Education & Training
- B.S. Symbolic Systems, Stanford University, 2000
- M.S. Computer Science, Stanford University, 2002
- Ph.D. Genomics and Computational Biology, University of Pennsylvania, 2009
Research Interest Summary
How does a fertilized egg know how to develop? For most animals and plants, the genetic instructions that guide early embryogenesis are inherited as RNA. During a short window of development, these RNA coordinate all cellular activity, including the processes that induce the first rounds of transcription from the embryonic genome. Eventually those maternally inherited RNA are destroyed, as newly transcribed embryonic RNA assume control of the embryo. This period of development is called the maternal-to-zygotic transition.
Maternally inherited RNA encode the instructions to reprogram an egg into pluripotent embryonic cells, the precursors to all cell types in the adult organism. Thus, we study eggs and their RNA to better understand the mechanisms underlying cellular identity and pluripotency, and how they have evolved. Our tool kit includes classical genetics and embryology in zebrafish, and high-throughput experimental and computational genomics across animals.
Yartseva V, Takacs CM, Vejnar CE, Lee MT‡, Giraldez AG‡. 2017. RESA identifies mRNA regulatory sequences with high resolution. Nature Methods 14, 201-207.
Reischauer S, Stone O, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsio J, Luo S, Tworus D, Augustine SA, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DY. 2016. Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Nature 535(7611), 294-8.
Lee MT#‡, Bonneau AR#, Giraldez AJ‡. Zygotic genome activation during the maternal-to-zygotic transition. 2014. Annu Rev Cell Dev Biol 30(1), 18.1-18.33.
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. 2014. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33(9), 981-993.
Lee MT#, Bonneau AR#, Takacs CM, Bazzini AB, DiVito KR, Fleming ES, Giraldez AJ. 2013. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 503(7476), 360-364.
Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim, TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. 2012. Quantitative biology of single neurons. J R Soc Interface 9(77), 3165-3183.
Bazzini AA#, Lee MT#, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078), 233-237.
Buckley PT#, Lee MT#, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J. 2011. Cytoplasmic intron retention provides multiple mechanisms for localizing dendritic mRNAs. Neuron 69(5), 877-884.
Lee MT, Kim J. 2008. Self containment, a property of modular RNA structures, distinguishes microRNAs. PLoS Comput Biol 4(8), e1000150.