publications

2026

JournalD. Bonet, M. Comajoan Cara, M. Barrabés, R. Smeriglio, D. Agrawal, K. Aounallah, M. Geleta, A. Dominguez Mantes, C. Thomassin, C. Shanks, E. C. Huang, M. Franquesa Monés, A. Luis, J. Saurina, M. Perera, C. López, B. Oriol Sabat, J. Abante, S. Moreno-Grau, D. Mas Montserrat, A. G. Ioannidis (2026, in print). snputils: A High-Performance Python Library for Genetic Variation and Population Structure. Molecular Biology and Evolution. (preprint: bioRxiv:2026.02.28.708618)

@article{Bonet_2026,
  title={snputils: A High-Performance Python Library for Genetic Variation and Population Structure},
  url={http://dx.doi.org/10.64898/2026.02.28.708618},
  DOI={10.64898/2026.02.28.708618},
  publisher={openRxiv},
  author={Bonet, David and Comajoan Cara, Marçal and Barrabés, Míriam and Smeriglio, Riccardo and Agrawal, Devang and Aounallah, Khaled and Geleta, Margarita and Dominguez Mantes, Albert and Thomassin, Christophe and Shanks, Cole and Huang, Edward C. and Franquesa Monés, Marc and Luis, Aina and Saurina, Joan and Perera, Maria and López, Cayetana and Sabat, Benet Oriol and Abante, Jordi and Moreno-Grau, Sonia and Mas Montserrat, Daniel and Ioannidis, Alexander G.},
  year={2026},
  month=Mar,
}

JournalD. Bonet, C. Shanks, M. Comajoan Cara, J. Abante, A. Ioannidis (2026). ARGformer: learning on ancestral recombination graphs with transformers. Bioinformatics, 42(Supplement_2), btag438. ECCB 2026.

@article{Bonet_2026,
  title={ARGformer: learning on ancestral recombination graphs with transformers},
  volume={42},
  ISSN={1367-4811},
  url={http://dx.doi.org/10.1093/bioinformatics/btag438},
  DOI={10.1093/bioinformatics/btag438},
  number={Supplement_2},
  journal={Bioinformatics},
  publisher={Oxford University Press (OUP)},
  author={Bonet, David and Shanks, Cole and Cara, Marçal Comajoan and Abante, Jordi and Ioannidis, Alexander G},
  year={2026},
  month=Aug,
}

ConferenceB. Ros, M. Olives-Verger, C. Fuses, J. M. Canals, J. Soriano, J. Abante (2026). Integration of Calcium Imaging Traces via Deep Generative Modeling. ICASSP 2026 - 2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Barcelona, Spain, pp. 6986-6990, doi: 10.1109/ICASSP55912.2026.11464071.

@inproceedings{Ros_2026,
  title={Integration of Calcium Imaging Traces via Deep Generative Modeling},
  url={http://dx.doi.org/10.1109/ICASSP55912.2026.11464071},
  DOI={10.1109/icassp55912.2026.11464071},
  booktitle={ICASSP 2026 - 2026 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)},
  publisher={IEEE},
  author={Ros, Berta and Olives-Verger, Mireia and Fuses, Caterina and Canals, Josep M. and Soriano, Jordi and Abante, Jordi},
  year={2026},
  month=May,
  pages={6986–6990},
}

PreprintR. Smeriglio, S. Moreno-Grau, D. Mas Montserrat, G. Venkataraman, D. Bonet, C. Fuses, M. A. Rivas, A. Savino, S. Di Carlo, J. Abante, A. G. Ioannidis (2026). Multi-ancestry admixture mapping reveals ancestry-associated disease loci in the UK Biobank. medRxiv, 2026.08.06.26359859.

