Selected Publications + Press

deep learning & automated machine learning in genomics

Bonet, D., Mas Montserrat, D. Giró-i-Nieto, X., Ioannidis, A. "HyperFast: Instant Classification for Tabular Data." Association for the Advancement of Artificial Intelligence (AAAI), 2024. *Best Paper Award, TRL-NeurIPS

Comajoan, M., Mas, D., Ioannidis, A. PopGenAdapt: Semi-Supervised Domain Adaptation for Genotype-to-Phenotype Prediction in Underrepresented Populations. Pacific Symposium for Biocomputing (PSB), 2024.

Dominguez Mantes, A., Mas Montserrat, D., Bustamante, C., Giró-i-Nieto, X., Ioannidis, A. "Neural ADMIXTURE for rapid genomic clustering." Nature Computational Science, 2023. [link] [news & views]

Nature Methods, research highlight

Barrabes, M., Mas Montserrat, D., Geleta, M., Giro-i-Nieto, X., Ioannidis, A. Adversarial Learning for Feature Shift Detection and Correction. Advances in Neural Information Processing Systems (NeurIPS), 2023

Mas Montserrat D. and Ioannidis A. Adversarial Attacks on Genotype Sequences. IEEE Int. Con. on Acoustics, Speech & Signal Processing (ICASSP), 2023. doi: 10.1109/ICASSP49357.2023.10096857

Kumar, A., Mas Montserrat, D., Bustamante, C., Ioannidis, A. "XGMix: Local-Ancestry Inference With Stacked XGBoost." Int'l Conference on Learning Representations (ICLR, 2020, AI4H) [link]. *Best Paper Award

computational population genetics

Gimbernat-Mayol, J., Dominguez Mantes, A., Mas Montserrat, D., Bustamante, C., Ioannidis, A. "Archetypal Analysis for Population Genetics." PLOS Computational Biology, 2022. [link]

Oriol Sabat, B., Mas Montserrat D., Giró-i-Nieto, X., Ioannidis A. "SALAI-Net: Species-agnostic local ancestry inference network." Bioinformatics, 2022. [link]

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] [news & views]

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"

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

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] [news & views]

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"

computational precision health

Bonet, D., Levin, M., Mas, D., Ioannidis, A. Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations. Pacific Symposium for Biocomputing (PSB), 2024.

Parikh, V.*, Ioannidis, A.*, et al. *co-first authors "Deconvoluting complex correlates of COVID19 severity with a multi-omic pandemic tracking strategy." Nature Communications, 2022. [link]

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

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

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 publications

Bonet, D., Mas Montserrat, D. Giró-i-Nieto, X., Ioannidis, A. "HyperFast: Instant Classification for Tabular Data." Association for the Advancement of Artificial Intelligence (AAAI), 2024.

Bonet, D., Levin, M., Mas, D., Ioannidis, A. Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations. Pacific Symposium for Biocomputing (PSB), 2024.

Dominguez Mantes, A., Mas Montserrat, D., Bustamante, C., Giró-i-Nieto, X., Ioannidis, A. Neural ADMIXTURE for rapid genomic clustering. Nature Computational Science, 2023.

Villa-Islas V., Izarraras-Gomez A., Larena M., Perez Campos E. M., Sandoval-Velasco M., Rodríguez-Rodríguez J. E., Bravo-Lopez M., Moguel B., Fregel R., Medina Tretmanis J., Velázquez-Ramírez D. A., Herrera-Muñóz A., Sandoval K., Nieves-Colón M. A., Zepeda G., Villanea F., Villanueva Medina E., Aguayo-Haro R., Valdiosera C., Ioannidis A., Moreno-Estrada A., Jay F., Huerta-Sanchez E., Sánchez-Quinto F., Ávila-Arcos M. C., Demographic history & genetic structure in pre-Hispanic Central Mexico. Science, 2023.

Mas Montserrat D. and Ioannidis A. Adversarial Attacks on Genotype Sequences. IEEE Int. Con. on Acoustics, Speech & Signal Processing (ICASSP), 2023. doi: 10.1109/ICASSP49357.2023.10096857

Gimbernat-Mayol, J., Dominguez Mantes, A., Mas Montserrat, D., Bustamante, C., Ioannidis, A. "Archetypal Analysis for Population Genetics." PLOS Computational Biology, 2022. [link]

Oriol Sabat, B., Mas Montserrat D., Giró-i-Nieto, X., Ioannidis A. SALAI-Net: Species-agnostic local ancestry inference network. Bioinformatics, 2022.

Perera, M., Mas Montserrat, D., Barrabes, M., Geleta, M., Giro-i-Nieto, X., Ioannidis, A. Generative Moment Matching Networks for Genotype Simulation. IEEE Engineering in Medicine & Biology Society (EMBC), 2022. doi: 10.1109/EMBC48229.2022.9871045

Bartusiak, E., Barrabés, M., Rymbekova, A., Gimbernat-Mayol, J., López, C., Barberis, L., Mas Montserrat, D., Giró-i-Nieto, X., Ioannidis, A. Predicting Dog Phenotypes from Genotypes. IEEE Engineering in Medicine & Biology Society (EMBC), 2022. doi: 10.1109/EMBC48229.2022.9870905

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, 2022. (*co-first author)

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)

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.

Lopez-Pineda A., Vernekar M., Moreno-Grau S., Rojas-Muñoz A., Moatamed B., Lee M.T.M., Nava-Aguilar M.A., Gonzalez-Arroyo G., Numakura K., Matsuda Y., Ioannidis A., Katsanis N., Takano T., Bustamante C. Validating and automating learning of cardiometabolic polygenic risk scores from direct-to-consumer genetic and phenotypic data: implications for scaling precision health research. Human genomics, 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.

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.

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

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 workshop papers

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

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.