Publications for All Faculty

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Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M

A high-resolution map of human evolutionary constraint using 29 mammals.
Nature. 2011;478(7370):476-82 - PMID: 21993624 - PMCID: PMC3207357 - DOI: 10.1038/nature10530

Limmer S, Haller S, Drenkard E, Lee J, Yu S, Kocks C, Ausubel FM, Ferrandon D

Pseudomonas aeruginosa RhlR is required to neutralize the cellular immune response in a Drosophila melanogaster oral infection model.
Proc Natl Acad Sci U S A. 2011;108(42):17378-83 - PMID: 21987808 - PMCID: PMC3198323 - DOI: 10.1073/pnas.1114907108

Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, , , , Dubinsky MC, Brant SR, Silverberg MS, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D'Amato M, McGovern DP, Cho JH, Rioux JD, Xavier RJ, Daly MJ

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.
Nat Genet. 2011;43(11):1066-73 - PMID: 21983784 - PMCID: PMC3378381 - DOI: 10.1038/ng.952

Zeitels SM, Barbu AM, Landau-Zemer T, Lopez-Guerra G, Burns JA, Friedman AD, Freeman MW, Halvorsen YD, Hillman RE

Local injection of bevacizumab (Avastin) and angiolytic KTP laser treatment of recurrent respiratory papillomatosis of the vocal folds: a prospective study.
Ann Otol Rhinol Laryngol. 2011;120(10):627-34 - PMID: 22097147 - DOI: 10.1177/000348941112001001

Russel S, Frand AR, Ruvkun G

Regulation of the C. elegans molt by pqn-47.
Dev Biol. 2011;360(2):297-309 - PMID: 21989027 - PMCID: PMC3618673 - DOI: 10.1016/j.ydbio.2011.09.025

Slatko BE, Kieleczawa J, Ju J, Gardner AF, Hendrickson CL, Ausubel FM

automated DNA sequencing technology.
Curr Protoc Mol Biol. 2011;Chapter 7:Unit7.2 - PMID: 21987057 - DOI: 10.1002/0471142727.mb0702s96

Sander JD, Maeder ML, Joung JK

Engineering designer nucleases with customized cleavage specificities.
Curr Protoc Mol Biol. 2011;Chapter 12:Unit12.13 - PMID: 21987054 - PMCID: PMC3379964 - DOI: 10.1002/0471142727.mb1213s96

Hayes GD, Riedel CG, Ruvkun G

The Caenorhabditis elegans SOMI-1 zinc finger protein and SWI/SNF promote regulation of development by the mir-84 microRNA.
Genes Dev. 2011;25(19):2079-92 - PMID: 21979920 - PMCID: PMC3197206 - DOI: 10.1101/gad.17153811

Szostak JW

An optimal degree of physical and chemical heterogeneity for the origin of life?
Philos Trans R Soc Lond B Biol Sci. 2011;366(1580):2894-901 - PMID: 21930580 - PMCID: PMC3158921 - DOI: 10.1098/rstb.2011.0140

Merquiol E, Uzi D, Mueller T, Goldenberg D, Nahmias Y, Xavier RJ, Tirosh B, Shibolet O

HCV causes chronic endoplasmic reticulum stress leading to adaptation and interference with the unfolded protein response.
PLoS One. 2011;6(9):e24660 - PMID: 21949742 - PMCID: PMC3176279 - DOI: 10.1371/journal.pone.0024660

Warner EA, Kotz KT, Ungaro RF, Abouhamze AS, Lopez MC, Cuenca AG, Kelly-Scumpia KM, Moreno C, O'Malley KA, Lanz JD, Baker HV, Martin LC, Toner M, Tompkins RG, Efron PA, Moldawer LL

Microfluidics-based capture of human neutrophils for expression analysis in blood and bronchoalveolar lavage.
Lab Invest. 2011;91(12):1787-95 - PMID: 21931299 - PMCID: PMC3957199 - DOI: 10.1038/labinvest.2011.94

Sander JD, Yeh JR, Peterson RT, Joung JK

Engineering zinc finger nucleases for targeted mutagenesis of zebrafish.
Methods Cell Biol. 2011;104:51-8 - PMID: 21924156 - DOI: 10.1016/B978-0-12-374814-0.00003-3

Desai KH, Tan CS, Leek JT, Maier RV, Tompkins RG, Storey JD,

Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.
PLoS Med. 2011;8(9):e1001093 - PMID: 21931541 - PMCID: PMC3172280 - DOI: 10.1371/journal.pmed.1001093

