Curriculum Vitae
Research Interests
- Understanding gene regulation dynamics through the study of epigenetic modifications, mainly DNA methylation.
- Understanding contributors to cancer relapse following immunotherapy and how alternative immunotherapies can slow or prevent relapse.
Education
University of California, Los Angeles, Los Angeles, California
Ph.D., Human Genetics, August 2016 - June 2021
- Advisor: Prof. Matteo Pellegrini
- Dissertation: Assessing human health using DNA methylation based predictive models
- Dissertation Committee: Matteo Pellegrini, Xia Yang, Jae-Hoon Sul, Aldons J. Lusis
- Supported by NIH T32 CA201160-01 Biomedical Big Data (2018 - 2019)
University of Utah, Salt Lake City, Utah
M.P.H., Public Health, August 2011 - June 2013
- Advisors: Professors Lisa Gren and David Sundwall
- Practicum: Disconcerting headache practice patterns in academic primary care.
University of Utah, Salt Lake City, Utah
B.S., Chemistry, August 2006 - December 2010
Experience
University of California, Los Angeles Postdoctoral Fellow, Pellegrini Lab, June 2021 – Present
- Manage several parallel research projects, completing simultaneous tasks and delegating appropriate tasks to assistants
- Carry out large scale data processing on high performance computing clusters and AWS
- Instituted lab wide version control best practice to ease collaboration and foster reproducibility
University of California, Los Angeles Graduate Student Researcher, Pellegrini Lab, August 2016 – June 2021
- Designed an integrated measure of type two diabetes and fit a DNA methylation based predictive model to this measure
- Built a high performance bisulfite sequencing processing platform written in C, C++, and Python
- Developed a novel statistical model of epigenetic aging to model non-linear epigenetic aging and open sourced the model as a Python package
- Built an analysis pipeline to assess inactivation of CAR T-cell therapy vectors following product infusion using DNA methylation and vector integration location
- Designed a targeted bisulfite sequencing method and implemented an optimized analysis pipeline
- Collaborated with researches, clinicians, and support staff to implement research projects and meet project goals
University of Utah School of Medicine Lab Specialist, Phillips Lab, February 2014 – August 2016
- Analyzed sequencing data to identify causative genetic variants in clinical cases diagnosed with iron homeostasis and heme synthesis disorders
- Integrated PacBio, Oxford Nanopore, and Illumina sequencing data to assemble a high quality reference genome for the Babraham pig breed with intact T-Cell Receptor loci for vaccine development
- Performed CRISPR KO analysis to identify ligands targeted by a ubiquitous cancer killing T-Cell line
Open Source Software Tools
BSBolt (Python, C, C++) – High performance bisulfite sequencing processing platform; bsbolt.readthedocs.io Epigenetic Pacemaker (Python) – Evolutionary model of epigenetic aging; epigeneticpacemaker.readthedocs.io
Computer Skills
- Languages
- Proficient - Python
- Competent - C, C++, R, Bash
- Unit Testing
- System - Linux/UNIX, MacOS
- Tools - Git, Jupyter, SGE, AWS, SLURM, Anaconda, Vim
Teaching
Research Immersion Laboratory in Genomic Biology at UCLA(Spring 2018, Spring 2019) Instructed laboratory class for upper division molecular biology students at UCLA. In the laboratory class I introduced bioinformatics tools and workflow utilized to perform a quarter long genome annotation project. (Review available upon request)
Mentoring
- Huling Huang (Bruins In Genomics Undergraduate Researcher, Summer 2018): Modeled non-linear epigenetic aging trends in publicly available datasets and compared epigenetic aging trends across distinct populations.
- Maria Malikwa (Santa Monica College Summer Scholars, Summer 2018): Designed a DNA methylation based predictor of folic acid levels in pregnant women.
- Ibrahime Wone (Santa Monica College Summer Scholars, Summer 2019): Built a non-linear DNA methylation based predictive model for type two diabetes progression.
- Adewale Oytetunde (UCLA-CSUN Stem Cell Bridges Program, August 2018 - August 2019): Modeled methylation dynamics during cellular differentiation and how the DNA methylation landscape is altered by induced pluripotency.
- Kalsuda Lapborisuth (UCLA Undergraduate Research Fellow, August 2018 - Present) Developing a simulation framework for modeling epigenetic age acceleration in response to physiological stress and is validating the framework using publicly available methylation datasets.
