Publications by Product

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Differential Gene Expression in Human Conducting Airway Surface Epithelia and Submucosal Glands

Anthony J. Fischer, Paul B. McCray Jr., Am J Respir Mol Biol, February 2009

Moderate kidney disease inhibits atherosclerosis regression

Manish P. Ponda, Edward Y. Skolnik, Atherosclerosis, 2009

Genome-wide transcriptome analysis of 150 cell samples

Irimia D., Toner M., Integrative Biology, January 1, 2009

Gene and Protein Expression Pilot Profiling and Biomarkers in an Experimental Mouse Model of Hypertensive Glaucoma

Molly M. Walsh, Paulo A. Ferreira, Experimental Biology and Medicine, Volume 234, Number 8, Pp 918-939

Induction of Alzheimer's-like changes in brain of mice expressing mutant APP fed excess methionine

McCampbell A, Wessner K, Marlatt MW, Wolffe C, Toolan D, Podtelezhnikov A, Yeh S, Zhang R, Szczerba P, Tanis KQ, Majercak J, Ray WJ,Savage M. Journal of Neurochemistry.  2011 Jan; 116(1):82-92. doi: 10.1111/j.1471-4159.2010.07087.x. Epub 2010 Dec 2. PMID: 21054384

Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18

Koide K, Slonim DK, Johnson KL, Tantravahi U, Cowan JM, Bianchi DW. Human Genetetics. 2011 Mar; 129(3):295-305. Epub 2010 Dec 9, PMID: 21152935, PMCID: PMC3206603

Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes

Iyer VV, Ierapetritou MG, Toxicology and Applied Pharmacology 2010 Nov 1;248(3):165-77

Adrenoceptors in Brain: Cellular Gene Expression and Effects on Astrocytic Metabolism and Ca2

Hertz, L, Nedergaard, M, Neurochemistry, Volume 57, Issue 4, November 2010, Pages 411-420

Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems

Morse AM, McIntyre LM, Journal of Biomolecular Techniques 2010 September; 21(3): 141-147

Molecular Classification of Thyroid Nodules Using High-Dimensionality Genomic Data

Chudova D, Kennedy, GC, The Journal of Clinical Endocrinology and Metabolism September 8, 2010

The gut transcriptome of a gall midge, Mayetiola destructor

Zhang, S, Chen, M, Journal of Insect Physiology Volume 56, Issue 9, September 2010, Pages 1198-1206 

Hepatic ISG expression is associated with genetic variation in IL28B and the outcome of IFN therapy for chronic hepatitis C

Honda, M, Kaneko, S, Gastroenterology, Volume 139, Issue 2 , Pages 499-509, August 2010.

Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

Abdueva, D, Davicioni, E, Journal of Molecular Diagnostic, 2010 Jul;12(4):409-17. Epub 2010 Jun 3.

VTA neurons show a potentially protective transcriptional response to MPTP

Phani, S, Iacovitti, L, Brain Research Volume 1343, 9 July 2010, Pages 1-13 

Jarid2 is among a set of genes differentially regulated by Nkx2. 5 during outflow tract morphogenesis

Barth JL, Lee K, Developmental Dynamics Volume 239, Issue 7, pages 2024_2033, July 2010

Circulating osteogenic cells: Characterization and relationship to rates of bone loss in postmenopausal women

Undale, A, Khosla, S, Bone Volume 47, Issue 1, Pages 83-92 (July 2010)

Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis

Buss, SN, Petri, WA, International Journal for Parasitology Volume 40, Issue 7, June 2010, Pages 833-843

Intrinsic response of thoracic propriospinal neurons to axotomy.

Siebert JR, Stelzner DJ, BMC Neuroscience  June 4, 2010, 11:69

Complement receptor 2-CD21-human naive B cells contain mostly autoreactive unresponsive clones

Isnardi I, Meffre E, Blood, 17 June 2010, Vol. 115, No. 24, pp. 5026-5036

Use of peripheral blood mRNA signatures to distinguish colorectal cancer patients from colonoscopy-negative patients.

Xu, Y, Cai, S, Journal of Clinical Oncology Vol 28, No 15_suppl (May 20 Supplement), 2010: 10564

Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells

Stadfeld, M, Hochedlinger, K, Nature 465, 175_181 (13 May 2010)

FIZZ1 potentiates the carbachol-induced tracheal smooth muscle contraction

Chen, H, Bowman, MR, European Respiratory Journal, April 22, 2010

Reversine Enhances Generation of Progenitor-Like Cells by Dedifferentiation of Annulus Fibrosus Cells

Saraiya, M, Risbud, MV, Tissue Engineering 16 Issue 4: April 5, 2010

Low malignant potential tumors with micropapillary features are molecularly similar to low-grade serous carcinoma of the ovary

May, T, Shaw, PA, Gynocologic Oncology Volume 117, Issue 1, April 2010, Pages 9-17 

The Transcription Factor ATF4 Promotes Skeletal Myofiber Atrophy during Fasting

Ebert, S, Adams, CM, Molecular Endocrinology, March 2, 2010

Elevated Tribbles homolog 2_specific antibody levels in narcolepsy patients

Cvetkovic-Lopes, V, Tafti, Mehdi, Journal of Clinical Investigation, 2010 March 1; 120(3): 713_719

Development and characterization of a human articular cartilage-derived chondrocyte cell line that retains chondrocyte phenotype

Hoffman BE, Majumdar MK, Journal of Cellular Physiology Volume 222, Issue 3, pages 695-702, March 2010

Comparison of Microarray Analysis of Fine Needle Aspirates and Tissue Specimen in Thyroid Nodule Diagnosis

Kundel, A, Fahley, TJ, Diagnostic Molecular Pharmacology March 2010 - Volume 19 - Issue 1

Fluorescence Activated Cell Sorting of Plant Protoplasts

Bargmann, B, Birnbaum, KD, Journal of Visualized Experiments 02/18/2010

Regulation of hematopoietic stem cell differentiation by a single ubiquitin ligase-substrate complex

Linsey Reavie, Iannis Aifantis; Nature Immunology, January 17, 2010

Class prediction models of thrombocytosis using genetic biomarkers

Gnatenko, DV, Bahou, WF, Blood, 7 January 2010, Vol. 115, No. 1, pp. 7-14

Research article poolMC: Smart pooling of mRNA samples in microarray experiments

Kainkaryam RM, Woolf, PJ, BMC Bioinformatics 2010, 11:299

Reactivation of adiponectin expression in obese patients after bariatric surgery

Hindle, AK, Brody, F, Surgical Endoscopy Volume 24, Number 6, 1367-1373

Prdm16 promotes stem cell maintenance in multiple tissues, partly by regulating oxidative stress

Chuikov S, Morrison SJ, Nature Cell Biology Volume: 12, 999-1006 (2010)

Long-term dynamic loading improves the mechanical properties of chondrogenic mesenchymal stem cell-laden hydrogel

Huang AH, Mauck, RL, European Cells and Materials, Vol. 19 2010 (pages 72-85)

Identification of Methylmercury Tolerance Gene Candidates in Drosophila

Mahapatra, C, Rand, DM, Toxicological Sciences (2010) 116 (1): 225-238

Global change of gene expression and cell physiology in YidC-depleted E. coli

Wang, P, Dalbey, RE, Journal of Bacteriology 2010

FOG1 requires NuRD to promote hematopoiesis and maintain lineage fidelity within the megakaryocytic_erythroid compartment.

Gregory, GD, Blobel, GA, Blood, 2010; 0: blood-2009-10-251280v1-blood-2009-10-251280

General Features of Certain RNA Populations from Gametes and Cumulus Cells

Payton R, Edward JL, Journal of Reproduction and Development  advpub(0), 1007140289, 2010

Genome response to tissue plasminogen activator in experimental ischemic stroke

Jickling, GC, Sharp, FR, BMC Genomics 2010, 11:254

Differential gene expression profile of retinoblastoma compared to normal retina

Ganguly, A, Shields, CL, Molecular Vision 2010; 16:1292-1303

Determination of Alternate Splicing Events Using the Affymetrix Exon 1.0 ST Arrays.

