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Rubinstein R, Thu CA, Goodman KM, Wolcott HN, Bahna F, Mannepalli S, Ahlsen G, Chevee M, Halim A, Clausen H, Maniatis T, Shapiro L, Honig B. (2015) Molecular logic of neuronal self-recognition through protocadherin domain interactions. Cell. 2015 Oct 22;163(3):629-42

Chen, W.V. and Maniatis, T. (2013) Clustered Protocadherins. Development 40 (16) : 3297 - 302.

Chiu, I., Morimoto, T.A., Goodarzi, H., Liao, J., Muratet, M., O’Keeffe, S., Phatnani, H., Painter, M., Carroll, M.C., Levy, S., Tavazoie, S., Myers, R.M. and Maniatis, T. (2013). A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an Amyotrophic Lateral Sclerosis mouse model. Cell Rep. 4(2):385-401.

Bilican, B., Serio, A., Shaw, C.E., Maniatis, T., and Chandran S. Unpickding neurodegeneration in a dish with human pluripotent stem cells: One cell type at a time. Cell Cycle. 12(15). [Epub ahead of print].

Gebhardt, J.C.M., Suter, D.M., Roy, R. Zhao, Z.W., Chapman, A.R. Basu, S., Maniatis, T. and Xie, X.S.(2013) Probing transcription factor DNA binding at the single molecule level in live mammalian cells. Nature Methods, 10(5):421-6.

Larabi, A., Devos, J.M., Ng Sze-Ling, Round,, A., Maniatis, T., and Panne, D. (2013). Crystal structure and mechanism of activation of TANK-binding kinase 1. Cell Reports Cell Rep. 3(3):734-46

Serio, A.,Bilican, B., Barmada, S.J.,. Ando, D.M, Siller, R., Burr, K., Haghi, G., Story, D., Nishimura, A. Carrasco, M., Phatnani, H., Shum, C., Wilmut, I., Maniatis, T., Shaw, C. E., Finkbeiner, S. A., & Chandran, S. (2013). Astrocyte pathology and non-cell autonomy in an induced pluripotent stem cell model of TDP-43 proteinopathy. Proc Natl Acad Sci USA. 110:4697-702.

Phatnani, H.P., Guarnieri, P., Friedman, B., Carrasco, M.A., Muratet, M., O’Keeffe,AS., Nwakezea, Florencia, C. Pauli-Behnd, Newberry, K.M., Sarah K. Meadows, S.K., Tapia, J.C., Myers, R.M. and Maniatis, T. (2013). An intricate interplay between astrocytes and motor neurons in ALS. Proc Natl Acad Sci U S A. 110(8):E756-65.

Amoroso, M.W., Croft, G.F., Williams, D.J., O’Keeffe, S.O., Carrasco, M.A., Davis, A.R., Roybon, L., Oakley, D.H., Maniatis, T., Henderson, C.E. and Wichterle, H. (2013). Accelerated high-yield generation of limb-innervating motor neurons from human stem cells. Journal of Neuroscience 33(2):574-586.

Guo, Y., Monahan, K., Wu, H., Gertz, J., Li, W., Myers, R.M., Maniatis, T. and Wu, Q. (2012). CTCF/Cohesin-mediated DNA Looping is required for protocadherin-alpha promoter choice. Proc. Natl. Acad. Sci. U.S.A. (in press).

NINDS ALS IPAC Consortium (Maniatis, T). (2012). Creation of an open-access, mutation-defined fibroblast resource for neurological disease research. PLoS One 7(8):e43099.

Maniatis, T. (2012) On the road from classical to modern molecular biology. Nat Med. 18(10):1499-502.

Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. (2012). Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. Sep 30. doi: 10.1038/nature11503. [Epub ahead of print]

Yamazaki T, Chen S, Yu Y, Yan B, Haertlein TC, Carrasco MA, Tapia JC, Zhai B, Das R, Lalancette-Hebert M, Sharma A, Chandran S, Sullivan G, Nishimura AL, Shaw CE, Gygi SP, Shneider NA, Maniatis T, Reed R. (2012). FUS-SMN Protein interactions link the motor neuron diseases ALS and SMA. Cell Rep. Sep 25. pii: S2211-1247(12)00265-3. doi: 10.1016/j.celrep.2012.08.025. [Epub ahead of print]

Li, Y., Xiao, H., Chiou, T.T., Jin, H., Bonhomme, B., Miralles, C.P., Pinal, N., Ali, R., Chen, W.V., Maniatis, T., De Blas, A.L. (2012). Molecular and Functional Interaction between Protocadherin-gC5 and GABAA Receptors. J Neurosci. 32:11780-97.

Lefebvre, J.L., Kostadinov, D., Chen, W.V., Maniatis, T., and Sanes, J.R. (2012). Protocadherins mediate dendritic self-avoidance in the mammalian nervous system. Nature. Jul 29. doi: 10.1038/nature11305. [Epub ahead of print] PMID: 22842903.

Chen, W.V., Alvarez, F.J., Lefebvre, J.L., Friedman, B., Nwakeze, C., Geiman, E., Smith, C., Chan, A., Tapia, J.C., Tasic, B. Sanes, J.R., and Maniatis, T. (2012) Functional Significance of isoform diversification in the protocadherin gamma gene cluster. Neuron, 75(3):402-9.

Monahan K, Rudnick ND, Kehayova PD, Pauli F, Newberry KM, Myers RM, Maniatis T. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-α gene expression. Proc Natl Acad Sci U S A. 2012 June 5 109(23):9125-30.

Bilican, B., Serio, A., Barmada, S.J., Nishimura, A.L., Sullivan, G.J., Carrasco, M, Phatnani, H.P., Puddifoot, C.A., Story, D., Fletcher, J., Park, I.H., Friedman, V.A., Daley, G.Q., Wyllie, D.J.A., Hardingham, G.E., Wilmut, I., Finkbeiner, S., Maniatis, T., Shaw, C.E. and Chandran, S. (2012). Mutant induced pluripotent stem cell lines recapitulate aspects of TDP-43 proteinopathies and reveal cell specific vulnerability. Proc. Nat. Acad. Sci. USA 2012 Apr 10;109(15):5803-8.

Zhao, M., Zhang, J., Phatnani, H., Scheu, S., and Maniatis, T. (2012) Stochastic Expression of the Interferon-β gene. PLoS Biol.10(1):e1001249.

Ng, Sze-Ling, Friedman, B.A., Schmid, S., Gertz, J., Myers, R.M., tenOever, B.R., and Maniatis, T. (2011). IκB kinase epsilon (IKKε) regulates the balance between type I and type II interferon responses. Proc. Natl. Acad. Sci. USA (108(52): 21170-5.

Kehayova P, Monahan K, Chen W, Maniatis T. (2011) Regulatory elements required for the activation and repression of the protocadherin-{alpha} gene cluster. Proc. Natl. Acad. Sci. USA 108(41):17195-200.

Ye J., Maniatis T. (2011) A Prion-like Trigger of Antiviral Signaling, Cell 146(3):348-50.

Friedman B.A. and Maniatis T. (2011) ExpressionPlot: A web-based framework for analysis of RNA-Seq and microarray gene expression data. Genome Biology Jul 28;12(7):R69.

Ye J, Maniatis T (2011) Negative Regulation of Interferon-β Gene Expression during Acute and Persistent Virus Infections. PLoS ONE 6(6): e20681. doi:10.1371/journal.pone.0020681

Ye, J., Chen, S., and Maniatis, T. (2011). Cardiac glycosides are potent inhibitors of interferon-β gene expression.  Nat Chem Biol.7:25-33.

Buchanan, S.M., Schalm, S.S. and Maniatis, T. Proteolytic processing of protocadherin proteins requires endocytosis. Proc Natl Acad Sci U S A. 107: 1774-9.

