Bioinformatics engineer

GEMMA R. TAKAHASHI

408-***-**** ********@***.*** github.com/grtakaha linkedin.com/in/gemma-takahashi Skilled in building automated data pipelines for the acquisition, preprocessing, and visualization of primarily sequence data from biological data stores. Seeking an interdisciplinary position that leverages strong knowledge of biological data, bioinformatics pipelines, and science communication. EDUCATION

PhD, University of California, Irvine, Molecular Biology and Biochemistry (MBB), September 2019-June 2025 Bioinformatics, GPA: 3.9

Relevant elective coursework: Stats Methods I, Machine Learning BS, California Institute of Technology, Geobiology, GPA: 3.3 June 2019 Relevant elective coursework: Introduction to Computer Programming, Introduction to Computer Science Research, Computer Language Shop (C), Computer Language Lab: C++, Learning Systems, Machine Learning & Data Mining

SKILLS

Programming and Data Science: Python, Java, Bash, R, C, C++, JavaScript, REST APIs, SPARQL, pandas, sklearn Environments: Windows (local), Linux (local, HPC cluster – UCI HPC3 with Slurm manager), Galaxy Open-Source Tools: for sequence manipulation (STAR, SignalP-6.0, Clustal Omega, BLAST, etc.); for protein structure visualization/prediction (UCSF Chimera/ChimeraX, RosettaFold, AlphaFold2, etc.) Databases: web and programmatic navigation of databases like Gene Ontology, GISAID, UniProt, NIH/NLM/NCBI databases (Gene, Nucleotide, etc.); submission to NCBI databases (SRA, TSA, WGS, etc.) Soft Skills: problem solving, communication, collaboration, public speaking (300+ student audience) RELEVANT EXPERIENCE

Martin Lab, UCI, Irvine, CA September 2019-Present Graduate Student, Cellular and Molecular Biosciences and MBB Advisor: Rachel Martin; Languages used: Python, Bash, R

• Designed and implemented automated, command-line, sequence data pipelines whose applications include:

o Informing the design of mutation-resistant SARS-CoV-2 inhibitors1,2. o Understanding microbial protein adaptations to extreme temperature3,4. o Characterizing protein diversity and function in carnivorous plants and eye lenses5–7.

• Aided lab members by writing scripts for processing of nuclear magnetic resonance (NMR) data. o Improved reproducibility, efficiency, and accuracy by eliminating hand-calculations. o Designed organized outputs, which included a clean log of both input and output file locations, as well as methods, tools, and versions used.

o Worked closely with lab members to fit specific needs (e.g. sorting, naming conventions, speed). o Taught lab members how to use scripts and how to continue to modify them for other purposes.

• Automated the generation of publication-quality protein sequence alignment figures6

(github.com/grtakaha/CASA).

o Eliminated the need for hours of error-prone formatting with each sequence alignment. o Allowed for fast, en masse comparison of sequences even prior to publication. o Found creative solutions to unexpected problems when implementing desired features (e.g. maintaining multi-line text box editability in Inkscape SVG). o Linked figure-generating tool with other custom scripts to add functionality (e.g. automatic annotation of key amino acid residues based on database records).

• Designed, developed, and led science outreach and teaching activities8–10. o Acquired data, designed activities, and gave lectures for a research-focused active learning module that taught protein structure and function to undergraduate-level biochemistry students9. o Consulted on the development of a remote, UCI-taught bioinformatics class (M128L). o Designed and assembled fifty COVID-friendly science kits for distribution at the Corona Public Library during 2020. Created worksheets and YouTube videos to teach children the science of color

(https://www.youtube.com/watch?v=7K37wQvJrpU,

https://www.youtube.com/watch?v=x8g1hQHrVFc).

o Gave tours, demos, invited talks, and/or poster presentations for organizations including: UCI’s Enhanced Academic Success Experience (EASE) Initiative, CSULB, Edwards Lifesciences, and the Sherman Library and Gardens.

PUBLICATIONS

(1) Cross, T. J.; Takahashi, G. R.; Diessner, E. M.; Crosby, M. G.; Farahmand, V.; Zhuang, S.; Butts, C. T.; Martin, R. W. Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease. Biochemistry 2020, 59 (39), 3741–3756. https://doi.org/10.1021/acs.biochem.0c00462.

(2) Diessner, E. M.; Takahashi, G. R.; Cross, T. J.; Martin, R. W.; Butts, C. T. Mutation Effects on Structure and Dynamics: Adaptive Evolution of the SARS-CoV-2 Main Protease. Biochemistry 2023, 62 (3), 747–758. https://doi.org/10.1021/acs.biochem.2c00479.

(3) Diessner, E. M.; Takahashi, G. R.; Martin, R. W.; Butts, C. T. Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases. Biomolecules 2023, 13 (2), 328. https://doi.org/10.3390/biom13020328.

(4) Diessner, E. M.; Takahashi, G. R.; Butts, C. T.; Martin, R. W. Comparative Analysis of Thermal Adaptations of Extremophilic Prolyl Oligopeptidases. Biophysical Journal 2024, 123 (18), 3143–3162. https://doi.org/10.1016/j.bpj.2024.07.013.

(5) Serebryany, E.; Martin, R. W.; Takahashi, G. R. The Functional Significance of High Cysteine Content in Eye Lens γ-Crystallins. Biomolecules 2024, 14 (5), 594. https://doi.org/10.3390/biom14050594.

(6) Takahashi, G. R.; Cumpio, F. M.; Butts, C. T.; Martin, R. W. The Computer-Assisted Sequence Annotation

(CASA) Workflow for Enzyme Discovery. Applications in Plant Sciences 2025, 13 (3). https://doi.org/10.1002/aps3.70009.

(7) Sprague-Piercy, M. A.; Bierma, J. C.; Crosby, M. G.; Carpenter, B. P.; Takahashi, G. R.; Paulino, J.; Hung, I.; Zhang, R.; Kelly, J. E.; Kozlyuk, N.; Chen, X.; Butts, C. T.; Martin, R. W. The Droserasin 1 PSI: A Membrane- Interacting Antimicrobial Peptide from the Carnivorous Plant Drosera Capensis. Biomolecules 2020, 10 (7), 1069. https://doi.org/10.3390/biom10071069.

(8) Dastgheib-Beheshti, S.; Long, Z. G.; Takahashi, G. R.; Martin, R. W. How Scientific Illustration Impacts Presentation and Understanding of Plant Adaptations at Multiple Scales. The Plant Science Bulletin.

(9) Kelz, J. I.*; Takahashi, G. R.*; Safizadeh, F.; Farahmand, V.; Crosby, M. G.; Uribe, J. L.; Kim, S. H.; Sprague- Piercy, M. A.; Diessner, E. M.; Norton-Baker, B.; Damo, S. M.; Martin, R. W.; Kadandale, P. Active Learning Module for Protein Structure Analysis Using Novel Enzymes. The Biophysicist 2022, 3 (1), 49–63. https://doi.org/10.35459/tbp.2021.000209.

(10) Kelz, J. I.; Uribe, J. L.; Rasekh, M. F.; Takahashi, G. R.; Gibson, W. S.; Link, R. D.; McKnelly, K. J.; Martin, R. W. Implementation of Specifications Grading in an Upper-Division Chemical Biology Lecture Course. The Biophysicist 2023, 4 (1), 11–29. https://doi.org/10.35459/tbp.2022.000239.

* These authors contributed equally to this work.

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