Subbaram, S, Chittur, SV, Microarray Methods for Drug Discovery, Methods in Molecular Biology, 2010, Volume 632, 63-72

Gene expression profile differences in embryos derived from prepubertal and adult Japanese Black cattle during in vitro development

Dorji, Yukihiro Ohkubo, Kazuchika Miyoshi and Mitsutoshi Yoshida, Reproduction, Fertility and Development 24(2) 370-381

KIF7 mutations cause fetal hydrolethalus and acrocallosal syndromes

Putoux A, Thomas S, Coene KL, Davis EE, Alanay Y, Ogur G, Uz E, Buzas D, Gomes C, Patrier S, Bennett CL, Elkhartoufi N, Frison MH,Rigonnot L, Joye N, Pruvost S, Utine GE, Boduroglu K, Nitschke P, Fertitta L, Thauvin-Robinet C, Munnich A, Cormier-Daire V, Hennekam R,Colin E, Akarsu NA, Bole-Feysot C, Cagnard N, Schmitt A, Goudin N, Lyonnet S, Encha-Razavi F, Siffroi JP, Winey M, Katsanis N, Gonzales M,Vekemans M, Beales PL, Attie-Bitach T. Nature Genetics. 2011 Jun; 43(6):601-6. Epub 2011 May 8. PMID: 21552264

Organelle-nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Tessa M. Burch-Smith, Jacob O. Brunkard, Yoon Gi Choi, and Patricia C. Zambryski. PNAS, December 20, 2011, 108(51): E1451-E1460, doi:10.1073/pnas.1117226108

Evidence for the Complexity of MicroRNA-Mediated Regulation in Ovarian Cancer: A Systems Approach

Shahab SW, Matyunina LV, Mezencev R, Walker LD, Bowen NJ, et al. PLoS ONE, 2011, 6(7): e22508. doi:10.1371/journal.pone.0022508

Single Transcription Factor Reprogramming of Hair Follicle Dermal Papilla Cells to Induced Pluripotent Stem Cells

Tsai, S.-Y., Bouwman, B. A., Ang, Y.-S., Kim, S. J., Lee, D.-F., Lemischka, I. R. and Rendl, M. Stem Cells, 2011, 29: 964-971. doi: 10.1002/stem.649

Cardiomyocyte-Specific Deletion of the Vitamin D Receptor Gene Results in Cardiac Hypertrophy Clinical Perspective

Songcang Chen, Christopher S. Law, Christopher L. Grigsby, Keith Olsen, Ting-Ting Hong, MD, Yan Zhang, MD, Yerem Yeghiazarians, David G. Gardner. Circultation, 2011, doi: 10.1161/CIRCULATIONAHA.111.032680

A Transcriptional Program Promotes Remodeling of GABAergic Synapses in Caenorhabditis elegans

Sarah C. Petersen, Joseph D. Watson, Janet E. Richmond,  Mihail Sarov, Walter W. Walthall, and David M. Miller III. The Journal of Neuroscience, October 2011, 31(43): 15362-15375, doi:10.1523/JNEUROSCI.3181-11.2011

Potential candidate genomic biomarkers of drug induced vascular injury in the rat

Deidre A. Dalmas, Marshall S. Scicchitano, David Mullins, Angela Hughes-Earle, Kay Tatsuoka, Michal Magid-Slav,  Kendall S. Frazier, Heath C. Thomas. Toxicology and Applied Pharmacology, Dec 2011, 257(2): 284-300, 

Distal Airway Stem Cells Yield Alveoli In Vitro and during Lung Regeneration following H1N1 Influenza Infection

Pooja A. Kumar, Yuanyu Hu, Yusuke Yamamoto, Neo Boon Hoe, Tay Seok Wei, Dakai Mu, Yan Sun, Lim Siew Joo, Rania Dagher, Elisabeth M. Zielonka, De Yun Wang, Bing Lim, Vincent T. Chow, Christopher P. Crum, Wa Xian, Frank McKeon. Cell, 28 October 2011, 147(3): 525-538, doi:10.1016/j.cell.2011.10.001

Molecular signature and pathway analysis of human primary squamous and adenocarcinoma lung cancers

Daraselia N, Wang Y, Budoff A, Lituev A, Potapova O, Vansant G, Monforte J, Mazo I, Ossovskaya VS. American Journal of Cancer Research. 2012; 2(1):93-103. Epub 2011 Nov 19. PMID: 22206048, PMCID: PMC3238469

The sphingosine 1-phosphate receptor S1P2 maintains the homeostasis of germinal center B cells and promotes niche confinement

Jesse A Green, Kazuhiro Suzuki, Bryan Cho, L David Willison, Daniel Palmer, Christopher D C Allen, Timothy H Schmidt, Ying Xu, Richard L Proia, Shaun R Coughlin & Jason G Cyster. Nature Immunology, 2011, 12: 672-680, doi:10.1038/ni.2047

Inhibition of RPE cell sterile inflammatory responses and endotoxin-induced uveitis by a cell-impermeable HSP90 inhibitor

Qin S, Ni M, Wang X, Maurier-Mahe F, Shurland DL, Rodrigues GA. Experimental Eye Research. 2011 Dec; 93(6):889-97. Epub 2011 Oct 18. PMID: 22019372

Neuroglobin-Deficiency Exacerbates Hif1A and c-FOS Response, but Does Not Affect Neuronal Survival during Severe Hypoxia In Vivo

Hundahl CA, Luuk H, Ilmjarv S, Falktoft B, Raida Z, et al. PLoS ONE, 2011, 6(12): e28160. doi:10.1371/journal.pone.0028160

FOG-1 and GATA-1 act sequentially to specify definitive megakaryocytic and erythroid progenitors

Mancini E, Sanjuan-Pla A, Luciani L, Moore S, Grover A, Zay A, Rasmussen KD, Luc S, Bilbao D, O'Carroll D, Jacobsen SE, Nerlov C. EMBO Journal. 2011 Nov 8; 31(2):351-65. doi: 10.1038/emboj.2011.390. PMID:22068055, PMCID: PMC3261555

Epigenetic Mechanisms of Groucho/Grg/TLE Mediated Transcriptional Repression

Sanjeevkumar R. Patel, Samina S. Bhumbra, Raghavendra S. Paknikar, Gregory R. Dressler. Molecular Cell, 2011, 45(2): 185-195, doi: 10.1016/j.molcel.2011.11.007

Systems biology of vaccination for seasonal influenza in humans

Helder I Nakaya, Jens Wrammert, Eva K Lee, Luigi Racioppi, Stephanie Marie-Kunze, W Nicholas Haining, Anthony R Means, Sudhir P Kasturi, Nooruddin Khan, Gui-Mei Li, Megan McCausland, Vibhu Kanchan, Kenneth E Kokko, Shuzhao Li, Rivka Elbein, Aneesh K Mehta, Alan Aderem, Kanta Subbarao, Rafi Ahmed & Bali Pulendran. Nature Immunology, 2011, 12, 786-795, doi:10.1038/ni.2067

Profiles of lacunar and nonlacunar stroke

Jickling GC, Stamova B, Ander BP, Zhan X, Tian Y, Liu D, Xu H, Johnston SC, Verro P, Sharp FR. Annals of Neurology. 2011 Sep; 70(3):477-85. doi: 10.1002/ana.22497. Epub 2011 Jul 27. PMID: 21796664, PMCID: PMC3201749

Human MAIT and CD8aa cells develop from a pool of type-17 pre-committed CD8+ T cells

Lucy J. Walker, Yu-Hoi Kang, Matthew O. Smith, Hannah Tharmalingham, Narayan Ramamurthy, Vicki M. Fleming, Natasha Sahgal, Alistair Leslie, Ye Oo, Alessandra Geremia, Thomas J. Scriba, Willem A. Hanekom, Georg M. Lauer, Olivier Lantz, David H. Adams, Fiona Powrie, Eleanor Barnes and Paul Klenerman. Blood, January 12, 2012, 119(2): 422-433; doi:10.1182/blood-2011-05-353789

