Publications for All Faculty - 2015

  • Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC Natural bacterial communities serve as quantitative geochemical biosensors. MBio. 2015;6(3):e00326-15 - PMID: 25968645 - PMCID: PMC4436078 - DOI: 10.1128/mBio.00326-15

  • 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 Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation. Immunity. 2015;43(4):715-26 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005

  • Haney CH, Samuel BS, Bush J, Ausubel FM Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants. 2015;1:15051 - PMID: 27250003

  • Zhang XC, Millet YA, Cheng Z, Bush J, Ausubel FM Jasmonate signalling in Arabidopsis involves SGT1b-HSP70-HSP90 chaperone complexes. Nat Plants. 2015;1:ePub - PMID: 27054042 - PMCID: PMC4819967 - DOI: 10.1038/nplants.2015.49

  • Haney CH, Samuel BS, Bush J, Ausubel FM Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants. 2015;1(6):ePub - PMID: 27019743 - PMCID: PMC4806546 - DOI: 10.1038/nplants.2015.51

  • 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, Quantifying Risk Factors for Long-Term Sleep Problems After Burn Injury in Young Adults. J Burn Care Res. 2015;38(2):e510-e520 - PMID: 27003738 - DOI: 10.1097/BCR.0000000000000315

  • Joung JK, Voytas DF, Kamens J Accelerating research through reagent repositories: the genome editing example. Genome Biol. 2015;16(1):255 - PMID: 26585970 - PMCID: PMC4653914 - DOI: 10.1186/s13059-015-0830-y

  • Lelyveld VS, Bjorkbom A, Ransey E, Sliz P, Szostak JW Pinpointing RNA-protein crosslinks with site-specific stable isotope labeled oligonucleotides. J Am Chem Soc. 2015;137(49):15378-15381 - PMID: 26583201 - PMCID: PMC4697197 - DOI: 10.1021/jacs.5b10596

  • Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat Biotechnol. 2015;33(12):1293-1298 - PMID: 26524662 - PMCID: PMC4689141 - DOI: 10.1038/nbt.3404

  • Tamehiro N, Park MH, Hawxhurst V, Nagpal K, Adams ME, Zannis VI, Golenbock DT, Fitzgerald ML 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. Biochemistry. 2015;54(46):6931-41 - PMID: 26506427 - PMCID: PMC4874254 - DOI: 10.1021/acs.biochem.5b00894

  • Bjorkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW Bidirectional direct sequencing of non-canonical RNA by two-dimensional analysis of mass chromatograms. J Am Chem Soc. 2015;137(45):14430-8 - PMID: 26495937 - PMCID: PMC7547889 - DOI: 10.1021/jacs.5b09438

  • Orr SK, Butler KL, Hayden D, Tompkins RG, Serhan CN, Irimia D Gene Expression of Proresolving Lipid Mediator Pathways Is Associated With Clinical Outcomes in Trauma Patients. Crit Care Med. 2015;43(12):2642-2650 - PMID: 26488221 - PMCID: PMC4651815 - DOI: 10.1097/CCM.0000000000001312

  • 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 Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation. Immunity. 2015;43(4):715-726 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005

  • Xiong Y, Sheen J Novel links in the plant TOR kinase signaling network. Curr Opin Plant Biol. 2015;28:83-91 - PMID: 26476687 - PMCID: PMC4612364 - DOI: 10.1016/j.pbi.2015.09.006

  • Rajamuthiah R, Jayamani E, Majed H, Conery AL, Kim W, Kwon B, Fuchs BB, Kelso MJ, Ausubel FM, Mylonakis E Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile. Bioorg Med Chem Lett. 2015;25(22):5203-7 - PMID: 26459212 - PMCID: PMC4718707 - DOI: 10.1016/j.bmcl.2015.09.066

  • Wyvekens N, Tsai SQ, Joung JK Genome Editing in Human Cells Using CRISPR/Cas Nucleases. Curr Protoc Mol Biol. 2015;112:31.3.1-31.3.18 - PMID: 26423589 - PMCID: PMC4852847 - DOI: 10.1002/0471142727.mb3103s112

  • Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813 - DOI: 10.1016/j.cell.2015.08.027

  • Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells. MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106 - DOI: 10.1128/mBio.01157-15

  • 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 The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. Circ Res. 2015;117(9):817-24 - PMID: 26358192 - PMCID: PMC4596485 - DOI: 10.1161/CIRCRESAHA.115.306807

  • Govindan JA, Jayamani E, Zhang X, Mylonakis E, Ruvkun G Dialogue between E. coli free radical pathways and the mitochondria of C. elegans. Proc Natl Acad Sci U S A. 2015;112(40):12456-61 - PMID: 26392561 - PMCID: PMC4603447 - DOI: 10.1073/pnas.1517448112

