CV
Caitlin Guccione
Bioinformatics Ph.D. Student
cguccion@ucsd.edu
(630) 336-3386
Interests : Cancer Microbiome, Mathematical Biology, Bioinformatics, Oncology
Education
Ph.D. Bioinformatics & Systems Biology
University of California, San Diego
September 2020 - Present
- Thesis : Cancer Microbiome + Microbial Modeling
- Advisors : Dr. Kit Curtius & Dr. Rob Knight
M.S. Applied Mathematics
University of Rhode Island
September 2018 - August 2020
- Final Project : Stochastic Models with Applications to Genetics, Cancer, AIDS & Biomedical Systems
B.S. Applied Mathematics & B.A. Computer Science
University of Rhode Island
September 2016 - May 2020
- Minor : Biological Sciences
- Honors : magna cum laude, University of Rhode Island Honors Program
- Extracurriculars : NCAA DI Student-Athlete, School Record Holder
Publications
Sepich-Poore GD * , Guccione C * , Laplane L, Pradeu T, Curtius K, Knight R. Cancer’s second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays. 2022 Mar 6:e2100252. doi: 10.1002/bies.202100252. Epub ahead of print. PMID: 35253252. * Authors contributed equally. PubMed
Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. Challenges in Determining the Role of Microbiome Evolution in Barrett’s Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms. 2021 Sep 22;9(10):2003. doi: 10.3390/microorganisms9102003. PMID: 34683324; PMCID: PMC8541168. PubMed
Loh JW, Guccione C, Di Clemente F, Riedlinger G, Ganesan S, Khiabanian H. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data. Bioinformatics. 2020 Apr 1;36(7):2173-2180. doi: 10.1093/bioinformatics/btz865. PMID: 31750888; PMCID: PMC7141867. PubMed
Preprints
Ghosh, P., Campos, V., Vo, D., Guccione, C., Goheen-Holland, V., Tindle, C., Mazzini, G., He, Y., Alexandrov, L., Lippman, S., Gurski, R., Das, S., Yadlapati, R., Curtius, K. and Sahoo, D., 2022. AI-assisted Discovery of an Ethnicity-influenced Driver of Cell Transformation in Esophageal and Gastroesophageal Junction Adenocarcinomas. bioRxiv
Presentations
Invited Seminars
- Community Assembly Dynamics of the Microbiome in Premalignant Barrett’s Esophagus
- Structural and Functional Genomics Annual Retreat, March 2022
Experience
Graduate Reserach Assistant
University of California, San Diego
September 2020 - Present
- Exploring the intersection of the human microbiome with gastrointestinal precancers and cancers
- Applying mathematical modeling to cancer evolution
Undergraduate Reserach Assistant
University of Rhode Island
January 2018 - September 2020
- Adviosr : Dr. Rachel Schwartz
- Performing various machine learning techniques using scikit-learn
- Developing a clearer picture of evolution to begin identifying which traits lead to speciation
- Categorizing potential noise in phylogenetic markers
- Poster presentation : Rethinking the Evolutionary Tree of Life using Machine Learning
Informatics Intern
Agios Pharmaceuticals
Summer 2019
- Created a user-friendly guide to setting up informatics projects with reproducible research techniques
- Implemented a LIMS (Laboratory Information Management System) using the Workflowr package in R for the informatics group
Discrete Mathematics & Theoretical Computer Science Research Experience for Undergraduates
Rutgers Cancer Institute of New Jersey
Summer 2018
- Adviosr : Dr. Hossein Khiabanian
- Determined evolutionary patterns in cancerous mutations by sequencing tumors
- Tracked the growth of particular mutations using mathematical trees
- Created a program which insured each sample had a correct purity reading
- Participated in Midsummer Combinatorial Workshop at Charles University, Prague
- Project website : Elucidating Tumor Evolutionary Patterns Using High-Depth Molecular Data
Data-Intensive Scientific Computing Research Experience for Undergraduates
University of Notre Dame
Summer 2018
- Adviosr : Dr. Douglas Thain
- Provided an easier and faster way to execute bioinformatic workflows for clinicians and scientists who do not specialize in computer science
- Used high throughput computing and Amazon Web Services
- Project video : Simplifying Bioinformatics Workflows
Awards
Training Grants
- NIH Training Grant in Bioinformatics (Fall 2020 - Summer 2021)
Travel Grants
- ACM Richard Tapia Scholarship (2019)
- Grace Hopper Scholar (2018)
Academic Honors
- Biology Department Alpha Research Award (Univ. of Rhode Island - 2020)
- Winifred P. Kelley Award of Academic Excellence (Univ. of Rhode Island - 2017)
- Winifred B. Keaney Award (Univ. of Rhode Island - 2020)
Professional Skills
- Programming Languages
- Python
- R / RStudio
- Java
- Perl
- C++
- C
- Mathematica
- MATLAB
- Linux Command Line
- Github
- Amazon Web Services
- Microsoft Office
Memberships
- Graduate Bioinformatics Council, 2020 - Current
- Community Event Chair, 2021 - Current
- Member of Outreach Committee, 2020- Current
- Graduate Women in Computing: Member, 2018 - Current
Outreach
- Organized Bioinformatics Workshop for Girls Inc. San Diego, April 2022
Invited Journal Referee
- Journal of Gastrointestinal Cancer
