Jeffrey M Trimarchi

Assistant Professor
Jeffrey Trimarchi photo

Professor Trimarchi received his B.A. in Biology from Amherst College in 1993. In 2001 he received his Ph.D. from the Massachusetts Institute of Technology, where his mentor was Dr. Jacqueline Lees. He was a postdoctoral research fellow at Harvard Medical School, where his mentor was Dr. Constance Cepko. Dr. Trimarchi joined the Genetics, Development and Cell Biology Department faculty at Iowa State University in spring 2010.

Research Description

The goal of my laboratory is to develop a systems level understanding of the development and degeneration of neurons.  Single cell transcriptomics in conjunction with gain and loss of function experiments are utilized to identify the gene expression networks responsible for generating neuronal diversity in the developing mouse, zebrafish and chicken retina, specifically among the retinal ganglion cells. These data can be used to enhance the efficiency with which ganglion cells are generated for potential uses in therapies for optic neuropathies such as glaucoma. A second avenue of research in the lab uses the same single cell technology to examine motor neurons that are resistant to the disease-causing mechanisms of Amyotrophic Lateral Sclerosis (ALS).  These experiments will identify new potential drug targets for intervention in ALS patients.


  • Zhu W, Gramlich OW, Laboissonniere L, Sheffield VC, Trimarchi JM, Tucker BA and Kuehn MH (2016) Transplantation of iPSC-derived TM cells rescues glaucoma phenotypes in vivo, accepted at PNAS.
  • Mullally M*, Albrecht C*, Horton M, Laboissonniere LA, Goetz JJ, Chowdhury R, Manning A, Wester AK, Bose Q, and Trimarchi JM. (2016)  Expression profiling of developing zebrafish retinal cells, doi:10.1089/zeb.2015.1184. (special issue on zebrafish education).
    *these authors contributed equally to this work
  • Goetz JJ, Laboissonniere LA, Wester AK, Lynch MR, and Trimarchi JM (2016). Polo-Like Kinase 3 Appears Dispensable for Normal Retinal Development Despite Robust Embryonic Expression. PLoS One 11, e0150878.
  • Goetz JJ and Trimarchi JM (2015) Transcriptomic analyses of Onecut1 and Onecut2 deficient retinas, Genomics Data, doi:10.1016/j.gdata.2015.03.010.
  • Goetz JJ, Martin GM, Chowdhury, R and Trimarchi JM.  (2014) Onecut transcription factors play overlapping and distinct roles in the developing and mature retina, PLoS ONE 9, e110194.
  • Chew, KS, Schmidt, TM, Rupp, AC, Kofuji, P, and Trimarchi, JM. (2014). Loss of gq/11 genes does not abolish melanopsin phototransduction. PLoS ONE 9, e98356.
  • Goetz JJ, Farris, C, Chowdhury, R and Trimarchi JM. (2014) Making of a retinal cell: Insights into retinal cell fate determination, Int. Review of Cell and Mol. Biology, 308, 273-321.
  • Mizeracka K, Trimarchi JM, Stadler MB, and Cepko CL. (2013). Analysis of gene expression in wild type and Notch1 mutant cells by single cell profiling, Dev. Dyn. doi 10.1002/dvdy.24006.
  • Emerson MM, Surzenko N, Goetz JJ, Trimarchi JM, and Cepko CL. (2013).  Otx2 and onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors, Dev.Cell. 26:59-72.
  • Farris, C and Trimarchi JM. (2013).  Plasma-seq: A novel strategy for metastatic prostate cancer analysis,  Genome Medicine. 5:35.
  • Goetz JJ and Trimarchi JM. (2012).  Transcriptome sequencing of single cells with SMART-Seq, Nat. Biotechnol. 30:763-5.
  • Goetz JJ and Trimarchi JM. (2012).  Single-cell profiling of developing and mature retinal neurons, J Vis Exp,  pii: 3824. doi: 10.3791/3824.
  • Hafler BP, Surzenko N, Beier K, Punzo C, Trimarchi J, Kong J, and Cepko CL.  (2012).  Olig2 defines subpopulations of retinal progenitor cells biased towards specific cell fates, Proc. Natl. Acad. Sci. U S A. 109:7882-7.
  • McEvoy J, Flores-Otero J, Zhang J, Nemeth K, Brennan R, Bradley C, Krafcik F, Rodriguez-Galindo C, Wilson M, Xiong S, Lozano G, Sage J, Fu L, Louhibi L, Trimarchi J, Pani A, Smeyne R, Johnson D, and Dyer MA. (2011). Coexpression of normally incompatible developmental pathways in retinoblastoma genesis, Cancer Cell 20:260-75.
  • Cherry, TJ, Trimarchi, JM, Stadler, M, And Cepko, CL.  (2009). Development and diversification of retinal amacrine interneurons at single cell resolution, Proc. Natl. Acad. Sci. U S A. 106:9495-9500.
  • Trimarchi, JM*, Cho, S*, and Cepko, CL.  (2009) Identification of genes expressed preferentially in the developing peripheral margin of the optic cup, Dev. Dyn., doi:10.1002/dvdy.21973. *these authors contributed equally to this work
