Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). - Alexander Yermanos; Victor Greiff; Nike Julia Krautler; Ulrike Menzel; Andreas Dounas; Enkelejda Miho; Annette Oxenius; Tanja Stadler; Sai T. Reddy (Bioinform., 2017)

Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. - Erand Smakaj; Lmar Babrak; Mats Ohlin; Mikhail Shugay; Bryan S. Briney; Deniz Tosoni; Christopher Galli; Vendi Grobelsek; Igor D'Angelo; Branden J. Olson; Sai T. Reddy; Victor Greiff; et al. (Bioinform., 2020)

immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. - Cédric R. Weber; Rahmad Akbar; Alexander Yermanos; Milena Pavlovic; Igor Snapkov; Geir Kjetil Sandve; Sai T. Reddy; Victor Greiff (Bioinform., 2020)

ePlatypus: an ecosystem for computational analysis of immunogenomics data. - Tudor-Stefan Cotet; Andreas Agrafiotis; Victor Kreiner; Raphael Kuhn; Danielle Shlesinger; Marcos Manero-Carranza; Keywan Khodaverdi; Evgenios Kladis; Aurora Desideri Perea; Dylan Maassen-Veeters; Wiona Glänzer; Solène Massery; et al. (Bioinform., 2023)

TCR clustering by contrastive learning on antigen specificity. - Margarita Pertseva; Oceane Follonier; Daniele Scarcella; Sai T. Reddy (Briefings Bioinform., 2024)

PLMFit: benchmarking transfer learning with protein language models for protein engineering. - Thomas Bikias; Evangelos Stamkopoulos; Sai T. Reddy (Briefings Bioinform., 2025)