Schalm SS, Ballif BA, Buchanan SM, Phillips GR, Maniatis T. (2010) Phosphorylation of protocadherin proteins by the receptor tyrosine kinase Ret. Proc Natl Acad Sci U S A. 107(31):13894-9.

Huang HR, Chen ZJ, Kunes S, Chang GD, Maniatis T.(2010) Endocytic pathway is required for Drosophila Toll innate immune signaling. Proc Natl Acad Sci. 107:8322-7.

Chiu, I.M., Phatnani, H., Kuligowski, M., Tapia, J.C., Carrasco, M.A., Zhang, M., Maniatis, T., and Carroll, M.C. (2009). Activation of innate and humoral immunity in the peripheral nervous system of ALS transgenic mice PNAS 106:20960-65.

Falvo, J.V., Lin, C.H., Tsytsykova, A.V., Hwang, P.K., Thanos, D., Goldfeld, A.E., and Maniatis, T. (2008). A dimer-specific function of the transcription factor NFATp
Proceedings of the National 105(50):19637.

Makeyev, E.V., and Maniatis, T. (2008). Multilevel Regulation of Gene Expression by MicroRNAs
Science 319:1789-90.

Makeyev, E.V., Zhang, J. Carrasco, M.A., and Maniatis, T. (2007). The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative pre-mRNA Splicing.
Molecular Cell 27(3):435.

Panne, D., McWhirter, S.M., Maniatis, T., and Harrison, S.C. (2007). Interferon response factor 3 is regulated by a dual phosphorylation dependent switch J. Biol. Chem. 282(31)22816-22822.

Panne, D., Maniatis, T., and Harrison, S.C.  (2007).  An Atomic Model of the Interferon-β Enhanceosome.  Cell 129(6):1111-23 (2007).

Di Giorgio, F.P., Carrasco, M.A., Siao, M.C., Maniatis, T., and Eggan, K.  (2007).  Non–cell autonomous effect of glia on motor neurons in an embryonic stem cell–based ALS model.
Nature Neuroscience:608-614.

tenOever, B.R., Ng, S., Chua, M.A., McWhirter, S.M., García-Sastre, A., and Maniatis, T. (2007). Multiple Functions of the IKK-Related Kinase IKK in Interferon-Mediated Antiviral Immunity.
Science 315(5816):1274-1278.

Ribich, S., Tasic, B., and Maniatis, T. (2006). Identification of long-range regulatory elements in the protocadherin-alpha gene cluster. Proc. Natl. Acad. Sci. 103, 19719-19724.

tenOever, B.R. and Maniatis, T. (2006). Parallel pathways of virus recognition. Immunity 24,510-512.

Maciag, K., Altschuler, S.J., Slack, M.D., Krogan, N.J., Emili, A., Greenblatt, J.F., Maniatis, T., and Wu, L.F. (2006). Systems-level analyses identify extensive coupling among gene expression machines.
Mol. Systems Biol. 2:2006.0003.

Zhou, R., Silverman, N., Hong, M., Liao, D.S., Chung, Y., Chen, Z.J., and Maniatis, T. (2005).  The role of ubiquitination in Drosophila innate immunity. J. Biol. Chem. 280, 34048-34055.

McWhirter, S.M., tenOever, B.R., and Maniatis, T. (2005). Connecting mitochondria and innate immunity. Cell 122, 645-647.

Takahara, T., Tasic, B., Maniatis, T., Akanuma, H., and Yanagisawa, S. (2005). Delay in synthesis of the 3’ splice site promotes trans-splicing of the preceding 5’ splice site. Mol. Cell 18, 245-251.

Ibrahim, E.C., Schaal, T.D., Hertel, K.J., Reed, R., and Maniatis, T. (2005). Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers.
Proc. Natl. Acad. Sci. USA 102, 5002-5007.

Panne, D., Maniatis, T. and Harrison, S.C. (2004). Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-b enhancer. EMBO J. 23, 4384-4393.