  • 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 CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat Med. 2015;21(11):1357-1363 - PMID: 26398868 - PMCID: PMC4746056 - DOI: 10.1038/nm.3975

  • Cervone F, Ausubel FM, Lorenzo G Enhancing immunity by engineering DAMPs. Oncotarget. 2015;6(30):28523-4 - PMID: 26387132 - PMCID: PMC4745668 - DOI: 10.18632/oncotarget.5251

  • Bushinsky DA, Williams GH, Pitt B, Weir MR, Freeman MW, Garza D, Stasiv Y, Li E, Berman L, Bakris GL Patiromer induces rapid and sustained potassium lowering in patients with chronic kidney disease and hyperkalemia. Kidney Int. 2015;88(6):1427-1433 - PMID: 26376130 - PMCID: PMC4678168 - DOI: 10.1038/ki.2015.270

  • Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells. MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106 - DOI: 10.1128/mBio.01157-15

  • Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813 - DOI: 10.1016/j.cell.2015.08.027

  • Siegel MO, Borkowska AG, Dubrovsky L, Roth M, Welti R, Roberts AD, Parenti DM, Simon GL, Sviridov D, Simmens S, Bukrinsky M, Fitzgerald ML HIV infection induces structural and functional changes in high density lipoproteins. Atherosclerosis. 2015;243(1):19-29 - PMID: 26343868 - PMCID: PMC4609619 - DOI: 10.1016/j.atherosclerosis.2015.08.036

  • Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol. 2015;33(10):1045-1052 - PMID: 26344404 - PMCID: PMC4676274 - DOI: 10.1038/nbt.3319

  • Govindan JA, Jayamani E, Zhang X, Breen P, Larkins-Ford J, Mylonakis E, Ruvkun G Lipid signalling couples translational surveillance to systemic detoxification in Caenorhabditis elegans. Nat Cell Biol. 2015;17(10):1294-303 - PMID: 26322678 - PMCID: PMC4589496 - DOI: 10.1038/ncb3229

  • Haney CH, Ausubel FM MICROBIOME. Plant microbiome blueprints. Science. 2015;349(6250):788-9 - PMID: 26293938 - DOI: 10.1126/science.aad0092

  • Phillips CM, Brown KC, Montgomery BE, Ruvkun G, Montgomery TA piRNAs and piRNA-Dependent siRNAs Protect Conserved and Essential C. elegans Genes from Misrouting into the RNAi Pathway. Dev Cell. 2015;34(4):457-465 - PMID: 26279487 - PMCID: PMC4550515 - DOI: 10.1016/j.devcel.2015.07.009

  • Ryan CM, Lee AF, Kazis LE, Shapiro GD, Schneider JC, Goverman J, Fagan SP, Wang C, Kim J, Sheridan RL, Tompkins RG 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. J Burn Care Res. 2015;37(1):64-74 - PMID: 26284638 - DOI: 10.1097/BCR.0000000000000287

  • Hubbard BP, Badran AH, Zuris JA, Guilinger JP, Davis KM, Chen L, Tsai SQ, Sander JD, Joung JK, Liu DR Continuous directed evolution of DNA-binding proteins to improve TALEN specificity. Nat Methods. 2015;12(10):939-942 - PMID: 26258293 - PMCID: PMC4589463 - DOI: 10.1038/nmeth.3515

  • 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 Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015;349(6252):1101-6 - PMID: 26229116 - PMCID: PMC5087275 - DOI: 10.1126/science.aac4812

  • Larsen AT, Fahrenbach AC, Sheng J, Pian J, Szostak JW Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization. Nucleic Acids Res. 2015;43(16):7675-87 - PMID: 26240387 - PMCID: PMC4652770 - DOI: 10.1093/nar/gkv761

  • Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases. Inflamm Bowel Dis. 2015;21(11):2507-2514 - PMID: 26241000 - PMCID: PMC4615315 - DOI: 10.1097/MIB.0000000000000524

  • Kamat NP, Tobé S, Hill IT, Szostak JW Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides. Angew Chem Int Ed Engl. 2015;54(40):11735-11739 - PMID: 26223820 - PMCID: PMC4600236 - DOI: 10.1002/anie.201505742

  • Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst. Nat Commun. 2015;6:7838 - PMID: 26194095 - PMCID: PMC4518307 - DOI: 10.1038/ncomms8838

  • 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 Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics. Proc Natl Acad Sci U S A. 2015;112(31):E4281-7 - PMID: 26195741 - PMCID: PMC4534235 - DOI: 10.1073/pnas.1512289112

  • Pringle PL, Stewart KO, Peloquin JM, Sturgeon HC, Nguyen D, Sauk J, Garber JJ, Yajnik V, Ananthakrishnan AN, Chan AT, Xavier RJ, Khalili H Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease. Inflamm Bowel Dis. 2015;21(10):2304-2310 - PMID: 26181430 - PMCID: PMC4567407 - DOI: 10.1097/MIB.0000000000000498

