36. Eldred, K.C., Avelis, C., Johnston, R.J., Jr.* and Roberts, E.* Modeling binary and graded cone cell fate patterning in the mouse retina.
bioRxiv 10.1101/650606  * indicates co-corresponding authors

35. Viets, K., Sauria, M., Chernoff, C., Rodriguez-Viales, R., Echterling,  M., Anderson, C., Tran, S., Dove, A., Goyal, R., Voortman, L., Gordus, A., Furlong, E., Taylor, J., and Johnston, R.J., Jr. Characterization of button loci that promote homologous chromosome pairing and cell-type-specific interchromosomal gene regulation.
Dev Cell, in press (bioRxiv 10.1101/445627)

34. Urban, E.A., and Johnston, R.J., Jr. (2018) Buffering and amplifying transcriptional noise during cell fate specification.
Front Genet, doi: 10.3389/fgene.2018.00591

33. Eldred, K.C., Hadyniak, S.E., Hussey, K.A., Brenerman, B., Zhang, P., Chamling, X., Sluch, V.M., Welsbie, D.S., Hattar, S., Taylor, J., Wahlin, K., Zack, D.J., and Johnston, R.J., Jr. (2018) Thyroid hormone signaling specifies cone subtypes in human retinal organoids.
Science, 362, 6411.

32. Datta, R.R., Ling. J, Ren, X., Xu, Z., Yucel, G., Yu, D., Moore, J., Baker, I., Kurland, J., Bulyk, M.L., Bishop, T., Struffi, P., Levina, R., Johnston, R., and Small, SJ. (2018) A Feed-forward Relay between Bicoid and Orthodenticle Regulates the Timing of Embryonic Patterning in Drosophila.
Genes Dev, 32, 723-736.

31. Duan, H., de Navas, L.F., Hu, F., Kailiang, S., Mavromatakis, Y.E., Viets., K., Zhou C., Kavaler, J., Johnston, R.J., Tomlinson, A., and Lai, E.C. (2018) The mir-279/996 cluster represses receptor tyrosine kinase signaling to determine cell fates in the Drosophila eye.
Development145, 7.

30. Anderson, C., Reiss, I., Zhou, C., Cho, A., Siddiqi, H., Morman, B., Aviles, C.M., Deford, P., Bergland, A., Roberts, E., Taylor, J., Vasiliauskas, D., and Johnston, R.J., Jr. (2017)
Natural variation in binding site affinity controls stochastic gene expression and color perception.
eLife, 6, e29593.

29. Yan, J., Anderson, C., Viets, K., Tran, S., Goldberg, G., Small, S., and Johnston, R.J., Jr. (2017)
Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies.
Development, 144, 844-855.

28. Viets, K.*, Eldred, K.C.*, and Johnston, R.J., (2016)
Mechanisms of photoreceptor patterning in vertebrates and invertebrates.
Trends Genet, 32, 638-659. * indicates equal contribution


27. Jukam, D., Viets, K., Anderson, C., Zhou, C., DeFord, P., Yan, J., Cao, J., and Johnston, R.J., Jr. (2016)
The insulator protein BEAF-32 is required for Hippo pathway activity in the terminal differentiation of neuronal subtypes.
Development, 143, 2389-2397.


26. Johnston, R.J., Jr., and Desplan, C. (2014)
Interchromosomal communication coordinates intrinsically stochastic expression between alleles.
Science, 343, 661-665.

25. Cochella, L., Tursun, B., Hsieh, Y.W., Galindo, S., Johnston, R.J., Chuang, C.F., and Hobert, O. (2014)
Two distinct types of neuronal asymmetries are controlled by the Caenorhabditis elegans zinc finger transcription factor die-1.
Genes Dev, 28, 34-43.

24. Hsiao, H.Y., Jukam, D., Johnston, R., and Desplan, C. (2013)
The neuronal transcription factor erect wing regulates specification and maintenance of Drosophila R8 photoreceptor subtypes.
Dev Biol, 381, 482s-490.

23. Johnston, R.J., Jr. (2013)
Lessons about terminal differentiation from the specification of color-detecting photoreceptors in the Drosophila retina.
Ann N Y Acad Sci, 1293, 33-44.

22. Thanawala, S.U., Rister, J., Goldberg, G.W., Zuskov, A., Olesnicky, E.C., Flowers, J.M., Jukam, D., Purugganan, M.D., Gavis, E.R., Desplan, C., and Johnston, R.J., Jr. (2013)
Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina.
Dev Cell, 25, 93-105.

21. Hsiao H.Y., Johnston, R.J., Jukam, D., Vasiliauskas, D., Desplan, C., and Rister, J. (2012)
Dissection and Immunohistochemistry of Larval, Pupal and Adult Drosophila Retinas.
J Vis Exp, 69, e4347.

