cv
Basics
Name | Carson D. Broeker |
Label | Research Scientist |
cbroeker6@gmail.com | |
Url | https://carsonbroeker.github.io/ |
Summary | Oncology researcher with a penchant for bioinformatics, data science, and machine learning |
Work
- 2023 - Present
Analyst Commodity
AbbVie
Created an application for the automatic processing of mass spectrometry data identifying novel metabolites from animal specimens treated with small molecule pharmaceuticals. This application also matched MS1 peak data to MS2+ peak data to determine level of support across different fragmention ions. Created automated workflows for other small department needs
- Software Development
- Data Science
- 2023 - 2023
Django Backend Developer PhD Intern
Institute for Cyber-Enabled Research, Michigan State University
- Django
- Git
- 2023 - 2023
Non-Regulated Bioanalysis PhD Intern
AbbVie
Created an autonomous centralized database for non-regulated bioanalysis method information, along with a machine learning pipeline for small molecule method prediction. Created a web application for querying database and method prediction information
- Python
- Data Engineering
- Data Science
- Machine Learning
- DevOps
- 2020 - 2022
Technician
Covid-19 Early Detection Program, Michigan State University
Responsible for processing incoming spit samples with chemical stabilization, RNA extraction, and preparation for qRT-PCR
- CLIA Operations
- Sterile Technique
- Highthroughput Processing
- 2019 - Present
PhD Candidate
Department of Biochemistry and Molecular Biology, Michigan State University
Engaged in many different research project broadly relating to mouse models of breast cancer and their development, genomics of breast cancer models, and developing artificial intelligence models to study breast cancer
- Cell Culture
- Murine Handling and Surgery
- Multi-Omics
- Bioinformatics
- Data Science
- Machine Learning
Education
-
Columbia, MO
BSc, Minor in Mathematics
University of Missouri
Biochemistry
- Chemistry I and II
- Organic Chemistry I and II
- Physical Chemistry I and II
- Genetics
- Biology
- Cancer Biology
- Biochemistry I and II
- Physical Biochemistry
- Calculus Based Physics I and II
- Modern Physics
- Math for Physical Chemistry
- Calculus I, II, and III
- Differential Equations
- Mathematical Statistics
- Discrete Math Structures
- Microeconomics
- Labs in Biology, Chemistry, Biochemistry, and Physics
-
East Lansing, MI
PhD
Michigan State University
Biochemistry and Molecular Biology
- Molecular Biology
- Methods in Macromolecular Analysis and Synthesis
- Protein Structure, Design, and Mechanisms
- Metabolism Regulation and Signal Transduction
- Cell Structure and Function
- Foundations of Data Science
- Applied Machine Learning
- Bioinformatics in R
- Drug Discovery and Medicinal Chemistry
Awards
- 2023
Ruth L. Kirschstein Predoctoral Individual National Research Service Award (F31)
National Cancer Institute
The NCI Ruth L. Kirschstein NRSA for Individual Predoctoral Fellows (F31) Award supports promising doctoral candidates who will perform dissertation research and training for a PhD degree in a scientific health-related field relevant to the mission of the NCI during the tenure of the award.
- 2022
Aitch Foundation Predoctoral Fellowship Award
Aitch Foundation
The Aitch Foundation supports awareness of and generates charitable contributions for research into early detection of hidden cancers.
Publications
-
2023.10.07 Integrative multi-omic sequencing reveals the MMTV-Myc mouse model mimics human breast cancer heterogeneity
Breast Cancer Research
This paper explores the heterogeneity found at the transcriptional and genomic level of MMTV-Myc mouse model tumors. We also find that many mouse models widely described as being representative of specific human breast cancer subtypes are quite heterogeneous and do not replicate the transcriptional state of the supposed matching human breast cancer subtype.
-
2022.06.23 Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling
JoVE (Journal of Visualized Experiments)
Herein, we detail a high throughput method of transpositional pooled saliva sampling for detection of Covid-19 in the Michigan State University student body.
-
2022.06.09 E2F Transcription Factors in Cancer, More than the Cell Cycle
Comprehensive Pharmacology
In this review, we detail the canonical and noncanonical functions of E2F transcription factors. While widely known to be important regulators of the cell cycle, E2F transcription factors take on a variety of other rules, including but not limited to apoptosis, DNA repair, angiogenesis, etc.
-
2021.09.25 Insight into mammary gland development and tumor prevention in a newly developed metastatic mouse model of breast cancer
bioRxiv
Previously unknown to play a role in breast cancer development, we detail the novel conditional E2F5 knockout mouse model. We profile the mouse model at the genomic and transcriptional level.
Skills
General Progamming and App Development | |
Python | |
R | |
Linux/Unix Systems | |
SQL/NoSQL | |
AWS Suite | |
High Performance Computing |
Software and Library Packages | |
Pandas | |
Numpy | |
Scipy | |
Seaborn | |
Matplotlib | |
Plotnine | |
SciKitLearn | |
TensorFlow | |
PyTorch | |
Apache Spark | |
NLTK | |
RDKit | |
Django | |
Shiny | |
Tidyverse | |
DESeq | |
Limma | |
Seurat | |
STAR | |
Salmon | |
Dplyr | |
ggplot2 | |
LaTeX | |
Git | |
NCBI Suite | |
GSEA | |
IGV | |
UCSC Genome Browser | |
Imaris | |
ImageJ | |
GATK | |
SAMTools |
Lab Techniques | |
PCR | |
qRT-PCR | |
Genotyping | |
Western Blotting | |
Bacterial Cloning | |
Transformation | |
Primer and sgRNA Design | |
CRISPR/CRISPRi/CRISPRa | |
Lentivirus Production and Transduction | |
Aseptic Cell Culture | |
GLP | |
CLIA | |
Rodent Handling and Colony Management | |
Rodent Survival Surgery | |
Rodent Necropsy | |
Rodent Oral Gavage | |
Microscope Assisted Dissection | |
Confocal Microscopy |
Soft Skills | |
Interpersonal Communication | |
Scientific Dissemination to Advanced and Lay Audiences | |
Interdisciplinary Knowledge | |
Punctual | |
Quickly Adaptable | |
Data Informed Decision Making | |
Detail to Big Picture Oriented | |
Able to Influence Key Decision Makers | |
Independent | |
Team Player | |
Intuitive Writing and Visualizations | |
Outcome Driven |
Languages
English | |
Native speaker |