Yale/NIDA Neuroproteomics Center Publications

Journal of Neuroscience, 2014

Cover legend: Artistic rendition of αβγ-synuclein knockout synapses, showing a deficit in cholera toxin-HRP positive vesicles (black vesicles). This experiment in synuclein-null neurons supports a physiological role for α-synuclein in synaptic vesicle endocytosis. For more information see the article by Vargas, K.J., Makhani, S., Davis, T., Westphal, C., Castillo, P.E., and Chandra, S.S. (2014). Synucleins regulate the kinetics of synaptic vesicle endocytosis. J. Neuroscience 34(28), 9364-9376. (PMCID: PMC4087213)

Journal of Cell Biology, 2012

Cover legend: GFP-Farp1 (green) promotes the polymerization of F-actin (red) in dendritic spines, the postsynaptic protrusions of excitatory synapses. Cheadle and Biederer reveal that Farp1 works with the synaptic adhesion molecule SynCAM 1 to promote spine assembly and organize presynaptic active zones. The postsynaptic marker Shank is stained blue. For more information see the article by Cheadle, L., Biederer, T. (2012) The novel synaptogenic protein Farp1 links postsynaptic cytoskeletal dynamics and transsynaptic organization. J Cell Biol. 199(6):985-1001. (PMCID: PMC3518221)

Journal of Biological Chemistry, 2010

Cover legend: SynCAM adhesion molecules connect pre- and postsynaptic membranes to organize synapses. The cover image shows a SynCAM 2 homodimer (left) and a SynCAM 1/2 heterodimer (right) based on the crystal structure and crystal packing of the first SynCAM 2 immunoglobulin domain. The strength of these trans-synaptic interactions is modulated by N-glycans (red) that reduce SynCAM 2 adhesion, likely through steric hindrance. In contrast, N-glycans (brown) facing away from SynCAM 1 may restrict its conformational freedom and position it toward binding. For more information see the article by Fogel, A.I., Li, Y., Wang, Q., Lam, T.T., Modis, Y. and Biederer, T. (2010) N-Glycosylation at the SynCAM immunoglobulin interface modulates synaptic adhesion. J. Biol. Chem. 285: 34864-34874. (PMCID: PMC2966101)
Rinehart 2009 JPG

Cell, 2009

Cover legend: K-Cl cotransporters (KCCs) control transmembrane electrolyte flux in a variety of physiologic settings, including the acute response to altered extracellular osmolarity. In this issue of Cell, Rinehart et al. (pp. 525–536) use targeted phosphoproteomics to reveal how phosphorylation at two conserved sites in KCCs controls their activity. The image depicts the activation of KCC3 in red blood cells in response to extracellular hypotonicity. KCC3 (blue) is shown embedded in the red blood cell membrane. Cotransporters that are phosphorylated at T991 and T1048 in the C terminus (highlighted in a white “flash”) are inactive, while those that are dephosphorylated at these sites are active, allowing K-Cl efflux from the cell and preventing cell swelling due to influx of water. For more information see the article by Rinehart, J., Maksimova, Y.D., Tanis, J.E., Stone, K.E., Hodson, C.A., Zhang, J, Risinger, M., Pan, W., Wu, D., Colangelo, C.M., Forbush, B., Joiner, C.H., Gulcicek, E.E., Gallagher, P.G., and Lifton, R.P. (2009) Sites of regulated phosphorylation that control K-Cl cotransporter activity. Cell. 138(3):525-36. (PMCID: PMC2811214)

205. Gunther, E.,Smith, L., Kostylev, M.,Cox, T., Kaufman, A., Lee, S.,Folta-Stogniew, E.,Maynard, G., Um, J., Stagi, M., Heiss, J., Stoner, A., Noble, J., Takahashi, H., Haas,L., Schneekloth, J., Merkel, J., Teran, C., Naderi, Z., Supattapone, S., Strittmatter, S.M. (2019) Rescue of transgenic Alzheimer’s pathophysiology by polymeric cellular Prion Protein antagonists. Cell Reports 26(1) 145-158 (PMID:30605671).


204. Wilson, R.S. and Nairn, A.C. (2018) Making brain proteomics true to type. Nature Biotechnology 36: 149-150 (PMID: 29406511).

203. Wilson, R.S. and Nairn, A.C. (2018) Cell-type-specific proteomics: A neuroscience perspective. Proteomes Special Issue on Neuroproteomics 6(4), 51 (PMCID:PMC6313874) (PMID:30544872)

202. Torregrossa, M., MacDonald, M., Stone, K.L., Lam, T.T., Nairn, A.C., Taylor, J.R. (2018) Phosphoproteomic analysis of cocaine memory extinction and reconsolidation in the nucleus accumbens, Psychopharmacology Epub ahead of print on Nov. 8, 2018 (PMID: 30411139).

201. Rao, V., Zavala, G., Roy, A., Mains, R., Eipper, B. (2018)  A pH-sensitive luminal His-cluster promotes interaction of PAM with V-ATPase along the secretory and endocytic pathways of peptidergic cells. J. Cellular Physiology (PMID: 30317586).

200. Peng, G., Wilson, R., Tang, Y., Lam, T. Nairn, A., Williams, K., Zhao, H. (2018) ProteomicsBrowser: MS/Proteomics Data Visualization and Investigation, Bioinformatics, 2018 Nov 21. doi: 10.1093/bioinformatics/bty958 Epub ahead of print on Nov. 21, 2018 (PMID: 30462190).

199. Park, J. (2018) Phosphorylation of the AMPAR-TARP complex in synaptic plasticity. Proteomes Special Issue on Neuroproteomics 6(4), 40 (PMCID:PMC6313930) (PMID: 30297624).

198. Milovanovic, D., Wu, Y., Bian, X. De Camilli, P. (2018) A liquid phase of synapsin and lipid vesicles. Science 361, 604-607(PMCID: PMC6191856) (PMID:29976799).

197. Miller, M., Wilson, R., Lam, T., Nairn, A., Picciotto, M., (2018) Evaluation of the phosphoproteome of mouse alpha 4/beta 2-containing nicotinic acetylcholine receptors in vitro and in vivo. Proteomes Special Issue on Neuroproteomics 6(4) 42 (PMCID: PMC6313896) (PMID: 30326594).

196. Mervosh, N., Wilson, R., Rauniyar, N., Hofford, R., Kutlu, M., Calipari, E., Lam, T. T., Kiraly, D., (2018) Granulocyte-colony stimulating factor alters the proteomic landscape of the ventral tegmental area. Proteomes Special Issue on Neuroproteomics 6(4), 35 (PMCID:PMC6313867) (PMID: 30249060).

195. Luxmi, R., Blaby-Haas, C., Kumar, D., Rauniyar, N., King, S., Mains, R., Eipper, B. (2018) Proteases shape the Chlamydomonas secretome: Comparison to classical neuropeptide processing machinery. Proteomes Special Issue on Neuroproteomics 6(4), 36 (PMCID:PMC6313938) (PMID: 30249063).

194. Li, D., Musante, V., Zhou, W., Picciotto, M.R., Nairn, A.C. (2018) Striatin-1 is a B subunit of protein phosphatase PP2A that regulates dendritic arborization and spine development in striatal neurons. J.Biol.Chem. 293(28):11179-11194 (PMCID: PMC6052221 Available on 2019-07-13) (PMID: 29802198).

193. Levy, A., Xiao, X., Shaw, J., Devi, S., Katrancha, S., Bennett, A., Greer, C. Howe, J., Machida, K., and Koleske, A. (2018) Noonan Syndrome-Associated SHP2 Dephosphorylates GluN2B to Regulate NMDA Receptor Function. Cell Reports 24, 1523-1535 (PMCID: PMC6234505) (PMID: 30089263).

192. Kumar, N., Leonzino, M., Hancock-Cerutti, W., Horenkamp, F., Li, P., Lees, J., Wheeler, H., Reinish, K., De Camilli, P. (2018) VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites. J. Cell Biology 217(10):3625-3639 (PMCID:PMC6168267 Available on 2019-04-01) (PMID:30093493).

191. Dong, R., Zhu, T., Benedetti, L., Gowrishankar, S., Deng, H., Cai, Y., Wang, X., Shen, K., De Camilli P. (2018) The inositol 5-phosphatase INPP5K participates in the fine control of ER organization J. Cell Biol. 217(10):3577-3592 (PMCID:PMC6168264 Available on 2019-04-01) (PMID: 30087126).

190. Cijsouw, T., Ramsey, A., Lam, T., Carbone, B., Blanpied, T., Biederer, T. (2018) Mapping the Proteome of the Synaptic Cleft Through Proximity Labeling Reveals New Cleft Proteins. Proteomes Special Issue on Neuroproteomics 6(4), 48 (PMCID:PMC6313906)(PMID:30487426).

189. Carlyle, B.C., Kitchen, R.R.,  Zhang, J., Wilson, R., Lam, T.T., Rozowsky, J.S., Williams, K., Sestan, N., Gerstein, M.B., Nairn, A.C. (2018) Isoform level interpretation of high-throughput proteomic data enabled by deep integration with RNA-seq. J. Proteome Research 17(10), 3431-3444 (PMID: 30125121).

