2012 Publications

2012 Publications

Toward a Systems Analysis of the Root.
Benfey PN.
Cold Spring Harb Symp Quant Biol. 2012 Dec 12. [Epub ahead of print]

Airway Epithelial Progenitors are Region-Specific and Show Differential Responses to Bleomycin-Induced Lung Injury.
Chen H, Matsumoto K, Brockway BL, Rackley CR, Liang J, Lee JH, Jiang D, Noble PW, Randell SH, Kim CF, Stripp BR.
Stem Cells. 2012 Jun 13. doi: 10.1002/stem.1150. [Epub ahead of print]

Hedgehog Controls Hepatic Stellate Cell Fate by Regulating Metabolism.
Chen Y, Choi SS, Michelotti GA, Chan IS, Swiderska M, Karaca GF, Xie G, Moylan CA, Garibaldi F, Premont R, Suliman HB, Piantodosi CA, Diehl AM.
Gastroenterology. 2012 Aug 8. [Epub ahead of print]

Tie2(+) Bone Marrow Endothelial Cells Regulate Hematopoietic Stem Cell Regeneration Following Radiation Injury.
Doan PL, Russell JL, Himburg HA, Helms K, Harris J, Lucas J, Holshausen K, Meadows SK, Daher P, Jeffords LB, Chao NJ, Kirsch DG, Chute JP.
Stem Cells. 2012 Nov 6. doi: 10.1002/stem.1275. [Epub ahead of print]

A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation.
Duncan CG, Barwick BG, Jin G, Rago C, Kapoor-Vazirani P, Powell DR, Chi JT, Bigner DD, Vertino PM, Yan H.
Genome Res. 2012 Aug 16. [Epub ahead of print]

Evidence for phenotypic plasticity in aggressive triple-negative breast cancer: human biology is recapitulated by a novel model system.
D'Amato NC, Ostrander JH, Bowie ML, Sistrunk C, Borowsky A, Cardiff RD, Bell K, Young LJ, Simin K, Bachelder RE, Delrow J, Dawson A, Yee LD, Mr??zek K, Clay TM, Osada T, Seewaldt VL.
PLoS One. 2012;7(9):e45684. doi: 10.1371/journal.pone.0045684. Epub 2012 Sep 25.

Individuals with increased inflammatory response to ozone demonstrate muted signaling of immune cell trafficking pathways.
Fry RC, Rager JE, Zhou H, Zou B, Brickey JW, Ting J, Lay JC, Peden DB, Alexis NE.
Respir Res. 2012 Oct 3;13:89. doi: 10.1186/1465-9921-13-89.

Global identification of MLL2-targeted loci reveals MLL2's role in diverse signaling pathways.
Guo C, Chang CC, Wortham M, Chen LH, Kernagis DN, Qin X, Cho YW, Chi JT, Grant GA, McLendon RE, Yan H, Ge K, Papadopoulos N, Bigner DD, He Y.
Proc Natl Acad Sci U S A. 2012 Oct 8. [Epub ahead of print]

Convergent differential regulation of parvalbumin in the brains of vocal learners.
Hara E, Rivas MV, Ward JM, Okanoya K, Jarvis ED.
PLoS One. 2012;7(1):e29457. Epub 2012 Jan 6.

β-Catenin-SOX2 signaling regulates the fate of developing airway epithelium.
Hashimoto S, Chen H, Que J, Brockway BL, Drake JA, Snyder JC, Randell SH, Stripp BR.
J Cell Sci. 2012 Feb 15;125(Pt 4):932-42. Epub 2012 Mar 15.

Plasticity of the myelination genomic fabric.
Iacobas S, Thomas NM, Iacobas DA.
Mol Genet Genomics. 2012 Mar;287(3):237-46. Epub 2012 Jan 13.

Statins improve outcome in murine models of intracranial hemorrhage and traumatic brain injury: a translational approach.
Indraswari F, Wang H, Lei B, James ML, Kernagis D, Warner DS, Dawson HN, Laskowitz DT.
J Neurotrauma. 2012 May 1;29(7):1388-400. Epub 2012 Apr 2.

