Publications for All Faculty

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Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time.

Nat Commun. 2017;8:14319 - PMID: 28230052 - PMCID: PMC5331214 - DOI: 10.1038/ncomms14319
Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM

Corrigendum: SIKs control osteocyte responses to parathyroid hormone.

Nat Commun. 2017;8:14745 - PMID: 28224982 - PMCID: PMC5322529 - DOI: 10.1038/ncomms14745
Gibbons SM, Kearney SM, Smillie CS, Alm EJ

Two dynamic regimes in the human gut microbiome.

PLoS Comput Biol. 2017;13(2):e1005364 - PMID: 28222117 - PMCID: PMC5340412 - DOI: 10.1371/journal.pcbi.1005364
Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

Elife. 2017;6:ePub - PMID: 28220755 - PMCID: PMC5319836 - DOI: 10.7554/eLife.20420
Chung HS, Sheen J

MAPK Assays in Arabidopsis MAMP-PRR Signal Transduction.

Methods Mol Biol. 2017;1578:155-166 - PMID: 28220422 - DOI: 10.1007/978-1-4939-6859-6_12
Li L, Prywes N, Tam CP, O'Flaherty DK, Lelyveld VS, Izgu EC, Pal A, Szostak JW

Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides.

J Am Chem Soc. 2017;139(5):1810-1813 - PMID: 28117989 - PMCID: PMC6326525 - DOI: 10.1021/jacs.6b13148
Nakazawa H, Chang K, Shinozaki S, Yasukawa T, Ishimaru K, Yasuhara S, Yu YM, Martyn JA, Tompkins RG, Shimokado K, Kaneki M

iNOS as a Driver of Inflammation and Apoptosis in Mouse Skeletal Muscle after Burn Injury: Possible Involvement of Sirt1 S-Nitrosylation-Mediated Acetylation of p65 NF-?B and p53.

PLoS One. 2017;12(1):e0170391 - PMID: 28099528 - PMCID: PMC5242494 - DOI: 10.1371/journal.pone.0170391
Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.

Proc Natl Acad Sci U S A. 2017;114(5):1135-1140 - PMID: 28096418 - PMCID: PMC5293017 - DOI: 10.1073/pnas.1616248114
Urbach JM, Ausubel FM

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events.

Proc Natl Acad Sci U S A. 2017;114(5):1063-1068 - PMID: 28096345 - PMCID: PMC5293065 - DOI: 10.1073/pnas.1619730114
Nowyhed HN, Chandra S, Kiosses W, Marcovecchio P, Andary F, Zhao M, Fitzgerald ML, Kronenberg M, Hedrick CC

ATP Binding Cassette Transporter ABCA7 Regulates NKT Cell Development and Function by Controlling CD1d Expression and Lipid Raft Content.

Sci Rep. 2017;7:40273 - PMID: 28091533 - PMCID: PMC5238393 - DOI: 10.1038/srep40273
Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW

Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes.

J Am Chem Soc. 2017;139(2):571-574 - PMID: 28055190 - PMCID: PMC7547879 - DOI: 10.1021/jacs.6b09760
Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.

Microbiome. 2016;4(1):68 - PMID: 28034306 - PMCID: PMC5200970 - DOI: 10.1186/s40168-016-0214-x
Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.

Cell Host Microbe. 2017;21(1):59-72 - PMID: 28017659 - PMCID: PMC5699477 - DOI: 10.1016/j.chom.2016.11.002
Izgu EC, Björkbom A, Kamat NP, Lelyveld VS, Zhang W, Jia TZ, Szostak JW

N-Carboxyanhydride-Mediated Fatty Acylation of Amino Acids and Peptides for Functionalization of Protocell Membranes.

J Am Chem Soc. 2016;138(51):16669-16676 - PMID: 27959544 - PMCID: PMC7547885 - DOI: 10.1021/jacs.6b08801
McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM

Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway.

BMC Biol. 2016;14(1):105 - PMID: 27927200 - PMCID: PMC5143455 - DOI: 10.1186/s12915-016-0334-6
Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.

Mol Ther. 2016;16(2):352-358 - PMID: 28178540 - DOI: 10.1038/sj.mt.6300357
Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH

Genome Editing Technologies: Defining a Path to Clinic: Genomic Editing: Establishing Preclinical Toxicology Standards, Bethesda, Maryland 10 June 2014.

Mol Ther. 2016;23(5):796-806 - PMID: 28142000
Mason SA, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Arnoldo BD, Tompkins RG, Herndon DN, Jeschke MG,

Hold the Pendulum: Rates of Acute Kidney Injury are Increased in Patients Who Receive Resuscitation Volumes Less than Predicted by the Parkland Equation.

Ann Surg. 2016;264(6):1142-1147 - PMID: 27828823 - PMCID: PMC5111808 - DOI: 10.1097/SLA.0000000000001615
Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA

The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).

J Biol Chem. 2017;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744 - DOI: 10.1074/jbc.M116.749663
Davidson D, Zhong MC, Pandolfi PP, Bolland S, Xavier RJ, Seed B, Li X, Gu H, Veillette A

The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors.

Cell Rep. 2016;17(10):2776-2788 - PMID: 27926878 - PMCID: PMC5656005 - DOI: 10.1016/j.celrep.2016.11.035
Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng AC, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ

TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation.

Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209 - PMCID: PMC5661940 - DOI: 10.1016/j.celrep.2016.11.042
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Cell. 2016;167(7):1897 - PMID: 27984736 - DOI: 10.1016/j.cell.2016.11.046
Van Der Sloot KW, Joshi AD, Bellavance DR, Gilpin KK, Stewart KO, Lochhead P, Garber JJ, Giallourakis C, Yajnik V, Ananthakrishnan AN, Alizadeh BZ, Xavier RJ, Khalili H

Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Inflamm Bowel Dis. 2017;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457 - DOI: 10.1097/MIB.0000000000000978
Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JJ, Xavier RJ, Yajnik V, Ananthakrishnan AN

Erratum to: Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

Dig Dis Sci. 2017;62(2):552 - PMID: 27864657 - DOI: 10.1007/s10620-016-4380-2
Arts RJ, Novakovic B, Ter Horst R, Carvalho A, Bekkering S, Lachmandas E, Rodrigues F, Silvestre R, Cheng SC, Wang SY, Habibi E, Gonçalves LG, Mesquita I, Cunha C, van Laarhoven A, van de Veerdonk FL, Williams DL, van der Meer JW, Logie C, O'Neill LA, Dinarello CA, Riksen NP, van Crevel R, Clish C, Notebaart RA, Joosten LA, Stunnenberg HG, Xavier RJ, Netea MG

Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity.

Cell Metab. 2016;24(6):807-819 - PMID: 27866838 - PMCID: PMC5742541 - DOI: 10.1016/j.cmet.2016.10.008
Total: 2466