Publications

Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.

Adams JC, Seed B, Lu N, Landry A, Xavier RJ
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023

Regulation of signaling pathways downstream of IGF-I/insulin by androgen in skeletal muscle of glucocorticoid-treated rats.

Yin HN, Chai JK, Yu YM, Shen CA, Wu YQ, Yao YM, Liu H, Liang LM, Tompkins RG, Sheng ZY
J Trauma. 2009;66(4):1083-90 - PMID: 19359918 - PMCID: PMC4085982

Exploration of O-spiroketal C-arylglucosides as novel and selective renal sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors.

Lv B, Xu B, Feng Y, Peng K, Xu G, Du J, Zhang L, Zhang W, Zhang T, Zhu L, Ding H, Sheng Z, Welihinda A, Seed B, Chen Y
Bioorg Med Chem Lett. 2009;19(24):6877-81 - PMID: 19896374

O-Spiro C-aryl glucosides as novel sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors.

Xu B, Lv B, Feng Y, Xu G, Du J, Welihinda A, Sheng Z, Seed B, Chen Y
Bioorg Med Chem Lett. 2009;19(19):5632-5 - PMID: 19700318

Screening for hyperlipidemia. In: Goroll A and Mulley A, eds.

Haydock GS and MW Freeman
Primary Care Medicine, 6th Edition. 2009;:ePub

Approach to the patient with hypercholesterolemia. In: Goroll A, May L, Mulley A, eds

MW Freeman
Primary Care Medicine, 6th Edition. 2009;:ePub

What to do about high cholesterol

M Freeman, Consultant editor, 4th edition. Buckley, Rita
President and Fellows of Harvard College. Harvard Health Publications. 2009;:ePub

Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes.

Stephenson LM, Miller BC, Ng A, Eisenberg J, Zhao Z, Cadwell K, Graham DB, Mizushima NN, Xavier R, Virgin HW, Swat W
Autophagy. 2009;5(5):625-35 - PMID: 19276668 - PMCID: PMC3737142

Building complex biological networks based upon model organisms: mapping the human autophagy interactome via a hybrid yeast-human protein interaction network.

Huett A, Xavier R
Autophagy. 2009;5(6):884-6 - PMID: 19535904

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.

Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, , Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D, Daly MJ
PLoS Genet. 2009;5(6):e1000534 - PMID: 19557189 - PMCID: PMC2694358

Emerging connections in the ethylene signaling network.

Yoo SD, Cho Y, Sheen J
Trends Plant Sci. 2009;14(5):270-9 - PMID: 19375376 - PMCID: PMC3063992

In vitro reconstitution of an abscisic acid signalling pathway.

Fujii H, Chinnusamy V, Rodrigues A, Rubio S, Antoni R, Park SY, Cutler SR, Sheen J, Rodriguez PL, Zhu JK
Nature. 2009;462(7273):660-4 - PMID: 19924127 - PMCID: PMC2803041

Low glucose uncouples hexokinase1-dependent sugar signaling from stress and defense hormone abscisic acid and C2H4 responses in Arabidopsis.

Cho YH, Sheen J, Yoo SD
Plant Physiol. 2009;152(3):1180-2 - PMID: 20034964 - PMCID: PMC2832269

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

Huett A, McCarroll SA, Daly MJ, Xavier RJ
Autophagy. 2009;5(1):96-9 - PMID: 19029815 - PMCID: PMC3204672

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

Imamura T, Kikuchi H, Herraiz MT, Park DY, Mizukami Y, Mino-Kenduson M, Lynch MP, Rueda BR, Benita Y, Xavier RJ, Chung DC
Int J Cancer. 2009;124(4):763-71 - PMID: 19030186 - PMCID: PMC2682346

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

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,
J Proteome Res. 2009;8(1):290-9 - PMID: 19053531 - PMCID: PMC2752204