  • Trimarchi, JM*, Harpavat, S*, Billings, NA, and Cepko CL.  (2008) Thyroid hormone components are expressed in three sequential waves during development of the chick retina, BMC Dev Biol, 8:101. *these authors contributed equally to this work
  • Kanadia, RN, Clark, VE, Punzo, C, Trimarchi, JM, and Cepko, CL.  (2008) Temporal requirement of the alternative splicing factors Sfrs1 for the survival of retinal neurons, Development ePress doi: 10.1242/dev.024620.
  • Nygaard, V, Liu, F, Holden, M., Kuo, WP, Trimarchi, J, et al.  (2008)  Validation of oligoarrays for quantitative exploration of the transcriptome.  BMC Genomics 9:258.
  • Trimarchi JM, Stadler, M, and Cepko CL. (2008) Individual retinal progenitor cells display extensive heterogeneity of gene expression.  PlosOne, 3:e1588.
  • Roesch, K, Jadhav, AP, Trimarchi, JM, Stadler, MB, Roska B , Sun, BB, and Cepko CL. (2008) The Transcriptome of Retinal Muller Glial Cells, J. Comp. Neurol., 509:225-238.
  • Kim, D, Ross, S, Trimarchi, JM, Aach, J, Greenberg, M, and Cepko, CL. (2008) Identification of molecular markers of bipolar cells in the murine retina, J.Comp.Neurol.  507:1795-1810.
  • Liu, F, Jenssen, TK, Trimarchi, J, Punzo, C et al. (2007).  Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.  BMC Genomics.  8:153.
  • Trimarchi JM, Stadler, M, Roska, B, Billings N, Sun, B, Bartch, B and Cepko CL. (2007) Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling.  J Comp Neurology, 502:1047-1065. *this paper is highlighted by the Faculty of 1000.
  • Galante, PA, Trimarchi, J, Cepko, CL, de Souza, SJ, Ohno-Machado, L and Kuo, WP.  (2007).  Automatic correspondence of tags and genes (ACTG):  A tool for the analysis of SAGE, MPSS and SBS data.  Bioinformatics.  23:903-905.
  • Kuo WP, Liu F, Trimarchi J, Punzo C, et al. (2006).  A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies.  Nat Biotechnol. 24:832-840.
  • Kuo WP, Kim EY, Trimarchi J, Jenssen TK, Vinterbo SA and Ohno-Machado L.  (2004).  A primer on gene expression and microarrays for machine learning researchers.  J Biomed Inform. 37:293-303.
  • Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho S, Yung R, Asch E, Ohno-Machado  L, Wong WH and Cepko CL. (2004). Genomic analysis of mouse retinal development.  PLOS biology 2:1411-1431.
  • Trimarchi JM and Lees JA.  (2002).  Sibling rivalry in the E2F family. Nature Reviews Molecular Cell Biology. 3:11-20.
  • Trimarchi JM, Courel M, Wen J, Fairchild B, and Lees JA.  (2001).  E2F-6 is a component of the Bmi-1 containing polycomb complex.  Proc. Natl. Acad. Sci. U S A. 98:1519-1524.
  • Humbert PO, Rogers C, Ganiatsas S, Landsberg RL, Trimarchi JM, Dandapani S, Brugnara C, Erdman S, Schrenzel M, Bronson RT, and Lees JA. (2000).  E2F4 is essential for normal erythrocyte maturation and neonatal viability.  Mol. Cell.  6:281-291.
  • Humbert PO, Verona R, Trimarchi JM, Rogers C, Dandapani S, and Lees JA  (2000).  E2f3 is critical for normal cellular proliferation.  Genes Dev. 14:690-703.
  • Trimarchi JM, Fairchild B, Verona R, Moberg K, Andon N, and Lees JA. (1998).  E2F-6, a member of the E2F family that can behave as a transcriptional repressor. Proc. Natl. Acad. Sci. U S A. 95:2850-5.
  • Foster PL, Trimarchi JM, and Maurer RA. (1996).  Two enzymes, both of which process recombination intermediates, have opposite effects on adaptive mutation in Escherichia coli. Genetics. 142:25-37.
  • Foster PL and Trimarchi JM. (1995).  Conjugation is not required for adaptive reversion of an episomal frameshift mutation in Escherichia coli.  J Bacteriol. 177:6670-1.
  • Foster PL, Gudmundsson G, Trimarchi JM, Cai H, and Goodman MF. (1995).  Proofreading-defective DNA polymerase II increases adaptive mutation in Escherichia coli.  Proc. Natl. Acad. Sci. U S A. 92:7951-5.
  • Foster PL and Trimarchi JM. (1995).  Adaptive reversion of an episomal frameshift mutation in Escherichia coli requires conjugal functions but not actual conjugation.  Proc. Natl. Acad. Sci. U S A. 92:5487-90.
  • Foster PL and Trimarchi JM.  (1994).  Adaptive reversion of a frameshift mutation in Escherichia coli by simple base deletions in homopolymeric runs.  Science. 265:407-9.
Area of Expertise: 
Development and Degeneration of Neurons
B.A. Biology, Amherst College, 1993
Ph.D., Biology, Massachusetts Institute of Technology, 2001
2114 Molecular Biology