Publications

The hybrid four-CBS-domain KIN?? subunit functions as the canonical ? subunit of the plant energy sensor SnRK1.

Ramon M, Ruelens P, Li Y, Sheen J, Geuten K, Rolland F
Plant J. 2013;75(1):11-25 - PMID: 23551663

How antibiotics kill bacteria: new models needed?

Wright GD, Hung DT, Helmann JD
Nat Med. 2013;19(5):544-5 - PMID: 23652106

Moving beyond translation: glucose-TOR signaling in the transcriptional control of cell cycle.

Xiong Y, Sheen J
Cell Cycle. 2013;12(13):1989-90 - PMID: 23759578 - PMCID: PMC3737295

Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL.

Sandoval GJ, Graham DB, Gmyrek GB, Akilesh HM, Fujikawa K, Sammut B, Bhattacharya D, Srivatsan S, Kim A, Shaw AS, Yang-Iott K, Bassing CH, Duncavage E, Xavier RJ, Swat W
Cancer Immunol Res. 2013;1(6):426-37 - PMID: 24778134 - PMCID: PMC4006353

Virulence profile: Frederick M Ausubel.

Ausubel FM
Virulence. 2013;4(8):730-3 - PMID: 24481134 - PMCID: PMC3925705

Bacterial toxins and small molecules elucidate endosomal trafficking.

Slater LH, Clatworthy AE, Hung DT
Trends Microbiol. 2013;22(2):53-5 - PMID: 24370463

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.

Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R
Cell. 2013;155(7):1507-20 - PMID: 24360274 - PMCID: PMC3905448

Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans.

Fischer SE, Pan Q, Breen PC, Qi Y, Shi Z, Zhang C, Ruvkun G
Genes Dev. 2013;27(24):2678-95 - PMID: 24352423 - PMCID: PMC3877757

Ancient signals: comparative genomics of green plant CDPKs.

Hamel LP, Sheen J, Séguin A
Trends Plant Sci. 2013;19(2):79-89 - PMID: 24342084 - PMCID: PMC3932502

Correction of Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair.

Low BE, Krebs MP, Joung JK, Tsai SQ, Nishina PM, Wiles MV
Invest Ophthalmol Vis Sci. 2013;55(1):387-395 - PMID: 24346171 - PMCID: PMC3921157

High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3.

De Nardo D, Labzin LI, Kono H, Seki R, Schmidt SV, Beyer M, Xu D, Zimmer S, Lahrmann C, Schildberg FA, Vogelhuber J, Kraut M, Ulas T, Kerksiek A, Krebs W, Bode N, Grebe A, Fitzgerald ML, Hernandez NJ, Williams BR, Knolle P, Kneilling M, Röcken M, Lütjohann D, Wright SD, Schultze JL, Latz E
Nat Immunol. 2013;15(2):152-60 - PMID: 24317040 - PMCID: PMC4009731

Endogenous ?-glucocerebrosidase activity in Abca12-/-epidermis elevates ceramide levels after topical lipid application but does not restore barrier function.

Haller JF, Cavallaro P, Hernandez NJ, Dolat L, Soscia SJ, Welti R, Grabowski GA, Fitzgerald ML, Freeman MW
J Lipid Res. 2013;55(3):493-503 - PMID: 24293640 - PMCID: PMC3934733

The cytokinin side chain commands shooting.

Sheen J
Dev Cell. 2013;27(4):371-2 - PMID: 24286823 - PMCID: PMC3887519

Nonenzymatic template-directed RNA synthesis inside model protocells.

Adamala K, Szostak JW
Science. 2013;342(6162):1098-100 - PMID: 24288333 - PMCID: PMC4104020

Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia.

Liu Y, Shoji-Kawata S, Sumpter RM, Wei Y, Ginet V, Zhang L, Posner B, Tran KA, Green DR, Xavier RJ, Shaw SY, Clarke PG, Puyal J, Levine B
Proc Natl Acad Sci U S A. 2013;110(51):20364-71 - PMID: 24277826 - PMCID: PMC3870705

Deletion of the Murine Cytochrome P450 Cyp2j Locus by Fused BAC-Mediated Recombination Identifies a Role for Cyp2j in the Pulmonary Vascular Response to Hypoxia.

