cv
Basics
| Name | Temitope Adeoye |
| tadeoye@usf.edu | |
| Summary | Applying systems biology methods in biophysics and genomics to better understand dysfunction in neurological disorders. |
Education
-
2019.08 - 2023.12 Tampa, Florida
Master of Science (MSc)
University of South Florida
Applied Physics: Computational Biophysics and Neurobiology
- Biophysics
- Applied Bioinformatics
- Theoretical Physics
-
2019.08 - 2025.05 Tampa, Florida
Doctor of Philosophy (PhD)
University of South Florida
Applied Physics: Computational Biophysics and Neurobiology
- Biophysics
- Applied Bioinformatics
- Theoretical Physics
-
2012.09 - 2017.01 Lagos, Nigeria
Work
-
2025.05 - 2025.08 Incoming Intern, Computational Biology, Neuroscience and Ophthalmology Therapeutic Area Genetics
Regeneron Genetics Centere
Primary work here will focus on integrating single-nucleus RNA-seq, single cell eQTL, and ATAC-seq data to annotate top hits from genetic perturbation studies with cell types or cell states, and pinpoint specific signatures associated with such signals
- Single-cell multi-omics
- GWAS
- Functional Genomics
- Variant Effect Prediction
- Bioinformatics
- Systems Biology
- Statistics
- Machine Learning
-
2022.05 - 2022.08 Research Intern, Human Multi-omics
Cajal Neuroscience
My work here focused on developing deep learning pipelines for mapping and contextualizing single-cell sequencing data to aid rapid integration of new datasets into reference atlases. The project involved implementing an interpretable deep learning approach with explainable embeddings to create biologically informed latent representations, and deploying standardized bioinformatic workflows to identify cell states, differential expression patterns, and trajectories in Alzheimer's and Parkinson's disease (PD) models.
- Single-cell multi-omics
- Bioinformatics
- Machine Learning
-
2021.08 - 2022.05 Bioinformatics Research Student
University of South Florida
Investigated the role of intrinsic disorder in Ebola and Marburg virus proteins and its potential implications for virulence.
- Intrinsically Disordered Proteins
-
2019.09 - 2025.05 Graduate Research Asssistant
Computational Biophysics Group, University of South Florida
Primary research has focused on applying theoretical and computational techniques as well as single-cell multi-omics to understand the molecular and cellular mechanisms of synaptic dysfunction in Alzheimer’s disease (AD). This has involved investigating neuronal signaling pathways and gene programs affected in AD and their impact on synaptic plasticity. These research experiences have resulted in two publications and multiple collaborations.
- Single-cell multi-omics
- Biophysics
- Bioinformatics
- Systems Biology
- Statistics
- Machine Learning
Awards
- 2024.08
Trainee Professional Development Award
Soceity for Neuroscience
This award is given to graduate students who demonstrate scientific merit and excellence in research.
- 2024.05
Tharp and Duckwall Summer Research Fellowship
College of Arts and Sciences, University of South Florida
This is awarded in recognition of accomplishments as a graduate student and in support of continuing research and scholarship activities.
- 2012.2017
University of Lagos Endowment Prize
University of Lagos
This award is given to students who maintain a GPA of 4.5 and above (3.6 on a 4.0 scale) in each semester.
- 2012.2017
Dean's Award
University of Lagos
Honors recognizing the best graduating student from the program, the Department of Physics
Certificates
| Deep Learning for Neuroscience | ||
| Neuromatch Academy | 2021-08-21 |
| Computational Neuroscience | ||
| Neuromatch Academy | 2020-07 |
Publications
-
2024.06.21 Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer’s Disease.
Aging and Disease
We integrate pathway activity analysis with weighted gene co-expression patterns to provide insights into the functional coherence and interplay among genes involved in perturbed biological processes in AD.
-
2022.07.11 Upregulated Ca2+ Release from the Endoplasmic Reticulum Leads to Impaired Presynaptic Function in Familial Alzheimer’s Disease.
MDPI
We perform in-silico experiments of intracellular Ca2+ signaling and exocytosis in a detailed biophysical model of hippocampal synapses to investigate the effect of aberrant Ca2+ signaling on neurotransmitter release in Familial ALzheimer's Disease.
Skills
| Programming/Scripting Languages | |
| Python | |
| R | |
| Bash | |
| MATLAB | |
| SQL | |
| FORTRAN |
| Machine Learning Frameworks | |
| Keras | |
| scikit-learn | |
| TensorFlow | |
| scipy | |
| PyTorch | |
| statsmodels |
| Research-relevant Open-source Libraries | |
| Single-cell (RNA, ATAC, & spatial) -omics libraries | |
| scanpy | |
| squidpy | |
| scvi-tools | |
| hdWGCNA | |
| GSVA | |
| SCENIC+ | |
| ArchR | |
| Biopython |
| Parallel Computing | |
| CUDA | |
| mpi4py |
| High Performance Computing | |
| Amazon Sagemaker | |
| Terra Community Workbench | |
| Google Cloud Platform |
| Code Development | |
| Git | |
| Github | |
| Visual Studio | |
| Docker | |
| Anaconda |
Projects
- 2022.03 - 2022.03
DEMON Neurohack Challenge - Trans-ethnic GWAS analysis.
Created a modular trans-ethnic GWAS pipeline that can perform essential GWAS analysis with flexibility
- GWAS
- Pipeline Automation
- PRSice
- MR-MEGA
- 2021.08 - 2021.08
Deep Image Decoding From Neural Activity
Developed a deep-image reconstruction model that utilizes recorded neural activity from the visual cortex.
- Visual Decoding
- Image Reconstruction
- Generative Modelling
- 2020.07 - 2020.07
Trial History Effects on trial-to-trial variability of neural and behavioural data
Developed a prediction model to investigate the effects of trial history on the trial-to-trial variability of neural and behavioral data
- Neural Variability
- Trial History
- Predictive Modeling