CBC-Funded Publications 2008

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2008

Amaral LA. A truer measure of our ignorance. Proc Natl Acad Sci U S A. 2008 May 13;105(19):6795-6. (PubMed)

Antoniou C, Fung LW. Potential artifacts in using a glutathione S-transferase fusion protein system and spin labeling electron paramagnetic resonance methods to study protein-protein interactions. Anal Biochem. 2008 May 1; 376(1): 160–162. (PubMed)

Antoniou C, Lam VQ, Fung LW. Conformational changes at the tetramerization site of erythroid alpha-spectrin upon binding beta-spectrin: a spin label EPR study. Biochemistry, 2008 Oct 7;47(40):10765-72. (PubMed)

Cao H, Xiao L, Park G, Wang X, Azim AC, Christman JW, van Breemen RB. An improved LC-MS/MS method for the quantification of prostaglandins E(2) and D(2) production in biological fluids. Anal Biochem. 2008 Jan 1;372(1):41-51. (PubMed)

Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Res. 2008 May;18(5):751-62. (PubMed)

Choi Y, van Breemen RB. Development of a screening assay for ligands to the estrogen receptor based on magnetic microparticles and LC-MS. Comb Chem High Throughput Screen. 2008 Jan;11(1):1-6. (PubMed)

Dietz BM, Liu D, Hagos GK, Yao P, Schinkovitz A, Pro SM, Deng S, Farnsworth NR, Pauli GF, van Breemen RB, Bolton JL. Angelica sinensis and Its Alkylphthalides Induce the Detoxification Enzyme NAD(P)H: Quinone Oxidoreductase 1 by Alkylating Keap1. Chem Res Toxicol. 2008. (PubMed)

Doan N, Gettins PG. alpha-Macroglobulins are present in some gram-negative bacteria: characterization of the alpha2-macroglobulin from Escherichia coli. J Biol Chem. 2008 Oct 17;283(42):28747-56. (PubMed)

Edghill EL, Flanagan SE, Patch AM, Boustred C, Parrish A, Shields B, Shepherd MH, Hussain K, Kapoor RR, Malecki M, MacDonald MJ, Støy J, Steiner DF, Philipson LH, Bell GI; Neonatal Diabetes International Collaborative Group, Hattersley AT, Ellard S. Insulin mutation screening in 1,044 patients with diabetes: mutations in the INS gene are a common cause of neonatal diabetes but a rare cause of diabetes diagnosed in childhood or adulthood. Diabetes. 2008 Apr;57(4):1034-42. (PubMed)

Green CB, Takahashi JS, Bass J. The meter of metabolism. Cell. 2008 Sep 5;134(5):728-42. (PubMed)

Guet CC, Bruneaux L, Min TL, Siegal-Gaskins D, Figueroa I, Emonet T, Cluzel P. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Res. 2008 Jul;36(12):e73. (PubMed)

Guo J, Liu A, Cao H, Luo Y, Pezzuto JM, van Breemen RB. Biotransformation of the chemopreventive agent 2′,4′,4-trihydroxychalcone (isoliquiritigenin) by UDP-glucuronosyltransferases. Drug Metab Dispos. 2008 Oct;36(10):2104-12. (PubMed)

Guo J, Liu D, Nikolic D, Zhu D, Pezzuto JM, van Breemen RB. In vitro metabolism of isoliquiritigenin by human liver microsomes. Drug Metab Dispos. 2008 Feb;36(2):461-8. (PubMed)

Hay N. p53 strikes mTORC1 by employing sestrins. Cell Metab. 2008 Sep;8(3):184-5. (PubMed)

Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP. Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol. 2008;4:188. (PubMed)

Kohsaka A, Bass J. Clock Genes and Metabolic Regulation. In: Squire LR, editor. 2008. Encyclopedia of Neuroscience. Oxford: Academic Press 1023-1029.

Kristjansdottir K, Wolfgeher D, Lucius N, Angulo DS, Kron SJ. Phosphoprotein profiling by PA-GeLC-MS/MS. J Proteome Res. 2008 Jul;7(7):2812-24. (PubMed)

Laposky AD, Bass J, Kohsaka A, Turek FW. Sleep and circadian rhythms: key components in the regulation of energy metabolism. FEBS Lett. 2008 Jan 9;582(1):142-51. (PubMed)

Laposky AD, Bradley MA, Williams DL, Bass J, Turek FW. Sleep-wake regulation is altered in leptin-resistant (db/db) genetically obese and diabetic mice. Am J Physiol Regul Integr Comp Physiol. 2008 Dec;295(6):R2059-66. (PubMed)

Lee BS, Krishnanchettiar S, Lateef SS, Gupta S. Capturing biotinylated proteins and peptides by avidin functional affinity electrophoresis. Methods Mol Biol. 2008;418:51-62. (PubMed)

Lee BS, Lasanthi GD, Jayathilaka P, Huang JS, Gupta S. Immobilized metal affinity electrophoresis: a novel method of capturing phosphoproteins by electrophoresis. J Biomol Tech. 2008 Apr;19(2):106-8. (PubMed)

Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew R, Wu CI. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol Biol Evol. 2008 May;25(5):929-38. (PubMed)

Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. The birth and death of microRNA genes in Drosophila. Nat Genetics 2008 Mar;40(3):351-5. (PubMed)

Molven A, Ringdal M, Nordbø AM, Raeder H, Støy J, Lipkind GM, Steiner DF, Philipson LH, Bergmann I, Aarskog D, Undlien DE, Joner G, Søvik O; Norwegian Childhood Diabetes Study Group, Bell GI, Njølstad PR. Mutations in the insulin gene can cause MODY and autoantibody-negative type 1 diabetes. Diabetes. 2008 Apr;57(4):1131-5. (PubMed)

