the Gingras Laboratory

The Lunenfeld-Tanenbaum Research Institute

 

Publications

                 

Recent Publications

2015:

Lambert, J.-P., Tucholska, M., Go, C., Knight, J.D.R. and Gingras, A.-C.* Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes.  J Proteomics. 2015 Apr 6; 118:81-94.

St-Denis, N., Gabriel, M., Turowec, J.P., Gloor, G., Li, S.-C., Gingras, A.-C. and Litchfield, D.W. Systematic investigation of hierarchical phosphorylation by protein kinase CK2  J. Proteomics. 2014 ; 118: 49-62.

Knight, J.D.R., Liu, G., Zhang, J.P., Pasculescu, A., Choi, H. and Gingras, A.-C.** A web-tool for visualizing quantitative interaction proteomics data  Proteomics. 2014 ; 15:1432-6 .

Tsou, C.-C., Avtonomov, D., Larsen, B., Tucholska, M., Gingras, A.-C.** and Nesvizhskii, A.I.** DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics  Nature Methods. 2014 ; 12: 258-64 .

Lant, B., Yu, B., Goudreault, M., Holmyard, D., Knight, J.D.R., Xu, P., Zhao, L., Chin, K., Zhen, M., Gingras, A.-C. and Derry, W.B. CCM-3/STRIPAK promotes seamless tube extension through endocytic recycling  Nature Communication. 2014 ; 6: 6449.

Scifo, E., Szwajda, A., Soliymani, R., Dębski, J., Uusi-Rauva, K., Dadlez, M., Gingras, A.-C., Tynnella, J., Jalanko, A., Baumann, M., Lalowski, M. Proteomic Analysis of the Palmitoyl Protein Thioesterase 1 Interactome in SH-SY5Y Human Neuroblastoma Cells  J Proteomics. 2014 ; 123:42-53.

Tian, R., Wang, H., Gish, G.D., Petsalaki, E., Pasculescu, A., Shi, Y., Bagshaw, R., Hunter, H., Gingras, A.-C., Weiss, A. and Pawson, T. Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor  Proc Natl Acad Sci U. 2014 ; 112: E1594-603.

Coyaud, E., Mis, M., Dunham, W.H., Couzens, A.L., Gingras, A.-C., Angers, S. and Raught, B. BioID-based identification of SCF β-TrCP1/2 E3 ligase substrates  Mol Cell Proteomics. 2014 ; pii: mcp.M114.045658.

Nishimura, T., Padamsi, Z., Fakim, H., Milette, S., Dunham, W.H., Gingras, A.-C. and Fabian, M.R. Human 4E-T promotes circularization and decay of genes targeted by multiple silencing mechanisms  Cell Reports. 2014 ; pii: S2211-1247.

Mui, M., Zhou, Y., Chughtai, N., Gruosso, T., Knight, J., Park, M., Blanchette, P., Gingras, A.-C.** and Branton, P.** The human adenovirus type 5 E4orf4 protein targets two phosphatase regulators of the Hippo signaling pathway in inducing tumor cell specific death  J Virology. 2014 ; JVI03710-14.

Marcon, E., Jain, H., Bhattacharya, A., Collins, B.C., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J.J., Larsen, B., Lin, Z.-Y., Loppnau, P., Nguyen, T., Olsen, J., Phanse, S., Pu, S., Ravichandran, M., Seitova, A., Whiteaker, J.R., Zhong, G., Zhao, L., Zhong, N., Aebersold, R., Arrowsmith, C.H., Emili, A., Frappier, L.D., Gingras, A.-C.,Gstaiger, M., Koide, S., Kossiakoff, T., Paulovich, A.G., Sidhu, S., Wodak, S.F., Graslund, S., Greenblatt, J.F., Edwards, A.M. Mass spectrometry to validate antibodies for immunoprecipitation assays  Nature Methods. 2014 ; in press.

St-Denis, N., Gupta, G.D., Lin, Z.-Y., Gonzalez-Badillo, B., Pelletier, L.** and Gingras, A.-C.** Myotubularin-related proteins 3 & 4 interact with PLK1 and CEP55 to control CEP55 recruitment to the midbody and ensure proper abscission  Mol Cell Proteomics. 2014 ; 14:946-60.

