Curriculum Vitae
Publications
Upcoming manuscripts
Del-Rio, G., Rego, M. A., Baumgart, S.L., Randall, Z.S., Kratter, A.W., Keriazes, M., Doyle, Z., Marcelino, R. S., Handika, H., Truong, H. C., and Schachner, E.R. In revision. Integrating specimens’ internal anatomy with external morphology in modern ornithological collections. Ibis
Chipps, S. A., Handika, H., Achmadi, S. A., Rowe, K. C., and Esselstyn, J. A. In review. The rapid radiation of Sulawesi shrews (Soricidae: Crocidura) is characterized by convergent evolution and low levels of gene flow. Systematic Biology
2025
Burgin, C. J., Zijlstra, J. S., Becker, M. A., Handika, H., Widness, J., Liphardt, S., Huckaby, D. G., and Upham, N. S. 2025. How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge. Journal of Mammalogy, gyaf047. https://doi.org/10.1093/jmammal/gyaf047
Giarla, T. C., Achmadi, A.S., Fabre, P. H., Handika, H., Chipps, A. S., Swanson, M.T., Nations, J. A., Morni, M. A., William-Dee, J., Inayah, N., Jayanti, E. D., Nurdin, M.R.T.J., Griffin, K. E., Khan, F. A. A., Heaney, L. R., Rowe, K. C., and Esselstyn, J. A. 2025. Systematics and historical biogeography of Crunomys and Maxomys (Muridae: Murinae), with the description of a new species from Sulawesi and new genus-level classification. Journal of Mammalogy, gyaf006. https://doi.org/10.1093/jmammal/gyaf006
Adams, A.L., Achmadi, A.S., Mursyid, A., Handika, H., Nurdin, M.R.T., Esselstyn, J.A., Perkins, S.L., Rowe, K.M., and Rowe, K.C. 2025. Wildlife disease surveillance from village to peak: Trypanosome infections of mammals on Sulawesi revealed higher prevalence in intact montane forests. THERYA, 16(1), 125-141.
2024
Handika, H. and Esselstyn, J. A. 2024. SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic datasets. Molecular Ecology Resources, 24(7). https://doi.org/10.1111/1755-0998.13964
Nations, J.A., Kohli, B.A., Handika, H., Achmadi, A.S., Polito, M.J., Rowe, K.C., and Esselstyn, J. A. 2024. The roles of isolation and interspecific interaction in generating the functional diversity of an insular mammal radiation. Oikos, p.e10888. https://doi.org/10.1111/oik.10888
Nations, J. A., Handika, H., Mursyid, A., Butsa, R. D., Apandi, Achmadi, A. S., and Esselstyn, J. A. 2024. Three new species of shrew (Soricidae: Crocidura) from West Sumatra, Indonesia: elevational and morphological divergence in syntopic, sister taxa. Journal of Mammalogy, 105 (2), 372-389. https://doi.org/10.1093/jmammal/gyad126
2023
Mursyid, A., Achmadi, A.S., Novarino, W., Handika, H., Nugroho, H.A., Anita, S., Adams, A.L., Rowe, K.M.C., and Rowe, K.C. 2023. Trypanosoma (Euglenozoa: Kinetoplastea) infections in rodents, bats, and shrews along an elevation and disturbance gradient in Central Sulawesi, Indonesia. Records of the Australian Museum, pp.663-671. http://dx.doi.org/10.3853/j.2201-4349.75.2023.1786
Achmadi, A. S., Fahri, F., Gazzard, A., Handika, H., Inayah, N., Kennerley, R. J., Lanusi, A. A., Nangoy, M., Nurdin, M. R. T. J. P., Rowe, K. C., and Sheherazade. 2023. Conservation status and priorities for Sulawesi's unique small mammal fauna. Oryx, 57(6), pp.690-691. https://doi.org/10.1017/S0030605323001059
Swanson, M.T., Henson, M.W., Handika, H., Achmadi, A.S., Anita, S., Rowe, K.C., and Esselstyn, J.A. 2023. Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture. Journal of Mammalogy, 104(1), pp.146-158. https://doi.org/10.1093/jmammal/gyac098
