Publications

Loss of a Class A Penicillin-Binding Protein Alters ?-Lactam Susceptibilities in Mycobacterium tuberculosis.

Wivagg CN, Wellington S, Gomez JE, Hung DT
ACS Infect Dis. 2015;2(2):104-10 - PMID: 27624961

Associations with rhizosphere bacteria can confer an adaptive advantage to plants.

Haney CH, Samuel BS, Bush J, Ausubel FM
Nat Plants. 2015;1:15051 - PMID: 27250003

Jasmonate signalling in Arabidopsis involves SGT1b-HSP70-HSP90 chaperone complexes.

Zhang XC, Millet YA, Cheng Z, Bush J, Ausubel FM
Nat Plants. 2015;1:ePub - PMID: 27054042 - PMCID: PMC4819967

Associations with rhizosphere bacteria can confer an adaptive advantage to plants.

Haney CH, Samuel BS, Bush J, Ausubel FM
Nat Plants. 2015;1(6):ePub - PMID: 27019743 - PMCID: PMC4806546

Quantifying Risk Factors for Long-Term Sleep Problems After Burn Injury in Young Adults.

Lee AF, Ryan CM, Schneider JC, Kazis LE, Li NC, Rose M, Liang MH, Wang C, Palmieri T, Meyer WJ, Pidcock FS, Reilly D, Sheridan RL, Tompkins RG,
J Burn Care Res. 2015;38(2):e510-e520 - PMID: 27003738

Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity.

Singhal PK, Sassi S, Lan L, Au P, Halvorsen SC, Fukumura D, Jain RK, Seed B
Proc Natl Acad Sci U S A. 2015;113(1):122-7 - PMID: 26699463 - PMCID: PMC4711836

Proton pump inhibitors affect the gut microbiome.

Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A
Gut. 2015;65(5):740-8 - PMID: 26657899 - PMCID: PMC4853569

In vivo high-resolution magic angle spinning magnetic and electron paramagnetic resonance spectroscopic analysis of mitochondria-targeted peptide in Drosophila melanogaster with trauma-induced thoracic injury.

Constantinou C, Apidianakis Y, Psychogios N, Righi V, Mindrinos MN, Khan N, Swartz HM, Szeto HH, Tompkins RG, Rahme LG, Tzika AA
Int J Mol Med. 2015;37(2):299-308 - PMID: 26648055 - PMCID: PMC4716799

Accelerating research through reagent repositories: the genome editing example.

Joung JK, Voytas DF, Kamens J
Genome Biol. 2015;16(1):255 - PMID: 26585970 - PMCID: PMC4653914

Pinpointing RNA-protein crosslinks with site-specific stable isotope labeled oligonucleotides.

Lelyveld VS, Bjorkbom A, Ransey E, Sliz P, Szostak JW
J Am Chem Soc. 2015;137(49):15378-15381 - PMID: 26583201 - PMCID: PMC4697197

Flow Cytometric Analysis of Mononuclear Phagocytes in Non-diseased Human Lung and Lung-draining Lymph Nodes.

Desch AN, Gibbings SL, Goyal R, Kolde R, Bednarek J, Bruno T, Slansky JE, Jacobelli J, Mason R, Ito Y, Messier E, Randolph GJ, Prabagar M, Atif SM, Segura E, Xavier RJ, Bratton DL, Janssen WJ, Henson PM, Jakubzick CV
Am J Respir Crit Care Med. 2015;193(6):614-626 - PMID: 26551758 - PMCID: PMC4824940

Early Leukocyte Gene Expression Associated with Age, Burn Size, and Inhalation Injury in Severely Burned Adults.

Sood RF, Gibran NS, Arnoldo BD, Gamelli RL, Herndon DN, Tompkins RG, Inflammation T, Investigators TH
J Trauma Acute Care Surg. 2015;80(2):250-7 - PMID: 26517785 - PMCID: PMC4731271

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition.

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK
Nat Biotechnol. 2015;33(12):1293-1298 - PMID: 26524662 - PMCID: PMC4689141

Kidney and Liver Injuries After Major Burns in Rats Are Prevented by Resolvin D2.

Inoue Y, Yu YM, Kurihara T, Vasilyev A, Ibrahim A, Oklu R, Zhao G, Nair AV, Brown D, Fischman AJ, Tompkins RG, Irimia D
Crit Care Med. 2015;44(5):e241-52 - PMID: 26509319 - PMCID: PMC4833510

LXR agonism up-regulates the macrophage ABCA1/syntrophin protein complex which can bind apoA-I and stabilized ABCA1 protein, but complex loss does not inhibit lipid efflux.