Carter EA, Bonab AA, Paul K, Yerxa J, Tompkins RG, Fischman AJ

Association of heat production with 18F-FDG accumulation in murine brown adipose tissue after stress.
J Nucl Med. 2011;52(10):1616-20 - PMID: 21914754 - PMCID: PMC4082963 - DOI: 10.2967/jnumed.111.090175

Stoddard FJ, White GW, Kazis LE, Murphy JM, Sorrentino EA, Hinson M, Kim Stubbs T, Chan G, Sheridan RL, Palmieri T, Kagan R, Herndon D, Tompkins RG

Patterns of medication administration from 2001 to 2009 in the treatment of children with acute burn injuries: a multicenter study.
J Burn Care Res. 2011;32(5):519-28 - PMID: 21811176 - DOI: 10.1097/BCR.0b013e31822bef92

Ryan CM, Antoon A, Fagan SP, Goverman J, Lawlor D, Sheridan RL, Tompkins RG

Considerations for preparedness for a pediatric burn disaster.
J Burn Care Res. 2011;32(5):e165-6 - PMID: 21772149 - DOI: 10.1097/BCR.0b013e31822ac9a4

Lindquist S, Karitkina D, Langnaese K, Posevitz-Fejfar A, Schraven B, Xavier R, Seed B, Lindquist JA

Phosphoprotein associated with glycosphingolipid-enriched microdomains differentially modulates SRC kinase activity in brain maturation.
PLoS One. 2011;6(9):e23978 - PMID: 21915273 - PMCID: PMC3167820 - DOI: 10.1371/journal.pone.0023978

Cuenca AG, Maier RV, Cuschieri J, Moore EE, Moldawer LL, Tompkins RG,

The Glue Grant experience: characterizing the post injury genomic response.
Eur J Trauma Emerg Surg. 2011;37(6):549-58 - PMID: 26815465 - PMCID: PMC6541206 - DOI: 10.1007/s00068-011-0148-8

Ng A, Xavier RJ

Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity.
Autophagy. 2011;7(9):1082-4 - PMID: 21606681 - PMCID: PMC3901792 - DOI: 10.4161/auto.7.9.16464

Zhao Y, Alonso C, Ballester I, Song JH, Chang SY, Guleng B, Arihiro S, Murray PJ, Xavier R, Kobayashi KS, Reinecker HC

Control of NOD2 and Rip2-dependent innate immune activation by GEF-H1.
Inflamm Bowel Dis. 2012;18(4):603-12 - PMID: 21887730 - PMCID: PMC3594873 - DOI: 10.1002/ibd.21851

MW Freeman

Lipoprotein Metabolism and the Treatment of Lipid Disorders, Chapter 42. In: DeGroot LJ and JL Jameson, eds
Endocrinology, 6th edition. 2010;:ePub

Yang W, Yamada M, Tamura Y, Chang K, Mao J, Zou L, Feng Y, Kida K, Scherrer-Crosbie M, Chao W, Ichinose F, Yu YM, Fischman AJ, Tompkins RG, Yao S, Kaneki M

Farnesyltransferase inhibitor FTI-277 reduces mortality of septic mice along with improved bacterial clearance.
J Pharmacol Exp Ther. 2011;339(3):832-41 - PMID: 21873557 - PMCID: PMC3226365 - DOI: 10.1124/jpet.111.183558

Hamel LP, Benchabane M, Nicole MC, Major IT, Morency MJ, Pelletier G, Beaudoin N, Sheen J, Séguin A

Stress-responsive mitogen-activated protein kinases interact with the EAR motif of a poplar zinc finger protein and mediate its degradation through the 26S proteasome.
Plant Physiol. 2011;157(3):1379-93 - PMID: 21873571 - PMCID: PMC3252155 - DOI: 10.1104/pp.111.178343

Trevino SG, Zhang N, Elenko MP, Lupták A, Szostak JW

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity.
Proc Natl Acad Sci U S A. 2011;108(33):13492-7 - PMID: 21825162 - PMCID: PMC3158193 - DOI: 10.1073/pnas.1107113108

Pattanayak V, Ramirez CL, Joung JK, Liu DR

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection.
Nat Methods. 2011;8(9):765-70 - PMID: 21822273 - PMCID: PMC3164905 - DOI: 10.1038/nmeth.1670
Total: 2501