@article{Smeriglio_2026,
  title={Multi-ancestry admixture mapping reveals ancestry-associated disease loci in the UK Biobank},
  url={http://dx.doi.org/10.64898/2026.08.06.26359859},
  DOI={10.64898/2026.08.06.26359859},
  publisher={openRxiv},
  author={Smeriglio, Riccardo and Moreno-Grau, Sonia and Mas Montserrat, Daniel and Venkataraman, Guhan and Bonet, David and Fuses, Caterina and Rivas, Manuel A. and Savino, Alessandro and Di Carlo, Stefano and Abante, Jordi and Ioannidis, Alexander G.},
  year={2026},
  month=Aug,
}

2025

ConferenceC. Fuses, G. Zavou, B. Ros, J.M. Canals, and J. Abante (2025). Context-Dependent Genetic Modifiers of Huntington’s Disease Revealed through Multimodal Machine Learning. Proceedings of 2025 Machine Learning in Computational Biology (MLCB). PMLR 311:128-147.

@InProceedings{pmlr-v311-abante25a,
  title = {Context-Dependent Genetic Modifiers of Huntington’s Disease Revealed Through Multimodal Machine Learning},
  author = {Fuses, Caterina and Zavou, Georgia and Ros, Berta and Canals, Josep M and Abante, Jordi},
  booktitle = {Proceedings of the 20th Machine Learning in Computational Biology meeting},
  pages = {128--147},
  year = {2025},
  editor = {Knowles, David A and Koo, Peter K},
  volume = {311},
  series = {Proceedings of Machine Learning Research},
  month = {10--11 Sep},
  publisher = {PMLR},
  pdf = {https://raw.githubusercontent.com/mlresearch/v311/main/assets/abante25a/abante25a.pdf},
  url = {https://proceedings.mlr.press/v311/abante25a.html},
}

JournalF. J. Molina-Ruiz, P. Sanders, C. Gomis, J. Abante, F. Londoño, G. Bombau, M. Galofre, G. Vinyes, V. Monforte, and J. M. Canals (2025). CD200-based cell sorting results in homogeneous transplantable striatal neuroblasts for cell therapy. Neurobiology of Disease, 106905.

@article{Molina_Ruiz_2025,
  title={CD200-based cell sorting results in homogeneous transplantable striatal neuroblasts for human cell therapy for Huntington’s disease},
  volume={209},
  ISSN={0969-9961},
  url={http://dx.doi.org/10.1016/j.nbd.2025.106905},
  DOI={10.1016/j.nbd.2025.106905},
  journal={Neurobiology of Disease},
  publisher={Elsevier BV},
  author={Molina-Ruiz, Francisco J. and Sanders, Phil and Gomis, Cinta and Abante, Jordi and Londoño, Francisco and Bombau, Georgina and Galofré, Mireia and Vinyes-Bassols, Gal la and Monforte, Veronica and Canals, Josep M.},
  year={2025},
  month=June,
  pages={106905},
}

PreprintM. Usman, O. Varea, P.I. Radeva, J.M. Canals, J. Abante, D. Ortiz (2025). Explainable AI model reveals disease-related mechanisms in single-cell RNA-seq data. ArXiv, 2501.03923v1.

@misc{https://doi.org/10.48550/arxiv.2501.03923,
  doi = {10.48550/ARXIV.2501.03923},
  url = {https://arxiv.org/abs/2501.03923},
  author = {Usman, Mohammad and Varea, Olga and Radeva, Petia and Canals, Josep and Abante, Jordi and Ortiz, Daniel},
  keywords = {Genomics (q-bio.GN), Computer Vision and Pattern Recognition (cs.CV), Machine Learning (cs.LG), FOS: Biological sciences, FOS: Biological sciences, FOS: Computer and information sciences, FOS: Computer and information sciences},
  title = {Explainable AI model reveals disease-related mechanisms in single-cell RNA-seq data},
  publisher = {arXiv},
  year = {2025},
  copyright = {Creative Commons Attribution Non Commercial No Derivatives 4.0 International},
}

2024

ConferenceR. Smeriglio, J. Rosell-Mirmi, P. Radeva, and J. Abante (2024). Leveraging protein-protein interactions in phenotype prediction through graph neural networks. 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 1–8.

