EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures. - Dario Ghersi; Roberto Sanchez (Bioinform., 2009)

SITEHOUND-web: a server for ligand binding site identification in protein structures. - Marylens Hernandez; Dario Ghersi; Roberto Sanchez (Nucleic Acids Res., 2009)

Disentangling function from topology to infer the network properties of disease genes. - Dario Ghersi; Mona Singh 001 (BMC Syst. Biol., 2013)

molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. - Dario Ghersi; Mona Singh 001 (Bioinform., 2014)

A novel approach to identify shared fragments in drugs and natural products. - Akshay Balasubramanya; Ishwor Thapa; Dhundy Bastola; Dario Ghersi (BIBM, 2015)

Genome-Wide Detection and Analysis of Multifunctional Genes. - Yuri Pritykin; Dario Ghersi; Mona Singh 001 (PLoS Comput. Biol., 2015)

Forecasting the Spread of Mosquito-Borne Disease using Publicly Accessible Data: A Case Study in Chikungunya. - Kathryn M. Cooper; Dhundy Bastola; Robin A. Gandhi; Dario Ghersi; Steven H. Hinrichs; Marsha Morien; Ann L. Fruhling (AMIA, 2016)

Recovering Bound Forms of Protein Structures Using the Elastic Network Model and Molecular Interaction Fields. - Dario Ghersi; Roberto Sanchez (BCB, 2016)

In-silico analysis of the "memory anti-Naïve" effect in anti-viral cross-reactive responses. - Filippo Castiglione; Dario Ghersi; Franco Celada (BIBM, 2017)

Analyzing T cell receptor alpha/beta usage in binding to the pMHC. - Ryan Ehrlich; Dario Ghersi (BIBM, 2017)

Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations. - Dario Ghersi; Abhishek Parakh; Mihaly Mezei (J. Comput. Chem., 2017)

Two critical positions in zinc finger domains are heavily mutated in three human cancer types. - Daniel Munro; Dario Ghersi; Mona Singh 001 (PLoS Comput. Biol., 2018)

Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage. - Qianran Li; Dario Ghersi; Ishwor Thapa; Ling Zhang; Hesham Ali 001; Kate Cooper 001 (BIBM, 2019)

FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis. - Matthew L. Hale; Ishwor Thapa; Dario Ghersi (BMC Bioinform., 2019)

Uncovering and characterizing splice variants associated with survival in lung cancer patients. - Sean West; Sushil Kumar; Surinder K. Batra; Hesham Ali 001; Dario Ghersi (PLoS Comput. Biol., 2019)

Cluster Analysis of Biological Networks. - Asuda Sharma; Hesham Ali 001; Dario Ghersi (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Biological Pathway Data Formats and Standards. - Ramakanth Chirravuri Venkata; Dario Ghersi (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Biological Pathway Analysis. - Ramakanth Chirravuri Venkata; Dario Ghersi (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

MeSH Indexing Using the Biomedical Citation Network. - William Gasper; Parvathi Chundi; Dario Ghersi (BCB, 2020)

Measurement of structural change in co-expression networks from cancer gene expression data. - Qianran Li; Dario Ghersi; Ishwor Thapa; Ling Zhang; Hesham Ali 001; Kate Cooper 001 (Int. J. Data Min. Bioinform., 2020)

NEEP: null empirically estimated p-values for high-throughput molecular survival analysis. - Sean West; Hesham Ali 001; Dario Ghersi (J. Open Source Softw., 2020)

Automatic Extension of Medical Subject Headings (MeSH) Thesaurus to Emerging Research. - William Gasper; Jiahao Ma; Dario Ghersi; Etienne Z. Gnimpieba; Venkataramana Gadhamshetty; Parvathi Chundi (BIBM, 2021)

SwarmTCR: a computational approach to predict the specificity of T cell receptors. - Ryan Ehrlich; Larisa Kamga; Anna Gil; Katherine Luzuriaga; Liisa K. Selin; Dario Ghersi (BMC Bioinform., 2021)

Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data. - William Gasper; Francesca Rossi 003; Matteo Ligorio; Dario Ghersi (PLoS Comput. Biol., 2022)

VIPER: Virus Inhibition Via Peptide Engineering and Receptor Mimicry. - Anna Sophie Klingenberg; Dario Ghersi (J. Comput. Biol., 2025)

TRain: T-cell receptor automated immunoinformatics. - Austin Seamann; Maia Bennett-Boehm; Ryan Ehrlich; Anna Gil; Liisa K. Selin; Dario Ghersi (BMC Bioinform., 2025)