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

Neely AN, Gardner J, Durkee P, Warden GD, Greenhalgh DG, Gallagher JJ, Herndon DN, Tompkins RG, Kagan RJ
J Burn Care Res. 2009;30(1):19-29 - PMID: 19060725

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

Medoff BD, Sandall BP, Landry A, Nagahama K, Mizoguchi A, Luster AD, Xavier RJ
Eur J Immunol. 2009;39(1):78-84 - PMID: 19130560 - PMCID: PMC2747028

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

Chen JJ, Cai X, Szostak JW
J Am Chem Soc. 2009;131(6):2119-21 - PMID: 19166350 - PMCID: PMC2722806

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

Clatworthy AE, Lee JS, Leibman M, Kostun Z, Davidson AJ, Hung DT
Infect Immun. 2009;77(4):1293-303 - PMID: 19168742 - PMCID: PMC2663173

Lack of lymphatic vessel phenotype in LYVE-1/CD44 double knockout mice.

Luong MX, Tam J, Lin Q, Hagendoorn J, Moore KJ, Padera TP, Seed B, Fukumura D, Kucherlapati R, Jain RK
J Cell Physiol. 2009;219(2):430-7 - PMID: 19170073 - PMCID: PMC2665001

Biosynthesis of the Caenorhabditis elegans dauer pheromone.

Butcher RA, Ragains JR, Li W, Ruvkun G, Clardy J, Mak HY
Proc Natl Acad Sci U S A. 2009;106(6):1875-9 - PMID: 19174521 - PMCID: PMC2631283

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

Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC
Plant Physiol. 2009;149(3):1435-51 - PMID: 19176722 - PMCID: PMC2649394

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

Powell JR, Kim DH, Ausubel FM
Proc Natl Acad Sci U S A. 2009;106(8):2782-7 - PMID: 19196974 - PMCID: PMC2650343

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

Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK
PLoS One. 2009;4(2):e4348 - PMID: 19198653 - PMCID: PMC2634973

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

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
Gut. 2009;58(6):799-804 - PMID: 19201773 - PMCID: PMC2757103

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

Soukas AA, Kane EA, Carr CE, Melo JA, Ruvkun G
Genes Dev. 2009;23(4):496-511 - PMID: 19240135 - PMCID: PMC2648650

Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.

Adams JC, Seed B, Lu N, Landry A, Xavier RJ
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023

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

Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT
Cell Host Microbe. 2009;5(3):298-307 - PMID: 19286138 - PMCID: PMC2756022

Enzymatic primer-extension with glycerol-nucleoside triphosphates on DNA templates.

Chen JJ, Tsai CH, Cai X, Horhota AT, McLaughlin LW, Szostak JW
PLoS One. 2009;4(3):e4949 - PMID: 19305495 - PMCID: PMC2654545

Coupled growth and division of model protocell membranes.

Zhu TF, Szostak JW
J Am Chem Soc. 2009;131(15):5705-13 - PMID: 19323552 - PMCID: PMC2669828

A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy.

Huett A, Ng A, Cao Z, Kuballa P, Komatsu M, Daly MJ, Podolsky DK, Xavier RJ
J Immunol. 2009;182(8):4917-30 - PMID: 19342671 - PMCID: PMC2752416

Using PATIMDB to create bacterial transposon insertion mutant libraries.

Urbach JM, Wei T, Liberati N, Grenfell-Lee D, Villanueva J, Wu G, Ausubel FM
Curr Protoc Mol Biol. 2009;Chapter 19:Unit 19.7 - PMID: 19343706 - PMCID: PMC4492697

Preparation of large monodisperse vesicles.

Zhu TF, Szostak JW
PLoS One. 2009;4(4):e5009 - PMID: 19347043 - PMCID: PMC2661144

Development of a second-generation antiandrogen for treatment of advanced prostate cancer.

