A custom FPGA for the simulation of gene regulatory networks. - Ilias Tagkopoulos; Charles A. Zukowski; German Cavelier; Dimitris Anastassiou (ACM Great Lakes Symposium on VLSI, 2003)

Multi-Class Biclustering and Classification Based on Modeling of Gene Regulatory Networks. - Ilias Tagkopoulos; Nikolai Slavov; Sun-Yuan Kung (BIBE, 2005)

A Transcriptional Approach to Gene Clustering. - Ilias Tagkopoulos (CIBCB, 2005)

Multi-Metric and Multi-Substructure Biclustering Analysis for Gene Expression Data. - Sun-Yuan Kung; Man-Wai Mak; Ilias Tagkopoulos (CSB, 2005)

Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix. - Sun-Yuan Kung; Man-Wai Mak; Ilias Tagkopoulos (J. Bioinform. Comput. Biol., 2006)

EVEVis: A multi-scale visualization system for dense evolutionary data. - Robert Miller; Vadim Mozhayskiy; Ilias Tagkopoulos; Kwan-Liu Ma (BioVis, 2011)

In Silico Evolution of Multi-scale Microbial Systems in the Presence of Mobile Genetic Elements and Horizontal Gene Transfer. - Vadim Mozhayskiy; Ilias Tagkopoulos (ISBRA, 2011)

A scalable multi-scale framework for parallel simulation and visualization of microbial evolution. - Vadim Mozhayskiy; Bob Miller; Kwan-Liu Ma; Ilias Tagkopoulos (TG, 2011)

A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support system. - Eren Gultepe; Hien Nguyen; Timothy E. Albertson; Ilias Tagkopoulos (ICCABS, 2012)

A robust, library-based, optimization-driven method for automatic gene circuit design. - Linh Hunyh; Ilias Tagkopoulos (ICCABS, 2012)

Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation. - Vadim Mozhayskiy; Ilias Tagkopoulos (BMC Bioinform., 2012)

Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution. - Vadim Mozhayskiy; Ilias Tagkopoulos (BMC Bioinform., 2012)

A flood-based information flow analysis and network minimization method for gene regulatory networks. - Andreas Pavlogiannis; Vadim Mozhayskiy; Ilias Tagkopoulos (BMC Bioinform., 2013)

A systems biology analysis of brain microvascular endothelial cell lipotoxicity. - Hnin H. Aung; Athanasios Tsoukalas; John C. Rutledge; Ilias Tagkopoulos (BMC Syst. Biol., 2014)

From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system. - Eren Gultepe; Jeffrey P. Green; Hien Nguyen; Jason Adams; Timothy E. Albertson; Ilias Tagkopoulos (J. Am. Medical Informatics Assoc., 2014)

A Distribution Adaptive Framework for Prediction Interval Estimation Using Nominal Variables. - Ameen Eetemadi; Ilias Tagkopoulos (CoRR, 2015)

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles. - Minseung Kim; Violeta Zorraquino; Ilias Tagkopoulos (PLoS Comput. Biol., 2015)

DeepPep: Deep proteome inference from peptide profiles. - Minseung Kim; Ameen Eetemadi; Ilias Tagkopoulos (PLoS Comput. Biol., 2017)

Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships. - Ameen Eetemadi; Ilias Tagkopoulos (Bioinform., 2019)

BWCNN: Blink to Word, a Real-Time Convolutional Neural Network Approach. - Albara Ah Ramli; Rex Liu; Rahul Krishnamoorthy; Vishal I B; Xiaoxiao Wang 002; Ilias Tagkopoulos; Xin Liu 002 (ICIOT, 2020)

Using Word Embeddings to Learn a Better Food Ontology. - Jason Youn; Tarini Naravane; Ilias Tagkopoulos (Frontiers Artif. Intell., 2020)

Special report: AI Institute for next generation food systems (AIFS). - Ilias Tagkopoulos; Stephen F. Brown; Xin Liu 002; Qing Zhao; Tarek I. Zohdi; J. Mason Earles; Nitin Nitin; Daniel E. Runcie; Danielle G. Lemay; Aaron D. Smith; Pamela C. Ronald; Hao Feng; et al. (Comput. Electron. Agric., 2022)

Algorithmic lifestyle optimization. - Ameen Eetemadi; Ilias Tagkopoulos (J. Am. Medical Informatics Assoc., 2022)

KGLM: Integrating Knowledge Graph Structure in Language Models for Link Prediction. - Jason Youn; Ilias Tagkopoulos (*SEM@ACL, 2023)

Semi-Automated Construction of Food Composition Knowledge Base. - Jason Youn; Fangzhou Li; Ilias Tagkopoulos (CoRR, 2023)

The AIFS Institute: Building a better food system through AI. - Ilias Tagkopoulos; J. Mason Earles; Danielle G. Lemay; Xin Liu 002; Nitin Nitin; Aaron D. Smith; Tarek I. Zohdi; Stephen F. Brown (AI Mag., 2024)

FoodAtlas: Automated knowledge extraction of food and chemicals from literature. - Jason Youn; Fangzhou Li; Gabriel Simmons; Shanghyeon Kim; Ilias Tagkopoulos (Comput. Biol. Medicine, 2024)

Interpreting Inflammation Prediction Model via Tag-based Cohort Explanation. - Fanyu Meng; Jules Larke; Xin Liu 002; Zhaodan Kong; Xin Chen; Danielle G. Lemay; Ilias Tagkopoulos (CoRR, 2024)

Predicting clinical trial success for Clostridium difficile infections based on preclinical data. - Fangzhou Li; Jason Youn; Christian Millsop; Ilias Tagkopoulos (Frontiers Artif. Intell., 2024)

SkillFlow: Efficient Skill and Code Transfer Through Communication in Adapting AI Agents. - Pagkratios Tagkopoulos; Fangzhou Li; Ilias Tagkopoulos (CoRR, 2025)