Publications for All Faculty

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Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N

Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.

Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737 - DOI: 10.1158/2159-8290.CD-15-1442
Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.

Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890 - DOI: 10.1016/j.jcmgh.2016.05.011
Sundberg TB, Liang Y, Wu H, Choi HG, Kim ND, Sim T, Johannessen L, Petrone A, Khor B, Graham DB, Latorre IJ, Phillips AJ, Schreiber SL, Perez J, Shamji AF, Gray NS, Xavier RJ

Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function In Vivo.

ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440 - DOI: 10.1021/acschembio.6b00217
O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

Cell Syst. 2016;2(5):323-334 - PMID: 27211859 - PMCID: PMC5032147 - DOI: 10.1016/j.cels.2016.04.011
Frydman GH, Bendapudi PK, Marini RP, Vanderburg CR, Tompkins RG, Fox JG

Coagulation Biomarkers in Healthy Chinese-Origin Rhesus Macaques (Macaca mulatta).

J Am Assoc Lab Anim Sci. 2016;55(3):252-9 - PMID: 27177557 - PMCID: PMC4865685
Ueki R, Liu L, Kashiwagi S, Kaneki M, Khan M, Hirose M, Tompkins RG, Martyn JA, Yasuhara S

Role of Elevated Fibrinogen in Burn-Induced Mitochondrial Dysfunction: Protective Effects of Glycyrrhizin.

Shock. 2016;46(4):382-9 - PMID: 27172157 - PMCID: PMC5026541 - DOI: 10.1097/SHK.0000000000000602
Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.

Nat Med. 2016;22(6):598-605 - PMID: 27158904 - PMCID: PMC5087285 - DOI: 10.1038/nm.4102
Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.

Science. 2016;352(6289):1116-20 - PMID: 27230380 - PMCID: PMC4996125 - DOI: 10.1126/science.aad9948
Taleban S, Stewart KO, Li DK, Singh P, Pardi DS, Sturgeon HC, Yajnik V, Xavier RJ, Ananthakrishnan AN, Khalili H

Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes.

Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770 - DOI: 10.1007/s10620-016-4180-8
Tsai SQ, Topkar VV, Joung JK, Aryee MJ

Open-source guideseq software for analysis of GUIDE-seq data.

Nat Biotechnol. 2016;34(5):483 - PMID: 27153277 - DOI: 10.1038/nbt.3534
Peloquin JM, Goel G, Villablanca EJ, Xavier RJ

Mechanisms of Pediatric Inflammatory Bowel Disease.

Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239 - DOI: 10.1146/annurev-immunol-032414-112151
Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, , Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Science. 2016;352(6285):565-9 - PMID: 27126040 - PMCID: PMC5240844 - DOI: 10.1126/science.aad3369
Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007
Prywes N, Michaels YS, Pal A, Oh SS, Szostak JW

Thiolated uridine substrates and templates improve the rate and fidelity of ribozyme-catalyzed RNA copying.

Chem Commun (Camb). 2016;52(39):6529-32 - PMID: 27109314 - DOI: 10.1039/c6cc02692c
Netea MG, Joosten LA, Latz E, Mills KH, Natoli G, Stunnenberg HG, O'Neill LA, Xavier RJ

Trained immunity: A program of innate immune memory in health and disease.

Science. 2016;352(6284):aaf1098 - PMID: 27102489 - PMCID: PMC5087274 - DOI: 10.1126/science.aaf1098
Zimmer S, Grebe A, Bakke SS, Bode N, Halvorsen B, Ulas T, Skjelland M, De Nardo D, Labzin LI, Kerksiek A, Hempel C, Heneka MT, Hawxhurst V, Fitzgerald ML, Trebicka J, Björkhem I, Gustafsson JÅ, Westerterp M, Tall AR, Wright SD, Espevik T, Schultze JL, Nickenig G, Lütjohann D, Latz E

Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming.

Sci Transl Med. 2016;8(333):333ra50 - PMID: 27053774 - PMCID: PMC4878149 - DOI: 10.1126/scitranslmed.aad6100
Tsai SQ, Joung JK

Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.

Nat Rev Genet. 2016;17(5):300-12 - PMID: 27087594 - PMCID: PMC7225572 - DOI: 10.1038/nrg.2016.28
Abrams JA, Xavier RJ, Rustgi AK

Timothy C. Wang, MD: Our next AGA President.

Gastroenterology. 2016;150(5):1231-1236 - PMID: 27018487 - DOI: 10.1053/j.gastro.2016.03.021
Adamala KP, Engelhart AE, Szostak JW

Collaboration between primitive cell membranes and soluble catalysts.

Nat Commun. 2016;7:11041 - PMID: 26996603 - PMCID: PMC4802160 - DOI: 10.1038/ncomms11041
Li L, Lelyveld VS, Prywes N, Szostak JW

Experimental and computational evidence for a loose transition state in phosphoroimidazolide hydrolysis.

J Am Chem Soc. 2016;138(12):3986-9 - PMID: 26974265 - PMCID: PMC7547882 - DOI: 10.1021/jacs.6b00784
Engelhart AE, Adamala KP, Szostak JW

A simple physical mechanism enables homeostasis in primitive cells.

Nat Chem. 2016;8(5):448-53 - PMID: 27102678 - PMCID: PMC4929987 - DOI: 10.1038/nchem.2475
Acharya M, Sokolovska A, Tam JM, Conway KL, Stefani C, Raso F, Mukhopadhyay S, Feliu M, Paul E, Savill J, Hynes RO, Xavier RJ, Vyas JM, Stuart LM, Lacy-Hulbert A

?v Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells.

Nat Commun. 2016;7:10917 - PMID: 26965188 - PMCID: PMC4792966 - DOI: 10.1038/ncomms10917
Kazis LE, Lee AF, Rose M, Liang MH, Li NC, Ren XS, Sheridan R, Gilroy-Lewis J, Stoddard F, Hinson M, Warden G, Stubbs K, Blakeney P, Meyer W, McCauley R, Herndon D, Palmieri T, Mooney K, Wood D, Pidcock F, Reilly D, Cullen M, Calvert C, Ryan CM, Schneider JC, Soley-Bori M, Tompkins RG

Recovery Curves for Pediatric Burn Survivors: Advances in Patient-Oriented Outcomes.

JAMA Pediatr. 2016;170(6):534-42 - PMID: 26953515 - DOI: 10.1001/jamapediatrics.2015.4722
Schwerd T, Pandey S, Yang HT, Bagola K, Jameson E, Jung J, Lachmann RH, Shah N, Patel SY, Booth C, Runz H, Düker G, Bettels R, Rohrbach M, Kugathasan S, Chapel H, Keshav S, Elkadri A, Platt N, Muise AM, Koletzko S, Xavier RJ, Marquardt T, Powrie F, Wraith JE, Gyrd-Hansen M, Platt FM, Uhlig HH

Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease.

Gut. 2017;66(6):1060-1073 - PMID: 26953272 - PMCID: PMC5532464 - DOI: 10.1136/gutjnl-2015-310382
Total: 2467