Morimoto RI. Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging. Genes Dev. 2008 Jun 1;22(11):1427-38. Review. (PubMed)

Nogueira V, Park Y, Chen CC, Xu PZ, Chen ML, Tonic I, Unterman T, Hay N. Akt determines replicative senescence and oxidative or oncogenic premature senescence and sensitizes cells to oxidative apoptosis. Cancer Cell. 2008 Dec 9;14(6):458-70. (PubMed)

Parker L, Engel-Hall A, Drew K, Steinhardt G, Helseth DL Jr, Jabon D, McMurry T, Angulo DS, Kron SJ. Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. J Mass Spectrom. 2008 Apr;43(4):518-27. (PubMed)

Poser I, Sarov M, Hutchins JR, Hériché JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW, Pelletier L, Kittler R, Hua S, Naumann R, Augsburg M, Sykora MM, Hofemeister H, Zhang Y, Nasmyth K, White KP, Dietzel S, Mechtler K, Durbin R, Stewart AF, Peters JM, Buchholz F, Hyman AA. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. 2008 May;5(5):409-15. Erratum in: Nat Methods. 2008 Aug;5(8):748. (PubMed)

Prahlad V, Cornelius T, Morimoto RI. Regulation of the cellular heat shock response in Caenorhabditis elegans by thermosensory neurons. Science. 2008 May 9;320(5877):811-4. (PubMed)

Prochazkova K, Satchell KJ. Structure-function analysis of inositol hexakisphosphate-induced autoprocessing of the Vibrio cholerae multifunctional autoprocessing RTX toxin. J Biol Chem. 2008 Aug 29;283(35):23656-64. (PubMed)

Rao PK, Rodriguez GM, Smith I, Li Q. Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-fourier transform mass spectrometry. Anal Chem. 2008 Sep 15;80(18):6860-9. (PubMed)

Rao PK, Roxas BA, Li Q. Determination of global protein turnover in stressed mycobacterium cells using hybrid-linear ion trap-fourier transform mass spectrometry. Anal Chem. 2008 Jan 15;80(2):396-406. (PubMed)

Ravindran S, Narayanan K, Eapen AS, Hao J, Ramachandran A, Blond S, George A. Endoplasmic reticulum chaperone protein GRP-78 mediates endocytosis of dentin matrix protein 1. J Biol Chem. 2008 Oct 31;283(44):29658-70. (PubMed)

Roxas BA, Li Q. Significance analysis of microarray for relative quantitation of LC/MS data in proteomics. BMC Bioinformatics. 2008 Apr 10;9:187. (PubMed)

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families. Gene. 2008 Jan 15;407(1-2):199-215. (PubMed)

Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, Goldman RD. The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev. 2008 Dec 15;22(24):3409-21. (PubMed)

Smart AG, Amaral LA, Ottino JM. Cascading failure and robustness in metabolic networks. Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13223-8. (PubMed)

Støy J, Greeley SA, Paz VP, Ye H, Pastore AN, Skowron KB, Lipton RB, Cogen FR, Bell GI, Philipson LH; United States Neonatal Diabetes Working Group. Diagnosis and treatment of neonatal diabetes: a United States experience. Pediatr Diabetes. 2008 Oct;9(5):450-9. (PubMed)

Ulanovskaya OA, Janjic J, Suzuki M, Sabharwal SS, Schumacker PT, Kron SJ, Kozmin SA. Synthesis enables identification of the cellular target of leucascandrolide A and neopeltolide. Nat Chem Biol. 2008 Jul;4(7):418-24. (PubMed)

Vicario S, Mason CE, White KP, Powell JR. Developmental stage and level of codon usage bias in Drosophila. Mol Biol Evol. 2008 Nov;25(11):2269-77. (PubMed)

Warmflash A, Dinner AR. Signatures of combinatorial regulation in intrinsic biological noise. Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17262-7. (PubMed)

Warren CM, Arteaga GM, Rajan S, Ahmed RP, Wieczorek DF, Solaro RJ. Use of 2-D DIGE analysis reveals altered phosphorylation in a tropomyosin mutant (Glu54Lys) linked to dilated cardiomyopathy. Proteomics. 2008 Jan;8(1):100-5. (PubMed)

Wu C, Delano DL, Mitro N, Su SV, Janes J, McClurg P, Batalov S, Welch GL, Zhang J, Orth AP, Walker JR, Glynne RJ, Cooke MP, Takahashi JS, Shimomura K, Kohsaka A, Bass J, Saez E, Wiltshire T, Su AI. Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet. 2008 May 9;4(5):e1000070. (PubMed)

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS One. 2008 Jul 30;3(7):e2803. (PubMed)

Yuan C, Sheng Q, Tang H, Li Y, Zeng R, Solaro RJ. Quantitative comparison of sarcomeric phosphoproteomes of neonatal and adult rat hearts. Am J Physiol Heart Circ Physiol. 2008 Aug;295(2):H647-56. (PubMed)

Yuan C, Solaro RJ. Myofilament proteins: From cardiac disorders to proteomic changes. 2008. Proteomics Clin Appl 2: 788-799. (InterScience)

Zhou D, Xue J, Lai JC, Schork NJ, White KP, Haddad GG. Mechanisms underlying hypoxia tolerance in Drosophila melanogaster: hairy as a metabolic switch. PLoS Genet. 2008 Oct;4(10):e1000221. (PubMed)