Publications

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

Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T
Mol Ther. 2016;16(2):352-358 - PMID: 28178540

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

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
Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890

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

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
Mol Ther. 2016;23(5):796-806 - PMID: 28142000

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

Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA
Microbiome. 2016;4(1):68 - PMID: 28034306 - PMCID: PMC5200970

Unusual Base-Pairing Interactions in Monomer-Template Complexes.

Zhang W, Tam CP, Wang J, Szostak JW
ACS Cent Sci. 2016;2(12):916-926 - PMID: 28058281 - PMCID: PMC5200924

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

Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B
Cell Host Microbe. 2016;21(1):59-72 - PMID: 28017659

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

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
Cell. 2016;167(7):1897 - PMID: 27984736

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

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
Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209

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

Izgu EC, Björkbom A, Kamat NP, Lelyveld VS, Zhang W, Jia TZ, Szostak JW
J Am Chem Soc. 2016;138(51):16669-16676 - PMID: 27959544

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

McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM
BMC Biol. 2016;14(1):105 - PMID: 27927200 - PMCID: PMC5143455

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

Davidson D, Zhong MC, Pandolfi PP, Bolland S, Xavier RJ, Seed B, Li X, Gu H, Veillette A
Cell Rep. 2016;17(10):2776-2788 - PMID: 27926878

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

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
Inflamm Bowel Dis. 2016;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457

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

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
J Biol Chem. 2016;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744

RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy.

Heath RJ, Goel G, Baxt LA, Rush JS, Mohanan V, Paulus GL, Jani V, Lassen KG, Xavier RJ
Cell Rep. 2016;17(9):2183-2194 - PMID: 27880896 - PMCID: PMC5192565

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

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
Cell Metab. 2016;24(6):807-819 - PMID: 27866838

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

Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JJ, Xavier RJ, Yajnik V, Ananthakrishnan AN
Dig Dis Sci. 2016;62(2):552 - PMID: 27864657

SIKs control osteocyte responses to parathyroid hormone.

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
Nat Commun. 2016;7:13176 - PMID: 27759007 - PMCID: PMC5075806

TNF-?/IL-10 Ratio Correlates with Burn Severity and May Serve as a Risk Predictor of Increased Susceptibility to Infections.

Tsurumi A, Que YA, Ryan CM, Tompkins RG, Rahme LG
Front Public Health. 2016;4:216 - PMID: 27761434 - PMCID: PMC5050217

KERIS: kaleidoscope of gene responses to inflammation between species.

Li P, Tompkins RG, Xiao W,
Nucleic Acids Res. 2016;45(D1):D908-D914 - PMID: 27789704 - PMCID: PMC5210651

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

Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JG, Xavier RJ, Yajnik V, Ananthakrishnan AN
Dig Dis Sci. 2016;62(1):197-206 - PMID: 27796768 - PMCID: PMC5218976

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.

Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK
Gut. 2016;:ePub - PMID: 27802154

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG
Cell. 2016;167(4):1099-1110.e14 - PMID: 27814507

Host and Environmental Factors Influencing Individual Human Cytokine Responses.

Ter Horst R, Jaeger M, Smeekens SP, Oosting M, Swertz MA, Li Y, Kumar V, Diavatopoulos DA, Jansen AF, Lemmers H, Toenhake-Dijkstra H, van Herwaarden AE, Janssen M, van der Molen RG, Joosten I, Sweep FC, Smit JW, Netea-Maier RT, Koenders MM, Xavier RJ, van der Meer JW, Dinarello CA, Pavelka N, Wijmenga C, Notebaart RA, Joosten LA, Netea MG
Cell. 2016;167(4):1111-1124.e13 - PMID: 27814508

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ
Cell. 2016;167(4):1125-1136.e8 - PMID: 27814509 - PMCID: PMC5131922

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits.

Aguirre-Gamboa R, Joosten I, Urbano PC, van der Molen RG, van Rijssen E, van Cranenbroek B, Oosting M, Smeekens S, Jaeger M, Zorro M, Withoff S, van Herwaarden AE, Sweep FC, Netea RT, Swertz MA, Franke L, Xavier RJ, Joosten LA, Netea MG, Wijmenga C, Kumar V, Li Y, Koenen HJ
Cell Rep. 2016;17(9):2474-2487 - PMID: 27818087 - PMCID: PMC5130901

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

Mason SA, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Arnoldo BD, Tompkins RG, Herndon DN, Jeschke MG,
Ann Surg. 2016;264(6):1142-1147 - PMID: 27828823 - PMCID: PMC5111808

Effect of terminal 3'-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension.

