Bar-Joseph studied computer science at Bachelor of Science (1997) and Master of Science (1999) level, both at the Hebrew University of Jerusalem. 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. Jaakkola. Following this, he was a postdoctoral associate at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) and the Whitehead Institute.
Bar-Joseph's research at Carnegie Mellon is primarily focused on developing computational methods to allow greater understanding of the interactions and dynamics of complex biological systems, particularly systems that change with time, such as the cell cycle.
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.