Melanie Lee Email & Phone Number

San Francisco, California, US

San Francisco, California, US

Los Angeles, California, US

• Mined genomic databases and publicly available data, and transformed data into a uniform format useful for primer design and haplotype classification.
• Designed PCR primers for a multiplexed primer set targeting 40 genes in the major histocompatibility complex.
• Wrote custom pipelines and scripts for analyzing next-generation sequencing (NGS) data.
• Created an end-to-end tool for QC-ing data, identifying off-target reads and cross-hybridizing primers.
• Evaluated primer specificity, efficiency, and determined most informative primer sets using machine learning.

Los Angeles, California, US

San Francisco, CA, US

* Consulted for a start-up company that harnesses the plant microbiome for sustainable agriculture.* Extracted microbial communities from a crowd-sourced dataset of airborne microbes using latent semantic analysis of taxon counts to understand microbial community structure.* Created geospatial visualizations in Python of microbial community dispersal.

• Created a content recommender web application that generates links to similar articles using topic modeling.
• Scrapped Wikipedia articles from the web and stored and retrieved content using sqllite3.
• Performed A/B testing to compare the effectiveness of recommendation algorithms.
• Created an interactive front end using Flask and Javascript and deployed on Amazon Web Services.

Berkeley, CA, US

• Designed and performed 2-photon calcium imaging, electroporation, electrophysiology, and in situ hybridization experiments in developing mouse retina to understand the development of direction selectivity.
• Assembled an integrated pipeline in Matlab and ImageJ for acquisition and analysis of simultaneous imaging and visual stimulation of populations of mouse direction-selective retinal ganglion cells.
• Wrote custom image processing code to segment data and to time-sync cellular responses with location of visual stimulus across the visual field, increasing reliability of detecting direction-selective cells in a field.

New York, NY, US

• Developed methods for sparse labeling of calcium indicators in neurons; restriction-free PCR-based cloning for development of transgenic zebrafish sparsely expressing genetically encoded calcium indicators in neurons.
• Wrote custom Matlab scripts to link optokinetic stimulation with real-time saccade detection to optimize acquisition of cellular responses to specific oculomotor behaviors in zebrafish.
• Designed and implemented an analysis suite for identifying spatiotemporal footprints of subcellular compartments, detecting and classifying behavior-linked response types, and visualizing spatiotemporal patterns in.

Rahway, New Jersey, US

• Applied Computer Science and Mathematics Division, Merck, Inc.
• Implemented a pipeline in Matlab for analyzing pressure pulse waveforms obtained from rat telemetry to quantify cardiovascular benefits of future hypertension drugs. Optimized computational efficiency and robustness.

Ithaca, NY, US

• Mathematical and Theoretical Biology Institute (MTBI) Summer Research Program
• Mathematically modeled and analyzed the effects of the HIV epidemic on the South African transport industry. Developed and simulated in Matlab and Maple three deterministic, and one stochastic model, and investigated.

Los Angeles, CA, US

• Research in Industrial Projects for Students Summer Research Program
• Implemented advanced image processing routines (Fourier transforms, wavelet transforms, and PDE-based image inpainting) in C++ and wrote prototype code for an existing image compositing software package.

Phd, Computational Biology

Ms, Applied Math

Bs, Applied Math