Publications

Pradiptajati Kusuma, Guy S Jacobs, Hirzi Luqman, Firda A Ma’ruf, Prisca C Limardi, Herawati Sudoyo, J Stephen Lansing, Safarina G Malik, Irene Gallego Romero (2026). Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers. bioRxiv.

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Clarissa Asha Febinia, Pradiptajati Kusuma, Hirzi Luqman, Joseph Lewis, Prisca C Limardi, Isabella Apriyana, Lidwina Priliani, Kristiawan, Herawati Sudoyo, Safarina G Malik, Guy S Jacobs (2026). Market access, subsistence transition, and the transformation of diet and health among hunter-gatherer communities in Indonesia. SocArXiv.

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Pradiptajati Kusuma, Irene Gallego Romero, Taufiq Hidayat, Herawati Sudoyo, J Stephen Lansing, Safarina G Malik, Guy S Jacobs (2026). The important role of community engagement and equal collaboration in population genetic research: Lessons from Bornean contemporary hunter-gatherers. Zenodo.

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Muhamad Fachrul, Pongsakorn Sukonthamarn, Pradiptajati Kusuma, Monika Meili Novita, Isabela Alvim, Isabella Apriyana, Chelzie Crenna Darusallam, Andreas Christian, Alice Groudko, Robert Kendle, Prisca Cynthia Limardi, Evan D Mee, Sukma Oktavianthi, Lance M Peter, Lidwina Priliani, Bertha Letizia Utami, Fredrik Sokoy, Simon Abdi K Frank, Desak Made Wihandani, Ni Nyoman Ayu Dewi, Agus Eka Darwinata, Murray P Cox, Nicholas E Banovich, Herawati Sudoyo, Safarina G Malik, Irene Gallego Romero (2026). Ancestral and environmental diversity shape the immune landscape in Indonesia. bioRxiv.

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Clarissa A Febinia, Hirzi Luqman, Pradiptajati Kusuma, Lidwina Priliani, Joseph Lewis, Desak Made Wihandani, Gde Ngurah Pinatih, Herawati Sudoyo, Alexandre Almeida, Safarina G Malik, Guy S Jacobs (2025). From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia. Cell Rep..

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Katalina Bobowik, Muhamad Fachrul, Chelzie Crenna Darusallam, Pradiptajati Kusuma, Herawati Sudoyo, Clarissa A Febinia, Safarina G Malik, Christine A Wells, Irene Gallego Romero (2025). Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood. PLoS One.

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Guy S Jacobs, Pradiptajati Kusuma, R Attenborough (2025). Deep histories in New Guinea: Insights from human genetics on regional demography and archaic introgression. In D. Gaffney and M. Tolla (eds.), West New Guinea: Social, Biological, and Material Histories. ANU Press: Canberra.

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Pradiptajati Kusuma, Guy S Jacobs, R Attenborough (2025). Deep histories in New Guinea: Insights from human genetics on local demography and social processes. In D. Gaffney and M. Tolla (eds.), West New Guinea: Social, Biological, and Material Histories. ANU Press: Canberra.

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R Attenborough, Guy S Jacobs, Pradiptajati Kusuma (2025). Deep histories in New Guinea: Insights from genetics on human adaptation to malaria and diverse environments. In D. Gaffney and M. Tolla (eds.), West New Guinea: Social, Biological, and Material Histories. ANU Press: Canberra.

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Neke Ibeh, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Safarina G Malik, Herawati Sudoyo, Davis J McCarthy, Irene Gallego Romero (2024). Profiling genetically driven alternative splicing across the Indonesian archipelago. Am. J. Hum. Genet..

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Pradiptajati Kusuma, Murray P Cox, Graeme Barker, Herawati Sudoyo, J Stephen Lansing, Guy S Jacobs (2023). Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics. Cell Rep..

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Heini M Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, Chelzie Crenna Darusallam, Mait Metspalu, Herawati Sudoyo, Murray P Cox, Irene Gallego Romero, Nicholas E Banovich (2022). Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries. Am. J. Hum. Genet..

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J Stephen Lansing, Guy S Jacobs, Sean S Downey, Peter K Norquest, Murray P Cox, Steven L Kuhn, John H Miller, Safarina G Malik, Herawati Sudoyo, Pradiptajati Kusuma (2022). Deep ancestry of collapsing networks of nomadic hunter--gatherers in Borneo. Evolut. Hum. Sci..