Tamehiro N, Park MH, Hawxhurst V, Nagpal K, Adams ME, Zannis VI, Golenbock DT, Fitzgerald ML
Biochemistry. 2015;54(46):6931-41 - PMID: 26506427 - PMCID: PMC4874254

Bidirectional direct sequencing of non-canonical RNA by two-dimensional analysis of mass chromatograms.

Bjorkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW
J Am Chem Soc. 2015;137(45):14430-14438 - PMID: 26495937

Gene Expression of Proresolving Lipid Mediator Pathways Is Associated With Clinical Outcomes in Trauma Patients.

Orr SK, Butler KL, Hayden D, Tompkins RG, Serhan CN, Irimia D
Crit Care Med. 2015;43(12):2642-2650 - PMID: 26488221 - PMCID: PMC4651815

Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.

Cao Z, Conway KL, Heath RJ, Rush JS, Leshchiner ES, Ramirez-Ortiz ZG, Nedelsky NB, Huang H, Ng A, Gardet A, Cheng SC, Shamji AF, Rioux JD, Wijmenga C, Netea MG, Means TK, Daly MJ, Xavier RJ
Immunity. 2015;43(4):715-726 - PMID: 26488816 - PMCID: PMC4672733

Novel links in the plant TOR kinase signaling network.

Xiong Y, Sheen J
Curr Opin Plant Biol. 2015;28:83-91 - PMID: 26476687 - PMCID: PMC4612364

Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile.

Rajamuthiah R, Jayamani E, Majed H, Conery AL, Kim W, Kwon B, Fuchs BB, Kelso MJ, Ausubel FM, Mylonakis E
Bioorg Med Chem Lett. 2015;25(22):5203-7 - PMID: 26459212 - PMCID: PMC4718707

Genome Editing in Human Cells Using CRISPR/Cas Nucleases.

Wyvekens N, Tsai SQ, Joung JK
Curr Protoc Mol Biol. 2015;112:31.3.1-31.3.18 - PMID: 26423589 - PMCID: PMC4852847

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.

Fu J, Bonder MJ, Cenit MC, Tigchelaar E, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A
Circ Res. 2015;117(9):817-24 - PMID: 26358192 - PMCID: PMC4596485

Dialogue between E. coli free radical pathways and the mitochondria of C. elegans.

Govindan JA, Jayamani E, Zhang X, Mylonakis E, Ruvkun G
Proc Natl Acad Sci U S A. 2015;112(40):12456-61 - PMID: 26392561 - PMCID: PMC4603447

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.

Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, , Gayther SA, Joung JK, Freedman ML
Nat Med. 2015;21(11):1357-1363 - PMID: 26398868 - PMCID: PMC4746056

Enhancing immunity by engineering DAMPs.

Cervone F, Ausubel FM, Lorenzo G
Oncotarget. 2015;6(30):28523-4 - PMID: 26387132 - PMCID: PMC4745668

Patiromer induces rapid and sustained potassium lowering in patients with chronic kidney disease and hyperkalemia.

Bushinsky DA, Williams GH, Pitt B, Weir MR, Freeman MW, Garza D, Stasiv Y, Li E, Berman L, Bakris GL
Kidney Int. 2015;88(6):1427-1433 - PMID: 26376130 - PMCID: PMC4678168

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813

HIV infection induces structural and functional changes in high density lipoproteins.

Siegel MO, Borkowska AG, Dubrovsky L, Roth M, Welti R, Roberts AD, Parenti DM, Simon GL, Sviridov D, Simmens S, Bukrinsky M, Fitzgerald ML
Atherosclerosis. 2015;243(1):19-29 - PMID: 26343868 - PMCID: PMC4609619

ConStrains identifies microbial strains in metagenomic datasets.

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D
Nat Biotechnol. 2015;33(10):1045-1052 - PMID: 26344404 - PMCID: PMC4676274

Lipid signalling couples translational surveillance to systemic detoxification in Caenorhabditis elegans.

Govindan JA, Jayamani E, Zhang X, Breen P, Larkins-Ford J, Mylonakis E, Ruvkun G
Nat Cell Biol. 2015;17(10):1294-303 - PMID: 26322678 - PMCID: PMC4589496

MICROBIOME. Plant microbiome blueprints.

Haney CH, Ausubel FM
Science. 2015;349(6250):788-9 - PMID: 26293938

piRNAs and piRNA-Dependent siRNAs Protect Conserved and Essential C. elegans Genes from Misrouting into the RNAi Pathway.

