Robert Foreman
San Diego,CA
Summary
Bioinformatics scientist with 12 years of experience and a Ph.D. from UCSD. Expertise in integrating computational methods with biological research to drive innovation and address complex challenges. Proven leadership in team management, data-driven strategy development, and contributions to biotech advancements. Strong work ethic, adaptability, and exceptional interpersonal skills enhance effectiveness in dynamic environments.
Overview
12
12
years of professional experience
Work History
Senior Bioinformatics Scientist
VELIA
San Diego, CA
01.2023 - Current
- Company Overview: Velia is a startup drug discovery company identifying micro-protein drug targets.
- Co-developed target ID platform to identify and prioritize novel open reading frames (ORFs) in human genome. Targets were identified with ribo-seq and mass spect, and prioritized with integrated ORF annotation (conservation, protein processing feature prediction, structural prediction, disease association, and internal assay results).
- Developed dashboard for cross-functional collaboration to review and prioritize targets between computational platform team and biology teams.
- Generated MoA and disease association hypotheses for prioritized targets by integrating bulk RNA-Seq, scRNA-Seq, and genetics across broad disease categories including: autoimmune, cancer, and metabolism.
- Velia is a startup drug discovery company identifying micro-protein drug targets.
Senior Bioinformatics Scientist
VIZGEN
San Diego, CA
01.2021 - 01.2023
- Company Overview: Vizgen is a spatial transcriptomics platform company commercializing MERFISH.
- Project leader for gene panel design webapp and R&D NPI. Bioinformatic and image analysis, developing validation and verification requirements, test plans, and managing cross-functional team through execution and product launch.
- Technical lead for MERFISH image decoding algorithm development. Performing and managing team prototyping and evaluating new solutions to improve detection sensitivity (+20%) and speed (4X).
- Technical lead for developing instrument and analysis metrics and root cause troubleshooting workflows.
- Vizgen is a spatial transcriptomics platform company commercializing MERFISH.
Bioinformatics Scientist
MONOCEROS BIOSYSTEMS
San Diego, CA
01.2019 - 01.2021
- Led data processing, analysis, and interpretation for small to medium drug discovery companies.
- Conducted clinical and pre-clinical pharmacodynamics analysis across diverse targets.
- Executed synthetic lethal cancer target discovery utilizing DepMap and dual CRISPRko datasets.
- Performed RNA-Seq and scRNA-Seq studies for disease hypothesis and target validation.
- Developed ASO oligonucleotide design algorithm and designed clinical-stage assets.
- Carried out off-target liability analysis in silico and in vivo to ensure safety.
- Spearheaded biomarker discovery projects using whole exome sequencing and expression biomarkers.
Graduate Research Scientist
UC SAN DIEGO
01.2013 - 01.2019
- Developed technology to measure live-cell phenotypes coupled with transcriptomic measurements from same single-cells.
- Developed algorithms, analysis software, and pipelines for characterizing dynamic cellular phenotypes, and integration of multi-modal datasets to decode information processing in mammalian signaling networks (calcium, ERK, and NFkB).
- Built custom microscopes, fluidics, and hardware control software. Fully implementing custom live-cell imaging acquisitions and MERFISH spatial transcriptomics experiments.
- Developed and performed all underlying wet-lab experiments including mammalian cell culturing, cloning, molecular biology, and in-vitro transcription (milligram scale preps).