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Pradiptajati Kusuma, Nicolas Brucato, Murray P Cox, Chandra Nuraini, Thierry Letellier, Philippe Grangé, Herawati Sudoyo, François-Xavier Ricaut (2021). A genomic perspective of the origin and dispersal of the Bajo Sea Nomads in Indonesia. In B. Bellina, R. Blench and J.-C. Galipaud (eds.), Sea Nomads of Southeast Asia. NUS Press: Singapore.

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Heini M Natri, Katalina S Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S Jacobs, Georgi Hudjashov, J Stephen Lansing, Herawati Sudoyo, Nicholas E Banovich, Murray P Cox, Irene Gallego Romero (2020). Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genet..

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Guy S Jacobs, Georgi Hudjashov, Lauri Saag, Pradiptajati Kusuma, Chelzie C Darusallam, Daniel J Lawson, Mayukh Mondal, Luca Pagani, François-Xavier Ricaut, Mark Stoneking, Mait Metspalu, Herawati Sudoyo, J Stephen Lansing, Murray P Cox (2019). Multiple deeply divergent Denisovan ancestries in Papuans. Cell.

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Nicolas Brucato, Veronica Fernandes, Pradiptajati Kusuma, Viktor Černý, Connie J Mulligan, Pedro Soares, Teresa Rito, Céline Besse, Anne Boland, Jean-Francois Deleuze, Murray P Cox, Herawati Sudoyo, Mark Stoneking, Luisa Pereira, François-Xavier Ricaut (2019). Evidence of Austronesian genetic lineages in East Africa and south Arabia: Complex dispersal from Madagascar and southeast Asia. Genome Biol. Evol..

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Nicolas Brucato, Veronica Fernandes, Stéphane Mazières, Pradiptajati Kusuma, Murray P Cox, Joseph Wainaina Ng'ang'a, Mohammed Omar, Marie-Claude Simeone-Senelle, Coralie Frassati, Farida Alshamali, Bertrand Fin, Anne Boland, Jean-Francois Deleuze, Mark Stoneking, Alexander Adelaar, Alison Crowther, Nicole Boivin, Luisa Pereira, Pascal Bailly, Jacques Chiaroni, François-Xavier Ricaut (2018). The Comoros show the earliest Austronesian gene flow into the Swahili Corridor. Am. J. Hum. Genet..

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Pradiptajati Kusuma, Nicolas Brucato, Murray P Cox, Thierry Letellier, Abdul Manan, Chandra Nuraini, Philippe Grangé, Herawati Sudoyo, Fran ̧cois-Xavier Ricaut (2017). The last sea nomads of the Indonesian archipelago: genomic origins and dispersal. Eur. J. Hum. Genet..

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Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Ignace Rakoto, Nelly Rabetokotany, Bodo Ravololomanga, Lucien M-A Rakotozafy, Mireille Mialy Rakotomalala, Michel Razafiarivony, Bako Rasoarifetra, Miakabola Andriamampianina Raharijesy, Lolona Razafindralambo, Ramilisonina, Fulgence Fanony, Sendra Lejamble, Olivier Thomas, Ahmed Mohamed Abdallah, Christophe Rocher, Amal Arachiche, Laure Tonaso, Veronica Pereda-Loth, Stéphanie Schiavinato, Nicolas Brucato, François-Xavier Ricaut, Pradiptajati Kusuma, Herawati Sudoyo, Shengyu Ni, Anne Boland, Jean-Francois Deleuze, Philippe Beaujard, Philippe Grangé, Sander Adelaar, Mark Stoneking, Jean-Aimé Rakotoarisoa, Chantal Radimilahy, Thierry Letellier (2017). Genomic landscape of human diversity across Madagascar. Proc. Natl. Acad. Sci. U. S. A..

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Nicolas Brucato, Pradiptajati Kusuma, Philippe Beaujard, Herawati Sudoyo, Murray P Cox, Fran ̧cois-Xavier Ricaut (2017). Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Sci. Rep..

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Alexander Mörseburg, Luca Pagani, François-Xavier Ricaut, Bryndis Yngvadottir, Eadaoin Harney, Cristina Castillo, Tom Hoogervorst, Tiago Antao, Pradiptajati Kusuma, Nicolas Brucato, Alexia Cardona, Denis Pierron, Thierry Letellier, Joseph Wee, Syafiq Abdullah, Mait Metspalu, Toomas Kivisild (2016). Multi-layered population structure in Island Southeast Asians. Eur. J. Hum. Genet..