188. Bian, X., Saheki, Y., and De Camilli, P. (2018) Ca2+ releases E-Syt1 autoinhibition to couple ER-plasma membrane tethering with lipid transport. EMBO J. 37:219-234 (PMCID: PMC5770786) (PMID:29222176).

187. Bertholomey, M.L., Stone, K.L., Lam, T.T., Bang, S., Wu, W., Nairn, A.C., Taylor, J.R., Torregrossa, M.M. (2018) Phosphoproteomic analysis of the amygdala response to adolescent glucocorticoid exposure reveals G-protein coupled receptor kinase 2 (GRK2) as a target for reducing motivation for alcohol. Proteomes Special Issue on Neuroproteomics 6(4), 41 (PMCID:PMC6313880) (PMID:30322021).

186. Benedetti, L., Barentineb, A., Messa, M., Wheeler, H., Bewersdorf, J., De Camilli, P.(2018) Light-activated protein interaction with high spatial subcellular confinement. Proc. Natl. Acad. Sci. 115(10):E2238-E2245 (PMCID:PMC5877946) (PMID:29463750).


185. Yuan, Q., Ren, C., Xu, W., Petri, B., Zhang, J., Zhang, Y., Kubes, P., Wu, D., Tang, W. (2017) PKN1 Directs Polarized RAB21 Vesicle Trafficking via RPH3A and Is Important for Neutrophil Adhesion and Ischemia-Reperfusion Injury. Cell Reports 19, 2586; published online Epub Jun 20, 2017, (PMCID: PMC5548392) (PMID:28636945).

184. Stefan, C.J., Trimble, W.S., Grinstein, S., Drin, G., Reinisch, K., De Camilli, P., Cohen, S., Valm, A.M., Lippincott-Schwartz, J., Levine, T.P., Iaea, D.B., Maxfield, F.R., Futter, C.E., Eden, E.R., Judith, D., van Vliet, A.R., Agostinis, P., Tooze, S.A., Sugiura, A., McBride, H.M. (2017). Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers. BMC Biol. 15: 102. (PMCID: PMC5663033) (PMID: 29089042).

183. Saheki, Y. and De Camilli, P. (2017) The extended–Synaptotagmins. Biochim. Biophys. Acta 1864(9): 1490-1493 (PMCID:PMC5642939) (PMID: 28363589).

182. Saheki Y, De Camilli P. 2017. Endoplasmic Reticulum-Plasma Membrane Contact Sites. Annual Rev Biochem. 86:659-684 (PMID: 28301744).

181. Musante, V., Li L., Kanyo, J., Lam, T.T., Colangelo, C.M., Cheng, S.K., Brody, H., Greengard, P., Le Novère N., Nairn, A.C. (2017) Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife 2017 June 14;6. pii: e24998 (PMCID:PMC5515580) PMID:28613156). 

180. Milovanovic, D. and De Camilli, P. (2017) Synaptic vesicles clusters at synapses: a distinct liquid phase? Neuron 93(5): 995-1002 (PMCID: PMC5347463) ( PMID: 28279363).

179. Miller, M.B., Yan, Y., Machida, K.,  Kiraly, D.D., Levy, A.D., Wu, Y.I., Lam, T.T., Abbott, T., Koleske, A.J., Eipper, B.A., Mains, R.E. (2017) Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity, ACS Chemical Neuroscience 8: 1554-1569 (PMCID: PMC5517348) (PMID: 28418645).

178. Lees, J.A., Messa, M., Sun, W.E., Wheeler, H., Torta, F., Wenk, M.R., De Camilli, P., and Reinisch, K.M. (2017) Lipid transport by TMEM24 at ER-PM contacts regulates pulsatile insulin secretion. Science 355 (6326): 709 (PMCID:PMC5414417) (PMID: 28209843).

177. Gorenberg, E., and Chandra, S.S. (2017). The Role of Co-Chaperones in Synaptic Proteostasis and Neurodegenerative Disease. Frontiers in Neuroscience (Roodveldt, C., Outeiro, T. F., Braun, J.E.A., Eds.) 11: 248 (PMCID: PMC5437171) (PMID:28579939

176. Carlyle, B., Kitchen, R., Kanyo J., Voss, E., Pletikos, M., Lam, T. T., Gerstein, M., Sestan, N., Nairn, A.C. (2017) A Multiregional Proteomic Survey of the Postnatal Human Brain, Nature Neuroscience 20: 1787-1795 (PMCID:PMC5894337) (PMID: 29184206).

175. Cao, M., Wu, Y., Ashrafi, G., McCartney, A.J., Wheeler, H., Bushong, E.A., Boassa, D., Ellisman, M.H., Ryan, T.A., and De Camilli, P. (2017)  Parkinson Sac Domain Mutation in Synaptojanin 1 Impairs Clathrin Uncoating at Synapses and Triggers Dystrophic Changes in Dopaminergic Axons. Neuron 93: 882-896 (PMCID: PMC5340420) (PMID: 28231468).

174. Andrade, E.C., Musante, V., Horiuchi, A., Matsuzaki, H., Harrison, A., Brody, H., Wu, T., Greengard, P., Taylor, J.R. and Nairn, A.C. (2017) ARPP-16 is a striatal-enriched inhibitor of protein phosphatase 2A regulated by microtubule-associated serine/threonine kinase 3 (Mast 3 kinase). J. Neurosci. 37(10): 2709-2722 (PMCID: PMC5354324) (PMID: 28167675).


173. Vishwanatha, K.S., Back, N., Lam, TuKiet T., Mains, R.E., Eipper, B.A. (2016) O-Glycosylation of a Secretory Granule Membrane Enzyme Is Essential for Its Endocytic Trafficking. J. Biol. Chem. 291(18):9835-50.  (PMCID: PMC4850319) (PMID: 26961877).

172. Serebryany E, Folta-Stogniew E, Liu J, Yan EC. (2016) Homodimerization enhances both sensitivity and dynamic range of the ligand-binding domain of type 1 metabotropic glutamate receptor. FEBS Lett. 590: 4308-4317. (PMCID: PMC5154874) (PMID: 27800613).

171. Saheki,Y., Bian,X., Schauder, C.M., Sawaki,Y., Surma, M.A.,Klose, C., Pincet,F., Reinisch,K.M., De Camilli, P. (2016) Control of plasma membrane lipid homeostasis by the extended synaptotagmins, Nature Cell Biology, 18: 504-515 (PMCID:PMC4848133) (PMID: 27065097).

170. Rich, M.T., Abbott, T., Chung, L., Gulcicek E.E., Stone, K.L., Colangelo, C.M., Lam, T.T., Nairn, A.C., Taylor, J.R., Torregrossa, M.M. (2016) Phosphoproteomic Analysis Reveals a Novel Mechanism of CaMKIIα Regulation Inversely Induced by Cocaine Memory Extinction versus Reconsolidation. J. Neuroscience 36(29):7613-27 (PMCID:PMC4951572) (PMID:27445140)

169. Reinisch KM, De Camilli P. (2016) SMP-domain proteins at membrane contact sites: Structure and function. Biochim Biophys Acta (PMCID 1861:924-927 (PMCID:PMC4902782) (PMID: 26686281).

168. Park J., Chávez, A.E., Mineur, Y.S., Morimoto-Tomita, M., Lutzu, S., Kim, K.S., Picciotto, M.R., Castillo P.E., Tomita, S. (2016) CaMKII Phosphorylation of TARPγ-8 Is a Mediator of LTP and Learning and Memory. Neuron 92(1):75-83. (PMCID:PMC5059846) (PMID: 27667007).

167. McClure-Begley, T. D., Esterlis, I., Stone, K. L., Lam, T. T., Grady, S.R., Colangelo, C.M., Lindstrom, J.M., Marks, M.J., and Picciotto, M.R. (2016) Evaluation of the Nicotinic Acetylcholine Receptor-Associated Proteome at Baseline and Following Nicotine Exposure in Human and Mouse Cortex. eNeuro 3 (PMCID: PMC4985585) (PMID: 27559543)

166. Hernandez, A., Tan, C., Mettlach, G., Pozo, K., Plattner, F., Bibb (2016) Cdk5 Modulates Long-Term Synaptic Plasticity and Motor Learning in Dorsolateral Striatum. Scientific Reports (Nature) Jul 22; 6:29812 (PMCID:PMC4957238) (PMID:27443506).

165. Henderson, M.X., Wirak; G.S., Zhang, Y., Dai, F., Ginsberg, S.D., Dolzhanskaya, N., Staropoli, J.F., Nijssen, P.C.G., Lam, TuKiet T., Roth, A.F., Davis, N.G., Dawson, G., Velinov, M., Chandra, S.S. (2016) Neuronal ceroid lipofuscinosis with DNAJC5/CSPalpha mutation has PPT1 pathology and exhibit aberrant protein palmitoylation. Acta Neuropathologics 131 (4), 621-37 (PMCID: PMC4791186) (PMID: 26659577).