2014:

Taipale, M., Tucker, G., Peng, J., Krykbaeva, I., Lin, Z.Y., Larsen, B., Choi, H., Berger, B., Gingras, A.-C.* and Lindquist, S.* A quantitative chaperone interaction network reveals the wiring of cellular protein homeostasis pathways  Cell. 2013 ; 158(2):434-48.

Lambert, J.P., Tucholska, M., Pawson, T and Gingras, A.-C.* A streamlined approach for the identification of chromatin-bound interactors by affinity purification coupled to mass spectrometry.  J Proteomics. 2013 ; 100: 55-9.

Gray, E.J.**, Petsalaki, E., James, D.A., Bagshaw, R.D., Stacey, M.M., Rocks, O., Gingras, A.-C.** and Pawson, T. Src Homology 2 Domain Containing Protein 5 (SH2D5) Binds the Breakpoint Cluster Region Protein, BCR, and Regulates Levels of Rac1-GTP  J Biol Chem. 1999 ; 289:35397-408 .

Sakamaki, J.I., Fu, A., Reeks, C., Depatie, C., Al Azzabi, M., Bardeesy, N., Gingras, A.-C., Yee, S.P. and Screaton, R.A. Role of the Sik2-p35-Pja2 complex in pancreatic beta cell functional compensation.   Nature Cell Biology. 2014 Jan 1; 16: 234-44.

Cullis J., Meiri, D., Radulovich N., LaRose J., Medrano M., Marcotte R., Marshall C.B., Moffat J., Neel B., Gingras A.-C., Rottapel, R. The RhoGEF GEF-H1 is required for RAS oncogene-driven pancreatic cancer.  Cancer Cell. 2014 Jan 1; 10: 282-95.

Raj, B., Irimia, M., Braunschweig, U., Sterne-Weiler, T., O’Hanlon, D., Lin, Z.-L., Chen, G.I., Easton, L., Ule, J., Gingras, A.-C., Eyras, E., and Blencowe, B.J. Global regulatory mechanism underlying the activation of an exon network required for neurogenesis.  Molcular Cell. 2014 Jan 1; 56(1):90-103.

Rojas, M., Gingras, A.-C. and Dever, T. Protein phosphatase PP1/GLC7 interaction domain in yeast eIF2g bypasses targeting subunit requirement for eIF2a dephosphorylation.  PNAS. 2014 Jan 1; 111: E1344-53.

Meiri D., Marshall CB., LaRose J., Mullin, M., Gingras A.-C., Ikura M. and Rottapel, R. Mechanistic insight into the GPCR-mediated activation of the microtubule-associated RhoA-specific guanine exchange factor, GEF-H1.  Nature Communication. 2014 Jan 1; 5:4857.

ONeill, D.J., Williamson, S.C., Alkharaif, D., Monteiro, I.C., Goudreault, M., Gaughan, L., Robson, C.N., Gingras, A.-C. and Binda, O. SETD6 controls the expression of estrogen-responsive genes and proliferation of breast carcinoma cells.  Epigenetics. 2014 Jan 1; 9(7):942-50.

Jovic, M., Kean, M.J., Dubankova, A., Boura, E., Gingras, A.-C., Brill, J.A. and Balla, T. Endosomal sorting of VAMP3 is regulated by PI4K2A.  J Cell Science. 2014 Jan 1; 127(Pt 17):3745-56.

Barsyte-Lovejoy, D., Li, F., Oudhoff, M.J., Tatlock, J.H., Dong, A., Wu, H., Freeman, S., Schapira, M., Senisterra, G.A., Kuznetsova, E., Marcellus, R., Allali-Hassani, A., Lambert, J.-P., Couzens, A.L., Aman, A., Gingras, A.-C., Al-awar, R., Fish, P.V., Gerstenberger, B.S., Roberts, L., Benn, C., Grimley, R.L., Braam, M.J.S., Sudol, M., Brown, P.J., Bunnage, M.E., Owen, D.R., Zaph, C., Vedadi, M. and Arrowsmith, C.H. (R)-PFI2: a potent, selective and cell-active inhibitor of the SETD7 methyltransferase activity  PNAS. 2014 Jan 1; 111(35):12853-8.

Philpott, M., Rogers, C., Yapp, C., Wells, C., Lambert, J.-P., Strain-Damerell, C., Burgess-Brown, N., Gingras, A.-C., Knapp, S. and Müller-Knapp, S. Assessing cellular efficacy of bromodomain inhibitors using Fluorescence Recovery After Photobleaching.  Epigeneics and Chrom. 2014 Jan 1; Jul 13;7:14.

