ralphi: a deep reinforcement learning framework for haplotype assembly
Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger, Victoria Popic
RECOMB (International Conference on Research in Computational Molecular Biology), Best Paper Award, 2025
Resolution of a human super-enhancer by targeted genome randomisation
Jonas Koeppel, Pierre Murat, Gareth Girling, Elin Madli Peets, Mélanie Gouley, Valentin Rebernig, Anant Maheshwari, Jacob Hepkema, Juliane Weller, Jenie Hannah Johnkingsly Jebaraj, Ronnie Crawford, Fabio Giuseppe Liberante, Leopold Parts
BioRxiv, 2025
Cue: a deep-learning framework for structural variant discovery and genotyping
Victoria Popic, Chris Rohlicek, F. Cunial, I. Hajirasouliha, D. Meleshko, K. Garimella, Anant Maheshwari
Nature Methods, 2023
Diagnostic classification of childhood cancer using multiscale transcriptomics
Federico Comitani, Joshua O Nash, S. Cohen-Gogo, A. Chang, Timmy T. Wen, Anant Maheshwari, Bipasha Goyal, E. Tio, Kevin Tabatabaei, C. Mayoh, Regis Zhao, Ben Ho, L. Brunga, J. E. Lawrence, P. Balogh, A. Flanagan, Sarah A. Teichmann, A. Huang, V. Ramaswamy, J. Hitzler, J. Wasserman, R. Gladdy, B. Dickson, U. Tabori, M. Cowley, S. Behjati, D. Malkin, A. Villani, M. Irwin, A. Shlien
Nature Medicine, 2023
Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival
Nathaniel D. Anderson, Y. Babichev, F. Fuligni, Federico Comitani, M. Layeghifard, Rosemarie E. Venier, S. Dentro, Anant Maheshwari, S. Guram, Claire Wunker, J. D. Thompson, K. Yuki, Huayun Hou, M. Zatzman, Nicholas Light, M. Bernardini, J. Wunder, I. Andrulis, P. Ferguson, A. Razak, C. Swallow, J. Dowling, R. Al-Awar, R. Marcellus, M. Rouzbahman, M. Gerstung, D. Durocher, L. Alexandrov, B. Dickson, R. Gladdy, A. Shlien
Nature Communications, 2021