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Pontus Skoglund, Cosimo Posth, Kendra Sirak, Matthew Spriggs, Frederique Valentin, Stuart Bedford, Geoffrey R Clark, Christian Reepmeyer, Fiona Petchey, Daniel Fernandes, Qiaomei Fu, Eadaoin Harney, Mark Lipson, Swapan Mallick, Mario Novak, Nadin Rohland, Kristin Stewardson, Syafiq Abdullah, Murray P Cox, Françoise R Friedlaender, Jonathan S Friedlaender, Toomas Kivisild, George Koki, Pradiptajati Kusuma, D Andrew Merriwether, Francois-X Ricaut, Joseph T S Wee, Nick Patterson, Johannes Krause, Ron Pinhasi, David Reich (2016). Genomic insights into the peopling of the Southwest Pacific. Nature.

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Pradiptajati Kusuma, Murray P Cox, Nicolas Brucato, Herawati Sudoyo, Thierry Letellier, Fran ̧cois-Xavier Ricaut (2016). Western Eurasian genetic influences in the Indonesian archipelago. Quat. Int..

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Nicolas Brucato, Pradiptajati Kusuma, Murray P Cox, Denis Pierron, Gludhug A Purnomo, Alexander Adelaar, Toomas Kivisild, Thierry Letellier, Herawati Sudoyo, François-Xavier Ricaut (2016). Malagasy genetic ancestry comes from an historical Malay Trading Post in Southeast Borneo. Mol. Biol. Evol..

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Pradiptajati Kusuma, Nicolas Brucato, Murray P Cox, Denis Pierron, Harilanto Razafindrazaka, Alexander Adelaar, Herawati Sudoyo, Thierry Letellier, François-Xavier Ricaut (2016). Contrasting linguistic and genetic origins of the Asian source populations of Malagasy. Sci. Rep..

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Monika Karmin, Lauri Saag, Mário Vicente, Melissa A Wilson Sayres, Mari Järve, Ulvi Gerst Talas, Siiri Rootsi, Anne-Mai Ilumäe, Reedik Mägi, Mario Mitt, Luca Pagani, Tarmo Puurand, Zuzana Faltyskova, Florian Clemente, Alexia Cardona, Ene Metspalu, Hovhannes Sahakyan, Bayazit Yunusbayev, Georgi Hudjashov, Michael DeGiorgio, Eva-Liis Loogväli, Christina Eichstaedt, Mikk Eelmets, Gyaneshwer Chaubey, Kristiina Tambets, Sergei Litvinov, Maru Mormina, Yali Xue, Qasim Ayub, Grigor Zoraqi, Thorfinn Sand Korneliussen, Farida Akhatova, Joseph Lachance, Sarah Tishkoff, Kuvat Momynaliev, François-Xavier Ricaut, Pradiptajati Kusuma, Harilanto Razafindrazaka, Denis Pierron, Murray P Cox, Gazi Nurun Nahar Sultana, Rane Willerslev, Craig Muller, Michael Westaway, David Lambert, Vedrana Skaro, Lejla Kovačevic, Shahlo Turdikulova, Dilbar Dalimova, Rita Khusainova, Natalya Trofimova, Vita Akhmetova, Irina Khidiyatova, Daria V Lichman, Jainagul Isakova, Elvira Pocheshkhova, Zhaxylyk Sabitov, Nikolay A Barashkov, Pagbajabyn Nymadawa, Evelin Mihailov, Joseph Wee Tien Seng, Irina Evseeva, Andrea Bamberg Migliano, Syafiq Abdullah, George Andriadze, Dragan Primorac, Lubov Atramentova, Olga Utevska, Levon Yepiskoposyan, Damir Marjanovic, Alena Kushniarevich, Doron M Behar, Christian Gilissen, Lisenka Vissers, Joris A Veltman, Elena Balanovska, Miroslava Derenko, Boris Malyarchuk, Andres Metspalu, Sardana Fedorova, Anders Eriksson, Andrea Manica, Fernando L Mendez, Tatiana M Karafet, Krishna R Veeramah, Neil Bradman, Michael F Hammer, Ludmila P Osipova, Oleg Balanovsky, Elza K Khusnutdinova, Knut Johnsen, Maido Remm, Mark G Thomas, Chris Tyler-Smith, Peter A Underhill, Eske Willerslev, Rasmus Nielsen, Mait Metspalu, Richard Villems, Toomas Kivisild (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res..

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Pradiptajati Kusuma, Murray P Cox, Denis Pierron, Harilanto Razafindrazaka, Nicolas Brucato, Laure Tonasso, Helena Loa Suryadi, Thierry Letellier, Herawati Sudoyo, François-Xavier Ricaut (2015). Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics.

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