Opportunity Awards

The CCBS Opportunity award competition is open to any UCI graduate student or postdoctoral researcher (including project scientists, specialists, etc.), who is present at the 2023 Sys Bio Retreat.  Any pair (or trio) of individuals who meet the above criteria may jointly submit a proposal for this year's competition following the instructions below. The progress reports from previous years' awardees are available below.

2023 - 2024

Testing and refining hypotheses

By hypothesis, we mean a provisional explanation for a phenomenon of interest. The successful project will use interdisciplinary methods to validate, distinguish between, or refine a hypothesis or hypotheses.  


•The proposed project must be a short-term (up to 1 year), feasible research investigation that answers a question related to the proposers’ research.•It must be interdisciplinary:  it must involve participation from at least two lab/research groups representing different disciplines or departments.•It must be a “new” project, and it must address the year’s theme.
•Your advisor/PI must agree to let you work on the project.•You/your team are expected to attend next year’s retreat and give a presentation on your progress (retreat registration fees are waived for opportunity awardees).
•Step I:  Before 5:00 PM on Wednesday, April 5, hand in (or email to Emi) a one paragraph abstract (can even be handwritten) briefly describing the nature of the project.
•Step II:  Send a more complete description (up to three pages) by email by MIDNIGHT on Monday, April 17, to Emi.
* The proposals will be judged by the CCBS faculty,  based on significance, interdisciplinarity, feasibility, responsiveness to theme.  *

2022 Award Winners!

Untangling Spaghetti and Meatballs: Theory-driven Feature Selection for Cell State Classification in Single Cell TranscriptomicsEmmanuel Dollinger (PI: S. Atwood and Q. Nie)

Venus Sosa Iglesias (PI: S. Atwood)

Kai Silkwood (PI: A. Lander)
Developmental & Cell Biology; Mathematics

Developmental & Cell Biology

Developmental & Cell Biology

Defining Epigenetic Drivers of Metastasis using the Cancer De-differentiation TheoryTatyana Lev (PI: D. Lawson)

Dennis Ma (PI: K. Kessenbrock)

Ashley Avila (PI: T. Downing)

SOM- Physiology & Biophysics

SOM - Biological Chemistry

Biomedical Engineering
Revealing the Role of Neutrophils in BCC Tumors Using Single-cell TrackingLulu Lai (PI: S. Atwood)

Pei Tan (PI: C. Miles)
Developmental & Cell Biology

Developing a system to understand the vasculature of endothelial cells and its role in mediating the progression of glioblastomaSarah Eldeen (PI: E. Botvinick)

Andres Guerrero (PI: P. Chang)
Biomedical Engineering

SOM - Radiological Sciences

Past Awardees

2018-2019 Awardees
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Characterizing the Transition Between Naïve and Primed States of Pluripotent ESCs in Different Mammalian SpeciesChristina Wilcox, Kate Williams PI - Ali Mortazavi

Linh Vuong, PI - Peter Donovan
Developmental & Cell Biology

Developmental & Cell Biology
Transcriptomic analysis of MCF-10A mammary epithelial acini in normal and invasive statesSorena Rahmanian, PI - Ali Mortazavi

Qingda Hu, PI - Elliot Botvinick
Developmental & Cell Biology

Biomedical Engineering and Surgery
Understanding cellular state transitions in the mammary gland microenvironment from a control theory perspectiveKevin Nee, PI - Kai Kessenbrock

Suoqin Jin, PI - Qing Nie
Biological Chemistry

Mathematics and Developmental & Cell Biology
Transitional states regulating macrophage heterogeneity in dystrophic muscleNick Pervolarakis, Quy
Nguyen, PI - Kai Kessenbrock

Jenna Kastenschmidt, PI - S. Armando Villalta
Biological Chemistry

Physiology & Biophysics
Methylation pseudotime: a novel tool for observing protein-DNA interactionsJulien Morival, PI - Tim Downing

Adam MacLean, PI - Qing Nie
Biomedical Engineering

Mathematics and Developmental & Cell Biology
Label-free, non-destructive determination of cell state using high throughput characterization of cell physical propertiesMatt Bovyn, PI - Jun Allard

Cody Combs, PI - Zuzanna Siwy
Physics and Astronomy and Mathematics

Physics and Astronomy
Optimal experimental design for feedback models of hematopoiesisLuis Martinez-Lomeli, PI - Babak Shahbaba/Volodymyr Minin

Abdon Iniguez, Shuxiong Wang, PI - John Lowengrub 

Prasanthi Tata, PI - Richard Van Etten

Mathematics, Biomedical Engineering and Chemical Engineering & Material Science

Hematology/Oncology, Department of Medicine

2019-2020 Awardees
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Variability and plasticity - That is: Research to understand diversity and difference, and its impact on phenotype and function.  Variability here refers to measurable differences across sets of genes, cells, molecules, networks, genotypes or organisms.

