July 1st 2022
CANDACE SAVONEN, M.S.
Business Address, Phone, & E-mail
Hutch Data Science Lab Phone: (734) 735 - 2469
Fred Hutchinson Cancer Center Email: firstname.lastname@example.org
Professional Social Media Handles
EDUCATION AND TRAINING
M.S. / 2018 Michigan State University, Neuroscience
Advisor: Alison Bernstein Ph.D.
Thesis project: Differentially methylated gene networks in Parkinson’s disease
B.S. / 2013 Oakland University, Biology
B.A. / 2013 Oakland University, Psychology
Fred Hutchinson Cancer Center
Johns Hopkins University
Other Non-JHU Professional Experience
Journal Articles (peer reviewed)
Savonen, Candace, Carrie Wright, Ava M. Hoffman, John Muschelli, Katherine Cox, Frederick J. Tan, and Jeffrey T. Leek. 2022. “Open-Source Tools for Training Resources OTTR.” Journal of Statistics and Data Science Education, October, 1–12. https://doi.org/10.1080/26939169.2022.2118646.
Shapiro, Joshua, Candace Savonen, Chante Bethell, Krutika Gaonkar, Yuankun Zhu, Miguel Brown, Nhat Duong, et al. 2021. “OMIC-14. OPENPBTA: AN OPEN PEDIATRIC BRAIN TUMOR ATLAS.” Neuro-Oncology 23 (Supplement_1): i40–40. https://doi.org/10.1093/neuonc/noab090.161.
Dang, Mai T., Michael V. Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, Sherjeel Arif, Li Zhai, et al. 2021. “Macrophages in SHH Subgroup Medulloblastoma Display Dynamic Heterogeneity That Varies with Treatment Modality.” Cell Reports 34 (13): 108917. https://doi.org/10.1016/j.celrep.2021.108917.
Kochmanski, Joseph, Candace Savonen, and Alison I. Bernstein. 2019. “A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-Methylcytosine and 5-Hydroxymethylcytosine Data in Neuroepigenetics.” Frontiers in Genetics 10 (September). https://doi.org/10.3389/fgene.2019.00801.
Saad, Manal H., Matthew Rumschlag, Michael H. Guerra, Candace L. Savonen, Alaina M. Jaster, Philip D. Olson, Adnan Alazizi, et al. 2019. “Differentially Expressed Gene Networks, Biomarkers, Long Noncoding RNAs, and Shared Responses with Cocaine Identified in the Midbrains of Human Opioid Abusers.” Scientific Reports 9 (1). https://doi.org/10.1038/s41598-018-38209-8.
Saad, Manal H., Candace L. Savonen, Matthew Rumschlag, Sokol V. Todi, Carl J. Schmidt, and Michael J. Bannon. 2018. “Opioid Deaths: Trends, Biomarkers, and Potential Drug Interactions Revealed by Decision Tree Analyses.” Frontiers in Neuroscience 12 (October). https://doi.org/10.3389/fnins.2018.00728.
Bannon, Michael J., Candace L. Savonen, Zachary J. Hartley, Magen M. Johnson, and Carl J. Schmidt. 2015. “Investigating the Potential Influence of Cause of Death and Cocaine Levels on the Differential Expression of Genes Associated with Cocaine Abuse.” Edited by Z. Carl Lin. PLOS ONE 10 (2): e0117580. https://doi.org/10.1371/journal.pone.0117580.
Bannon, Michael J., Candace L. Savonen, Hui Jia, Fabien Dachet, Steven D. Halter, Carl J. Schmidt, Leonard Lipovich, and Gregory Kapatos. 2015. “Identification of Long Noncoding RNAs Dysregulated in the Midbrain of Human Cocaine Abusers.” Journal of Neurochemistry 135 (1): 50–59. https://doi.org/10.1111/jnc.13255.
Articles, Editorials and Other Publications Not Peer Reviewed
Dang, Mai T., Michael Gonzalez, Krutika S. Gaonkar, Komal S. Rathi, Patricia Young, Sherjeel Arif, Li Zhai, et al. 2020. “Single-Cell Transcriptomic Profile Reveals Macrophage Heterogeneity in Medulloblastoma and Their Treatment-Dependent Recruitment,” February. https://doi.org/10.1101/2020.02.12.945642.
Savonen, Candace, Carrie Wright, Ava M. Hoffman, John Muschelli, Katherine Cox, Frederick J. Tan, and Jeffrey T. Leek. 2022a. “Open-Source Tools for Training Resources – OTTR.” https://arxiv.org/abs/2203.07083.
Blog post: https://www.ccdatalab.org/blog/7/25/19/overcoming-the-steep-data-science-learning-curve-in-childhood-cancer-research-using-workshop
Blog post: https://www.ccdatalab.org/blog/2020/5/29/openpbta-someone-is-wrong-on-the-internet-and-its-probably-us
Educational Resources and Software Tools
The ITN is a collaborative effort of researchers to catalyze informatics research through training opportunities (NCI UE5CA254170). ITN Courses are published on Leanpub and Coursera and on their own Bookdown websites.
Published ITN Courses:
A course to cover the basics of creating documentation and tutorials to maximize the usability of informatics tools.
Equip learners with reproducibility skills they can apply to their existing analyses scripts and projects. This course opts for an “ease into it” approach.
To equip learners with a deeper knowledge of the capabilities of reproducibility tools and how they can apply to their existing analyses scripts and projects.
To help learners find resources and tools to help them process and interpret their genomic data.
A self-guided tutorial to help users analyze processed gene expression data from refine.bio repository.
A short format workshop (3 – 5 days) to introduce pediatric cancer researchers to the basics of single-cell and bulk RNA-seq data analysis.
Classroom Instruction – Workshops
Increasing data analysis skills in the pediatric cancer community with the Childhood Cancer Data Lab training workshops
Differentially methylated gene networks in Parkinson’s disease
Microglia are more active in schizophrenia as evidenced by gene expression signatures
Differential expression of lncRNAs in the ventral midbrain of cocaine abusers
Dopamine-cell specific expression of long non-coding RNAs in the ventral midbrain
My interest is in making genomic data science tools more easily attainable to those who are looking to impactfully apply them to their areas of knowledge and expertise. I am passionate about creating educational materials which emphasize reproducibility and using scalable methods to disseminate educational materials. I have been involved in creating and delivering bioinformatic education materials for cancer genomics. My neuroscience background has helped me empathize with researchers who are looking to bridge the data science knowledge gap.
Bioinformatics, Data Science, Data Analysis, Education, Reproducibility, Gene Expression, Genomics