CBC-Funded Publications 2009

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2009

Abdul-Hay SO, Edirisinghe P, Thatcher GR. Selective modulation of amyloid-beta peptide degradation by flurbiprofen, fenofibrate, and related compounds regulates Abeta levels. J Neurochem. 2009 Nov;111(3):683-95. (PubMed)

Abdul-Hay SO, Luo J, Ashghodom RT, Thatcher GR. NO-flurbiprofen reduces amyloid-beta, is neuroprotective in cell culture, and enhances cognition in response to cholinergic blockade. J Neurochem. 2009 Nov;111(3):766-76. (PubMed)

Adamian L, Gussin HA, Tseng YY, Muni NJ, Feng F, Qian H, Pepperberg DR, Liang J. Structural model of rho1 GABAC receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function. Protein Sci. 2009 Nov;18(11):2371-83. (PubMed)

Arble DM, Bass J, Laposky AD, Vitaterna MH, Turek FW. Circadian timing of food intake contributes to weight gain. Obesity (Silver Spring). 2009 Nov;17(11):2100-2. (PubMed)

Barick KC, Aslam M, Lin YP, Bahadur D, Prasad PV, Dravid VP. Novel and efficient MR active aqueous colloidal Fe3O4 nanoassemblies. J. Mater. Chem., 2009, 19, 7023 – 7029. (DOI: 10.1039/b911626e)

Barick KC, Aslam M, Prasad PV, Dravid VP, Bahadur D. Nanoscale assembly of amine functionalized colloidal iron oxide. J Magn Magn Mater. 2009 May;321(10):1529-1532. (PubMed)

Barrière A, Yang SP, Pekarek E, Thomas CG, Haag ES, Ruvinsky I. Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 2009 Mar;19(3):470-80. (PubMed)

Ben-Zvi A, Miller EA, Morimoto RI. Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14914-9. (PubMed)

Bhaskar PT, Nogueira V, Patra KC, Jeon SM, Park Y, Robey RB, Hay N. mTORC1 hyperactivity inhibits serum deprivation-induced apoptosis via increased hexokinase II and GLUT1 expression, sustained Mcl-1 expression, and glycogen synthase kinase 3beta inhibition. Mol Cell Biol. 2009 Sep;29(18):5136-47. (PubMed)

Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009 Feb 20;136(4):642-55. Review. (PubMed)

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. Unlocking the secrets of the genome. Nature. 2009 Jun 18;459(7249):927-30. (PubMed)

Chen PR, Nishida S, Poor CB, Cheng A, Bae T, Kuechenmeister L, Dunman PM, Missiakas D, He C. A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus. Mol Microbiol. 2009 Jan;71(1):198-211. (PubMed)

Chen WS, Peng XD, Wang Y, Xu PZ, Chen ML, Luo Y, Jeon SM, Coleman K, Haschek WM, Bass J, Philipson LH, Hay N. Leptin deficiency and beta-cell dysfunction underlie type 2 diabetes in compound Akt knockout mice. Mol Cell Biol. 2009 Jun;29(11):3151-62. (PubMed)

Chou ST, Khandros E, Bailey LC, Nichols KE, Vakoc CR, Yao Y, Huang Z, Crispino JD, Hardison RC, Blobel GA, Weiss MJ. Graded repression of PU.1/Sfpi1 gene transcription by GATA factors regulates hematopoietic cell fate. Blood. 2009 Jul 30;114(5):983-94. (PubMed)

Dai Q, Saikia M, Li NS, Pan T, Piccirilli JA. Efficient Chemical Synthesis of AppDNA by Adenylation of Immobilized DNA-5′-monophosphate. Org. Lett., 2009, 11 (5): 1067–1070. (PubMed)

Dechat T, Adam SA, Goldman RD. Nuclear lamins and chromatin: when structure meets function. Adv Enzyme Regul. 2009;49(1):157-66. (PubMed)

Dellefave LM, Pytel P, Mewborn S, Mora B, Guris DL, Fedson S, Waggoner D, Moskowitz I, McNally EM. Sarcomere mutations in cardiomyopathy with left ventricular hypertrabeculation. Circ Cardiovasc Genet. 2009 Oct;2(5):442-9. (PubMed)

Ebalunode JO, Dong X, Ouyang Z, Liang J, Eckenhoff RG, Zheng W. Structure-based shape pharmacophore modeling for the discovery of novel anesthetic compounds. Bioorg Med Chem. 2009 Jul 15;17(14):5133-8. (PubMed)

