Jeremy Schmutz
Investigator

Jeremy Schmutz began programming computers when he was five years old. He graduated from North Central College in three years with a B.S. in computer science and a B.A. in biology. During college, he worked on DNA sequencing technology at Argonne National Laboratory that led to his first research position developing parallel sequencing systems at a small silicon valley startup company. In 1996, Schmutz joined the newly formed sequencing group at the Stanford Human Genome Center (SHGC) to develop the computational infrastructure necessary for large scale DNA sequencing. Schmutz and his group finished and assembled the human sequence of chromosomes 5, 16 and 19. He also led the quality assessment of the human genome sequence that evaluated the accuracy and completeness of the final human genome sequence. Currently, Schmutz leads the informatics and production sequencing groups at the SHGC and continues to work on genome sequencing projects of plants and fungi. He joins HudsonAlpha in 2008.

Research interests

• Whole genome sequencing and assembly
• Constructing complex data collection and analysis systems in order to answer specific scientific questions
• Genomic changes in populations in response to selective environmental pressures
• Understanding the structural organization of genomes through comparative analysis of the genomes of related species

Selected publications
Stickney, H. L., Schmutz J., Woods, I. G., Holtzer C. C., Dickson, M. C., Kelly, P. D., Myers, R. M. and Talbot, W. S. (2002). Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 12: 1929-1934.

MGC Program Team. (2002). Generation and initial analysis of more than 14,000 non-redundant, full-length human and mouse cDNA sequences by the NIH Mammalian Gene Collection Program. Proc. Natl. Acad. Sci. USA. 99: 16899-16903.

Grimwood, J., Gordon, L.A., Terry, A., Olsen, A., Schmutz, J.,..., Branscomb, E., Rokhsar, D. S., Myers, R. M., Rubin, E. M., and Lucas, S. M. (2004) The DNA sequence and biology of human chromosome 19. Nature. 428: 529-535.

Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM. (2004). Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res. 14, 2397-405.

Schmutz, J., Wheeler, J., Grimwood, J., Dickson, M., ..., and Myers, R. M. (2004) Quality assessment of the human genome sequence. Nature. 429: 365-368.

Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, ..., Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM and Rubin EM. (2004). The DNA sequence and comparative analysis of human chromosome 5. Nature 431:268-274.

Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villareal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D. and Kingsley, D. M. (2005) Widespread parallel evolution of stickleback armor plates determined by ancestral genetic variation in Ectodysplasin. Science. 307: 1928-1933.

Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsen U, ... Schmutz J, ... Rokhsar D. (2006) The genome of black cottonwood, Populus trichocarpa (Torr, & Gray). Science 313, 1596-1604.

Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis, Nature Biotechnology 25: 319-326.

Palenik B, Grimwood J, Aerts A …. Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV (2007). The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PNAS 104: 7705-7710.