164. Fleming, M.R., Brown, M.R., Kronengold, J., Zhang, Y., Jenkins, D.P., Barcia, G., Nabbout, R., Bausch, A.E., Ruth, P., Lukowski, R., Navaratnam, D.S. and Kaczmarek, L.K. (2016) Stimulation of Slack K+ channels alters mass at the plasma membrane by triggering disassociation of a phosphatase-regulatory complex. Cell Reports 16: 2281-2288. (PMCID: PMC5123741) (PMID: 27545877).

163. Dong, R., Saheki, Y., Swarup, S., Lucast, L., Harper, J.W., and De Camilli, P. (2016)  Endosome-ER contacts control actin nucleation and retromer function through VAP-dependent regulation of PI4P.  Cell 166: 408-423.  (PMCID: PMC4963242) (PMID: 27419871)

162. Clarke, D., Sethi, A., Li, S., Kumar, S., Chang, R.W., Chen, J., Gerstein, M. (2016) Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation. Structure 24, 826-837 (PMCID:PMC4883016) (PMID: 27066750).

161. Baskin JM, Wu X, Christiano R, Oh MS, Schauder CM, Gazzerro E, Messa M, Baldassari S, Assereto S, Biancheri R, Zara F, Minetti C, Raimondi A, Simons M, Walther TC, Reinisch KM, De Camilli P. (2016) The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane. Nat Cell Biol. 18(1):132-8, doi: 10.1038/ncb3271 (PMCID: PMC4689616) (PMID:26571211)


160. Plattner F, Hayashi K, Hernández A, Benavides DR, Tassin TC, Tan C, Day J, Fina MW, Yuen EY, Yan Z, Goldberg MS, Nairn AC, Greengard P, Nestler EJ, Taussig R, Nishi A, Houslay MD, Bibb JA.(2015) The role of ventral striatal cAMP signaling in stress-induced behaviors. Nat Neurosci. 18(8):1094-100. (PMCID:PMC4519694) (PMID:26192746)

159. Nakatsu F, Messa M, Nández R, Czapla H, Zou Y, Strittmatter SM, De Camilli P. (2015) Sac2/INPP5F is an inositol 4-phosphatase that functions in the endocytic pathway. J Cell Biol. 209(1):85-95 (PMCID:PMC4395491) (PMID:25869668).

158. Idevall-Hagren O, and De Camilli P. (2015) Detection and manipulation of phosphoinositides.  Biochim. Biophys. Acta. 6: 736-45 (PMCID: PMC4863076) (PMID: 25514766).

157. Gowrishankar S, Yuan P, Wu Y, Schrag M, Paradise S, Grutzendler J, De Camilli P, Ferguson SM. (2015) Massive accumulation of luminal protease-deficient axonal lysosomes at Alzheimer's disease amyloid plaques. Proc Natl Acad Sci U S A. 112(28):E3699-708. (PMCID: PMC4507205) (PMID:26124111)

156. Engmann, O., Giralt, A., Gervasi, N., Marion-Poll, L., Gasmi, L., Filhol, O., Picciotto, M.R., Gilligan, D., Greengard, P., Nairn, A.C., Hervé, D., Girault, J.A. (2015). DARPP-32 interaction with adducin may ediate rapid environment effects on striatal neurons. Nat Commun. 6:10099 | DOI: 10.1038/ncomms100996 (PMCID: PMC4675091) (PMID:26639316)

155. Colangelo, C., Shifman, M., Cheung, K., Stone, K.L., Carriero, N., Gulcicek, E., Lam, T.T., Wu, T., Bjornson, R.D., Bruce, C., Nairn, A.C., Rinehart, J., Miller, P.L., and Williams, K. (2015) YPED: An integrated bioinformatics suite and database for mass spectrometry based proteomics research. Genomics, Proteomics, and Bioinformatics  13, 25-35 (PMCID: PMC4411476) (PMID: 25712262).

154. Colangelo, C., Ivosev, G., Chung, L., Abbott, T., Shifman, M., Sakaue, F., Cox, D., Kitchen, R., Burton, L., Tate, S., Gulcicek, E., Bonner, R., Rinehart, J., Nairn, A., and Williams, K. (2015) Development, Implementation, and Verification of a Targeted Proteome Assay Pipeline. Proteomics 15: 1202-1214 (PMCID: PMC4698340) (PMID: 25476245).

153. Chung J, Torta F, Masai K, Lucast L, Czapla H, Tanner LB, Narayanaswamy P, Wenk MR, Nakatsu F, De Camilli P. (2015) Intracellular Transport. PI4P/phosphatidylserine countertransport at ORP5- and ORP8-mediated ER-plasma membrane contacts. Science 349(6246):428-32 (PMCID: PMC4638224) (PMID: 26206935)

152. Chung, J., Nakatsu, F., Baskin, J.M., De Camilli, P. (2015) Plasticity of PI4KIIIα interactions at the plasma membrane. EMBO Rep. 16(3): 312-20 (PMCID: PMC4364870) (PMID: 25608530).


151. Zhang, Y. and Chandra, S.S. (2014). Oligomerization of Cysteine String Protein alpha mutants causing adult neuronal ceroid lipofuscinosis. Biochim Biophys Acta 1842(11):2136-46 (PMCID: PMC4188699) (PMID:25064588).

150. Xu, J.; Chatterjee, M.; Baguley, T. D.; Brouillette, J.; Kurup, P.; Kanyo, J.; Zhang, Y.; Seyb, K.; Ononenyi, C.; Anderson, G.M.; Gresack, J.; Cuny, G.D.; Glicksman, M.A.; Greengard, P.; Lam, T.T.; Nairn, A.G.; Tautz, L.; Ellman, J.A.; Lombroso, P.J. (2014) Inhibitors of the tyrosine phosphatase STEP Reverse Cognitive Deficits in a Mouse Model of Alzheimer’s Disease. PLOS Biology, 12(8):e1001923. (PMCID: PMC4122355) (PMID: 25093460).

149. Wu, Y., O'Toole, E.T., Girard, M., Ritter, B., Messa, M., Liu, X., McPherson, P., Ferguson, S.M., De Camilli P. (2014) A dynamin 1-, dynamin 3- and clathrin-independent pathway of synaptic vesicle recycling mediated by bulk endocytosis. Elife. 2014 Jun 24; 3:e01621. doi: 10.7554/eLife.01621. (PMCID: PMC4107917) (PMID: 24963135).

148. Wu, X., Chi, R.J., Baskin, J.M., Lucast, L., Burd, C.G., De Camilli, P., and Reinisch, K.M. (2014) Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex. Dev. Cell.  28: 19-29 (PMCID: PMC4349574)(PMID: 24360784).

147. Vargas, K.J., Makhani, S., Davis, T., Westphal, C., Castillo, P.E., and Chandra, S.S. (2014). Synucleins regulate the kinetics of synaptic vesicle endocytosis. J. Neuroscience. 34, 9364-9376. (PMCID: PMC4087213) (PMID: 25009269).

146. Uys, JD, PJ Mulholland and DM Townsend (2014) Glutathione and redox signaling in substance abuse. Biomedicine and Pharmacotherapy 68(6): 799-807 (PMCID: PMC4455547) (PMID: 25027386).

145. Shibata, S., Arroyo, J.P., Castañeda-Bueno, M., Puthumana, J., Zhang, J., Uchida, S., Stone, K.L., Lam, T.T., Lifton, R.P. (2014) Angiotensin II signaling via protein kinase C phosphorylates Kelch-like 3, preventing WNK4 degradation. Proc. Natl. Acad. Sci. U S A. 111(43):15556-61 (PMCID: PMC4217463) (PMID: 25313067).

144. Shen, H., Giordano, F., Wu, Y., Chan, J., Zhu, C., Milosevic, I., Wu, X., Yao, K., Chen, B., Baumgart, T., Sieburth, D., De Camilli, P. (2014) Coupling between endocytosis and sphingosine kinase 1 recruitment. Nat. Cell Biol. 16(7): 652-62 (PMCID: PMC4230894) (PMID: 24929359).

143. Sharma V1, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B (2014) Panorama: A Targeted Proteomics Knowledge Base. J. Proteome Res. 13(9), 4205-10 (PMCID: PMC4156235) (PMID: 25102069).

142. Schauder CM, Wu X, Saheki Y, Narayanaswamy P, Torta F, Wenk MR,  De Camilli P, and Reinisch, KM.  (2014). Structure of a lipid-bound Extended-Synaptotagmin indicates a role in lipid transfer. Nature.  510: 552-555 (PMCID: PMC4135724) (PMID: 24847877).

141. Plattner, F., Hernandéz, A., Kistler, T. M., Pozo, K., Zhong, P., Yuen, E., Hawasli, A., Cooke, S., Tan, C., Guo, A., Weiderhold, T., Yan, Z., Bibb, J.A. (2014) Memory enhancement by targeting Cdk5 regulation of NR2B. Neuron 81: 1070-83 (PMCID: PMC4010123) (PMID:24607229)

140. Pirruccello M, Nandez R, Idevall-Hagren O, Alcazar-Roman A, Abriola L, Berwick SA, Lucast L, Morel D, De Camilli P. Identification of inhibitors of inositol 5-phosphatases through multiple screening strategies. ACS Chem Biol. 2014 Jun 20;9(6):1359-68. (PMCID: PMC4076014) (PMID: 24742366)  

139. Nandez R, Balkin DM, Messa M, Paradise S, Czapla H, Hein MY, Mann M, and De Camilli P. (2014) A role of OCRL in clathrin-coated pit fission and uncoating revealed by studies of Lowe syndrome cells. Elife. 2014 Aug 8;3:e02975. doi: 10.7554/eLife.02975 (PMCID: PMC4358339) (PMID: 25107275).