Regulation of trabecular meshwork cell contraction and intraocular pressure by miR-200c.
Luna C, Li G, Huang J, Qiu J, Wu J, Yuan F, Epstein DL, Gonzalez P.
PLoS One. 2012;7(12):e51688. doi: 10.1371/journal.pone.0051688. Epub 2012 Dec 14.

Connective tissue growth factor-mediated upregulation of neuromedin u expression in trabecular meshwork cells and its role in homeostasis of aqueous humor outflow.
Iyer P, Maddala R, Pattabiraman PP, Rao PV.
Invest Ophthalmol Vis Sci. 2012 Jul 26;53(8):4952-62. Print 2012.

Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad.
Jameson SA, Natarajan A, Cool J, DeFalco T, Maatouk DM, Mork L, Munger SC, Capel B.
PLoS Genet. 2012;8(3):e1002575. Epub 2012 Mar 15.

A chemical genetic approach identifies piperazine antipsychotics as promoters of CNS neurite growth on inhibitory substrates.
Johnstone AL, Reierson GW, Smith RP, Goldberg JL, Lemmon VP, Bixby JL.
Mol Cell Neurosci. 2012 Jun;50(2):125-35. Epub 2012 May 3.

Genes with bimodal expression are robust diagnostic targets that define distinct subtypes of epithelial ovarian cancer with different overall survival.
Kernagis DN, Hall AH, Datto MB.
J Mol Diagn. 2012 May-Jun;14(3):214-22. Epub 2012 Apr 9.

Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal Cancer.
Kim MK, Osada T, Barry WT, Yang XY, Freedman JA, Tsamis KA, Datto M, Clary BM, Clay T, Morse MA, Febbo PG, Lyerly HK, Hsu DS.
Mol Cancer Ther. 2012 Feb 16. [Epub ahead of print]

Resveratrol worsens survival in SCID mice with prostate cancer xenografts in a cell-line specific manner, through paradoxical effects on oncogenic pathways.
Klink JC, Tewari AK, Masko EM, Antonelli J, Febbo PG, Cohen P, Dewhirst MW, Pizzo SV, Freedland SJ.
Prostate. 2012 Nov 28. doi: 10.1002/pros.22619. [Epub ahead of print]

A Dominant Allele of Arabidopsis Pectin-Binding Wall-Associated Kinase Induces a Stress Response Suppressed by MPK6 but Not MPK3 Mutations.
Kohorn BD, Kohorn SL, Todorova T, Baptiste G, Stansky K, McCullough M.
Mol Plant. 2012 Jul;5(4):841-51. Epub 2011 Dec 7.

Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Contributes to Malaria Resistance.
Lamonte G, Philip N, Reardon J, Lacsina JR, Majoros W, Chapman L, Thornburg CD, Telen MJ, Ohler U, Nicchitta CV, Haystead T, Chi JT.
Cell Host Microbe. 2012 Aug 16;12(2):187-99.

Gene expression profiling of peritoneal metastases from appendiceal and colon cancer demonstrates unique biologic signatures and predicts patient outcomes.
Levine EA, Blazer DG 3rd, Kim MK, Shen P, Stewart JH 4th, Guy C, Hsu DS.
J Am Coll Surg. 2012 Apr;214(4):599-606; discussion 606-7. Epub 2012 Feb 17.

Highly Conductive Carbon Nanotube Matrix Accelerates Developmental Chloride Extrusion in Central Nervous System Neurons by Increased Expression of Chloride Transporter KCC2.
Liedtke W, Yeo M, Zhang H, Wang Y, Gignac M, Miller S, Berglund K, Liu J.
Small. 2012 Dec 10. doi: 10.1002/smll.201201994. [Epub ahead of print]

Effect of (S)-3,5-DHPG on microRNA expression in mouse brain.
Lusardi TA, Thompson SJ, MacDonald IC, Lan JQ, Theofilas P, Saugstad JA.
Exp Neurol. 2012 Jun;235(2):497-507. Epub 2012 Jan 28.

