Scott R. Manalis Uses Physics and Engineering to Study Cancer Cells
Scott Manalis, Ph.D., a CSBC Investigator at the Massachusetts Institute of Technology (MIT), has always been interested in coming up with new types of measurements and ways to push the limits of quantitative approaches. His enthusiasm for using a wide range of analytical skills to solve complex problems led him to study Physics at the University of California, Santa Barbara and Stanford University.
Dr. Christina Leslie: Solving Cancer Biology Questions with Computational Models
Christina Leslie, Ph.D., a CSBC investigator at Memorial Sloan Kettering, trained as a mathematician in differential geometry and Lie theory. However, after graduate school, she moved into computational biology and cancer research.
In this interview, she describes her career path, systems biology approaches, and her recent findings related to immune cell heterogeneity in cancer.