Zhou GL, Beloiartsev A, Yu B, Baron DM, Zhou W, Niedra R, Lu N, Tainsh LT, Zapol WM, Seed B, Bloch KD
PLoS Genet. 2013;9(11):e1003950 - PMID: 24278032 - PMCID: PMC3836722

Pathogen-Triggered Ethylene Signaling Mediates Systemic-Induced Susceptibility to Herbivory in Arabidopsis.

Groen SC, Whiteman NK, Bahrami AK, Wilczek AM, Cui J, Russell JA, Cibrian-Jaramillo A, Butler IA, Rana JD, Huang GH, Bush J, Ausubel FM, Pierce NE
Plant Cell. 2013;25(11):4755-66 - PMID: 24285796 - PMCID: PMC3875748

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis.

Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A
Cell. 2013;155(6):1409-21 - PMID: 24269006 - PMCID: PMC3956118

Pseudomonas syringae Effector HopF2 Suppresses Arabidopsis Immunity by Targeting BAK1.

Zhou J, Wu S, Chen X, Liu C, Sheen J, Shan L, He P
Plant J. 2013;77(2):235-45 - PMID: 24237140 - PMCID: PMC4224013

Autophagy is redundant for the host defense against systemic Candida albicans infections.

Smeekens SP, Malireddi RK, Plantinga TS, Buffen K, Oosting M, Joosten LA, Kullberg BJ, Perfect JR, Scott WK, van de Veerdonk FL, Xavier RJ, van de Vosse E, Kanneganti TD, Johnson MD, Netea MG
Eur J Clin Microbiol Infect Dis. 2013;33(5):711-22 - PMID: 24202731

Genetic Regulation of Caenorhabditis elegans Lysosome Related Organelle Function.

Soukas AA, Carr CE, Ruvkun G
PLoS Genet. 2013;9(10):e1003908 - PMID: 24204312 - PMCID: PMC3812091

Long-Lasting Effects of BCG Vaccination on Both Heterologous Th1/Th17 Responses and Innate Trained Immunity.

Kleinnijenhuis J, Quintin J, Preijers F, Benn CS, Joosten LA, Jacobs C, van Loenhout J, Xavier RJ, Aaby P, van der Meer JW, van Crevel R, Netea MG
J Innate Immun. 2013;6(2):152-8 - PMID: 24192057 - PMCID: PMC3944069

Preparation of Fatty Acid or Phospholipid Vesicles by Thin-film Rehydration.

Zhu TF, Budin I, Szostak JW
Methods Enzymol. 2013;533:267-74 - PMID: 24182932 - PMCID: PMC4310237

Vesicle Extrusion Through Polycarbonate Track-etched Membranes using a Hand-held Mini-extruder.

Zhu TF, Budin I, Szostak JW
Methods Enzymol. 2013;533:275-82 - PMID: 24182933 - PMCID: PMC4310236

Preparation of Fatty Acid micelles.

Zhu TF, Budin I, Szostak JW
Methods Enzymol. 2013;533:283-8 - PMID: 24182934 - PMCID: PMC4310231

Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules.

Shaw SY, Tran K, Castoreno AB, Peloquin JM, Lassen KG, Khor B, Aldrich LN, Tan PH, Graham DB, Kuballa P, Goel G, Daly MJ, Shamji AF, Schreiber SL, Xavier RJ
ACS Chem Biol. 2013;8(12):2724-33 - PMID: 24168452 - PMCID: PMC3951132

mRNA display: from basic principles to macrocycle drug discovery.

Josephson K, Ricardo A, Szostak JW
Drug Discov Today. 2013;19(4):388-399 - PMID: 24157402

Reply to Cauwels et al.: Of men, not mice, and inflammation.