  • Baxt LA, Xavier RJ Role of Autophagy in the Maintenance of Intestinal Homeostasis. Gastroenterology. 2015;149(3):553-62 - PMID: 26170139 - PMCID: PMC4550567 - DOI: 10.1053/j.gastro.2015.06.046

  • Bakris GL, Pitt B, Weir MR, Freeman MW, Mayo MR, Garza D, Stasiv Y, Zawadzki R, Berman L, Bushinsky DA, Effect of Patiromer on Serum Potassium Level in Patients With Hyperkalemia and Diabetic Kidney Disease: The AMETHYST-DN Randomized Clinical Trial. JAMA. 2015;314(2):151-61 - PMID: 26172895 - DOI: 10.1001/jama.2015.7446

  • Joung JK Unwanted mutations: Standards needed for gene-editing errors. Nature. 2015;523(7559):158 - PMID: 26156364 - DOI: 10.1038/523158a

  • Ramezani A, Dubrovsky L, Pushkarsky T, Sviridov D, Karandish S, Raj DS, Fitzgerald ML, Bukrinsky M Stimulation of Liver X Receptor Has Potent Anti-HIV Effects in a Humanized Mouse Model. J Pharmacol Exp Ther. 2015;354(3):376-83 - PMID: 26126533 - PMCID: PMC4538872 - DOI: 10.1124/jpet.115.224485

  • 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 Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy. Cell Rep. 2015;11(12):1905-1918 - PMID: 26095365 - PMCID: PMC4507440 - DOI: 10.1016/j.celrep.2015.05.045

  • Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JJ, Aryee MJ, Joung JK Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015;523(7561):481-5 - PMID: 26098369 - PMCID: PMC4540238 - DOI: 10.1038/nature14592

  • Wyvekens N, Topkar VV, Khayter C, Joung JK, Tsai SQ Dimeric CRISPR RNA-guided FokI-dCas9 nucleases (RFNs) directed by truncated gRNAs for highly specific genome editing. Hum Gene Ther. 2015;26(7):425-431 - PMID: 26068112 - PMCID: PMC4509490 - DOI: 10.1089/hum.2015.084

  • Rajamuthiah R, Jayamani E, Conery AL, Fuchs BB, Kim W, Johnston T, Vilcinskas A, Ausubel FM, Mylonakis E A Defensin from the Model Beetle Tribolium castaneum Acts Synergistically with Telavancin and Daptomycin against Multidrug Resistant Staphylococcus aureus. PLoS One. 2015;10(6):e0128576 - PMID: 26062137 - PMCID: PMC4465704 - DOI: 10.1371/journal.pone.0128576

  • Causton B, Ramadas RA, Cho JL, Jones K, Pardo-Saganta A, Rajagopal J, Xavier RJ, Medoff BD CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation. J Immunol. 2015;195(2):683-94 - PMID: 26041536 - PMCID: PMC4489191 - DOI: 10.4049/jimmunol.1402983

  • Kim W, Conery AL, Rajamuthiah R, Fuchs BB, Ausubel FM, Mylonakis E Identification of an Antimicrobial Agent Effective against Methicillin-Resistant Staphylococcus aureus Persisters Using a Fluorescence-Based Screening Strategy. PLoS One. 2015;10(6):e0127640 - PMID: 26039584 - PMCID: PMC4454602 - DOI: 10.1371/journal.pone.0127640

  • Adamala K, Engelhart AE, Kamat NP, Jin L, Szostak JW Construction of a liposome dialyzer for the preparation of high-value, small-volume liposome formulations. Nat Protoc. 2015;10(6):927-938 - PMID: 26020615 - PMCID: PMC4982460 - DOI: 10.1038/nprot.2015.054

  • 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 Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Genes Dev. 2015;29(10):1018-31 - PMID: 25995187 - PMCID: PMC4441050 - DOI: 10.1101/gad.259796.115

  • 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 The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells. Elife. 2015;4:ePub - PMID: 25998054 - PMCID: PMC4441007 - DOI: 10.7554/eLife.05920

  • 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 Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model. PLoS Genet. 2015;11(5):e1005239 - PMID: 26000857 - PMCID: PMC4441453 - DOI: 10.1371/journal.pgen.1005239

  • Hwang WY, Fu Y, Reyon D, Gonzales AP, Joung JK, Yeh JR Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided Nucleases. Methods Mol Biol. 2015;1311:317-34 - PMID: 25981483 - DOI: 10.1007/978-1-4939-2687-9_21

  • Wlodarska M, Kostic AD, Xavier RJ An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases. Cell Host Microbe. 2015;17(5):577-591 - PMID: 25974300 - PMCID: PMC4498258 - DOI: 10.1016/j.chom.2015.04.008

