ReFHap: a reliable and fast algorithm for single individual haplotyping. - Jorge Duitama; Thomas Huebsch; Gayle McEwen; Eun-Kyung Suk; Margret R. Hoehe (BCB, 2010)

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. - Jorge Duitama; Pramod Kumar Srivastava; Ion I. Mandoiu (ICCABS, 2011)

Workshop: Bioinformatics pipeline for fosmid based molecular haplotype sequencing. - Jorge Duitama; Eun-Kyung Suk; Sabrina Schulz; Gayle McEwen; Thomas Huebsch; Margret R. Hoehe (ICCABS, 2011)

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. - Jorge Duitama; Justin Kennedy; Sanjiv Dinakar; Yözen Hernández; Yufeng Wu; Ion I. Mandoiu (BMC Bioinform., 2011)

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. - Sergio Pulido-Tamayo; Jorge Duitama; Kathleen Marchal (Nucleic Acids Res., 2016)

NGSEP3: accurate variant calling across species and sequencing protocols. - Daniel Tello; Juanita Gil; Cristian D. Loaiza; John J. Riascos; Nicolás Cardozo; Jorge Duitama (Bioinform., 2019)

FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data. - Fabio Herrera-Rocha; Miguel Fernández-Niño; Jorge Duitama; Mónica P. Cala; María José Chica; Ludger A. Wessjohann; Mehdi D. Davari; Andrés Fernando González Barrios (J. Cheminformatics, 2024)