Phillips CM, Brown KC, Montgomery BE, Ruvkun G, Montgomery TA
Dev Cell. 2015;34(4):457-465 - PMID: 26279487 - PMCID: PMC4550515

Is Real-Time Feedback of Burn-Specific Patient-Reported Outcome Measures in Clinical Settings Practical and Useful? A Pilot Study Implementing the Young Adult Burn Outcome Questionnaire.

Ryan CM, Lee AF, Kazis LE, Shapiro GD, Schneider JC, Goverman J, Fagan SP, Wang C, Kim J, Sheridan RL, Tompkins RG
J Burn Care Res. 2015;37(1):64-74 - PMID: 26284638

Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.

Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM, Chen L, Tsai SQ, Sander JD, Joung JK, Liu DR
Nat Methods. 2015;12(10):939-942 - PMID: 26258293 - PMCID: PMC4589463

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.

Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Segal E
Science. 2015;349(6252):1101-6 - PMID: 26229116 - PMCID: PMC5087275

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization.

Larsen AT, Fahrenbach AC, Sheng J, Pian J, Szostak JW
Nucleic Acids Res. 2015;43(16):7675-87 - PMID: 26240387 - PMCID: PMC4652770

Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ
Inflamm Bowel Dis. 2015;21(11):2507-2514 - PMID: 26241000 - PMCID: PMC4615315

Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides.

Kamat NP, Tobé S, Hill IT, Szostak JW
Angew Chem Int Ed Engl. 2015;54(40):11735-11739 - PMID: 26223820 - PMCID: PMC4600236

Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease.

Quévrain E, Maubert MA, Michon C, Chain F, Marquant R, Tailhades J, Miquel S, Carlier L, Bermúdez-Humarán LG, Pigneur B, Lequin O, Kharrat P, Thomas G, Rainteau D, Aubry C, Breyner N, Afonso C, Lavielle S, Grill JP, Chassaing G, Chatel JM, Trugnan G, Xavier R, Langella P, Sokol H, Seksik P
Gut. 2015;65(3):415-25 - PMID: 26045134 - PMCID: PMC5136800

Pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in Arabidopsis.

Groen SC, Humphrey PT, Chevasco D, Ausubel FM, Pierce NE, Whiteman NK
J Insect Physiol. 2015;84:90-102 - PMID: 26205072 - PMCID: PMC4721946

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ
Nat Commun. 2015;6:7838 - PMID: 26194095 - PMCID: PMC4518307

Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.

Kuo SY, Castoreno AB, Aldrich LN, Lassen KG, Goel G, Dan?ík V, Kuballa P, Latorre I, Conway KL, Sarkar S, Maetzel D, Jaenisch R, Clemons PA, Schreiber SL, Shamji AF, Xavier RJ
Proc Natl Acad Sci U S A. 2015;112(31):E4281-7 - PMID: 26195741 - PMCID: PMC4534235

Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Pringle PL, Stewart KO, Peloquin JM, Sturgeon HC, Nguyen D, Sauk J, Garber JJ, Yajnik V, Ananthakrishnan AN, Chan AT, Xavier RJ, Khalili H
Inflamm Bowel Dis. 2015;21(10):2304-2310 - PMID: 26181430 - PMCID: PMC4567407

Role of Autophagy in the Maintenance of Intestinal Homeostasis.

Baxt LA, Xavier RJ
Gastroenterology. 2015;149(3):553-62 - PMID: 26170139 - PMCID: PMC4550567

Effect of Patiromer on Serum Potassium Level in Patients With Hyperkalemia and Diabetic Kidney Disease: The AMETHYST-DN Randomized Clinical Trial.

Bakris GL, Pitt B, Weir MR, Freeman MW, Mayo MR, Garza D, Stasiv Y, Zawadzki R, Berman L, Bushinsky DA,
JAMA. 2015;314(2):151-161 - PMID: 26172895

Unwanted mutations: Standards needed for gene-editing errors.

Joung JK
Nature. 2015;523(7559):158 - PMID: 26156364

Stimulation of Liver X Receptor Has Potent Anti-HIV Effects in a Humanized Mouse Model.

Ramezani A, Dubrovsky L, Pushkarsky T, Sviridov D, Karandish S, Raj DS, Fitzgerald ML, Bukrinsky M
J Pharmacol Exp Ther. 2015;354(3):376-83 - PMID: 26126533 - PMCID: PMC4538872

Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.