Teo, G., Liu, G., Zhang, J.P., Nesvizhskii, A.I., Gingras, A.-C. and Choi, H. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software  J. Proteomics. 2013 ; 100: 37-43.

Liu, Y.C., Couzens, A.L., Deshwar, A.R., McBroom-Cerajewski, L.D.B., Zhang, X., Puviindran, V., Scott, I.C., Gingras, A.-C., Hui, C.C. and Angers, S. The PPFIA1-PP2A protein complex promotes trafficking of Kif7 to the ciliary tip and Hedgehog signaling  Science Signaling. 2013 ; 7(355):ra11 .

Kurat C.F., Lambert J.-P., Petschnigg J., Friesen H., Pawson T., Rosebrock A., Gingras A.-C., Fillingham J., and Andrews, B. Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation  Proc Natl Acad Sci U. 2013 ; 111:14124-9.

2013:

Lambert JP, Ivosev G, Couzens AL, Larsen B, Taipale M, Lin ZY, Zhong Q, Lindquist S, Vidal M, Aebersold R, Pawson T, Bonner R, Tate S, Gingras AC. Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.  Nat Methods. 2013 ; In Press.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.  Nat Methods. 2013 ; 10(8):730-6.

Couzens, A.L., Knight, J.D.R., Kean, M.J., Teo, G., Weiss, A., Dunham, W.H., Lin, Z.Y., Bagshaw, R.D., Sicheri, F., Pawson, T., Wrana, J., Choi, H., Gingras, A.-C.* Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions.  Science Signaling. 2012 ; 6: rs15.

Zheng Y, Zhang C, Croucher DR, Soliman MA, St-Denis N, Pasculescu A, Taylor L, Tate SA, Hardy WR, Colwill K, Dai AY, Bagshaw R, Dennis JW, Gingras AC, Daly RJ, Pawson T. Temporal regulation of EGF signalling networks by the scaffold protein Shc1.  Nature. 2013 ; 499(7457):166-71.

Rivkin E, Almeida SM, Ceccarelli DF, Juang YC, MacLean TA, Srikumar T, Huang H, Dunham WH, Fukumura R, Xie G, Gondo Y, Raught B, Gingras AC, Sicheri F, Cordes SP. The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.  Nature. 2013 ; 498(7454):318-24.

Oudhoff MJ, Freeman SA, Couzens AL, Antignano F, Kuznetsova E, Min PH, Northrop JP, Lehnertz B, Barsyte-Lovejoy D, Vedadi M, Arrowsmith CH, Nishina H, Gold MR, Rossi FM, Gingras AC, Zaph C. Control of the hippo pathway by Set7-dependent methylation of Yap.  Dev Cell. 2013 ; 26(2):188-94.

Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using target-decoy approach.  Mol Cell Proteomics. 2013 ; In Press.

Garg J, Lambert JP, Karsou A, Marquez S, Shah NS, Bertucci V, Retnasothie DV, Radovani E, Pawson T, Gingras AC, Pearlman RE, Fillingham JS. Conserved Asf1-importin β physical interaction in growth and sexual development in the ciliate Tetrahymena thermophila.  J Proteomics. 2013 ; In Press.

Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks  Mol Syst Biol. 2013 ; 9:655.

Scifo E, Szwajda A, Dębski J, Uusi-Rauva K, Kesti T, Dadlez M, Gingras AC, Tyynelä J, Baumann MH, Jalanko A, Lalowski M. Drafting the CLN3 protein interactome in SH-SY5Y human neuroblastoma cells: a label-free quantitative proteomics approach.  J Proteome Res. 2013 ; 12(8):3822.

Louria-Hayon, I., Frelin, C., Ruston, J., Gish, G., Jin, J., Kofler, M.M., Lambert, J.-P., Adissu, H., Milyavsky, M., Herrington, R., Minden, M.D., Dick, J.E., Gingras, A.-C., Iscove, N.I. and Pawson, T. Lnk adaptor suppresses radiation resistance and radiation-induced B-cell malignancies by inhibiting IL-11 signaling.  PNAS. 2013 Jan 1; 110: 20599-604.

