Selected Publications + Press

computational genomics

Ioannidis, A., Blanco-Portillo, J., Sandoval, K...Mentzer, A., Moreno-Estrada, A. "Paths and timings of the peopling of Polynesia inferred from genomic networks." Nature, 2021. [link] [review]

The Economist, "To the ends of the Earth: Genes reveal how humans reached remote corners of Pacific"
The Times of London, "Ancient statues on distant islands linked by sailors' genetic legacy"
Le Figaro, "L’histoire du peuplement de la Polynésie s'éclaircit grâce à la génétique"
Reuters, "Genetic study reveals how ancient seafarers settled vast Polynesia"
Science, "'No one could have predicted.' DNA offers surprises on how Polynesia was settled"

Mantes, A., Montserrat, D., Bustamante, C., Giró-i-Nieto, X., Ioannidis, A. "Neural ADMIXTURE: rapid population clustering with autoencoders" [BioRxiv] 2021.

Kumar, A., Montserrat, D., Bustamante, C. and Ioannidis, A. "XGMix: Local-Ancestry Inference With Stacked XGBoost." International Conference on Learning Representations (ICLR, 2020, AI4H) [link]

*Awarded Best Paper

Ioannidis, A., Blanco-Portillo, J., Sandoval, K...Bustamante, C., Moreno-Estrada, A. "Native American gene flow into Polynesia predating Easter Island settlement." Nature, 2020. [link] [review]

The Guardian, "Indigenous Americans had contact with Polynesians 800 years ago, DNA reveals"
Le Monde, "Des croisements anciens entre Polynésiens et Amérindiens mis en évidence par la génétique"
BBC, "Evidence of epic prehistoric Pacific voyages"
Reuters, "Study shows ancient contact between Polynesian and South American peoples"
Smithsonian Magazine, "Native Americans and Polynesians Met Around 1200 A.D."
Nature Reviews Genetics, "An odyssey to Oceania"

Montserrat, D., Bustamante, C. and Ioannidis, A. "LAI-Net: Local-Ancestry Inference With Neural Networks" IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP, 2020). IEEE. [link]

Hilmarsson, H., Kumar, A., Rastogi, R., Bustamante, C., Mas Montserrat, D., Ioannidis, A. "High Resolution Ancestry Deconvolution for Next Generation Genomic Data" [BioRxiv] 2021.

Montserrat, D.M., Bustamante, C. and Ioannidis, A. "Class-Conditional VAE-GAN for Local-Ancestry Simulation."

Machine Learning for Computational Biology at NeurIPS (MLCB/NeurIPS, 2019) [link]

precision health & machine learning in medicine

Parikh, V.*, Ioannidis, A.*, et al. *co-first authors "Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy" Nature Communications, 2022. (in press) [pre-print link]

Wojcik, G. Murphy, J., Edelson, J., Gignoux, C., Ioannidis, A., Manning, A., Rivas, M., Buyske, S., Hendricks, A., "Opportunities and challenges for the use of common controls in sequencing studies," Nature Reviews Genetics, 2022. [link]

COVID-19 Host Genetics Initiative, "Mapping the human genetic architecture of COVID-19," Nature, 2021. [link]

Pineda, A., Pourshafeie, A., Ioannidis, A., Leibold, C., Chan, A., Bustamante, C., Frankovich, J., Wojcik, G., "Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients." Journal of Biomedical Informatics, 2021. [link]

Montserrat, D., Bustamante C., Ioannidis, A. "Active Learning for Efficient Construction of Diverse Biobanks," International Conference on Learning Representations (ICLR, 2020, Workshop ML-RL)

superconducting computing logic

Herr, Q.P., Herr, A.Y., Oberg, O.T. and Ioannidis, A.G. "Ultra-low-power superconductor logic," Journal of Applied Physics, 2011, 109(10), p.103903. [link]

"Superconducting Niobium Chip Smashes Silicon Power," MIT Technology Review
"Will the NSA Finally Build Its Superconducting Spy Computer," IEEE Spectrum

Olaya, D., Dresselhaus, P.D., Benz, S.P., Herr, A., Herr, Q.P., Ioannidis, A.G., Miller, D.L. and Kleinsasser, A.W. "Digital circuits using self-shunted Nb/Nb_x Si_(1−x)/Nb Josephson junctions," Applied Physics Letters, 2010, 96(21), p.213510. [link]

Oberg, O.T., Herr, Q.P., Ioannidis, A.G. and Herr, A.Y. "Integrated power divider for superconducting digital circuits." IEEE Transactions on Applied Superconductivity, 2010, 21(3), pp.571-574. [link]

Complete Publication List

Peer reviewed journal articles

Parikh V.*, Ioannidis, A.*, et al., Bustamante, C., Rivas, M., Ashley, E. Deconvoluting complex correlates of COVID19 with a multi-omic pandemic tracking strategy. Nature Communications (accepted), medRxiv doi:10.1101/2021.08.04.21261547 (*co-first author)

Gimbernat-Mayol J., Mas Montserrat D., Bustamante C., Ioannidis A. Archetypal Analysis for Population Genetics. PLOS Computational Biology (accepted) doi:10.1101/2021.11.28.470296

Oriol Sabat, B., Mas Montserrat D., Giró-i-Nieto, X., Ioannidis A. SALAI-Net: Species-agnostic local ancestry inference network. Bioinformatics (accepted)

Wojcik, G., Murphy, J., Edelson, J., Gignoux, C., Ioannidis, A., Manning, A., Rivas, M., Buyske, S., Hendricks, A. Opportunities & challenges for the use of common controls in sequencing studies. Nature Reviews Genetics, 2022.