Publications
- Larison, B., Pinho, G. M., Hagani, A., Zoller, J. A., Li, C. Z., Finno, C. J., Farrell, C., Kaelin, C. B., Barsh, G. S., Wooding, B., Robeck, T. R., Maddox, D., Pellegrini, M. & Horvath, S. Epigenetic models predict age and aging in plains zebras and other equids. bioRxiv (2021)
- Pinho, G. M., Martin, J. G. A., Farrell, C., Haghani, A., Zoller, J. A., Zhang, J., Snir, S., Pellegrini, M., Wayne, R. K., Blumstein, D. T. & Horvath, S. Hibernation slows epigenetic aging in yellow-bellied marmots. BioRxiv 2021.03.07.434299 (2021)
- Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform. GigaScience (2021)
- Li, S., Ma, F., Yokota, T., Jr., G. G., Palermo, A., Wang, Y., Farrell, C., Wang, Y.-C., Wu, R., Zhou, Z., Pan, C., Morselli, M., Teitell, M. A., Ryazantsev, S., Fishbein, G. A., ten Hoeve, J., Arboleda, V. A., Bloom, J., Dillon, B., Pellegrini, M., Lusis, A. J., Graeber, T. G., Arumugaswami, V. & Deb, A. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2–induced systemic toxicity. JCI Insight 6, (2021).
- Farrell, C., Snir, S. & Pellegrini, M. The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. Bioinformatics 36, 4662–4663 (2020).
- Nowicki, T. S., Farrell, C., Morselli, M., Rubbi, L., Campbell, K. M., Macabali, M. H., Berent-Maoz, B., Comin-Anduix, B., Pellegrini, M. & Ribas, A. Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy. Cancer Discov. (2020). doi:10.1158/2159-8290.CD-20-0300
- Morselli, M., Farrell, C., Rubbi, L., Fehling, H. L., Henkhaus, R. & Pellegrini, M. Targeted bisulfite sequencing for biomarker discovery. Methods (2020). doi:10.1016/j.ymeth.2020.07.006
- Wu, R., Ma, F., Tosevska, A., Farrell, C., Pellegrini, M. & Deb, A. Cardiac fibroblast proliferation rates and collagen expression mature early and are unaltered with advancing age. JCI Insight 5, (2020).
- Levine, M., McDevitt, R. A., Meer, M., Perdue, K., Di Francesco, A., Meade, T., Farrell, C., Thrush, K., Wang, M., Dunn, C., Pellegrini, M., de Cabo, R. & Ferrucci, L. A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin. Elife 9, (2020).
- Crowther, M. D., Dolton, G., Legut, M., Caillaud, M. E., Lloyd, A., Attaf, M., Galloway, S. A. E., Rius, C., Farrell, C. P., Szomolay, B., Ager, A., Parker, A. L., Fuller, A., Donia, M., McCluskey, J., Rossjohn, J., Svane, I. M., Phillips, J. D. & Sewell, A. K. Genome-wide CRISPR-Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1. Nat. Immunol. 21, 178–185 (2020).
- Snir, S., Farrell, C. & Pellegrini, M. Human epigenetic ageing is logarithmic with time across the entire lifespan. Epigenetics 14, 912–926 (2019).
- Phillips, J., Farrell, C., Wang, Y., Singal, A. K., Anderson, K., Balwani, M., Bissell, M., Bonkovsky, H., Seay, T., Paw, B., Desnick, R. & Bloomer, J. Strong correlation of ferrochelatase enzymatic activity with Mitoferrin-1 mRNA in lymphoblasts of patients with protoporphyria. Mol. Genet. Metab. 128, 391–395 (2019).
- Orozco, L. D., Farrell, C., Hale, C., Rubbi, L., Rinaldi, A., Civelek, M., Pan, C., Lam, L., Montoya, D., Edillor, C., Seldin, M., Boehnke, M., Mohlke, K. L., Jacobsen, S., Kuusisto, J., Laakso, M., Lusis, A. J. & Pellegrini, M. Epigenome-wide association in adipose tissue from the METSIM cohort. Human Molecular Genetics 27, 1830–1846 (2018).
- Yaish, H. M., Farrell, C. P., Christensen, R. D., MacQueen, B. C., Jackson, L. K., Trochez-Enciso, J., Kaplan, J., Ward, D. M., Salah, W. K. & Phillips, J. D. Two novel mutations in TMPRSS6 associated with iron-refractory iron deficiency anemia in a mother and child. Blood Cells Mol. Dis. 65, 38–40 (2017).
- Farrell, C. P., Overbey, J. R., Naik, H., Nance, D., McLaren, G. D., McLaren, C. E., Zhou, L., Desnick, R. J., Parker, C. J. & Phillips, J. D. The D519G Polymorphism of Glyceronephosphate O-Acyltransferase Is a Risk Factor for Familial Porphyria Cutanea Tarda. PLoS One 11, e0163322 (2016).
- Farrell, C. P., Parker, C. J. & Phillips, J. D. Exome sequencing for molecular characterization of non-HFE hereditary hemochromatosis. Blood Cells Mol. Dis. 55, 101–103 (2015).
