Publications for All Faculty

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Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, Finnerty CC, López CM, Honari S, Moore EE, Minei JP, Cuschieri J, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Jeschke MG, Klein MB, Gamelli RL, Gibran NS, Brownstein BH, Miller-Graziano C, Calvano SE, Mason PH, Cobb JP, Rahme LG, Lowry SF, Maier RV, Moldawer LL, Herndon DN, Davis RW, Xiao W, Tompkins RG,

Genomic responses in mouse models poorly mimic human inflammatory diseases.

Proc Natl Acad Sci U S A. 2013;110(9):3507-12 - PMID: 23401516 - PMCID: PMC3587220 - DOI: 10.1073/pnas.1222878110
Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK

Robust, synergistic regulation of human gene expression using TALE activators.

Nat Methods. 2013;10(3):243-5 - PMID: 23396285 - PMCID: PMC3584229 - DOI: 10.1038/nmeth.2366
Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, Defelice M, H?lková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Nat Genet. 2013;45(3):299-303 - PMID: 23396133 - PMCID: PMC3901305 - DOI: 10.1038/ng.2543
Fukumoto T, Kano A, Ohtani K, Inoue M, Yoshihara A, Izumori K, Tajima S, Shigematsu Y, Tanaka K, Ohkouchi T, Ishida Y, Nishizawa Y, Tada Y, Ichimura K, Gomi K, Yoo SD, Sheen J, Akimitsu K

Phosphorylation of D-allose by hexokinase involved in regulation of OsABF1 expression for growth inhibition in Oryza sativa L.

Planta. 2013;237(5):1379-91 - PMID: 23397192 - DOI: 10.1007/s00425-013-1853-9
O'Rourke EJ, Kuballa P, Xavier R, Ruvkun G

?-6 Polyunsaturated fatty acids extend life span through the activation of autophagy.

Genes Dev. 2013;27(4):429-40 - PMID: 23392608 - PMCID: PMC3589559 - DOI: 10.1101/gad.205294.112
Buffen K, Oosting M, Mennens S, Anand PK, Plantinga TS, Sturm P, van de Veerdonk FL, van der Meer JW, Xavier RJ, Kannegati TD, Netea MG, Joosten LA

Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1? (IL-1?).

J Biol Chem. 2013;288(12):8658-66 - PMID: 23386602 - PMCID: PMC3605684 - DOI: 10.1074/jbc.M112.412841
Cuenca AG, Gentile LF, Lopez MC, Ungaro R, Liu H, Xiao W, Seok J, Mindrinos MN, Ang D, Ozrazgat Baslanti T, Bihorac A, Efron PA, Cuschieri J, Warren HS, Tompkins RG, Maier RV, Baker HV, Moldawer LL,

Development of a Genomic Metric That Can Be Rapidly Used to Predict Clinical Outcome in Severely Injured Trauma Patients.

Crit Care Med. 2013;41(5):1175-1185 - PMID: 23388514 - PMCID: PMC3652285 - DOI: 10.1097/CCM.0b013e318277131c
Tremblay JP, Xiao X, Aartsma-Rus A, Barbas C, Blau HM, Bogdanove AJ, Boycott K, Braun S, Breakefield XO, Bueren JA, Buschmann M, Byrne BJ, Calos M, Cathomen T, Chamberlain J, Chuah M, Cornetta K, Davies KE, Dickson JG, Duchateau P, Flotte TR, Gaudet D, Gersbach CA, Gilbert R, Glorioso J, Herzog RW, High KA, Huang W, Huard J, Joung JK, Liu D, Liu D, Lochmüller H, Lustig L, Martens J, Massie B, Mavilio F, Mendell JR, Nathwani A, Ponder K, Porteus M, Puymirat J, Samulski J, Takeda S, Thrasher A, Vandendriessche T, Wei Y, Wilson JM, Wilton SD, Wolfe JH, Gao G

Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic Diseases.

Mol Ther. 2013;21(2):266-268 - PMID: 23369965 - PMCID: PMC3594019 - DOI: 10.1038/mt.2013.4
Gao X, Chen X, Lin W, Chen S, Lu D, Niu Y, Li L, Cheng C, McCormack M, Sheen J, Shan L, He P

Bifurcation of Arabidopsis NLR Immune Signaling via Ca(2+)-Dependent Protein Kinases.

PLoS Pathog. 2013;9(1):e1003127 - PMID: 23382673 - PMCID: PMC3561149 - DOI: 10.1371/journal.ppat.1003127
Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B

Identification of a candidate therapeutic autophagy-inducing peptide.

Nature. 2013;494(7436):201-6 - PMID: 23364696 - PMCID: PMC3788641 - DOI: 10.1038/nature11866
Shi Z, Montgomery TA, Qi Y, Ruvkun G

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes.