Eriksson JE, Dechat T, Grin B, Helfand B, Mendez M, Pallari HM, Goldman RD. Introducing intermediate filaments: from discovery to disease. J Clin Invest. 2009 Jul;119(7):1763-71. (PubMed)

Gauhar Z, Sun LV, Hua S, Mason CE, Fuchs F, Li TR, Boutros M, White KP. Genomic mapping of binding regions for the Ecdysone receptor protein complex. Genome Res. 2009 Jun;19(6):1006-13. (PubMed)

Gidalevitz T, Krupinski T, Garcia S, Morimoto RI. Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity. PLoS Genet. 2009 Mar;5(3):e1000399. (PubMed)

Glavaski-Joksimovic A, Virag T, Chang QA, West NC, Mangatu TA, McGrogan MP, Dugich-Djordjevic M, Bohn MC. Reversal of dopaminergic degeneration in a parkinsonian rat following micrografting of human bone marrow-derived neural progenitors. Cell Transplant. 2009;18(7):801-14. (PubMed)

Gondi VB, Hagihara K, Rawal VH. Diastereoselective and enantioselective synthesis of tertiary alpha-hydroxy phosphonates through hydrogen-bond catalysis. Angew Chem Int Ed Engl. 2009;48(4):776-9. (PubMed)

Gu Y, Grossman RL. Sector and Sphere: Towards Simplified Storage and Processing of Large Scale Distributed Data. Philosophical Transactions of the Royal Society A. 2009 Volume 367, Number 1897, pages 2429-2445. (pubs.rgrossman.com)

Harney AS, Lee J, Manus LM, Wang P, Ballweg DM, LaBonne C, Meade TJ. Targeted inhibition of Snail family zinc finger transcription factors by oligonucleotide-Co(III) Schiff base conjugate. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13667-72. (PubMed)

He B, Velaparthi S, Pieffet G, Pennington C, Mahesh A, Holzle DL, Brunsteiner M, van Breemen R, Blond SY, Petukhov PA. Binding ensemble profiling with photoaffinity labeling (BEProFL) approach: mapping the binding poses of HDAC8 inhibitors. J Med Chem. 2009 Nov 26;52(22):7003-13. (PubMed)

Heydemann A, Ceco E, Lim JE, Hadhazy M, Ryder P, Moran JL, Beier DR, Palmer AA, McNally EM. Latent TGF-beta-binding protein 4 modifies muscular dystrophy in mice. J Clin Invest. 2009 Dec;119(12):3703-12. Erratum in: J Clin Invest. 2010 Feb;120(2):645. (PubMed)

Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009 Jun 26;137(7):1259-71. (PubMed)

Huang Z, Dore LC, Li Z, Orkin SH, Feng G, Lin S, Crispino JD. GATA-2 reinforces megakaryocyte development in the absence of GATA-1. Mol Cell Biol. 2009 Sep;29(18):5168-80. (PubMed)

Hurst SJ, Hill HD, Macfarlane RJ, Wu J, Dravid VP, Mirkin CA. Synthetically programmable DNA binding domains in aggregates of DNA-functionalized gold nanoparticles. Small. 2009 Oct;5(19):2156-61. (PubMed)

Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A. Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol. 2009 Nov;5(11):e1000559. (PubMed)

Joshi HM, Lin YP, Aslam M, Prasad PV, Schultz EA, Edelman, R, Meade T, Dravid VP. Effects of shape and size of cobalt ferrite nanostructures on their MRI contrast and thermal activation. J Phys Chem C. 2009 Vol. 113 (41): pp: 17761-17767. (J. Phys. Chem.)

Kawai T, Ng MC, Hayes MG, Yoshiuchi I, Tsuchiya T, Robertson H, Cox NJ, Polonsky KS, Bell GI, Ehrmann DA. Variation in the perilipin gene (PLIN) affects glucose and lipid metabolism in non-Hispanic white women with and without polycystic ovary syndrome. Diabetes Res Clin Pract. 2009 Dec;86(3):186-92. (PubMed)

Kirk JA, MacGowan GA, Evans C, Smith SH, Warren CM, Mamidi R, Chandra M, Stewart AF, Solaro RJ, Shroff SG. Left ventricular and myocardial function in mice expressing constitutively pseudophosphorylated cardiac troponin I. Circ Res. 2009 Dec 4;105(12):1232-9. (PubMed)