138. Meyer, D., Torres-Altoro, M.I., Tan, Z., Tozzi, A., Di Filippo, M., DiNapoli, V., Plattner, F., Kansy, J.W., Benkovic, S.A., Huber, J., Miller, D.B., Greengard, P., Calibressi, P., Rosen, C.L., Bibb, J.A. (2014) Ischemic stroke injury is mediated by aberrant Cdk5, J. Neurosci., 34(24) 8259-8267. (PMCID: PMC4051977) (PMID: 24920629)

137. Messa, M., Fernández-Busnadiego, R., Sun, E.W., Chen, H., Czapla, H., Wrasman, K., Wu, Y., Ko, G., Ross, T., Wendland, B., De Camilli, P. (2014) Epsin deficiency impairs endocytosis by stalling the actin-dependent invagination of endocytic clathrin-coated pits. Elife. 3:e03311. doi: 10.7554/eLife.03311 (PMCID: PMC4161027) (PMID: 25122462).

136. McClure-Begley T.D., Papke R.L., Stone K.A., Stokes, C., Levy A.D., Gelernter J., Xie P., Lindstrom J.M., Picciotto M.R. (2014) Rare human nicotinic acetylcholine receptor alpha 4 subunit (CHRNA4) variants affect expression and function of high affinity nicotinic acetylcholine receptors. J. Pharmacol. Exp. Therapeutics 348: 410-420 (PMCID: PMC3935145) (PMID: 24385388).

135. Ma, X.M., Miller, M.B., Vishwanatha, K.S., Gross, M., Wang, Y., Abbott, T., Lam, T.T., Mains, R.E., Eipper, B.A. (2014) Non-enzymatic domains of Kalirin7 contribute to spine morphogenesis through interactions with phosphoinositides and Abl. Mol. Biol. Cell 25(9):1458-71 (PMCID: PMC4004595) (PMID: 24600045).

134. Lee, M., Skoura, A., Park, E.J., Landskroner-Eiger, S., Jozsef, L., Luciano, A., Murata, T, Pasula, S., Dong, Y., Bouaouina, M., Calderwood, D., Ferguson, S.M., De Camilli, P., and Sessa, W.C. (2014) Dynamin-2 regulation of integrin endocytosis, but not VEGF signaling, is critical for developmental angiogenesis.  Development 141: 1465-1472  (PMCID: PMC3957370) (PMID: 24598168).

133. Kitchen, R.R., Rozowsky, J.S., Gerstein, M.B., and Nairn, A.G. (2014) Decoding neuroproteomics: integrating the genome, translatome, and functional neuroanatomy. Nature Neuroscience 17(11): 1491-1499. (PMCID: PMC4737617) (PMID: 25349915)

132. Idevall-Hagren O and De Camilli P. (2013) Manipulation of plasma membrane phosphoinositides using photoinduced protein-protein interactions. Methods Mol. Biol. 1148:109-148  (PMID: 24718798).

131. Frohlich F, Christiano R, Alcazar-Roman A, De Camilli  P, and Walther TC.  (2014) A role for eisosomes in maintenance of plasma membrane phosphoinositide levels.  Mol. Biol. Cell. 25(18): 2797-806 (PMCID: PMC4161514) (PMID: 25057013).

130. Chung, L, Colangelo, CM, and Zhao, H.(2014) Data Pre-Processing of Label-Free Multiple Reaction Monitoring (MRM) Experiments.  Biology (Basel) 3(2):383-402 (PMCID: PMC4085614) (PMID:24905083).

129. Cheadle, L. and Biederer, T.  (2014) Activity-dependent regulation of dendritic complexity by Semaphorin 3A through Farp1. Journal of Neuroscience 34:7999-8009 (PMCID: PMC4044256) (PMID:24899721

128. Cates, H, Thibault, M, Pfau, M, Heller, E, Eagle, A,  Gajewski, P, Bagot, R, Colangelo, C Abbott, T, Rudenko, G,  Neve, R, Nestler, R, Robison, A. (2014) Threonine 149 Phosphorylation Enhances ΔFosB Transcriptional Activity to Control Psychomotor Responses to Cocaine.  J. Neuroscience 34(34): 11461-11469 (PMCID: PMC4138349) (PMID: 25143625).

127. Cao, M., Milosevic, I., Giovedi, S., and De Camilli, P. (2014) Up-regulation of Parkin in endophilin mutant mice. J. Neurosci. 34: 16544-16549  (PMCID: PMC4252559) (PMID: 25471590).


126. Zhang, Y., Tang, W., Zhang, H., Niu, X., Xu, Y., Zhang, J., Gao, K., Pan, W., Boggon, T.J., Toomre, D., Min, W., and Wu, D. (2013) A Network of Interactions Enables CCM3 and STK24 to Coordinate UNC13D-Driven Vesicle Exocytosis in Neutrophils. Dev Cell 27: 215-26 (PMCID: PMC3834565) (PMID: 24176643).

125. Wu, M., Wu, X., and De Camilli, P. (2013) Calcium oscillations-coupled conversion of actin travelling waves to standing oscillations. Proc. Natl. Acad. Sci. USA. 4: 1339-1344 (PMCID: PMC3557052) (PMID: 23297209).

124. Wiseman, S.L., Shimizu, Y., Palfrey, H.C. and Nairn, A.C. (2013) Eukaryotic elongation factor-2 kinase (EF2K) is degraded by the proteasome in response to stimulation via the SCFβTRCP ubiquitin E3 ligase. J. Biol. Chem. 288: 17803-17811 (PMCID: PMC3682579) (PMID: 23640883).

123. Westphal, C. and Chandra, S.S. (2013). Monomeric synucleins generate membrane curvature. J. Biol. Chem. 288: 1829-1840 (PMCID: PMC3548493) (PMID: 23184946).

122. Shibata, S., Zhang, J., Puthumana, J., Stone, K.L., and Lifton, R.P. (2013) Kelch-like 3 and Cullin 3 regulate electrolyte homeostasis via ubiquitination and degradation of WNK4. Proc. Natl. Acad. Sci. U.S.A. 110: 7838-7843 (PMCID: PMC3651502) (PMID: 23576762).

121. Shibata, S., Rinehart, J., Zhang, J., Moeckel, G., Castañeda-Bueno, M., Stiegler, A.L., Boggon, T.J., Gamba, G., Lifton, R.P. (2013) Mineralocorticoid receptor phosphorylation regulates ligand binding and renal response to volume depletion and hyperkalemia. Cell Metabolism 18(5): 660-671 (PMCID: PMC3548493, PMID: 24206662).

120. Robison, A.J., Vialou, V., Mazei-Robison, M., Feng, J. Kourrich, S., Collins, M., Wee, S-M., Koob, G., Turecki, G., Neve, R., Thomas, M., Nestler, E. (2013) Behavioral and Structural Responses to Chronic Cocaine Require a Feedforward Loop Involving ΔFosB and Calcium/Calmodulin-Dependent Protein Kinase II in the Nucleus Accumbens Shell. J. Neurosci. 33: 4295-4307  (PMCID: PMC3658178) (PMID: 23467346).

119. Park, R., Shen, H., Liu, L., Liu, X., Ferguson, S.M., and De Camilli, P. (2013) Dynamin triple knockout cells reveal off target effects of a commonly used dynamin inhibitor. J. Cell Sci. 126: 5305-5312 (PMCID:PMC3828596) (PMID: 24046449).

118. Newton, S.S., Fournier, N.M., Duman, R.S. (2013) Vascular growth factors in neuropsychiatry. Cell. Mol. Life Sci. 70(10): 1739-52 (PMCID: PMC3951730, PMID: 23475069).

117. McClure-Begley, T., Stone, K.L., Marks, M.J., Grady, S.R., Colangelo, C.M., Lindstrom, J.M., and Picciotto, M.R. (2013) Exploring the nicotinic acetylcholine receptor-associated proteome with iTRAQ and transgenic mice, Genomics, Proteomics & Bioinformatics, 11(4): 207-18 (PMCID: PMC3806329, PMID: 23891776).

116. Krebs CE, Karkheiran S, Powell JC, Cao M, Makarov V, Darvish H, Di Paolo G, WalkerRH, Shahidi GA, Buxbaum JD, De Camilli P, Yue Z, and Paisan-Ruiz C.  2013. The Sac1 domain of SYNJ1 identified mutated in a family with early-onsetprogressive Parkinsonism with generalized seizures.  Hum. Mutat. 34: 1200-1207. (PMCID: PMC3790461) (PMID:23804563)

115. Kim, I., Pan, W., Jones, S.A., Zhang, Y., Zhuang, X., and Wu, D. (2013). Clathrin and AP2 are required for PtdIns(4,5)P2-mediated formation of LRP6 signalosomes. J. Cell Biol. 200: 419-428. (PMCID: PMC3575536) (PMID: 23400998).