Education
Ph.D. - Bioinformatics and Systems Biology
UC San Diego
San Diego, CA01.2019
Bachelor of Science - Biology and Cell Physiology
UNC Charlotte
Charlotte01.2012
Skills
- Python
- R
- BASH
- SQL
- MATLAB
- Git
- Plotly
- Seaborn
- Matplotlib
- Streamlit
- AWS
- GCP
- Nextflow
- Snakemake
- Pandas
- Numpy
- Tensorflow
- Keras
- Ensemble modeling
- Convolutional Neural Networks
- Target identification
- Data analysis
- Machine learning
- Cross-functional collaboration
- Image analysis
- Statistical modeling
- Biomarker discovery
- Project management
- RNA sequencing
- Problem solving
- Effective communication
- Communication
- Supervised Learning
- Unsupervised Learning
- Dimensionality Reduction
- Linear Regression
- Nonlinear Regression
- Problem formulation
- Sequence Algorithms
- Mixed Linear Models
- Network Analysis
- Design of Experiments
- Deep learning
- Information Theory
- Image Analysis
- Signal Processing
- DepMap
- CCLE
- TCGA
- L1000
- ClinVar
- UK Biobank
- GTEx
- ENCODE
- Single-cell RNA Sequencing
- WES
- CRISPR screening
- Multi-omic data integration
- Ribo-seq
- Virtual ligand screening
- Genetics
- Cell Segmentation and Tracking
- Oligo Design
- Immunology
- Cancer genetics
- DNA damage and repair
- Innate immunity
- Fibrotic diseases
- Inflammatory Bowel Disease
- Metabolic disease
- Alternative splicing
- Synthetic lethality and genetic dependency
- Transcriptional Regulation
- Signaling Networks
- Secreted factors
- Hormone signaling
- GPCR signaling
- Membrane biology
- Spatial Transcriptomics
- Live Cell Imaging
- Mammalian Cell Culture
- Molecular Biology
Publications
- Handa S, Jiang Y, Tao S, Foreman R, Schinazi RF, Miller JF, Ghosh P, Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex, Nucleic Acids Research, 46, 18, 2018, 9711-9725
- Foreman R, Wollman R, Mammalian gene expression variability is explained by underlying cell state., Molecular Systems Biology, 16, e9146
- Zhang T, Foreman R, Pilko A, Wollman R, Identifying chromatin features that regulate gene expression distribution., Scientific Reports, 10, 20566, 2020
- Metzig M, Tang Y, Mitchell S, Taylor B, Foreman R, Wollman R, Hoffmann R, An incoherent feedforward loop interprets NFkB/RelA dynamics to determine TNF-induced necroptosis decisions., Molecular Systems Biology, 16, e9677, 2020
- Littman R, Hemminger Z, Foreman R, Arneson D, Zhang G, Gomez-Pinilla F, Yang X, Wollman R, Joint cell segmentation ana cell type annotation for spatial transcriptomics., Molecular Systems Biology, 17, e10108, 2021
- Hong SG, Ashby J, Kennelly J, Wu M, Steel M, Chattopadhyay E, Foreman R, Tontonoz P, Tarling E, Turowski P, Gallagher-Jones M, Mack J, Mechanosensitive membrane domains regulate calcium entry in arterial endothelial cells to protect against inflammation., Journal Clinical Investigation, 134, 13, 2024
Awards And Acknowledgements
Technology Fellow at UCLA Collaborator, 01/01/19, Fellowship offered to teach interdisciplinary workshops in spatial transcriptomics and consult/collaborate with other labs.
Timeline
Senior Bioinformatics Scientist
VELIA
01.2023 - Current
Senior Bioinformatics Scientist
VIZGEN
01.2021 - 01.2023
Bioinformatics Scientist
MONOCEROS BIOSYSTEMS
01.2019 - 01.2021
Graduate Research Scientist
UC SAN DIEGO
01.2013 - 01.2019
Ph.D. - Bioinformatics and Systems Biology
UC San Diego
Bachelor of Science - Biology and Cell Physiology
UNC Charlotte
Similar Profiles
Hazuki SanoHazuki Sano
Nightclub Hostess at VeliaNightclub Hostess at Velia
Jose RamosJose Ramos
Sandwich Artist at VeliaSandwich Artist at Velia
Emiliano BravoEmiliano Bravo
Kitchen Line Cook at Velia (Hospital Restaurant).Kitchen Line Cook at Velia (Hospital Restaurant).
MICHELLE SANDOVALMICHELLE SANDOVAL
Customer Service Representative at UbiquityCustomer Service Representative at Ubiquity
Ivan Segovia-JimenezIvan Segovia-Jimenez
Senior Interior Designer at Anne Rae DesignSenior Interior Designer at Anne Rae Design