Akkaynak, D., Allen, J.J., Mäthger, L.M., Chiao, C.C. and Hanlon, R.T. 2013. Quantification of cuttlefish (Sepia officinalis) camouflage: a study of color and luminance using in situ spectrometry. J. Comp. Physiol A. 199 (3): 211-225.

Allen, J.J., Bell, G.R.R., Kuzirian, A.M., Hanlon, R.T. 2013. Cuttlefish skin papillae possess morphology suggesting a muscular hydrostat function for rapid changeability. J Morphology 274 (6): 645-656.   DOI: 10.1002/jmor.20121

Bell, G.R.R., Kuzirian, A.M., Senft, S.L., Mäthger, L.M., Wardill, T.J., and Hanlon, R.T. 2013. Chromatophore radial muscle fibers anchor in flexible squid skin. Invertebrate Biology 132 (2): 120-132.

Bilandžija, H., Ma, L., Parkhurst, A., and Jeffery, W. R. (2013). A potential benefit of albinism in Astyanax cavefish:  Downregulation of the oca2 gene increases L-tyrosine and catecholamine levels as an alternative to melanin synthesis.  PLoS ONE 8 (11): e80823. doi: 10.1371/journal.pone.0080823

Chiao, C.C., Ulmer, K. M., Siemann, L., Buresch, K.C., Chubb, C. and Hanlon, R.T. 2013. How visual edge features influence cuttlefish camouflage patterning. Vision Research 83: 40-47.

Chowanadisai, W., Graham, D. M., Keen, C. L., Rucker, R. B., & Messerli, M. A. (2013). A zinc transporter gene required for development of the nervous system. Commun. Int. Biol. 2013: 6:e26207

Chowanadisai, W., Graham, D. M., Keen, C. L., Rucker, R. B. & Messerli, M. A. (2013). Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12) Proc. Natl. Acad. Sci. USA 2013 110: 9903-9908.

Crook, R.J., Hanlon, R.T. and Walters, E.T. 2013. Squid have nociceptors that display widespread long-term sensitization and spontaneous activity after bodily injury. J. Neuroscience 33 (24): 10021-10026.

Graham, D. M., Huang, L., Robinson, K. R., & Messerli, M. A. (2013). Epidermal keratinocyte polarity and motility require Ca2+ influx through TRPV1. J. Cell Sci. 126:4602-4613. July 2013. http://dx.doi.org/10.1242/jcs.122192

Hanlon, R. T., Buresch, K, Staudinger, M.D., & Moustahfid, H. (2013). Doryteuthis pealeii, Longfin Inshore Squid. Pgs. 205-240. In: Rosa, R., O’Dor, R. & Pierce, G. J., (eds.) Advances in Squid Biology, Ecology, and Fisheries. Part 1 – Myopsid Squids. Nova Science Publishers, Inc. Hauppauge, NY.

Hanlon, R.T., Chiao, C.-C., Mäthger, L.M. and Marshall, N.J. 2013. A fish-eye view of cuttlefish camouflage using in-situ spectrometry. Biological Journal of the Linnean Society 109 (3): 535-551.

Helm, R. R., Siebert, S., Tulin, S., Smith, J., & Dunn, C. Characterization of differential transcript abundance through time during Nematostella vectensis development.  BMC Genomics.14(1):266, 2013. http://www.ncbi.nlm.nih.gov/pubmed/23601508

Hinaux, H., Poulain, J. Da Silva, C., Noirot, C., Jeffery, W. R., Casane, D., & S. Retaux (2013). De novo sequencing of Astyanax mexicanus surface fish and Pachon cavefish transcriptomes reveals enrichment of mutations in putative cavefish eye genes. PLoS ONE 8(1): e53553. doi:10.1371/journal.pone.0053553.s

Jeffery, W. R. The tunicate Ciona: a model system for studying the relationship between regeneration and aging. (accepted for publication in Invertebrate Reproduction & Development).

Kowalko J. E., Rohner, N., Linden, T. A., Rompani, S. B., Warren, W. C, Borowsky, R., Tabin C. J., Jeffery, W. R., & M. Yoshizawa (2013). Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus.  Proc. Natl. Acad. Sci. USA 110 (42)  16933-16938.  doi:10.1073/pnas.1317192110

Kowalko, J. E., Rohner, N., Rompani, S. B., Peterson, B. K., Linden, T., Yoshizawa, M., Kay E. H., Hoekstra H. E., Jeffery, W. R., Borowsky, R., & Tabin, C. J. (2013). Genetic analysis of the loss of schooling behavior in cavefish reveals both sight-dependent and independent mechanisms. Curr. Biol. 23: 1874-1883. doi: 10.1016/j.cub.2013.07.056

Kreit, E., Mäthger, L., Hanlon, R.T., Dennis, P.B., Naik, R.R., Forsythe, E. and Heikenfeld, J. 2013. Biological vs. electronic adaptive coloration: how can one inform the other? Journal of the Royal Society Interface. 10 (78): article 20120601 (DOI: 10.1098/rsif.2012.0601)

Lau BY, Fogerson SM, Walsh RB, Morgan J.R. Cyclic AMP promotes axon regeneration, lesion repair and neuronal survival in lampreys after spinal cord injury. Exp Neurol. 2013. Volume 250, December 2013, Pages 31–42. http://www.ncbi.nlm.nih.gov/pubmed/24041988

Laubichler, M., Maienschein, J. and Juergen Renn, “Computational Perspectives in the History of Science: To the Memory of Peter Damerow,” Isis. 2013. 104:119-130.

Laubichler, M., Maienschein, J. Developmental Evolution, in Michael Ruse, editor, Darwin Encyclopedia  (Cambridge University Press, 2013), pp. 375-382.

