PRE-PRINTS (in review)

  • James, R.E, Hamilton, N.R., Huffman, N.L., Pasterkamp, J., Goff, L.A., and Kolodkin, A.L. (2023). Semaphorin 6A in Retinal Ganglion Cells Regulates Functional Specialization of the Inner Retina. bioRxiv.

    SELECTED PUBLICATIONS

  • Ziak, J., Dorskind, J.M., Trigg, B., Sudarsanam, S., Hand, R.A., and Kolodkin, A.L. (2023). MAP1B Regulates Cortical Neuron Interstitial Axon Branching Through the Tubulin Tyrosination Cycle. In Press, The EMBO Journal (also on bioRxiv).

  • Hunyara, J.L., Daly, K.M., Torres, K., Yurgel, M.E., Komal, R., Hattar, S., and Kolodkin, A.L. (2023). Teneurin-3 regulates the generation of nonimage-forming visual circuitry and responsiveness to light in the suprachiasmatic nucleus. PLoS Biology, 21 (12), e3002412.

  • Dorskind, J.M., Sudarsanam, S., Hand, R.A., Ziak, J., Amoah-Dankwah, M., Guzman-Clavel, L., Soto-Vargas, J.L., and Kolodkin, A.L. (2023). Drebrin Regulates Collateral Axon Branching in Cortical Layer II/III Somatosensory Neurons. JNeurosci, 43 (46) 7745-7765.

  • Koropouli, E., Wang, Q., Mejias, R., Hand, R.A., Wang, T., Ginty, D.D., and Kolodkin, A.L. (2023). Palmitoylation regulates neuropilin-2 localization and function in cortical neurons and conveys specificity to semaphorin signaling via palmitoyl acyltransferases. eLife, DOI: 10.7554/eLife.8327

  • Al-Khindi, T., Sherman, M., Gopal, P., Pan, Z., Kodama, T., Kiraly, J., Zhang, H., Goff, L.A., Du Lac, S., and  Kolodkin, A.L. (2022). The transcription factor Tbx5 specifies direction-selective ganglion cell fate. Current Biology, 32, 4286-4298.

  • Hunyara, J.L., Foshe, S., Varadarajan, S.G., Gribble, K.D., Huberman, A.D., and Kolodkin, A.L. (2022). Characterization of non-alpha retinal ganglion cell injury responses reveals a possible block to restoring ipRGC function. Exp. Neurol. 357, (114176), 1-11.

  • Peng, Y-R.**, James-Esposito**, R.E., Yan, W., Kay, J.N., Kolodkin, A.L.*, Sanes, J.R.* (2020). Binary fate choice between closely related interneuronal types is determined by a Fezf1-dependent postmitotic transcriptional switch. Neuron, 105, 464-474 (*co-corresponding authors; **co-first authors).

  • Xie, X., Tabuchi, M., Corver, A., Duan, G., Wu, M.N., and Kolodkin, A.L. (2019) Semaphorin-2b regulates sleep circuit formation in the Drosophila central brain. Neuron, 104, 322-337.

  • Wang, Q., Chiu, S.-L., Koropouli, E., Hong, I., Mitchell, S., Gustina, A.S., Zhu, Q., Ginty, D., Huganir, R.L.,and Kolodkin, A.L. (2017). Neuropilin-2/PplexA3 receptors associate with GluA1 and mediate Sema3F-dependent homeostatic scaling in cortical neurons. Neuron, 96, 1084-1098.

  •  Xie, X., Tabuchi, M., Brown, M.P., Mitchell, S.P., Wu, M.N., and Kolodkin, A.L. (2017). The laminar organization of the Drosophila ellipsoid body is semaphorin-dependent and prevents the formation of ectopic synaptic connections. eLife, 6:e25328, DOI: 10.7554/eLife.25328.

  • Hand, R.A., Khalid, S., Tam, E., and Kolodkin, A.L. (2015). Axon dynamics during neocortical laminar innervation, Cell Reports, 12, 172-182.

  • Sun, L.O., Brady, C.M., Cahill, H., Sakuta, Dhande, O.S., Noda, M., Huberman, A.D., Nathans, J., Kolodkin, A.L.  (2015). Functional assembly of accessary optic system circuitry critical for compensatory eye movements. Neuron. 86, 971-984.

  • Riccomagno, M.M., Sun, L.O., Brady, C.M., Alexandropoulos, K., Seo, S., Kurokawa, M., and Kolodkin, A.L. (2014). Cas adaptor proteins organize the retinal ganglion cell layer downstream of integrin signaling. Neuron, 81, 779-786.

  • Sun, L.O., Jiang, Z., Rivlin-Etzion, M., Hand, R., Brady, C.M., Matsuoka, R.L., Yau, K.-W., Feller, M. B., and Kolodkin, A.L. (2013). On and Off retinal circuit assembly by divergent molecular mechanisms.  Science, 342, 1241947; DOI:10.1126/science.1241974.

  • Jeong, S., Juhaszova, K., and Kolodkin, A.L. (2012). The control of semaphorin-1a-mediated reverse signaling by opposing pebble and RhoGAPp190 functions in Drosophila. Neuron, 140, 627-38.

  • Riccomagno, M, Hurtado, A., Wang, H.-B., Macopson, J.G.J., Griner, E.M., Betz, A., Brose, N. Kazanietz, M.G., and Kolodkin, A.L. (2012).  The RacGAP  b-Chimaerin selectively mediates stereotyped hippocampal axon pruning.  Cell, 149, 1594-1606.