2021
Esselstyn, J.A., Achmadi, A.S., Handika, H., Swanson, M. T., Giarla, T.C., and Rowe, K.C. 2021. Fourteen new, endemic species of shrew (genus Crocidura) from Sulawesi reveal a spectacular island radiation. Bulletin of the American Museum of Natural History, 454(1), pp.1-108. https://doi.org/10.1206/0003-0090.454.1.1
Handika, H., Achmadi, A.S., Esselstyn, J.A., and Rowe, K.C. 2021. Molecular and morphological systematics of the Bunomys division (Rodentia: Muridae), an endemic radiation on Sulawesi. Zoologica Scripta, 50(2), pp. 141–154. https://doi.org/10.1111/zsc.12460
Nations, J.A., Mursyid, A., Busta, R.D., Adrian, S.P., Handika, H., Achmadi, A.S., and Esselstyn, J.A. 2021. The first report of albinism in a Sundaland endemic rodent. Mammalia, 85(2), pp.168-172. https://doi.org/10.1515/mammalia-2020-0047
2020
Harapan, T.S., Agung, A.P., Handika, H., Novarino, W., Tjong, D.H., and Tomlinson, K.W. 2020. New records and potential geographic distribution of Elongated Caecilian, Ichthyophis elongatus Taylor, 1965 (Amphibia, Gymnophiona, Ichthyophiidae), endemic to West Sumatra, Indonesia. Check List, 16(6), pp. 1695-1701. https://doi.org/10.15560/16.6.1695
Winterhoff, M.L., Achmadi, A.S., Roycroft, E.J., Handika, H., Putra, R.T.J., Rowe, K.M.C., Perkins, S., and Rowe, K.C. 2020. Native and introduced trypanosome parasites in endemic and introduced murine rodents of Sulawesi. The Journal of Parasitology, 106(5), pp.523-536. https://doi.org/10.1645/19-136
2019 and earlier
Esselstyn, J.A., Achmadi, A.S., Handika, H., Giarla, T.C., and Rowe, K.C. 2019. A new climbing shrew from Sulawesi highlights the tangled taxonomy of an endemic radiation. Journal of Mammalogy, 100(6), pp.1713-1725. https://doi.org/10.1093/jmammal/gyz077
Janra, M.N., Noske, R.A., Chornelia, A., Handika, H., Mursyid, A., Agung, A., and Saputra, A. 2018. A second breeding record of Chestnut-naped Forktails Enicurus ruficapillus in Sumatra, and observations suggesting females alone incubate. Kukila, 21, pp.13-16.
Demos, T.C., Achmadi, A.S., Handika, H., Rowe, K.C., and Esselstyn, J.A. 2017. A new species of shrew (Soricomorpha: Crocidura) from Java, Indonesia: possible character displacement despite interspecific gene flow. Journal of Mammalogy, 98(1), pp.183-193. https://doi.org/10.1093/jmammal/gyw183
Demos, T.C., Achmadi, A.S., Giarla, T.C., Handika, H., Rowe, K.C., and Esselstyn, J.A. 2016. Local endemism and within‐island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity. Molecular ecology, 25(20), pp.5158-5173. https://doi.org/10.1111/mec.13820
Esselstyn, J.A., Achmadi, A.S., Handika, H., and Rowe, K.C. 2015. A hog-nosed shrew rat (Rodentia: Muridae) from Sulawesi Island, Indonesia. Journal of Mammalogy, 96(5), pp.895-907. https://doi.org/10.1093/jmammal/gyv093
Handika, H., Nurdin, J., and Rizaldi. 2013. Small Terrestrial Mammals Community on Mount Singgalang, West Sumatra. Jurnal Biologi Universitas Andalas, 2(2), pp.103-109. https://doi.org/10.25077/jbioua.2.2.%25p.2013
Manuscripts in prep
Handika, H., Lürig, M. D., Nichtawitz, K. L., Dobon, O. M., Yarava, V. S., Shi, B. D., Elliott, M. J., Fortes, J. A. B., and Porto, A. In prep. BioCosmos: computer vision and large-language models for large-scale image-based biodiversity exploration and trait discovery.
