Publications for All Faculty

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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
Irimia D, Mindrinos M, Russom A, Xiao W, Wilhelmy J, Wang S, Heath JD, Kurn N, Tompkins RG, Davis RW, Toner M

Genome-wide transcriptome analysis of 150 cell samples.

Integr Biol (Camb). 2009;1(1):99-107 - PMID: 20023796 - PMCID: PMC3763906 - DOI: 10.1039/b814329c
Pham TN, Klein MB, Gibran NS, Arnoldo BD, Gamelli RL, Silver GM, Jeschke MG, Finnerty CC, Tompkins RG, Herndon DN

Impact of oxandrolone treatment on acute outcomes after severe burn injury.

J Burn Care Res. 2008;29(6):902-6 - PMID: 18849836 - PMCID: PMC3958934 - DOI: 10.1097/BCR.0b013e31818ba14d
Guttormsen HK, Stuart LM, Shi L, Carroll MC, Chen J, Kasper DL, Ezekowitz RA, Takahashi K

Deficiency of mannose-binding lectin greatly increases antibody response in a mouse model of vaccination.

Clin Immunol. 2009;130(3):264-71 - PMID: 18996748 - PMCID: PMC2660855 - DOI: 10.1016/j.clim.2008.09.012
Irazoqui JE, Ng A, Xavier RJ, Ausubel FM

Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions.

Proc Natl Acad Sci U S A. 2008;105(45):17469-74 - PMID: 18981407 - PMCID: PMC2582251 - DOI: 10.1073/pnas.0809527105
Wang MC, O'Rourke EJ, Ruvkun G

Fat metabolism links germline stem cells and longevity in C. elegans.

Science. 2008;322(5903):957-60 - PMID: 18988854 - PMCID: PMC2760269 - DOI: 10.1126/science.1162011
Zuo Y, Zhuang DZ, Han R, Isaac G, Tobin JJ, McKee M, Welti R, Brissette JL, Fitzgerald ML, Freeman MW

ABCA12 maintains the epidermal lipid permeability barrier by facilitating formation of ceramide linoleic esters.

J Biol Chem. 2008;283(52):36624-35 - PMID: 18957418 - PMCID: PMC2605993 - DOI: 10.1074/jbc.M807377200
Manning-Tobin JJ, Moore KJ, Seimon TA, Bell SA, Sharuk M, Alvarez-Leite JI, de Winther MP, Tabas I, Freeman MW

Loss of SR-A and CD36 activity reduces atherosclerotic lesion complexity without abrogating foam cell formation in hyperlipidemic mice.

Arterioscler Thromb Vasc Biol. 2009;29(1):19-26 - PMID: 18948635 - PMCID: PMC2666043 - DOI: 10.1161/ATVBAHA.108.176644
Ramon M, Rolland F, Sheen J

Sugar sensing and signaling.

Arabidopsis Book. 2008;6:e0117 - PMID: 22303242 - PMCID: PMC3243355 - DOI: 10.1199/tab.0117
Isenbarger TA, Carr CE, Johnson SS, Finney M, Church GM, Gilbert W, Zuber MT, Ruvkun G

The most conserved genome segments for life detection on Earth and other planets.

Orig Life Evol Biosph. 2008;38(6):517-33 - PMID: 18853276 - DOI: 10.1007/s11084-008-9148-z
Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ

Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant.

PLoS One. 2008;3(10):e3391 - PMID: 18852889 - PMCID: PMC2566595 - DOI: 10.1371/journal.pone.0003391
Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S, Stone CD, Brunt EM, Xavier RJ, Sleckman BP, Li E, Mizushima N, Stappenbeck TS, Virgin HW

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells.

Nature. 2008;456(7219):259-63 - PMID: 18849966 - PMCID: PMC2695978 - DOI: 10.1038/nature07416
Ruvkun G

The perfect storm of tiny RNAs.

Nat Med. 2008;14(10):1041-5 - PMID: 18841145 - DOI: 10.1038/nm1008-1041
Huang R, Barber TA, Schmidt MA, Tompkins RG, Toner M, Bianchi DW, Kapur R, Flejter WL

A microfluidics approach for the isolation of nucleated red blood cells (NRBCs) from the peripheral blood of pregnant women.

Prenat Diagn. 2008;28(10):892-9 - PMID: 18821715 - PMCID: PMC4482103 - DOI: 10.1002/pd.2079
Litovchick A, Szostak JW

Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display.

Proc Natl Acad Sci U S A. 2008;105(40):15293-8 - PMID: 18824687 - PMCID: PMC2556359 - DOI: 10.1073/pnas.0805837105
Finnerty CC, Jeschke MG, Herndon DN, Gamelli R, Gibran N, Klein M, Silver G, Arnoldo B, Remick D, Tompkins RG,

Temporal cytokine profiles in severely burned patients: a comparison of adults and children.

Mol Med. 2008;14(9-10):553-60 - PMID: 18548133 - PMCID: PMC2424320 - DOI: 10.2119/2007-00132.Finnerty
Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.

Nucleic Acids Res. 2009;37(Database issue):D279-83 - PMID: 18812396 - PMCID: PMC2686427 - DOI: 10.1093/nar/gkn606
Galletti R, Denoux C, Gambetta S, Dewdney J, Ausubel FM, De Lorenzo G, Ferrari S

The AtrbohD-mediated oxidative burst elicited by oligogalacturonides in Arabidopsis is dispensable for the activation of defense responses effective against Botrytis cinerea.

Plant Physiol. 2008;148(3):1695-706 - PMID: 18790995 - PMCID: PMC2577270 - DOI: 10.1104/pp.108.127845
Thomson CE, McCulloch M, Sorenson A, Barnett SC, Seed BV, Griffiths IR, McLaughlin M

Myelinated, synapsing cultures of murine spinal cord--validation as an in vitro model of the central nervous system.

Eur J Neurosci. 2008;28(8):1518-35 - PMID: 18793322 - PMCID: PMC2777255 - DOI: 10.1111/j.1460-9568.2008.06415.x
Fischer SE, Butler MD, Pan Q, Ruvkun G

Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7.

Nature. 2008;455(7212):491-6 - PMID: 18784652 - PMCID: PMC2756026 - DOI: 10.1038/nature07274
Mansy SS, Szostak JW

Thermostability of model protocell membranes.

Proc Natl Acad Sci U S A. 2008;105(36):13351-5 - PMID: 18768808 - PMCID: PMC2528865 - DOI: 10.1073/pnas.0805086105
McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease.

Nat Genet. 2008;40(9):1107-12 - PMID: 19165925 - PMCID: PMC2731799 - DOI: 10.1038/ng.215
KJ Moore and MW Freeman

Targeting innate immunity for CV benefit

Drug Discovery Today: Therapeutic Strategies. 2008;5:15-23
Total: 2470