Osteogenic effects of a potent Src-over-Abl-selective kinase inhibitor in the mouse

Murrills RJ, Fukayama S, Boschelli F, Matteo JJ, Owens J, Golas JM, Patel D, Lane G, Liu YB, Carter L, Jussif J, Spaulding V, Wang YD,Boschelli DH, McKew JC, Li XJ, Lockhead S, Milligan C, Kharode YP, Diesl V, Bai Y, Follettie M, Bex FJ, Komm B, Bodine PV. Journal of Pharmacology Experimental Therapeutics. 2012 Mar; 340(3):676-87. Epub 2011 Dec 9. PMID: 22171089

Regulation of behavioral plasticity by systemic temperature signaling in Caenorhabditis elegans

Takuma Sugi, Yukuo Nishida & Ikue Mori. Nature Neuroscience, 2011, 14:984-992; doi:10.1038/nn.2854

Perivascular Human Endometrial Mesenchymal Stem Cells Express Pathways Relevant to Self-Renewal, Lineage Specification, and Functional Phenotype

Trimble L.B. Spitzer, Angela Rojas, Zara Zelenko, Lusine Aghajanova, David W. Erikson, Fatima Barragan, Michelle Meyer, John S. Tamaresis, Amy E. Hamilton, Juan C. Irwin and Linda C. Giudice. Biology of Reproduction, Feb  2012,  vol. 86 no. 2 58; doi: 10.1095/ biolreprod.111.095885 

Functional heterogeneity of human effector CD8 T cells

Takata H, Naruto T, Takiguchi M. Blood. 2012 Feb 9; 119(6):1390-8. Epub 2011 Dec 14. PMID: 22174157

Transient ischemic attacks characterized by RNA profiles in blood

Zhan X, Jickling GC, Tian Y, Stamova B, Xu H, Ander BP, Turner RJ, Mesias M, Verro P, Bushnell C, Johnston SC, Sharp FR. Neurology. 2011 Nov 8; 77(19):1718-24. Epub 2011 Oct 12. PMID: 21998319

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

Massimiliano Caiazzo, Maria Teresa Dell'Anno, Elena Dvoretskova, Dejan Lazarevic, Stefano Taverna, Damiana Leo, Tatyana D. Sotnikova, Andrea Menegon, Paola Roncaglia, Giorgia Colciago, Giovanni Russo, Piero Carninci, Gianni Pezzoli, Raul R. Gainetdinov, Stefano Gustincich, Alexander Dityatev & Vania Broccoli. Nature. August 2011, 476: 224-227, doi:10.1038/nature10284

Programming the magnitude and persistence of antibody responses with innate immunity

Sudhir Pai Kasturi, Ioanna Skountzou, Randy A. Albrecht, Dimitrios Koutsonanos, Tang Hua, Helder I. Nakaya, Rajesh Ravindran, Shelley Stewart, Munir Alam, Marcin Kwissa, Francois Villinger, Niren Murthy, John Steel, Joshy Jacob, Robert J. Hogan, Adolfo Garcia-Sastre, Richard Compans & Bali Pulendran. Nature. February 2011; 470, 543-547.doi:10.1038/nature09737

Peritoneal macrophages are distinct from monocytes and adherent macrophages

Krithika Selvarajan, Leni Moldovan, Aluganti Narasimhulu Chandrakala, Dmitry Litvinov, Sampath Parthasarathy. Atherosclerosis. 2011 Dec; 219(2):475-83. doi:10.1016/j.atherosclerosis.2011.09.014

Transcriptomic analyses of murine resolution-phase macrophages.

Melanie J. Stables, Sonia Shah, Evelyn B. Camon, Ruth C. Lovering, Justine Newson, Jonas Bystrom, Stuart Farrow, and Derek W. Gilroy. Blood, October 19, 2011; doi: 10.1182/blood-2011-04-345330. Published online: October 19, 2011

AML1/RUNX1 functions as a cytoplasmic attenuator of NF-kB signaling in the signaling in the repression of myeloid tumors

Masahiro Nakagawa, Munetake Shimabe, Naoko Watanabe-Okochi, Shunya Arai, Akihide Yoshimi, Akihito Shinohara, Nahoko Nishimoto, Keisuke Kataoka, Tomohiko Sato, Keiki Kumano, Yasuhito Nannya, Motoshi Ichikawa, Yoichi Imai, and Mineo Kurokawa. Blood, December 15, 2011 vol. 118 no. 256626-6637. doi: 10.1182/blood-2010-12-326710. Published online: October 21, 2011

Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue

Richard D. Kennedy, Max Bylesjo, Peter Kerr, Timothy Davison, Julie M. Black, Elaine W. Kay, Robert J. Holt, Vitali Proutski,Miika Ahdesmaki, Vadim Farztdinov, Nicolas Goffard,  Peter Hey, Fionnuala McDyer, Karl Mulligan, Julie Mussen, Eamonn O'Brien, Gavin Oliver, Steven M. Walker, Jude M. Mulligan, Claire Wilson, Andreas Winter, Diarmuid O'Donoghue, Hugh Mulcahy, Jacintha O'Sullivan, Kieran Sheahan, John Hyland, Rajiv Dhir, Oliver F. Bathe, Ola Winqvist, Upender Manne, Chandrakumar Shanmugam, Sridhar Ramaswamy, Eduardo J. Leon, William I. Smith Jr, Ultan McDermott, Richard H. Wilson, Daniel Longley, John Marshall, Robert Cummins, Daniel J. Sargent, Patrick G. Johnston and D. Paul Harkin. Journal of Clinical Oncology 2011.35.4498. doi:10.1200/JCO.2011.35.4498JCO. Published online: November 7, 2011

Molecular discrimination of cutaneous squamous cell carcinoma from actinic keratosis and normal skin

Seong Hui Ra, Xinmin Li and Scott Binder. Modern Pathology 24, 963-973; July 2011; doi:10.1038/modpathol.2011.39

Roles of Beta-catenin signaling in phenotypic expression and proliferation of articular cartilage superficial zone cells

Yasuhara R, Ohta Y, Yuasa T, Kondo N, Hoang T, Addya S, Fortina P, Pacifici M, Iwamoto M, Enomoto-Iwamoto M. Laboratory Investigation. 2011 Dec;91(12):1739-52. doi: 10.1038/labinvest.2011.144. Epub 2011 Oct 3. PMID: 21968810

Ossifying Fibromyxoid Tumor of Soft Parts: A Clinicopathologic, Proteomic, and Genomic Study

Graham RP, Dry S, Li X, Binder S, Bahrami A, Raimondi SC, Dogan A, Chakraborty S, Souchek JJ, Folpe AL. The American Journal of Surgical Pathology, 2011 Nov;35(11):1615-25. PMID:21997683; PMCID: PMC3193600

Changes in transcriptional output of human peripheral blood mononuclear cells following resistance exercise

Carlson LA, Tighe SW, Kenefick RW, Dragon J, Westcott NW, Leclair RJ. European Journal of Applied Physiology. 2011 Dec;111(12):2919-29. Epub 2011 Mar 25.

Mammary Gland Morphological and Gene Expression Changes Underlying Pregnancy Protection of Breast Cancer Tumorigenesis

Yogi Misra, Pamela A. Bentley, Jeffrey P. Bond, Scott Tighe, Timothy Hunter, and Feng-Qi Zhao. Physiol. Genomics, January 1, 2012 vol. 44 no. 1 76-88. doi:10.1152/physiolgenomics.00056.2011. Published online before print November 15, 2011

Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

Xu Q, Ni S, Wu F, Liu F, Ye X, et al. PLoS ONE 6(10): e26905. 2011. doi:10.1371/journal.pone.0026905

Transcriptional responses to loss or gain of function of the leucine-rich repeat kinase 2 (LRRK2) gene uncover biological processes modulated by LRRK2 activity

Elena V. Nikonova, Yulan Xiong, , Keith Q. Tanis, Valina L. Dawson, Robert L. Vogel, Eva M. Finney, David J. Stone, Ian J. Reynolds, Jonathan T. Kern and Ted M. Dawson. Human Molecular Genetics, 2011.  doi: 10.1093/hmg/ddr451. First published online: October 4, 2011

Whole genome RNA expression profiling of endoscopic biliary brushings provides data suitable for biomarker discovery in cholangiocarcinoma

Chapman MH, Tidswell R, Dooley JS, Sandanayake NS, Cerec V, Deheragoda M, Lee AJ, Swanton C, Andreola F, Pereira SP. J Hepatol. 2012 Apr;56(4):877-85. Published online 14 December 2011.

