Publications for All Faculty - 2015

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):715-26 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005

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 - DOI: 10.1021/acsinfecdis.5b00119

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 - DOI: 10.1038/nplants.2015.49

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 - DOI: 10.1038/nplants.2015.51

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 - DOI: 10.1097/BCR.0000000000000315

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 - DOI: 10.1073/pnas.1522401112

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 - DOI: 10.1136/gutjnl-2015-310376

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 - DOI: 10.3892/ijmm.2015.2426

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 - DOI: 10.1186/s13059-015-0830-y

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 - DOI: 10.1021/jacs.5b10596

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 - DOI: 10.1164/rccm.201507-1376OC

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 - DOI: 10.1097/TA.0000000000000905

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 - DOI: 10.1038/nbt.3404

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 - DOI: 10.1097/CCM.0000000000001397

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 - DOI: 10.1021/acs.biochem.5b00894

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 - DOI: 10.1021/jacs.5b09438

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 - DOI: 10.1097/CCM.0000000000001312

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 - DOI: 10.1016/j.immuni.2015.10.005

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 - DOI: 10.1016/j.pbi.2015.09.006

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 - DOI: 10.1016/j.bmcl.2015.09.066

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 - DOI: 10.1002/0471142727.mb3103s112

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 - DOI: 10.1016/j.cell.2015.08.027

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 - DOI: 10.1128/mBio.01157-15

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 - DOI: 10.1161/CIRCRESAHA.115.306807

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 - DOI: 10.1073/pnas.1517448112

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 - DOI: 10.1038/nm.3975

Enhancing immunity by engineering DAMPs.

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

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 - DOI: 10.1038/ki.2015.270

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 - DOI: 10.1128/mBio.01157-15

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 - DOI: 10.1016/j.cell.2015.08.027

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 - DOI: 10.1016/j.atherosclerosis.2015.08.036

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 - DOI: 10.1038/nbt.3319

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 - DOI: 10.1038/ncb3229

MICROBIOME. Plant microbiome blueprints.

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

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 - DOI: 10.1016/j.devcel.2015.07.009

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 - DOI: 10.1097/BCR.0000000000000287

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 - DOI: 10.1038/nmeth.3515

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 - DOI: 10.1126/science.aac4812

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 - DOI: 10.1093/nar/gkv761

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 - DOI: 10.1097/MIB.0000000000000524

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 - DOI: 10.1002/anie.201505742

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 - DOI: 10.1136/gutjnl-2014-307649

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 - DOI: 10.1016/j.jinsphys.2015.07.011

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 - DOI: 10.1038/ncomms8838

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 - DOI: 10.1073/pnas.1512289112

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 - DOI: 10.1097/MIB.0000000000000498

Role of Autophagy in the Maintenance of Intestinal Homeostasis.

Baxt LA, Xavier RJ
Gastroenterology. 2015;149(3):553-62 - PMID: 26170139 - PMCID: PMC4550567 - DOI: 10.1053/j.gastro.2015.06.046

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 - DOI: 10.1001/jama.2015.7446

Unwanted mutations: Standards needed for gene-editing errors.

Joung JK
Nature. 2015;523(7559):158 - PMID: 26156364 - DOI: 10.1038/523158a

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 - DOI: 10.1124/jpet.115.224485

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 - DOI: 10.1016/j.celrep.2015.05.045

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 - DOI: 10.1038/nature14592

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 - DOI: 10.1089/hum.2015.084

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 - DOI: 10.1371/journal.pone.0128576

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 - DOI: 10.4049/jimmunol.1402983

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 - DOI: 10.1371/journal.pone.0127640

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 - DOI: 10.1038/nprot.2015.054

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 - DOI: 10.1101/gad.259796.115

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 - DOI: 10.7554/eLife.05920

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 - DOI: 10.1371/journal.pgen.1005239

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 - DOI: 10.1007/978-1-4939-2687-9_21

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 - DOI: 10.1016/j.chom.2015.04.008

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 - DOI: 10.1093/nar/gkv452

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 - DOI: 10.1038/mt.2015.54

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 - DOI: 10.1016/j.burns.2015.03.017

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 - DOI: 10.1021/jacs.5b02707

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 - DOI: 10.1371/journal.pone.0124595

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 - DOI: 10.1039/c5lc00311c

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 - DOI: 10.1161/CIR.0000000000000211

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 - DOI: 10.1186/s13059-015-0637-x

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 - DOI: 10.1073/pnas.1504154112

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 - DOI: 10.1021/jacs.5b02150

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 - DOI: 10.1038/ng.3258

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 - DOI: 10.1016/j.jnutbio.2014.12.005

Targeted Plant Genome Editing via the CRISPR/Cas9 Technology.