Pal A, Das RS, Zhang W, Lang M, McLaughlin LW, Szostak JW
Chem Commun (Camb). 2016;52(80):11905-11907 - PMID: 27722518

The metabolic stress response to burn trauma: current understanding and therapies.

Porter C, Tompkins RG, Finnerty CC, Sidossis LS, Suman OE, Herndon DN
Lancet. 2016;388(10052):1417-1426 - PMID: 27707498

Corrigendum: Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.

Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG
Nat Med. 2016;22(10):1192 - PMID: 27711068

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages.

Mills EL, Kelly B, Logan A, Costa AS, Varma M, Bryant CE, Tourlomousis P, Däbritz JH, Gottlieb E, Latorre I, Corr SC, McManus G, Ryan D, Jacobs HT, Szibor M, Xavier RJ, Braun T, Frezza C, Murphy MP, O'Neill LA
Cell. 2016;167(2):457-470.e13 - PMID: 27667687

Characterization of candidate genes in inflammatory bowel disease-associated risk loci.

Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ
JCI Insight. 2016;1(13):e87899 - PMID: 27668286 - PMCID: PMC5033062

A perspective on single cell behavior during infection.

Avraham R, Hung DT
Gut Microbes. 2016;:0 - PMID: 27658058 - PMCID: PMC5153611

Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication.

Jia TZ, Fahrenbach AC, Kamat NP, Adamala KP, Szostak JW
Nat Chem. 2016;8(10):915-21 - PMID: 27657866 - PMCID: PMC5061144

Changes in neutrophil migration patterns upon contact with platelets in a microfluidic assay.

Frydman GH, Le A, Ellett F, Jorgensen J, Fox JG, Tompkins RG, Irimia D
J Leukoc Biol. 2016;101(3):797-806 - PMID: 27630219 - PMCID: PMC5295852

Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, , , MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Fä ...
Nat Commun. 2016;7:12869 - PMID: 27619887 - PMCID: PMC5027274

Genomic analysis of the evolution of fluoroquinolone resistance in Mycobacterium tuberculosis prior to tuberculosis diagnosis.

Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT
Antimicrob Agents Chemother. 2016;60(11):6600-6608 - PMID: 27572408 - PMCID: PMC5075065

On the origin of life.

Szostak JW
Medicina (B Aires). 2016;76(4):199-203 - PMID: 27576276

A highly reactive imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.

Walton T, Szostak JW
J Am Chem Soc. 2016;138(36):11996-2002 - PMID: 27552367

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease.

Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, Gevers D, Ting A, Robson SC, Moss AC
Inflamm Bowel Dis. 2016;22(9):2182-90 - PMID: 27542133 - PMCID: PMC4995064

Proteasome dysfunction triggers activation of SKN-1A/Nrf1 by the aspartic protease DDI-1.

Lehrbach NJ, Ruvkun G
Elife. 2016;5:ePub - PMID: 27528192 - PMCID: PMC4987142

Prevention of Burn-Induced Inflammatory Responses and Muscle Wasting By GTS-21, A Specific Agonist for ?7 Nicotinic Acetylcholine Receptors.

Kashiwagi S, Khan MA, Yasuhara S, Goto T, Tompkins RG, Kaneki M, Martyn JA
Shock. 2016;47(1):61-69 - PMID: 27529131 - PMCID: PMC5167674

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, , , MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Fä ...
Nat Commun. 2016;7:12342 - PMID: 27503255 - PMCID: PMC4980482

A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition.

Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DP, Duerr RH
Gastroenterology. 2016;151(4):724-32 - PMID: 27492617 - PMCID: PMC5037008

Understanding human immune function using the resources from the Human Functional Genomics Project.

Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwe ...
Nat Med. 2016;22(8):831-833 - PMID: 27490433

Accelerating global innovation to address antibacterial resistance: introducing CARB-X.

Outterson K, Rex JH, Jinks T, Jackson P, Hallinan J, Karp S, Hung DT, Franceschi F, Merkeley T, Houchens C, Dixon DM, Kurilla MG, Aurigemma R, Larsen J
Nat Rev Drug Discov. 2016;15(9):589-90 - PMID: 27469032

Molecular Imaging of Smoke-Induced Changes in Nuclear Factor-Kappa B Expression in Murine Tissues Including the Lung.

Syrkina O, Hales CH, Bonab AA, Hamrahi V, Paul K, Jung WJ, Tompkins RG, Fischman AJ, Carter EA
J Burn Care Res. 2016;37(6):335-342 - PMID: 27437954

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.

Avraham R, Haseley N, Fan A, Bloom-Ackermann Z, Livny J, Hung DT
Nat Protoc. 2016;11(8):1477-1491 - PMID: 27442864

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.

Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S
Genome Med. 2016;8(1):75 - PMID: 27412252 - PMCID: PMC4944441

A microRNA program in the C. elegans hypodermis couples to intestinal mTORC2/PQM-1 signaling to modulate fat transport.

Dowen RH, Breen PC, Tullius T, Conery AL, Ruvkun G
Genes Dev. 2016;30(13):1515-28 - PMID: 27401555 - PMCID: PMC4949325

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.

Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG
Nat Med. 2016;22(8):952-960 - PMID: 27376574 - PMCID: PMC5084084

Introduction to Gene Editing and Manipulation Using CRISPR/Cas9 Technology.

Newman M, Ausubel FM
Curr Protoc Mol Biol. 2016;115:31.4.1-6 - PMID: 27366890 - PMCID: PMC4963815

Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides.

Prywes N, Blain JC, Del Frate F, Szostak JW
Elife. 2016;5:ePub - PMID: 27351102 - PMCID: PMC4959843

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62.

DeJesus R, Moretti F, McAllister G, Wang Z, Bergman P, Liu S, Frias E, Alford J, Reece-Hoyes JS, Lindeman A, Kelliher J, Russ C, Knehr J, Carbone W, Beibel M, Roma G, Ng A, Tallarico JA, Porter JA, Xavier RJ, Mickanin C, Murphy LO, Hoffman GR, Nyfeler B
Elife. 2016;5:ePub - PMID: 27351204 - PMCID: PMC4924995

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK
Nat Biotechnol. 2016;34(8):869-874 - PMID: 27347757 - PMCID: PMC4980201

Microbiota as Therapeutic Targets.

Xavier RJ
Dig Dis. 2016;34(5):558-565 - PMID: 27331403

Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors.

Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT
Cell Chem Biol. 2016;23(6):666-77 - PMID: 27321573 - PMCID: PMC4920728

Caenorhabditis elegans responses to bacteria from its natural habitats.

Samuel BS, Rowedder H, Braendle C, Félix MA, Ruvkun G
Proc Natl Acad Sci U S A. 2016;113(27):E3941-9 - PMID: 27317746 - PMCID: PMC4941482

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, , Xavier RJ
Sci Transl Med. 2016;8(343):343ra81 - PMID: 27306663 - PMCID: PMC5032909

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ
Proc Natl Acad Sci U S A. 2016;113(26):E3667-75 - PMID: 27298372 - PMCID: PMC4932963

Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.

Lassen KG, McKenzie CI, Mari M, Murano T, Begun J, Baxt LA, Goel G, Villablanca EJ, Kuo SY, Huang H, Macia L, Bhan AK, Batten M, Daly MJ, Reggiori F, Mackay CR, Xavier RJ
Immunity. 2016;44(6):1392-1405 - PMID: 27287411 - PMCID: PMC4936415

The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.

Boada-Romero E, Serramito-Gómez I, Sacristán MP, Boone DL, Xavier RJ, Pimentel-Muiños FX
Nat Commun. 2016;7:11821 - PMID: 27273576 - PMCID: PMC4899871

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

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
Cell. 2016;165(6):1551 - PMID: 27259157

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

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
Science. 2016;352(6289):1116-20 - PMID: 27230380 - PMCID: PMC4996125

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

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
Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737

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

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
ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440

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

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ
Cell Syst. 2016;2(5):323-334 - PMID: 27211859 - PMCID: PMC5032147

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

Ueki R, Liu L, Kashiwagi S, Kaneki M, Khan M, Hirose M, Tompkins RG, Martyn JA, Yasuhara S
Shock. 2016;46(4):382-9 - PMID: 27172157 - PMCID: PMC5026541

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

Frydman GH, Bendapudi PK, Marini RP, Vanderburg CR, Tompkins RG, Fox JG
J Am Assoc Lab Anim Sci. 2016;55(3):252-9 - PMID: 27177557 - PMCID: PMC4865685

Mechanisms of Pediatric Inflammatory Bowel Disease.

Peloquin JM, Goel G, Villablanca EJ, Xavier RJ
Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239

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

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
Nat Med. 2016;22(6):598-605 - PMID: 27158904 - PMCID: PMC5087285

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

Tsai SQ, Topkar VV, Joung JK, Aryee MJ
Nat Biotechnol. 2016;34(5):483 - PMID: 27153277

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

Taleban S, Stewart KO, Li DK, Singh P, Pardi DS, Sturgeon HC, Yajnik V, Xavier RJ, Ananthakrishnan AN, Khalili H
Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

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
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857

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

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

Prywes N, Michaels YS, Pal A, Oh SS, Szostak JW
Chem Commun (Camb). 2016;52(39):6529-32 - PMID: 27109314

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

Netea MG, Joosten LA, Latz E, Mills KH, Natoli G, Stunnenberg HG, O'Neill LA, Xavier RJ
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A simple physical mechanism enables homeostasis in primitive cells.

