You can also find my articles on my Google Scholar profile.

By Year By Topic

Cancer Progression

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
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

Cancer Research

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

Causal Discovery

19.
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

Causal Inference

12.
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

Cell Perturbation Experiments

20.
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

Complex Networks

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

Computational Biology

13.
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
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
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

Computational Oncology

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
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

Conditional Average Treatment Effect

12.
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

Deconfounding

19.
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

Drug Hypersensitivity

18.
Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 2025. PDFLink
17.
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

Evaluation Metrics

20.
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

Heterogeneous Treatment Effect

12.
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

High Dimensional Statistics

10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. 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

Immune Checkpoint Inhibitors

18.
Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 2025. PDFLink

Immunology

16.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
15.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
11.
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

In silico Cell Models

20.
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

Infectious Disease

11.
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

Keystone Theory

16.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI
15.
Keystone Epitope Theory: An Ecological Perspective on RNA Viruses, Tumor Immunoediting, and Vaccine Design Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI

Machine Learning

10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. 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
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

MicroRNA

13.
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
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

Multi-task Learning

10.
High Dimensional Data Enrichment: Interpretable, Fast, and Data-Efficient Amir Asiaee, Samet Oymak, Kevin R. Coombes, Arindam Banerjee. arXiv, 2023. 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

Natural Language Processing

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

NK Cell

16.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI

Probabilistic Graphical Models

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

Randomized Controlled Trial

12.
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

SCAR

18.
Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 2025. PDFLink
17.
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

Sentiment Analysis

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

SJS/TEN

18.
Immune checkpoint inhibitors as independent and synergistic drivers of SJS/TEN Eric Milan Mukherjee, Dodie Park, Amir Asiaee, Matthew S. Krantz, Cosby A. Stone, Michelle Martin-Pozo, Elizabeth Phillips. JAMA oncology, 2025. PDFLink
17.
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

Social Networks

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

Social Networks Analysis

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

Statistical Shape Analysis

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

Structur Learning

19.
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

Synthetic Data

14.
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

T Cell

16.
Keystone Theory: Implications for Effective T and Natural Killer Cell Interoperability Simon Mallal, Amir Asiaee. Zenodo, 2025. PDFDOI

Transcription Factor

13.
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