@inproceedings{Smeriglio_2024,
  title={Leveraging protein-protein interactions in phenotype prediction through graph neural networks},
  url={http://dx.doi.org/10.1109/CIBCB58642.2024.10702170},
  DOI={10.1109/cibcb58642.2024.10702170},
  booktitle={2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)},
  publisher={IEEE},
  author={Smeriglio, Riccardo and Rosell-Mirmi, Joana and Radeva, Petia and Abante, Jordi},
  year={2024},
  month=Aug,
  pages={1–8},
}

JournalY.R. Shen, S. Zaballa, X. Bech, A. Sancho-Balsells, I. Rodríguez-Navarro, C. Cifuentes-Díaz, G. Seyit-Bremer, S. H. Chun, T. Straub, J. Abante, I. Merino-Valverde, L. Richart, V. Gupta, H.-Y. Li, I. Ballasch, N. Alcázar, J. Alberch, J. M. Canals, M. Abad, and D. del Toro (2024). Expansion of the neocortex and protection from neurodegeneration by in vivo transient reprogramming. Cell Stem Cell.

@article{Shen_2024,
  title={Expansion of the neocortex and protection from neurodegeneration by in vivo transient reprogramming},
  volume={31},
  ISSN={1934-5909},
  url={http://dx.doi.org/10.1016/j.stem.2024.09.013},
  DOI={10.1016/j.stem.2024.09.013},
  number={12},
  journal={Cell Stem Cell},
  publisher={Elsevier BV},
  author={Shen, Yi-Ru and Zaballa, Sofia and Bech, Xavier and Sancho-Balsells, Anna and Rodríguez-Navarro, Irene and Cifuentes-Díaz, Carmen and Seyit-Bremer, Gönül and Chun, Seung Hee and Straub, Tobias and Abante, Jordi and Merino-Valverde, Iñaki and Richart, Laia and Gupta, Vipul and Li, Hao-Yi and Ballasch, Ivan and Alcázar, Noelia and Alberch, Jordi and Canals, Josep M. and Abad, Maria and Serrano, Manuel and Klein, Rüdiger and Giralt, Albert and del Toro, Daniel},
  year={2024},
  month=Dec,
  pages={1741–1759.e8},
}

2023

ConferenceA. Meléndez, C. López, D. Bonet, G. Sant, D. M. Montserrat, J. Abante, M. Rivas, F. Marqués, and A. Ioannidis (2023). Assessing Tree-Based Phenotype Prediction on the UK Biobank. 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 3804–3810.

@inproceedings{Mel_ndez_2023,
  title={Assessing Tree-Based Phenotype Prediction on the UK Biobank},
  url={http://dx.doi.org/10.1109/BIBM58861.2023.10385960},
  DOI={10.1109/bibm58861.2023.10385960},
  booktitle={2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  publisher={IEEE},
  author={Meléndez, Alex and López, Cayetana and Bonet, David and Sant, Gerard and Montserrat, Daniel Mas and Abante, Jordi and Rivas, Manuel and Marqués, Ferran and Ioannidis, Alexander G.},
  year={2023},
  month=Dec,
  pages={3804–3810},
}

JournalJ. Abante, P. L. Wang, J. Salzman (2023). DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery. Genome Biology 24, 240.

@article{Abante_2023,
  title={DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery},
  volume={24},
  ISSN={1474-760X},
  url={http://dx.doi.org/10.1186/s13059-023-03038-0},
  DOI={10.1186/s13059-023-03038-0},
  number={1},
  journal={Genome Biology},
  publisher={Springer Science and Business Media LLC},
  author={Abante, Jordi and Wang, Peter L. and Salzman, Julia},
  year={2023},
  month=Oct,
}

JournalY. Fang, Z. Ji (†), W. Zhou (†), J. Abante (†), M.A. Koldobskiy, H. Ji, and A.P. Feinberg (2023). DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence. Nucleic Acids Research, 51(5), 2046–2065. † Equal contribution.

@article{Fang_2023,
  title={DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence},
  volume={51},
  ISSN={1362-4962},
  url={http://dx.doi.org/10.1093/nar/gkad050},
  DOI={10.1093/nar/gkad050},
  number={5},
  journal={Nucleic Acids Research},
  publisher={Oxford University Press (OUP)},
  author={Fang, Yuqi and Ji, Zhicheng and Zhou, Weiqiang and Abante, Jordi and Koldobskiy, Michael A and Ji, Hongkai and Feinberg, Andrew P},
  year={2023},
  month=Feb,
  pages={2046–2065},
}