Engelhart AE, Adamala KP, Szostak JW
Nat Chem. 2016;8(5):448-53 - PMID: 27102678 - PMCID: PMC4929987

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

Tsai SQ, Joung JK
Nat Rev Genet. 2016;17(5):300-12 - PMID: 27087594

Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming.

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
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ABCA7 Deficiency Accelerates Amyloid-? Generation and Alzheimer's Neuronal Pathology.

Sakae N, Liu CC, Shinohara M, Frisch-Daiello J, Ma L, Yamazaki Y, Tachibana M, Younkin L, Kurti A, Carrasquillo MM, Zou F, Sevlever D, Bisceglio G, Gan M, Fol R, Knight P, Wang M, Han X, Fryer JD, Fitzgerald ML, Ohyagi Y, Younkin SG, Bu G, Kanekiyo T
J Neurosci. 2016;36(13):3848-59 - PMID: 27030769 - PMCID: PMC4812140

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

Abrams JA, Xavier RJ, Rustgi AK
Gastroenterology. 2016;150(5):1231-6 - PMID: 27018487

Collaboration between primitive cell membranes and soluble catalysts.

Adamala KP, Engelhart AE, Szostak JW
Nat Commun. 2016;7:11041 - PMID: 26996603 - PMCID: PMC4802160

Mutation of the Glucosinolate Biosynthesis Enzyme Cytochrome P450 83A1 Monooxygenase Increases Camalexin Accumulation and Powdery Mildew Resistance.

Liu S, Bartnikas LM, Volko SM, Ausubel FM, Tang D
Front Plant Sci. 2016;7:227 - PMID: 26973671 - PMCID: PMC4774424

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

Li L, Lelyveld VS, Prywes N, Szostak JW
J Am Chem Soc. 2016;138(12):3986-3989 - PMID: 26974265

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

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

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
Gut. 2016;66(6):1060-1073 - PMID: 26953272

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

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
JAMA Pediatr. 2016;170(6):534-542 - PMID: 26953515

New Regulatory Roles of Galectin-3 in the High-affinity IgE Receptor Signaling.

Bambouskova M, Polakovicova I, Halova I, Goel G, Draberova L, Bugajev V, Doan A, Utekal P, Gardet A, Xavier RJ, Draber P
Mol Cell Biol. 2016;36(9):1366-82 - PMID: 26929198 - PMCID: PMC4836217

NH125 kills methicillin-resistant Staphylococcus aureus persisters by lipid bilayer disruption.

Kim W, Fricke N, Conery AL, Fuchs BB, Rajamuthiah R, Jayamani E, Vlahovska PM, Ausubel FM, Mylonakis E
Future Med Chem. 2016;8(3):257-69 - PMID: 26910612 - PMCID: PMC4976882

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C
Genome Med. 2016;8(1):17 - PMID: 26884067 - PMCID: PMC4756455

Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates.

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Chem Commun (Camb). 2016;52(18):3684-6 - PMID: 26857159

Planetary Protection and Mars Special Regions-A Suggestion for Updating the Definition.

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Astrobiology. 2016;16(2):119-125 - PMID: 26848950

On the Mechanism of Berberine-INF55 (5-Nitro-2-phenylindole) Hybrid Antibacterials.

Dolla NK, Chen C, Larkins-Ford J, Rajamuthiah R, Jagadeesan S, Conery AL, Ausubel FM, Mylonakis E, Bremner JB, Lewis K, Kelso MJ
Aust J Chem. 2016;67:1471-1480 - PMID: 26806960 - PMCID: PMC4720975

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM, Ait-Si-Ali S, Akematsu T, Akporiaye ET, Al-Rubeai M, Albaiceta GM, Albanese C, Albani D, Albert ML, Aldudo J, Algül H, Alirezaei M, Alloza I, Almasan A, Almonte-Beceril M, Alnemri ES, Alonso C, Altan-Bonnet N, Altieri DC, Alvarez S, Alvarez-Erviti L, Alves S, A ...
Autophagy. 2016;12(1):1-222 - PMID: 26799652 - PMCID: PMC4835977

The burn outcome questionnaires: Patient and family reported outcome metrics for children of all ages.

Ryan CM, Cartwright S, Schneider JC, Tompkins RG, Kazis LE
Burns. 2016;42(5):1144-5 - PMID: 26803370

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

Mason SA, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Arnoldo BD, Tompkins RG, Herndon DN, Jeschke MG,
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