Jeremy Schmutz

Jeremy SchmutzJeremy 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, Jeremy joined the newly formed Sequencing Group at the Stanford Human Genome Center to develop the computational infrastructure necessary for large scale DNA sequencing. Jeremy 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, Jeremy leads the Informatics and Production Sequencing Groups at the Genome Center and continues to work on genome sequencing projects of plants and fungi. He joined 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

The International Brachypodium Initiative. (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463 (7282): 763-768. (PDF)

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T ... Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. (2010). Genome sequence of the palaeopolyploid soybean. Nature. 463 (7278): 178-183. (PDF)

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J ... Mayer KF, Messing J, Rokhsar DS. (2009). The Sorghum bicolor genome and the diversification of grasses. Nature. 457 (7229): 551-6. (PDF)

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. (PDF)

Colosimo PF, Hosemann KE, Balabhadra S, Villareal G, Dickson M, Grimwood J, Schmutz J, Myers RM, Schluter D, Kingsley DM. (2005). Widespread parallel evolution of stickleback armor plates determined by ancestral genetic variation in Ectodysplasin. Science. 307: 1928- 1933. (PDF)

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. (PDF)

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

Grimwood J, Gordon LA, Terry A, Olsen A, Schmutz J ... Branscomb E, Rokhsar DS, Myers RM, Rubin EM, Lucas SM. (2004). The DNA sequence and biology of human chromosome 19. Nature. 428: 529-535. (PDF)

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. (PDF)

Stickney HL, Schmutz J, Woods IG, Holtzer CC, Dickson MC, Kelly PD, Myers RM, Talbot WS. (2002). Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 12: 1929-1934. (PDF)