safwan

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i'm a first year graduate student at the University of Washington. i'm interested in all things computer science and protein design :)

a little context (about me)

I'm a student in the molecular information systems lab (MISL) working with Dr. Jeff Nivala on some pretty sweet protein based stuff. My research interests lie at the intersection of protein engineering and synthetic biology, with a focus on designing novel proteins that can recognize and respond to specific molecular cues. I'm particularly interested in how custom protein interactions can be harnessed to build new biological functions or control cellular behavior.

Outside of lab, I love working on my car (a beautiful '09 Acura TL), hiking/camping, climbing, longboarding, playing pretty much any team sport, and working (or delaying working) on my science fiction novel. I'm also absurdly passionate about ice cream, so you'll often find me behind the counter scooping at Many Bennies - the most awesome ice cream shop in Seattle.

research/teaching experiences + publications

Research Assistant - Protein Design and Synthetic Biology

Molecular Information Science Lab (MISL) - University of Washington

September 2024 - Present (11 months)
  • Proficient in computational protein design software (AlphaFold, RFDiffusion, ProteinMPNN, Chai-1, Protein Generator).
  • Adept in high-efficiency plasmid to cell transformation of BL21(DE3) and 5-alpha E. coli strains.
  • Experienced in genetic engineering techniques such as Gibson assembly and site-directed mutagenesis for plasmid modification.
  • More details to come (top-secret research in progress)!

Research Assistant - Distributed Systems

Distributed Systems Computing Group - University of Minnesota

June 2023 - June 2024 (1 year, 1 month)
  • Developed lightweight, scalable classroom video-based applications with the capability to recognize faces, facial expressions, and characters on a whiteboard.
  • Implemented a machine learning approach via support vector machines (SVMs) for video analytics, using Docker containers to pipeline the applications, allowing each processing step to be individually scaled and easily implemented on small IoT devices.
  • Presented performance and technical results to Cisco Systems, the project funders.

Teaching Assistant

Introduction to Machine Architecture (CSCI 2021) - University of Minnesota

September 2022 - May 2023 (9 months)
  • Worked with students of diverse backgrounds and experiences to debug code issues, explain core concepts, and promote group collaboration.
  • Held office hours as well as demo sessions of 60+ students for projects and labs to explain key machine architecture and memory principles in both C and x86 Assembly.

Research Assistant - Chemical Biology

Distefano Lab - University of Minnesota

September 2021 - June 2022 (10 months)
  • Publication:
    Schey, G. L., Hildebrandt, E. R., Wang, Y., Diwan, S., Passetti, H. A., Potts, G. W., Sprague-Getsy, A. M., Leoni, E. R., Kuebler, T. S., Sham, Y. Y., Hougland, J. L., Beese, L. S., Schmidt, W. K., & Distefano, M. D. (2024). Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase. International Journal of Molecular Sciences, 25(10), 5324.
  • Synthesized peptide libraries using manual solid-phase peptide synthesis.
  • Ran and assessed aforementioned libraries with yeast and rat farnesyltransferase (yFTase and rFTase) reactions to determine susceptibility for prenylation.
  • Assisted in recombinant enzyme expression in E. coli to obtain transferase for susceptibility experiments.
  • Characterized reagent and post-enzymatic reaction peptide libraries using GC-MS (gas chromatography-mass spectrometry), UV-Vis Spectroscopy, and MALDI-MS (matrix-assisted laser desorption ionization-mass spectrometry).

professional experiences

Software Cloud Engineer

Medtronic

July 2023 - September 2024 (1 year, 3 months)
  • Successfully integrated a new insertable cardiac monitor (ICM) into the Medtronic CareLink Remote Monitoring System by developing micro-service infrastructure for protected health information (PHI) transmissions.
  • Developed .NET REST APIs for microservice communication and data transfer during patient device-to-cloud transmission processing.
  • Ensured optimal uptime (an increase of approximately 20%) for shared Azure cloud deployments through Dynatrace monitoring and microservice code fixes.
  • Co-led organization-wide .NET upgrade at Medtronic, safeguarding data quality and security throughout the transition.
  • Improved efficiency in the CareLink codebase by developing scripts for streamlined package version updates, enhancing overall development agility and shared environment consistency.

Research and Development Engineer

FemtoFluidics

March 2023 - February 2024 (1 year)
  • Developed a novel and proprietary SOP for pentapeptide library syntheses and assisted in the design of a procedure for enzyme-linked immunosorbent assays (ELISA) on magnetic beads. Sourced potential material/equipment vendors.
  • Successfully synthesized pentapeptide libraries via solid-phase peptide synthesis.
  • Developed a novel protocol for peptide synthesis on magnetic beads as a replacement for standard resin.

Software Engineering Intern

Medtronic

June 2022 - August 2022 (3 months)
  • Implemented REST APIs using C# and .NET to integrate heart monitor data into CareLink.
  • Increased consistency between SQL and Apache HBase by building record reconciliation capabilities from both databases within a single C# implementation.
  • Developed Azure pipelines to build and deploy code into a testing environment and release necessary artifacts.
  • Assisted team in transitioning from deprecated virtual machine development environments, ensuring successful setup of Kubernetes and Docker infrastructure.

Software Engineer Intern

UnitedHealth Group - Optum

June 2021 - August 2021 (3 months)
  • Analyzed data irregularities and created a mapping between two databases, MS SQL Server and ServiceNow through Python data analysis libraries to synchronize the data.
  • Built a live dashboard for data visualization and synchronization status using Tableau.
  • Created an update plan for future consistent data integration between the two databases, using newly built tables in MS SQL Server and ServiceNow APIs.
  • Designed and presented biweekly presentations to update company executives on project status.

Intern

University of Minnesota Nano-Center

March 2019 - May 2019 (3 months)
  • Explored practical applications of the nanosciences in fields such as medicine, computing, and chemistry.
  • Synthesized and analyzed nanoparticles through the use of devices such as the Dynamic Light Scattering (DLS) Instrument, Nanoparticle Tracking Analyzer, Zeta Potential Analyzer, and Laser Diffraction tools.
  • Explored the administrative areas of a lab, management, training, and facilitation of events.
  • Observed training of new lab users and discussed research topics with students and industry clients.
  • Attended UMN-hosted conference related to the nanosciences, applications of nanotechnology and analysis devices.

education

University of Washington

Paul G. Allen School of Computer Science & Engineering

2024 - 2029

Master of Science and Doctor of Philosophy in Computer Science

GPA: 4.0

University of Minnesota

College of Science and Engineering

2019 - 2023

Bachelor of Science in Computer Science | Bachelor of Science in Chemistry

GPA: 3.95