RNA Processing and Cell State Plasticity in the Colon Crypt

  • Amber Habrowski (Microbiology & Molecular Genetics) - Mariam Waterman Lab
  • Gabriela Balderrama (Developmental & Cell Biology) - Ali Mortazabi Lab









Multi-scale Analysis of Histone Acetylation Variability in the Cancer Genome to Predict Changes in Chromatin Function and Architecture

  • Navied Akhtar (Biomedical Engineering) - Tim Downing Lab
  • Alvaro Fletcher (Mathematics) - German Enciso Lab
  • Tessa Morris (Biomedical Engineering) - Anya Grosberg Lab







Elucidating Fibroblast and Pericyte Plasticity and their Roles in Cancer Using Temporal Single Cell RNA Sequencing of Microphysiological Cancer Models

  • Kevin Nee (Biological Chemistry) - Kai Kessenbrock Lab
  • Stephanie Hachey (Molecular Biology & Biochemistry) - Chris Hughes Lab

Plasticity and Diversity of Metastatic Breast Cancer Cells Revealed by Transcriptome Analysis

  • Gabriela Balderrama (Developmental & Cell Biology) - Ali Mortazavi Lab
  • Anastasia Ionkina (Chemistry) - Jennifer Prescher Lab

Identifying Altered Transcriptional Dynamics and Signaling Pathways in Vitiligo Affected Epidermis

  • Jessica Flesher (SOM Dermatology) - Anand Ganesan Lab
  • Lihua Zhang (Mathematics) - Qing Nie Lab
  • Suoqin Jin (CCBS) - Qing Nie Lab

Targeted Epigenetic Tools for the Control of Variability in Cardiac Differentiation of Patient-Derived iPSCs

  • Julien Morival (Biomedical Engineering) - Tim Downing Lab
  • Lily Widyastuti (Biological Chemistry) - Michael Zaragoza Lab

Variability and Plasticity of RAC1 and RHOA Signaling on Keratinocytes During Epidermal Regeneration

  • Rachel Cinco (Biomedical Engineering) - Michelle Digman Lab
  • Morgan Dragan (Biological Chemistry) - Xing Dai Lab

Examining the Mechanical Properties of Cells with Lamin A/C Mutations

  • Cody Combs (Physics and Astronomy) - Zusanna Siwy Lab
  • Richard Tran (Biomedical Engineering) - Anya Grosberg Lab
  • Michael Zaragoza Lab
2020-2021 Awardees
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Enriching Models with Health Data - Take advantage of existing data from medicine, health systems, epidemiology, or any other health related professions to build, enhance, or improve mathematical, computational or statistical models that inform scientific understanding, clinical practice, and/or public policy.  Datasets such as the Cancer Genome Atlas, Cell and Brain Atlases, health records, and COVID-19 epidemiological data are some of the many types of starting points that could be considered.


Connecting Oncogenic Transcription Factor Myc-Max Search Dynamics on DNA with its Genome Association ProfilingCarmen Al Masiri, PI - Jin Yu

Yi Dai, PI - Jing Zhang
Physics and Astronomy

Computer Science
Predicting Circadian Phase Clock Heterogeneity in Normal and Diseased Human Epidermis at a Single-cell LevelJunyan Duann, PIs - Bogi Anderson & John Lowengrub

Michelle Ngo, PIs - Babak Shahbaba & John Lowengrub

Rolando Ruiz, PIs - Arthur Lander & Anand Ganesan
Biological Chemistry


Development and Cell Biology
Modeling Clonal Evolution in MPNJonathan Vo, PI - John Lowengrub

Eric Bourgain-Chang, PI - Qing Nie

Brianna Hoover, PI - Angela Fleischman



Identifying Statin-Sensitivity Biomarkers in Blood CancersDennis Juarez, PI - David Fruman

Yingxin Cao, PI - Xiaohui Xie
Molecular Biology & Biochemistry

Computer Science
DNA Methylation and Copy Number Variation in Machine Learning Approaches for Predicting Tumor Progression in Colorectal CancerCharmeine Ko, PI - James Brody

Annie Trinh, PI - Tim Downing
Biomedical Engineering

Biomedical Engineering