Importance of Correlation between Gene Expression Levels: Application to the Type I Interferon Signature in Rheumatoid Arthritis

Reynier F, Petit F, Paye M, Turrel-Davin F, Imbert PE, Hot A, Mougin B, Miossec P. PLoS One. 2011;6(10):e24828. Epub 2011 Oct 17. PMID: 22043277; PMCID: PMC3197194

Sustained axon regeneration induced by co-deletion of PTEN and SOCS3

Fang Sun, Kevin K. Park, Stephane Belin, Dongqing Wang, Tao Lu, Gang Chen, Kang Zhang, Cecil Yeung, Guoping Feng, Bruce A. Yankner & Zhigang He. Nature 480, 372-375; 15 December 2011. doi:10.1038/nature10594

Gene Expression Analysis of Whole Blood, Peripheral Blood Mononuclear Cells, and Lymphoblastoid Cell Lines from the Framingham Heart Study

Roby Joehanes, Andrew Danner Johnson, Jennifer Joanna Barb, Nalini Raghavachari, Poching Liu, Kimberly Ann Woodhouse, Christopher Joseph O'Donnell, Peter J. Munson, and Daniel Levy. Physiological Genomics, November 1, 2011. doi: 10. 1152/ physiolgenomics. 00130. 2011

Gene expression in accumbens GABA neurons from inbred rats with different drug-taking behavior

B. M. Sharp, H. Chen, S. Gong, X. Wu, Z. Liu, K. Hiler, W. L. Taylor, S. G. Matta. Genes, Brain and Behavior, October 2011. 10(7): 778-788. doi: 10.1111/j.1601-183X.2011.00716.x. First published online: 1 August 2011.

Directed Conversion of Alzheimer's Disease Patient Skin Fibroblasts into Functional Neurons

Liang Qiang, Ryousuke Fujita, Toru Yamashita, Sergio Angulo, Herve Rhinn, David Rhee, Claudia Doege, Lily Chau, Laetitia Aubry, William B. Vanti, Herman Moreno, Asa Abeliovich. Cell. 5 August 2011, Vol. 146, Issue 3, pp. 359-371. doi: 10.1016/j.cell.2011.07.007

Transcriptome Analysis of Epithelial and Stromal Contributions to Mammogenesis in Three Week Prepartum Cows

Casey T, Dover H, Liesman J, DeVries L, Kiupel M, et al. PLoS ONE 6(7): e22541. 2011. doi:10.1371/journal.pone.0022541

Comparative Transcriptome Analysis of Human Trophectoderm and Embryonic Stem Cell-Derived Trophoblasts Reveal Key Participants in Early Implantation

Aghajanova L, Shen S, Rojas AM, Fisher SJ, Irwin JC, Giudice LC; Biol Reprod. 2012 Jan 16;86(1):1-21. Print 2012 Jan.

Rational Design of Therapeutic siRNAs: Minimizing Off-targeting Potential to Improve the Safety of RNAi Therapy for Huntington's Disease

Ryan L Boudreau, Ryan M Spengler and Beverly L Davidson. Molecular Therapy 19, 2169-2177 (December 2011) | doi:10.1038 mt.2011.185

Genetics of Sputum Gene Expression in Chronic Obstructive Pulmonary Disease

Qiu W, Cho MH, Riley JH, Anderson WH, Singh D, et al. 2011 PLoS ONE 6(9): e24395. doi:10.1371/journal.pone.0024395

Lineage-committed osteoclast precursors circulate in blood and settle down into bone

Akinori Muto, Toshihide Mizoguchi, Nobuyuki Udagawa, Susumu Ito, Ichiro Kawahara, Yoshimitsu Abiko, Atsushi Arai, Suguru Harada, Yasuhiro Kobayashi, Yuko Nakamichi, Josef M Penninger, Toshihide Noguchi, Naoyuki Takahashi PhD, Article first published online: 21 NOV 2011DOI: 10.1002/jbmr.490

Splice variants of tissue factor promote monocyte endothelial interactions by triggering the expression of cell adhesion molecules via integrin mediated signaling

R. SRINIVASAN, E. OZHEGOV, Y. W. VAN DEN BERG, B. J. ARONOW, R. S. FRANCO, M. B. PALASCAK, J. T. FALLON, W. RUF, H.H. VERSTEEG, V.Y. BOGDANOV Article first published online: 29 SEP 2011 DOI: 10.1111/j.1538-7836.2011.04454.x

CD140a identifies a population of highly myelinogenic, migration-competent and efficiently engrafting human oligodendrocyte progenitor cells

Fraser J Sim, Crystal R McClain, Steven J Schanz, Tricia L Protack, Martha S Windrem & Steven A Goldman Nature Biotechnology Volume: 29, 934-941 (2011) doi:10.1038/nbt.1972. Published online September 25, 2011

Genes and pathways affected by CAG-repeat RNA-based toxicity in Drosophila

Shin-Yi Shieh, Nancy M Bonini; Hum. Mol. Genet. (2011) doi: 10.1093/hmg/ddr420; First published online: September 20, 2011 

Distinct Populations of Hepatic Stellate Cells in the Mouse Liver Have Different Capacities for Retinoid and Lipid Storage

D'Ambrosio DN, Walewski JL, Clugston RD, Berk PD, Rippe RA, et al. 2011 . PLoS ONE 6(9): e24993. doi:10.1371/journal.pone.0024993. Published September 16, 2011 

Molecular profiling and gene expression analysis in cutaneous sarcoidosis: The role of interleukin-12, interleukin-23, and the T-helper 17 pathway

Marc A. Judson, Richard M. Marchell, MaryAnn Mascelli, Alexa Piantone, Elliot S. Barnathan, Kevin J. Petty, Dion Chen, Hongtao Fan, Heidi Grund, Keying Ma, Frederic Baribaud, Carrie Brodmerkel,  Journal of the American Academy of Dermatology, Available online 15 September 2011, ISSN 0190-9622, 10.1016/j.jaad.2011.06.017.

Crx broadly modulates the pineal transcriptome

Louise Rovsing, Samuel Clokie, Diego M. Bustos, Kristian Rohde, Steven L. Coon, Thomas Litman, Martin F. Rath, Morten Moller, David C. Klein Journal of Neurochemistry Volume 119, Issue 2, pages 262-274, October 2011. Article first published online: Sept 2, 2011

Overexpression of Cloned RhsA Sequences Perturbs the Cellular Translational Machinery in Escherichia coli

Aggarwal K, Lee KH. J Bacteriol. 2011 Sep; 193(18):4869-80. Epub 2011 Jul 15. PubMed PMID: 21764923; PubMed Central PMCID: PMC3165670.

