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Nathaniel Fisher

Bioinformatics & Biotechnology Researcher

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About

I recently graduated with an M.S. in Bioinformatics from Boston University. Currently I work in the integrative Cardiovascular Metabolism and Pathophysiology Program (iCaMP) at Boston University where I am investigating mitochondrial genetic diversity across tissues in the human body and developing new approaches for variant calling and Nuclear-embedded mitochondrial DNA sequence (NUMT) filtering using mitochondrial WGS and RNA-seq data. Previously I worked in DNA process development at Moderna and genetic toolkit development in non-model bacteria at Joyn Bio. I also completed my B.A. in Biological Sciences from Cornell University where I did research in Environmental Microbiology and Ecosystem Ecology. In addition to mitochondrial genetics and cardiovascular disease, I have broad interests including environmental biotechnology, cancer biology, and deep learning applications in genomics. Outside of work I love sailing, swimming, and playing penny (Irish) whistle.

Projects

Shiny RNA-seq App

Customizing visualizations is a fun and engaging way to learn about a dataset. Here I deleloped a Shiny app that enables users to interactively analyze a publicly available RNA-seq dataset from soybean Glycine max at three different growth stages. The app allows users to explore the dataset by selecting differentially expressed genes, visualizing gene expression patterns, and performing gene ontology enrichment analysis. The app is hosted on a Shiny server and can be accessed here.

Shiny RNA-seq App

Mitoproximal Database Website

Below is a link to the Mitoproximal Proetin Database. I worked with classmates Jason Cunha, Iris Xu, and Christian Landaverde to create an SQL database and website to share the work of Fetterman and Leyfer (2023) who developed a data driven approach to identify nuclear proteins relevant to mitochondrial function. Take a look at the database and associated paper to learn more!

Mitop db

Heart Failure GWAS using the All of Us Dataset

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scRNAseq

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Curriculum vitae

    Nathaniel Fisher

    nmf35[at]cornell[dot]edu

    Education

    2024, M.S. in Bioinformatics
    Boston University, Boston, MA
    Grade: 4.0
    2019, B.A. in Biological Sciences (magna cum laude)
    Cornell University, Ithaca, NY
    Grade: 3.87
    Honors Thesis: Nutrient Limitations to Denitrification in Northeastern Hardwood Forests
    2021, CHEM 271, Chemical Biology
    University of California, Berkeley, CA
    Grade: A+

    Research Experience

    2024-present Bioinformatics Analyst, Boston University School of Medicine, Boston, MA
  • Member of iCaMP Lab (Integrative Cardiovascular Metabolism and Physiopathology)
  • Adapted and wrote bash scripts for quality control and variant calling of 17,000+ RNA-Seq samples
  • Collaborated on parallelizing WGS analysis pipeline, reducing runtime by 50x
    • 2022-2023 Senior Research Associate, Moderna, Norwood, MA
  • Designed novel plasmid-based approach for DNA production
  • Executed experiments for new gene editing technologies
  • Tested and implemented processes for optimizing plasmid production
    • 2020-2022 Strain Engineer, Joyn Bio LLC, Boston, MA
  • Automated data processing and analysis of CRISPR PAM library interference assays
  • Developed marker-less genome integration method
  • Conducted RNA-Seq and metabolic engineering experiments
    • 2016-2019 Research Assistant, Goodale Lab, Cornell University, Ithaca, NY
  • Adapted denitrification enzymatic assay for soil samples
  • Studied nutrient limitations on microbial denitrification activity
  • Installed root cores for forest root biomass study
    • 2018-2019 Undergraduate Researcher, Thies Lab, Cornell University, Ithaca, NY
  • Isolated chromium-resistant bacterial strains
  • Studied effects of bacterial strains on plant growth in chromium-contaminated soils
    • 2018 Research Assistant, Baars Lab, North Carolina State University, Raleigh, NC
  • Developed methods for small molecule extraction and quantitation from soils