McWhirter, S.M., Fitzgerald, K.A., Rosains, J., Rowe, D.C., Golenbock, D.T., and Maniatis, T. (2004). IFN-regulatory factor 3-dependent gene expression is defective in Tbk1-deficient mouse embryonic fibroblasts. Proc. Natl. Acad. Sci. USA 101, 233-238.

Silverman, N., Zhou, R., Erlich, R.L., Hunter, M., Bernstein, E., Schneider, D., and Maniatis, T. (2003). Immune activation of NF-kB and JNK requires Drosophila TAK1. J. Biol. Chem. 278, 48928-48934.

Stöven, S., Silverman, N., Junell, A., Hedengren-Olcott, M., Erturk, D., Engström, Y., Maniatis, T., and Hultmark, D. (2003). Caspase-mediated processing of the Drosophila NF-kB factor Relish.
Proc. Natl. Acad. Sci. USA 100, 5991-5996.

Fitzgerald, K.A., McWhirter, S.M., Faia, K.L., Rowe, D.C., Latz, E., Golenbock, D.T., Coyle, A.J., Liao, S.-M., and Maniatis, T. (2003).  IKKe and TBK1 are essential components of the IRF3 signaling pathway.  Nature Immunol. 4, 491-496.

Tasic, B., Nabholz, C.E., Baldwin, K.K., Kim, Y., Rueckert, E.H., Ribich, S.A., Cramer, P., Axel, R., and Maniatis, T. (2002).  Promoter choice determines splice site selection in protocadherin a and g pre-mRNA splicing.  Mol. Cell 10, 21-33.

Maniatis, T. and Tasic, B. (2002).   Alternative pre-mRNA splicing and proteome expansion in metazoans.  Nature 418, 236-243.

Maniatis, T. and Reed, R. (2002).  An extensive network of coupling among gene expression machines.  Nature 416, 499-506.

Lin, C.H., Hare, B.J., Wagner, G., Harrison, S.C., Maniatis, T., and Fraenkel, E. (2001).  A small domain of CBP/p300 binds diverse proteins:  Solution structure and functional studies. Mol. Cell 8, 581-590.

Silverman, N. and Maniatis, T. (2001).  NF-kB signaling pathways in mammalian and insect innate immunity.  Genes & Dev. 15, 2321-2342.

Graveley, B.R., Hertel, K.J., and Maniatis, T. (2001).  The role of U2AF35 and U2AF65 in enhancer-dependent splicing.  RNA 7, 806-818.

Peters, R.T. and Maniatis, T. (2001).  A new family of IKK-related kinases may function as IkB kinase kinases.  Biochim. Biophys. Acta 1471, M57-M62.

Wu, Q., Zhang, T., Cheng, J.-F., Kim, Y., Grimwood, J., Schmutz, J., Dickson, M., Noonan, J.P., Zhang, M.Q., Myers, R.M., and Maniatis, T. (2001).  Comparative DNA sequence analysis of mouse and human protocadherin gene clusters.  Genome Res. 11, 389-404.

Agalioti, T., Lomvardas, S., Parekh, B., Yie, J., Maniatis, T., and Thanos, D. (2000).  Ordered recruitment of chromatin modifying and general transcription factors to the IFN-b promoter.
Cell 103, 667-678.

Silverman, N., Zhou, R., Stöven, S., Pandey, N., Hultmark, D., and Maniatis, T. (2000). A Drosophila IkB kinase complex required for Relish cleavage and antibacterial immunity. Genes & Dev. 14, 2461-2471.

Wu, Q. and Maniatis, T. (2000).  Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes.  Proc. Natl. Acad. Sci. USA 97, 3124-3129.

Peters, R.T., Liao, S.-M., and Maniatis, T. (2000).  IKKe is part of a novel PMA-inducible IkB kinase complex.  Mol. Cell 5, 513-522.

Wu, Q. and Maniatis, T. (1999).  A striking organization of a large family of human neural cadherin-like cell adhesion genes.  Cell 97, 779-790.

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