Tate, S., Larsen, B., Bonner, R and Gingras, A.-C. Label-free quantitative proteomics trends for protein-protein interactions [review]  J Proteomics. 2012 ; 81:91-101 .

Knight, J.D.R., Pawson, T. and Gingras, A.-C.** Profiling the kinome: current capabilities and future challenges [review]  J Proteomics. 2012 ; 81:43-55 .

2012:

Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI. Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.  Curr Protoc Bioinfor. 2012 ; Chapter 8:Unit8.

Liu G, Zhang J, Choi H, Lambert JP, Srikumar T, Larsen B, Nesvizhskii AI, Raught B, Tyers M, Gingras AC. Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data.  Curr Protoc Bioinfor. 2012 ; Chapter 8:Unit8.

Filippakopoulos, P., Picaud, S., Mangos, M., Keates, T., Lambert, J.-P., Barsyte-Lovejoy, D., Felletar, I., Volkmer, R., Muller, S., Pawson, T., Gingras, A-C., Arrowsmith, CH., and Knapp, S. Histone recognition and large structural analysis of the human bromodomain family.  Cell. 2012 ; 149(1):214-31.

Oberg EA, Nifoussi SK, Gingras AC, Strack S. Selective proteasomal degradation of the Bβ subunit of protein phosphatase 2A by the E3 ubiquitin ligase adaptor Kelch-like 15.  J Biol Chem. 2012 ; 287(52):43378-89.

Mak AB, Nixon AM, Kittanakom S, Stewart JM, Chen GI, Curak J, Gingras AC, Mazitschek R, Neel BG, Stagljar I, Moffat J. Regulation of CD133 by HDAC6 promotes β-catenin signaling to suppress cancer cell differentiation.  Cell Rep. 2012 ; 2(4):951-63.

Gomez-Ferreria MA, Bashkurov M, Mullin M, Gingras AC, Pelletier L. CEP192 interacts physically and functionally with the K63-deubiquitinase CYLD to promote mitotic spindle assembly.  Cell Cycle. 2012 ; 11(19):3555-8.

Belozerov VE, Lin ZY, Gingras AC, McDermott JC, Michael Siu KW. High-resolution protein interaction map of the Drosophila melanogaster p38 mitogen-activated protein kinases reveals limited functional redundancy.  Mol Cell Biol. 2012 ; 32(18):3695-706.

van Zuylen WJ, Doyon P, Clement JF, Khan KA, DAmbrosio LM, Do F, St-Amant-Verret M, Wissanji T, Emery G, Gingras AC, Meloche S, Servant MJ. Proteomic profiling of the TRAF3 interactome network reveals a new role for the ER-to-Golgi transport compartments in innate immunity.  PLoS Pathog. 2012 ; 8(7):e1002747.

Costa B, Kean MJ, Ast V, Knight JD, Mett A, Levy Z, Ceccarelli DF, Badillo BG, Eils R, Konig R, Gingras AC, Fainzilber M. STK25 protein mediates TrkA and CCM2 protein-dependent death in pediatric tumor cells of neural origin.  J Biol Chem. 2012 ; 287(35):29285-9.

Morita M, Ler LW, Fabian MR, Siddiqui N, Mullin M, Henderson VC, Alain T, Fonseca BD, Karashchuk G, Bennett CF, Kabuta T, Higashi S, Larsson O, Topisirovic I, Smith RJ, Gingras AC, Sonenberg N. A novel 4EHP-GIGYF2 translational repressor complex is essential for mammalian development.  Mol Cell Biol. 2012 ; 32(17):3585-93.

Gomez-Ferreria, M.A., Bashkurov, M., Helbig, A., Larsen, B., Pawson, T., Gingras, A.-C. and Pelletier, L. NEDD1 phosphorylation is modulated by CEP192 and regulates its binding to gamma-tubulin.  J Cell Science. 2012 ; In press.

Jovic, M., Kean, M.J., Szentpetery, Z., Polevoy, G., Gingras, A.-C., Brill, J.A. and Balla, T. Two PI 4-kinases control lysosomal delivery of the Gaucher disease enzyme, B-glucocerebrosidase.  Mol Biol Cell. 2012 ; In press.

Al-hakim, A.K., Bashkurov, M., Gingras, A.-C., Durocher, D and Pelletier, L. Interaction proteomics identify NEURL4 and the HECT E3 ligase HERC2 as novel modulators of centrosome architecture.  Mol Cell Proteomics. 2012 ; Epub PMID:22261722.

