MetaFlow: an interactive user-friendly workflow for automated analysis of whole genome shotgun sequencing metagenomic data. - Usama Bakry; Mohamed Fares; Ali Kishk; Mohamed El-Hadidi (BIBM, 2018)

AmpliconNet: Sequence Based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation. - Ali Kishk; Mohamed El-Hadidi (BIBM, 2018)

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research. - Judit Kumuthini; Lyndon Zass; Sumir Panji; Samson P. Salifu; Jonathan K. Kayondo; Victoria Nembaware; Mamana Mbiyavanga; Ajayi Olabode; Ali Kishk; Gordon Wells; Nicola J. Mulder (BMC Bioinform., 2019)

Project-based learning course on metabolic network modelling in computational systems biology. - Thomas Sauter; Tamara Bintener; Ali Kishk; Luana Presta; Tessy Prohaska; Daniel Guignard; Ni Zeng; Claudia Cipriani; Sundas Arshad; Thomas Pfau; Patricia Martins Conde; Maria Pires Pacheco (PLoS Comput. Biol., 2022)

Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas. - Ali Kishk; Maria Pires Pacheco; Tony Heurtaux; Thomas Sauter (Briefings Bioinform., 2024)