Research Training Program: T32 in Integrated Training in Quantitative and Experimental Cancer Systems Biology (ICSB)

There is an outstanding need for a national cadre of quantitatively sophisticated oncologists, with deep training in both biological aspects of cancer and computational tools to further understanding and treatment. In the Research Training Program, OHSU leverages the strengths of both its cancer program, ranging from basic science to translation, and its computational capacity, spanning from genomics to mechanistic modeling. OHSU was recently ranked as the top young university in life sciences research in the world in the Nature Index. A key strength of the training program is required co-mentorship by both quantitative and wet-lab basic or clinical faculty. Post-doctoral trainees arriving with expertise in either biology or computation will receive extensive training in the complementary field, both didactic and research-based. Graduate trainees will engage both fields from day one in a specially designed curriculum building on existing courses and established faculty expertise, centered in the Departments of Biomedical Engineering and the Department of Cell, Developmental & Cancer Biology. The training faculty have outstanding track records in mentorship and research productivity, complemented by a healthy cohort of junior faculty to maintain program viability over the long term. Nearly 40 faculty are available to trainees, with an average of >$800,000/year in research funding.

The T32 program will award training fellowships typically on an annual basis depending on the number of trainee slots awarded by NIH and when prior trainees cycle off the fellowship.  In a typical year, fellowship applications will be processed roughly according to the following schedule: RFA posted in September, applications due in November, awardees notified in January , beginning of fellowship February 1.  Fellowships are awarded under the condition that both trainee and mentors participate in training activities, which include a two-hour session every other week in addition to annual activities.  In addition to stipend support, trainees are eligible to receive funds for T32-related travel and/or education.

The Research Training Program: T32 in Integrated Training in Quantitative and Experimental Cancer Systems Biology (ICSB) provides foundational basic and translational training to enable understanding and management of the behavior of cancer ecosystems, from both experimental and computational perspectives. Our proposal for ICSB is motivated by the appreciation that critical aspects of cancer genesis, progression, and response to therapy depend on inter- and intracellular interactions involving tumor-intrinsic and -extrinsic processes.

The goal of this ICSB program is to train postdoctoral fellows and graduate students in the productive application of both quantitative and experimental systems biology approaches for elucidation of the fundamental properties and behavior of evolving cancer systems, with the goals of enabling earlier detection of potentially lethal cancers, and/or developing more durable and tolerable treatment strategies for early and established cancers.

Lisa Coussens, Ph.D. - Program Co-Director
Cell, Developmental & Cancer Biology
Investigates immunemediated mechanisms regulating solid tumor development and response to therapies

Daniel Zuckerman, Ph.D. - Program Co-Director
Biomedical Engineering
Uses physics-based computational methods to study molecular, meso- and cell-scale systems

Anupriya Agarwal, Ph.D.
Knight Cancer Institute, Division of Hematology and Medical Oncology
Focuses on understanding the interplay of nature (genetic factors) and nurture (microenvironment) leading to leukemia initiation, progression, and drug resistance

Sudarshan Anand, Ph.D.
Cell, Developmental and Cancer Biology
Focuses on the function of noncoding RNAs in the tumor microenvironment

Kimberly Beatty, Ph.D.
Biomedical Engineering
Develops innovative chemical tools to elucidate the molecular basis of human diseases

Jonathan Brody, Ph.D.
Cell, Developmental & Cancer Biology & Department of Surgery
Focuses on many molecular aspects of pancreatic cancer, including developing ways to target a novel pro-survival network in pancreatic cancer cells and optimizing current targeted therapies used in the clinic

Lucia Carbone, Ph.D.
Knight Cardiovascular Institute, Epigenetics Consortium
Studies mechanisms of chromosomal instability during species evolution and organism development, with a focus on non-human primates

Young Hwan Chang, Ph.D.
Biomedical Engineering
Uses systems theory, computational biology, and machine learning/deep learning approaches to quantify multiscale imaging and provide quantitative architectural analysis of proteins, cells and tissues

Mushui Dai, M.D., Ph.D.
Molecular & Medical Genetics
Focuses on understanding tumor suppressor and oncogenic pathways in cancer using multidisciplinary approaches including molecular, cellular and biochemical, and mouse genetic analyses

