1. Cai, A.Q., Radtke, K., Linville, A., Lander, A.D., Nie, Q., and Schilling, T.F. (2012). Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development 139, 2150-2155. PMCID 3357909. This work combines experiments and modeling to reveal the regulatory roles played by cellular retinoic acid binding proteins during development.
2. Cardarelli, F., Lanzano, L., and Gratton, E. (2012). Capturing directed molecular motion in the nuclear pore complex of live cells. Proc Natl Acad Sci U S A 109, 9863-9868. PMCID 3382504. This work leverages fluorescence dynamics to elucidate that paths and rates of motion of molecules as they go through nuclear pores.
3. Chan, C., Liu, X., Wang, L., Bardwell, L., Nie, Q., and Enciso, G. (2012). Protein scaffolds can enhance the bistability of multisite phosphorylation systems. PLoS Comput Biol 8, e1002551. PMCID 3380838. This work elucidates how scaffolds and compartments contribute to signaling specificity within cells.
4. Gokoffski, K.K., Wu, H.H., Beites, C.L., Kim, J., Kim, E.J., Matzuk, M.M., Johnson, J.E., Lander, A.D., and Calof, A.L. (2011). Activin and GDF11 collaborate in feedback control of neuroepithelial stem cell proliferation and fate. Development 138, 4131-4142. PMCID:3171217. This work shows how two secreted feedback factors control lineage branching in a neural epithelium.
5. Gordon, E.A., Whisenant, T.C., Zeller, M., Kaake, R.M., Gordon, W.M., Krotee, P., Patel, V., Huang, L., Baldi, P., and Bardwell, L. (2013). Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. Cell Signal 25, 2518-2529. NIHMSID 526352. This work, a collaboration between Cell Biology and Computer Science groups, used computational techniques to identify and validate new MAP kinase substrates.
6. Hinde, E., Cardarelli, F., Digman, M.A., and Gratton, E. (2010). In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow. Proc Natl Acad Sci U S A 107, 16560-16565. PMCID:2944750. This work uses a novel fluorescence fluctuation-based technique to track the flow of molecules in and around chromatin.
7. Lander, A.D., Gokoffski, K.K., Wan, F.Y., Nie, Q., and Calof, A.L. (2009). Cell lineages and the logic of proliferative control. PLoS Biol 7, e15. PMCID 2628408. This work shows how feedback circuits tightly control cell proliferation to allow organs to grow to and maintain proper sizes.
8. Lander, A.D., Lo, W.C., Nie, Q., and Wan, F.Y. (2009b). The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol 1, a002022. PMCID:2742077. This work uses modeling to reveal the tradeoffs that exist among mechanisms for achieving robustness and noise-tolerance in morphogen gradients.
9. Lee, B., Villarreal-Ponce, A., Fallahi, M., Ovadia, J., Sun, P., Yu, Q.C., Ito, S., Sinha, S., Nie, Q., and Dai, X. (2014). Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Developmental Cell 29, 47-58. This work involved a collaboration between a lab in Biochemistry and one in Mathematics to investigate transcriptional mechanisms in epidermal development.
10. McHale, P.T., and Lander, A.D. (2014). The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage. PLoS Comput Biol. DOI: 10.1371/journal.pcbi.1003802. This manuscript presents mathematical theory that shows that symmetric patterns of stem cell division significantly lower the risk of accumulation of mutations, provided that early mutations increase the probability of later ones (as occurs frequently in the development of cancer).
11. Mjolsness, E., Orendorff, D., Chatelain, P., and Koumoutsakos, P. (2009). An exact accelerated stochastic simulation algorithm. J Chem Phys 130, 144110. PMCID:2852436. The authors of this work develop a novel algorithm for fast stochastic simulation that substantially outperforms other algorithms on a class of hard problems.
12. Park, E., Williams, B., Wold, B.J., and Mortazavi, A. (2012). RNA editing in the human ENCODE RNA-seq data. Genome Res 22, 1626-1633. PMCID 3431480. This work reveals the extent and nature of RNA editing throughout the human genome.
13. Srinivasan, S., Hu, J.S., Currle, D.S., Fung, E.S., Hayes, W.B., Lander, A.D., and Monuki, E.S. (2014). A BMP-FGF morphogen toggle switch drives the ultrasensitive expression of multiple genes in the developing forebrain. PLoS Comput Biol 10, e1003463. PMCID 3923663. This manuscript uses a combination of experimental and mathematical methods to identify the gene regulatory logic underlying the formation of sharp spatial boundaries in forebrain development.
14. Stringari, C., Cinquin, A., Cinquin, O., Digman, M.A., Donovan, P.J., and Gratton, E. (2011). Phasor approach to fluorescence lifetime microscopy distinguishes different metabolic states of germ cells in a live tissue. Proc Natl Acad Sci U S A 108, 13582-13587. PMCID:3158156. This work uses the technique of fluorescence lifetime imaging to visualize metabolic states in cells within living tissues.
15. Wang, L., Nie, Q., and Enciso, G. (2010a). Nonessential sites improve phosphorylation switch. Biophys J 99, L41-43. PMCID:2941022. This work reveals a novel role for the large numbers of seemingly redundant phosphorylation sites that occur on many proteins.
16. Wang, L., Xin, J., and Nie, Q. (2010). A critical quantity for noise attenuation in feedback systems. PLoS Comput Biol 6, e1000764. PMCID 2861702. This work explores the mathematics behind the feedback strategies that biological systems use to filter noise, and resolves confusion about what kinds of feedback, and how many feedback loops, are most effective.
17. Xu, J., Reddy, B.J., Anand, P., Shu, Z., Cermelli, S., Mattson, M.K., Tripathy, S.K., Hoss, M.T., James, N.S., King, S.J., et al. (2012). Casein kinase 2 reverses tail-independent inactivation of kinesin-1. Nat Commun 3, 754. PMCID 3574636. This work shows that the motor protein, kinesin, self-inactivatives by a previously unknown mechanism, and reveals a non-enzymatic role for Casein kinase 2 in its re-activation. This work reveals a novel pathway for regulating the activity of cargo-bound kinesin.
18. Zhang, L., Lander, A.D., and Nie, Q. (2012). A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. BMC Syst Biol 6, 93. PMCID 3434027. This work shows how feedback interactions in cell lineage progression drive morphogenesis in the intestine.
19. Zhang, L., Radtke, K., Zheng, L., Cai, A.Q., Schilling, T.F., and Nie, Q. (2012). Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Mol Syst Biol 8, 613. PMCID 3472692. This paper elucidates the positive role of gene expression noise in making tissue patterning boundaries more precise.
20. Zhou, S., Lo, W.C., Suhalim, J.L., Digman, M.A., Gratton, E., Nie, Q., and Lander, A.D. (2012). Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc. Curr Biol 22, 668-675. PMCID 3338872. This work uses genetics, modeling, and fluorescence dynamics measurements to elucidate how molecular gradients set up patterns in organs and tissues.