Genome Res. 2013;23(3):497-508 - PMID: 23363624 - PMCID: PMC3589538 - DOI: 10.1101/gr.149112.112
Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK

Efficient genome editing in zebrafish using a CRISPR-Cas system.

Nat Biotechnol. 2013;31(3):227-9 - PMID: 23360964 - PMCID: PMC3686313 - DOI: 10.1038/nbt.2501
Lu XM, Tompkins R, Fischman A

Burn injury-induced IRS-1 degradation in mouse skeletal muscle.

Int J Burns Trauma. 2013;3(1):37-48 - PMID: 23386984 - PMCID: PMC3560490
Slater LH, Hett EC, Mark K, Chumbler NM, Patel D, Lacy DB, Collier RJ, Hung DT

Identification of Novel Host-Targeted Compounds That Protect From Anthrax Lethal Toxin-Induced Cell Death.

ACS Chem Biol. 2013;8(4):812-822 - PMID: 23343607 - PMCID: PMC3638717 - DOI: 10.1021/cb300555n
Conway KL, Kuballa P, Khor B, Zhang M, Shi HN, Virgin HW, Xavier RJ

ATG5 regulates plasma cell differentiation.

Autophagy. 2013;9(4):528-37 - PMID: 23327930 - PMCID: PMC3627668 - DOI: 10.4161/auto.23484
Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, Alm EJ, Erdman SE

Probiotic bacteria induce a 'glow of health'.

PLoS One. 2013;8(1):e53867 - PMID: 23342023 - PMCID: PMC3547054 - DOI: 10.1371/journal.pone.0053867
Cortez-Retamozo V, Etzrodt M, Newton A, Ryan R, Pucci F, Sio SW, Kuswanto W, Rauch PJ, Chudnovskiy A, Iwamoto Y, Kohler R, Marinelli B, Gorbatov R, Wojtkiewicz G, Panizzi P, Mino-Kenudson M, Forghani R, Figueiredo JL, Chen JW, Xavier R, Swirski FK, Nahrendorf M, Weissleder R, Pittet MJ

Angiotensin II Drives the Production of Tumor-Promoting Macrophages.

Immunity. 2013;38(2):296-308 - PMID: 23333075 - PMCID: PMC3582771 - DOI: 10.1016/j.immuni.2012.10.015
Lu XM, Tompkins RG, Fischman AJ

Nitric oxide activates intradomain disulfide bond formation in the kinase loop of Akt1/PKB? after burn injury.

Int J Mol Med. 2013;31(3):740-50 - PMID: 23314241 - PMCID: PMC3597556 - DOI: 10.3892/ijmm.2013.1241
Zhang S, Zhang N, Blain JC, Szostak JW

Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension.

J Am Chem Soc. 2013;135(2):924-32 - PMID: 23252395 - PMCID: PMC3548433 - DOI: 10.1021/ja311164j
Cezairliyan B, Vinayavekhin N, Grenfell-Lee D, Yuen GJ, Saghatelian A, Ausubel FM

Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans.

PLoS Pathog. 2013;9(1):e1003101 - PMID: 23300454 - PMCID: PMC3536714 - DOI: 10.1371/journal.ppat.1003101
Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans.

Nat Commun. 2013;4:1342 - PMID: 23299892 - PMCID: PMC3625375 - DOI: 10.1038/ncomms2343
Carr CE, Rowedder H, Vafadari C, Lui CS, Cascio E, Zuber MT, Ruvkun G

Radiation resistance of biological reagents for in situ life detection.

Astrobiology. 2013;13(1):68-78 - PMID: 23330963 - DOI: 10.1089/ast.2012.0869
Zhao G, Yu YM, Kaneki M, Tompkins RG, Fischman AJ

Simvastatin Protects Hepatocytes From Apoptosis by Suppressing the TNF-?/Caspase-3 Signaling Pathway in Mice With Burn Injury.

Ann Surg. 2013;257(6):1129-36 - PMID: 23275311 - PMCID: PMC4102342 - DOI: 10.1097/SLA.0b013e318273fdca
Tabach Y, Billi AC, Hayes GD, Newman MA, Zuk O, Gabel H, Kamath R, Yacoby K, Chapman B, Garcia SM, Borowsky M, Kim JK, Ruvkun G

Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence.

Nature. 2013;493(7434):694-8 - PMID: 23364702 - PMCID: PMC3762460 - DOI: 10.1038/nature11779
Zhang S, Zhang N, Blain JC, Szostak JW

Synthesis of N3´-P5´-Phosphoramidate DNA by Non-enzymatic Template-directed Primer Extension.

J Am Chem Soc. 2013;135(2):924-32 - PMID: 23252395 - PMCID: PMC3548433 - DOI: 10.1021/ja311164j
Total: 2481