Publications for All Faculty

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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
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
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
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
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
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
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
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
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
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
Keung AJ, Joung JK, Khalil AS, Collins JJ

Chromatin regulation at the frontier of synthetic biology.

Nat Rev Genet. 2015;16(3):159-71 - PMID: 25668787 - PMCID: PMC4846386 - DOI: 10.1038/nrg3900
Heuberger BD, Pal A, Del Frate F, Topkar VV, Szostak JW

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

J Am Chem Soc. 2015;137(7):2769-75 - PMID: 25654265 - PMCID: PMC4985000 - DOI: 10.1021/jacs.5b00445
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

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

Cell Host Microbe. 2015;17(2):260-273 - PMID: 25662751 - PMCID: PMC4689191 - DOI: 10.1016/j.chom.2015.01.001
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
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

A new antibiotic with potent activity targets MscL.

J Antibiot (Tokyo). 2015;68(7):453-62 - PMID: 25649856 - PMCID: PMC4430313 - DOI: 10.1038/ja.2015.4
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

Exome Sequencing in Suspected Monogenic Dyslipidemias.

Circ Cardiovasc Genet. 2015;8(2):343-50 - PMID: 25632026 - PMCID: PMC4406825 - DOI: 10.1161/CIRCGENETICS.114.000776
Kirienko NV, Ausubel FM, Ruvkun G

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

Proc Natl Acad Sci U S A. 2015;112(6):1821-6 - PMID: 25624506 - PMCID: PMC4330731 - DOI: 10.1073/pnas.1424954112
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

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

Cell. 2015;160(3):447-60 - PMID: 25619688 - PMCID: PMC4312520 - DOI: 10.1016/j.cell.2015.01.002
Nakazawa H, Yamada M, Tanaka T, Kramer J, Yu YM, Fischman AJ, Martyn JA, Tompkins RG, Kaneki M

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

PLoS One. 2015;10(1):e0116633 - PMID: 25594415 - PMCID: PMC4296934 - DOI: 10.1371/journal.pone.0116633
Jayamani E, Rajamuthiah R, Larkins-Ford J, Fuchs BB, Conery AL, Vilcinskas A, Ausubel FM, Mylonakis E

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

Antimicrob Agents Chemother. 2015;59(3):1728-37 - PMID: 25583713 - PMCID: PMC4325797 - DOI: 10.1128/AAC.04198-14
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

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

Cell Metab. 2015;21(1):65-80 - PMID: 25565206 - PMCID: PMC5198835 - DOI: 10.1016/j.cmet.2014.12.005
Jeschke MG, Pinto R, Kraft R, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Klein MB, Arnoldo BD, Tompkins RG, Herndon DN,

Morbidity and Survival Probability in Burn Patients in Modern Burn Care.

Crit Care Med. 2015;43(4):808-15 - PMID: 25559438 - PMCID: PMC4359665 - DOI: 10.1097/CCM.0000000000000790
Osborn MJ, Gabriel R, Webber BR, DeFeo AP, McElroy AN, Jarjour J, Starker CG, Wagner JE, Joung JK, Voytas DF, von Kalle C, Schmidt M, Blazar BR, Tolar J

Fanconi Anemia Gene Editing by the CRISPR/Cas9 System.

Hum Gene Ther. 2015;26(2):114-26 - PMID: 25545896 - PMCID: PMC4326027 - DOI: 10.1089/hum.2014.111
Warren HS, Tompkins RG, Moldawer LL, Seok J, Xu W, Mindrinos MN, Maier RV, Xiao W, Davis RW

Mice are not men.

Proc Natl Acad Sci U S A. 2015;112(4):E345 - PMID: 25540422 - PMCID: PMC4313842 - DOI: 10.1073/pnas.1414857111
Total: 2459