Regulation of Gene Expression in Ovarian Cancer Cells by Luteinizing Hormone Receptor Expression and Activation

Juan Cui, Brooke M Miner, Joanna B Eldredge, Susanne W Warrenfeltz, Phuongan Dam, Ying Xu. Cui et al. BMC Cancer 2011, 11:280

Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-1-Associated Neurocognitive Disorders

Borjabad A, Morgello S, Chao W, Kim S-Y, Brooks AI, et al. 2011 PLoS Pathog 7(9): e1002213. doi:10.1371/journal.ppat.1002213

Gene Expression Analysis of the Embryonic Subplate

Franziska M. Oeschger, Wei-Zhi Wang, Sheena Lee, Fernando Garcia-Moreno, Andre M. Goffinet, Maria L. Arbones, Sonja Rakic and Zoltan Molnar, Cereb. Cortex (2011) doi: 10.1093/cercor/bhr197, August 22, 2011

Gene Expression Differences in Oocytes Derived From Adult and Prepubertal Japanese Black Cattle during In Vitro Maturation

Dorji , Y Ohkubo, K Miyoshi, M Yoshida Article first published online: 22 AUG 2011 DOI: 10.1111/j.1439-0531.2011.01887.x

Genome-wide gene expression profiling of nucleus accumbens neurons projecting to ventral pallidum using both microarray and transcriptome sequencing

Chen H, Liu Z, Gong S, Wu X, Taylor WL, Williams RW, Matta SG and Sharp BM (2011). Front. Neurosci. 5:98. doi: 10.3389/fnins.2011.00098

Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Charissa de Bekker, Oskar Bruning, Martijs J Jonker, Timo M Breit and Han AB Wosten. Genome Biology 2011, 12:R71 doi:10.1186/gb-2011-12-8-r71 Published: 4 August 2011

Association between c-myc amplification and pathological complete response to neoadjuvant chemotherapy in breast cancer

Yasojima H, Shimomura A, Naoi Y, Kishi K, Baba Y, Shimazu K, Nakayama T, Kim SJ, Tamaki Y, Noguchi S. Eur J Cancer. 2011 Aug;47(12):1779-88. Epub 2011 Jul 7.

Microarray analyses of laser-captured hippocampus reveal distinct gray and white matter signatures associated with incipient Alzheimer's disease

Blalock EM, Buechel HM, Popovic J, Geddes JW, Landfield PW. J Chem Neuroanat. 2011 Oct;42(2):118-26. Epub 2011 Jul 2.

Non-Invasive Genomic Detection of Melanoma

Wachsman W, Chang S, British Journal of Dermatology Volume 164, Issue 4, pages 797-806, April 2011

Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression

Wartman L, Ley T, J Clin Invest. 2011 Mar 23. pii: 45284. doi: 10.1172/JCI45284. [Epub ahead of print]

A Unique Hybrid Renal Mononuclear Phagocyte Activation Phenotype in Murine Systemic Lupus Erythematosus Nephritis

Bethunaickan R, Davidson A, J Immunol. 2011 Apr 15;186(8):4994-5003. Epub 2011 Mar 16.

Highly Activated Cytotoxic CD8 T Cells Express Protective IL-10 at the Peak of Coronavirus-Induced Encephalitis

Trandem K, Perlman S, J Immunol. 2011 Mar 15;186(6):3642-52. Epub 2011 Feb 11.

Inositol 1, 4, 5-trisphosphate receptors are essential for the development of the second heart field

Nakazawa M, Yamagishi H, J Mol Cell Cardiol. 2011 Mar 5. [Epub ahead of print]

Modelling asthma in macaques: longitudinal changes in cellular and molecular markers

Ayanoglu G, Wardle R, Eur Respir J. 2011 Mar;37(3):541-52. Epub 2010 Jul 22.

NKp46 identifies an NKT cell subset susceptible to leukemic transformation in mouse and human

Yu J, Caliguiri M, J Clin Invest. 2011 Mar 1. pii: 43242. doi: 10.1172/JCI43242. [Epub ahead of print]

Rara haploinsufficiency modestly influences the phenotype of acute promyelocytic leukemia in mice

Welch J, Ley T, Blood. 2011 Feb 24;117(8):2460-8. Epub 2010 Dec 29.

A spatial and temporal map of C. elegans gene expression

Spencer W, Miller D, Genome Res. 2011 Feb;21(2):325-41. Epub 2010 Dec 22.

Differential gene expression profiles of neurothekeomas and nerve sheath myxomas by microarray analysis

Sheth S, Dry S, Mod Pathol. 2011 Mar;24(3):343-54. Epub 2011 Feb 4.

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Novershtern N, Regev A, Cell. 2011 Jan 21;144(2):296-309.

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Mahoney S, Gifford D, Genome Biol. 2011 Jan 13;12(1):R2. [Epub ahead of print]

Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans

Hallem E, Ringstad N, Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):254-9. Epub 2010 Dec 20.

Altered mRNA expression after long_term soleus electrical stimulation training in humans with paralysis

Adams C, Shields R, Muscle & Nerve, Volume 43, Issue 1, pages 65-75, January 2011

Transient Enhanced IL-2R Signaling Early during Priming Rapidly Amplifies Development of Functional CD8+ T Effector-Memory Cells

Iris Castro, Michael J. Dee and Thomas R. Malek, The Journal of Immunology November 1, 2012 vol. 189 no. 9 4321-4330

Retinoblastoma treatment: impact of the glycolytic inhibitor 2-deoxy-d-glucose on molecular genomics expression in LHBETATAG retinal tumors

Yolanda Pina, Samuel K Houston, Timothy G Murray, Tulay Koru-Sengu, Christina Decatur, William K Scott, Lubov Nathanson, Jennifer Clarke, and Theodore J Lampidis, Clin Ophthalmol. 2012; 6: 817-830. Published online 2012 May 29. doi:  10.2147/OPTH.S29688

Repression of bacterial lipoprotein production by Francisella novicida facilitates evasion of innate immune recognition

Crystal L. Jones, Timothy R. Sampson, Helder I. Nakaya, Bali Pulendran, David S. Weiss, Cellular Microbiology, Volume 14, Issue 10, pages 1531-1543, October 2012

Probiotic Interference of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 with the Opportunistic Fungal Pathogen Candida albicans

Gerwald A. Kohler, Senait Assefa, and Gregor Reid, Infectious Diseases in Obstetrics and GynecologyVolume 2012 (2012), Article ID 636474, 14 pagesdoi:10.1155/2012/636474

Posttranscriptional Regulation of Cell-Cell Interaction Protein-Encoding Transcripts by Zfs1p in Schizosaccharomyces pombe

Melissa L. Wells, Weichun Huang, Leping Li, Kevin E. Gerrish, David C. Fargo, Fatih Ozsolak and Perry J. Blackshear, Mol. Cell. Biol. October 2012 vol. 32 no. 20 4206-4214

Myocardial Alternative RNA Splicing and Gene Expression Profiling in Early Stage Hypoplastic Left Heart Syndrome

Marco Ricci, Yanji Xu, Harriet L. Hammond, David A. Willoughby, Lubov Nathanson, Maria M. Rodriguez, Matteo Vatta, Steven E. Lipshultz, Joy Lincoln, PLoS ONE 7(1): e29784. doi:10.1371/journal.pone.0029784

Microfluidics separation reveals the stem-cell–like deformability of tumor-initiating cells

Weijia Zhang, Kazuharu Kai, Dong Soon Choi, Takayuki Iwamoto, Yen H. Nguyen, Helen Wong, Melissa D. Landis, Naoto T. Ueno, Jenny Chang and Lidong Qin, PNAS November 13, 2012 vol. 109 no. 46 18707-18712

Microarray-Based Gene Profiling Analysis of Muller Glia-Derived Retinal Stem Cells in Light-Damaged Retinas from Adult Zebrafish

Zhao Qin, Pamela A. Raymond, Retinal Development, Methods in Molecular BiologyVolume 884, 2012, pp 255-261

Phosphorylation of serine 212 confers novel activity to human estrogen receptor?

Sawako Shindo, Tsutomu Sakuma1, Masahiko Negishi, James Squires, Steroids, Volume 77, Issue 5, April 2012, Pages 448-453

Differentiation of small bowel and pancreatic neuroendocrine tumors by gene-expression profiling

Jennifer C. Carr, Erin A. Boese, Philip M. Spanheimer, Fadi S. Dahdaleh, Molly Martin, Daniel Calva, Blanca Schafer, David M. Thole, Terry Braun, Thomas M. O'Dorisio, M. Sue O'Dorisio, James R. Howe, Surgery. 2012 Dec;152(6):998-1007. doi: 10.1016/j.surg.2012.08.040.

