Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. - Shobha Potluri; Aly Azeem Khan; A. Kuzminykh; Janusz M. Bujnicki; Alan M. Friedman; Chris Bailey-Kellogg (Pacific Symposium on Biocomputing, 2004)

BASIC: BCR assembly from single cells. - Stefan Canzar; Karlynn E. Neu; Qingming Tang; Patrick C. Wilson; Aly A. Khan (Bioinform., 2017)

Predicting protein-protein interactions through sequence-based deep learning. - Somaye Hashemifar; Behnam Neyshabur; Aly A. Khan; Jinbo Xu (Bioinform., 2018)

Integrating RNA expression and visual features for immune infiltrate prediction. - Derek Reiman; Lingdao Sha; Irvin Ho; Timothy Tan; Denise Lau; Aly A. Khan (PSB, 2019)

Evaluation of Hyperbolic Attention in Histopathology Images. - Renyu Zhang; Aly A. Khan; Robert L. Grossman (BIBE, 2020)

Evaluating and interpreting caption prediction for histopathology images. - Renyu Zhang; Christopher Weber; Robert L. Grossman; Aly A. Khan (MLHC, 2020)

BALanCe: Deep Bayesian Active Learning via Equivalence Class Annealing. - Renyu Zhang; Aly A. Khan; Robert L. Grossman; Yuxin Chen 001 (CoRR, 2021)

Pseudocell Tracer - A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination. - Derek Reiman; Godhev Kumar Manakkat Vijay; Heping Xu; Andrew Sonin; Dianyu Chen; Nathan Salomonis; Harinder Singh; Aly A. Khan (PLoS Comput. Biol., 2021)

Privacy preserving validation for multiomic prediction models. - Talal Ahmed; Mark A. Carty; Stephane Wenric; Jonathan R. Dry; Ameen A. Salahudeen; Aly A. Khan; Eric Lefkofsky; Martin C. Stumpe; Raphael Pelossof (Briefings Bioinform., 2022)

Scalable Batch-Mode Deep Bayesian Active Learning via Equivalence Class Annealing. - Renyu Zhang; Aly A. Khan; Robert L. Grossman; Yuxin Chen 001 (ICLR, 2023)

Enhancing Instance-Level Image Classification with Set-Level Labels. - Renyu Zhang; Aly A. Khan; Yuxin Chen 001; Robert L. Grossman (ICLR, 2024)

TRIBAL: Tree Inference of B Cell Clonal Lineages. - Leah L. Weber; Derek Reiman; Mrinmoy Saha Roddur; Yuanyuan Qi; Mohammed El-Kebir; Aly A. Khan (RECOMB, 2024)

Computational prediction of protein interactions in single cells by proximity sequencing. - Junjie Xia; Hoang Van Phan; Luke Vistain; Mengjie Chen; Aly A. Khan; Savas Tay (PLoS Comput. Biol., 2024)