Doctor of Philosophy, Oral Biology
Aug 2023 – present
University at Buffalo, Buffalo, NY · Lab of Dr. Kathryn M. Kauffman
- Advanced to candidacy December 2024. GPA 3.98.
Education
Continuing Education
Aug 2019 – May 2021
University of Vermont, Burlington, VT · GPA 3.89
- Biochemistry 301/302 — year-long graduate-level biochemistry
- One Health: Antimicrobial Resistance
- Understanding Human Pregnancy
Bachelor of Science, Medical Laboratory Science
Aug 2015 – May 2019
University of Vermont, Burlington, VT · Public Health concentration, Microbiology minor · GPA 3.35
- Completed all coursework required for medical school applicants
- Full-time public health practicum, UVM Vaccine Testing Center (Spring 2019)
- 6-credit Emergency Medical Technician course; national certification expired March 2022
High School Diploma
Sep 2011 – May 2014
Northfield Mount Hermon School, Mount Hermon, MA
Funding
Mark Diamond Research Fund (MDRF) Grant
2026
Graduate Student Association, University at Buffalo · $5,000
- “Characterization of novel secreted natural products in the keystone pathogen Porphyromonas gingivalis” — mass-spectrometry identification of secreted molecules from size-fractionated culture supernatants across a panel of genetically distinct P. gingivalis strains.
Technical skills
Computational
Languages & tooling
Python, R, Bash, Git/GitHub; MATLAB (working knowledge)
High-performance computing
SLURM job submission and array jobs on the UB Center for Computational Research cluster; batch pipeline design for genome-scale analysis
Comparative & pan-genomics
Prokka, Panaroo, cblaster, BLAST+; gene presence/absence analysis across strain panels
Mobile genetic elements
Prophage and integrative conjugative element identification and manual curation (ICEfinder); anti-phage defense system detection (DefenseFinder); host–element association
Biosynthetic gene clusters
RODEO; RiPP precursor and tailoring-enzyme identification, cluster architecture comparison, and family assignment
Regulatory sequence analysis
MEME Suite / FIMO promoter motif discovery, scanning, and filtering
Protein structure
ColabFold / AlphaFold2 structure prediction; interpretation of pLDDT and predicted aligned error
Protein language models & ML
ProtT5 embeddings via HuggingFace Transformers; UMAP projection and clustering; leakage-controlled benchmark design for function prediction
Data analysis & visualization
pandas, matplotlib, Plotly; publication figures and self-contained interactive browser tools
Sequence data management
Geneious, SequenceServer, HOMD; reproducible reference database construction for metaproteomic search
Laboratory
Anaerobic microbiology
Routine anaerobic culture of Porphyromonas gingivalis and other oral taxa; anaerobic chamber operation and maintenance
Nucleic acids
DNA and RNA extraction from pure and mixed samples, cDNA synthesis, PCR, RT-qPCR, Sanger sequencing and alignment
Protein & peptide
Protease inhibition assays (cathepsin S, chymotrypsin); solid-phase extraction; size-based fractionation of culture supernatant for mass spectrometry
Genetic manipulation
Knockout construct design for P. gingivalis precursor loci
Animal models
IACUC-approved ligature-induced periodontitis mouse model; microCT acquisition and AnalyzePro analysis
Culturomics
Isolation and identification of clinical oral microbiome isolates; isolate database development
Clinical research & regulatory
Trial operations
Phase I–III coordination; protocol, SOP, and informed-consent development; IND submissions; regulatory and sponsor communications; randomization; adverse event documentation; source-document quality control; biorepository study coordination
Research experience
PhD Student — Kauffman Lab
Jul 2024 – present
Department of Oral Biology, School of Dental Medicine, University at Buffalo
- Leading an independent dissertation project on mobile genetic elements and associated natural product biosynthetic systems in Porphyromonas gingivalis, with emphasis on microbial ecology, virulence, and periodontal disease.
- Building scalable computational pipelines on UB high-performance computing systems for analysis of microbial genomes, mobile genetic elements, and protein function.
PhD Student — Diaz Lab
Aug 2023 – Jul 2024
Department of Oral Biology, School of Dental Medicine, University at Buffalo
- Developed working proficiency in R, Python, and MATLAB for bioinformatic analysis integrated with UB high-performance computing workflows.
- Independently developed, submitted, and executed an IACUC-approved ligature-induced periodontitis mouse model to study the oral–gut axis, including microCT imaging and AnalyzePro-based analysis.
- Contributed to laboratory operations, organization, onboarding, and training of new students and postdoctoral researchers.
Laboratory Research Technician
Aug 2022 – Aug 2023
UB Microbiome Center · Diaz Lab, Department of Oral Biology, University at Buffalo
- Contributed to a collaborative culturomics project with Sunstar Group: culture and identification of clinical oral microbiome isolates, and development of an individualized isolate database for downstream biofilm and community modeling.
- Conducted microbiome bench research across clinical and mouse specimens — protocol development for bacterial cell lysis, DNA extraction, PCR, Sanger sequencing, sequence alignment, and microbial DNA isolation from mixed samples.
- Managed laboratory purchasing, budget tracking across funding sources, and core equipment maintenance including anaerobic chambers and incubator systems.
Clinical Research Coordinator II
Apr 2021 – Aug 2022
Dana-Farber Cancer Institute, Boston, MA
- First coordinator dedicated exclusively to development of the pediatric Cellular Immune Therapy Program (CTIP), including creation of workflows, SOPs, and shared document templates across oncology groups.
- Led a quality-control project across disease groups to troubleshoot research sample collection and improve clinical–operational communication.
