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2009
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 Aalto-Setala K, Conklin BR, Lo B (2009) Obtaining consent for future research with induced pluripotent cells: Opportunities and challenges. PLoS Biol. 7:e42.

Aiba K, Nedorezov T, Piao Y, Nishiyama A, Matoba R, Sharova LV, Sharov AA, Yamanaka S, Niwa H, Ko MS (2009) Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells. DNA Res. 16:73–80.

Auffray C, Fogg DK, Narni-Mancinelli E, Senechal B, Trouillet C, Saederup N, Leemput J, Bigot K, Campisi L, Abitbol M, Molina T, Charo I, Hume DA, Cumano A, Lauvau G, Geissmann F (2009) CX3CR1+ CD115+ CD135+ common macrophage/DC precursors and the role of CX3CR1 in their response to inflammation. J. Exp. Med. 206:595–606.

Berglund J, Pollard KS, Webster MT (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7:e26.

Bock-Marquette I, Shrivastava S, Pipes GC, Thatcher JE, Blystone A, Shelton JM, Galindo CL, Melegh B, Srivastava D, Olson EN, DiMaio JM (2009) Thymosin beta4 mediated PKC activation is essential to initiate the embryonic coronary developmental program and epicardial progenitor cell activation in adult mice in vivo. J. Mol. Cell. Cardiol. 46:728–738.

Can AS, Bersot TP, Gonen M (2009) Anthropometric indices and their relationship with cardiometabolic risk factors in a sample of Turkish adults. Public Health Nutr. 12:538–546.

Can AS, Ozbayrakci S, Palaoglu KE, Bersot TP (2009) Comparison between Turkish Cardiovascular Risk Platform and United States National Cholesterol Education Program Adult Treatment Panel III definitions of the metabolic syndrome in Turkish adults. J. Cardiometab. Syndr. 4:26–32.

Conklin BR (2009) Journal club. A geneticist wonders why we need to sleep. Nature 461:573.

Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, Muth AN, Lee TH, Miano JM, Ivey KN, Srivastava D (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460:705–710.

Cordes KR, Srivastava D (2009) MicroRNA regulation of cardiovascular development. Circ. Res. 104:724–732.

Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM (2009) Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J. Bacteriol. 191:782–794.

Daley GQ, Lensch MW, Jaenisch R, Meissner A, Plath K, Yamanaka S (2009) Broader implications of defining standards for the pluripotency of iPSCs. Cell Stem Cell 4:200–201.

Ellis J, Bruneau BG, Keller G, Lemischka IR, Nagy A, Rossant J, Srivastava D, Zandstra PW, Stanford WL (2009) Alternative induced pluripotent stem cell characterization criteria for in vitro applications. Cell Stem Cell 4:198–199.

Farese RV, Jr., Walther TC (2009) Lipid droplets finally get a little R-E-S-P-E-C-T. Cell 139:855–860.

Fish JE, Srivastava D (2009) MicroRNAs: Opening a new vein in angiogenesis research. Sci. Signal. 2:pe1.

Guo Y, Cordes KR, Farese RV, Jr., Walther TC (2009) Lipid droplets at a glance. J. Cell Sci. 122:749–752.

Hirami Y, Osakada F, Takahashi K, Okita K, Yamanaka S, Ikeda H, Yoshimura N, Takahashi M (2009) Generation of retinal cells from mouse and human induced pluripotent stem cells. Neurosci. Lett. 458:126–131.

Hong H, Takahashi K, Ichisaka T, Aoi T, Kanagawa O, Nakagawa M, Okita K, Yamanaka S (2009) Suppression of induced pluripotent stem cell generation by the p53-p21 pathway. Nature 460:1132–1135.

Hsieh F, Chen S-C, Pollard KS (2009) A nearly exhaustive search for CpG islands on whole chromosomes. Int. J. Biostat. 5:article 14.

Ieda M, Tsuchihashi T, Ivey KN, Ross RS, Hong T-T, Shaw RM, Srivastava D (2009) Cardiac fibroblasts regulate myocardial proliferation through beta-1 integrin signaling. Dev. Cell 16:233–244.