    • DEIA Statement

           I am committed to questioning existing hierarchies and uplifting underrepresented perspectives to improve research and work towards a more just society. In one effort to increase DEI awareness and action at my previous company, I organized and facilitated three rounds of small discussion groups for my company, each of which followed a larger training on a core component of DEI. In these discussions, coworkers voiced concerns and provided ideas for the future, which were documented for continued initiatives.
           DEI efforts require consistent commitment at multiple scales. In my daily interactions, I focus on active listening, maintaining an open mind, and recognizing all that I do not know before drawing conclusions. I also intend to advance equity and accessibility through my work as a volunteer English language tutor with ELNOR, an organization that provides English language education to students living in refugee camps and contexts. I am glad for the efforts to raise awareness of DEI and look forward to continuing to participate in putting words to action. I want to help create environments where everybody is included, and diverse perspectives are valued.

    Grants, Honors, and Awards

  • 2019 Granted Honors in Biological Sciences
  • 2019 Graduated with Distinction in all subjects (Top 30% of class)
  • 2018 Awarded NSF REU Summer Fellowship in Basic and Environmental Soil Science Training
  • 2017 Writing in the Majors Prize Honorable Mention
  • 2016 Member of Cornell delegation to UN Framework Convention on Climate Change COP 22

    • Technical Skills and Experience

  • Computational: R, Python, Linux, Snakemake, Git, SQL, Cloud Computing, Next Generation Sequencing analysis pipelines, Shiny, Web Development (HTML, JavaScript, CSS)
  • Molecular Biology: RNA-Seq, Whole Genome Sequencing, PCR, qPCR, Golden Gate Assembly, Gibson Assembly, nucleic acid extraction, protein purification, cell-free systems
  • Microbiology: Microbial culturing, non-model bacterial transformation (electroporation, conjugation, natural competence, and chemical competence), genetic toolkit development for undomesticated bacteria

    • Publications

    1. Rai V, Fisher N, Duckworth OW, Baars O, 2020. Extraction and Detection of Structurally Diverse Siderophores in Soil. Frontiers in Microbiology 11, 1–13. doi:10.3389/fmicb.2020.581508

    Conference Presentations

    Oral Presentations
    1. Fisher N. Controls on Denitrification at Three Soil Depths West of Watershed 6. Hubbard Brook Ecosystem Study, 56th Annual Cooperator’s Meeting, Woodstock, NH, July 2019.
    Poster Presentations
    1. Nathaniel Fisher, Liying Xue, Xianbang Sun, Jesse D. Moreira1, Yi Li, Karan Kacy Smith, Jason Cunha, Brian Tao, Zachary Milstone, Robert F. Padera, Marc E. Lenburg, Daniel Levy, Emelia J. Benjamin, Scott Ladenheim, Deepa M. Gopal, Chunyu Liu, Seung Hoan Choi, Jessica L. Fetterman. Mitochondrial Genetic Variation Across Human Tissues. Bioinformatics Student-Organized Symposium. Boston, MA. June 2024.
    2. N and Goodale C. Controls on Denitrification at Three Depths in a Northeastern Hardwood Forest. Hubbard Brook LTER Mid-Term Review. Woodstock, NH. June 2019.
    3. Fisher N, Liu S, Gardner TG, and Baars O. Relationships between Nutrient Content, Microbial Communities, and Presence of Siderophores in North Carolina Soils. SSSA International Soils Meeting. San Diego, CA. January 2019.

    Professional Organizations

  • Student Member, American Society of Microbiology (2021-2022)
  • Student Member, Soil Science Society of America (2018-2019)

    • General Research Interests

    Human disease genomics, mitochondrial genetics, parallel computing, quantum computing, computational biology technologies applied to metabolic engineering, regulatory circuit redesign, and protein engineering, developing computational tools to improve design and data analysis of experiments, environmental applications for biotechnology