Peptides: A Package for Data Mining of Antimicrobial Peptides. - Daniel Osório 004; Paola Rondón-Villarreal; Rodrigo Torres (R J., 2015)

minval: An R package for MINimal VALidation of Stoichiometric Reactions. - Daniel Osório 004; Janneth González; Andrés Pinzón Velasco (R J., 2017)

Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2. - James J. Cai; Daniel Osório 004 (ICCABS, 2020)

scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. - Daniel Osório 004; Yan Zhong 003; Guanxun Li; Jianhua Z. Huang; James J. Cai (Patterns, 2020)

Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. - Daniel Osório 004; James J. Cai (Bioinform., 2021)

g2f as a Novel Tool to Find and Fill Gaps in Metabolic Networks. - Daniel Osório 004; Kelly Botero; Andrés Pinzón Velasco; Nicolás Mendoza-Mejía; Felipe Rojas-Rodríguez; George E. Barreto; Janneth González (R J., 2021)

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. - Daniel Osório 004; Marieke L. Kuijjer; James J. Cai (Bioinform., 2022)

Interpretable multi-modal data integration. - Daniel Osório 004 (Nat. Comput. Sci., 2022)

scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. - Daniel Osório 004; Yan Zhong 003; Guanxun Li; Qian Xu; Yongjian Yang 003; Yanan Tian; Robert S. Chapkin; Jianhua Z. Huang; James J. Cai (Patterns, 2022)

Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data. - Daniel Osório 004; Anna Capasso; S. Gail Eckhardt; Uma Giri; Alexander Somma; Todd M. Pitts; Christopher H. Lieu; Wells A. Messersmith; Stacey M. Bagby; Harinder Singh; Jishnu Das; Nidhi Sahni; et al. (Nat. Comput. Sci., 2024)