Warren HS, Tompkins RG, Mindrinos MN, Xiao W, Davis RW
Proc Natl Acad Sci U S A. 2013;110(34):E3151 - PMID: 24137663 - PMCID: PMC3752239

Reply to Osterburg et al.: To study human inflammatory diseases in humans.

Tompkins RG, Warren HS, Mindrinos MN, Xiao W, Davis RW
Proc Natl Acad Sci U S A. 2013;110(36):E3371 - PMID: 24137798 - PMCID: PMC3767510

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK
Nat Biotechnol. 2013;31(12):1137-42 - PMID: 24108092 - PMCID: PMC3858462

Autophagy at the crossroads of metabolism and cellular defense.

Begun J, Xavier RJ
Curr Opin Gastroenterol. 2013;29(6):588-596 - PMID: 24100719

Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer.

Zhang S, Blain JC, Zielinska D, Gryaznov SM, Szostak JW
Proc Natl Acad Sci U S A. 2013;110(44):17732-7 - PMID: 24101473 - PMCID: PMC3816440

Synthesis and structure-activity relationships of phenyl-substituted coumarins with anti-tubercular activity that target FadD32.

Kawate T, Iwase N, Shimizu M, Stanley SA, Wellington S, Kazyanskaya E, Hung DT
Bioorg Med Chem Lett. 2013;23(22):6052-9 - PMID: 24103299

A Small Volatile Bacterial Molecule Triggers Mitochondrial Dysfunction in Murine Skeletal Muscle.

Tzika AA, Constantinou C, Bandyopadhaya A, Psychogios N, Lee S, Mindrinos M, Martyn JA, Tompkins RG, Rahme LG
PLoS One. 2013;8(9):e74528 - PMID: 24098655 - PMCID: PMC3787027

Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling.

Tabach Y, Golan T, Hernández-Hernández A, Messer AR, Fukuda T, Kouznetsova A, Liu JG, Lilienthal I, Levy C, Ruvkun G
Mol Syst Biol. 2013;9:692 - PMID: 24084807 - PMCID: PMC3817400

Genetic Variants Synthesize to Produce Paneth Cell Phenotypes that Define Subtypes of Crohn's Disease.

Vandussen KL, Liu TC, Li D, Towfic F, Modiano N, Winter R, Haritunians T, Taylor KD, Dhall D, Targan SR, Xavier RJ, McGovern DP, Stappenbeck TS
Gastroenterology. 2013;146(1):200-9 - PMID: 24076061 - PMCID: PMC3899786

Plant immune response to pathogens differs with changing temperatures.

Cheng C, Gao X, Feng B, Sheen J, Shan L, He P
Nat Commun. 2013;4:2530 - PMID: 24067909 - PMCID: PMC3901997

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis.

Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Törkvist L, Goel G, Lagacé C, Annese V, Bitton A, Begun J, Brant SR, Bresso F, Cho JH, Duerr RH, Halfvarson J, McGovern DP, Radford-Smith G, Schreiber S, Schumm PL, Sharma Y, Silverberg MS, Weersma RK, , , , D'Amato M, Vermeire S, Franke A, Lettre G, Xavier RJ, Daly MJ, Rioux JD
PLoS Genet. 2013;9(9):e1003723 - PMID: 24068945 - PMCID: PMC3772057

Dual Regulation of the lin-14 Target mRNA by the lin-4 miRNA.

Shi Z, Hayes G, Ruvkun G
PLoS One. 2013;8(9):e75475 - PMID: 24058689 - PMCID: PMC3772890

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Knights D, Lassen KG, Xavier RJ
Gut. 2013;62(10):1505-10 - PMID: 24037875 - PMCID: PMC3822528

Axl mediates acquired resistance of head and neck cancer cells to the epidermal growth factor receptor inhibitor erlotinib.

Giles KM, Kalinowski FC, Candy PA, Epis MR, Zhang PM, Redfern AD, Stuart LM, Goodall GJ, Leedman PJ
Mol Cancer Ther. 2013;12(11):2541-58 - PMID: 24026012

Locus-specific editing of histone modifications at endogenous enhancers.