20. Sood, P., Johnston, R.J., Jr., and Kussell, E. (2012)
Stochastic de-repression of Rhodopsins in single photoreceptors of the fly retina.
PLoS Comput Biol, 8, e1002357.

19. Vasiliauskas, D., Mazzoni, E.O, Sprecher, S.G., Brodetskiy, K., Johnston R.J., Jr., Lidder, P., Vogt, N., Celik, A., and Desplan, C. (2011)
Feedback from rhodopsin controls rhodopsin exclusion in Drosophila photoreceptors.
Nature, 479, 108-112.

18. Johnston, R.J., Jr.*, Otake, Y.*, Sood, P., Vogt, N., Behnia, R., Vasiliauskas, D., McDonald, E., Xie, B., Koenig, S., Wolf, R., Cook, T., Gebelein, B., Kussell, E., Nakagoshi, H., and Desplan, C. (2011)
Interlocked feedforward loops control cell-type-specific Rhodopsin expression in the Drosophila eye.
Cell, 145, 956-968. * indicates equal contribution

17. Johnston, R.J., Jr., and Desplan, C. (2010)
Stochastic mechanisms of cell fate specification that yield random or robust outcomes.
Annu Rev Cell Dev Biol, 26, 689-719.

16. Johnston, R.J., Jr., and Desplan, C. (2010)
A penetrating look at stochasticity in development.
Cell, 140, 610-612.

15. Vasiliauskas, D., Johnston, R., and Desplan, C. (2009)
Maintaining a stochastic neuronal cell fate decision.
Genes Dev, 23, 385-390.

14. Johnston, R.J., Jr., and Desplan, C. (2008)
Stochastic neuronal cell fate choices.
Curr Opin Neurobiol, 18, 20-27.

13. Mazzoni, E.O., Celik, A., Wernet, M.F., Vasiliauskas, D., Johnston, R.J., Cook, T.A., Pichaud, F., and Desplan, C. (2008)
Iroquois complex genes induce co-expression of rhodopsins in Drosophila.
PLoS Biol, 6, e97.

12. Sarin, S., O’Meara, M.M., Flowers, E.B., Antonio, C., Poole, R.J., Didiano, D., Johnston R.J., Jr., Chang, S, Narula, S., and Hobert, O. (2007)
Genetic screens for Caenorhabditis elegans mutants defective in left/right asymmetric neuronal fate specification.
Genetics, 176, 2109-2130.

11. Johnston, R.J., Jr., Copeland, J.W., Fasnacht, M., Etchberger, J.F., Liu, J., Honig, B., and Hobert, O. (2006) An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans.
Development, 133, 3317-3328.

10. Johnston, R.J., Jr., and Hobert, O. (2005)
A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA.
Development, 132, 5451-5460.

9. Johnston, R.J., Jr., Chang, S., Etchberger, J.F., Ortiz, C.O., and Hobert, O. (2005)
MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision.
Proc Natl Acad Sci USA, 102, 12449-12454.

8. Chang, S., Johnston, R.J., Jr., Frokjaer-Jensen, C., Lockery, S., and Hobert, O. (2004)
MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode.
Nature, 430, 785-789.

 7. Johnston, R.J., and Hobert, O. (2003)
A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans.
Nature, 426, 845-849.

6. Chang, S.*, Johnston, R.J., Jr.*, and Hobert, O (2003)
A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans.
Genes Dev, 17, 2123-2137. * indicates equal contribution

5. Hobert, O., Johnston, R.J., Jr., and Chang, S. (2002)
Left-right asymmetry in the nervous system: the Caenorhabditis elegans model.
Nat Rev Neurosci, 3, 629-640.

4. Melia, T.J., Weber, T., McNew, J.A., Fisher, L.E., Johnston, R.J., Parlati, F., Mahal, L.K., Sollner, T.H., and Rothman, J.E. (2002)
Regulation of membrane fusion by the membrane-proximal coil of the t-SNARE during zippering of SNAREpins.
J Cell Biol, 158, 929-940.

3. McNew, J.A., Parlati, F., Fukuda, R., Johnston, R.J., Paz, K., Paumet, F., Sollner, T.H., and Rothman, J.E. (2000)
Compartmental specificity of cellular membrane fusion encoded in SNARE proteins.
Nature, 407, 153-159.

2. McNew, J.A., Weber, T., Parlati, F., Johnston, R.J., Melia, T.J., Sollner, T.H., and Rothman, J.E. (2000)
Close is not enough: SNARE-dependent membrane fusion requires an active mechanism that transduces force to membrane anchors.
J Cell Biol, 150, 105-117.

1. Weber, T., Parlati, F., McNew, J.A., Johnston, R.J., Westermann, B., Sollner, T.H., and Rothman, J.E. (2000)
SNAREpins are functionally resistant to disruption by NSF and alphaSNAP.
J Cell Biol, 149, 1063-1072.