Kelder T, Pico AR, Hanspers K, van Iersel MP, Evelo C, Conklin BR (2009) Mining biological pathways using WikiPathways web services. PLoS One 4:e6447.

Kita-Matsuo H, Barcova M, Prigozhina N, Salomonis N, Wei K, Jacot JG, Nelson B, Spiering S, Haverslag R, Kim C, Talantova M, Bajpai R, Calzolari D, Terskikh A, McCulloch AD, Price JH, Conklin BR, Chen HS, Mercola M (2009) Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. PLoS One 4:e5046.

Koliwad SK, Kuo T, Shipp LE, Gray NE, Backhed F, So AY, Farese RV, Jr., Wang JC (2009) Angiopoietin-like 4 (ANGPTL4, fasting-induced adipose factor) is a direct glucocorticoid receptor target and participates in glucocorticoid-regulated triglyceride metabolism. J. Biol. Chem. 284:25593–25601.

Koshiba-Takeuchi K, Mori AD, Kaynak BL, Cebra-Thomas J, Sukonnik T, Georges RO, Latham S, Beck L, Henkelman RM, Black BL, Olson EN, Wade J, Takeuchi JK, Nemer M, Gilbert SF, Bruneau BG (2009) Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature 461:95–98.

Krahmer N, Guo Y, Farese RV, Jr., Walther TC (2009) SnapShot: Lipid Droplets. Cell 139:1024-1024 e1.

Kwon C, Qian L, Cheng P, Nigam V, Arnold J, Srivastava D (2009) A regulatory pathway involving Notch1/beta-catenin/Isl1 determines cardiac progenitor cell fate. Nat. Cell Biol. 11:951–957.

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M (2009) The bovine lactation genome: Insights into the evolution of mammalian milk. Genome Biol. 10:R43.

Li G, Bien-Ly N, Andrews-Zwilling Y, Xu Q, Bernardo A, Ring K, Halabisky B, Deng C, Mahley RW, Huang Y (2009) GABAergic interneuron dysfunction impairs hippocampal neurogenesis in adult apolipoprotein E4 knockin mice. Cell Stem Cell 5:634–645.

Ling H, Waterworth DM, Stirnadel HA, Pollin TI, Barter PJ, Kesaniemi YA, Mahley RW, McPherson R, Waeber G, Bersot TP, Cohen JC, Grundy SM, Mooser VE, Mitchell BD (2009) Genome-wide linkage and association analyses to identify genes influencing adiponectin levels: The GEMS Study. Obesity (Silver Spring) 17:737–744.

Lo B, Conklin BR (2009) Consent: Criteria should be drawn up for tissue donors. Nature 461:593.

Mahley RW, Huang Y (2009) Alzheimer disease: Multiple causes, multiple effects of apolipoprotein E4, and multiple therapeutic approaches. Ann. Neurol. 65:623–625.

Mahley RW, Weisgraber KH, Huang Y (2009) Apolipoprotein E: Structure determines function, from atherosclerosis to Alzheimer's disease to AIDS. J. Lipid Res. 50 Suppl:S183–S188.

Maitra M, Schluterman MK, Nichols HA, Richardson JA, Lo CW, Srivastava D, Garg V (2009) Interaction of Gata4 and Gata6 with Tbx5 is critical for normal cardiac development. Dev. Biol. 326:368–377.

Miura K, Okada Y, Aoi T, Okada A, Takahashi K, Okita K, Nakagawa M, Koyanagi M, Tanabe K, Ohnuki M, Ogawa D, Ikeda E, Okano H, Yamanaka S (2009) Variation in the safety of induced pluripotent stem cell lines. Nat. Biotechnol. 27:743–745.

Nagata S, Toyoda M, Yamaguchi S, Hirano K, Makino H, Nishino K, Miyagawa Y, Okita H, Kiyokawa N, Nakagawa M, Yamanaka S, Akutsu H, Umezawa A, Tada T (2009) Efficient reprogramming of human and mouse primary extra-embryonic cells to pluripotent stem cells. Genes Cells 14:1395–1404.

