Industrial methodology for process verification in research (IMPROVER): toward systems biology verification. - Pablo Meyer 001; Julia Hoeng; John Jeremy Rice; Raquel Norel; Jörg Sprengel; Katrin Stolle; Thomas Bonk; Stephanie Corthesy; Ajay K. Royyuru; Manuel C. Peitsch; Gustavo Stolovitzky (Bioinform., 2012)

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. - Adi L. Tarca; Mario Lauria; Michael Unger; Erhan Bilal; Stéphanie Boué; Kushal Kumar Dey; Julia Hoeng; Heinz Koeppl; Florian Martin 002; Pablo Meyer 001; Preetam Nandy; Raquel Norel; et al. (Bioinform., 2013)

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. - Pablo Meyer 001; Thomas Cokelaer; Deepak Chandran; Kyung Hyuk Kim; Po-Ru Loh; George Tucker; Mark Lipson; Bonnie Berger; Clemens Kreutz; Andreas Raue; Bernhard Steiert; Jens Timmer; et al. (BMC Syst. Biol., 2014)

Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria. - Pablo Meyer 001; Guillermo A. Cecchi; Gustavo Stolovitzky (BMC Syst. Biol., 2014)

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. - Michael Biehl; Peter J. Sadowski; Gyan Bhanot; Erhan Bilal; Adel Dayarian; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Michael D. Zeller; Sahand Hormoz (Bioinform., 2015)

A crowd-sourcing approach for the construction of species-specific cell signaling networks. - Erhan Bilal; Theodore Sakellaropoulos; Challenge Participants; Ioannis N. Melas; Dimitris E. Messinis; Vincenzo Belcastro; Kahn Rhrissorrakrai; Pablo Meyer 001; Raquel Norel; Anita Iskandar; Elise Blaese; John Jeremy Rice; et al. (Bioinform., 2015)

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. - Adel Dayarian; Roberto Romero; Zhiming Wang; Michael Biehl; Erhan Bilal; Sahand Hormoz; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Gyan Bhanot; Feng Luo 001; Adi L. Tarca (Bioinform., 2015)

Inter-species pathway perturbation prediction via data-driven detection of functional homology. - Christoph Hafemeister; Roberto Romero; Erhan Bilal; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Richard Bonneau; Adi L. Tarca (Bioinform., 2015)

Where are we at regarding species translation? A review of the sbv IMPROVER challenge. - Julia Hoeng; Manuel C. Peitsch; Pablo Meyer 001; Igor Jurisica (Bioinform., 2015)

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. - Sahand Hormoz; Gyan Bhanot; Michael Biehl; Erhan Bilal; Pablo Meyer 001; Raquel Norel; Kahn Rhrissorrakrai; Adel Dayarian (Bioinform., 2015)

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. - Kahn Rhrissorrakrai; Vincenzo Belcastro; Erhan Bilal; Raquel Norel; Carine Poussin; Carole Mathis; Rémi H. J. Dulize; Nikolai V. Ivanov; Leonidas G. Alexopoulos; John Jeremy Rice; Manuel C. Peitsch; Gustavo Stolovitzky; et al. (Bioinform., 2015)

Enzyme function is regulated by its localization. - Stacey M. Gifford; Pablo Meyer 001 (Comput. Biol. Chem., 2015)

Advances in systems biology - New trends and perspectives. - Enrique Hernández-Lemus; Wentian Li; Pablo Meyer 001 (Comput. Biol. Chem., 2015)

DREAMTools: a Python package for scoring collaborative challenges. - Thomas Cokelaer; Mukesh Bansal; Christopher Bare; Erhan Bilal; Brian M. Bot; Elias Chaibub Neto; Federica Eduati; Mehmet Gönen; Steven M. Hill; Bruce R. Hoff; Jonathan R. Karr; Robert Küffner; et al. (F1000Research, 2015)

