[2] He is Director of the European Molecular Biology Laboratory (EMBL) site in Heidelberg, in south-west Germany.

[2] He is on the board of editorial reviewers of Science,[5] and is a senior editor of the journal Molecular Systems Biology.

[6] In 2000, Bork was elected as a Member of the European Molecular Biology Organization,[7] and in 2008 he received the Nature "mid-career achievement" award for science mentoring in Germany.

[8] He was appointed a member of the German National Academy of Sciences Leopoldina in 2014.

[9] In 2021, Bork was awarded the Novozymes Prize "for developing groundbreaking, publicly available and integrative bioinformatic tools" by the Novo Nordisk Foundation[10].