Kozlov KN, Myasnikova E, Samsonova AA, Surkova S, Reinitz J, Samsonova M. GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly (Austin). 2009 Apr-Jun;3(2):151-6. (PubMed)

Krishnaswamy S, Kanteti R, Duke-Cohan JS, Loganathan S, Liu W, Ma PC, Sattler M, Singleton PA, Ramnath N, Innocenti F, Nicolae DL, Ouyang Z, Liang J, Minna J, Kozloff MF, Ferguson MK, Natarajan V, Wang YC, Garcia JG, Vokes EE, Salgia R. Ethnic differences and functional analysis of MET mutations in lung cancer. Clin Cancer Res. 2009 Sep 15;15(18):5714-23. (PubMed)

Lange Y, Ye J, Duban ME, Steck TL. Activation of membrane cholesterol by 63 amphipaths. Biochemistry. 2009 Sep 15;48(36):8505-15. (PubMed)

Lee JH, Bugarija B, Millan EJ, Walton NM, Gaetz J, Fernandes CJ, Yu WH, Mekel-Bobrov N, Vallender TW, Snyder GE, Xiang AP, Lahn BT. Systematic identification of cis-silenced genes by trans complementation. Hum Mol Genet. 2009 Mar 1;18(5):835-46. (PubMed)

Lee JH, Gaetz J, Bugarija B, Fernandes CJ, Snyder GE, Bush EC, Lahn BT. Chromatin analysis of occluded genes. Hum Mol Genet. 2009 Jul 15;18(14):2567-74. (PubMed)

Li Q, Fung LW. Structural and dynamic study of the tetramerization region of non-erythroid alpha-spectrin: a frayed helix revealed by site-directed spin labeling electron paramagnetic resonance. Biochemistry. 2009 Jan 13;48(1):206-15. (PubMed)

Li Q, Roxas BA. An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. BMC Bioinformatics. 2009 Feb 2;10:43. (PubMed)

Li X, Cassidy JJ, Reinke CA, Fischboeck S, Carthew RW. A microRNA imparts robustness against environmental fluctuation during development. Cell. 2009 Apr 17;137(2):273-82. (PubMed)

Liang J. Geometry of protein shape and its evolutionary pattern for function prediction and characterization. Conf Proc IEEE Eng Med Biol Soc. 2009;2009:2324-7. (PubMed)

Lin W, Hyeon T, Lanza GM, Zhang M, Meade TJ. Magnetic nanoparticles for early detection of cancer by Magnetic Resonance Imaging. MRS Bulletin 2009, 34, 441-448. (MRS Bulletin)

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science. 2009 Feb 27;323(5918):1218-22. (PubMed)

Lu HM, Liang J. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES. PLoS Comput Biol. 2009 Oct;5(10):e1000526. (PubMed)

Lucchetta EM, Carthew RW, Ismagilov RF. The endo-siRNA pathway is essential for robust development of the Drosophila embryo. PLoS One. 2009 Oct 23;4(10):e7576. (PubMed)

Major JL, Meade TJ. Bioresponsive, cell-penetrating, and multimeric MR contrast agents. Acc Chem Res. 2009 Jul 21;42(7):893-903. (PubMed)

Manolopoulou M, Guo Q, Malito E, Schilling AB, Tang WJ. Molecular basis of catalytic chamber-assisted unfolding and cleavage of human insulin by human insulin-degrading enzyme. J Biol Chem. 2009 May 22;284(21):14177-88. (PubMed)

Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR, Radulescu O, Vanario-Alonso CE, Sharp DH, Samsonova M, Reinitz J. Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Comput Biol. 2009 Mar;5(3):e1000303. (PubMed)

Manu, Surkova S, Spirov AV, Gursky VV, Janssens H, Kim AR, Radulescu O, Vanario-Alonso CE, Sharp DH, Samsonova M, Reinitz J. Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biol. 2009 Mar;7(3):e1000049. (PubMed)

Marcheva B, Ramsey KM, Affinati A, Bass J. Clock genes and metabolic disease. J Appl Physiol. 2009 Nov;107(5):1638-46. (PubMed)

Marko JF. Micromechanics of Single Supercoiled DNA Molecules. In: The IMA Volumes in Mathematics and its Applications. Mathematics of DNA Structure, Function and Interactions. Springer. 2009. Vol. 150, 225-249. (Springerlink)

