Alika K. Maunakea, Ph.D.

Associate Professor

Portrait of Alika K. Maunakea, Phd, Associate Professor, IBR, John A. Burns School of Medicine, University of Hawaiʻi at Mānoa

Short Bio

Dr. Maunakea received his B.Sc. degree in Biology at Creighton University (2001) and Ph.D. in Biomedical Sciences at the University of California, San Francisco (2008). He completed Postdoctoral training at the National Institutes of Health (2012) and joined the John A. Burns School of Medicine at the University of Hawaiʻi, Mānoa in the Fall of 2012. Dr. Maunakea was recruited as an Assistant Professor in the Department of Native Hawaiian Health, where he has established an independent laboratory and an Epigenomics Core Facility to investigate how epigenomic information may improve our 

understanding of the mechanistic relationships of gene-environment interactions that underlie the development of diseases of health disparities, including autism and cardiometabolic diseases. It is anticipated that such studies will contribute to the development of more effective targeted diagnostic, preventative, and therapeutic strategies to reduce health disparities. In 2018, Dr. Maunakea earned tenure and was promoted to Associate Professor.

Research Interests

In studying epigenetics for over 20 years, Dr. Maunakea has made several important contributions that have helped advance the field. In particular, he has developed and applied novel high-throughput, genome-wide technologies that survey DNA methylation and histone modifications (Ching et al., 2005; Corley, Zhang, Zheng, Lum-Jones, & Maunakea, 2015; Kraushaar et al., 2013), both central components of epigenetic processes, and has discovered novel roles for DNA methylation in regulating alternative promoter usage (Maunakea, Nagarajan, et al., 2010) and in pre-mRNA splicing (Maunakea, Chepelev, Cui, & Zhao, 2013). 


Currently, the primary goal of the Maunakea lab is to better understand the molecular basis of environmental and epigenetic interactions that consequently influence cellular phenotypes relevant to health outcomes, in particular those that underlie neurological deficiencies, cardiometabolic disorders, and cancer. The majority of the research in the lab involve investigating how DNA methylation and histone modifications collectively operate to inform transcript heterogeneity through interactions with the basal transcription machinery, pre-mRNA splicing factors, and chromatin-associated proteins in the context of normal development and how alterations to these components of the chromatin landscape contribute to disease. To enable this research, high-throughput massively parallel genomic sequencing coupled with various immunoprecipitation technologies (i.e. MeDIP-Seq, ChIP-Seq, ChIA-PET, HiC-Seq, etc) and transcriptomic assays (i.e. RNA-Seq, Ampli-Seq, etc) are integrated using bioinformatic tools. It is anticipated that results from these research activities will lead to a better understanding of disease etiology, and thereby provide new avenues for disease diagnosis, prevention, and treatment. Partnerships and collaborations with several other divisions within the University of Hawaiʻi at Mānoa (i.e. Institute for Biogenesis Research, Pacific Biosciences Research Center, Office of Public Health Studies, Hawaiʻinuiakea School of Hawaiian Knowledge, University of Hawaiʻi Cancer Center), University of Hawaiʻi at Hilo, Chaminade University of Honolulu, Shriners Hospitals for Children Honolulu collectively contribute to research and educational activities in the Maunakea lab. 

Inherent in the traditional Native Hawaiian concept of health (mauli ola) is the understanding that environmental factors, including nutrition and social behaviors, trans-generationally impact health outcomes in individuals and communities. Epigenetic mechanisms may now explain molecular links between these environmental factors and health outcomes. Research in the Maunakea lab focuses on elucidating the molecular functions of epigenetic mechanisms and how they play a role in gene-environment interactions that underlie diseases of health disparity afflicting the Native Hawaiian and Pacific Islander community through a Community-based Participatory Research (CBPR) approach and community partnerships such as with MAʻO Organic Farms. These studies also involve investigating the relationship between the human gut microbiome composition (using a 16S metagenomics approach), epigenetic regulation of immune cell function, and health.


The Maunakea lab also serves as a hub for the Epigenomics Core Facility at the University of Hawaiʻi, the State’s only next-generation sequencing service that integrates this technology with epigenome-wide surveys of DNA methylation (such as MeDIP-Seq), chromatin structure and histone modifications (such as ChIP-Seq), and transcriptomic analyses (such as RNA-Seq). This Core includes a laboratory technician, bioinformatics specialist, and research assistant all of whom have extensive training in molecular techniques related to the Core’s services as well as in processing and analyzing high-throughput data derived from such techniques. It is meant to enable investigators to perform “omics” research, particularly those interested in chromatin organization and function.

Contributions to the Epigenomic Research Enhancement Fund:

Epigenomic Research Enhancement Fund

University of Hawaiʻi Foundation




This fund is to assist in supporting the mission of the Epigenomic Research Program within the Maunakea lab, Department of Native Hawaiian Health, John A. Burns School of Medicine. The mission of the Epigenomic Research Program is to aid in the development of research and educational opportunities focused on enhancing and applying epigenomic data to enable the reduction of diseases of health disparities in Native Hawaiian and Pacific Islander communities. 

As the translational (bench to bedside) component of the Maunakea lab, the Epigenomic Research Program entails developing new disease diagnostic and risk stratification approaches, identifying novel molecular targets for disease treatment, and augmenting preventive strategies by gathering and applying clinically-relevant epigenomic information.

Selected Publications