Begun J, Lassen KG, Jijon HB, Baxt LA, Goel G, Heath RJ, Ng A, Tam JM, Kuo SY, Villablanca EJ, Fagbami L, Oosting M, Kumar V, Schenone M, Carr SA, Joosten LA, Vyas JM, Daly MJ, Netea MG, Brown GD, Wijmenga C, Xavier RJ
Cell Rep. 2015;11(12):1905-1918 - PMID: 26095365 - PMCID: PMC4507440

Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JJ, Aryee MJ, Joung JK
Nature. 2015;523(7561):481-5 - PMID: 26098369 - PMCID: PMC4540238

Dimeric CRISPR RNA-guided FokI-dCas9 nucleases (RFNs) directed by truncated gRNAs for highly specific genome editing.

Wyvekens N, Topkar VV, Khayter C, Joung JK, Tsai SQ
Hum Gene Ther. 2015;26(7):425-431 - PMID: 26068112 - PMCID: PMC4509490

A Defensin from the Model Beetle Tribolium castaneum Acts Synergistically with Telavancin and Daptomycin against Multidrug Resistant Staphylococcus aureus.

Rajamuthiah R, Jayamani E, Conery AL, Fuchs BB, Kim W, Johnston T, Vilcinskas A, Ausubel FM, Mylonakis E
PLoS One. 2015;10(6):e0128576 - PMID: 26062137 - PMCID: PMC4465704

CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.

Causton B, Ramadas RA, Cho JL, Jones K, Pardo-Saganta A, Rajagopal J, Xavier RJ, Medoff BD
J Immunol. 2015;195(2):683-94 - PMID: 26041536 - PMCID: PMC4489191

Identification of an Antimicrobial Agent Effective against Methicillin-Resistant Staphylococcus aureus Persisters Using a Fluorescence-Based Screening Strategy.

Kim W, Conery AL, Rajamuthiah R, Fuchs BB, Ausubel FM, Mylonakis E
PLoS One. 2015;10(6):e0127640 - PMID: 26039584 - PMCID: PMC4454602

Construction of a liposome dialyzer for the preparation of high-value, small-volume liposome formulations.

Adamala K, Engelhart AE, Kamat NP, Jin L, Szostak JW
Nat Protoc. 2015;10(6):927-938 - PMID: 26020615 - PMCID: PMC4982460

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.

Black JC, Atabakhsh E, Kim J, Biette KM, Van Rechem C, Ladd B, Burrowes PD, Donado C, Mattoo H, Kleinstiver BP, Song B, Andriani G, Joung JK, Iliopoulos O, Montagna C, Pillai S, Getz G, Whetstine JR
Genes Dev. 2015;29(10):1018-31 - PMID: 25995187 - PMCID: PMC4441050

The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells.

Khor B, Gagnon JD, Goel G, Roche MI, Conway KL, Tran K, Aldrich LN, Sundberg TB, Paterson AM, Mordecai S, Dombkowski D, Schirmer M, Tan PH, Bhan AK, Roychoudhuri R, Restifo NP, O'Shea JJ, Medoff BD, Shamji AF, Schreiber SL, Sharpe AH, Shaw SY, Xavier RJ
Elife. 2015;4:ePub - PMID: 25998054 - PMCID: PMC4441007

Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model.

Rahman SH, Kuehle J, Reimann C, Mlambo T, Alzubi J, Maeder ML, Riedel H, Fisch P, Cantz T, Rudolph C, Mussolino C, Joung JK, Schambach A, Cathomen T
PLoS Genet. 2015;11(5):e1005239 - PMID: 26000857 - PMCID: PMC4441453

Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided Nucleases.

Hwang WY, Fu Y, Reyon D, Gonzales AP, Joung JK, Yeh JR
Methods Mol Biol. 2015;1311:317-34 - PMID: 25981483

An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases.

Wlodarska M, Kostic AD, Xavier RJ
Cell Host Microbe. 2015;17(5):577-591 - PMID: 25974300 - PMCID: PMC4498258

PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.

Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y
Nucleic Acids Res. 2015;43(W1):W154-W159 - PMID: 25958392 - PMCID: PMC4489270

Genome editing technologies: defining a path to clinic.

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. 2015;23(5):796-806 - PMID: 25943494 - PMCID: PMC4427885

Do standard burn mortality formulae work on a population of severely burned children and adults?

Tsurumi A, Que YA, Yan S, Tompkins RG, Rahme LG, Ryan CM
Burns. 2015;41(5):935-45 - PMID: 25922299

Uncovering the Thermodynamics of Monomer Binding for RNA Replication.

Izgu EC, Fahrenbach AC, Zhang N, Li L, Zhang W, Larsen A, Blain JC, Szostak JW
J Am Chem Soc. 2015;137(19):6373-82 - PMID: 25901790 - PMCID: PMC4984997

Repurposing Salicylanilide Anthelmintic Drugs to Combat Drug Resistant Staphylococcus aureus.

