A.W.L.
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Alexander Larsen

Computational Biology • Deep Learning • Bioinformatics

Computational Biologist — TUM / Helmholtz Munich & Roche

About Me Resume
ORCID

About

I work at the intersection of deep learning, bioinformatics, and molecular design for pharmaceutical development. My current focus is on building computational approaches for siRNA, ASOs, and sequence-based therapeutics — combining predictive modeling, multimodal biological data analysis, foundation model integration, and agentic workflows to support drug discovery and design.

My background spans NGS, CRISPR-Cas, clinical and research data analysis, and bioinformatic software development, from fast-paced diagnostic settings to high-dimensional biological modeling. Over time my work has grown from classical bioinformatics pipelines into PyTorch-based ML systems for therapeutic design, including feature engineering, workflow automation, and decision-support tooling.

I enjoy working across technical and scientific boundaries to build systems that are rigorous, practical, and useful to real research teams, and I bring experience in cross-functional collaboration, scientific communication, grant writing, and software development.

6+ Publications
4 Amplification Chemistries
10+ Years in Bioinformatics
PhD Computational Biology, TUM

Skills

Machine Learning & Deep Learning

PyTorch Neural Networks Transformers LSTMs VAEs ConvNN / ResNet DNA/RNA LLMs Gradient Saliency Random Forests XGBoost SVM / KNN Ensemble Methods PCoA / PCA DESeq2

Software Engineering

Python Perl SQL Bash C++ R JavaScript HTML / CSS Docker Nextflow AWS Git REST APIs Django SLURM / HPC

Bioinformatics

Metagenomics NGS / Illumina NextSeq Whole Exome Sequencing CRISPR-Cas siRNA / ASO Design Sequence Alignment RNA Structure (Vienna/Nupack) GATK / Samtools Bowtie2 / BWA Kraken2 / CLARK BLAST Annovar / ClinVar Hidden Markov Models MSA / UPGMA DeBruijn Graphs

Laboratory & Communication

DNA/RNA/Protein Extraction Western Blotting PCR Mass Spectrometry Neuronal Electrophysiology Grant Writing SOP Writing Public Speaking Team Management Mentoring

Experience

Computational Biologist Doktorand

Roche — Basel, Switzerland / Penzberg, Germany

Sep 2025 – Present
  • Hybrid role between Penzberg, Basel, and Helmholtz for molecular design with Basel's RNA Hub and the Computational Science department under gRED.
  • Building generative and predictive models for siRNA/ASO therapeutic design, including chemically modified oligonucleotides.
  • Developed scalable, reproducible pipelines for training, inference, and benchmarking across deep learning, foundation model / LLM, and generative modeling projects.

Machine Learning Researcher — Doktorand

Helmholtz Munich — Munich, Germany

Jun 2024 – Aug 2025
  • Generative modeling for RNA therapeutics: predicting siRNA efficacy with engineered features, chemically modified sequences, and foundation model embeddings.
  • Deep learning architectures: ResNet, AttentionPooling, LSTMs, VAEs with integrated gradient saliency maps for model explainability.
  • Curated the largest known publicly available dataset of chemically modified siRNAs for mRNA knockdown.
  • Benchmarking XGBoost, RF, Lasso/Ridge models; patent PaddleOCR data extraction; genetic algorithms and beam search for siRNA generative design.

Bioinformatics Scientist I → Manager

Sherlock Biosciences — Boston, MA

Nov 2020 – Jan 2024
  • Led the Bioinformatics Division; managed employee reviews, project tracking, and cross-team coordination with experimental and theoretical groups.
  • Developed and maintained full company bioinformatics pipelines (Python, Perl, SQL, Bash, Docker, Vienna) optimizing RNA structure, CRISPR performance, LAMP constraints, and SDA across four amplification/readout chemistries.
  • Achieved 99%+ reduction in genomic feature space across all amplification technologies, dramatically reducing clinical diagnostic failure post-deployment.
  • Identified novel thermostable CRISPR-Cas proteins for publication and patent.
  • Supported grant applications for MIT/Harvard BROAD, B&M Gates Foundation, and US Department of Defence FDA-cleared diagnostics contracts.

Clinical Bioinformatician I & II

Aperiomics Inc. — Sterling, VA

Jun 2018 – Nov 2020
  • Designed automated COVID-19 report end-to-end software covering analysis, formatting, and clinical sign-off.
  • Built a metagenomic analysis library that automatically queries patient data for report statistics formatting (Python, Bash, SQL, CSS/HTML, Git, Django, Docker, AWS CLI).
  • Designed automated multi-process Human Microbiome Project WGS metagenomic pipeline on cluster.
  • Presented bioinformatics clinical value to investors, poster talks, and local events.