Knight, J.R., Tian, R., Lee, R.E.C., Wang, F., Beauvais, A., Zou, H., Megeney, L.A., Gingras, A.-C., Pawson., T., Figeys, D. and Kothary, R. A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts.  Skeletal Muscle. 2012 ; 2(1):5.

Kean, M.J., Couzens, A.L. and Gingras, A.-C.** Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins [method / protocol]  Methods. 2011 ; 57:400-8 .

Gingras, A.-C.** and Raught, B. Beyond hairballs: the use of quantitative mass spectrometry data to understand protein-protein interactions [review / perspective]  FEBS Lett. 2011 ; 586:2723-31.

Braun, P. and Gingras, A.-C. Protein interactions in the 20th century: from egg white to complex networks [review]  Proteomics. 2011 ; 12:1478-98 .

Dunham, W., Mullin, M. and Gingras, A.-C.** Affinity-Purification coupled to Mass Spectrometry: Basic Principles and Strategies [review]  Proteomics. 2011 ; 12:1576-90.

Lambert, J.-P., Pawson, T. and Gingras, A.-C.** Mapping physical interactions within chromatin by proteomic approaches  Proteomics. 2011 ; 12:1609-22.

2011:

Choi, H., Larsen, B., Lin., Z.-Y., Breitkreutz, A., Mellacheruvu, D., Fermin, D., Qin, Z.S., Tyers, M., Gingras, A.-C.*, Nesvizhskii, A.I*. SAINT: probabilistic scoring of affinity purification - mass spectrometry data.  Nature Methods. 2010 ; 8:70-3.

Kean, M.J., Ceccarelli, D., Goudreault, M., Tate, S., Larsen, B., Sanches, M., Gibson, L.D., Derry., W.B., Scott, I.C., Pelletier, L., Baillie, G.S., Sicheri, F., and Gingras, A.-C.* Structure-function analysis of core STRIPAK: a signaling complex implicated in Golgi polarization  J Biol Chem. 2010 ; PMID 21561863.

Ceccarelli, D.F., Laister, R.C., Kean, M.J., Goudreault, M., Scott, I., Derry, W.B., Gingras, A.-C.* and Sicheri, F.* CCM3/PDCD10 is a scaffold for GCKIII kinases.  J Biol Chem. 2011 Jun 27; PMID 21561863.

Skarra, D.V., Goudreault, M., Choi, H., Mullin, M., Nesvizhskii, A., Gingras, A.-C.*, and Honkanen, R*. Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5.  Proteomics. 2010 ; in press.

Dunham, W.H., Larsen, B., Tate, S., Gonzalez Badillo, B., Tehami, Y., Kislinger, T., and Gingras, A.-C.* A cost-benefit analysis of multidimensional fractionation of affinity purification mass spectrometry samples  Proteomics. 2011 Jun 27; PMID 21630450.

Li, Z., Vizeacoumar, F., Bahr, S., Li, J., Warringer, J., Vizeacoumar, F., VanderSluis, B., Bellay, J., DeVit, M., Fleming, J., Stephens, A., Haase, J., Lin, Z.-Y., Baryshnikova, A., Min, R., Lu, H., Yan, Z., Jin, K., Barker, S., Datti, A., Giaever, G., Nislow, C., Bulawa, C., Costanzo, M., Myers, C., Gingras, A.-C., Zhang, Z., Blomberg, A., Bloom, K., Andrews, B. and Boone, C. Systematic exploration of essential gene function with temperature-sensitive mutants  Nature Biotech. 2010 ; 29:361-7.

Templeton, G., Nimixk, M., Morrice, N.A., Campbell, D.G., Goudreault, M., Gingras, A.-C., Takemiya, A., Shimazaki, K.I., Moorhead, G.B. Identification and characterization of Atl-2, an Arabidopsis homolog of an ancient protein phosphatase (PP1) regulatory subunit.  Biochem J. 2010 ; 435(1):73-83.

Olhovsky, M., Williton, K., Dai, A., Pasculescu, A., Lee, J.P., Goudreault, M., Wells, C.D., Park, J.G., Gingras, A.-C., Linding, R., Pawson, T., and Colwill, K. OpenFreezer: A web-based laboratory information and workflow management system for reagents.  Nature Methods. 2010 ; in press.