Maienschein, J. Stem cell research utilizing embryonic tissue SHOULD be conducted,  with response, in Arthur Caplan and Robert Arp, editors, Contemporary Debates in Bioethics (Wiley-Blackwell, 2013), pp. 237-247.

Maienschein, J. “Finding Goodness Among Ought and Is Debates in Stem Cell Research,” in Victorio Hösle, editor, Dimensions of Goodness (Cambridge Scholar Publishers, 2013), pp. 225-242.

Materna, S., Swartz, S. and Smith, J. Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin. Development. 140(8):1796-806, (2013). http://www.ncbi.nlm.nih.gov/pubmed/23533178

Mäthger, L.M., Hanlon, R.T., Hakansson, J. and Nilsson, D.-E. 2013. The W-shaped pupil in cuttlefish (Sepia officinalis): a function in maximizing visual field. Vision Research 83: 19-24.

Mäthger, L.M., Senft, S., Gao, M., Karaveli, S., Bell, G., Zia, R., Kuzirian, A.M., Dennis, P.B., Crookes-Goodson, W.J., Naik, R.R., Kattawar, G. and Hanlon, R.T. 2013. Bright white scattering from protein spheres in color changing, flexible cuttlefish skin. Advanced Functional Materials 23 (32): 3980-3989.

Morgan J. R., Comstra, H. S., Cohen, M., & Faundez, V. (2013). Presynaptic membrane retrieval and endosome biology: defining molecularly heterogeneous synaptic vesicles. Cold Spring Harbor Perspect Biol. Oct 1;5(10)PubMed PMID: 24086045.

Morgan J. R., Jiang, J., Oliphint, P. A., Jin, S., Gimenez, L. E., Busch, D. J., Foldes, A. E., Zuo, Y., Sousa, R., & Lafer, E. M.  (2013). Role for an Hsp70 nucleotide exchange factor in the regulation of synaptic vesicle endocytosis.  Journal of Neuroscience.  33:8009-8021.

Nilsson, D.-E., Warrant, E. J., Johnsen, S., Hanlon, R. T., and Shashar, N. 2013. The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales. BMC Evolutionary Biology 13: article 187.

O’Quin, K. E., Yoshizawa, M., Doshi, P., & W. R. Jeffery (2013).  Quantitative genetic analysis of retinal degeneration in the blind cavefish. PLoS ONE 8(2): e57281. doi:10.1371/journal.pone.0057281.

Rohner, H., Jarosz, D. F., Kowalko, J. E., Yoshizawa, M., Jeffery, W. R., Borowsky, R. L., Lindquist, S., & Tabin, C. J. (2013). Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in a cavefishScience 342: 1372-1375.  doi: 10.1126/science.1240276

Shashar, N. and Hanlon, R.T. 2013. Spawning behavior dynamics at communal egg beds in the squid Doryteuthis (Loligo) pealeii (Mollusca: Cephalopoda). J. Experimental Marine Biology and Ecology 447:65-74.

Staudinger, M.D., Buresch, K.C., Mäthger, L.M., Fry, C., McAnulty, S., Ulmer, K.M. and Hanlon, R.T. 2013. Defensive responses of cuttlefish to different teleost predators. 2013. Biological Bulletin 225 (3): 161-174.

Smith, J. J., Kuraku, S., Holt, C., Sauka-Spengler, T., Jiang, N., Campbell, M. S., Yandell, M. D., Manousaki, T., Meyer, A., Bloom, O. E., Morgan J. R., Buxbaum, J. D., Sachidanadam, R., Sims, C., Garruss, A. S., Cook, M., Krumlauf, R., Wiedemann, L. M., Sower, S. A., Decatur, W. A., Hall, J. A., Amemiya, C. T., Saha, N. R., Buckley, K. M., Rast, J. P., Das, S., Hirano, M., McCurley, N., Guo, P., Rohner, N., Tabin, C. J., Piccinelli, P., Elgar, G., Ruffier, M., Aken, B. L., Searle, S. M. J., Muffato, M., Pignatelli, M., Herrero, J., Jones, M., Brown, C. T., Chung-Davidson, Y-W., Nanlohy, K. G., Libants, S. V., Yeh, C-Y., McCauley, D. W., Langeland, J. A., Pancer, Z., Fritzsch, B., de Jong, P. J., Zhu, B., Fulton, L. L., Theising, B., Flicek, P., Bronner, M., Warren, W. C., Clifton, S. W., Wilson, R. K., & Li, W. (2013) Sequencing of the sea lamprey (Petromyzon marinus) provides insights into vertebrate evolution.  Nature Genetics.  45:415-421.

Tulin, S., Aguiar, D.,Istrail, S., & Smith, J. A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Accepted for publication in EvoDevo Journal.

Ulmer, K.M., Buresch, K.C., Kossodo, M., Mäthger, L.M., Siemann, L.A., and Hanlon, R.T. 2013. Visual background features in the vertical dimension have a strong influence on cuttlefish camouflage. Biological Bulletin 224(2): 110-118.

Vang, S., Wu, H. T., Fischer, A., Miller, D. H., MacLaughlan, S., Douglass E., Steinhoff, M., Collins, C., Smith, P. J. S., Brard, L., & Brodsky, A. S. (2013). Identification of Ovarian Cancer Metastatic miRNAs. PLoS ONE 8(3): e58226.

Wardill, T.J., Gonzalez-Bellido, P.T., Crook, R.J. and Hanlon, R.T. 2013. Neural control of tuneable skin iridescence in squid. Proc Roy Soc B 279: 4243-4252.

Books and Book Chapters

Chiao, C.C. and Hanlon, R.T. 2013. Animal camouflage. Pgs 21-25. In: McGraw-Hill Yearbook of Science and Technology, New York, 433p.