Meerschaert K, Tun MP, Remue E, De Ganck A, Boucherie C, Vanloo B, Degeest G, Vandekerckhove J, Zimmermann P, Bhardwaj N, Lu H, Cho W, Gettemans J. The PDZ2 domain of zonula occludens-1 and -2 is a phosphoinositide binding domain. Cell Mol Life Sci. 2009 Dec;66(24):3951-66. (PubMed)

Mukhopadhyay A, McGuire T, Peng CY, Kessler JA. Differential effects of BMP signaling on parvalbumin and somatostatin interneuron differentiation. Development. 2009 Aug;136(15):2633-42. (PubMed)

Myasnikova E, Surkova S, Panok L, Samsonova M, Reinitz J. Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila. Bioinformatics. 2009 Feb 1;25(3):346-52. (PubMed)

Nakahata Y, Sahar S, Astarita G, Kaluzova M, Sassone-Corsi P. Circadian control of the NAD+ salvage pathway by CLOCK-SIRT1 Science. 2009 May 1;324(5927):654-7. (PubMed)

Nangia Y, Wangoo N, Sharma S, Wu JS, Dravid V, Shekhawat GS, Raman Suri R. Facile biosynthesis of phosphate capped gold nanoparticles by a bacterial isolate Stenotrophomonas maltophilia. Appl. Phys. Lett. 2009 94, 233901. (doi:10.1063/1.3141519)

Neretti N, Wang PY, Brodsky AS, Nyguyen HH, White KP, Rogina B, Helfand SL. Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2277-82. (PubMed)

Pavon-Eternod M, Gomes S, Geslain R, Dai Q, Rosner MR, Pan T. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 2009 Nov;37(21):7268-80. (PubMed)

Pedró Rosa LE, Reddy DR, Queener SF, Miller LW. Selective antifolates for chemically labeling proteins in mammalian cells. Chembiochem. 2009 Jun 15;10(9):1462-4. (PubMed)

Pisarev A, Poustelnikova E, Samsonova M, Reinitz J. FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res. 2009 Jan;37(Database issue):D560-6. (PubMed)

Poor CB, Chen PR, Duguid E, Rice PA, He C. Crystal structures of the reduced, sulfenic acid, and mixed disulfide forms of SarZ, a redox active global regulator in Staphylococcus aureus. J Biol Chem. 2009 Aug 28;284(35):23517-24. (PubMed)

Powers ET, Morimoto RI, Dillin A, Kelly JW, Balch WE. Biological and chemical approaches to diseases of proteostasis deficiency. Annu Rev Biochem. 2009;78:959-91. (PubMed)

Prahlad V, Morimoto RI. Integrating the stress response: lessons for neurodegenerative diseases from C. elegans. Trends Cell Biol. 2009 Feb;19(2):52-61. Review. (PubMed)

Prochazkova K, Shuvalova LA, Minasov G, Voburka Z, Anderson WF, Satchell KJ. Structural and molecular mechanism for autoprocessing of MARTX toxin of Vibrio cholerae at multiple sites. J Biol Chem. 2009 Sep 25;284(39):26557-68. (PubMed)

Qin Z, Kastrati I, Ashgodom RT, Lantvit DD, Overk CR, Choi Y, van Breemen RB, Bolton JL, Thatcher GR. Structural modulation of oxidative metabolism in design of improved benzothiophene selective estrogen receptor modulators. Drug Metab Dispos. 2009 Jan;37(1):161-9. (PubMed)

Rajapakse HE, Reddy DR, Mohandessi S, Butlin NB, Miller LW. Luminescent Terbium Protein Labels for Time-Resolved Microscopy and Screening. Angew Chem Int Edit. 2009 Vol. 48 Issue 27:4990-4992. (InterScience)

Ralat LA, Ren M, Schilling AB, Tang WJ. Protective role of Cys-178 against the inactivation and oligomerization of human insulin-degrading enzyme by oxidation and nitrosylation. J Biol Chem. 2009 Dec 4;284(49):34005-18. (PubMed)

Ramsey KM, Bass J. Obeying the clock yields benefits for metabolism. Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4069-70. (PubMed)

Ramsey KM, Yoshino J, Brace CS, Abrassart D, Kobayashi Y, Marcheva B, Hong HK, Chong JL, Buhr ED, Lee C, Takahashi JS, Imai S, Bass J. Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science. 2009 May 1;324(5927):651-4. (PubMed)

Rao PK, Li Q. Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis. J Proteomics Bioinform. 2009 Jan 15;2(1):19-31. (PubMed)