Gingras, A.-C.** Protein Phosphatases, from Molecules to Networks [meeting review]  EMBO Reports. 2010 ; 12:1211-13.

2010:

Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M*, Gingras AC*. ProHits: integrated software for mass spectrometry-based interaction proteomics.  Nat Biotechnol. 2010 Aug 19; 28(10):1015-7.

Nakada S, Tai I, Panier S, Al-Hakim A, Iemura S, Juang YC, O'Donnell L, Kumakubo A, Munro M, Sicheri F, Gingras AC, Natsume T, Suda T, Durocher D. Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1.  Nature. 2010 Aug 19; 466(7309):941-6.

Sydorskyy Y, Srikumar T, Jeram SM, Wheaton S, Vizeacoumar FJ, Makhnevych T, Chong YT, Gingras AC, Raught B. A novel mechanism for SUMO system control: regulated Ulp1 nucleolar sequestration.  Mol Cell Biol. 2010 Jul 19; .

Choi H, Kim S, Gingras AC, Nesvizhskii AI. Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data.  Mol Syst Biol. 2010 Jun 22; 6:385.

Mak AB, Ni Z, Hewel JA, Chen GI, Zhong G, Karamboulas K, Blakely K, Smiley S, Marcon E, Roudeva D, Li J, Olsen JB, Wan C, Punna T, Isserlin R, Chetyrkin S, Gingras AC, Emili A, Greenblatt J, Moffat J. A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.  Mol Cell Proteomics.. 2010 May ; 9(5):811-23.

Bidinosti M, Ran I, Sanchez-Carbente MR, Martineau Y, Gingras AC, Gkogkas C, Raught B, Bramham CR, Sossin WS, Costa-Mattioli M, DesGroseillers L, Lacaille JC, Sonenberg N. Postnatal deamidation of 4E-BP2 in brain enhances its association with raptor and alters kinetics of excitatory synaptic transmission.  Mol Cell.. 2010 Mar 26; 37(6):797-808.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pal C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C The genetic landscape of a cell.  Science.. 2010 Jan 22; 327(5964):425-31.

Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL. Quantitative analysis of fitness and genetic interactions on a genome scale.  Nat Methods. 2010 Nov 11; 7:1017-24.

O'Donnell L, Panier S, Wildenhain J, Tkach JM, Al-Hakim A, Landry MC, Escribano-Diaz C, Szilard RK, Young JT, Munro M, Canny MD, Kolas NK, Zhang W, Harding SM, Ylanko J, Mendez M, Mullin M, Sun T, Habermann B, Datti A, Bristow RG, Gingras AC, Tyers M, Brown G and Durocher D. The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination.  Mol Cell. 1999 ; 40:619-31.

2009:

Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI, Aebersold R, Raught B, Gingras AC*. A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to th  Mol Cell Proteomics.. 2009 Nov ; 8(1):157-71.

Gingras AC*. Journal Club: 35 years later, mRNA caps still matter.  Nat Rev Mol Cell Bio. 2009 Nov ; 10(11):734.

Lawo S, Bashkurov M, Mullin M, Ferreria MG, Kittler R, Habermann B, Tagliaferro A, Poser I, Hutchins JR, Hegemann B, Pinchev D, Buchholz F, Peters JM, Hyman AA, Gingras AC, Pelletier L. HAUS, the 8-subunit human Augmin complex, regulates centrosome and spindle integrity.  Curr Biol.. 2009 May 26; 19(10):816-26.

2008:

Nakada S, Chen GI, Gingras AC*, Durocher D*. PP4 is a gamma H2AX phosphatase required for recovery from the DNA damage checkpoint.  EMBO Rep.. 2008 Aug 24; 9(10):1019-26.

Chen GI, Tisayakorn S, Jorgensen C, D'Ambrosio LM, Goudreault M, Gingras AC*. PP4R4/KIAA1622 forms a novel stable cytosolic complex with phosphoprotein phosphatase 4.  J Biol Chem.. 2008 Aug 24; 283(43):29273-84.

Rong L, Livingstone M, Sukarieh R, Petroulakis E, Gingras AC, Crosby K, Smith B, Polakiewicz RD, Pelletier J, Ferraiuolo MA, Sonenberg N. Control of eIF4E cellular localization by eIF4E-binding proteins, 4E-BPs.  RNA.. 2008 Jul 14; 14(7):1318-27.

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