As of 2008[update], he is the Chief Technology Officer and Senior Vice President at Illumina. Prior to this position, he was a principal investigator and Senior Research Associate at the Stanford Genome Technology Center at Stanford University, focusing on developing analytical techniques for molecular diagnostics.
He is principal investigator for several grants including grants from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health  for the development of array-based Pyrosequencing.
In 1998, he described together with Pål Nyren and Mathias Uhlen  a solution-based variant of the pyrosequencing technology and co-founded Pyrosequencing AB (renamed to Biotage in 2003). He co-invented Molecular Inversion Probe assay and co-founded ParAllele BioScience to develop this multiplexed technology for genetic testing. ParAllele was acquired by Affymetrix in May 2005. In 2005, he co-founded NextBio, a search engine for life science data that was acquired by Illumina in 2013. He also serves on the board of directors of IntegenX and Aurora Biofuels. In 2008 he co-founded Avantome, a DNA sequencing company acquired by Illumina July 2008.
Among his approximately 50 peer-reviewed journal articles are the publications describing Pyrosequencing and Molecular Inversion Probe assays and other techniques:
- Absalan, F; Ronaghi, M (2007). "Molecular inversion probe assay". Methods in Molecular Biology. 396: 315–30. PMID 18025701. doi:10.1007/978-1-59745-515-2_20.
- Hardenbol, P; Banér, J; Jain, M; Nilsson, M; Namsaraev, EA; Karlin-Neumann, GA; Fakhrai-Rad, H; Ronaghi, M; Willis, TD; Landegren, U; Davis, RW (Jun 2003). "Multiplexed genotyping with sequence-tagged molecular inversion probes". Nature Biotechnology. 21 (6): 673–8. PMID 12730666. doi:10.1038/nbt821.
- "Prediction of protein orientation upon immobilization on biological and nonbiological surfaces". Proceedings of the National Academy of Sciences. 103 (40): 14773–8. Oct 2006. PMC . PMID 17001006. doi:10.1073/pnas.0605841103.
- Ronaghi, M (Jan 2001). "Pyrosequencing sheds light on DNA sequencing". Genome Research. 11 (1): 3–11. PMID 11156611. doi:10.1101/gr.11.1.3.
- Ronaghi, M; Uhlén, M; Nyrén, P (Jul 1998). "A sequencing method based on real-time pyrophosphate". Science. 281 (5375): 363–365. PMID 9705713. doi:10.1126/science.281.5375.363.
- Ronaghi, M; Karamohamed, S; Pettersson, B; Uhlén, M; Nyrén, P (Nov 1996). "Real-time DNA sequencing using detection of pyrophosphate release". Analytical Biochemistry. 242 (1): 84–9. PMID 8923969. doi:10.1006/abio.1996.0432.
He also holds about 20 patents.
- Illumina | 2008 Release: Illumina Appoints Mostafa Ronaghi as Senior Vice President and Chief Technology Officer
- genome.gov | 2004 Release: NHGRI Seeks Next Generation of Sequencing Technologies
- Ronaghi, M; Uhlén, M; Nyrén, P (Jul 1998). "A sequencing method based on real-time pyrophosphate". Science. 281 (5375): 363–365. PMID 9705713. doi:10.1126/science.281.5375.363
- Illumina | Illumina Signs Agreement to Acquire NextBio, Leader in Analyzing and Aggregating Complex Genomic Data
- tradingmarkets.com | 2008 Release: Illumina To Acquire Privately-Held Avantome For $25 Million In Cash Upfront
- [Pyrosequencing Array for DNA Sequencing]