Professor Vlahoviček won the EMBO Young Investigator Programme installation grant and has been running an internationally competitive research group in Croatia for past 18 years. He had several international appointments, including the 10-year stay at the International Center for Genetic Engineering in Trieste, Italy and a 4-year adjunct professorship at the University of Oslo, Norway. He also served a two-year mandate as a guest-professor at the university of Skövde, Sweden. His bioinformatics group develops computational tools and uses machine learning techniques to tackle open questions in developmental genomics and metagenomics.

He published his research in influential journals, including Nature, Cell, and PNAS, and his publications have been widely cited. He is a recipient of the National award for science and the Annual science award of the Croatian academy.

He has been a reviewer in a number of scientific journals, as well as national and international funding bodies and programmes, such as ESF Programme, EC FP7 Programme, EC H2020 Programme, Estonian National Funding Agency, Hungarian National Funding Agency, Flanders Research Foundation, The Netherlands ZonMw Vidi Programme, Croatian National Funding Agencies. He reviewed program applications for Croatian pre-accession and accession structural funds.