114. Ivanov, A.R., Colangelo, C.M., Dufresne, C.P., Friedman, D.B., Lilley, K.S., Mechtler, K., Phinney, B.S., Rose, K.L., Rudnick, P.A., Searle, B.C., Shaffer, S.A., Weintraub, S.T. (2013) Interlaboratory studies and initiatives developing standards for proteomics. Proteomics 13(6):904-909 (PMCID: PMC3863631) (PMID: 23319436).

113. Giordano, F., Saheki, Y., Idevall-Hagren, O., Colombo, S.F., Pirruccello, M., Milosevic, I., Gracheva, E.O., Bagriantsev, S.N., Borgese, N., De Camilli, P. (2013) PI(4,5)P2-Dependent and Ca(2+)-Regulated ER-PM Interactions Mediated by the Extended Synaptotagmins. Cell. 153: 1494-1509 (PMCID: PMC3716012) (PMID: 23791178).

112. Devereaux, K., Dall’Armi, C., Alcazar-Roman, A., Ogasawara, Y., Zhou, X., Wang, F., Yamamoto, A., De Camilli, P., and Di Paolo, G. (2013) Regulation of mammalian autophagy by Class II and III Pi 3-kinases through PI3P synthesis. PLOS ONE. 8:e76405. (PMCID: PMC3789715) (PMID:24098492).

111. Destaing, O., Ferguson, S.M., Grichine, A., Oddou, C., De Camilli, P., Albiges-Rizo, C., and Baron, R. (2013) Essential function of dynamin in the invasive properties and actin architecture of v-SRC induced podosomes/invadosomes. PLOS ONE. 10: e77956. (PMCID: PMC3857171) (PMID: 24348990).

110. Craft, G.E., Chen, A., Nairn, A.C. (2013) Recent Advances in Quantitative Neuroproteomics. Methods (Elsevier) issue on Quantitative Proteomics 61(3) 186-218 (PMCID: PMC3891841) (PMID: 23623823).

109. Colangelo CM, Chung L, Bruce C, Chung KH (2013) Review of Software Tools for Design and Analysis of Large scale MRM Proteomic Datasets in Methods (Elsevier) issue on Quantitative Proteomics 61(3): 287-98 (PMCID:PMC3775261) (PMID: 23702368).

108. Cai X, Xu Y, Cheung AK, Tomlinson RC, Alcazar-Roman A, Murphy L. Billich A,Zhang B, Feng Y, Klumpp M, Rondeau JM, Fazal AN, Wilson CJ, Myer V, JobertyG, Bouwmeester T, Babow MA, Finan PM, Porter JA, Ploegh HL, Baird D, DeCamilli P, Tallarico JA, and Huang Q. (2013) PIKfyve, a Class III PI kinase, is the target of the small molecular IL-12/IL-23 inhibitor apilimod and a player in toll-likereceptor signaling.  Chem. Biol.  20: 912-921 (PMCID: PMC4878021) (PMID:23890009)

107. Bruce, C., Stone, K., Gulcicek, E., and Williams, K. (2013) Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein-Profiling Technologies. Current Protocols Bioinformatics 41:13.21.1-13.21.17. (PMCID: PMC3688054) (PMID: 23504934).

106. Armbruster M, Messa M, Ferguson SM, De Camilli P, and Ryan TA. (2013) Dynamin phosphorylation controls optimization of endocytosis for brief action potential bursts. eLife, e00845. (PMCID: PMC3728620) (PMID: 23908769).

105. Antinone, S.E., Ghadge, G.D., Lam, T., Roos, R., and Green, W.N. (2013) Human Superoxide Dismutase (SOD1) is palmitoylated and familial ALS-linked SOD1 mutants are abnormally palmitoylated. J. Biol. Chem. 288: 21606-17 (PMCID: PMC3724620) (PMID: 23760509).


104. Zhang,Y., Henderson, M.X., Colangelo, C.M., Ginsberg, S., Bruce, C., Wu, T., and Chandra, S.S. (2012) Identification of CSPα clients reveals a role in dynamin 1 regulation. Neuron 74(1):136-50. (PMCID: PMC3328141) (PMID: 22500636) (YPED Repository).

103. Wu, M., and De Camilli, P. (2012) Supported native plasma membranes as platforms for reconstitution and visualization of endocytic membrane budding. in Lipids, Methods in Cell Biology (Wenk, M.R., Di Paolo, G., eds) Academic Press, volume 108:3-18. (PMID: 22325595) .

102. Sousa, L., Lax, I., Shen, H., Ferguson, S.M., De Camilli, P., and Schlessinger, J. (2012) Suppression of EGFR endocytosis by dynamin depletion reveals that EGFR signaling occurs primarily at the plasma membrane. Proc. Nat. Acad. Sci. 109:4419-2 (PMCID: PMC3311323) (PMID: 22371560) .

101. Shen H, Pirruccello M and De Camilli P. (2012) SnapShot: Membrane Curvature Sensors and Generators. Cell. 150: 1300-1300.e2 doi.1016/j.cell.2012.08.017. (PMID: 22980986).

100. Sathyanesan, M., Girgenti, M.J., Banasr, M., Stone, K., Bruce, C., Guilchicek, E., Wilczak-Havill, K., Nairn, A., Williams, K., Sass, S., Duman, J.G., Newton, S.S. (2012) A molecular characterization of the choroid plexus and stress-induced gene regulation. Transl Psychiatry 2(7): e139. (PMCID: PMC3410626) (PMID: 22781172) (YPED Repository).

99. Saheki, Y., and De Camilli, P. (2012) Synaptic vesicle endocytosis in The Synapse. (M. Sheng, B. Sabatini, and T.C. Südhof eds) Cold Spring Harb. Perspect. Biol. 4:  a005645. doi: 10.1101/cshperspect.a005645. (PMCID: PMC3428771)(PMID: 22763746).

98.  Rodriguez L, Simeonato E, Scimeni P, Anselmi F, Cali B, Crispino G, Ciubotaru CB, Bortolozzi M, Ramiro FG, Majumder P, Arslan E, De Camilli P, Pozzan T, and Mammano F. (2012). Reduced phosphatidylinositol 4,5-bisphosphate synthesis impairs inner ear Ca2+ signaling and high frequency hearing acquisition. Proc. Natl. Acad. Sci. 109: 14013-14018. (PMCID: PMC3435166) (PMID: 22891314).

97.  Pirruccello, M., and De Camilli, P. (2012) The Inositol 5-phosphatases: insights from the Lowe Syndrome Protein OCRL. Trends. Biochem. Sci. 37(4):134-143. (PMCID: PMC3323734) (PMID: 22381590).

96.  Nakatsu, F., Baskin, J.M., Chung, J., Tanner, L.B., Shui, G., Lee, S.Y., Pirruccello, M., Hao, M., Ingolia, N.T., Wenk, M.R., and De Camilli, P. (2012). PtdIns4P synthesis at the plasma membrane and its impact on PtdIns(4,5)P2 dynamics to control plasma membrane identity. J. Cell Biol. 199: 1003-1016. (PMCID: PMC3518224) (PMID: 23229899).

95.  Lou, X, Fan F, Messa M, Raimondi A, Wu Y, Looger LL, Ferguson SM, De Camilli P. (2012) Reduced release probability prevents vesicle depletion and transmission failure at dynamin mutant synapses. Proc Natl Acad Sci 109(8):E515-23. (PMCID: PMC3286982) (PMID:22308498).

94.  Idevall-Hagren O, Dickson EJ, Hille B, Toomre DK, and De Camilli P. (2012) Optogenetic control of phosphoinositide metabolism. Proc. Natl. Acad. Sci. 109: 2316-2323. (PMCID: PMC3435206, PMID: 22847441).

93.  Ferguson, S.M., and De Camilli, P. (2012) Dynamin, a membrane-remodeling GTPase. Nature Rev. Mol. Cell Biol. 13: 75-88. (PMCID: PMC3519936) (PMID: 22233676).

92.  Clarke, D., Bhardwaj, N., Gerstein, M.B. (2012) Novel insights through the integration of structural and functional genomics data with protein networks. J Struct Biol 179: 320-326. (PMCID: PMC4830681, PMID: 22343087).

91.  Cheadle, L., Biederer, T. (2012) The novel synaptogenic protein Farp1 links postsynaptic cytoskeletal dynamics and transsynaptic organization. J Cell Biol. 199: 985-1001. (PMCID: PMC3518221, PMID: 23209303).


90.  Yip, K.Y., Utz, L., Sitwell, S., Hu, X., Sidhu, S.S., Turk, B.E., Gerstein, M., Kim, P.M. (2011) Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. BMC Biology 9:53. (PMCID: PMC3224579) (PMID: 21835011).

89.  Shen, H., Ferguson, S.M., Dephoure, N., Park, R., Volpicelli-Daley, L., Gygi, S., Schlessinger, J., and De Camilli P. (2011) Constitutive activated Cdc42-associated kinase (Ack) phosphorylation at arrested endocytic clathrin-coated pits of cells that lack dynamin. Mol Biol Cell. 22(4): 493-502. (PMCID: PCM3038647) (PMID: 21169560).