Tran C, Ouk S, Clegg NJ, Chen Y, Watson PA, Arora V, Wongvipat J, Smith-Jones PM, Yoo D, Kwon A, Wasielewska T, Welsbie D, Chen CD, Higano CS, Beer TM, Hung DT, Scher HI, Jung ME, Sawyers CL
Science. 2009;324(5928):787-90 - PMID: 19359544 - PMCID: PMC2981508

The cytoskeletal scaffold Shank3 is recruited to pathogen-induced actin rearrangements.

Huett A, Leong JM, Podolsky DK, Xavier RJ
Exp Cell Res. 2009;315(12):2001-11 - PMID: 19371741 - PMCID: PMC2693461

Retraction for Litovchick and Szostak. "Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display".

Litovchick A, Szostak JW
Proc Natl Acad Sci U S A. 2009;106(17):7263 - PMID: 19380733 - PMCID: PMC2678432

Long-term superior performance of a stem cell/hepatocyte device for the treatment of acute liver failure.

Yagi H, Parekkadan B, Suganuma K, Soto-Gutierrez A, Tompkins RG, Tilles AW, Yarmush ML
Tissue Eng Part A. 2009;15(11):3377-88 - PMID: 19397469 - PMCID: PMC2792056

High-frequency modification of plant genes using engineered zinc-finger nucleases.

Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF
Nature. 2009;459(7245):442-5 - PMID: 19404258 - PMCID: PMC2743854

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

Cheng X, Gupta A, Chen C, Tompkins RG, Rodriguez W, Toner M
Lab Chip. 2009;9(10):1357-64 - PMID: 19417901 - PMCID: PMC4064257

Origins of life: Systems chemistry on early Earth.

Szostak JW
Nature. 2009;459(7244):171-2 - PMID: 19444196

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ
Nucleic Acids Res. 2009;37(14):4587-602 - PMID: 19491311 - PMCID: PMC2724271

Modulation of allergen-specific T-lymphocyte function by virus-like particles decorated with HLA class II molecules.

Leb VM, Jahn-Schmid B, Kueng HJ, Schmetterer KG, Haiderer D, Neunkirchner A, Fischer GF, Hartl A, Thalhamer J, Steinberger P, Bohle B, Seed B, Pickl WF
J Allergy Clin Immunol. 2009;124(1):121-8 - PMID: 19500826

A soma-to-germline transformation in long-lived Caenorhabditis elegans mutants.

Curran SP, Wu X, Riedel CG, Ruvkun G
Nature. 2009;459(7250):1079-84 - PMID: 19506556 - PMCID: PMC2716045

Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells.

Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L
Cell Stem Cell. 2009;5(1):97-110 - PMID: 19540188 - PMCID: PMC2720132

High-throughput screen for novel antimicrobials using a whole animal infection model.

Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM
ACS Chem Biol. 2009;4(7):527-33 - PMID: 19572548 - PMCID: PMC2745594

Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics.

Elenko MP, Szostak JW, van Oijen AM
J Am Chem Soc. 2009;131(29):9866-7 - PMID: 19572753 - PMCID: PMC2716146

Cell polarity factor Par3 binds SPTLC1 and modulates monocyte serine palmitoyltransferase activity and chemotaxis.

Tamehiro N, Mujawar Z, Zhou S, Zhuang DZ, Hornemann T, von Eckardstein A, Fitzgerald ML
J Biol Chem. 2009;284(37):24881-90 - PMID: 19592499 - PMCID: PMC2757191

A genomic score prognostic of outcome in trauma patients.

Warren HS, Elson CM, Hayden DL, Schoenfeld DA, Cobb JP, Maier RV, Moldawer LL, Moore EE, Harbrecht BG, Pelak K, Cuschieri J, Herndon DN, Jeschke MG, Finnerty CC, Brownstein BH, Hennessy L, Mason PH, Tompkins RG,
Mol Med. 2009;15(7-8):220-7 - PMID: 19593405 - PMCID: PMC2707513

Mannose-binding lectin and innate immunity.