Expression Profiling of Archival Tumors for Long-term Health Studies

Levi Waldron, Shuji Ogino, Yujin Hoshida, Kaori Shima, Amy E. McCart Reed, Peter T. Simpson, Yoshifumi Baba, Katsuhiko Nosho, Nicola Segata, Ana Cristina Vargas, Margaret C. Cummings, Sunil R. Lakhani, Gregory J. Kirkner, Edward Giovannucci, John Quackenbush, Todd R. Golub, Charles S. Fuchs, Giovanni Parmigiani, and Curtis Huttenhower, Clin Cancer Res November 15, 2012 18; 6136, Published OnlineFirst November 7, 2012; doi: 10.1158/1078-0432.CCR-12-1915

Correlations of gene expression with ratings of inattention and hyperactivity/impulsivity in tourette syndrome: a pilot study

Yingfang Tian, Boryana Stamova, Bradley P Ander, Glen C Jickling, Joan R Gunther, Blythe A Corbett, Netty GP Bos-Veneman, Pieter J Hoekstra, Julie B Schweitzer and Frank R Sharp, BMC Medical Genomics 2012, 5:49 doi:10.1186/1755-8794-5-49

Gene and protein expression signature of endometrial glandular and stromal compartments during the window of implantation

Gloria E. Evans, Jose A. Martinez-Conejero, Gregory T.M. Phillipson, Carlos Simon, Les A. McNoe, Peter H. Sykes, Jose A.Horcajadas, Enid Y.N. Lam, Cristin G. Print, Iris L. Sin, John J. Evans, Fertility and Sterility, Volume 97, Issue 6, June 2012, Pages 1365–1373.e2"

Lentiviral Vector Induced Insertional Haploinsufficiency of Ebf1 Causes Murine Leukemia

Dirk Heckl, Adrian Schwarzer, Reinhard Haemmerle, Doris Steinemann, Cornelia Rudolph, Britta Skawran, Sabine Knoess, Johanna Krause, Zhixiong Li, Brigitte Schlegelberger, Christopher Baum and Ute Modlich, Molecular Therapy (2012); 20 6, 1187–1195. doi:10.1038/mt.2012.59

Implications for Powering Biomarker Discovery Studies

Sian M. Dibben, Robert J. Holt, Timothy S. Davison, Claire L. Wilson, Janet Taylor, Ian Paul, Kieran McManus, Paul J. Kelly, Vitali Proutski, D. Paul Harkin, Peter Kerr, Dean A. Fennell, Jacqueline A. James, Richard D. Kennedy, The Journal of Molecular Diagnostics, Volume 14, Issue 2, March–April 2012, Pages 130–139

Differential gene expression profiling of primary cutaneous melanoma and sentinel lymph node metastases

Stephen S Koh, Jia-Perng J Wei, Xinmin Li, Rong R Huang, Ngan B Doan, Richard A Scolyer, Alistair J Cochran and Scott W Binder, Modern Pathology (2012) 25, 828-837; doi:10.1038/modpathol.2012.32; published online 9 March 2012

Integrated analysis of mRNA and microRNA expression in mature neurons, neural progenitor cells and neuroblastoma cells

Da-Zhi Liu, Bradley P. Ander, Yingfang Tian, Boryana Stamova, Glen C. Jickling, Ryan R. Davis, Frank R. Sharp, Gene, Volume 495, Issue 2, 10 March 2012, Pages 120–127

Gene expression analysis of whole blood, peripheral blood mononuclear cells, and lymphoblastoid cell lines from the Framingham Heart Study

Roby Joehanes, Andrew D. Johnson, Jennifer J. Barb, Nalini Raghavachari, Poching Liu, Kimberly A. Woodhouse, Christopher J. O'Donnell, Peter J. Munson, and Daniel Levy, Physiol. Genomics January 1, 2012 vol. 44 no. 1 59-75

Analytical performance verification of a molecular diagnostic for cytology-indeterminate thyroid nodules

P. Sean Walsh, Jonathan I. Wilde, Edward Y. Tom, Jessica D. Reynolds, Daphne C. Chen, Darya I. Chudova, Moraima Pagan, Daniel G. Pankratz, Mei Wong, James Veitch, Lyssa Friedman, Robert Monroe, David L. Steward, Mark A. Lupo, Richard B. Lanman and Giulia C. Kennedy, The Journal of Clinical Endocrinology & Metabolism December 1, 2012 vol. 97 no. 12 E2297-E2306, Published online before print October 18, 2012, doi: 10.1210/jc.2012-1923

Molecular signature and pathway analysis of human primary squamous and adenocarcinoma lung cancers

Nikolai Daraselia, Yipeng Wang, Adam Budoff, Alexander Lituev, Olga Potapova, Gordon Vansant, Joseph Monforte, Ilya Mazo, and Valeria S Ossovskaya; Am J Cancer Res. 2012; 2(1): 93–103. Published online 2011 November 19.

DBA-Lectin Reactivity Defines Mouse Uterine Natural Killer Cell Subsets with Biased Gene Expression

Zhilin Chen, Jianhong Zhang, Kota Hatta, Patricia D.A. Lima, Hakim Yadi, Francesco Colucci, Aureo T. Yamada and B. Anne Croy; Published online before print August 8, 2012, doi: 10.1095/?biolreprod.112.102293 Biology of Reproduction August 8, 2012 biolreprod.112.102293

Characterization of Circulating Endothelial Cells in Acute Myocardial Infarction

S. Damani, A. Bacconi, O. Libiger, A. H. Chourasia, R. Serry, R. Gollapudi, R. Goldberg, K. Rapeport, S. Haaser, S. Topol, S. Knowlton, K. Bethel, P. Kuhn, M. Wood, B. Carragher, N. J. Schork, J. Jiang, C. Rao, M. Connelly, V. M. Fowler, E. J. Topol; Sci. Transl. Med. 4, 126ra33 (2012)

Pre-B cell leukemia homeobox 1 is associated with lupus susceptibility in mice and humans

Carla M. Cuda, Shiwu Li, Shujuan Liang, Yiming Yin, Hari Hara S. K. Potula, Zhiwei Xu, Mayami Sengupta, Yifang Chen, Edward Butfiloski, Henry Baker, Lung-Ji Chang, Igor Dozmorov, Eric S. Sobel and Laurence Morel; Published online before print December 16, 2011, doi: 10.4049/?jimmunol.1002362 The Journal of Immunology January 15, 2012 vol. 188 no. 2 604-614

Single-stranded microRNA mimics

Guillaume Chorn, Molly Klein-McDowell, Lihong Zhao, Matthew A. Saunders, W. Michael Flanagan, Aarron T. Willingham and Lee P. Lim;Published in Advance August 21, 2012, doi: 10.1261/rna.031278.111 RNA 2012. 18: 1796-1804

IL-2 Receptor Signaling Is Essential for the Development of Klrg1+ Terminally Differentiated T Regulatory Cells

Guoyan Cheng, Xiaomei Yuan, Matthew S. Tsai, Eckhard R. Podack, Aixin Yu and Thomas R. Malek; Published online before print July 11, 2012, doi: 10.4049/?jimmunol.1103768 The Journal of Immunology August 15, 2012 vol. 189 no. 4 1780-1791

A metabolic prosurvival role for PML in breast cancer

Arkaitz Carracedo, Dror Weiss, Amy K. Leliaert, Manoj Bhasin, Vincent C.J. de Boer, Gaelle Laurent, Andrew C. Adams, Maria Sundvall, Su Jung Song, Keisuke Ito, Lydia S. Finley, Ainara Egia, Towia Libermann, Zachary Gerhart-Hines, Pere Puigserver, Marcia C. Haigis, Elefteria Maratos-Flier, Andrea L. Richardson, Zachary T. Schafer, and Pier P. Pandolfi; J Clin Invest. 2012;122(9):3088–3100. doi:10.1172/JCI62129

Motor axon exit from the mammalian spinal cord is controlled by the homeodomain protein Nkx2. 9 via Robo-Slit signaling

Arlene Bravo-Ambrosio, Grant Mastick and Zaven Kaprielian; Posted online before print March 7, 2012, doi: 10.1242/dev.072256 April 15, 2012 Development 139, 1435-1446.

