In 2007 she joined the Institute of Molecular Oncology at the Biomedical Sciences Research Center “Alexander Fleming” as a Principal Investigator (Researcher C from 2007 -2008 and Researcher B from 2008 until today) . In the same year she was elected as an Adjunct Assistant Professor of the Department of Computer and Information Science at the School of Engineering of the University of Pennsylvania.
Recently (2009) she got elected as a Full Professor of Bioinformartics at the Department of Computer and Communication at the University of Thessaly. Currently she is teaching the 'Introduction to Bioinformatics' at the undergraduate level at the university of Thessaly and at the graduate level in the Master program “Technology of Computer Sciences in Medicine and Biology" from the Department of Informatics and Telecommunication at the National and Kapodistrian University of Athens.

Artemis Hatzigeorgiou is the co-author of the Stuttgart Neural Network Simulator (SNNS) , a world wide used (with more than 1000 registered users) open-source software for the simulation of Artificial Neural Networks. In 2003 she developed DIANA-microT, one of the first published microRNA target prediction programs worldwide. She has published in top tier journals as Nature, Science, Proc. Nat. Acad. Sci. USA, Am J. Hum. Genet., Genes Dev. , Nat. Methods, Gen. Research. Her works are cited more than 2,700 times according to the ISI Web of Knowledge (h- index 19) .
She has served as a reviewer panelist for the National Science Foundation and the National Institute of Health at the USA, for the Seventh Framework Program (FP7) of the European Community and at the General Secretary for Research and Technology in Greece. She is since 1996 the co-founder of the computer science company Synaptic, Ltd, located at Herakleion, Crete.