Clarence Mah Email & Phone Number

San Diego, Ca, Us

San Diego, California, United States

Greater San Diego Area

PI: Dr. Gene YeoMaintained and expanded bento-tools (more below), an open-source Python package for subcellular spatial transcriptomics analysis (version control, unit testing, continuous integration, documentation, tutorials, etc.)Devised deep learning and computer vision algorithms to predict RNA dynamics and cell morphology from spatial omics data (variational autoencoders, remote sensing).Created in-house high-content image analysis pipeline (Nextflow) handling stitching, image registration, background normalization, spot detection, barcode decoding, and visualization. Used for decoding MERFISH and in-situ sequencing imaging data.

Greater San Diego Area

PIs: Dr. Gene Yeo and Dr. Hannah CarterThesis: “Computational Frameworks for Functional Subcellular Analysis of Spatial Transcriptomics Data”Created bento-tools, an open-source Python package for subcellular spatial transcriptomics analysis (53 stars, 16k+ downloads). Part of the Scverse ecosystem (interfaces with Scanpy, Squidpy, SpatialData, AnnData). First author, published in Genome Biology.Graduate Student Researcher (continued)Developed novel machine learning algorithms (neural networks, random forests, SOMs, tensor decomposition) to interrogate RNA processing and cell biology using spatial transcriptomics and imaging (Xenium, Molecular Cartography, CosMx, MERFISH, etc.).Versatile experience performing large-scale data analysis and algorithm optimization using HPCs, GPUs (PyTorch) and parallel processing (Dask, joblib).Extensive experience analyzing NGS datasets: single-cell RNA-seq, RNA-seq, ATAC-seq, ChIP-seq, CLIP-seq, etc. for single-cell analysis (Seurat, Scanpy) differential expression (DESeq2), gene enrichment (GSEA, AUCell, GO), peak calling (MACS2), motif analysis (Homer), alt. splicing (RMATS, IRFinder), MHC binding affinity prediction (netMHCpan).Frequently performed analyses with large public data i.e. ENCODE, ENCORE, TCGA, and GTEx.

San Diego, California, United States

Used deep learning models to predict RNA binding protein-mediated alternative splicing.

Uc San Diego

PI: Jill MesirovAuthored one of the earliest vignettes for exploratory single-cell RNA-seq analysis using Scanpy. First author, published in F1000 Research.Authored a vignette on inferring copy number variation from Illumina methylation arrays.First author, published in F1000 Research.Identified multi-omic signatures characterizing novel subtypes of medulloblastoma with distinct clinical outcomes. Analyzed copy number variation, gene expression, proteomics, phospho-proteomics, and single-cell RNA-seq data for Bayesian classification and survival analysis. Middle author, published in Cancer Cell.Identified subtype-specific enhancer regulatory networks of glioblastoma cancer stem cells integrating H3K27ac ChIP-seq, methylation arrays, and RNA-seq data. Middle author, published in Journal of Experimental Medicine.Created and maintained reproducible multi-tool bioinformatics analysis workflows.Developed prototype Python GUI builder feature for GenePattern Notebook (GenePattern + Jupyter Notebooks).

Uc San Diego

Assisted in creation of behavioral study to design and optimize an experimental framework for a neurally controlled speech prosthesis.Designed/optimized a visual interface for a neurally controlled speech prosthesis.Proposed implementation of Microsoft Kinect sensor in clinical environment for data collection of patient movement/environment interaction.

Scripps Institution Of Oceanography

Investigated transcriptional regulators of peroxisome biogenesis disorders by analyzing annotated regulatory motifs as well as de novo motif discovery.

Responsible for keeping track of FDA regulations for lab and manufacturing safety.Carried out quality testing on medical devices and products.

Doctor Of Philosophy - Phd, Bioinformatics And Systems Biology

Activities and Societies: Graduate Bioinformatics Council

Bachelor Of Science (B.S.), Bioinformatics

Activities and Societies: Biomedical Engineering Society, Undergraduate Bioinformatics Club, Society of Asian Scientists and Engineers

High School