Handika, H., Moncrieff, A. E., Del-Rio, G., Canton, R., Delgado, F., Jaiswal, A., Gan, J. B., Henderson, C., Rutledge, S. L., Hernández-Canchola, G., Babb-Biernacki, S. J., Chipps, A. S., Pérez-Amaya, N., Chornelia, A., Morales-Martínez, D. M., McCallum, Q., Thom, G., and Esselstyn, J. A. In prep. NAHPU: An integrated approach to natural history data collection, disease surveillance, and teaching the next generation of naturalists.
Handika, H., Rowe, K.C., Achmadi, A.S., Swanson, M. T., and Esselstyn, J.A. In prep. A new species of Frateromys from the Northern Peninsula of Sulawesi, Indonesia.
Handika, H., Rowe, K.C., Achmadi, A.S., Zulkurnia Irsaf, Swanson, M. T., and Esselstyn, J.A. In prep. An island of islands: complex gene tree discordance and local endemism on a recent, rapid rodent radiation on Sulawesi.
Handika, H., Del-Rio, G. D., and Esselstyn, J. A. In prep. ULLAR: An Ultrafast, scalable, Accessible, and Reproducible phylogenomic pipeline.
Book chapter
Snider, M., Hernández, L. A., Mweetw, T., Handika, H., Ou, S., and Zulian, V. In revision. Decolonizing the Field: International Perspectives on Equity, Belonging, and Nature in Conservation Science. In “Inclusive Nature” (L. Parr, ed.). Johns Hopkins University Press
Teaching, Mentoring, & Workshops
Courses Taught
Louisiana State University, USA
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Spring 2021, 2025
BIOL 1209 Introduction to Biology
Teaching assistant
This course is an introduction to the principles of biology that covers topics on ecology, evolution, and diversity. I taught lab section and assisted with grading. My class size was about 50 students.
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Fall 2024
BIOL 2153 Principles of Genetics
Teaching assistant
This course covers several topics, including Mendelian inheritance, gene mapping, population genetics, and genomics. I taught recitation sections and assisted with homework, exam preparation, and grading. My class size was about 60 students divided into two sections.
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Fall 2021
BIOL 4141 Mammalogy
Teaching assistant
This course covers the evolution and systematics of mammals. I taught lab section using specimens from the museum collection. My class size was 16 students.
Andalas University, Indonesia
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Fall 2012
PAB 125 Computer Application for Biology
Instructor
This course introduces students to computer applications in biology that covers topics on basic computational statistics, geographic information system (GIS), and scientific photography. I developed the syllabus, taught lectures, and graded assignments. My class size was 70 students.
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2011–2012
PAB 505 Taxonomy of Vertebrates
Teaching assistant
Pedagogical Training
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Fall 2019
BASC 7000 Methods of Instruction in College Life Science Laboratories
1 credit hour · Louisiana State University, USA
Workshops Taught
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May 2025
Efficient and reproducible avian and mammalian specimen data acquisition: from fieldwork to museum database
Instructor · The Society for the Preservation of Natural History Collections (SPNHC)
This workshop covers recording avian and mammalian specimen data efficiently and reproducibly, from the field catalog to the museum database.
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May 2024
Molecular Analyses of Indonesian Mammals
Instructor · Generasi Biologi Indonesia
This workshop covers an introduction to mammalian phylogenetics, multi-locus DNA sequencing analyses, and genomic analyses using current methods and software. The workshop was tailored with data from Indonesian mammals, but the methodologies are applicable to studies utilizing both Sanger and short-read sequencing data.
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April 2023
Coding for Conservation: Integrating GitHub to Your Workflow
Instructor · Tambora Muda, RLadies Jakarta, and RLadies Bogor, with logistical support from the University of Indonesia
This workshop introduced students to version control and collaborative coding using GitHub. I taught the basics of Git and GitHub, including creating a repository, staging, making commits, and creating pull requests. I also introduced an advanced approach to R dependency management and writing cross-platform code.