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE
Nat Biotechnol. 2013;31(12):1133-6 - PMID: 24013198 - PMCID: PMC3858395

Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases.

Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF
G3 (Bethesda). 2013;3(10):1707-1715 - PMID: 23979943 - PMCID: PMC3789795

Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice from Salmonella Infection.

Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, Jijon HB, Zhang M, Aldrich LN, Villablanca EJ, Peloquin JM, Goel G, Lee IA, Mizoguchi E, Shi HN, Bhan AK, Shaw SY, Schreiber SL, Virgin HW, Shamji AF, Stappenbeck TS, Reinecker HC, Xavier RJ
Gastroenterology. 2013;145(6):1347-57 - PMID: 23973919 - PMCID: PMC3840157

Differences in Resuscitation in Morbidly Obese Burn Patients May Contribute to High Mortality.

Rae L, Pham TN, Carrougher G, Honari S, Gibran NS, Arnoldo BD, Gamelli RL, Tompkins RG, Herndon DN
J Burn Care Res. 2013;34(5):507-14 - PMID: 23966116 - PMCID: PMC3800202

Out of Context: Clinical Practice Guidelines and Patients With Multiple Chronic Conditions: A Systematic Review.

Wyatt KD, Stuart LM, Brito JP, Carranza Leon B, Domecq JP, Prutsky GJ, Egginton JS, Calvin AD, Shah ND, Murad MH, Montori VM
Med Care. 2013;52 Suppl 3:S92-S100 - PMID: 23969592

Beclin 2 Functions in Autophagy, Degradation of G Protein-Coupled Receptors, and Metabolism.

He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B
Cell. 2013;154(5):1085-99 - PMID: 23954414 - PMCID: PMC4231430

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK
Nucleic Acids Res. 2013;41(19):e181 - PMID: 23945932 - PMCID: PMC3799455

Dislodgement of port-A catheters in pediatric oncology patients: 11 years of experience.

Wang SC, Tsai CH, Hou CP, Lee SY, Ko SF, Hsiao CC, Chen YC, Chuang JH, Sheen JM
World J Surg Oncol. 2013;11(1):191 - PMID: 23941644 - PMCID: PMC3765137

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.

Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J
Nat Biotechnol. 2013;31(8):688-91 - PMID: 23929339 - PMCID: PMC4078740

Functional profiling of the gut microbiome in disease-associated inflammation.

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C
Genome Med. 2013;5(7):65 - PMID: 23906180 - PMCID: PMC3978847

Identification of novel inhibitors of non-replicating M. tuberculosis using a carbon starvation model.

Grant SS, Kawate T, Nag PP, Silvis MR, Gordon K, Stanley SA, Kazyanskaya E, Nietupski R, Golas A, Fitzgerald M, Cho S, Franzblau SG, Hung DT
ACS Chem Biol. 2013;8(10):2224-34 - PMID: 23898841 - PMCID: PMC3864639

Notch-induced transcription factors are predictive of survival and 5-fluorouracil response in colorectal cancer patients.

Candy PA, Phillips MR, Redfern AD, Colley SM, Davidson JA, Stuart LM, Wood BA, Zeps N, Leedman PJ
Br J Cancer. 2013;109(4):1023-30 - PMID: 23900217 - PMCID: PMC3749585

CRISPR RNA-guided activation of endogenous human genes.

Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK
Nat Methods. 2013;10(10):977-9 - PMID: 23892898 - PMCID: PMC3794058

Mild Obesity Is Protective After Severe Burn Injury.

Jeschke MG, Finnerty CC, Emdad F, Rivero HG, Kraft R, Williams FN, Gamelli RL, Gibran NS, Klein MB, Arnoldo BD, Tompkins RG, Herndon DN
Ann Surg. 2013;258(6):1119-29 - PMID: 23877367 - PMCID: PMC3963145

Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System.