  • Sadreyev IR, Ji F, Cohen E, Ruvkun G, Tabach Y PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles. Nucleic Acids Res. 2015;43(W1):W154-W159 - PMID: 25958392 - PMCID: PMC4489270 - DOI: 10.1093/nar/gkv452

  • 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. Mol Ther. 2015;23(5):796-806 - PMID: 25943494 - PMCID: PMC4427885 - DOI: 10.1038/mt.2015.54

  • Tsurumi A, Que YA, Yan S, Tompkins RG, Rahme LG, Ryan CM Do standard burn mortality formulae work on a population of severely burned children and adults?. Burns. 2015;41(5):935-45 - PMID: 25922299 - DOI: 10.1016/j.burns.2015.03.017

  • Izgu EC, Fahrenbach AC, Zhang N, Li L, Zhang W, Larsen A, Blain JC, Szostak JW Uncovering the Thermodynamics of Monomer Binding for RNA Replication. J Am Chem Soc. 2015;137(19):6373-82 - PMID: 25901790 - PMCID: PMC4984997 - DOI: 10.1021/jacs.5b02707

  • Rajamuthiah R, Fuchs BB, Conery AL, Kim W, Jayamani E, Kwon B, Ausubel FM, Mylonakis E Repurposing Salicylanilide Anthelmintic Drugs to Combat Drug Resistant Staphylococcus aureus. PLoS One. 2015;10(4):e0124595 - PMID: 25897961 - PMCID: PMC4405337 - DOI: 10.1371/journal.pone.0124595

  • Hou HW, Bhattacharyya RP, Hung DT, Han J Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics. Lab Chip. 2015;15(10):2297-2307 - PMID: 25882432 - PMCID: PMC4437799 - DOI: 10.1039/c5lc00311c

  • 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 Future Translational Applications From the Contemporary Genomics Era: A Scientific Statement From the American Heart Association. Circulation. 2015;131(19):1715-36 - PMID: 25882488 - PMCID: PMC4825323 - DOI: 10.1161/CIR.0000000000000211

  • Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 2015;16(1):67 - PMID: 25887922 - PMCID: PMC4414286 - DOI: 10.1186/s13059-015-0637-x

  • Benedetti M, Pontiggia D, Raggi S, Cheng Z, Scaloni F, Ferrari S, Ausubel FM, Cervone F, De Lorenzo G Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns. Proc Natl Acad Sci U S A. 2015;112(17):5533-8 - PMID: 25870275 - PMCID: PMC4418913 - DOI: 10.1073/pnas.1504154112

  • 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 Discovery of a Small-Molecule Probe for V-ATPase Function. J Am Chem Soc. 2015;137(16):5563-8 - PMID: 25860544 - PMCID: PMC4416280 - DOI: 10.1021/jacs.5b02150

  • 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 Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015;47(5):469-78 - PMID: 25822089 - PMCID: PMC4414868 - DOI: 10.1038/ng.3258

  • 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 Intake of farmed Atlantic salmon fed soybean oil increases hepatic levels of arachidonic acid-derived oxylipins and ceramides in mice. J Nutr Biochem. 2015;26(6):585-95 - PMID: 25776459 - DOI: 10.1016/j.jnutbio.2014.12.005

  • Li JF, Zhang D, Sheen J Targeted Plant Genome Editing via the CRISPR/Cas9 Technology. Methods Mol Biol. 2015;1284:239-55 - PMID: 25757776 - DOI: 10.1007/978-1-4939-2444-8_12

  • Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis KA, Urrutia RA, Faubion WA A novel role for KLF14 in T regulatory cell differentiation. Cell Mol Gastroenterol Hepatol. 2015;1(2):188-202.e4 - PMID: 25750932 - PMCID: PMC4349492 - DOI: 10.1016/j.jcmgh.2014.12.007

  • Tompkins RG Genomics of injury: The Glue Grant experience. J Trauma Acute Care Surg. 2015;78(4):671-686 - PMID: 25742245 - PMCID: PMC4389222 - DOI: 10.1097/TA.0000000000000568

  • Cheng Z, Li JF, Niu Y, Zhang XC, Woody OZ, Xiong Y, Djonovi? S, Millet Y, Bush J, McConkey BJ, Sheen J, Ausubel FM Pathogen-secreted proteases activate a novel plant immune pathway. Nature. 2015;521(7551):213-6 - PMID: 25731164 - PMCID: PMC4433409 - DOI: 10.1038/nature14243

  • 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 Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2015;125(3):1363 - PMID: 25729854 - PMCID: PMC4362234 - DOI: 10.1172/JCI79657

  • 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 Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods. 2015;12(4):323-325 - PMID: 25730492 - PMCID: PMC4712044 - DOI: 10.1038/nmeth.3313

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