Ip WK, Takahashi K, Ezekowitz RA, Stuart LM
Immunol Rev. 2009;230(1):9-21 - PMID: 19594626

Formation of protocell-like vesicles in a thermal diffusion column.

Budin I, Bruckner RJ, Szostak JW
J Am Chem Soc. 2009;131(28):9628-9 - PMID: 19601679 - PMCID: PMC2710859

Productive steps toward an antimicrobial targeting virulence.

Barczak AK, Hung DT
Curr Opin Microbiol. 2009;12(5):490-6 - PMID: 19631578 - PMCID: PMC2763366

Microarray analysis suggests that burn injury results in mitochondrial dysfunction in human skeletal muscle.

Tzika AA, Mintzopoulos D, Mindrinos M, Zhang J, Rahme LG, Tompkins RG
Int J Mol Med. 2009;24(3):387-92 - PMID: 19639232 - PMCID: PMC3207251

Chemical tools for dissecting bacterial physiology and virulence.

Stanley SA, Hung DT
Biochemistry. 2009;48(37):8776-86 - PMID: 19653697

Conformational analysis of DNA repair intermediates by time-resolved fluorescence spectroscopy.

Lin S, Horning DP, Szostak JW, Chaput JC
J Phys Chem A. 2009;113(35):9585-7 - PMID: 19673467 - PMCID: PMC2733762

Preliminary evidence for the effects of morphine on posttraumatic stress disorder symptoms in one- to four-year-olds with burns.

Stoddard FJ, Sorrentino EA, Ceranoglu TA, Saxe G, Murphy JM, Drake JE, Ronfeldt H, White GW, Kagan J, Snidman N, Sheridan RL, Tompkins RG
J Burn Care Res. 2009;30(5):836-43 - PMID: 19692914

Origin of life on earth.

Ricardo A, Szostak JW
Sci Am. 2009;301(3):54-61 - PMID: 19708528

A genome-wide genetic screen for host factors required for hepatitis C virus propagation.

Li Q, Brass AL, Ng A, Hu Z, Xavier RJ, Liang TJ, Elledge SJ
Proc Natl Acad Sci U S A. 2009;106(38):16410-5 - PMID: 19717417 - PMCID: PMC2752535

Effect of insulin levels on the phosphorylation of specific amino acid residues in IRS-1: implications for burn-induced insulin resistance.

Lu XM, Hamrahi VF, Tompkins RG, Fischman AJ
Int J Mol Med. 2009;24(4):531-8 - PMID: 19724894 - PMCID: PMC4084762

Validation of the riboleukogram to detect ventilator-associated pneumonia after severe injury.

Cobb JP, Moore EE, Hayden DL, Minei JP, Cuschieri J, Yang J, Li Q, Lin N, Brownstein BH, Hennessy L, Mason PH, Schierding WS, Dixon DJ, Tompkins RG, Warren HS, Schoenfeld DA, Maier RV
Ann Surg. 2009;250(4):531-9 - PMID: 19730236 - PMCID: PMC3047595

Reconstructing the emergence of cellular life through the synthesis of model protocells.

Mansy SS, Szostak JW
Cold Spring Harb Symp Quant Biol. 2009;74:47-54 - PMID: 19734203

Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly.

Lapaquette P, Glasser AL, Huett A, Xavier RJ, Darfeuille-Michaud A
Cell Microbiol. 2009;12(1):99-113 - PMID: 19747213 - PMCID: PMC3743084

Identification of antifungal compounds active against Candida albicans using an improved high-throughput Caenorhabditis elegans assay.

Okoli I, Coleman JJ, Tampakakis E, Tempakakis E, An WF, Holson E, Wagner F, Conery AL, Larkins-Ford J, Wu G, Stern A, Ausubel FM, Mylonakis E
PLoS One. 2009;4(9):e7025 - PMID: 19750012 - PMCID: PMC2737148

Efficient and rapid template-directed nucleic acid copying using 2'-amino-2',3'-dideoxyribonucleoside-5'-phosphorimidazolide monomers.

Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW
J Am Chem Soc. 2009;131(40):14560-70 - PMID: 19757789 - PMCID: PMC2759813

Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays.

Maeder ML, Thibodeau-Beganny S, Sander JD, Voytas DF, Joung JK
Nat Protoc. 2009;4(10):1471-501 - PMID: 19798082 - PMCID: PMC2858690

Autophagy, immunity and human disease.

Heath RJ, Xavier RJ
Curr Opin Gastroenterol. 2009;25(6):512-20 - PMID: 19826372 - PMCID: PMC2849745

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.

Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR
Nature. 2009;461(7268):1282-6 - PMID: 19865172 - PMCID: PMC3256734

C. elegans major fats are stored in vesicles distinct from lysosome-related organelles.

O'Rourke EJ, Soukas AA, Carr CE, Ruvkun G
Cell Metab. 2009;10(5):430-5 - PMID: 19883620 - PMCID: PMC2921818

PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.

Spandidos A, Wang X, Wang H, Seed B
Nucleic Acids Res. 2009;38(Database issue):D792-9 - PMID: 19906719 - PMCID: PMC2808898

Common variants at five new loci associated with early-onset inflammatory bowel disease.

Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, , Silber G, Wrobel I, Quiros A, , Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dasso ...
Nat Genet. 2009;41(12):1335-40 - PMID: 19915574 - PMCID: PMC3267927

Flip-flop-induced relaxation of bending energy: implications for membrane remodeling.

Bruckner RJ, Mansy SS, Ricardo A, Mahadevan L, Szostak JW
Biophys J. 2009;97(12):3113-22 - PMID: 20006948 - PMCID: PMC2793357

Plant science. DNA binding made easy.

Voytas DF, Joung JK
Science. 2009;326(5959):1491-2 - PMID: 20007890

Targeted mutagenesis in zebrafish using customized zinc-finger nucleases.

Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR
Nat Protoc. 2009;4(12):1855-67 - PMID: 20010934 - PMCID: PMC2814337

RNA editing genes associated with extreme old age in humans and with lifespan in C. elegans.

Sebastiani P, Montano M, Puca A, Solovieff N, Kojima T, Wang MC, Melista E, Meltzer M, Fischer SE, Andersen S, Hartley SH, Sedgewick A, Arai Y, Bergman A, Barzilai N, Terry DF, Riva A, Anselmi CV, Malovini A, Kitamoto A, Sawabe M, Arai T, Gondo Y, Steinberg MH, Hirose N, Atzmon G, Ruvkun G, Baldwin CT, Perls TT
PLoS One. 2009;4(12):e8210 - PMID: 20011587 - PMCID: PMC2788130

CD36 ligands promote sterile inflammation through assembly of a Toll-like receptor 4 and 6 heterodimer.

Stewart CR, Stuart LM, Wilkinson K, van Gils JM, Deng J, Halle A, Rayner KJ, Boyer L, Zhong R, Frazier WA, Lacy-Hulbert A, El Khoury J, Golenbock DT, Moore KJ
Nat Immunol. 2009;11(2):155-61 - PMID: 20037584 - PMCID: PMC2809046

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus.

Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E, Adams DJ, Xavier RJ, Farzan M, Elledge SJ
Cell. 2009;139(7):1243-54 - PMID: 20064371 - PMCID: PMC2824905

Targeting multiple biofilm pathways.

Hett EC, Hung DT
Chem Biol. 2009;16(12):1216-8 - PMID: 20064430

Toward a systems-level analysis of infection biology: a new method for conducting genetic screens in human cells.

Stanley SA, Hung DT
Sci Transl Med. 2009;1(11):11ps13 - PMID: 20371455