Mark T. W. Ebbert, Assistant Professor
Sanders-Brown Center on Aging
University of Kentucky
Lexington, KY 40536, USA

Current Research

Lab Mission

Our purpose and mission are to meaningfully impact human health and disease, where we are primarily focused on Alzheimer's disease and other neurodegenerative diseases. Other diseases include amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We are also heavily involved in human genomics. We’re looking for individuals who are genuinely excited and motivated by the prospect of improving human health and disease.


We believe wet lab + dry lab = better science. That's why, to accomplish our goals, we are employing cutting-edge approaches in both the "wet" and "dry" labs, including long-read sequencing, Bioinformatics, and Computational Biology. The wet-lab approaches include Bionano Genomics, PacBio, and Oxford Nanopore Technologies, while the dry-lab approaches range from algorithms to understand the underlying biology, to large-scale disease studies. Equally important, however, is that we are determined to collaborate with molecular biologists to truly understand the disease from DNA through molecular pathways. We can only succeed if we work openly with other labs to make the most meaningful difference possible.

Current Projects

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Alzheimer's disease

Alzheimer's disease is well known for its symptoms involving memory loss, and is the only top disease lacking a meaningful treatment. We want to contribute to Alzheimer's disease research: (1) help develop a meaningful treatment, and (2) develop a pre-symptomatic disease diagnostic because, unlike other diseases, the body can't heal from neurodegenerative diseases like Alzheimer's disease—once sympotoms onset, it's too late. Dr. Ebbert has a strong background in developing disease diagnostics. We are performing a long-read DNA and RNA sequencing in large Alzheimer's disease cohorts to identify "structural" DNA variants (≥50 contiguous nucleotides) and aberrant RNA isoforms directly involved in disease.

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We're fascinated with genomics. Genomics is foundational to understanding human health and disease (or biology of any kind). We, along with our collaborators, seek to improve our understanding of the human genome and downstream factors. We are specifically focused on characterizing and understanding structural DNA variants (≥50 contiguous nucleotides) and RNA isoforms. For example, the top genes implicated in Alzheimer's disease average ~12 RNA isoforms; RNA sequencing studies have historically treated all of these isoforms as a single "gene", which is a major oversimplification of the underlying biology. We're working to better understand how these isoforms vary across tissue, cell type, and disease.

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Amyotrophic lateral sclerosis

Amyotrophic Lateral Sclerosis (ALS, or Lou Gehrig's disease) is a fatal neurodegenerative disease that often strikes relatively suddenly between 45 and 55. Symptoms include progressive muscle weakness in the extremities and/or muscles required for swallowing or breathing. Longevity can range from six months to five years. It is also genetically linked to Frontotemporal Dementia (FTD). Our approaches involve long-read and single-cell sequencing.

lab milestones


Total Publications


First or corresponding-author Publications


Book Chapters

Key Publications

Explore key publications by category
Long-read RNAseq in Alzheimer's disease brain — Nature Biotechnology
Dark and Camouflaged genes — Genome Biology
Long-read sequencing in C9orf72 — Molecular Neurodegeneration
Poly(GR) mouse model — Nature Medicine
Methylation in ALS — Acta Neuropathologica
Variant Tool Chest — BMC Bioinformatics
Genetic Interactions in Alzheimer's disease — Biological Psychiatry
Tumor Grafts from Women Reflect Tumor Pathology and Outcome — Nature Medicine
Epistasis in Alzheimer's disease — Alzheimer's and Dementia
Tracking HIV Infection Through Viral Sequence — J. Clin. Virology
PCR Duplicate Removal Unnecessary — BMC Bioinformatics
An Algorithm to Characterize Systematic Error to Present Personalized Clinical Test Scores — J. Clin. Biinformatics
Review: Bridging the Gap Between Statistical and Biological Epistasis
Review: Genetic Discoveries in AD Using CSF Amyloid and Tau
Review: Genetics of Alzheimer's disease
TREM2 R47H in the Cache County Study
PAM50 Breast Cancer Subtyping
Feel free to get in touch.