Nakamura K, Salomonis N, Tomoda K, Yamanaka S, Conklin BR (2009) G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies. PLoS One 4:e7780.

Neumann SA, Tingley WG, Conklin BR, Shrader CJ, Peet E, Muldoon MF, Jennings JR, Ferrell RE, Manuck SB (2009) AKAP10 (I646V) functional polymorphism predicts heart rate and heart rate variability in apparently healthy, middle-aged European-Americans. Psychophysiology 46:466–472.

Nigam V, Srivastava D (2009) Notch1 represses osteogenic pathways in aortic valve cells. J. Mol. Cell. Cardiol. 47:828–834.

Nishimura K, Nakagawa T, Ono K, Ogita H, Sakamoto T, Yamamoto N, Okita K, Yamanaka S, Ito J (2009) Transplantation of mouse induced pluripotent stem cells into the cochlea. Neuroreport 20:1250–1254.

Niwa A, Umeda K, Chang H, Saito M, Okita K, Takahashi K, Nakagawa M, Yamanaka S, Nakahata T, Heike T (2009) Orderly hematopoietic development of induced pluripotent stem cells via Flk-1(+) hemoangiogenic progenitors. J. Cell. Physiol. 221:367–377.

Ohnuki M, Takahashi K, Yamanaka S (2009) Generation and characterization of human induced pluripotent stem cells. Curr. Protoc. Stem Cell Biol. Chapter 4:Unit 4A 2.

Okano H, Yamanaka S, Tsuji S (2009) Possibility of iPS cells. Brain Nerve 61:711–718.

Pico AR, Smirnov IV, Chang JS, Yeh RF, Wiemels JL, Wiencke JK, Tihan T, Conklin BR, Wrensch M (2009) SNPLogic: An interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic Acids Res. 37:D803–D809.

Pollard KS (2009) What makes us human? Sci. Am. 300:44–49.

Riazi AM, Takeuchi JK, Hornberger LK, Zaidi SH, Amini F, Coles J, Bruneau BG, Van Arsdell GS (2009) NKX2-5 regulates the expression of beta-catenin and GATA4 in ventricular myocytes. PLoS One 4:e5698.

Richards JB, Waterworth D, O?Rahilly S, Hivert MF, Loos RJF, Perry JRB, Tanaka T, Timpson NJ, Semple RK, Soranzo N, Song K, Rocha N, Grundberg E, Dupuis J, Florez JC, Langenberg C, Prokopenko I, Saxena R, Sladek R, Aulchenko Y, Evans D, Waeber G, Erdmann J, Burnett M-S, Sattar N, Devaney J, Willenborg C, GIANT Consortium, Hingorani A, Witteman JCM, Vollenweider P, Hengstenberg C, Ferrucci L, Melzer D, Deanfield J, Hall AS, Egan JM, Thompson JR, Ricketts SL, K?nig IR, Grundy S, Wichmann H-E, Barter P, Mahley R, Kesaniemi A, Rader DJ, Reilly MP, Epstein SE, Stewart AFR, Duijn CMV, Schunkert H, Burling K, Deloukas P, Pastinen T, Samani NJ, McPherson R, Smith GD, Frayling TM, Wareham NJ, Meigs JB, Mooser V, Spector TD. A genome-wide association study reveals variants in ARL15 that influence adiponectin levels. PLoS Genet. In press.

Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR (2009) Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PLoS Comput. Biol. 5:e1000553.

Senju S, Haruta M, Matsunaga Y, Fukushima S, Ikeda T, Takahashi K, Okita K, Yamanaka S, Nishimura Y (2009) Characterization of dendritic cells and macrophages generated by directed differentiation from mouse induced pluripotent stem cells. Stem Cells 27:1021–1031.

Shieh JT, Srivastava D (2009) Heart malformation: What are the chances it could happen again? Circulation 120:269–271.

Shih MY, Kane MA, Zhou P, Yen CL, Streeper RS, Napoli JL, Farese RV, Jr. (2009) Retinol esterification by DGAT1 is essential for retinoid homeostasis in murine skin. J. Biol. Chem. 284:4292–4299.

