Research Projects

My research integrates fieldwork, natural history collections, genomics, and the development of digital tools to address speciation, biogeography, and conservation questions. In particular, it centers on identifying patterns of small mammal diversity and understanding speciation processes within and across islands in the Indo-Australian Archipelago. I have also engaged in projects focusing on other taxa and in different regions. Most of the tools I develop are taxon-agnostic. My collaborative work involves more than a dozen people in some projects. I strive to make research using natural history collections and genomic data accessible to students and researchers with limited technical knowledge and access to computing resources.

Small Mammal Diversity & Speciation

Understanding patterns that generate species diversity within a complex island system

Lenomys meyeri

This project studies small mammal diversity and speciation in Sulawesi and islands on the Sunda Shelf, Southeast Asia. During the Pleistocene, the islands on the Sunda Shelf—such as Sumatra, Java, and Borneo— were connected as a continuous landmass. In contrast, Sulawesi were formed from separate islands. The isolated mountains on these islands promote other opportunities for speciation. We conduct extensive fieldwork, perform genomic studies, and describe undocumented species as necessary.

My dissertation focuses on the in-situ diversification of hill rats (the Bunomys species group) in Sulawesi. I aim to improve phylogenetic resolution and understand how the island's geological history has shaped the group's diversity. Ultimately, I aim to deepen our understanding of speciation on a large, isolated island like Sulawesi and aid conservation efforts by improving our knowledge of species diversity and endemism.

Publications:
Handika et. al. ( , )
Demos et. al. ( , )
Esselstyn et. al. ( , , )
Giarla et. al. ( )
Nations et. al. ( )

Inclusive, Open, and Accessible Software

Developing digital tools empowering new learners in evolutionary studies

SEGUL app preview

My software project spans a broad spectrum of collection-based evolutionary studies, from data collection in the field (NAHPU), species identification through innovative digital field guide (RINJA), a phylogenomic pipeline (ULLAR), genomic data wrangling and summarization (SEGUL), to taxonomic database (MDD app, website, and tooling). My goal for this project is to develop software to improve the efficiency, data integration, and accessibility of biodiversity research. Additionally, I aim to reduce the ecological footprint of genomic studies while allowing underfunded labs to benefit from the decreasing cost of genomic sequencing. The development of the apps leverages emerging technologies in software development (e.g., Rust, Flutter, and CI/CD ). Especially for genomic studies, I take advantage of advancements in CPU technology and heterogenous computing to accelerate data processing and minimize reliance on expensive and power-hungry High-Performance Computing Clusters.

Publications:
Handika and Esselstyn ( )
Handika et al. ( )
Burgin et al. ( )

GPU-Agnostic, Low-cost Machine Learning Approaches

Developing on-devices, cross-platform machine-learning methods to improve biodiversity research

This project aims to implement emerging machine-learning (ML) approaches to aid natural history studies and enhance our understanding of biodiversity. It will be part of my postdoc at Porto's lab, the University of Florida, starting Summer 2025. The goal is to develop low-cost, user-friendly, and cross-platform (mobile and desktop) on-device large language models (LLMs) and computer vision ML approaches. My work will include integrating the models into the software I currently develop. The LLM models will summarize and translate digital field notes. The computer vision models will extract data from paper-based natural history catalogs and identify phenotypic patterns from specimen images. In collaboration with Del-Rio's lab (University of Florida), another potential work is to develop a cross-platform ML tool to identify selective sweep in genomic data.

Other Projects

Projects that I am involved in outside my main research

Mammalian Microbiomes and Host-Parasites Interaction

This project is part of our ongoing research on Sulawesi Island, Indonesia. We aim to understand the microbial communities in the gut regions of shrews and rodents. Additionally, we focus on detecting Trypanosoma parasites in native rodents of Sulawesi to study host-parasite interactions across elevational gradients.

Publications:
Adams et al. ( )
Mursyid et. al. ( )
Swanson et. al. ( )
Winterhoff et. al. ( )
Herbarium Universitas Andalas

Specimen Digitization

This project is led by Dr. Nurainas at the Herbarium Universitas Andalas (ANDA) funded through the collection and data mobilization grant provided by the Global Biodiversity Information Facility (GBIF). We aim to digitize >65,000 sheets of the herbarium specimens at ANDA and make the data accessible through the GBIF portal.

Published datasets:
Nurainas et. al. ( , , )

Genomics and Systematics of Antbirds in the Neotropics

I mentored to students: Marky Mutchler (the University of Chicago) and Ryan Zucker (Cornell University). Both of them are under the supervision of Dr. Glaucia Del-Rio, the University of Florida. We aim to understand the genomic basis of speciation and systematics of antbirds in the Neotropics. My involement is primarily in the phylogenomic analyses of the studies.