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. - Jonathan R. Karr; Alex H. Williams; Jeremy D. Zucker; Andreas Raue; Bernhard Steiert; Jens Timmer; Clemens Kreutz; Simon Wilkinson; Brandon A. Allgood; Brian M. Bot; Bruce R. Hoff; Michael R. Kellen; et al. (PLoS Comput. Biol., 2015)

Disease Progression Modeling Workbench 360. - Parthasarathy Suryanarayanan; Prithwish Chakraborty; Piyush Madan; Kibichii Bore; William Ogallo; Rachita Chandra; Mohamed F. Ghalwash; Italo Buleje; Sekou L. Remy; Shilpa Mahatma; Pablo Meyer 001; Jianying Hu (CoRR, 2021)

Leveraging Clinical Context for User-Centered Explainability: A Diabetes Use Case. - Shruthi Chari; Prithwish Chakraborty; Mohamed F. Ghalwash; Oshani Seneviratne; Elif K. Eyigöz; Daniel M. Gruen; Fernando J. Suarez Saiz; Ching-Hua Chen; Pablo Meyer Rojas; Deborah L. McGuinness (CoRR, 2021)

Distillation to Enhance the Portability of Risk Models Across Institutions with Large Patient Claims Database. - Steve Nyemba; Chao Yan 004; Ziqi Zhang 005; Amol Rajmane; Pablo Meyer 001; Prithwish Chakraborty; Bradley A. Malin (CoRR, 2022)

Human-centered explainability for life sciences, healthcare, and medical informatics. - Sanjoy Dey; Prithwish Chakraborty; Bum Chul Kwon; Amit Dhurandhar; Mohamed F. Ghalwash; Fernando J. Suarez Saiz; Kenney Ng; Daby Sow; Kush R. Varshney; Pablo Meyer 001 (Patterns, 2022)

Improving Primary Healthcare Workflow Using Extreme Summarization of Scientific Literature Based on Generative AI. - Gregor Stiglic; Leon Kopitar; Lucija Gosak; Primoz Kocbek; Zhe He 001; Prithwish Chakraborty; Pablo Meyer 001; Jiang Bian 001 (CoRR, 2023)

Informing clinical assessment by contextualizing post-hoc explanations of risk prediction models in type-2 diabetes. - Shruthi Chari; Prasant Acharya; Daniel M. Gruen; Olivia Zhang; Elif K. Eyigöz; Mohamed F. Ghalwash; Oshani Seneviratne; Fernando J. Suarez Saiz; Pablo Meyer 001; Prithwish Chakraborty; Deborah L. McGuinness (Artif. Intell. Medicine, 2023)

Multi-view biomedical foundation models for molecule-target and property prediction. - Parthasarathy Suryanarayanan; Yunguang Qiu; Shreyans Sethi; Diwakar Mahajan; Hongyang Li; Yuxin Yang; Elif K. Eyigöz; Aldo Guzmán-Sáenz; Daniel E. Platt; Timothy H. Rumbell; Kenney Ng; Sanjoy Dey; et al. (CoRR, 2024)

Explanation Ontology: A general-purpose, semantic representation for supporting user-centered explanations. - Shruthi Chari; Oshani Seneviratne; Mohamed F. Ghalwash; Sola Shirai; Daniel M. Gruen; Pablo Meyer 001; Prithwish Chakraborty; Deborah L. McGuinness (Semantic Web, 2024)

Genetics-Driven Personalized Disease Progression Model. - Haoyu Yang; Sanjoy Dey; Pablo Meyer 001 (CoRR, 2025)

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects. - Hongyang Li; Sanjoy Dey; Bum Chul Kwon; Michael M. Danziger; Michal Rosen-Tzvi; Jianying Hu; James Kozloski; Ching-Huei Tsou; Bharath Dandala; Pablo Meyer 001 (CoRR, 2025)

MetaExplainer: A Framework to Generate Multi-Type User-Centered Explanations for AI Systems. - Shruthi Chari; Oshani Seneviratne; Prithwish Chakraborty; Pablo Meyer 001; Deborah L. McGuinness (CoRR, 2025)