Publications for All Faculty

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Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT

A functional genomic screen identifies cellular cofactors of hepatitis C virus replication.

Cell Host Microbe. 2009;5(3):298-307 - PMID: 19286138 - PMCID: PMC2756022 - DOI: 10.1016/j.chom.2009.02.001
Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK

Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN).

PLoS One. 2009;4(2):e4348 - PMID: 19198653 - PMCID: PMC2634973 - DOI: 10.1371/journal.pone.0004348
Festen EA, Goyette P, Scott R, Annese V, Zhernakova A, Lian J, Lefèbvre C, Brant SR, Cho JH, Silverberg MS, Taylor KD, de Jong DJ, Stokkers PC, Mcgovern D, Palmieri O, Achkar JP, Xavier RJ, Daly MJ, Duerr RH, Wijmenga C, Weersma RK, Rioux JD

Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis.

Gut. 2009;58(6):799-804 - PMID: 19201773 - PMCID: PMC2757103 - DOI: 10.1136/gut.2008.166918
Powell JR, Kim DH, Ausubel FM

The G protein-coupled receptor FSHR-1 is required for the Caenorhabditis elegans innate immune response.

Proc Natl Acad Sci U S A. 2009;106(8):2782-7 - PMID: 19196974 - PMCID: PMC2650343 - DOI: 10.1073/pnas.0813048106
Cheng X, Gupta A, Chen C, Tompkins RG, Rodriguez W, Toner M

Enhancing the performance of a point-of-care CD4+ T-cell counting microchip through monocyte depletion for HIV/AIDS diagnostics.

Lab Chip. 2009;9(10):1357-64 - PMID: 19417901 - PMCID: PMC4064257 - DOI: 10.1039/b818813k
Soukas AA, Kane EA, Carr CE, Melo JA, Ruvkun G

Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans.

Genes Dev. 2009;23(4):496-511 - PMID: 19240135 - PMCID: PMC2648650 - DOI: 10.1101/gad.1775409
Chen JJ, Cai X, Szostak JW

N2'-->p3' phosphoramidate glycerol nucleic acid as a potential alternative genetic system.

J Am Chem Soc. 2009;131(6):2119-21 - PMID: 19166350 - PMCID: PMC2722806 - DOI: 10.1021/ja809069b
Imamura T, Kikuchi H, Herraiz MT, Park DY, Mizukami Y, Mino-Kenduson M, Lynch MP, Rueda BR, Benita Y, Xavier RJ, Chung DC

HIF-1alpha and HIF-2alpha have divergent roles in colon cancer.

Int J Cancer. 2009;124(4):763-71 - PMID: 19030186 - PMCID: PMC2682346 - DOI: 10.1002/ijc.24032
Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC

Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis.

Plant Physiol. 2009;149(3):1435-51 - PMID: 19176722 - PMCID: PMC2649394 - DOI: 10.1104/pp.108.132985
Butcher RA, Ragains JR, Li W, Ruvkun G, Clardy J, Mak HY

Biosynthesis of the Caenorhabditis elegans dauer pheromone.

Proc Natl Acad Sci U S A. 2009;106(6):1875-9 - PMID: 19174521 - PMCID: PMC2631283 - DOI: 10.1073/pnas.0810338106
Huett A, McCarroll SA, Daly MJ, Xavier RJ

On the level: IRGM gene function is all about expression.

Autophagy. 2009;5(1):96-9 - PMID: 19029815 - PMCID: PMC3204672 - DOI: 10.4161/auto.5.1.7263
Clatworthy AE, Lee JS, Leibman M, Kostun Z, Davidson AJ, Hung DT

Pseudomonas aeruginosa infection of zebrafish involves both host and pathogen determinants.