Silva J, Nichols J, Theunissen TW, Guo G, van Oosten AL, Barrandon O, Wray J, Yamanaka S, Chambers I, Smith A (2009) Nanog is the gateway to the pluripotent ground state. Cell 138:722–737.

Srivastava D, Kwon C (2009) Signaling pathways involved in cardiogenesis. In: Handbook of Cell Signaling, 2nd edition (Bradshaw RA, Dennis EA, Eds) Academic Press, Oxford, pp 2601–2609.

Stone SJ, Levin MC, Zhou P, Han J, Walther TC, Farese RV, Jr. (2009) The endoplasmic reticulum enzyme DGAT2 is found in mitochondria-associated membranes and has a mitochondrial targeting signal that promotes its association with mitochondria. J. Biol. Chem. 284:5352–5361.

Takahashi K, Narita M, Yokura M, Ichisaka T, Yamanaka S (2009) Human induced pluripotent stem cells on autologous feeders. PLoS One 4:e8067.

Takeuchi JK, Bruneau BG (2009) Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors. Nature 459:708–711.

Tanaka Y, Ikeda T, Kishi Y, Masuda S, Shibata H, Takeuchi K, Komura M, Iwanaka T, Muramatsu S, Kondo Y, Takahashi K, Yamanaka S, Hanazono Y (2009) ERas is expressed in primate embryonic stem cells but not related to tumorigenesis. Cell Transplant 18:381–389.

Taura D, Noguchi M, Sone M, Hosoda K, Mori E, Okada Y, Takahashi K, Homma K, Oyamada N, Inuzuka M, Sonoyama T, Ebihara K, Tamura N, Itoh H, Suemori H, Nakatsuji N, Okano H, Yamanaka S, Nakao K (2009) Adipogenic differentiation of human induced pluripotent stem cells: Comparison with that of human embryonic stem cells. FEBS Lett. 583:1029–1033.

Taura D, Sone M, Homma K, Oyamada N, Takahashi K, Tamura N, Yamanaka S, Nakao K (2009) Induction and isolation of vascular cells from human induced pluripotent stem cells--brief report. Arterioscler. Thromb. Vasc. Biol. 29:1100–1103.

Taylor S, Pollard K (2009) Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values. Stat. Appl. Genet. Mol. Biol. 8:Article 8.

Tsubooka N, Ichisaka T, Okita K, Takahashi K, Nakagawa M, Yamanaka S (2009) Roles of Sall4 in the generation of pluripotent stem cells from blastocysts and fibroblasts. Genes Cells 14:683–694.

Villanueva CJ, Monetti M, Shih M, Zhou P, Watkins SM, Bhanot S, Farese RV, Jr. (2009) Specific role for acyl CoA:Diacylglycerol acyltransferase 1 (Dgat1) in hepatic steatosis due to exogenous fatty acids. Hepatology 50:434–442.

Walther TC, Farese RV, Jr. (2009) The life of lipid droplets. Biochim. Biophys. Acta 1791:459–466.

Yamanaka S (2009) Elite and stochastic models for induced pluripotent stem cell generation. Nature 460:49–52.

Yamanaka S (2009) A fresh look at iPS cells. Cell 137:13–17.

Yamanaka S (2009) Ekiden to iPS Cells. Nat. Med. 15:1145–1148.

Yen CL, Cheong ML, Grueter C, Zhou P, Moriwaki J, Wong JS, Hubbard B, Marmor S, Farese RV, Jr. (2009) Deficiency of the intestinal enzyme acyl CoA:monoacylglycerol acyltransferase-2 protects mice from metabolic disorders induced by high-fat feeding. Nat. Med. 15:442–446.

Yokoo N, Baba S, Kaichi S, Niwa A, Mima T, Doi H, Yamanaka S, Nakahata T, Heike T (2009) The effects of cardioactive drugs on cardiomyocytes derived from human induced pluripotent stem cells. Biochem. Biophys. Res. Commun. 387:482–488.

Yoshida Y, Takahashi K, Okita K, Ichisaka T, Yamanaka S (2009) Hypoxia enhances the generation of induced pluripotent stem cells. Cell Stem Cell 5:237–241.

 

 


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