Hwang WY, Fu Y, Reyon D, Maeder ML, Kaini P, Sander JD, Joung JK, Peterson RT, Yeh JR
PLoS One. 2013;8(7):e68708 - PMID: 23874735 - PMCID: PMC3706373

Genetic risk factors for Clostridium difficile infection in ulcerative colitis.

Ananthakrishnan AN, Oxford EC, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
Aliment Pharmacol Ther. 2013;38(5):522-30 - PMID: 23848254 - PMCID: PMC3755009

Natural selection in a bangladeshi population from the cholera-endemic ganges river delta.

Karlsson EK, Harris JB, Tabrizi S, Rahman A, Shlyakhter I, Patterson N, O'Dushlaine C, Schaffner SF, Gupta S, Chowdhury F, Sheikh A, Shin OS, Ellis C, Becker CE, Stuart LM, Calderwood SB, Ryan ET, Qadri F, Sabeti PC, Larocque RC
Sci Transl Med. 2013;5(192):192ra86 - PMID: 23825302 - PMCID: PMC4367964

Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) Assembly.

Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK
Curr Protoc Mol Biol. 2013;Chapter 12:Unit12.16 - PMID: 23821439 - PMCID: PMC3767754

CD36 coordinates NLRP3 inflammasome activation by facilitating intracellular nucleation of soluble ligands into particulate ligands in sterile inflammation.

Sheedy FJ, Grebe A, Rayner KJ, Kalantari P, Ramkhelawon B, Carpenter SB, Becker CE, Ediriweera HN, Mullick AE, Golenbock DT, Stuart LM, Latz E, Fitzgerald KA, Moore KJ
Nat Immunol. 2013;14(8):812-20 - PMID: 23812099 - PMCID: PMC3720827

Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32.

Stanley SA, Kawate T, Iwase N, Shimizu M, Clatworthy AE, Kazyanskaya E, Sacchettini JC, Ioerger TR, Siddiqi NA, Minami S, Aquadro JA, Schmidt Grant S, Rubin EJ, Hung DT
Proc Natl Acad Sci U S A. 2013;110(28):11565-70 - PMID: 23798446 - PMCID: PMC3710825

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.

Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD
Nat Biotechnol. 2013;31(9):822-6 - PMID: 23792628 - PMCID: PMC3773023

Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses.

Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D
J Innate Immun. 2013;6(3):253-62 - PMID: 23796786 - PMCID: PMC4045018

Competition between model protocells driven by an encapsulated catalyst.

Adamala K, Szostak JW
Nat Chem. 2013;5(7):634 - PMID: 23787756

Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis.

Hett EC, Slater LH, Mark KG, Kawate T, Monks BG, Stutz A, Latz E, Hung DT
Nat Chem Biol. 2013;9(7):466 - PMID: 23774875

Radiation Resistance of Sequencing Chips for in situ Life Detection.

Carr CE, Rowedder H, Lui CS, Zlatkovsky I, Papalias CW, Bolander J, Myers JW, Bustillo J, Rothberg JM, Zuber MT, Ruvkun G
Astrobiology. 2013;13(6):560-9 - PMID: 23734755

Card9 Mediates Intestinal Epithelial Cell Restitution, T-helper 17 Responses, and Control of Bacterial Infection in Mice.

Sokol H, Conway KL, Zhang M, Choi M, Morin B, Cao Z, Villablanca EJ, Li C, Wijmenga C, Yun SH, Shi HN, Xavier RJ
Gastroenterology. 2013;145(3):591-601.e3 - PMID: 23732773 - PMCID: PMC3781941

A cytoprotective perspective on longevity regulation.

Shore DE, Ruvkun G
Trends Cell Biol. 2013;23(9):409-20 - PMID: 23726168 - PMCID: PMC4057428

Conformational stability, vibrational spectra, HOMO-LUMO and NBO analysis of 1,3,4-thiadiazolidine-2,5-dithione with experimental (FT-IR and FT-Raman) techniques and scaled quantum mechanical calculations.