Temporal Network Based Analysis of Cell Specific Vein Graft Transcriptome Defines Key Pathways and Hub Genes in Implantation Injury

Bhasin M, Huang Z, Pradhan-Nabzdyk L, Malek JY, LoGerfo PJ, et al. (2012) PLoS ONE 7(6): e39123. doi:10.1371/journal.pone.0039123

Cross-Species Transcriptional Network Analysis Defines Shared Inflammatory Responses in Murine and Human Lupus Nephritis

Celine C. Berthier, Ramalingam Bethunaickan, Tania Gonzalez-Rivera, Viji Nair, Meera Ramanujam, Weijia Zhang, Erwin P. Bottinger, Stephan Segerer, Maja Lindenmeyer, Clemens D. Cohen, Anne Davidson and Matthias Kretzler; Published online before print June 20, 2012, doi: 10.4049/?jimmunol.1103031 The Journal of Immunology July 15, 2012 vol. 189 no. 2 988-1001

Expression Profiling of Hereditary versus Sporadic Prostate Cancer Suggests CYR61, EGR3, KLF6 and SNF1LK as Differentially Expressed Genes

D. Nguyen Bentzon, M. Morck Mortensen, T. Orntoft, L. Dyrskjot and M. Borre; Open Journal of Urology, Vol. 2 No. 2, 2012, pp. 55-66. doi: 10.4236/oju.2012.22010

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells

Micah J. Benson, Tarmo Aijo, Xing Chang, John Gagnon, Utz J. Pape, Vivek Anantharaman, L. Aravind, Juha-Pekka Pursiheimo, Shalini Oberdoerffer, X. Shirley Liu, Riitta Lahesmaa, Harri Lähdesmäki and Anjana Rao; Published online before print September 18, 2012, doi: 10.1073/pnas.1214414109 PNAS September 18, 2012

Vascular disrupting activity and the mechanism of action of EHT 6706, a novel anticancer tubulin polymerization inhibitor

Anne-Sophie Belzacq-Casagrande, Florence Bachelot, Catherine De Oliveira, Severine Coutadeur, Florence Maurier-Mahe, Emeline Throo, Cedric Chauvignac, Laure Pognante, Angelique Petibon, Thierry Taverne, Investigational New Drugs April 2013, Volume 31, Issue 2, pp 304-319

Multiple sclerosis-linked and interferon-beta-regulated gene expression in plasmacytoid dendritic cells

Latt Latt Aung, Andrew Brooks, Steven A. Greenberg, Michael L. Rosenberg, Suhayl Dhib-Jalbut, Konstantin E. Balashov; Journal of Neuroimmunology 15 September 2012 Vol. 250, Issue 1, Pages 99-105, DOI: 10.1016/j.jneuroim.2012.05.013

Global Identification of New Substrates for the Yeast Endoribonuclease, RNase Mitochondrial RNA Processing (MRP)

Jason Aulds, Sara Wierzbicki, Adrian McNairn and Mark E. Schmitt; Journal of Biological Chemistry September 12, 2012, doi: 10.1074 jbc.M112.389023

Impact of lactobacilli on orally acquired listeriosis

Cristel Archambaud, Marie-Anne Nahoria, Guillaume Soubigoud, Christophe Becavina, Laure Lavale, Pierre Lechatg, Tamara Smokvinaf, Philippe Langellae, Marc Lecuith, and Pascale Cossarta; Published online before print September 24, 2012, doi: 10.1073/pnas.1212809109

Identification of novel pathways involved in the pathogenesis of human adamantinomatous craniopharyngioma

Cynthia L. Andoniadou, Carles Gaston-Massuet, Rukmini Reddy, Ralph P. Schneider, Maria A. Blasco, Paul Le Tissier, Thomas S. Jacques, Larysa H. Pevny, Mehul T. Dattani, Juan Pedro Martinez-Barbera; Acta Neuropathologica August 2012, Volume 124, Issue 2, pp 259-271

Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity

Michael C. Abt, Lisa C. Osborne, Laurel A. Monticelli, Travis A. Doering, Theresa Alenghat, Gregory F. Sonnenberg, Michael A. Paley, Marcelo Antenus, Katie L. Williams, Jan Erikson, E. John Wherry, David Artis Immunity 27 July 2012 (Vol. 37, Issue 1, pp. 158-170

T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling

Kristine Germar, Marei Dose, Tassos Konstantinou, Jiangwen Zhang, Hongfang Wang, Camille Lobry, Kelly L. Arnett, Stephen C. Blacklow, Iannis Aifantis, Jon C. Aster, and Fotini Gounari. PNAS, December 13, 2011, 108(50): 20060-20065. doi:10.1073/pnas.1110230108

Laser Capture Microdissection with Genome-Wide Expression Profiling Displayed Gene Expression Signatures in Endometrioid Endometrial Cancer

Mokhtar NM, Ramzi NH, Yin-Ling W, Rose IM, Hatta Mohd Dali AZ, Jamal R. Cancer Investigation. February 2012, Vol. 30, No. 2, Pages 156-164. doi:10.3109/07357907.2011.633290

Transient Enhanced IL-2R Signaling Early during Priming Rapidly Amplifies Development of Functional CD8+ T Effector-Memory Cells

Iris Castro, Michael J. Dee and Thomas R. Malek, The Journal of Immunology November 1, 2012 vol. 189 no. 9 4321-4330

Molecular profiling supports the role of epithelial-to-mesenchymal transition (EMT) in ovarian cancer metastasis

Loukia N Lili, Lilya V Matyunina , L DeEtte Walker, Stephen L Wells, Benedict B Benigno , John F McDonald  Journal of Ovarian Research 2013, 6:49 doi:10.1186/1757-2215-6-49

The Role of Oxidative Stress in Nervous System Aging

Sims-Robinson C, Hur J, Hayes JM, Dauch JR, Keller PJ, et al. (2013) The Role of Oxidative Stress in Nervous System Aging. PLoS ONE 8(7): e68011. doi:10.1371/journal.pone.0068011

Increased ID2 Levels in Adult Precursor B Cells as Compared with Children Is Associated with Impaired Ig Locus Contraction and Decreased Bone Marrow Output

Kristin Jensen, Magdalena B. Rother, Berit Sletbakk Brusletto,Ole K. Olstad, Hans Christian Dalsbotten Aass, Menno C. van Zelm,Peter Kierulf and Kaare M. Gautvik

Alternatively Spliced Tissue Factor Contributes to Tumor Spread and Activation of Coagulation in Pancreatic Ductal Adenocarcinoma

Dusten Unruh, Kevin Turner,Ramprasad Srinivasan ,Begüm Kocatürk, Xiaoyang Qi, Zhengtao Chu,Bruce J. Aronow, David R. Plas, Catherine A. Gallo, Holger Kalthoff, Daniel Kirchhofer, Wolfram Ruf, Syed A. Ahmad, Fred V. Lucas, Henri H. Versteeg, Vladimir Y. Bogdanov DOI: 10.1002/ijc.28327

The Time Course of Gene Expression during Reactive Gliosis in the Optic Nerve

Qu J, Jakobs TC (2013) The Time Course of Gene Expression during Reactive Gliosis in the Optic Nerve. PLoS ONE 8(6): e67094. doi:10.1371/journal.pone.0067094

Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation

Marc A Kerenyi, Zhen Shao, Yu-Jung Hsu, Guoji Guo, Sidinh Luc, Kassandra O'Brien, Yuko Fujiwara, Cong Peng, Minh Nguyen, Stuart H Orkin eLife 2013;2:e00633

Lichen planopilaris is characterized by immune privilege collapse of the hair follicle's epithelial stem cell niche

Matthew J. Harries, Katja Meyer, Iskander Chaudhry, Jennifer Kloepper, Enrique Poblet, Christopher E. M. Griffiths,Ralf Paus DOI: 10.1002/path.4233

The Ubiquitin Ligase FBXW7 Modulates Leukemia-Initiating Cell Activity by Regulating MYC Stability

Bryan King,Thomas Trimarchi,Linsey Reavie,Luyao Xu,Jasper Mullenders,Panagiotis Ntziachristos,Beatriz Aranda-Orgilles,Arianne Perez-Garcia,Junwei Shi,Christopher Vakoc,Peter Sandy,Steven S. Shen,Adolfo Ferrando,Iannis Aifantis Cell, Volume 153, Issue 7, 1552-1566, 20 June 2013

Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse Large B-Cell Lymphoma

Kim Linton, Christopher Howarth, Mark Wappett, Gillian Newton, Cynthia Lachel, Javeed Iqbal, Stuart Pepper, Richard Byers, Wing (John) Chan, John Radford, The Journal of Molecular Diagnostics, Volume 14, Issue 3, May-June 2012, Pages 223-232

Fibroblast Growth Factor-1 is a mesenchymal stromal cell secreted factor stimulating proliferation of osteoarthritic chondrocytes in co-culture

Ling Wu, Jeroen Leijten, Clemens A. van Blitterswijk, and Marcel Karperien, Stem Cells and Development. -Not available-, ahead of print. doi:10.1089/scd.2013.0118.