- Independently coordinated 4–6 Phase I and Phase II clinical trials simultaneously.
- Managed regulatory submissions, sponsor communications, and day-to-day clinical research operations.
Clinical Research Coordinator
May 2019 – Apr 2021
University of Vermont Vaccine Testing Center, Burlington, VT
- Developed standard study procedures and helped coordinate a Phase III AstraZeneca clinical trial for prevention of COVID-19 illness.
- Supported clinical operations across scheduling, informed consent, participant screening, source document QC, data entry, randomization, vendor platform support, adverse event documentation, and supply management.
- Contributed to development of study protocols, informed consents, IND applications, source documents, human challenge model studies, and online databases for vaccine and biorepository studies.
- Worked on domestic, international, multi-site, pharmaceutical-sponsored, and investigator-initiated trials.
- Independently coordinated a biorepository study salvaging COVID-positive hospital samples for research use.
Public Health Intern (full-time)
Jan 2019 – May 2019
Vaccine Testing Center, Burlington, VT
- Semester-long project compiling and organizing clinical trial metadata to support analysis of a 16S rRNA microbiome dataset from a Bangladeshi birth cohort.
- Completed over 100 literature reviews; developed skills in hypothesis generation, scientific writing, and interpretation of microbiome sequencing data.
Part-Time Laboratory Assistant
Sep 2016 – Oct 2017
Francklyn Lab, Department of Biochemistry, University of Vermont
Publications & preprints
Matrishin CB, Haase EM, Miles AK, Steimer S, Soh D, Smardz M, Diaz PI, Kauffman KM. Pervasive integrative and conjugative elements shape Porphyromonas gingivalis gene repertoires. bioRxiv, 5 August 2026. doi:10.64898/2026.08.04.741601
Handelmann C, Miles AK, Ye Y, Freire M, Dewhirst FE, Chen T, Mark Welch J, Kauffman KM. maniFasta and the AllOralsDB: simplifying construction of comprehensive reference databases for metaproteomics. bioRxiv, 10 August 2026. doi:10.64898/2026.08.08.739415
Graham NR, Whitaker AN, Strother CA, Miles AK, Grier D, McElvany BD, Bruce EA, Poynter ME, Pierce KK, Kirkpatrick BD, Stapleton RD, An G, Botten JW, Crothers JW, Diehl SA. Kinetics and isotype assessment of antibodies targeting the spike protein receptor binding domain of SARS-CoV-2 in COVID-19 patients as a function of age and biological sex. medRxiv, 2020. doi:10.1101/2020.07.15.20154443
Software
Miles AK. Graspetide Crosslink Explorer. Interactive browser tool for comparing crosslink topologies across characterized graspetide families. ashleykmiles.com/explorer.html
Miles AK. 3D Graspetide Precursor UMAP. Interactive projection of ProtT5 protein language-model embeddings for graspetide precursors, colorable by biosynthetic branch, taxonomy, and oral/non-oral origin. ashleykmiles.com/umap3d.html
Handelmann C, Miles AK, et al. maniFasta. Reproducible construction of comprehensive reference databases for metaproteomics; contributor. doi:10.64898/2026.08.08.739415
Presentations
Characterization of widespread graspetide biosynthetic gene clusters in the periodontal pathogen Porphyromonas gingivalis
2026
Miles AK, Matrishin CB, Kauffman KM — presented at UB Student Research Day 2026; the 36th Annual Buffalo Conference on Microbial Pathogenesis; and the Gordon Research Conference on Proteases, Inhibitors and Therapeutics (Il Ciocco, Tuscany, Italy)
Strain heterogeneity in subgingival plaque isolates of Fusobacterium nucleatum subspecies animalis
2024
Suzuki T, Miles A, Steimer S, Dada I, Shimizu Y, Diaz PI — UB Student Research Day 2024; IADR General Session 2024
Microbiome clusters associated with diarrheal outcomes in a Bangladeshi birth cohort
2020
Colgate ER, Eckstrom KM, Haque R, Dickson DM, Carmolli MP, Miles AK, Alam M, Gordon JI, Petri WA, Kirkpatrick BD — ASTMH Symposium 2020
Teaching
Teaching Assistant
Jan 2017 – May 2019
University of Vermont, Burlington, VT
- Human Cell Biology (introductory) — helped establish a course laboratory development committee and weekly TA meetings with the course director to refine laboratory instruction; shared bi-weekly pre-lab lectures; exam and quiz development and grading.
- Recombinant DNA Technology (mid-level, lab-exclusive, 3 h × 2/week) — bi-weekly pre-lab lectures, exam and quiz development, laboratory notebook monitoring, and technical troubleshooting.
Service
Organizing Committee Member, Finger Lakes Microbiome Symposium
Jul 2023 – present
University at Buffalo
Organizing Committee Member, Oral Biology Seminar
Aug 2023 – present
Department of Oral Biology, School of Dental Medicine, University at Buffalo
Volunteer service abroad
Oct 2014 – Jun 2015
Sea turtle conservation (Turtle Trax / Oyster Worldwide, Costa Rica) · Emergency room volunteer intern (St. James Hospital, Malta) · Permaculture eco-village community volunteer (Sunseed Technologies, Almería, Spain)
Other work experience
Program Manager, Vermont Swim School
Sep 2015 – May 2019
Burlington, VT
- Trained and managed eight staff swim instructors over three years; annual supervisory training including emergency response and inclusive-workplace practice.
Interim Aquatics Director, The EDGE Sports & Fitness
Apr 2018 – Sep 2018
South Burlington, VT
- Chemical balance and safety compliance for three bodies of water; departmental payroll; staffing coverage.