He gained his PhD from the Massachusetts Institute of Technology in computer science in 2003, under the supervision of David K. Gifford and Tommi S.

[1] Following this, he was a postdoctoral associate at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) and the Whitehead Institute.

[3][12] At MIT, Bar-Joseph's group developed a novel algorithm to discover regulatory networks of gene modules in yeast.

These modules are groups of genes that work together to perform tasks such as respiration, protein synthesis and response to external stress.

[16] He co-chaired the Research in Computational Molecular Biology (RECOMB) conference in 2009 and 2010 and joined the board of the journal Bioinformatics as an Associate Editor in 2013.