88.  Rozowsky, J. , Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N., Bhardwaj, N., Rubin, M., Snyder, M., Gerstein, M. (2011) AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology 7:522. (PMCID: PMC3208341) (PMID: 21811232).

87.  Rinehart J, Vazquez N, Kahle KT, Hodson CA, Ring AM, Gulcicek EE, Louvi, A., Bobadilla, N., Gamba, G., and Lifton, R.P. (2011) WNK2 kinase is a novel regulator of essential neuronal cation-chloride cotransporters. J. Biol. Chem. 286: 30171-30180. (PMC: PMC3191056) (PMID: 21733846).

86.  Raimondi, A., Ferguson, S.M., Lou, X., Armbruster, M., Paradise, S., Giovedi, S., Messa, M., Kono, N., Takashi, J., Cappello, V., O’Toole, E., Ryan, T.A., and De Camilli, P. (2011) Overlapping role of dynamin isoforms in synaptic vesicle endocytosis. Neuron 70:1100-1114. (PMCID: PMC3190241) (PMID: 21689597).

85.  Pirruccello, M., Swan, L.E., Folta-Stogniew, E., and De Camilli, P. (2011) Recognition of the F&H motif by the Lowe Syndrome protein OCRL.  Nat Struct Mol Biol. 2011 18(7):789-795. (PMCID: PMC3130824) (PMID: 21666675).

84.  Milosevic, I., Giovedi, S., Lou, X., Raimondi, A., Collesi, C., Paradise, S., O’Toole, E., Ferguson, S., Cremona, O., DeCamilli, P. (2011) Recruitment of endophilin to clathrin coated pit necks is required for uncoating but is dispensable for fission. Neuron 72: 587-601. (PMCID: PMC3258500) (PMID: 22099461).

83.  Luo, R. and Zhao H. (2011). Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data. Annals of Applied Statistics, Ann Appl Stat. 5(2A):725–745. (PMCID: PMC3233205) (PMID: 22162986).

82.  Kiraly, D.D., Stone, K.L., Colangelo, C.M., Abbott, T., Wang, Y., Mains, R.E., Eipper, B.A. (2011). Identification of Kalirin-7 as a Potential Post-Synaptic Density Signaling Hub. J Proteome Res. 10(6):2828-2841. (PMCID: PMC3107868) (PMID: 21488700).

81.  Gianoulis, T.A., Agarwal, A., Snyder, M., Gerstein, M.B. (2011) The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biology, 12:R32. (PMCID: PMC3129682) (PMID: 21453526).

80.  Bordner, K.A., George, E.D., Carlyle, B.C., Duque, A., Kitchen, R.R., Lam, T.T., Colangelo, C.M., Stone, K.L., Abbott, T.B., Mane, S.M., Nairn, A.C., Simen, A.A. (2011) Functional genomic and proteomic analysis reveals disruption of myelin related genes and translation in a mouse model of early life neglect. Front Psychiatry. 2:18. (PMCID: PMC3098717) (PMID: 21629843) (YPED Repository).

79.  Bianchetta MJ, Lam TT, Jones SN, Morabito MA. (2011). Cyclin-dependent kinase 5 regulates PSD-95 ubiquitination in neurons. J Neurosci. 31:12029-35. (PMCID: PMC3190401) (PMID: 21849563) (YPED Repository).


78.  Yim, Y.I., Sun, T., Wu, L.G., Raimondi, A., De Camilli, P., Eisenberg, E., Greene, L.E. (2010) Endocytosis and clathrin-uncoating defects at synapses of auxilin knockout mice. Proc Natl Acad Sci 2;107(9):4412-7. (PMCID: PMC2840126) (PMID:20160091).

77.  Xu, W., Wang, P., Petri, B., Zhang, Y., Tang, W., Sun, L., Kress, H., Mann, T., Shi, Y., Kubes, P., Wu, D. (2010) Integrin-induced PIP5K1C kinase polarization regulates neutrophil polarization, directionality, and in vivo infiltration. Immunity 33(3):340-50. (PMCID: PMC2947797) (PMID:20850356).

76.  Wu, M., Huang, B., Graham, M., Raimondi, A., Heuser, J.E., Zhuang, X., De Camilli, P. (2010) Coupling between clathrin-dependent endocytosis budding and F-BAR-dependent tubulation in a cell-free system. Nat. Cell Bio. 9: 902-908. (PMCID: PMC3338250) (PMID: 20729836).

75.  Volpicelli-Daley, L.A., Lucast, L., Gong, L.W., Sasaki, J., Sasaki, T., Abrams, C.S., Kanaho, Y., and De Camilli P. (2010) Phosphatidylinositol 4-phosphatase 5-kinases and phosphatidylinositol 4,5-bisphosphate synthesis in the brain. J. Biol. Chem. 285: 28708-28714. (PMCID: PMC2937898) (PMID: 20622009).

74.  Swan, L.E., Tomasini, L., Pirruccello, M., Lunardi, J., and De Camilli, P. (2010) Two closely related endocytic proteins that share a common OCRL binding motif with APPL1. Proc. Nat. Acad. Sci. 107: 3511-16. (PMCID: PMC2840420) (PMID: 20133602).

73.  Sumioka A, Yan D, Tomita S. (2010). TARP phosphorylation regulates synaptic AMPA receptors through lipid bilayers. Neuron 66: 755-67. (PMCID: PMC2887694) (PMID: 20547132).

72.  Rajagopal, C., Stone, K., Mains, R., and Eipper, B. (2010) Secretion Stimulates Intramembrane Proteolysis of a Secretory Granule Membrane Enzyme. J. Biol. Chem. 285: 34632-42. (PMCID: PMC2966079) (PMID: 20817724) (YPED Repository).

71.  Nakatsu F, Perera R, Lucast L, Zoncu R, Domin J, Gertler F, Toomre D, and De Camilli P. (2010) Dual role of the inositol 5-phosphatase SHIP2 in clathrin-coated pit dynamics and signaling. J. Cell Biol. 190: 307-315. (PMCID: PMC2922640) (PMID: 20679431).

70.  Lam, H.Y.K., Kim, P.M., Tonikian, R., Mok J., Turk, B., Bader, G., Boone. C., Snyder, M., Gerstein, M.B. (2010) MOTIPS: An Automated Motif Analysis Pipeline for Predicting Targets of Modular Protein Domains, BMC Bioinformatics 11: 243. (PMCID: PMC2882932) (PMID: 20459839).

69.  Hu, F., Padukkavidana, T., Vægter, C.B., Brady, O.A., Zheng, Y., Mackenzie, I.R., Feldman, H.H., Nykjaer, A., Strittmatter, S.M. (2010) Sortilin-Mediated Endocytosis Determines Levels of the Fronto-Temporal Dementia Protein, Progranulin. Neuron 68: 654-667. (PMCID: PMC2990962) (PMID: 21092856).

68.  Gimbel, D.A., Nygaard, H.B., Coffey, E.E., Gunther, E.C., Lauren, J., Gimbel, Z.A., Strittmatter, S.M. (2010) Memory Impairment in Transgenic Alzheimer Mice Requires Cellular Prion Protein. J. Neurosci, 30: 6367-6674. (PMCID: PMC3323924) (PMID: 20445063).

67.  Fogel, A.I., Li, Y., Wang, Q., Lam, T.T., Modis, Y. and Biederer, T. (2010) N-Glycosylation at the SynCAM immunoglobulin interface modulates synaptic adhesion. J. Biol. Chem. 285: 34864-34874 (featured on cover). (PMCID: PMC2966101) (PMID: 20739279).

66.  Alexander, J.K., Govind, A.P., Drisdel, R.C., Blanton, M.P., Vallejo, Y., Lam, T.T. and Green, W.N. (2010) Palmitoylation of Nicotinic Acetylcholine Receptors. J. Molec. Neurosci. 40:12-20. (PMCID: PMC3523180) (PMID: 19693711).


65.  Zoncu, R., Perera, R., Balkin DM, Toomre D, and De Camilli P. (2009) A phosphoinositide switch controls the maturation and signaling properties of APPL endosomes. Cell 136:1110-1121. (PMCID: PMC2705806) (PMID: 19303853)

64.  Verstreken, P., Ohyama, T., Haueter, C., Habets, R., Lin, Y.Q., Swan, L.E., Ly, C.V., Venken, K., De Camilli. P., and Bellen, H.J. (2009) Tweek, an evolutionary conserved protein with no obvious motifs, is required for synaptic vesicle recycling. Neuron 63:203-215. (PMCID: PMC2759194) (PMID: 19640479).

63.  Vasudevan L, Jeromin A, Volpicelli-Daley L, De Camilli P, Holowka D, and Baird B. (2009) The beta and gamma isoforms of type I PIP5 kinase regulate distinct stages of Ca2+ signaling in mast cells. J. Cell Sci.122:2567-2574. (PMCID: PMC2704887) (PMID: 19549683).

62.  Stone, K.L. and Williams, K.R (2009) Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins in The Protein Protocols Handbook, 3rd edition (Walker, J., ed.) 937-946.

