TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. - Samuel Sledzieski; Chengchen Zhang; Ion I. Mandoiu; Mukul S. Bansal (PSB, 2021)

virDTL. - Sumaira Zaman; Samuel Sledzieski; Bonnie Berger; Yi-Chieh Wu; Mukul S. Bansal (Zenodo, 2021)

Topsy-Turvy: integrating a global view into sequence-based PPI prediction. - Rohit Singh 001; Kapil Devkota; Samuel Sledzieski; Bonnie Berger; Lenore Cowen (Bioinform., 2022)

virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. - Sumaira Zaman; Samuel Sledzieski; Bonnie Berger; Yi-Chieh Wu; Mukul S. Bansal (J. Comput. Biol., 2023)

TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions. - Samuel Sledzieski; Kapil Devkota; Rohit Singh 001; Lenore Cowen; Bonnie Berger (Bioinform., 2023)

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. - Samuel Sledzieski; Charlotte Versavel; Rohit Singh 001; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski; Hollie Putnam; Bonnie Berger; et al. (RECOMB, 2025)