Quin Lamothe

● NextFlow pipelines for patient variant calling ● AWS support, interagency clinical data transfers ● bcftools for patient .vcf, .bed file annotation and filtering ● Bioinformatic web application development on 'Argus', 'MetaMorph' and 'Rinae'. ● Design and deployment of agentic workflows for bioinformatic purposes

● Creating molecule objects from SMILES for intramolecular property calculations with RDkit. ● Visualizing oligonucleotide therapeutic predictions using RDkit and py3Dmol. ● Using SMARTS to modify molecule objects. ● Tokenizing and Embedding molecule objects, oligonucleotides and peptides. ● Developing Snakemake and Snakemake/papermill workflows. ● Reviewing contemporary bioinformatic machine learning research publications. ● NGS pipeline operation and maintenance. ● Analyzing clinical NGS data. ● Managing a team of bioinformatic engineering interns.

● Development of Metamorph software for ASO sequence and efficacy prediction ● Development of NGS pipelines for differential expression analysis using Python, R and Bash ● Analysis of RNA sequencing data from CRISPR and ASO experiments on humans and mice ● Visualization methods like UMAP with k-means clustering for DE Gene Ontology analysis ● Deployment of HOMER, Cytoscape/iRegulon, netZooR and netZooPy PANDA and PUMA ● Spring tension modeling for depiction of TF-gene regulatory networks ● miRNA identification and assessment ● Modeling Oligonucleotide/protein dynamics and interaction ● Unix/Linux shell scripting

● Rare neurodevelopmental disease research ● Computational synthetic oligonucleotide and engineered transcription repressor design ● Developing scripts to access clinical database APIs ● Developing bioinformatic pipelines ● Parsing and formatting clinical and bioinformatic data ● Clinical data and bioinformatic pipeline management ● Developing graphics to descript and illustrate clinical data

● Engineering and refactoring machine learning methods ● Developing methods to one-hot encode multimodal oncological data ● Leading meetings to discuss purpose, assign tasks, and update progress reports ● Reviewing and amending machine learning code in JAX, TensorFlow and PyTorch ● Reviewing and presenting contemporary bioinformatic machine learning research papers ● Managing project Github, approving pull requests and updating issues

● Collecting data from various clinical databases pertaining to rare neurodevelopmental conditions and diseases. ● Developing scripts which interact with clinical database FTP sites and APIs. ● Bioinformatic data analysis, data source verification. ● Developing ETL infrastructure / maintaining pipelines ● Developing methods for data annotation and visualization. ● Preparing training data for drug discovery LLMs

● Aligning and assembling NGS and ONT data using common bioinformatics command line tools. ● Development of screening, alignment and assembly algorithms for NGS data derived from novel reptile tissue samples. ● Bioinformatic pipeline development. ● Mitochondrial DNA analysis.

● Assessing and storing whole genome and whole transcriptome paired end data derived from tissue samples of rare lizards and snakes ● Using Geneious, and the UCSC Genome Browser ● Converting Perl scripts to Python

● Developed a private DNA fragmentation web app using Flask. ● Implemented FASTA file upload methods and data visualization. ● Collaborated with a team of bioinformatics professionals. ● Version control with Git, GitHub.