Career Profile
Biomedical data specialist with a passion for data harmonization, seeking new opportunities working with life science data ecosystems. I have spent the last 5 years working to build biomedical data platforms, and my 10+ years of research experience in molecular biology and genomics allow me to understand the needs of the scientific community and serve as a liaison between users, stakeholders, and developers.
Experience
Data modeling to support a cohort browser for patient health data. My efforts focused on the OMOP common data model for clinical data and building/providing expertise needed to support product strategy, as well as ETL and integration with complex variant information and omics data.
- Mapping of clinical datasets to OMOP CDM
- Market research on clinical data models and analysis ecosystems
- Led PoC for a data obfuscation tool that reduced complexity of testing workflow
- Helped lead PoC for Collibra data catalog
- Member of OHDSI Genomics Working Group
Data wrangling and product management for the Computational Genome Analysis Platform project, an end-to-end platform for clinical genomics workflows from raw sequencing data to variant interpretation. I led the data model design and managed data submissions to the platform, and planned and defined new platform features.
- Data model design
- Onboarded new users and projects
- Software development for data ingestion and mapping to data model
- Product management of data submission tool and variant interpretation module
- Led interviews with clinicians to understand user needs
- Define product requirements for software developers
Data wrangling for the 4D Nucleome Data Coordination and Integration Center, a repository for genomics and microscopy experimental data and metadata. I work with a large consortium of 100+ labs to ingest new datasets, implement data standards, and adhere to FAIR principles. I use REST APIs with python to manage data and metadata, and contribute to data model and software development.
- Data model design
- Managed new data submissions
- Scientific publication and user-facing documentation
- Optimized ontology processing code and submitted terms to public ontologies
- Participated in consortium working groups to set genomics and microscopy data standards
- Member of Common Fund Data Ecosystem Ontology Working Group
I studied the large ciliate Stentor coeruleus, a model for single cell regeneration. I was involved in the Stentor genome project, and investigated the role of CDKs in regeneration of cellular features.
- Managed collaborations with scientists at other institutions
- Generated and analyzed RNA-Seq data
- Discovered Stentor’s unusual 15 bp intron size
- Used HMMs and molecular evolution approaches to classify Stentor kinases into families
- Mentored graduate students
I studied the maintenance and replication of the plastid genome in the Apicomplexan parasite Toxoplasma gondii. I constructed conditional genetic mutants and used fluorescence microscopy and qPCR assays to show that the histone-like HU protein is essential for apicoplast DNA replication and proper plastid segregation.
I examined the function of the mtDNA polymerase PolIA in the parasite Trypanosoma brucei. I used RNAi to knock down the gene and designed assays with DNA damaging agents to probe a function in mtDNA repair.
I was investigating the role of p53 in DNA double strand break repair. I worked with mice and measured rates of homologous recombination and non-homologous end-joining in p53+/+, p53+/-, and p53-/- mouse cells.
Skills
Python
Excellent written and oral communication
SQL
Use of Cloud environments (AWS)
Genomics and microscopy data standards
Use of HPC Environments (Slurm)
Biomedical data modeling
Product requirement definition
Genomics data analysis
Extensive research experience
Experience with EHR/clinical data
Agile/scrum experience
Biomedical ontologies and OWL/RDF
Engagement with End Users
Use of REST APIs
Detail-oriented
Publications
Reiff, S.B., Schroeder, A.J., Kırlı, K., Cosolo, A., Bakker, C., Mercado, L., Lee, S., Veit, A.D., Balashov, A.K., Vitzthum, C., Ronchetti, W., Pitman, K.M., Johnson, J., Ehmsen, S.R., Kerpedjiev, P., Abdennur, N., Imakaev, M., Öztürk, S.U., Çamoğlu, U., Mirny, L.A., Gehlenborg, N., Alver, B.H., and Park, P.J. (2022) The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. Nat Comms 13: 2365. doi: 10.1101/2021.10.14.464435
Reiff, S.B. and Marshall, W.F. (2017) A large kinome in a large cell: Stentor coeruleus possesses highly expanded kinase families and novel domain architectures. bioRxiv doi: 10.1101/168187
Slabodnick, M.M.*, Ruby, J.G.*, Reiff, S.B.*, Swart, E.C.*, Gosai, S., Prabakaran, S., Witkowska, E., Larue, G.E., Fisher, S., Freeman, R.M. Jr., Gunawardena, J., Chu, W., Stover, N.A., Gregory, B.D., Nowacki, M., DeRisi, J., Roy, S.W., Marshall, W.F., and Sood, P. (2017) The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr. Biol. 27(4): 569-575. (* - equal contributions)
Reiff, S.B. and Marshall, W.F. (2015) Stentor, Its Cell Biology and Development. eLS. doi: 10.1002/9780470015902.a0025978 (Review)
Reiff, S.B., Vaishnava, S, and Striepen, B. (2012) The HU Protein is Important for Apicoplast Genome Maintenance and Inheritance in Toxoplasma gondii. Eukaryot. Cell 11(7): 905-915.
Reiff, S.B. and Striepen, B. (2009) Malaria: The Gatekeeper Revealed. Nature 459(7249): 918-919. (Commentary)
van Dooren, G.G., Reiff, S.B., Tomova, C., Meissner, M., Humbel, B.M., and Striepen, B. (2009) A Novel Dynamin-Related Protein Has Been Recruited for Apicoplast Fission in Toxoplasma gondii. Curr. Biol. 19(4): 267-276.
Striepen, B., Jordan, C., Reiff, S., and van Dooren,G.G. (2007) Building the Perfect Parasite: Cell Division in the Apicomplexa. PLoS Path. 6(3): e78. (Review)