Li JF, Zhang D, Sheen J
Methods Mol Biol. 2015;1284:239-55 - PMID: 25757776 - DOI: 10.1007/978-1-4939-2444-8_12

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 - DOI: 10.1016/j.jcmgh.2014.12.007

Genomics of injury: The Glue Grant experience.

Tompkins RG
J Trauma Acute Care Surg. 2015;78(4):671-686 - PMID: 25742245 - PMCID: PMC4389222 - DOI: 10.1097/TA.0000000000000568

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 - DOI: 10.1038/nature14243

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 - DOI: 10.1172/JCI79657

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 - DOI: 10.1038/nmeth.3313

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 - DOI: 10.1016/j.chom.2015.01.001

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 - DOI: 10.1038/nrg3900

Replacing Uridine with 2-Thio-Uridine Enhances the Rate and Fidelity of Nonenzymatic RNA Primer Extension.

Heuberger BD, Pal A, Del Frate F, Topkar VV, Szostak JW
J Am Chem Soc. 2015;137(7):2769-75 - PMID: 25654265 - PMCID: PMC4985000 - DOI: 10.1021/jacs.5b00445

A new antibiotic with potent activity targets MscL.

Iscla I, Wray R, Blount P, Larkins-Ford J, Conery AL, Ausubel FM, Ramu S, Kavanagh A, Huang JX, Blaskovich MA, Cooper MA, Obregon-Henao A, Orme I, Tjandra ES, Stroeher UH, Brown MH, Macardle C, van Holst N, Ling Tong C, Slattery AD, Gibson CT, Raston CL, Boulos RA
J Antibiot (Tokyo). 2015;68(7):453-62 - PMID: 25649856 - PMCID: PMC4430313 - DOI: 10.1038/ja.2015.4

Exome Sequencing in Suspected Monogenic Dyslipidemias.

Stitziel NO, Peloso GM, Abifadel M, Cefalù AB, Fouchier S, Motazacker MM, Tada H, Larach DB, Awan Z, Haller JF, Pullinger CR, Varret M, Rabès JP, Noto D, Tarugi P, Kawashiri MA, Nohara A, Yamagishi M, Risman M, Deo R, Ruel I, Shendure J, Nickerson DA, Wilson JG, Rich SS, Gupta N, Farlow DN, , Neale BM, Daly MJ, Kane JP, Freeman MW, Genest J, Rader DJ, Mabuchi H, Kastelein JJ, Hovingh GK, Averna MR, Gabriel S, Boileau C, Kathiresan S
Circ Cardiovasc Genet. 2015;8(2):343-50 - PMID: 25632026 - PMCID: PMC4406825 - DOI: 10.1161/CIRCGENETICS.114.000776

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

Kirienko NV, Ausubel FM, Ruvkun G
Proc Natl Acad Sci U S A. 2015;112(6):1821-6 - PMID: 25624506 - PMCID: PMC4330731 - DOI: 10.1073/pnas.1424954112

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

Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW
Cell. 2015;160(3):447-60 - PMID: 25619688 - PMCID: PMC4312520 - DOI: 10.1016/j.cell.2015.01.002

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

Nakazawa H, Yamada M, Tanaka T, Kramer J, Yu YM, Fischman AJ, Martyn JA, Tompkins RG, Kaneki M
PLoS One. 2015;10(1):e0116633 - PMID: 25594415 - PMCID: PMC4296934 - DOI: 10.1371/journal.pone.0116633

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

Jayamani E, Rajamuthiah R, Larkins-Ford J, Fuchs BB, Conery AL, Vilcinskas A, Ausubel FM, Mylonakis E
Antimicrob Agents Chemother. 2015;59(3):1728-37 - PMID: 25583713 - PMCID: PMC4325797 - DOI: 10.1128/AAC.04198-14

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

Palsson-McDermott EM, Curtis AM, Goel G, Lauterbach MA, Sheedy FJ, Gleeson LE, van den Bosch MW, Quinn SR, Domingo-Fernandez R, Johnson DG, Jiang J, Israelsen WJ, Keane J, Thomas C, Clish C, Vanden Heiden M, Xavier RJ, O'Neill LA
Cell Metab. 2015;21(1):65-80 - PMID: 25565206 - PMCID: PMC5198835 - DOI: 10.1016/j.cmet.2014.12.005