Marijo Šimunović, Lovro Vrček, Mile Šikić, Anton Bankevich (2026). GNNome-Decision: Enhancing GNN Training for de Novo Genome Assembly by Targeting Decision Nodes. In BMC Bioinformatics.

Martin Schmitz, Lovro Vrček, Kenji Kawaguchi, Mile Šikić (2026). DipGNNome: Diploid de Novo Genome Assembly with Geometric Deep Learning and Beam-Search. In RECOMB-CG.

Martin Schmitz, Lovro Vrček, Kenji Kawaguchi, Mile Šikić (2026). GNNome-Decision: Enhancing GNN Training for de Novo Genome Assembly by Targeting Decision Nodes. In RECOMB-CG.

Maxime Rochkoulets, Lovro Vrček, Mile Šikić (2026). Entropy, Disagreement, and the Limits of Foundation Models in Genomics. Poster at LMRL workshop @ ICLR 2026.

Prasad Sarashetti, Josipa Lipovac, Qi Jia, Ling Wang, Zhe Li, Lovro Vrček, Ying Chen, Fei Yao, YY Sia, Dehui Lin, Xinyi Zhang, Daniel Muliaditan, Hwee Meng Low, See Ting Leong, Chiea Chuen Khor, Eleanor Wong, Weiling Zheng, Kresimir Krizanovic, John C Chambers, William Y K Hwang, Patrick Tan, Jonathan Göke, Mile Sikic, Jianjun Liu (2025). A Complete Telomere-to-Telomere Diploid Reference Genome for South Asian Population. bioRxiv preprint.

Lovro Vrček, Xavier Bresson, Thomas Laurent, Martin Schmitz, Kenji Kawaguchi, Mile Šikić (2025). Geometric deep learning framework for de novo genome assembly. Genome Research, 35(4).

Marijo Šimunović, Lovro Vrček, Mile Šikić (2023). Graph Neural Network Meets de Bruijn Genome Assembly. In ISPA 2023.

Steven Lindner, Ivor Lončarić, Lovro Vrček, Maite Alducin, J. Iñaki Juaristi, Peter Saalfrank (2023). Femtosecond Laser-Induced Desorption of Hydrogen Molecules from Ru(0001): A Systematic Study Based on Machine-Learned Potentials. The Journal of Physical Chemistry C.

Lovro Vrček, Xavier Bresson, Thomas Laurent, Martin Schmitz, Mile Šikić (2023). Reconstruction of short genomic sequences with graph convolutional networks. In 46th MIPRO ICT and Electronics Convention (MIPRO).

Lovro Vrček, Petar Veličković, Mile Šikić (2020). A step towards neural genome assembly. Poster at LMCA workshop @ NeurIPS 2020.

Lovro Vrček, Megan Hong Hui Huang, Robert Vaser, Mile Šikić (2020). Deep learning approach to determining the type of long reads. Poster at ISMB 2020 - MLCSB COSI.

Lovro Vrček, Mile Šikić (2020). Supervised learning approach to long read classification. Poster at IWDS 2019.