Publications for All Faculty

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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
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
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
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
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
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
Total: 2467