Infect Immun. 2009;77(4):1293-303 - PMID: 19168742 - PMCID: PMC2663173 - DOI: 10.1128/IAI.01181-08
Neely AN, Gardner J, Durkee P, Warden GD, Greenhalgh DG, Gallagher JJ, Herndon DN, Tompkins RG, Kagan RJ

Are topical antimicrobials effective against bacteria that are highly resistant to systemic antibiotics?

J Burn Care Res. 2009;30(1):19-29 - PMID: 19060725 - DOI: 10.1097/BCR.0b013e3181921eed
Medoff BD, Sandall BP, Landry A, Nagahama K, Mizoguchi A, Luster AD, Xavier RJ

Differential requirement for CARMA1 in agonist-selected T-cell development.

Eur J Immunol. 2009;39(1):78-84 - PMID: 19130560 - PMCID: PMC2747028 - DOI: 10.1002/eji.200838734
Qian WJ, Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD,

Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.

J Proteome Res. 2009;8(1):290-9 - PMID: 19053531 - PMCID: PMC2752204 - DOI: 10.1021/pr800467r
Spandidos A, Wang X, Wang H, Dragnev S, Thurber T, Seed B

A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance.

BMC Genomics. 2008;9:633 - PMID: 19108745 - PMCID: PMC2631021 - DOI: 10.1186/1471-2164-9-633
Clay NK, Adio AM, Denoux C, Jander G, Ausubel FM

Glucosinolate metabolites required for an Arabidopsis innate immune response.

Science. 2009;323(5910):95-101 - PMID: 19095898 - PMCID: PMC2630859 - DOI: 10.1126/science.1164627
Avruch J, Xavier R, Bardeesy N, Zhang XF, Praskova M, Zhou D, Xia F

Rassf family of tumor suppressor polypeptides.

J Biol Chem. 2009;284(17):11001-5 - PMID: 19091744 - PMCID: PMC2670104 - DOI: 10.1074/jbc.R800073200
Neafsey DE, Schaffner SF, Volkman SK, Park D, Montgomery P, Milner DA, Lukens A, Rosen D, Daniels R, Houde N, Cortese JF, Tyndall E, Gates C, Stange-Thomann N, Sarr O, Ndiaye D, Ndir O, Mboup S, Ferreira MU, Moraes Sdo L, Dash AP, Chitnis CE, Wiegand RC, Hartl DL, Birren BW, Lander ES, Sabeti PC, Wirth DF

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.

Genome Biol. 2008;9(12):R171 - PMID: 19077304 - PMCID: PMC2646275 - DOI: 10.1186/gb-2008-9-12-r171
Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB

Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.

Nat Methods. 2009;6(1):67-9 - PMID: 19079253 - PMCID: PMC2613166 - DOI: 10.1038/nmeth.1286
Zhou D, Medoff BD, Chen L, Li L, Zhang XF, Praskova M, Liu M, Landry A, Blumberg RS, Boussiotis VA, Xavier R, Avruch J

The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells.

Proc Natl Acad Sci U S A. 2008;105(51):20321-6 - PMID: 19073936 - PMCID: PMC2600581 - DOI: 10.1073/pnas.0810773105
Gopalan S, Ausubel FM

A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

PLoS One. 2008;3(12):e3891 - PMID: 19066631 - PMCID: PMC2588659 - DOI: 10.1371/journal.pone.0003891
Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.

Nucleic Acids Res. 2009;37(2):506-15 - PMID: 19056825 - PMCID: PMC2632909 - DOI: 10.1093/nar/gkn962
Hitomi J, Christofferson DE, Ng A, Yao J, Degterev A, Xavier RJ, Yuan J

Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway.

Cell. 2008;135(7):1311-23 - PMID: 19109899 - PMCID: PMC2621059 - DOI: 10.1016/j.cell.2008.10.044
Troemel ER, Félix MA, Whiteman NK, Barrière A, Ausubel FM

Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans.

PLoS Biol. 2008;6(12):2736-52 - PMID: 19071962 - PMCID: PMC2596862 - DOI: 10.1371/journal.pbio.0060309
Total: 2467