Xavier RJ, Dinesh P
Spectrochim Acta A Mol Biomol Spectrosc. 2013;113C:171-181 - PMID: 23727670

piggyBac transposase tools for genome engineering.

Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB, Bushman FD, Sinn PL, Craig NL
Proc Natl Acad Sci U S A. 2013;110(25):E2279-87 - PMID: 23723351 - PMCID: PMC3690869

CCT chaperonin complex is required for efficient delivery of anthrax toxin into the cytosol of host cells.

Slater LH, Hett EC, Clatworthy AE, Mark KG, Hung DT
Proc Natl Acad Sci U S A. 2013;110(24):9932-7 - PMID: 23716698 - PMCID: PMC3683768

Competition between model protocells driven by an encapsulated catalyst.

Adamala K, Szostak JW
Nat Chem. 2013;5(6):495-501 - PMID: 23695631 - PMCID: PMC4041014

RhoGTPases - NODes for effector-triggered immunity in animals.

Stuart LM, Boyer L
Cell Res. 2013;23(8):980-1 - PMID: 23689278 - PMCID: PMC3731559

Activation of caspase-1 by the NLRP3 inflammasome regulates the NADPH oxidase NOX2 to control phagosome function.

Sokolovska A, Becker CE, Ip WK, Rathinam VA, Brudner M, Paquette N, Tanne A, Vanaja SK, Moore KJ, Fitzgerald KA, Lacy-Hulbert A, Stuart LM
Nat Immunol. 2013;14(6):543-553 - PMID: 23644505 - PMCID: PMC3708594

How Does Genotype Influence Disease Phenotype in Inflammatory Bowel Disease?

Ananthakrishnan AN, Xavier RJ
Inflamm Bowel Dis. 2013;19(9):2021-30 - PMID: 23644824 - PMCID: PMC3720704

Comprehensive Protein-Based Artificial MicroRNA Screens for Effective Gene Silencing in Plants.

Li JF, Chung HS, Niu Y, Bush J, McCormack M, Sheen J
Plant Cell. 2013;25(5):1507-22 - PMID: 23645631 - PMCID: PMC3694689

Cutting Edge: cell-autonomous control of IL-7 response revealed in a novel stage of precursor B cells.

Sandoval GJ, Graham DB, Bhattacharya D, Sleckman BP, Xavier RJ, Swat W
J Immunol. 2013;190(6):2485-9 - PMID: 23420891 - PMCID: PMC3649847

Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection.

Lupfer C, Thomas PG, Anand PK, Vogel P, Milasta S, Martinez J, Huang G, Green M, Kundu M, Chi H, Xavier RJ, Green DR, Lamkanfi M, Dinarello CA, Doherty PC, Kanneganti TD
Nat Immunol. 2013;14(5):480-8 - PMID: 23525089 - PMCID: PMC3631456

Concomitant BRAF and PI3K/mTOR Blockade Is Required for Effective Treatment of BRAFV600E Colorectal Cancer.

Coffee EM, Faber AC, Roper J, Sinnamon MJ, Goel G, Keung L, Wang WV, Vecchione L, de Vriendt V, Weinstein BJ, Bronson RT, Tejpar S, Xavier RJ, Engelman JA, Martin ES, Hung KE
Clin Cancer Res. 2013;19(10):2688-98 - PMID: 23549875 - PMCID: PMC3815598

Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling.

Zhou JY, Krovvidi RK, Gao Y, Gao H, Petritis BO, De A, Miller-Graziano C, Bankey PE, Petyuk VA, Nicora CD, Clauss TR, Moore RJ, Shi T, Brown JN, Kaushal A, Xiao W, Davis RW, Maier RV, Tompkins RG, Qian WJ, Camp DG, Smith RD,
Proteomics Clin Appl. 2013;7(7-8):571-83 - PMID: 23589343 - PMCID: PMC3737403

Efficacy of Phosphodiesterase 5 inhibitor on distant burn-induced muscle autophagy, microcirculation and survival rate.

