Mark Emerson

Assistant Professor

Main Affiliation








Mark Emerson


Dr. Emerson investigates the gene regulatory networks that are involved in the formation of vertebrate cone photoreceptors during development. The Emerson lab uses cis-regulatory assays, imaging, and next-generation sequencing approaches to uncover the basic processes involved in the development of the vertebrate retina. The long-term goals of his research team are to leverage this information for the development of therapies for human blindness and to uncover the genetic changes that underlie the evolution of visual systems.


Postdoctoral Fellow, Harvard Medical School 2006-2012

Ph.D. in Neuroscience, Harvard University, 2005

B.A. in Neuroscience, Oberlin College, 1997


Courses Taught

Biology 379, Developmental Neurobiology

Biology 206, Introduction to Genetics

Biology/Neuroscience, Graduate Neuroscience I

Biology, Graduate Genetics



Ghinia Tegla MG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM. (2020) OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification. Elife 9. pii: e54279


Patoori S, Jean-Charles N, Gopal A, Sulaiman S, Gopal S, Wang B, Souferi B, Emerson MM. (2020) Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells. Neural Development 15: 5.


Schick E, McCaffery SD, Keblish EE, Thakurdin C, Emerson MM. (2019) Lineage tracing analysis of cone photoreceptor-associated cis-regulatory elements in the developing chicken retina. Scientific Reports 9: 9358.


Buenaventura DF, Corseri A, Emerson MM. (2019) Identification of genes with enriched expression in early developing mouse cone photoreceptors. Investigative Ophthalmology & Visual Science 60(8): 2787-2799.


Souferi B, Emerson MM. (2019). Quantitative analysis of the ThrbCRM1-centered gene regulatory network. Biology Open, 8(4): 039115.


Jean-Charles N, Buenaventura DF, Emerson MM (2018) Identification and characterization of early photoreceptor cis-regulatory elements and their relation to Onecut1. Neural Development 13(1): 26.


Buenaventura DF, Ghinia-Tegla MG, Emerson MM (2018) Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells. Developmental Biology 443(1): 35-49.


Zhou J, Benito-Martin A, Mighty J, Chang L, Ghoroghi S, Wu H, Wong M, Guariglia S, Baranov P, Young M, Gharbaran R, Emerson M, Mark MT, Molina H, Canto-Solar MV, Selgas HP, Redenti S (2018). Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA, and membrane proteins. Scientific Reports 8(1): 2823.


Wang S, Sengel C, Emerson MM, Cepko CL (2014). A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. Developmental Cell 30(5): 513-527.


Emerson MM, Surzenko N, Goetz JJ, Trimarchi J, Cepko CL. (2013) Otx2 and Onecut1 Promote the Fates of Cone Photoreceptors and Horizontal Cells and Repress Rod Photoreceptors. Developmental Cell. 26(1):



Emerson, MM, Long, JB, Van Vactor, D. (2013) Drosophila semaphorin2b is Required for the Axon Guidance of a Subset of Embryonic Neurons. Developmental Dynamics. 242(7): 861-73.


Emerson, MM, Cepko CL. (2011) Identification of a Retina-specific Otx2 Enhancer Element Active in Immature Developing Photoreceptors. Developmental Biology. 360 (1): 241-255.


Billings, NA, Emerson MM, Cepko CL. (2010) Analysis of Thyroid Response Element Activity During Retinal Development. PLoS One. 5 (10): e13739.


*Samson M, *Emerson MM, Cepko CL. (2009) Robust marking of photoreceptor cells and pinealocytes with several reporters under control of the Crx gene. Developmental Dynamics. 238(12):3218-25.


Gates J, Mahaffey JP, Rogers SL, Emerson M, Rogers EM, Sottile SL, Van Vactor D, Gertler FB, Peifer M. (2007) Enabled plays key roles in embryonic epithelial morphogenesis in Drosophila. Development, 134(11):2027-39.


Ashmore LJ, Sathyanarayanan S, Silvestre DW, Emerson MM, Schotland P, Sehgal A. (2003) Novel insights into the regulation of the timeless protein. Journal of Neuroscience, 23(21), 7810-19.


*Wills Z, *Emerson M, Rusch J, Bikoff J, Baum B, Perrimon N, Van Vactor D. (2002) A Drosophila homolog of cyclase-associated proteins collaborates with the Abl tyrosine kinase to control midline axon pathfinding. Neuron, 36(4), 611-22.


*Yang Z, *Emerson M, Su HS, Sehgal A. (1998) Response of the timeless protein to light correlates with behavioral entrainment and suggests a nonvisual pathway for circadian photoreception.  Neuron 21(1), 215-23.


Ousley A, Zafarullah K, Chen Y, Emerson M, Hickman L, Sehgal A. (1998)  Conserved regions of the timeless (tim) clock gene in Drosophila analyzed through phylogenetic and functional studies.  Genetics 148(2), 815-25.

Additional Information