Transcriptome analysis of the ependymal barrier during murine neurocysticercosis.
Mishra PK, Teale JM.
J Neuroinflammation. 2012 Jun 25;9(1):141. [Epub ahead of print]

Oncogene dependent control of miRNA biogenesis and metastatic progression in a model of undifferentiated pleomorphic sarcoma.
Mito JK, Min HD, Ma Y, Carter JE, Brigman BE, Dodd L, Dankort D, McMahon M, Kirsch DG.
J Pathol. 2012 Sep 6. doi: 10.1002/path.4099. [Epub ahead of print]

The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition.
Pajerowska-Mukhtar KM, Wang W, Tada Y, Oka N, Tucker CL, Fonseca JP, Dong X.
Curr Biol. 2012 Jan 24;22(2):103-12. Epub 2012 Jan 12.

Up-regulated expression of extracellular matrix remodeling genes in phagocytically challenged trabecular meshwork cells.
Porter KM, Epstein DL, Liton PB.
PLoS One. 2012;7(4):e34792. Epub 2012 Apr 18.

Analysis of EBV-Regulated Host Gene Expression Changes through Primary B-Cell Outgrowth Reveals Delayed Kinetics of LMP1-Mediated NFκB Activation.
Price AM, Tourigny JP, Forte E, Salinas RE, Dave SS, Luftig MA.
J Virol. 2012 Aug 1. [Epub ahead of print]

SplicerEX: a tool for the automated detection and classification of mRNA changes from conventional and splice-sensitive microarray expression data.
Robinson TJ, Forte E, Salinas RE, Puri S, Marengo M, Garcia-Blanco MA, Luftig MA.
RNA. 2012 Aug;18(8):1435-45. Epub 2012 Jun 26.

Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network.
Simmons Kovacs LA, Mayhew MB, Orlando DA, Jin Y, Li Q, Huang C, Reed SI, Mukherjee S, Haase SB.
Mol Cell. 2012 Mar 9;45(5):669-79. Epub 2012 Feb 2.

Changes in the molecular phenotype of nucleus pulposus cells with intervertebral disc aging.
Tang X, Jing L, Chen J.
PLoS One. 2012;7(12):e52020. doi: 10.1371/journal.pone.0052020. Epub 2012 Dec 19.

Functional interaction between responses to lactic acidosis and hypoxia regulates genomic transcriptional outputs.
Tang X, Lucas JE, Chen JL, LaMonte G, Wu J, Wang MC, Koumenis C, Chi JT.
Cancer Res. 2012 Jan 15;72(2):491-502. Epub 2011 Dec 1.

Toward a molecular pathogenic pathway for Yersinia pestis YopM.
Uittenbogaard AM, Chelvarajan RL, Myers-Morales T, Gorman AA, Brickey WJ, Ye Z, Kaplan AM, Cohen DA, Ting JP, Straley SC.
Front Cell Infect Microbiol. 2012;2:155. doi: 10.3389/fcimb.2012.00155. Epub 2012 Dec 11.

Histological and molecular evaluation of patient-derived colorectal cancer explants.
Uronis JM, Osada T, McCall S, Yang XY, Mantyh C, Morse MA, Lyerly HK, Clary BM, Hsu DS.
PLoS One. 2012;7(6):e38422. Epub 2012 Jun 4.

MicroRNA-127 Inhibits Lung Inflammation by Targeting IgG Fcγ Receptor I.
Xie T, Liang J, Liu N, Wang Q, Li Y, Noble PW, Jiang D.
J Immunol. 2012 Mar 1;188(5):2437-44. Epub 2012 Jan 27.

Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma.
Xu X, Rock JR, Lu Y, Futtner C, Schwab B, Guinney J, Hogan BL, Onaitis MW.
Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4910-5. Epub 2012 Mar 12.

Adaptive response of vascular endothelial cells to an acute increase in shear stress magnitude.
Zhang J, Friedman MH.
Am J Physiol Heart Circ Physiol. 2012 Feb;302(4):H983-91. Epub 2011 Dec 2.

A novel role for type 1 angiotensin receptors on T lymphocytes to limit target organ damage in hypertension.
Zhang JD, Patel MB, Song YS, Griffiths R, Burchette J, Ruiz P, Sparks MA, Yan M, Howell DN, Gomez JA, Spurney RF, Coffman TM, Crowley SD.
Circ Res. 2012 Jun 8;110(12):1604-17. Epub 2012 Apr 24.