Brian Druker, M.D., Ph.D.
Knight Cancer Institute, Division of Hematology and Medical Oncology
Uses integrated genomic and functional approaches to identify and validate new therapeutic targets in leukemia, and determining mechanisms of disease resistance to targeted agents

Catherine Galbraith, Ph.D.
Biomedical Engineering
Studies mechanisms of cell organization and migration in health and disease, and foundation funding to investigate the mechanobiology of metastasis

James Galbraith, Ph.D.
Biomedical Engineering
Studies mechanisms of cell organization and migration in health and disease, and foundation funding to investigate the mechanobiology of metastasis

Summer Gibbs, Ph.D.
Biomedical Engineering
Develops fluorescence imaging technology to improve cancer care, is highly translational with novel fluorophores under development for near term clinical translation, including for image-guided tumor resection

Jeremy Goecks, Ph.D.
Biomedical Engineering
Pursues projects at the intersection of scientific computing and computational cancer systems biology

Alexander Guimaraes, M.D., Ph.D.
Diagnostic Radiology
Develops quantitative, diagnostic tools aimed at accurately assessing the efficacy of novel small molecule targeted agents in the preclinical and clinical setting

Laura Heiser, Ph.D.
Biomedical Engineering
Uses integrated experimental and computational approaches to identify mechanisms of therapeutic response and resistance in cancer, and elucidate the role of microenvironmental signals in mediating cellular phenotype

Molly Kulesz-Martin, Ph.D.
Dermatology
Investigates clonal lineage models of benign, malignant, and metastatic keratinocytes with respect to altered differentiation, tumorigenic, and metastatic properties of skin/oral SCC

Sanjay Malhotra, Ph.D.
Cell, Developmental & Cancer Biology
Focuses on the design and discovery of synthetic and natural product inspired small molecules, which can provide insight into biological mechanisms and disease targets

Daniel Marks, M.D., Ph.D.
Pediatrics
Focuses on systems physiology and neuroscience of the sickness response to cancer and its treatment

Julia Maxson, Ph.D.
Knight Cancer Institute, Division of Hematology and Medical Oncology
Studies molecular evolution of leukemia using genomic, epigenomic and functional studies, involving close collaboration between wet lab biologists and computational scientists

Gordon Mills, M.D., Ph.D.,
Cell, Developmental and Cancer Biology
Uses systems biology approaches to predict tumor behavior and response to therapy with an emphasis on patient management and translational research

Amy Moran, Ph.D.
Cell, Developmental and Cancer Biology
Focuses on cross-talk between sex hormones and immune cell development and function

Xiaolin Nan, Ph.D.
Biomedical Engineering
Uses quantitative single-molecule and super-resolution imaging to understand spatial and temporal organization of oncogenic signaling

Naoki Oshimori, Ph.D.
Cell, Developmental and Cancer Biology
Uses murine models of squamous cell carcinoma (SCC), SCC cell lines, and SCC patient samples to identify cellular crosstalk and molecular pathways crucial for malignant progression

Ferdinando Pucci, Ph.D.
Oto. Head & Neck Surgery
Studies tumor-host communication with a focus on tumor-lymph node crosstalk

David Qian, Ph.D.
School of Medicine, Knight Cancer Institute
Studies molecular and cellular mechanisms of chemotherapy stress response and resistance, and the epigenetics of hypoxia

Megan Ruhland, Ph.D.
Cell, Developmental and Cancer Biology
Studies the immune system's response to cancer with the goal of re-educating immune cells to fight disease

Pepper Schedin, Ph.D.
Cell, Developmental and Cancer Biology
Studies the normal mammary gland microenvironment, and demonstrated that physiologically normal stromal plasticity contributes significantly to breast cancer risk, and poor prognosis of breast cancers that arise in young women

Carsten Schultz, Ph.D.
Chemical Physiology & Biochemistry
Develops tools to help understand the cell biology of signaling networks

Rosalie Sears, Ph.D.
Molecular & Medical Genetics
Focuses on cellular signaling pathways and transcriptional control mechanisms regulating cell phenotypes in response to microenvironmental influences and therapeutic stress, spanning basic, systems, and translational biology

