Selected Publications + Press

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]

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]

Parikh, V.*, Ioannidis, A.*, et al.  *co-first  "Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy" [medRxiv] 2021.

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)

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]