61.  Stone, K.L. , Gulcicek E. E. and Williams, K.R (2009) Enzymatic Digestion of Proteins in Solution and in SDS Polyacrylamide Gels in The Protein Protocols Handbook, 3rd edition (Walker, J., ed.) 901-913.

60.  Rinehart, J., Maksimova, Y.D. , Tanis, J.E., Stone, K.E., Hodson, C.A., Zhang, J., Risinger, M., Pan, W., Wu, D., Colangelo, C.M., Forbush, B., Joiner, C.H., Gulcicek, E.E., Gallagher, P.G., and Lifton, R.P. (2009) Sites of regulated phosphorylation that control K-Cl cotransporter activity. Cell. 138(3):525-36. (PMCID: PMC2811214) (PMID: 19665974).

59.  Rajagopal, C., Stone, K., Francone, V, Mains, R., Eipper, B. (2009) Secretory Granule to the Nucleus: Role of a multiply phosphorylated intrinsically unstructured domain. J. Biol. Chem., 284:25723-25734. (PMCID: PMC2757974) (PMID: 19635792).

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57.  Pang, H., Tong. T., Zhao. H. (2009) Shrinkage-based diagonal discriminant analysis and its applications in high-dimensional data. Biometrics, 61: 1021-1029. (PMCID: PMC2794982) (PMID: 19302409)

56.  McCrea H and De Camilli P (2009) Mutations in Phosphoinositide Metabolizing Enzymes and Human Disease. Physiology. 24:8-16. (PMCID: PMC3499097) (PMID: 19196647)

55.  Mao, Y.S., Yamaga, M., Zhu, X., Wei, Y., Sun, H.Q., Wang, J., Yun, M., Wang, Y., Di Paolo, G., Bennett, M., Mellman, I., Abrams, C.S., De Camilli, P., Lu, C.Y., and Yin, H. (2009) Essential and unique roles of PIP5K-γ and -α in FCγ receptor-mediated phagocytosis. J. Cell Biol. 184:281-296. (PMCID: PMC2654300) (PMID: 19153220).

54.  Mao, Y., Balkin, D. M., Zoncu, R., Erdmann, K., Tomasini, L., Hodsdon, M. E., De Camilli, P. (2009) A PH domain within the Lowe Syndrome protein OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolism. EMBO J. 28:1831-1842. (PMCID: PMC2711190) (PMID: 19536138).

53.  Luo, R., Colangelo, C.M., Sessa, W.C., Zhao, H. (2009) Bayesian analysis of iTRAQ data with nonrandom missingness: Identification of differentially expressed proteins. Stat Biosci. 1(2):228-245. (PMCID: PMC3172970) (PMID: 21927625)

52.  Liu, Y., Kim, I., Zhao, H., (2009) Protein interaction predictions from diverse sources. New Developments in Biostatistics and Bioinformatics, (Eds J.Fan, X. Lin, and J.S. Liu), pp 159-178. World Scientific, New Jersey.

51.  Li, X., Zhao, H. (2009) Weighted random subspace method for high dimensional data classification. Statistics and Its Interfaces, 2:153-159. (PMCID: PMC3170928) (PMID: 21918713)

50.  Laurén, J., Gimbel, D.A., Nygaard, H.B., Gilbert JW, Strittmatter SM. (2009) Cellular Prion Protein Mediates Impairment of Synaptic Plasticity by Amyloid-ß Oligomers. Nature 457:1128-1132. (PMCID: PMC2748841) (PMID: 19242475).

49.  Hirunsatit, R., George, E.D., Lipska, B.K., Elwafi, H.M., Sander, L., Yrigollen, C.M., Gelernter, J., Mutirangura, A., Grigorenko, E.L., Lappalainen, J., Nairn, A.C., Kleinman, J.E., and Simen. A.A. (2009) Twenty-one-base-pair insertion polymorphism creates an enhancer element and potentiates SLC6A1 GABA transporter promoter. Pharmacogenetics and Genomics. 19: 53-65, (PMCID: PMC2791799) (PMID: 19077666).

48.  Frost A, Unger VM and De Camilli P. (2009) The BAR domain superfamily: Membrane-molding macro-molecules. Cell. 137: 191-196. (PMCID: PMC4832598, PMID: 19379681).

47.  Ferguson S, Raimondi A, Paradise S, Shen H, Mesaki K, Destaing O, Ko G, Cremona O, O'Toole E, and De Camilli P. (2009) Coordinated actions of actin and BAR proteins upstream of dynamin at endocytic clathrin-coated pits. Dev. Cell. 17:811-822. (PMCID: PMC2861561) (PMID: 20059951).

46.  Fairn GD, Ogata K, Botelho RJ, Stahl PD, Anderson RA, De Camilli P, Meyer T, Wodak S, and Grinstein S. (2009) An electrostatic switch displaces phosphatidylinositol phosphate kinases from the membrane during phagocytosis. J. Cell. Biol. 187:701-714 (PMCID: PMC2806594) (PMID: 19951917).


45.  Yu, W., He, Z., Liu, J. and Zhao, H. (2008) Improving mass spectrometry peak detection using multiple peak alignment results. J Proteome. Res 7, 123-129. (PMID: 18030999).

44.  Voronov, S.V., Frere, S.G., Giovedi, S., Pollina, E. A., Schmidt, C., Akeson, E.C., Wenk, M.R., Zhang, H., Cimasoni, L., Borel, C., Antonorakis, S.E., Arancio, O., Davisson, M.T., Gardiner, K., De Camilli, P. and Di Paolo, G. (2008) SYNJ1-linked phosphoinositide dyshomeostasis and cognitive deficits in mouse models of Down Syndrome. Proc. Nat. Acad. Sci. 105: 9415-9420. (PMCID: PMC2453748) (PMID: 18591654).

43.  Tong, T., Zhao, H., (2008) Practical guidelines for assessing power and false discovery rate for a fixed sample size in microarray experiments. Statistics in Medicine, 27: 1960-1972. (PMCID: PMC3157366) (PMID: 18338314)

42.  Pan, W., S.C. Choi, H. Wang, Y. Qin, L. Volpicelli-Daley, L. Swan, L. Lucast, C. Khoo, X. Zhang, L. Li, C.S. Abrams, S.Y. Sokol, and D. Wu, (2008) Wnt3a-mediated formation of phosphatidylinositol 4,5-bisphosphate regulates LRP6 phosphorylation. Science 321 (5894): 1350-1353. (PMCID: PMC2532521) (PMID: 18772438).

41.  Liu, Y., Kim, I., Zhao, H. (2008) Protein interaction predictions from diverse sources. Drug Discovery Today, 13: 409-416. (PMCID: PMC3164358) (PMID: 18468558)

40.  Liu, J., Yu, W., Wu, B. and Zhao, H. (2008) Bayesian mass spectra peak alignment from mass charge ratios. Cancer Inform. 6:217-241. (PMCID: PMC2623297) (PMID: 19259411)

39.  Hayashi, M., Raimondi, A., O'Toole E, Paradise S, Collesi C, Cremona O, Ferguson SM, and De Camilli, P. (2008) Cell and stimulus dependent heterogeneity of synaptic vesicle endocytic recycling revealed by studies of dynamin 1-null neurons. Proc. Nat. Acad. Sci. 105: 2175-2180. (PMCID: PMC2538894) (PMID: 18250322).

38.  Gong, L.W. and De Camilli P. (2008) Regulation of postsynaptic AMPA responses by synaptojanin I. Proc. Nat. Acad. Sci. 105: 17561-17566. (PMCID: PMC2579885) (PMID: 18987319).

37.  Frost, A., Perera, R., Roux, A., Spasov, K., Destaing, O., Egelman, E.H., De Camilli, P. and Unger, V.M. (2008) Structural basis of membrane invagination by F-BAR domains. Cell 132, 807-817. (PMCID: PMC2384079) (PMID: 18329367).

36.  Destaing O, Sanjay A, Itzstein C, Horne WC, Toomre D, De Camilli P, Baron R. The tyrosine kinase activity of c-Src regulates actin dynamics and organization of podosomes in osteoclasts. Mol Biol Cell. 2008 Jan;19(1):394-404. (PMCID: PMC2174183) (PMID: 17978100

35.  Chen, L., Tong, T., Zhao, H. (2008) Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics, 24: 2015-2022. (PMCID: PMC2732206) (PMID: 18635565). 

34.  Bjornson, R.D., Carriero, N.J., Colangelo, C., Shifman, M., Cheung, K.H., Miller, P.L. and Williams, K. (2008) X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. J Proteome. Res 7(1), 293-299. (PMCID:PMC3863625) (PMID: 17902638).


33.  Zoncu, R., Perera, R.M., Sebastian, R., Nakatsu, F., Chen, H., Balla, T., Ayala, G., Toomre, D. and De Camilli, P.V. (2007) Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate. Proc. Natl. Acad. Sci. 104, 3793-3798. (PMCID: PMC1805489) (PMID: 17360432).

32.  Yu, W., Liu, J., Colangelo, C., Gulcicek, E. and Zhao, H. (2007) A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC-MS spectrometry. Comput. Biol. Chem 31, 215-221. (PMCID: PMC4878675)   (PMID: 17499548).