Liu, Y., Hunter-Anderson, R., Cheronet, O., Eakin, J., Camacho, F., Pietrusewsky, M., Rohland, N., Ioannidis, A., Athens, J., Douglas, M., Ikehara-Quebral, R., Bernardos, R., Culleton, B., Mah, M., Adamski, N., Broomandkhoshbacht, N., Callan, K., Lawson, A., Mandl, K., Michel, M., Oppenheimer, J., Stewardson, K., Zalzala, F., Kidd, K., Kidd, J., Schurr, T., Auckland, K., Hill, A., Mentzer, A., Quinto-Cortés, C., Robson, K., Kennett, D., Patterson, N., Bustamante, C., Moreno-Estrada, A., Spriggs, M., Vilar, M., Lipson, M., Pinhasi, R., Reich, D., Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science, 377(6601): 72-79, 2022.

Rodriguez-Rodriguez J.*, Ioannidis A.*, Medina-Muñoz, S., Barberena-Jonas, C., Blanco-Portillo, J., Quinto-Cortés, C.D. and Moreno-Estrada, A. The genetic legacy of the Manila galleon trade in Mexico. Philosophical Transactions of the Royal Society B, 377(1852): 20200419, 2022. (*co-first author)

Ioannidis A., Blanco-Portillo J., et al., Mentzer A., Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature, 597:522-526, 2021.

Venkataraman G., DeBoever C., Tanigawa Y., Aguirre M., Ioannidis A., Mostafavi H., Spencer C., Poterba T., Bustamante C., Daly M., Pirinen M., Rivas M. Bayesian model comparison for rare-variant association studies. American Journal of Human Genetics, 102(12):2354-2367, 2021.

Ioannidis A., Blanco-Portillo J., et al., Bustamante C., Moreno-Estrada, A. Native American gene flow into Polynesia predating Easter Island settlement. Nature, 583:572-577, 2020.

Mas Montserrat D., Bustamante C., Ioannidis A. LAI-Net: Local-Ancestry Inference with Neural Networks. IEEE Int. Con. on Acoustics, Speech & Signal Processing (ICASSP) (pp. 1314-1318), 2020.

Lopez Pineda A., Pourshafeie A., Ioannidis A., Leibold C., Chan A., Bustamante C., Frankovich J., Wojcik G. Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients. Journal of Biomedical Informatics, 113:103664, 2020.

Herr Q., Herr A., Oberg O., Ioannidis A. Ultra-low-power superconductor logic. Journal of Applied Physics, 109(10):103903, 2011.

Oberg O., Herr Q., Ioannidis A., Herr A. Integrated power divider for superconducting digital circuits. IEEE Transactions on Applied Superconductivity, 21(3):571-574, 2011.

Olaya D., Dresselhaus P., Benz S., Herr A., Herr Q., Ioannidis A., Miller D., Kleinsasser A. Digital circuits using self-shunted Nb/NbxSi1-x/Nb Josephson junctions. Applied Physics Letters, 96(10):213510, 2010.

Peer reviewed conference papers

Perera, M., Montserrat, D., Barrabes, M., Geleta, M., Giro-i-Nieto, X., Ioannidis, A., 2022. Generative Moment Matching Networks for Genotype Simulation. IEEE Engineering in Medicine & Biology Society (EMBC), 2022. doi: 10.1101/2022.04.14.488350

Bartusiak, E., Barrabés, M., Rymbekova, A., Gimbernat-Mayol, J., López, C., Barberis, L., Montserrat, D., Giró-i-Nieto, X., Ioannidis, A., Predicting Dog Phenotypes from Genotypes. IEEE Engineering in Medicine & Biology Society (EMBC), 2022. doi: 10.1101/2022.04.13.488108

Hilmarsson H., Kumar A., Rastogi R., Mas Montserrat D., Bustamante C., Ioannidis A. XGFix: Fast and Scalable Phasing Error Correction with Local Ancestry Inference. Conference on Neural Information Processing Systems (NeurIPS) LMRL, 2020.

Aguirre M., Sokol J., Venkataraman G., Ioannidis A. A deep learning classifier for local ancestry inference. Conference on Neural Information Processing Systems (NeurIPS) LMRL, 2020. arXiv:2011.02081

Kumar A., Mas Montserrat D., Bustamante C., Ioannidis A. XGMix: Local-Ancestry Inference with Stacked XGBoost. Int. Conference on Learning Representations (ICLR) AI4AH, 2020. doi:10.1101/2020.04.21.053876 (best paper award)

Mas Montserrat D., Bustamante C., Ioannidis A. Class-Conditional VAE-GAN for Local-Ancestry Simulation. Machine Learning for Computational Biology at NeurIPS (MLCB/NeurIPS), 2019.