Rajamuthiah R, Fuchs BB, Conery AL, Kim W, Jayamani E, Kwon B, Ausubel FM, Mylonakis E
PLoS One. 2015;10(4):e0124595 - PMID: 25897961 - PMCID: PMC4405337

Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics.

Hou HW, Bhattacharyya RP, Hung DT, Han J
Lab Chip. 2015;15(10):2297-2307 - PMID: 25882432 - PMCID: PMC4437799

Future Translational Applications From the Contemporary Genomics Era: A Scientific Statement From the American Heart Association.

Fox CS, Hall JL, Arnett DK, Ashley EA, Delles C, Engler MB, Freeman MW, Johnson JA, Lanfear DE, Liggett SB, Lusis AJ, Loscalzo J, MacRae CA, Musunuru K, Newby LK, O'Donnell CJ, Rich SS, Terzic A
Circulation. 2015;131(19):1715-36 - PMID: 25882488 - PMCID: PMC4825323

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C
Genome Biol. 2015;16(1):67 - PMID: 25887922 - PMCID: PMC4414286

Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns.

Benedetti M, Pontiggia D, Raggi S, Cheng Z, Scaloni F, Ferrari S, Ausubel FM, Cervone F, De Lorenzo G
Proc Natl Acad Sci U S A. 2015;112(17):5533-8 - PMID: 25870275 - PMCID: PMC4418913

Discovery of a Small-Molecule Probe for V-ATPase Function.

Aldrich LN, Kuo SY, Castoreno AB, Goel G, Kuballa P, Rees MG, Seashore-Ludlow BA, Cheah JH, Latorre IJ, Schreiber SL, Shamji AF, Xavier RJ
J Am Chem Soc. 2015;137(16):5563-8 - PMID: 25860544 - PMCID: PMC4416280

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A
Nat Genet. 2015;47(5):469-78 - PMID: 25822089 - PMCID: PMC4414868

Intake of farmed Atlantic salmon fed soybean oil increases hepatic levels of arachidonic acid-derived oxylipins and ceramides in mice.

Midtbø LK, Borkowska AG, Bernhard A, Rønnevik AK, Lock EJ, Fitzgerald ML, Torstensen BE, Liaset B, Brattelid T, Pedersen TL, Newman JW, Kristiansen K, Madsen L
J Nutr Biochem. 2015;26(6):585-95 - PMID: 25776459

Targeted Plant Genome Editing via the CRISPR/Cas9 Technology.

Li JF, Zhang D, Sheen J
Methods Mol Biol. 2015;1284:239-55 - PMID: 25757776

A novel role for KLF14 in T regulatory cell differentiation.

Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis KA, Urrutia RA, Faubion WA
Cell Mol Gastroenterol Hepatol. 2015;1(2):188-202.e4 - PMID: 25750932 - PMCID: PMC4349492

Genomics of injury: The Glue Grant experience.

Tompkins RG
J Trauma Acute Care Surg. 2015;78(4):671-686 - PMID: 25742245 - PMCID: PMC4389222

Pathogen-secreted proteases activate a novel plant immune pathway.

Cheng Z, Li JF, Niu Y, Zhang XC, Woody OZ, Xiong Y, Djonovi? S, Millet Y, Bush J, McConkey BJ, Sheen J, Ausubel FM
Nature. 2015;521(7551):213-6 - PMID: 25731164 - PMCID: PMC4433409

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA
J Clin Invest. 2015;125(3):1363 - PMID: 25729854 - PMCID: PMC4362234

Simultaneous generation of many RNA-seq libraries in a single reaction.

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J
Nat Methods. 2015;12(4):323-325 - PMID: 25730492 - PMCID: PMC4712044

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Oreši? M, Huttenhower C, Knip M, , Xavier RJ
Cell Host Microbe. 2015;17(2):260-273 - PMID: 25662751 - PMCID: PMC4689191

Chromatin regulation at the frontier of synthetic biology.

Keung AJ, Joung JK, Khalil AS, Collins JJ
Nat Rev Genet. 2015;16(3):159-71 - PMID: 25668787 - PMCID: PMC4846386

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Mitophagy confers resistance to siderophore-mediated killing by Pseudomonas aeruginosa.

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Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease.

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Role of Protein Farnesylation in Burn-Induced Metabolic Derangements and Insulin Resistance in Mouse Skeletal Muscle.

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Insect-derived Cecropins Display Activity Against Acinetobacter baumannii in a Whole-Animal High-Throughput Caenorhabditis elegans Model.

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Pyruvate Kinase M2 Regulates Hif-1? Activity and IL-1? Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages.

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