31.  Yu, E.Z., Burba, A.E. and Gerstein, M. (2007) PARE: a tool for comparing protein abundance and mRNA expression data. BMC. Bioinformatics. 8, 309 - 313. (PMCID: PMC2000916) (PMID: 17718915).

30.  Volpicelli-Daley, L. and De Camilli, P. (2007) Phosphoinositides' link to neurodegeneration. Nat. Med. 13, 784-786. (PMID: 17618267).

29.  Stone, K.L., Crawford, M., McMurray, W., Williams, N. and Williams, K.R. (2007) Identification of Proteins Based on MS/MS Spectra and Location of Post-translational Modifications. In: Peptide Characterization and Application (Fields, G., Ed.), Vol. 386, pp. 57-77. Humana Press, Totowa, NJ. (PMID: 18604942).

28.  Stone, K., Bjornson, R.D., Blasko, G., Cofrancesco, R., Carriero, N.J., Colangelo, C., Crawford, J., Crawford, M., DaSilva, N., Deluca, J., Elliott, J., Elliott, M., Flory, P., Folta-Stogniew, E., Gulcicek, E., Kong, Y., Lam, T., Lee, J., Lin, A., LoPresti, M., Mane, S., McMurray, W., Tikhonova, I., Westman, S., Williams, N., Wu, T., Zhao, H. and Williams, K. (2007) Invited Review. Keck Foundation Biotechnology Resource Laboratory, Yale University, Yale Journal Biology & Medicine 80, 195-211.

27.  Shifman, M.A., Li, Y., Colangelo, C.M., Stone, K.L., Wu, T.L., Cheung, K.H., Miller, P.L. and Williams, K.R. (2007) YPED: a web-accessible database system for protein expression analysis. J Proteome. Res 6, 4019-4024. (PMCID:PMC3863627) (PMID: 17867667).

26.  Olausson, P., Jentsch, J.D., Krueger, D.D., Tronson, N.C., Nairn, A.C. and Taylor, J.R. (2007) Orbitofrontal cortex and cognitive-motivational impairments in psychostimulant addiction: evidence from experiments in the non-human primate. Ann. N. Y. Acad. Sci. 1121, 610-638. (PMID: 17698993).

25.  Mani, M., Lee, S.Y., Lucast, L., Cremona, O., Di Paolo, G., De Camilli, P. and Ryan, T.A. (2007) The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals. Neuron 56, 1004-1018. (PMCID:PMC3653591) (PMID: 18093523).

24.  Krueger, D.D. and Nairn, A.C. (2007) Expression of PKC substrate proteins, GAP-43 and neurogranin, is downregulated by cAMP signaling and alterations in synaptic activity. Eur. J Neurosci. 26, 3043-3053. (PMID: 18005072).

23.  Fogel, A.I., Akins, M.R., Krupp, A.J., Stagi, M., Stein, V. and Biederer, T. (2007) SynCAMs organize synapses through heterophilic adhesion. J Neurosci. 27, 12516-12530. (PMID: 18003830).

22.  Ferguson, S.M., Brasnjo, G., Hayashi, M., Wölfel, M., Collesi, C., Giovedi, S., Raimondi, A., Gong, L.W., Paradise, S., O'Toole, E., Flavell, R., Cremona, O., Miesenböck, Ryan, T.A. and De Camilli, P. (2007) A Selective Activity Dependent Requirement for Dynamin 1 in Synaptic Vesicle Endocytosis. Science. 316: 570-574. (PMID: 17463283).

21.  Erdmann, K.S., Mao, Y., McCrea, H.J., Zoncu, R., Lee, S., Paradise, S., Modregger, J., Biemesderfer, D., Toomre, D. and De Camilli, P. (2007) A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway. Dev. Cell 13, 377-390. (PMCID: PMC2025683) (PMID: 17765681).

20.  Andrade, E.C., Krueger, D.D. and Nairn, A.C. (2007) Recent advances in neuroproteomics. Curr. Opin. Mol. Ther. 9, 270-281. (PMCID:PMC3373961) (PMID: 17608026).


19.  Yu, W., Wu, B., Liu, J., Li, X., Stone, K., Williams, K.R. and Zhao, H. (2006) MALDI-MS data analysis for disease biomarker discovery. Methods Mol. Biol. 328, 199-216. (PMID: 16785651).

18.  Yu, W., Wu, B., Lin, N., Stone, K., Williams, K. and Zhao, H. (2006) Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Comput. Biol. Chem 30, 27-38. (PMID: 16298163).

17.  Yu, W., Wu, B., Huang, T., Li, X., Williams, K. and Zhao, H. (2006) Statistical methods in proteomics. In: Springer Handbook of Engineering Statistics (Pham, H., Ed.), pp. 623-638

16.  Yu, W., Li, X., Liu, J., Wu, B., Williams, K.R. and Zhao, H. (2006) Multiple peak alignment in sequential data analysis: a scale-space-based approach. IEEE/ACM. Trans. Comput. Biol. Bioinform. 3, 208-219, (PMID: 17048459).

15.  Wu, T. (2006) Two-Dimensional Difference Gel Electrophoresis. In: New and Emerging Proteomics Techniques (Nedelkov, D. and Nelson, R., Eds.), Vol. 328, Chapter 5, pp. 71-96. Humana Press, Totowa, NJ.

14.  Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K. and Zhao, H. (2006) Ovarian Cancer Classification based on Mass Spectrometry Analysis of Sera. Cancer Informatics. 2, 123-132. (PMCID:PMC2675484) (PMID:19458764)

13.  Perera, R.M., Zoncu, R., Lucast, L., De Camilli, P. and Toomre, D. (2006) Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages. Proc. Natl. Acad. Sci. 103, 19332-19337. (PMCID: PMC1693868) (PMID: 17158794).

12.  Itoh, T. and De Camilli, P. (2006) BAR, F-BAR (EFC) and ENTH/ANTH domains in the regulation of membrane-cytosol interfaces and membrane curvature. Biochim. Biophys. Acta 1761, 897-912. (PMID: 16938488). 

11.  Folta-Stogniew, E. (2006) Oligomeric states of proteins determined by size-exclusion chromatography coupled with light scattering, absorbance, and refractive index detectors. In: New and Emerging Proteomics Techniques (Nedelkov, D. and Nelson, R., Eds.), Vol. 328, pp. 97-112. Humana Press, Totowa, NJ, (PMID: 16785643)

10.  Di Paolo, G. and De Camilli, P. (2006) Phosphoinositides in cell regulation and membrane dynamics. Nature 443, 651-657. (PMID: 17035995)

9. Colangelo, C.M. and Williams, K.R. (2006) Isotope-coded affinity tags for protein quantification. Methods Mol. Biol. 328, 151-158. (PMID: 16785647)

8. Bruce, C., Shifman, M.A., Miller, P. and Gulcicek, E.E. (2006) Probabilistic enrichment of phosphopeptides by their mass defect. Anal. Chem 78, 4374-4382. (PMCID: PMC2547851) (PMID: 16808444).


7. Svenningsson, P., Nairn, A.C. and Greengard, P. (2005) DARPP-32 mediates the actions of multiple drugs of abuse. AAPS J. 7(2): E353-60. (PMCID: PMC2750972) (PMID:16353915).

6. Shin, H.W., Hayashi, M., Christoforidis, S., Lacas-Gervais, S., Hoepfner, S., Wenk, M.R., Modregger, J., Uttenweiler-Joseph, S., Wilm, M., Nystuen, A., Frankel, W.N., Solimena, M., De Camilli, P. and Zerial, M. (2005) An enzymatic cascade of Rab5 effectors regulates phosphoinositide turnover in the endocytic pathway. J Cell Biol. 170: 607-618 (PMCID: PMC2171494) (PMID: 16103228).

5. Shifman, M., Sun, K., Colangelo, C., Cheung, K., Miller, P. and Williams, K. (2005) YPED: A Proteomics Database for Protein Expression Analysis. Symposium of American Medical Informatics Association (AMIA), October 22-26, 2005, Washington, DC. (PMCID: PMC1560545) (PMID: 16779398).

4. Lee, S.Y., Voronov, S., Letinic, K., Nairn, A.C., Di Paolo, G. and De Camilli, P. (2005) Regulation of the interaction between PIPKI gamma and talin by proline-directed protein kinases. J Cell Biol. 168: 789-799 (PMCID: PMC2171813) (PMID: 15738269).

3. Jin, M., Bateup, H., Padovan, J.C., Greengard, P., Nairn, A.C. and Chait, B.T. (2005) Quantitative analysis of protein phosphorylation in mouse brain by hypothesis-driven multistage mass spectrometry. Anal. Chem 77, 7845-7851. (PMID: 16351129).

2. Gulcicek, E.E., Colangelo, C.M., McMurray, W., Stone, K., Williams, K., Wu, T., Zhao, H., Spratt, H., Kurosky, A., Wu, B. (2005) Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. In Current Protocols in Bioinformatics (A. D. Baxevanis, D. B. Davison, R. D. M. Page, G. A. Petsko, L. D. Stein and G. D. Stormo, eds) pp 13.1.1 - 13.1.31. John Wiley & Sons Inc, Hoboken, NJ. (PMCID:PMC3863626) (PMID: 18428746).


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