2026
33.Keystone Epitope Theory in Deep Time: How Viral Endogenization and Sexual Dimorphism Wrote the Genomic Syllabus of Immunity.
Simon Mallal, Amir Asiaee, Elizabeth Phillips.
Zenodo, 2026.
PDFDOI 32.Keystone Epitope Theory: Implications for the Investigation of Multiple Sclerosis
Simon Mallal, Amir Asiaee, Natalie Mallal, Elizabeth Phillips.
Zenodo, 2026.
PDFDOI 31.Widespread data leakage inflates performance estimates in cancer drug response prediction
Amir Asiaee, Jared Strauch, Leila Azinfar, Samhita Pal, Heather H. Pua, James P. Long, Kevin R. Coombes.
bioRxiv, 2026--02, 2026.
PDFLink 30.Sharp Bounds for Treatment Effect Generalization under Outcome Distribution Shift
Amir Asiaee, Samhita Pal, Cole Beck, Jared D. Huling.
arXiv preprint arXiv:2602.09595, 2026.
PDFLink 29.A shape-constrained regression and wild bootstrap framework for reproducible drug synergy testing
Amir Asiaee, James P. Long, Samhita Pal, Heather H. Pua, Kevin R. Coombes.
bioRxiv, 2026--02, 2026.
PDFLink 28.Risk-Equalized Differentially Private Synthetic Data: Protecting Outliers by Controlling Record-Level Influence
Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin.
arXiv, 2026.
PDFDOI 27.Projected Boosting with Fairness Constraints: Quantifying the Cost of Fair Training Distributions
Amir Asiaee, Kaveh Aryan.
arXiv preprint arXiv:2602.05713, 2026.
PDFLink 26.PRISM: Differentially Private Synthetic Data with Structure-Aware Budget Allocation for Prediction
Amir Asiaee, Chao Yan, Zachary B. Abrams, Bradley A. Malin.
arXiv, 2026.
PDFDOI 25.Fix Representation (Optimally) Before Fairness: Finite-Sample Shrinkage Population Correction and the True Price of Fairness Under Subpopulation Shift
Amir Asiaee, Kaveh Aryan.
arXiv preprint arXiv:2602.05707, 2026.
PDFLink 24.Fairness Under Group-Conditional Prior Probability Shift: Invariance, Drift, and Target-Aware Post-Processing
Amir Asiaee, Kaveh Aryan.
arXiv preprint arXiv:2602.05144, 2026.
PDFLink 2025
23.AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes
Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P. Long.
Briefings in bioinformatics, 26(5), bbaf426, 2025.
PDFLink 22.DAG DECORation: Continuous Optimization for Structure Learning under Hidden Confounding
Samhita Pal, James O'quinn, Kaveh Aryan, Heather Pua, James P. Long, Amir Asiaee.
arXiv, 2025.
PDFDOI 21.Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN
Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone Jr, Michelle Martin-Pozo, Elizabeth Phillips.
JAMA oncology, 11(12), 1542--1545, 2025.
PDFLink 20.Demographics, Overlap, and Latency of Severe Cutaneous Adverse Reactions in an FDA Database
Eric M. Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Jane Phillips.
medRxiv, 2025.
PDFDOI 19.Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability
Simon Mallal, Amir Asiaee.
Zenodo, 2025.
PDFDOI 18.Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design
Simon Mallal, Amir Asiaee.
Zenodo, 2025.
PDFDOI 17.Generating Synthetic Multi-national Longitudinal Cohorts for Clinically Grounded HIV Research
Zhuohui J. Liang, Zhuohang Li, Nicholas J. Jackson, Yanink Caro-Vega, Ronaldo I. Moreira, Fabio Paredes, Jordany Bernadin, Diana Varela, Carina Cesar, Alessandro Blasimme, Jessica M. Perkins, Amir Asiaee, Stephany N. Duda, Bradley A. Malin, Bryan E. Shepherd, Chao Yan.
medRxiv, 2025.
PDFDOI 16.Transcriptome Complexity Disentangled: A Regulatory Molecules Approach
Amir Asiaee, Zachary B. Abrams, Heather H. Pua, Kevin R. Coombes.
International journal of molecular sciences, 26(6), 2510, 2025.
PDFLink 15.Improving Precision of RCT-Based CATE Estimation using Data Borrowing with Double Calibration
Amir Asiaee, Chiara Di Gravio, Cole Beck, Yuting Mei, Samhita Pal, Jared D. Huling.
arXiv, 2025.
PDFDOI 14.Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms
Amir Asiaee, Natalie Mallal, Elizabeth Phillips, Simon Mallal.
bioRxiv, 2025--08, 2025.
PDFLink 13.Causal Discovery with Mixed Latent Confounding via Precision Decomposition
Amir Asiaee, Samhita Pal, James O'quinn, James P. Long.
arXiv preprint arXiv:2512.24696, 2025.
PDFLink 2024
12.Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning
Jared Strauch, Amir Asiaee.
bioRxiv, 2024--05, 2024.
PDFLink 11.Quantifying Differential Rhythmicity based on Effect Sizes with LimoRhyde2
Dora Obodo, Amir Asiaee.
bioRxiv, 2024--05, 2024.
PDFLink 2023
10.High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient
Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee.
arXiv, 2023.
PDFDOI 2022
9.SITH : An R package for visualizing and analyzing a spatial model of intratumor heterogeneity
Phillip B. Nicol, Dániel L. Barabási, Kevin R. Coombes, Amir Asiaee.
Computational and Systems Oncology, 2(2), e1033, 2022.
PDFDOI 2021
8.Oncogenetic network estimation with disjunctive Bayesian networks
Phillip B. Nicol, Kevin R. Coombes, Courtney Deaver, Oksana Chkrebtii, Subhadeep Paul, Amanda E. Toland, Amir Asiaee.
Computational and Systems Oncology, 1(2), e1027, 2021.
PDFDOI 2020
7.Explaining Gene Expression Using Twenty-One MicroRNAs
Amir Asiaee, Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes.
Journal of Computational Biology, 27(7), 1157--1170, 2020.
PDFDOI 2019
6.Elastic Statistical Shape Analysis of Biological Structures with Case Studies: A Tutorial
Min Ho Cho, Amir Asiaee, Sebastian Kurtek.
Bulletin of Mathematical Biology, 81(7), 2052--2073, 2019.
PDFDOI 5.Data enrichment: Multi-task learning in high dimension with theoretical guarantees
Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee.
Adaptive and Multitask Learning Workshop at the ICML. IMLS, Long Beach, CA, 2019.
PDFLink 2018
4.Thirty biologically interpretable clusters of transcription factors distinguish cancer type
Zachary B. Abrams, Mark Zucker, Min Wang, Amir Asiaee Taheri, Lynne V. Abruzzo, Kevin R. Coombes.
BMC Genomics, 19(1), 738, 2018.
PDFDOI 2015
3.Revisiting non-progressive influence models: scalable influence maximization in social networks
Golshan Golnari, Asiaee T. Amir, Arindam Banerjee, Zhi-Li Zhang.
Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 316--325, 2015.
PDF 2013
2.Influence maximization for informed agents in collective behavior
Amir Asiaee Taheri, Mohammad Afshar, Masoud Asadpour.
Distributed Autonomous Robotic Systems: The 10th International Symposium, 389--402, 2013.
PDF 2012
1.If you are happy and you know it... tweet
Amir Asiaee T., Mariano Tepper, Arindam Banerjee, Guillermo Sapiro.
Proceedings of the 21st ACM international conference on Information and knowledge management, 1602--1606, 2012.
PDFDOI