Daniel Ji Email & Phone Number

Los Angeles, Ca, Us

Los Angeles, Ca, Us

• Building AlphaFold screening pipeline for LRRK2 protein-protein interactions

• CryoEM ML data analysis & model development for deleterious particle detection

• Worked with Prof. Joel Wertheim, Prof. Sergei Pond, Prof. Niema Moshiri, Steven Weaver, Stephen Shank, as part of a CDC contract with UCSDWeaver, S., Dávila Conn, V. M., Ji, D., Verdonk, H., Ávila-Ríos, S., Leigh Brown, A., Wertheim, J. O., & Kosakovsky Pond, S. L. (2024). AUTO-TUNE: Selecting the distance threshold for inferring HIV transmission clusters. Frontiers in Bioinformatics, 4. https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2024.1400003• Involved in the development of the Secure HIV-TRACE tool suite, a web-based application facilitating health departments in the local detection of molecular clusters of HIV. Engaged in crucial refactoring of the existing codebase using Python, C++, and JavaScript to boost code sustainability and maintenance.

• Collaborated with Associate Teaching Professor Niema Moshiri and OMGenomics Labs Founder Robert Aboukhalil to develop and enhance multiple bioinformatics tools.ViralWasm Tool Suite• ViralWasm-Consensus: Developed an end-to-end pipeline for consensus genome generation, using minimap2, fastp, and ViralConsensus. Uses React.js and implements BioWasm library, utilizing WebAssembly to serve the C/C++ tools from the browser, serverless.• ViralWasm-Epi: Developed an end-to-end pipeline for multi-sequence alignment and molecular clustering, using ViralMSA, minimap2, and tn93. A secure, user-friendly, and client-side WebAssembly-based site that employs Pyodide and BioWasm to run Python/C++ tools in-browser. Ensured full compatibility with the source ViralMSA Python code using SharedArrayBuffer, Atomics, and WebWorkers, and features dynamic code fetching and automatic updating.• Built additional standalone tools for both tool pipelines: TN93, ViralConsensus, ViralMSA. GEMF Online Tools• Nominated to present the GEMF Online Tools at the Undergraduate Research Conference, an annual UCSD conference to celebrate excellence in undergraduate research. • Created GEMF-FAVITES-WASM, a React-based, comprehensive WebAssembly port of GEMF, (Generalized Epidemic Modeling Framework), a Python-wrapped C tool for simulating epidemics based on contact networks and node transition graphs. Enabled serverless and secure in-browser compilation of C and Python code via Emscripten and Pyodide.• Created GEMF Designer, a React application that visualizes epidemic interactions, including both infectious and non-infectious states. Offers a real-time, interactive graph displaying transitions between user-defined states. Finalized state transition data is exported for integration with the GEMF tool.

Redwood City, California, United States

• Led the efforts in developing a robust data validation schema and workflow as part of backend ingestion pipeline on the CryoET Data Portal for 250TB+ of data, 300+ datasets, and 15,000+ tomograms• Worked closely with domain experts at the Chan Zuckerberg Imaging Institute to ensure a high standard of data integrity, resolving dozens of unique data errors • Proactively reached out to multiple open-source libraries and collaborated with teams to fix bugs and implement new features• Primary software technologies used: Pydantic, Pytest, AWS S3, AWS Lambda, JSON Schema, LinkML

• Spearheaded the development of Virtual Advising System 2.0's Angular frontend, optimizing a critical communication platform frequently utilized by students, college advisors, and department advisors.• Fostered collaboration with backend developers, ensuring a clean and intuitive interface with increased security and fluidity.

• Supported a cohort of 50 students in learning Python programming and provided dedicated guidance on diverse computer science topics, including finite state machines and image processing.• Drove lab initiatives to introduce students to HTML, CSS, and JS, equipping them with essential skills for their final web application projects.• Cultivated a positive learning environment, promoting a welcoming atmosphere to explore and ask questions, without judgement or nervousness.

• Addressed multiple programming tasks as part of TRIUMPH, a collaborative, public health initiative developed to create interventions to reduce the transmission of HIV. Collaborated with a range of professors, graduate students, software engineers, epidemiologists, and public health officials. • Built Molecular Data Vis, a React web application designed to visualize and understand molecular transmission networks through various interactive graphs, diagrams, and statistics. Robust enough to handle 10,000+ nodes and edges.• Wrote R code and Python scripts to assist with data filtering and visualization generation, creating interactive, clear, and maintainable HIV case geographic heatmaps respective to a variety of metrics.

• Introduced a class of 20 students to foundational concepts of robotics, including robot construction and wiring, Raspberry Pi configuration, Python programming.• Assisted students in building image processing, feedback control, and finite state machine algorithms. • Continuously enhanced the learning experience by proactively incorporating student feedback into teaching and lab session improvements.

Duarte, California, United States

• Launched website from scratch using React, Express, Node, Perl, and AWS cloud, which accesses multiple Bioinformatics databases to utilize Research Professor Dr. Hongzhi Li’s scripts for searching genes and proteins.• Implemented user-friendly, dynamic front-end with robust back-end and API on an AWS Ubuntu Lightsail Instance to return sequence alignments, phylogenetic trees, and more from Dr. Li’s programs.