I am a computational biologist passionate about engaging with exciting biology and converting data into knowledge that improves patients’ lives. My Industry roles focus on drug discovery in cancer and other indications using genomics, transcriptomics, proteomics, and high content image analysis. These experiences complement my PhD and postdoc on quantitative genetics in Drosophila and methods development in image analysis & Genome Wide Association Studies (GWAS).
Scorpion Therapeutics
Small Molecule, Proteomics-Based Drug Discovery in Cancer
Intact Mass Spec Compound-Protein Interaction Classifier
My proudest achievement at Scorpion was the development of a fully automated Python program to quantify and classify covalent compound-protein binding interactions for hit screening. This work processed deconvoluted m/z spectra and applied agnostic peak finding, simple reinforcement learning, and a computationally inexpensive framework compatible with high-performance computing (HPC) environments.
Comprehensive Cysteinome Mapping with Proteomics
One of my earlier projects at Scorpion was leading the data curation and quality control for our in-house Data-Dependent Acquisition (DDA) TMT-ABPP proteomics library screen. Here, we aimed to map the cysteinome (accessible cysteines that our compounds could target) and understand which cancer-relevant targets we could target and chemical motifs that enabled that. This work enabled further exploration across the organization looking into novel target identification.
New Target Identification
Throughout my time at Scorpion, I worked to identify new targets for expanding our company’s pipeline. To achieve this, I worked with mutation, and gene dependency and gene expression from DepMap, as well as raw RNA transcript reads and DNA methylation data from publicly available datasets. I also contributed with cell line selection and close collaboration with scientists at the bench and running the instrumentation.
Faze Medicines
Small Molecule, High-Content Imaging Drug Discovery in Cancer & ALS
Indication Selection and Target Identification
My earliest work at Faze Medicines datamining the Cancer Dependency Map (DepMap) led to target identification and target validation of a gene associated with biomolecular condensates. Faze was in the process of screening compounds to target this protein though it was halted due to the company’s dissolution.
Uncovering Phase Separating Oncofusions
I led the computational efforts aimed at identifying potentially phase separating oncofusions–chimeric proteins that cause or are associated with cancer–and their affiliated indications. The top candidates were nominated for laboratory-based experiments, feeding the pipeline for future drug discovery efforts.
High-Throughput Imaging Screens
During my time at Faze, I was the lead computational contributor on two high-throughput, high-content imaging screens: one for small molecules and one genetic/CRISPR. Both focused on finding targets that modulated condensate dynamics in cancer cells lines carrying a specific condensate-associated oncofusion, previously identified in my oncofusion work.
Academic
Insect Flight Performance
Flies are called flies because they fly. And yet, despite their use as a genetic model, we know surprisingly little about the genetic modifiers affecting flight in a natural population…until now!
Insect Climbing Performance
Flies’ ability to climb is an established metric of their health. I developed a novel (and award-winning) approach to quantify climbing performance in an automated and high-throughput framework that avoids systematic bias and increases data transparency.
Fellowship Research
What do a mind-controlling, host-parasite interaction and bacteria sequenced from a meter-long core of a New England salt pond have in common? Both were the focus of separate, interdisciplinary research projects I participated in during my graduate career.
Non-Academic
Advocate
Throughout my undergraduate and graduate schooling, I worked to promote physical, mental and emotional health through exercise. From creating a healthy housing choice at Colby College to an initiative for free fitness classes for graduate and medical students at Brown University, I designed and implemented programs that empower students to make healthy lifestyle choices.
Athletic
As a fitness and racing enthusiast, I transitioned my life from the pool as an NCAA Division III swimmer onto land where I am now a certified group fitness instructor. I enjoy training for triathlons, going for long road bike rides, and leading Astronaut Training, a social workout club I founded at Brown University.
Artistic
Perspective can make big things look small and small things look big. I enjoy taking advantage of this phenomenon to view the world a bit differently. I pose and photograph toy dinosaurs and dolls interacting with the natural and urban worlds, as well as Boston’s fluffiest pup.
Contact me
Feel free to reach out with questions, requests for papers, FreeClimber help, and career opportunities.
Adam Spierer 