Rao PK, Li Q. Protein Turnover in Mycobacterial Proteomics. Molecules. 2009 14(9), 3237-3258. (mdpi)

Rao PK, Singh CR, Jagannath C, Li Q. Phagosomal proteomes modulated by mycobacterial infections. Int J Clin Exp Med. 2009 2(3):233-247. (ijcem)

Reynaud D, Lancki DW, Pongubala JMR, Warmflash A, Dinner AR, Singh H. 2009. In: Cell Determination during Hematopoiesis, Series: Cell Biology Research Progress, Chapter 1. Gene regulatory networks directing cell fates within the hematopoietic system, pp. 1-23. Editor(s): Brown G, Ceredig R. (novapublishers)

Rizk SS, Luchniak A, Uysal S, Brawley CM, Rock RS, Kossiakoff AA. An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11011-5. (PubMed)

Robey RB, Hay N. Is Akt the "Warburg kinase"?-Akt-energy metabolism interactions and oncogenesis. Semin Cancer Biol. 2009 Feb;19(1):25-31. (PubMed)

Roxas BA, Li Q. Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis. Int J Clin Exp Med. 2009 Nov 10;2(4):309-28. (PubMed)

Sawardecker EN, Amundsen CA, Sales-Pardo M, Amaral LAN. Comparison of methods for the detection of node group membership in bipartite networks. 2009 Eur. Phys. J. B 72, 671-677. (springerlink.com)

Sawardecker EN, Sales-Pardo M, Amaral LAN. Detection of node group membership in networks with group overlap. 2009 Eur. Phys. J. B 67, 277-284. (arxiv.org)

Scruggs SB, Hinken AC, Thawornkaiwong A, Robbins J, Walker LA, de Tombe PP, Geenen DL, Buttrick PM, Solaro RJ. Ablation of ventricular myosin regulatory light chain phosphorylation in mice causes cardiac dysfunction in situ and affects neighboring myofilament protein phosphorylation. J Biol Chem. 2009 Feb 20;284(8):5097-106. (PubMed)

Shekhawat GS, Lambert MP, Sharma S, Velasco PT, Viola KL, Klein WL, Dravid VP. Soluble state high resolution atomic force microscopy study of Alzheimer’s beta-amyloid oligomers. Appl Phys Lett. 2009 Nov 2;95(18):183701. (PubMed)

Skoko D, Li M, Huang Y, Mizuuchi M, Cai M, Bradley CM, Pease PJ, Xiao B, Marko JF, Craigie R, Mizuuchi K. Barrier-to-autointegration factor (BAF) condenses DNA by looping. Proc Natl Acad Sci U S A. 2009 Sep 29;106(39):16610-5. (PubMed)

Song Y, Pipalia NH, Fung LW. The L49F mutation in alpha erythroid spectrin induces local disorder in the tetramer association region: Fluorescence and molecular dynamics studies of free and bound alpha spectrin. Protein Sci. 2009 Sep;18(9):1916-25. (PubMed)

Song Y, Xu X, MacRenaris KW, Zhang XQ, Mirkin CA, Meade TJ. Multimodal gadolinium-enriched DNA-gold nanoparticle conjugates for cellular imaging. Angew Chem Int Ed Engl. 2009;48(48):9143-7. (PubMed)

Spooner CJ, Cheng JX, Pujadas E, Laslo P, Singh H. A recurrent network involving the transcription factors PU.1 and Gfi1 orchestrates innate and adaptive immune cell fates. Immunity. 2009 Oct 16;31(4):576-86. (PubMed)

Steiner DF, Park SY, Støy J, Philipson LH, Bell GI. A brief perspective on insulin production. Diabetes Obes Metab. 2009 Nov;11 Suppl 4:189-96. (PubMed)

Taimen P, Pfleghaar K, Shimi T, Möller D, Ben-Harush K, Erdos MR, Adam SA, Herrmann H, Medalia O, Collins FS, Goldman AE, Goldman RD. A progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization. Proc Natl Acad Sci U S A. 2009 Dec:8; 106(49): 20788–20793. (PubMed)

Thurn KT, Paunesku T, Wu A, Brown EM, Lai B, Vogt S, Maser J, Aslam M, Dravid V, Bergan R, Woloschak GE. Labeling TiO2 nanoparticles with dyes for optical fluorescence microscopy and determination of TiO2-DNA nanoconjugate stability. Small. 2009 Jun;5(11):1318-25. (PubMed)