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January 2022
Introduction to Phylogenetics
Instructor · Andalas University, Indonesia
This workshop covers the fundamental concepts of phylogenetics, including phylogenetic tree construction and interpretation. It also introduces students to multi-locus DNA sequencing analyses using IQ-TREE.
Student Mentees
- students mentored
- 29 students mentored
- current mentees
- 10 current mentees
- awards and grants
- 5 awards and grants
Fieldwork, survey design, scientific, and/or grant writing 8
- 1
Fatimah
BS, Biology · Andalas University, Indonesia
Received $5,300 from the Mohammed Bin Zayed Conservation Fund to study the Mentawai Langurs.
2014–2017
- 2
Ahmad Mursyid
BS, Biology · Andalas University, Indonesia
2012–2018
- 3
Zulkurnia Irsaf
BS, Biology · Tadulako University, Indonesia
2018–2020
- 4
Tri S. Harapan
BS, Biology · Andalas University, Indonesia
2020
- 5
Fajar Alfitrian
BS, Biology · Soedirman University, Indonesia
2023–2025
- 6
Alfath Fanidya
MS, Biology · Bogor Agricultural University, Indonesia
Received $13,000 from the Fonseca Species Conservation Fund to study the Javan bamboo rats.
2023–2024
- 7
Lutfi S. Maulidiyah
BS, Biology · University of Lampung, Indonesia
2023–2025
- 8
Akbar F. Hilmi
BS, Biology · University of Lampung, Indonesia
2023–2025
Specimen curation 3
- 9
Ericka Boyden
BS, Biology · Louisiana State University
Fall 2019–Spring 2020
- 10
Brittany E. Thames
BS, Biology · Louisiana State University
Spring 2019
- 11
Emily A. Bowers
BS, Biology · Louisiana State University
Fall 2020–Spring 2021
Genomic analyses 3
- 12
Murky Mutchler
BS, Biology · Louisiana State University / PhD, the University of Chicago
Won a poster award at the 2021 Wilson Ornithological Society Meeting.
2021
- 13
Ryan Zucker
BS, Biology · Cornell University
2024
- 14
Indri Lestari
BS, Biology · Andalas University, Indonesia
Fall 2025
Interdisciplinary research and software development 15
- 15
Filipe Delgado
MS, Computer Science · Georgia Institute of Technology
Fall 2025
- 16
Cody Henderson Current
MS, Computer Science · Georgia Institute of Technology
Fall 2025–now
- 17
Lawrence B. Gan Current
MS, Computer Science · Georgia Institute of Technology
Fall 2025–now
- 18
Aakanksha Jaiswal
MS, Computer Science · Georgia Institute of Technology
Fall 2025–Spring 2026
- 19
Kira L. Nichtawitz Current
BS, Computer Science · University of Florida
Florida Museum Undergraduate Internship Program awardee for Fall 2026.
Fall 2025–now
- 20
Julian D. Perez
BS, Computer Engineering · University of Florida
Fall 2025
- 21
Ethan E. Wolfe
BS, Data Science · University of Florida
Fall 2025
- 22
Zahara M. Shuemaker
BS, Computer Science · University of Florida
Fall 2025
- 23
Justin K. Sobayo Current
BS, Computer Science · University of Florida
Florida Museum Undergraduate Internship Program awardee for Fall 2026.