Associate Research Assistant

University of Wisconsin Madison — Madison, WI

Apr 2013 – May 2016
  • Characterized circadian rhythm genes and their temporal effect on long-term memory formation in Drosophila (Prof. Jerry Yin / Robin Fropf).
  • Additional research: zebrafish embryonic development, crayfish nerve reading frequencies, and rat hippocampal electrical activity (Prof. Tony Stretton).

Publications

ORCID iD ORCID: 0009-0003-9175-6005
In Preparation

Larsen, A., Butnaru, D., Rotrattanadumrong, R., Yonchev, D., Gagneur, J., & Marsico, A. (2026). FENNEC: Fine-Tuned Ensemble Neural Networks Accelerate Chemically Modified siRNA Design and Screening. Manuscript in preparation, Institute of Computational Biology, Helmholtz Zentrum München; Roche Innovation Center Basel; TUM School of Computation, Information and Technology.

Published

Phillips, E.; Silverman, A.; Joneja, A.; Liu, M.; Brown, C.; Carlson, P.; Coticchia, C.; Shytle, K.; Larsen, A.; Goyal, N.; et al. (2023). Detection of viral RNAs at ambient temperature via reporter proteins produced through the target-splinted ligation of DNA probes. Nature Biomedical Engineering. doi:10.1038/s41551-023-01028-y

Published

Pena JM, Manning BJ, Li X, Fiore ES, Carlson L, Shytle K, Nguyen PP, Azmi I, Larsen A, Wilson MK, Singh S, DeMeo MC, Ramesh P, Boisvert H, Blake WJ. (2023). Real-Time, Multiplexed SHERLOCK for in Vitro Diagnostics. Journal of Molecular Diagnostics, 25(7):428–437. doi:10.1016/j.jmoldx.2023.03.009

Published

Larsen, A. W., Chen, Y., Crandall, K. A., Icenhour, C. R., & Valencia, A. C. (2022). Characterization of the Interstitial Cystitis/Bladder Pain Syndrome Microbiome in Clinically Diagnosed Patients. Clinical Immunology & Research. doi:10.33425/2639-8494.1047

Published

Baugher, D., Larsen, A. W., Chen, Y., Icenhour, C. R., & Valencia, C. A. (2021). Female Urinary Microbiome Analysis and Artificial Intelligence Enhances the Infectious Diagnostic Yield in Precision Medicine. Microbiology & Infectious Diseases. doi:10.33425/2639-9458.1126

Published

Valencia, C. A., Baugher, D., Larsen, A., Chen, A., & Icenhour, C. (2020). Female Urinary Metagenomic Analysis and Natural Language Processing Enhances the Infectious Diagnostic Yield in Precision Medicine. Open Forum Infectious Diseases. doi:10.1093/ofid/ofaa439.1859

Education & Certifications

Computational Biology PhD

Technical University of Munich / Helmholtz Munich

Jun 2024 – Jan 2028 (expected) — Munich, DE

Generative Modeling for RNA Therapeutics. Traditional Models vs Deep-Learning Foundation Models.

M.S. Bioinformatics

University of Maryland Global Campus

Mar 2019 – Nov 2021 — Adelphi, MD

Alignment, Statistical Analysis, SQL Databases, Protein Structure, Biotechnology and Biomanufacturing.

B.S. Neurobiology

University of Wisconsin–Madison

Sep 2012 – May 2016 — Madison, WI

Selective honors biology program (UW Madison Biocore) facilitating group-directed research, scientific writing, and analysis.

edX / MIT / UC Berkeley Certificates

MIT • UC Berkeley • University of Maryland

May 2018 – Present

  • Bioinformatics MicroMasters Certificate
  • BIF001x: DNA Sequences • BIF002x: Proteins • BIF003x: Statistical Analysis
  • Foundations of Data Science: Computational Thinking with Python
  • MITx 6.431x: Probability and Uncertainty
  • MITx 18.6501x: Fundamentals of Statistics

GitHub

Open-source projects, bioinformatics tools, machine learning experiments, and more. Additional projects available on request.

View on GitHub

Photography

Highlights from a year-long road trip spanning 48 states, parts of Canada and Mexico.

Contact

Let's get in touch.

alarsen525@gmail.com linkedin.com/in/a-w-larsen github.com/Zinthrow ORCID ORCID: 0009-0003-9175-6005
Basel, Switzerland / Munich, Germany