Hosokawa S, Nagashima M, Maeyama Y, Koseki H, Yomogida K, Mehr C, Rutledge M, Greenfeld H, Kaneki M, Tompkins RG, Martyn JJ, Yasuhara SE
Am J Physiol Endocrinol Metab. 2013;304(9):E922-33 - PMID: 23512808

Evaluation of Intragastric Vs Intraperitoneal Glucose Tolerance Tests in the Evaluation of Insulin Resistance in a Rodent Model of Burn Injury and Glucagon-Like Polypeptide-1 Treatment.

Watada S, Yu YM, Fischman AJ, Kurihara T, Shen CA, Tompkins RG, Fagan S
J Burn Care Res. 2013;35(1):e66-72 - PMID: 23511296 - PMCID: PMC4053788

Benchmarks for Multidimensional Recovery After Burn Injury in Young Adults: The Development, Validation, and Testing of the American Burn Association/Shriners Hospitals for Children Young Adult Burn Outcome Questionnaire.

Ryan CM, Schneider JC, Kazis LE, Lee A, Li NC, Hinson M, Bauk H, Peck M, Meyer WJ, Palmieri T, Pidcock FS, Reilly D, Tompkins RG,
J Burn Care Res. 2013;34(3):e121-e142 - PMID: 23511284

Determination of Burn Patient Outcome by Large-Scale Quantitative Discovery Proteomics.

Finnerty CC, Jeschke MG, Qian WJ, Kaushal A, Xiao W, Liu T, Gritsenko MA, Moore RJ, Camp DG, Moldawer LL, Elson C, Schoenfeld D, Gamelli R, Gibran N, Klein M, Arnoldo B, Remick D, Smith RD, Davis R, Tompkins RG, Herndon DN,
Crit Care Med. 2013;41(6):1421-1434 - PMID: 23507713 - PMCID: PMC3660437

Mitochondria-targeted antioxidant promotes recovery of skeletal muscle mitochondrial function after burn trauma assessed by in vivo 31P nuclear magnetic resonance and electron paramagnetic resonance spectroscopy.

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

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Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity.

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Dectin-1 activation controls maturation of ?-1,3-glucan-containing phagosomes.

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Glucose-TOR signalling reprograms the transcriptome and activates meristems.

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MicroRNAs Visit the ER.

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DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity.

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MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability.

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Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death.

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TALEN-based Gene Correction for Epidermolysis Bullosa.

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Persistent bacterial infections, antibiotic tolerance, and the oxidative stress response.

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Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis.

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Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death.

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Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants.

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Succinate is an inflammatory signal that induces IL-1? through HIF-1?.

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Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling.

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From genetics of inflammatory bowel disease towards mechanistic insights.

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Polarity gene discs large homolog 1 regulates the generation of memory T cells.

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Resolvin D2 restores neutrophil directionality and improves survival after burns.

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Identification of a candidate therapeutic autophagy-inducing peptide.

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Angiotensin II Drives the Production of Tumor-Promoting Macrophages.

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Effector-triggered versus pattern-triggered immunity: how animals sense pathogens.

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Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation.

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Genomic responses in mouse models poorly mimic human inflammatory diseases.

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

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

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

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

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

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

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

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

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

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

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

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

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ACS Chem Biol. 2013;8(4):812-822 - PMID: 23343607 - PMCID: PMC3638717

Radiation resistance of biological reagents for in situ life detection.

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Astrobiology. 2013;13(1):68-78 - PMID: 23330963

ATG5 regulates plasma cell differentiation.

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Autophagy. 2013;9(4):528-37 - PMID: 23327930 - PMCID: PMC3627668

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

Lu XM, Tompkins RG, Fischman AJ
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Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans.

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Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans.

Cezairliyan B, Vinayavekhin N, Grenfell-Lee D, Yuen GJ, Saghatelian A, Ausubel FM
PLoS Pathog. 2013;9(1):e1003101 - PMID: 23300454 - PMCID: PMC3536714