Fall 2026–now
- 24
Shyaam Shanmugam Current
BS, Computer Science · University of Florida
Spring 2026–now
- 25
Danna Lee Current
MS, Computer Science · Georgia Institute of Technology
Summer 2026–now
- 26
Jia Yu Current
MS, Computer Science · Georgia Institute of Technology
Summer 2026–now
- 27
Phillip Kim Current
MS, Computer Science · Georgia Institute of Technology
Fall 2026–now
- 28
Eric Wan Current
MS, Computer Science · Georgia Institute of Technology
Fall 2026–now
- 29
Daniel Y. Cheng Current
BS, Computer Science · University of Florida
Fall 2026–now
Outreach & Services
Outreach
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Mammalian collection tours
LSU Museum of Natural History, USA
2018–2025
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Research Talk Show
Gita Bangsa Middle School, Indonesia
23 August 2021
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Personal Development Talk Show
KCA-LH Rafflesia FMIPA Unand Conservation Club, Indonesia
18 October 2020
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Getting to know neglected flora and fauna in Indonesia
Tambora Muda, Indonesia
22 May 2020
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Night at the Museum
LSU Museum of Natural History, USA
14 November 2019
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Night at the Museum
LSU Museum of Natural History, USA
11 August 2018
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Meet the Scientists
Museums Victoria, Australia
22 August 2015
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Earth Day Celebration
KCA-LH Rafflesia FMIPA Unand Conservation Club, Indonesia
2009–2020
In the Media
News media profiles
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The Indonesian Ministry of Finance Magazine, Media Keuangan · June 2017
Berniat Terus Meneliti Tikus
Intending to Keep Researching Rats
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DetikNews-ABC Australia Plus · 16 January 2017
Media interviews
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Science Next · 27 January 2020
What Could Recovery Look Like for Blazing Australia?
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Kompas.Com-ABC Australia Plus · 26 November 2015
Kisah Mahasiswa Indonesia Terlibat Penemuan Tikus Hidung Babi
The Story of an Indonesian Student Involved in the Discovery of the Hog-Nosed Rat
Popular Articles
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Hal yang Perlu Dilakukan agar Kuliah S2 di Luar Negeri
Things to Do to Study for a Master's Degree Abroad
Republika-ABC AustraliaPlus · 16 February 2017
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Langkah-Langkah Kuliah ke Luar Negeri: Dari A-Z
Steps to Study Abroad: From A-Z
DetikNews-ABC AustraliaPlus · 7 June 2016
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Menentukan Topik Penelitian: Dilema Kecepatan Tamat dan Kualitas Penelitian
Determining a Research Topic: The Dilemma of Graduating Quickly vs. Research Quality
Republika-ABC AustraliaPlus · 10 May 2016
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Pengalaman Heru Handika Menyikapi Kerja Sama dengan Peneliti Asing
Heru Handika's Experience Collaborating with Foreign Researchers
TribunNews-ABC AustraliaPlus · 8 May 2016
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Jurus Kuliah ke Luar Negeri Berkat Jaringan Pertemanan
Tips for Studying Abroad Thanks to Friendship Networks
DetikNews-ABC AustraliaPlus · 15 April 2016
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Kiat Meningkatkan TOEFL Melebihi 550
Tips for Increasing a TOEFL Score Above 550
Republika-ABC AustraliaPlus · 7 March 2016
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Mengenal LoA dan Cara Mendapatkan 'Surat Sakti' S2/S3 di Luar Negeri
Getting to Know the LoA and How to Get the 'Magic Letter' for Master's/PhD Studies Abroad
DetikNews-ABC AustraliaPlus · 3 February 2016
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Bagaimana Menulis Esai Untuk Mendapatkan Beasiswa LPDP
How to Write an Essay to Get an LPDP Scholarship
Republika-ABC AustraliaPlus · 11 January 2016
Memberships & Service
IUCN SSC Small Mammal Specialist Group
2017–present
- Contributed to the IUCN Red List assessments of 76 small mammal species native to Sulawesi, Indonesia
The American Society of Mammalogists
2016–present
- Biodiversity committee (2024–present)
- Mammal Diversity Database curation team (2024–present)
The Society of Systematic Biologists
2020–present
- Ernst Mayr Award judge (2025)
KCA-LH Rafflesia Nature Conservation Club, Andalas University
Permanent member since 2009
- Secretary (2011–2012)
- Training undergraduate student members on jungle survival, land navigation, search and rescue, and tropical forest ecology
- Led and participated in mountain and cave expeditions across Sumatra, Indonesia
- Led and participated in organizing conservation training and seminars for students, faculty, and the public
Student Association of the Indonesian Endowment Fund in Victoria, Australia
2015–2017
- Mentorship programs for new Indonesian students studying in Melbourne, Australia
- Developing guidelines for Indonesian students to study in Melbourne, Australia