CV

Education

• Ph.D. in Data Science and Engineering (expected 2025)
  • University of Tennessee, Knoxville
• M.S. in Computer Science (2017)
  • University of Missouri – St. Louis
• B.S. in Biology (2011)
  • University of Missouri – Columbia
• B.A. in Philosophy (2011)
  • University of Missouri – Columbia

Work Experience

• Graduate Research Assistant, Oak Ridge National Laboratory & University of Tennessee Knoxville
  • Aug 2020 – Present
  • Group: Computational and Predictive Biology (Advisor: Dr. Dan Jacobson)
  • Responsibilities:
    • Designed LLM-powered agentic pipelines integrating multi-omics data with curated literature to reverse engineer gene-disease associations.
    • Developed the RWRtoolkit, enabling random-walk restart analytics across multiplex networks; authored the API, documentation, and benchmarking suite.
    • Created high-throughput simulations for network-based gene knockouts and phenotype prediction.
    • Worked on explainable AI for Predictive Expression Networks (PENs) in exascale workflows on Frontier, Andes, and Summit supercomputers.
    • Engineered robust software packages for open science and peer-reviewed publication.
• Software Engineer, Monsanto / Bayer Crop Science
  • Jun 2017 – Aug 2020
  • Location: St. Louis, MO
  • Responsibilities:
    • Delivered mobile crop management apps using React Native for asynchronous field data collection.
    • Built full-stack applications with React/Redux front ends and ExpressJS/Scala-based back ends.
    • Automated regulatory and financial pipelines using ML microservice architecture.
    • Participated in CI/CD workflows and cross-functional DevOps collaboration.
• Adjunct Faculty, University of Missouri – St. Louis
  • Jan 2019 – Aug 2020
  • Department: Computer Science
  • Courses taught:
    • Web Development (HTML/JS/PHP)
    • Advanced Web Development (Node/React/Express)
    • Object-Oriented Programming (Java)
    • Linux Systems Programming (Bash/C)
• Graduate Research Assistant, University of Missouri – St. Louis
  • Jan 2017 – Aug 2017
  • Responsibilities:
    • Applied network theory to metabolomics data to uncover Alzheimer’s Disease biomarkers.
    • Taught Introduction to Computing and tutored programming in C/C++, Java, and mobile development.
• Outreach Educator, Missouri Botanical Garden
  • Aug 2013 – Aug 2014
  • Responsibilities:
    • Applied network theory to metabolomics data to uncover Alzheimer’s Disease biomarkers.
    • Taught Introduction to Computing and tutored programming in C/C++, Java, and mobile development.

Technological Proficiencies

• Languages: Python, R, Bash, NodeJS, HTML/CSS, PostgreSQL, Scala, Java, C, C++
• Frameworks/Toolkits: MPI, Dask, OpenAI API, React Native, ReactJS, Redux, ExpressJS, Akka
• Cloud & HPC Platforms: Azure Cloud AI, AWS, OLCF (Frontier, Andes), Perlmutter (NERSC)
• DevOps & Infrastructure: Docker, Apptainer, GitHub Actions, CI/CD pipelines, REST APIs

Publications

Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits

Klein, M. C., Meng, Z., Bailey‐Bale, J., Milner, S., Shi, P., Muchero, W., Chen, J., Tschaplinski, T. J., Jacobson, D., Lagergren, J., Lane, M., O’Brien, C., Chhetri, H., Abeyratne, C. R., Shu, M., Freer‐Smith, P., Buckley, T. N., Magney, T. S., Monroe, J. G., … Taylor, G. (2025). Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits. New Phytologist. https://doi.org/10.1111/nph.70343

Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis

Vasileva, D. P., Chhetri, H. B., Hochanadel, L. H., Streich, J. C., Lagergren, J. H., Lane, M. J., et al. (2025). “Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis.” bioRxiv. https://doi.org/10.1101/2025.07.14.664384

Population and adaptation history of 739 Thlaspi arvense natural accessions

Wu, X., Epstein, R., Esfahanian, M., Gautam, B., Griffiths, M., Perez, J., … Lane, M., et al. (2025). “Population and adaptation history of 739 Thlaspi arvense natural accessions.” bioRxiv. https://doi.org/10.1101/2025.03.21.644658

RWRtoolkit: multi‑omic network analysis using random walks on multiplex networks in any species

Kainer, D., Lane, M., Sullivan, K. A., et al. (2025). “RWRtoolkit: multi‑omic network analysis using random walks on multiplex networks in any species.” GigaScience.