Lawrence Sherman, Ph.D.
Oregon National Primate Research Center, Neuroscience Division.
Uses genetically-engineered mouse models and studies in human tissues to evaluate: (a) how chemotherapy influences the extracellular matrix of the hippocampus, and how blocking these changes can prevent cognitive changes in cancer patients following long-term high dose cancer therapies; and (b) how mutations linked to the peripheral nerve tumor predisposition syndrome schwannomatosis contribute to tumorassociated pain

Mara Sherman, Ph.D.
Cell, Developmental and Cancer Biology
Uses genetically-engineered mouse models, organoids, and patient derived models of pancreatic cancer to investigate how the tumor microenvironment impacts disease progression and response to therapy, with a focus on cancer-associated fibroblasts

Paul Spellman, Ph.D.
Molecular & Medical Genetics
Uses genomic technologies to understand the biology of cancer and develop strategies for early detection and prediction of therapeutic efficacy

Matthew Thayer, Ph.D.
Chemical Physiology & Biochemistry
Uses molecular genetic approaches to study novel cis-acting loci controlling chromosome-wide DNA replication and chromosome stability

Reid Thompson, M.D., Ph.D.
Radiation Medicine & Biomedical Engineering
Research interests focus on immunotherapy, genomics, clinical data science, precision medicine, and artificial intelligence in medical imaging

Jeffrey Tyner, Ph.D.
Cell, Developmental and Cancer Biology
Uses an integrative functional genomics approach on primary human specimens of heme malignancy

Josh Walker, M.D., Ph.D.
Radiation Medicine
Focuses on the rational combination of radiotherapy and immune modulation to prime and reactivate tumor-specific CD8 T cell immunity

Melissa Wong, Ph.D.
Cell, Developmental and Cancer Biology
Focuses on regulation of intestinal stem cells in development, tissue repair and disease, and developmental cell-cell fusion mechanism to generate hybrid cells in the context of metastatic cancer

Scott Wong, Ph.D.
Vaccine and Gene Therapy Institute
Utilizes molecular virology, biochemistry, functional genomics, immunological methods and nonhuman primate animal models to identify viral-determinants associated with gamma-herpesvirus mediated malignancies in simian immunodeficiency virus (SIV) infected rhesus macaques

Guanming Wu, Ph.D.
Department of Medical Informatics and Clinical Epidemiology
Focuses on (i) development of comprehensive open-source biological pathway and network databases and (ii) systems biology data analysis for cancer and other complex diseases

Zheng Xia, Ph.D.
Computation Biology Program & Molecular Microbiology and Immunology
Develops new computational biology tools for omics-data analysis to identify novel biological mechanisms in different physiological conditions like cancer

Xiangshu Xiao, Ph.D.
Chemical Physiology & Biochemistry
Develops innovative small molecule tools to understand and treat breast cancer and ovarian cancer

Daniel Zuckerman, Ph.D.
Biomedical Engineering
Develops and applies methods for computer simulation and experimental data analysis across bio-scales

Postdoctoral

Tahereh Ziglari, Ph.D.
Project: Novel prognostic/diagnostic tools to detect incipient 
tumorigenesis: contribution of extracellular vesicle-derived bio markers from senescent cells in induction of pro- or antitumorigenic immunity
Mentors: Ferdinando Pucci & Laura Heiser

Benjamin Sarno, Ph.D.
Project: Liquid-Biopsy Biomarker Screening for Therapeutic Design of Triple-Negative Breast Cancer Patients

Mentors: Gordon Mills & Jeremy Goecks

Predoctoral

Katie Blise, Ph.D. Candidate
Project: Single-Cell Spatial Analyses of the Tumor-Immune Ecosystem

Mentors: Lisa Coussens & Jeremy Goecks

Mona Hosseini, Ph.D. Candidate
Project: The mechanisms of RUNX1 mutations impacting hematopoiesis in familial platelet disorder syndrome

Mentors: Anupriya Agarwal & Emek Demir

Trainee Publications & Accolades

Katie Blise, graduate student in the Goecks lab and predoctoral trainee in the ICSB T32 training program (mentors: Drs. Lisa Coussens and Jeremy Goecks), has a recent 1st author publication titled, "Single-cell spatial architectures associated with clinical outcome in head and neck squamous cell carcinoma" in Nature-Precision Oncology.