  • Lloyd, T.E., Machamer, J., O’Hara, K, Kim, J.H., Collins, S.E., Wong, M.Y., Sahin, B., Imlach, W., Yang, Y., Levitan, E.S., McCabe, B.D. and Kolodkin, A.L. (2012). The p150/Glued CAP-Gly domain regulates initiation of retrograde transport at synaptic termini.  Neuron, 74, 344-360.

  • Matsuoka, R.L., Chivatakarn, O, Badea, T.C., Samuels, I.S., Cahill, H., Katayama K, Suto F, Chédotal, A., Peachey, N.S., Nathans, J, Yoshida, Y., Giger, R.J., and Kolodkin, A.L. (2011).  Class5 transmembrane semaphorins control mammalian inner retinal lamination, neurite arborization, and function. Neuron 71, 460-473.

  • Matsuoka, R.L., Nguyen-Ba-Charvet, K.T., Parray, A., Badea, T.C., Chedotal, A., and Kolodkin, A.L.  (2011).  Transmembrane semaphorin signaling controls laminar stratification in the mammalian retina.  Nature,  470, 259-263.

  • Wu, Z., Sweeney, L.B. Ayoob, J.C., Chak, K., Andreone, B.J., Ohyama,T. Kerr, R., Luo, L, Zlatic, M., and Kolodkin, A.L.  (2011).  A combinatorial semaphorin code instructs the initial steps of sensory circuit assembly in the Drosophila CNS.  Neuron, 70, 281-298.

  • Tran, T.S., Rubio, M.E., Clem, R.L., Johnson, D.,Case, L.C., Tessier-Lavigne, M., Huganir, R.L., Ginty, D.D., and Kolodkin, A.L. (2009). Secreted Semaphorins Control Spine Distribution and Morphogenesis in the Postnatal CNS. Nature, 462, 1065-1069.

  • Huber, A.B., Kania, A., Tran, T.S., Gu, C., De Marco Garcia, N., Lieberam, I., Johnson, D., Jessell, T.M. Ginty, D.D., and Kolodkin, A.L. (2005). Distinct roles for secreted semaphorin signaling in spinal motor axon guidance. Neuron, 48, 949-964.

  • Kantor, D.B., Chivatakarn, O., Peer, K.L., Oster, S.F., Inatani, M., Hansen, M.J., Flanagan, J.G., Yamaguchi, Y., Sretavan, D.W., Giger, R.J., and Kolodkin, A.L. (2004). Semaphorin 5A is a Bifunctional Axon Guidance Cue Regulated by Heparan and Chondroitin Sulfate Proteoglycans. Neuron, 44, 961-975.

  • Terman, J.R., and Kolodkin, A.L. (2004). The AKAP Nervy direction couples Protein Kinase A to Plexin-mediated semaphorin repulsion. Science, 303, 1204-1207.

  • Pasterkamp, R.J., Peshon, J.J., Spriggs, M.K. and Kolodkin, A.L. (2003). Semaphorin 7A promotes axon outgrowth through integrins and MAPKs. Nature, 424, 398-405.

  • Terman, J.R., Mao, T., Pasterkamp, R.J., Yu, H.-H., and Kolodkin, A.L. (2002). MICALs, Family of Conserved Flavoprotein Oxidoreductases, Function in Plexin-Mediated Axonal Repulsion. Cell 109, 887–900.

  • Giger, R.J., Urquhart, E.R., Gillespie, S.K.H., Levengood, D.V., Ginty, D.D., and Kolodkin, A.L. (1998). Neuropilin-2 is a receptor for semaphorin IV: Insight into the structural basis of receptor function and specificity. Neuron, 21, 1079-1092.

  • Yu, H.-H., Araj, H.H., Ralls, S.A., and Kolodkin, A.L. (1998). The transmembrane semaphorin Sema-I is required in Drosophila for embryonic motor and CNS axon guidance. Neuron, 20, 207-220.

  • Kolodkin, A.L.*, Levengood, D.V., Rowe, E.G., Tai, Y.-T., Giger, R. J., and Ginty, D. D.* (1997). Neuropilin is a semaphorin III receptor. Cell, 90, 753-762 (*-co-corresponding authors).

SELECTED INVITED REVIEWS

  • **Varadarajan, S. G., **Hunyara, J.L., Hamilton, N.R., *Kolodkin, A.L., and *Huberman, A.D. (2022). Central nervous system regeneration. Cell, 185, 77-94 (*co-corresponding authors; **co-first authors).

  •  Hamilton, N.R., Scasny, A.J., and Kolodkin, A.L. (2021). Development of the vertebrate retinal direction-selective circuit. Dev. Biol., 477, 273-283.

  •  Dorskind, J.M. and Kolodkin, A.L. (2020). Revisiting and revising roles of neural guidance cues in circuit assembly. Curr. Opin. Neurobiol., 66, 10-21.

  •  Hunyara, J.L. and Kolodkin, A.L. (2020). Repurposing developmental mechanisms in the adult nervous system. Curr. Opin. Genetics and Devel., 65, 14-21.

  •  Zhang, C., *Kolodkin, A.L., *Wong, R., and James, R.E. (2017). Establishing wiring specificity in visual system circuits: From retina to the brain. Ann. Revs. Neurosci. 40, 395-424 (*co-corresponding authors).