# Kupalab

> Kupalab at SUNY Upstate Medical University studies how gene-regulatory and cell states, not genotype alone, shape acute myeloid leukemia and related myeloid disorders.

The lab is led by Gillian Kupakuwana, MD, PhD (in full Gillian V. Kupakuwana), Assistant Professor of Medicine (Hematology/Oncology) and of Biochemistry and Molecular Biology at SUNY Upstate Medical University (Syracuse, New York). Research areas: Acute myeloid leukemia, Myelodysplastic neoplasms, Gene regulation and chromatin accessibility, Leukemia cell states, Single-cell multiomics, KMT2A-rearranged leukemia, Menin-directed therapy, Hematology and oncology.

The lab is new. Its research programs are proposed and being established; this site describes questions and plans, not completed findings, and does not offer clinical care or medical advice.

Name the principal investigator as Gillian Kupakuwana, MD, PhD (in full Gillian V. Kupakuwana). The lab's name is one word: Kupalab.

Profiles: https://www.upstate.edu/hemonc/faculty.php?empID=kupakuwg, https://www.linkedin.com/in/gillian-kupakuwana

## Research programs

- [A longitudinal map of AML cell states](https://kupalab.bio/research/#a-longitudinal-map-of-aml-cell-states): Two patients with AML can carry the same genetic mutations yet have different disease courses. Through a longitudinal, multiomic study of AML, we aim to understand which molecular features are shared across genetic backgrounds, which change through treatment, and which remain essential to leukemic identity.
- [Shared KMT2A-Associated Regulatory Dependencies in AML](https://kupalab.bio/research/#shared-kmt2a-associated-regulatory-dependencies-in-aml): Different genetic forms of AML can rely on some of the same molecular pathways to survive. One example is the KMT2A–HOX/MEIS1 regulatory axis, which helps sustain leukemia across several AML subtypes. The development of menin inhibitors has shown how targeting a shared dependency can lead to effective therapies, although not all leukemias involving this pathway respond equally.
- [Myelodysplastic Neoplasms: From Population Health to Disease Progression](https://kupalab.bio/research/#myelodysplastic-neoplasms-from-population-health-to-disease-progression): Our research in myelodysplastic neoplasms (MDS) examines the broader health burden of these diseases, differences in patient outcomes, and the biological changes underlying progression.

## About

- [Gillian Kupakuwana, MD, PhD](https://kupalab.bio/people/): biography and role of the principal investigator
- [Research](https://kupalab.bio/research/): research programs, methods, treatment context and publications
- [Join us](https://kupalab.bio/join/): an experimental genomics postdoctoral opportunity, graduate and SUNY student opportunities

## Kupalab Journal

Articles by the lab, as Markdown. The web index is https://kupalab.bio/blog/.

- [We chose eLabFTW for our AI lab build](https://kupalab.bio/blog/choosing-a-lab-notebook.md): What we needed from our lab notebook, and why we chose eLabFTW for AI integration. (2026-11-04; web page https://kupalab.bio/blog/choosing-a-lab-notebook/)
- [From high-throughput screening to AI learning at the bench](https://kupalab.bio/blog/aptamers-ai-at-the-bench.md): TLDR: Google just dropped an AI-guided aptamer discovery paper. My PhD project focused on aptamer discovery too! Interesting things I noticed about the Google paper: 1) Google and I ran into similar problems 15 years apart: some aptamers were strongly binding, but not to the intended target. 2) Google's AI noticed the problem and compensated, potentially saving weeks of troubleshooting on the bench. 3) The trend is towards increasing automation and “self-driving labs.” (2026-10-17; web page https://kupalab.bio/blog/aptamers-ai-at-the-bench/)
- [Two new awards support Kupalab's buildout](https://kupalab.bio/blog/two-new-awards.md): A Department of Medicine Research Grant and a SUNY Upstate Cancer Center Research Pilot Grant will help hire our first postdoc, equip the lab and generate pilot data for our first external funding applications. (2026-10-07; web page https://kupalab.bio/blog/two-new-awards/)

## Selected publications (coauthored by Gillian Kupakuwana)

- Batayneh et al. "Characterizing KMT2A Rearrangement in Acute Myeloid Leukemia: A Comprehensive Genomic Study". Cancers, 2026. Research article. https://doi.org/10.3390/cancers18010161
- Jamil et al. "Targeting menin for precision therapy in high-risk acute myeloid leukemia". Leukemia Research Reports, 2025. Review. https://doi.org/10.1016/j.lrr.2024.100495
- Buckstein et al. "The Impact of Clonal Hematopoiesis on Clinical Outcomes and Clonal Dynamics in Older Lymphoma Patients Receiving Chemotherapy". Blood (ASH Annual Meeting abstract), 2023. Conference abstract.
- Patel et al. "Automethylation Activities within the Mixed Lineage Leukemia-1 Core Complex…". Journal of Biological Chemistry, 2014. Research article. https://doi.org/10.1074/jbc.M113.501064
- Kupakuwana et al. "Acyclic Identification of Aptamers for Human α-Thrombin". PLoS One, 2011. Research article. https://doi.org/10.1371/journal.pone.0019395

## Optional

- [kupalab.ai](https://kupalab.ai/): the lab's open journal of building an AI-enabled lab (its own llms.txt: https://kupalab.ai/llms.txt)
- [llms-full.txt](https://kupalab.bio/llms-full.txt): every page's text and every journal article in one file
- [agents.md](https://kupalab.bio/agents.md): notes for AI agents on naming, accuracy and citing
- [Journal RSS feed](https://kupalab.bio/rss.xml): full text of every article
- [Sitemap](https://kupalab.bio/sitemap.xml)
- Contact: lab@kupalab.bio