Recent Publications

2009

SG Fonseca, M Burcin, J Gromada and F Urano (2009) Endoplasmic reticulum stress in beta cells and development of diabetes. Curr. Opin. Pharmacol., in press.

SG Fonseca, F Urano, M Burcin and J Gromada (2009) Stress hypERactivation in the beta cell. Islets, in press.

S Ishigakin, SG Fonseca, CM Oslowski, A Jurczyk, JR Shearstone, LJ Zhu, MA Permutt, DL Greiner, R Brotell and F Urano (2009) AATF mediates anti-apoptotic effect of the unfolded protein response through transcriptional regulation of AKT1. Cell Death Differ., in press.

U Dasgupta, T Bamba, S Chiantia, P Karim, A Abou Tayoun, I Yonamine, SS Rawat, RP Rao, K Nagashima, E Fukusaki, V Puri, P Dolph, P Schwille, JK Acharya and U Acharya (2009) Ceramide kinase regulates PLC and PIP2 in phototransduction. Proc. Natl. Acad. Sci. USA, in press.

MJ Parsons, H Pisharath, S Yusuff, JC Moore, AF Siekmann, ND Lawson and SD Leach (2009) Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas. Mech. Dev., 126: 898-912.

E Lieberman-Aiden, NL van Berkum, L Williams, M Imakaev, T Ragoczy, A Telling, I Amit, BR Lajoie, PJ Sabo, MO Dorschner, R Sandstrom, B Bernstein, MA Bender, M Groudine, A Gnirke, JA Stamatoyannopoulos, L Mirny, ES Lander and J Dekker (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326: 289-293.

JA Erkmann and PD Kaufman (2009) A negatively charged residue in place of histone H3K56 supports chromatin assembly factor association but not genotoxic stress resistance. DNA Repair (Amst), epub ahead of print.

AF Siekmann, C Standley, KE Fogarty, SA Wolfe and ND Lawson (2009) Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev., 23: 2272-2277.

BR Lajoie, NL van Berkum, A Sanyal and J Dekker (2009) My5C: web tools for chromosome conformation capture studies. Nat. Methods, 6: 690-691.

NL van Berkum and J Dekker (2009) Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol. Biol., 567: 189-213.

Y-W Chen, V Boyartchuk and BC Lewis (2009) Differential roles of insulin-like growth factor receptor- and insulin receptor-mediated signaling in the phenotypes of hepatocellular carcinoma cells. Neoplasia, 11: 835-845.

JD Osborne, J Flatow, M Holko, SM Lin, WA Kibbe, LJ Zhu, MI Danila, G Feng and RL Chisholm (2009) Annotating the human genome with Disease Ontology. BMC Genomics, 10: S6.

E Campeau, VE Ruhl, F Rodier, CL Smith, BL Rahmberg, JO Fuss, J Campisi, P Yaswen, PK Cooper and PD Kaufman (2009) A versatile viral system for expression and depletion of proteins in mammalian cells. PLoS ONE, 4: e6529.

HY Chang, O Cuvier and J Dekker (2009) Gene dates, parties and galas: symposium on chromatin dynamics and higher order organization.  EMBO Rep. 10: 689-693.

B D'haene, C Attanasio, D Beysen, J Dostie, E Lemire, P Bouchard, M Field, K Jones, B Lorenz, B Menten, K Buysse, F Pattyn, M Friedli, C Ucla, C Rossier, C Wyss, F Speleman, A De Paepe, J Dekker, SE Antonarakis and E De Baere (2009) Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet. 5: e1000522.

CA Grove, F deMasi, MI Barrasa, DE Newburger, MJ Alkema, ML Bulyk and AJ Walhout (2009) A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.  Cell, 138: 314-327.

MK Santra, N Wajapeyee and MR Green (2009) F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage. Nature, 459: 722-725.

A Miele, K Bystricky and J Dekker (2009) Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet., 5: e1000478.

P Oza, SL Jaspersen, A Miele, J Dekker and CL Peterson (2009) Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev., 23: 912-927.

JS Reece-Hoyes, B Deplancke, MI Barrasa, J Hatzold, RB Smit, HE Arda, PA Pope, J Gaudet, B Conradt, AJ Walhout (2009) The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res., 37: 3689-3698.

LD Covassin, AF Siekmann, MC Kacergis, E Laver, JC Moore, JA Villefranc, BM Weinstein and ND Lawson (2009) A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development. Dev. Biol., 329: 212-226.

Q Zhang, BT Helfand, TL Jang, LJ Zhu, L Chen, XJ Yang, J Kozlowski, N Smith, SD Kundu, G Yang, AA Raji, B Javonovic, M Pins P Lindholm, Y Guo, WJ Catalona and C Lee (2009).  Nuclear factor-kB-mediated transforming growth factor-beta-induced expression of vimentin is an independent predictor of biochemical recurrence after radical prostatectomy.  Clin Cancer Res., 15:3557-3567. 

Z Sheng, SZ Wang and MR Green (2009) Transcription and signalling pathways involved in BCR-ABL-mediated misregulation of 24p3 and 24p3R. EMBO J., 28: 866-876.

C Kakiuchi, S Ishigaki, CM Oslowski, SG Fonseca, T Kato and F Urano (2009) Valproate, a mood stabilizer, induces WFS1 expression and modulates its interaction with ER stress protein GRP94. PLoS ONE, 4: e4134.

S Padmanabhan, A Mukhopadhyay, SD Narasimhan, G Tesz, MP Czech and HA Tissenbaum (2009) A PP2A regulatory subunit regulates C. elegans insulin/IGF-1 signaling by modulating AKT-1 phosphorylation. Cell, 136: 939-951.

X Wang, RP Rao, T Kosakowska-Cholody, MA Masood, E Southon, H Zhang, C Berthet, K Nagashima, TK Veenstra, L Tessarollo, U Acharya and JK Acharya (2009) Mitochondrial degeneration and not apoptosis is the primary cause of lethality in ceramide transfer protein mutant mice. J. Cell Biol., 184: 143-158.

NJ Martinez and AJ Walhout (2009) The interplay between transcription factors and microRNAs in genome-scale regulatory networks. BioEssays, 31: 435-445.

SA Johnsen, C Güngör, T Prenzel, S Riethdorf, N Taniguchi-Ishigaki, L Riethdorf, T Rau, B Tursun, JD Furlow, G Sauter, M Scheffner, K Pantel, F Gannon and I Bach (2009) Regulation of estrogen-dependent transcription by LIM cofactors CLIM and RLIM in breast cancer. Cancer Res., 69: 128-136.

A Miele and J Dekker (2009) Mapping cis- and trans-chromatin interaction networks using Chromosome Conformtion Capture (3C). Methods Mol. Biol., 464: 105-121.

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