Publication Toward deep learning sequence–structure co-generation for protein design Chentong Wang, Sarah Alamdari, Carles Domingo-Enrich, Ava P. Amini, Kevin Kaichuang Yang Current Opinion in Structural Biology | March 2025
Publication Optimizing the mouse orthotopic liver transplantation model: Learning curve, technical enhancements, and keys to success Zipei Wang, Li Dai, Daqiang Zhao, Peixiang Lan, Yuanyuan Zhao, Lai Wei, Dong Chen, Bo Zhang, Dunfeng Du, Zhishui Chen Liver Transplantation | March 2025, Vol 31: pp. 1123-1134
Publication Evidence Aggregator: AI reasoning applied to rare disease diagnostics Hope Twede, Ashley Conard, Lynn Pais, Samantha Brye, Emily O’Heir, Greg Smith, Ron Paulsen, Christina A. Austin-Tse, Alex Bloemendal, Cas Simons, Scott Saponas, Miah Wander, Daniel G. MacArthur, Heidi Rehm March 2025
Publication Multi-Modal Mamba Modeling for Survival Prediction (M4Survive): Adapting Joint Foundation Model Representations Ho Hin Lee, Alberto Santamaria-Pang, Jameson Merkow, Matthew P Lungren, Ivan Tarapov ArXiv | March 2025
Publication Impact of Lewis Acids on the Reactivity of a High-Valent Cu(III) Complex. Raju Eerlapally, Divya Lakshmi Hareendran, Lucia Velasco, Asterios Charisiadis, Maxime Sauvan, Jayashrita Debnath, Dooshaye Moonshiram, A. Draksharapu Inorganic chemistry | March 2025
Publication Koala: Efficient Pipeline Training through Automated Schedule Searching on Domain-Specific Language Yu Tang, Lujia Yin, Qiao Li, Hongyu Zhu, Hengjie Li, Xingcheng Zhang, Linbo Qiao, Dongsheng Li, Jiaxin Li ACM Transactions on Architecture and Code Optimization | March 2025, Vol 22: pp. 1-25
Publication Deep learning guided design of protease substrates Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Kaichuang Yang, Sangeeta N. Bhatia, Ava P. Amini bioRxiv | March 2025
Publication Artificial variables help to avoid over-clustering in single-cell RNA sequencing Alan DenAdel, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin Crawford American journal of human genetics | March 2025
Publication Scalable Universal T-Cell Receptor Embeddings from Adaptive Immune Repertoires Paidamoyo Chapfuwa, Ilker Demirel, Lorenzo Pisani, Javier Zazo, Elon Portugaly, H. Jabran Zahid, Julia Greissl ICLR 2025 | March 2025 Github
Publication Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm Meghana Kshirsagar, Artur Meller, Ian R. Humphreys, Samuel Sledzieski, Yixi Xu, Rahul Dodhia, Eric Horvitz, Bonnie Berger, Gregory R. Bowman, Juan M. Lavista Ferres, David Baker, Minkyung Baek Nature Communications | February 2025 Project