Experience

AI PREMie

• Ireland
• Medical and Diagnostic Laboratories
• 1 - 100 Employee

• Machine Learning Research Assistant

  • Oct 2023 - Present

  Dublin, County Dublin, Ireland



Revolution Medicines

• United States
• Biotechnology
• 100 - 200 Employee

• Data Science Intern

  • Jan 2023 - Jun 2023

  Redwood City, California, United States Can we use structural alignment methods to efficiently identify new classes of targets in drug discovery? • Proteins with similar sequences often have similar structure, but proteins with vastly different sequences may also have similar structure. I sought to determine if structural alignment of cancer driver proteins reveals relationships hidden by sequential alignment of proteins. Used AlphaFold predicted structures to hierarchically cluster proteins by structure (DALI) or sequence… Show more Can we use structural alignment methods to efficiently identify new classes of targets in drug discovery? • Proteins with similar sequences often have similar structure, but proteins with vastly different sequences may also have similar structure. I sought to determine if structural alignment of cancer driver proteins reveals relationships hidden by sequential alignment of proteins. Used AlphaFold predicted structures to hierarchically cluster proteins by structure (DALI) or sequence (BLAST) and developed polar dendrogram web tools visualize and compare similarity. Identified a number of novel clusterings in structure that were undetected by sequential alignment because of remote homologies.

• Computational Biology & Cancer Targets Co-op @ RevMed

  • Jul 2022 - Jan 2023

  San Francisco Bay Area • Predicting Drug Permeability with Graph Convolution Networks (GCNs): Currently, candidate drug permeability is screened via an arbitrary molecular weight threshold. There is next to zero correlation, however, between MW and permeability. I developed a GCN and GAN with DeepChem that predicts tricomplex permeability with 75% accuracy, performing significantly better than arbitrary MW cutoffs. • Data Automation for HTP Analysis: developed a tool to process raw MS data for cross-linking… Show more • Predicting Drug Permeability with Graph Convolution Networks (GCNs): Currently, candidate drug permeability is screened via an arbitrary molecular weight threshold. There is next to zero correlation, however, between MW and permeability. I developed a GCN and GAN with DeepChem that predicts tricomplex permeability with 75% accuracy, performing significantly better than arbitrary MW cutoffs. • Data Automation for HTP Analysis: developed a tool to process raw MS data for cross-linking experiments in discovery biology and target validation, cutting manual data analysis time by hours. Built a pipeline to growth rate normalize cell viability assays in 384 well plates, allowing more accurate representation of depth of inhibition and potency for tricomplex drugs.



Northeastern University

• United States
• Higher Education
• 700 & Above Employee

• Research Assistant @ Apfeld Neurobiology Lab

  • Dec 2021 - May 2023

  How do innate immunity signaling pathways in neuronal tissue reduce oxidative stress, an agent of neurodegenerative disease? • Wet Lab: Studying TGF-β sma pathway (via functional and behavioral assays) to identify novel peroxide-defense mechanisms and gain insight into anti-oxidation signaling in neuronal tissue. Evaluating novel Lactococcus lactis as alternative peroxide-producing catalase-negative bacterial model to induce C. elegans signaling. • Computational: Performed splice… Show more How do innate immunity signaling pathways in neuronal tissue reduce oxidative stress, an agent of neurodegenerative disease? • Wet Lab: Studying TGF-β sma pathway (via functional and behavioral assays) to identify novel peroxide-defense mechanisms and gain insight into anti-oxidation signaling in neuronal tissue. Evaluating novel Lactococcus lactis as alternative peroxide-producing catalase-negative bacterial model to induce C. elegans signaling. • Computational: Performed splice variant RNA-seq analysis on sma-2 and sma-4 mutant C. elegans to identify sma regulatory control of downstream oxidative resilience and neuroendocrine signaling pathways. Updated Pharedox (C. elegans image analysis library) with dynamic GUI for user control of segmentation analysis and midline adjustment. Also automates visualizations for image intensity profile, 410/470 ratiometric CDF curve, and matrix correlation plots between animal tissues.

• Teaching Assistant @ Northeastern COS, COE, Khoury College

  • Sep 2020 - May 2022

  Boston, Massachusetts, United States • Teaching assistant for Biology Project Lab (BIOL2309), Discrete Structures (CS1800), and Cornerstone of Engineering (GE1501) • GE1501: Graded AutoCAD, SolidWorks, C++, and Arduino assignments; guided project prototyping • CS1800: Held biweekly office hours to review set theory, equivalence relations, graph/network theory • BIOL2309: Prepared stock solutions and lab protocol kits, maintained C. elegans/bacterial stocks



Takeda

• Japan
• Pharmaceutical Manufacturing
• 700 & Above Employee

• Bioanalytics & Automation Sciences Co-op @ Takeda Global Biologics

  • Jun 2021 - Dec 2021

  Cambridge, Massachusetts, United States How can we generate, process, and analyze biochemical data quicker to discover new cancer immunotherapeutic leads? • Developed data adaptor for HTP Lunatic (protein quantification assay) for automated aggregation to Genedata Screener • Developed data automation tool on intranet to convert sample fulfillment requests in Mosaic SampleBank to interpretable formats for the Lynx liquid handlers • Scripted numerous assay analysis notebooks to automate data visualization and analysis for… Show more How can we generate, process, and analyze biochemical data quicker to discover new cancer immunotherapeutic leads? • Developed data adaptor for HTP Lunatic (protein quantification assay) for automated aggregation to Genedata Screener • Developed data automation tool on intranet to convert sample fulfillment requests in Mosaic SampleBank to interpretable formats for the Lynx liquid handlers • Scripted numerous assay analysis notebooks to automate data visualization and analysis for CAR-T killing assays Show less



Montclair State University

• United States
• Higher Education
• 700 & Above Employee

• Research And Teaching Assistant @ Montclair State University

  • Jun 2016 - Aug 2019

  Montclair, New Jersey, United States Am I more likely to lie to myself to gain social acceptance, and if so what role does the prefrontal cortex play in this behavior? • Designed and directed an experiment studying the modes of overclaiming in the mPFC via transcranial magnetic stimulation • Published in Journal of Brain Sciences 2020; presented at Sense to Synapse 2019 [Rockefeller University], EPA 2020 • Summer Teaching Assistant for Weston Scholars program, working with high school students to design investigation… Show more Am I more likely to lie to myself to gain social acceptance, and if so what role does the prefrontal cortex play in this behavior? • Designed and directed an experiment studying the modes of overclaiming in the mPFC via transcranial magnetic stimulation • Published in Journal of Brain Sciences 2020; presented at Sense to Synapse 2019 [Rockefeller University], EPA 2020 • Summer Teaching Assistant for Weston Scholars program, working with high school students to design investigation of drosophila ovipositioning Paper abstract: https://www.mdpi.com/2076-3425/10/8/535 Show less