Tian F, Chen J, Bao S, Shi L, Liu X, Grossman R. A graph model based study on regulatory impacts of transcription factors of Drosophila melanogaster and comparison across species. Biochem Biophys Res Commun. 2009 Sep 4;386(4):559-62. (PubMed)

Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP, Grossman RL. Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. Bioinformatics. 2009 Nov 15;25(22):3001-4. (PubMed)

Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol. 2009 Mar 27;387(2):451-64. (PubMed)

Turner JR. Intestinal mucosal barrier function in health and disease. Nat Rev Immunol. 2009 Nov;9(11):799-809. (PubMed)

Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E, Kossiakoff A. Crystal structure of full-length KcsA in its closed conformation. Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6644-9. (PubMed)

Vakulenko S, Manu, Reinitz J, Radulescu O. Size regulation in the segmentation of Drosophila: interacting interfaces between localized domains of gene expression ensure robust spatial patterning. Phys Rev Lett. 2009 Oct 16;103(16):168102. (PubMed)

Venken KJ, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, Wan KH, Koriabine M, de Jong PJ, White KP, Bellen HJ, Hoskins RA. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods. 2009 Jun;6(6):431-4. (PubMed)

Villareal DT, Koster JC, Robertson H, Akrouh A, Miyake K, Bell GI, Patterson BW, Nichols CG, Polonsky KS. Kir6.2 variant E23K increases ATP-sensitive K+ channel activity and is associated with impaired insulin release and enhanced insulin sensitivity in adults with normal glucose tolerance. Diabetes. 2009 Aug;58(8):1869-78. (PubMed)

Volchenboum SL, Kristjansdottir K, Wolfgeher D, Kron SJ. Rapid validation of Mascot search results via stable isotope labeling, pair picking, and deconvolution of fragmentation patterns. Mol Cell Proteomics. 2009 Aug;8(8):2011-22. (PubMed)

Warren CM, Kobayashi T, Solaro RJ. Sites of intra- and intermolecular cross-linking of the N-terminal extension of troponin I in human cardiac whole troponin complex. J Biol Chem. 2009 May 22;284(21):14258-66. (PubMed)

Westerheide SD, Anckar J, Stevens SM Jr, Sistonen L, Morimoto RI. Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1. Science. 2009 Feb 20;323(5917):1063-6. (PubMed)

Wong KE, Szeto FL, Zhang W, Ye H, Kong J, Zhang Z, Sun XJ, Li YC. Involvement of the vitamin D receptor in energy metabolism: regulation of uncoupling proteins. Am J Physiol Endocrinol Metab. 2009 Apr;296(4):E820-8. (PubMed)

Wu CI, Shen Y, Tang T. Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res. 2009 May;19(5):734-43. (PubMed)

Xu H, Freitas MA. Automated diagnosis of LC-MS/MS performance. Bioinformatics. 2009 May 15;25(10):1341-3. (PubMed)

Xu H, Freitas MA. MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. Proteomics. 2009 Mar;9(6):1548-55. (PubMed)

Xu H, Wang L, Sallans L, Freitas MA. A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra. Proteomics. 2009 Apr;9(7):1763-70. (PubMed)

Yu B, Qin Z, Wijewickrama GT, Edirisinghe P, Bolton JL, Thatcher GR. Comparative methods for analysis of protein covalent modification by electrophilic quinoids formed from xenobiotics. Bioconjug Chem. 2009 Apr;20(4):728-41. (PubMed)

Zhao J, Camp SM, Chiang ET, Schilling AB, Dudek SM, Garcia JGN. Identification of novel in vitro protein kinase A phosphorylation sites on recombinant non-muscle myosin light chain kinase: nano-liquid chromatography tandem mass spectrometry methodology. J of Organ Dysfunction. 2009, Vol. 5, No. 4:242-253. (informa)

Zhao J, Singleton PA, Brown ME, Dudek SM, Garcia JG. Phosphotyrosine protein dynamics in cell membrane rafts of sphingosine-1-phosphate-stimulated human endothelium: role in barrier enhancement. Cell Signal. 2009 Dec;21(12):1945-60. (PubMed)

Zhuang M, Calabrese MF, Liu J, Waddell MB, Nourse A, Hammel M, Miller DJ, Walden H, Duda DM, Seyedin SN, Hoggard T, Harper JW, White KP, Schulman BA. Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. Mol Cell. 2009 Oct 9;36(1):39-50. (PubMed)