COCONUT online: Collection of Open Natural Products database. - Maria Sorokina; Peter Merseburger; Kohulan Rajan; Mehmet Aziz Yirik; Christoph Steinbeck (J. Cheminformatics, 2021)

MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle. - Mehmet Aziz Yirik; Maria Sorokina; Christoph Steinbeck (J. Cheminformatics, 2021)

Chemical graph generators. - Mehmet Aziz Yirik; Christoph Steinbeck (PLoS Comput. Biol., 2021)

Surge: a fast open-source chemical graph generator. - Brendan D. McKay; Mehmet Aziz Yirik; Christoph Steinbeck (J. Cheminformatics, 2022)

Generation of weighted trees, block trees and block graphs. - Tínaz Ekim; Mordechai Shalom; Mehmet Aziz Yirik (CoRR, 2024)

ChemReservoir - An Open-Source Framework for Chemically-Inspired Reservoir Computing. - Mehmet Aziz Yirik; Jakob Lykke Andersen; Rolf Fagerberg; Daniel Merkle (CoRR, 2025)