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June 8th 2023

CURRICULUM VITAE

CANDACE SAVONEN, M.S.

PROFESSIONAL DATA

Business Address, Phone, & E-mail

Hutch Data Science Lab                                        Phone: (734) 735 - 2469

Fred Hutchinson Cancer Center                                 Email: csavonen@fredhutch.org 

Professional Social Media Handles

        github: cansavvy

        website: cansavvy.com

Pronouns

        She/Her

EDUCATION AND TRAINING

Degrees

     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

PROFESSIONAL EXPERIENCE

Fred Hutchinson Cancer Center

Johns Hopkins University

Alex’s Lemonade Stand Foundation

Graduate Student Work


PUBLICATIONS

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

Afiaz, Awan, Andrey Ivanov, John Chamberlin, David Hanauer, Candace Savonen, Mary J Goldman, Martin Morgan, et al. 2023. “Evaluation of Software Impact Designed for Biomedical Research: Are We Measuring What’s Meaningful?” https://arxiv.org/abs/2306.03255.

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.

Savonen, Candace, Carrie Wright, Ava M. Hoffman, Elizabeth M. Humphries, Katherine E. L. Cox, Frederick J. Tan, and Jeffrey T. Leek. 2023. “Motivation, Inclusivity, and Realism Should Drive Data Science Education.” https://arxiv.org/abs/2305.06213.

PRACTICE ACTIVITIES

Media Dissemination

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

PART II

TEACHING

Educational Resources and Software Tools

        github: https://github.com/fhdsl/Tools_for_Reproducible_Workflows_in_R 

github: https://github.com/jhudsl/OTTR_Template/ 

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.

github: https://github.com/jhudsl/Documentation_and_Usability 

Equip learners with reproducibility skills they can apply to their existing analyses scripts and projects. This course opts for an “ease into it” approach.

github: https://github.com/jhudsl/Adv_Reproducibility_in_Cancer_Informatics 

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.

github: https://github.com/jhudsl/Reproducibility_in_Cancer_Informatics 

To help learners find resources and tools to help them process and interpret their genomic data.

github: https://github.com/fhdsl/Choosing_Genomics_Tools 

A self-guided tutorial to help users analyze processed gene expression data from refine.bio repository.

github: https://github.com/AlexsLemonade/refinebio-examples 

A short format workshop (3 – 5 days) to introduce pediatric cancer researchers to the basics of single-cell and bulk RNA-seq data analysis.

github: https://github.com/AlexsLemonade/training-modules

Classroom Instruction – Workshops

PRESENTATIONS

Scientific Meetings

Oral Presentations

DataTrail - building inclusive data science communities

Increasing data analysis skills in the pediatric cancer community with the Childhood Cancer Data Lab training workshops

Poster Presentations

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

ADDITIONAL INFORMATION

Personal statement

My interest is in making data science tools more easily attainable to those who are looking to impactfully apply them to their areas of knowledge and background. I am passionate about creating educational materials which emphasize reproducibility and using scalable methods to disseminate educational materials. I believe that as a part of the data science community, we need to work to become a more inclusive work environment. This would not only create better science, but would widen the circle for individuals who are currently underrepresented in data science. 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.

Keywords

Bioinformatics, Data Science, Data Analysis, Education, Reproducibility, Gene Expression, Genomics