A benchmark for microRNA quantification algorithms using the OpenArray platform. - Matthew N. McCall; Alexander S. Baras; Alexander Crits-Christoph; Roxann Ingersoll; Melissa A. McAlexander; Kenneth W. Witwer; Marc K. Halushka (BMC Bioinform., 2016)

miRge 2.0 for comprehensive analysis of microRNA sequencing data. - Yin Lu; Alexander S. Baras; Marc K. Halushka (BMC Bioinform., 2018)

Adversarial U-net with spectral normalization for histopathology image segmentation using synthetic data. - Faisal Mahmood 001; Richard Chen 001; Daniel Borders; Gregory N. McKay; Kevan J. Salimian; Alexander S. Baras; Nicholas J. Durr (Digital Pathology, 2019)

Weakly Supervised Prostate Tma Classification Via Graph Convolutional Networks. - Jingwen Wang; Richard J. Chen; Ming Y. Lu; Alexander S. Baras; Faisal Mahmood 001 (ISBI, 2020)

Deep Adversarial Training for Multi-Organ Nuclei Segmentation in Histopathology Images. - Faisal Mahmood 001; Daniel Borders; Richard J. Chen; Gregory N. McKay; Kevan J. Salimian; Alexander S. Baras; Nicholas J. Durr (IEEE Trans. Medical Imaging, 2020)

Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples. - Andrew H. Song; Mane Williams; Drew F. K. Williamson; Guillaume Jaume; Andrew Zhang; Bowen Chen; Robert Serafin; Jonathan T. C. Liu; Alexander S. Baras; Anil V. Parwani; Faisal Mahmood 001 (CoRR, 2023)

Multimodal Prototyping for cancer survival prediction. - Andrew H. Song; Richard J. Chen; Guillaume Jaume; Anurag J. Vaidya; Alexander S. Baras; Faisal Mahmood 001 (ICML, 2024)

Computational methods and biomarker discovery strategies for spatial proteomics: a review in immuno-oncology. - Haoyang Mi; Shamilene Sivagnanam; Won Jin Ho; Shuming Zhang; Daniel Bergman; Atul Deshpande; Alexander S. Baras; Elizabeth M. Jaffee; Lisa M. Coussens; Elana J. Fertig; Aleksander S. Popel (Briefings Bioinform., 2024)

CEMIL: Contextual Attention Based Efficient Weakly Supervised Approach for Histopathology Image Classification. - Tawsifur Rahman; Alexander S. Baras; Rama Chellappa (WACV, 2025)

AI-driven 3D Spatial Transcriptomics. - Cristina Almagro-Pérez; Andrew H. Song; Luca L. Weishaupt; Ahrong Kim; Guillaume Jaume; Drew F. K. Williamson; Konstantin Hemker; Ming Y. Lu; Kritika Singh; Bowen Chen; Long Phi Le; Alexander S. Baras; et al. (CoRR, 2025)