Multi‑omic network analysis identifies dysregulated neurobiological pathways in opioid addiction

Sullivan, K. A., Kainer, D., Lane, M., et al. (2024). “Multi‑omic network analysis identifies dysregulated neurobiological pathways in opioid addiction.” Biological Psychiatry.

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

Sullivan, K. A., Lane, M., Cashman, M., Miller, J. I., Pavicic, M., Walker, A. M., et al. (2024). “Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior.” Communications Biology, 7(1), 1360. https://doi.org/10.1038/s42003-024-06943-7

MENTOR: Multiplex Embedding of Networks for Team‑Based Omics Research

Sullivan, K. A., Miller, J. I., Townsend, A., … Lane, M. (2024). “MENTOR: Multiplex Embedding of Networks for Team‑Based Omics Research.” bioRxiv.

Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits

Klein, M. C., Meng, Z., Bailey-Bale, J., Milner, S., Shi, P., Muchero, W., … Lane, M., et al. (2024). “Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits.” bioRxiv. https://doi.org/10.1101/2024.07.11.603099

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Meena, M. G., Lane, M. J., Tannous, J., et al. (2023). “A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs.” PNAS Nexus.

Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress

Cashman, M., Vergara, V. G. M., Lane, M., et al. (2023). “Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress.” ACM Conference.

Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US military veterans

Kimbrel, N. A., Ashley-Koch, A. E., Qin, X. J., Lindquist, J. H., … Lane, M. J., et al. (2023). “Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US military veterans.” JAMA Psychiatry, 80(2), 135–145.

Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease

Levin, M. G., Huffman, J. E., Verma, A., … Lane, M. (2023). “Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease.” Nature Cardiovascular Research.

Exploring the role of plant lysin motif receptor‑like kinases in regulating plant‑microbe interactions in the bioenergy crop Populus

Cope, K. R., Prates, E. T., Miller, J. I., … Lane, M. (2023). “Exploring the role of plant lysin motif receptor‑like kinases in regulating plant‑microbe interactions in the bioenergy crop Populus.” Computational and Structural Biotechnology Journal.

Lipo‑Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth

Rush, T. A., Tannous, J., Lane, M. J., … Ané, J.-M. (2022). “Lipo‑Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth.” mSystems.

Antiviral Strategies Against SARS‑CoV‑2: A Systems Biology Approach

Prates, E. T., Garvin, M. R., Jones, P., … Lane, M. (2022). “Antiviral Strategies Against SARS‑CoV‑2: A Systems Biology Approach.” Methods in Molecular Biology.

Synchronized genetic activities in Alzheimer’s brains revealed by heterogeneity‑capturing network analysis

Climer, S., Templeton, A.R., Garvin, M., Jacobson, D., Lane, M., et al. (2020). “Synchronized genetic activities in Alzheimer’s brains revealed by heterogeneity‑capturing network analysis.” bioRxiv.

Eyeing the patterns: Data visualization using doubly‑seriated color heatmaps

Lane, M., Maiocco, A., Bhatia, S.K., Climer, S. (2020). “Eyeing the patterns: Data visualization using doubly‑seriated color heatmaps.” Advances in Computers.

Talks

Binding Pathways to Break Addiction

June 05, 2025

Talk at National Institute on Drug Abuse: National Institute of Health, Washington D.C., United States

AI Systems Biology for Addiction: Large Scale Multi-Omics Network Modeling and AI Agents for Mechanistic Discovery

June 05, 2025

Talk at Platform for Advanced Scientific Computing (PASC) 2025 Conference, Brugg, Switzerland

Decoding the Genetic Networks of Addiction: High-Performance Computing for Insight into Opioid and Nicotine Dependency

June 05, 2024

Talk at Platform for Advanced Scientific Computing (PASC) 2024 Conference, Zurich, Switzerland

Teaching

Linux Systems Programming: Bash && C

Introduction to Object Oriented Programming with Java

Advanced Web Programming with Javascript

Introduction to Web Programming: HTML, Javascript, and PHP

Introduction to Computing with C++

Service and leadership

• Educational Outreach Leader

  East TN STEM Hub (Aug 2021 – Dec 2024)

  • Developed and led workshops in JavaScript robotics, static web design, and Python data analysis.

• Board Member

  TN STEM Innovation Network – Statewide CS Advisory Board

  • Promoting equitable access to K-12 computer science education across Tennessee.

• HSCC Coordinator & Instructor

  BDPA St. Louis (Feb 2018 – Aug 2020)

  • Led teams to top national finishes using HTML/CSS, NodeJS, MySQL curriculum.

Other Interests

• Open-source software contributor
• Advocate for inclusive STEM education
• Data visualization, science communication, and illustration.
• Philosophy of Science