Chronic rhinosinusitis with nasal polyps is characterized by B-cell inflammation and EBV-induced protein 2 expression

Kathryn E. Hulse, James E. Norton, Lydia Suh, Qiu Zhong, Mahboobeh Mahdavinia, Patrick Simon, Robert C. Kern, David B. Conley, Rakesh K. Chandra, Bruce K. Tan, Anju T. Peters, Leslie C. Grammer III, Kathleen E. Harris, Roderick G. Carter, Atsushi Kato, Robert P. Schleimer, Journal of Allergy and Clinical Immunology, Volume 131, Issue 4, April 2013, Pages 1075-1083.e7

Exon-level Expression Profiling of Ocular Tissues

Alex H. Wagner, V. Nikhil Anand, Wan-Heng Wang, Jon E. Chatterton, Duo Sun, Allan R. Shepard, Nasreen Jacobson, Iok-Hou Pang, Adam P. DeLuca, Thomas L. Casavant, Todd E. Scheetz, Robert F. Mullins, Terry A. Braun, Abbot F. Clark, Experimental Eye Research, Volume 111, June 2013, Pages 105-111,

In vitro culture of mouse embryos reduces differential gene expression between inner cell mass and trophectoderm

G. Giritharan, L. Delle Piane, A. Donjacour, F. J. Esteban, J. A. Horcajadas, E. Maltepe, P. Rinaudo, Reproductive Sciences March 2012 vol. 19 no. 3 243-252

An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo

Meng How Tan, Kin Fai Au, Denise E Leong, Kira Foygel, Wing H Wong, and Mylene WM Yaob, Mol Syst Biol. 2013; 9: 632.Published online 2013 January 8. doi: 10.1038, msb.2012.65

Linear mRNA amplification from as little as 5ng total RNA for global gene expression analysis

Alan Dafforn, Pengchin Chen, Glenn Deng, Michael Herrler, Dawn Iglehart, Sriveda Koritala, Susan Lato, Susheela Pillarisetty, Reshma Purohit, Martin Wang, Shenglong Wang, and Nurith Kurn. Nov 2004, BioTechniques 37:854-857

Novel Isothermal, Linear Nucleic Acid Amplification Systems for Highly Multiplexed Applications

Nurith Kurn, Pengchin Chen, Joe Don Heath, Anne Kopf-Sill, Kathryn M. Stephens, Shenglong Wang, September 2005, Clinical Chemistry 51: 1973-1981

Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors

Masayuki Akimoto, Hong Cheng, Dongxiao Zhu, Joseph A. Brzezinski, Ritu Khanna, Elena Filippova, Edwin C. T. Oh, Yuezhou Jing, Jose-Luis Linares, Matthew Brooks, Sepideh Zareparsi, Alan J. Mears, Alfred Hero, Tom Glaser, and Anand Swaroop. Published online February 2006, PNAS Vol. 103, no. 10, 3890-3895

Limited role for SREBP-1c in defective glucose-induced insulin secretion from Zucker diabetic fatty rat islets: a functional and gene profiling analysis

Laura E. Parton, Patrick J. McMillen, Yingnian Shen, Elizabeth Docherty, Erin Sharpe, Frederique Diraison, Celia P. Briscoe, and Guy A. Rutter. Am J Physiol Endocrinol Metab 291: E982-E994, June 2006; doi:10.1152/ajpendo.00067.2006 0193-1849/06

Genome-wide expression profile of human trabecular meshwork cultured cells, nonglaucomatous and primary open angle glaucoma tissue

Liton PB, Luna C, Challa P, Epstein DL, Gonzalez P. July 2006, Molecular Vision, 12:774-90

Reversal of Hox1 Gene Subfunctionalization in the Mouse

Petr Tvrdik and Mario R. Capecchi. August 2006, Developmental Cell, Vol 11, 239-250

Cutting Edge: Role of TANK-Binding Kinase 1 and Inducible I_B Kinase in IFN Responses against Viruses in Innate Immune Cells

Kosuke Matsui, Yutaro Kumagai, Hiroki Kato, Shintaro Sato, Tatsukata Kawagoe, Satoshi Uematsu, Osamu Takeuchi, and Shizuo Akira. The Journal of Immunology, November 2006, 177: 5785-5789

Rb induces a proliferative arrest and curtails Brn-2 expression in retinoblastoma cells.

David Cobrinik, Richard O Francis, David H Abramson, and Thomas C Lee. Dec 2006, Mol Cancer. 2006; 5: 72. doi: 10.1186/1476-4598-5-7

Comparison of Amplification Methods to Produce Affymetrix GeneChip Target Material.

Dennis Burian, Vicky White, Mark Huggins, Doris Kupfer, Dennis V. Canfield, James E. Whinnery. Civil Aerospace Medical Institute, Federal Aviation Administration DO report, April 2007

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays

Herbert Auer, David L Newsom, Norma J Nowak, Kirk M McHugh, Sunita Singh, Chack-Yung Yu, Yan Yang, Gail D Wenger, Julie M Gastier- Foster and Karl Kornacker BMC Genomics April 2007, 8:111 doi:10.1186/1471-2164-8-111

Big Results from Small Samples: Evaluation of Amplification Protocols for Gene Expression Profiling.

Agnes Viale, Juan Li, Jay Tiesman, Susan Hester, Aldo Massimi, Chandi Griffin, George Grills, Greg Khitrov, Kathryn Lilley, Kevin Knudtson, Bill Ward, Karl Kornacker, Chin-yi Chu, Herbert Auer, and Andrew I. Brooks, July 2007, Journal of Biomolecular Techniques, Volume 18, issue 3, 150-161. Winner of the JBT "Outstanding Manuscript" Award

Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.

Li Li, Lihua Ying, Maarten Naesens, Wenzhong Xiao, Tara Sigdel, Sue Hsieh, Jon Martin, Rong Chen, Kang Liu, Michael N. Mindrinos, Ron Davis, and Minnie Sarwal; Physiology Genomics, 2008 Jan 17;32(2):190-7. Epub 2007 Oct 30

Maternal infection leads to abnormal gene regulation and brain atrophy in mouse offspring: implications for genesis of neurodevelopmental disorders.

Fatemi SH, Reutiman TJ, Folsom TD, Huang H, Oishi K, Mori S, Smee DF, Pearce DA, Winter C, Sohr R, Juckel G.; Schizophrenia Research. 2008 Feb;99(1-3):56-70. Epub 2008 Jan 9.

An Erythroid Differentiation Signature Predicts Response to Lenalidomide in Myelodysplastic Syndrome

Benjamin L. Ebert, Naomi Galili, Pablo Tamayo, Jocelyn Bosco, Raymond Mak, Jennifer Pretz, Shyam Tanguturi, Christine Ladd-Acosta, Richard Stone, Todd R. Golub, Azra Raza. February 2008, PLoS Medicine Vol. 5, No. 2, e35. doi:10.1371/journal.pmed.0050035

Isolation and Molecular Characterization of Cancer Stem Cells in MMTV-Wnt-1 Murine Breast Tumors

Robert W. Cho, Xinhao Wang, Maximilian Diehn, Kerby Shedden, Grace Y. Chen, Gavin Sherlock, Austin Gurney, John Lewicki, Michael F. Clarke Stem Cells Vol. 26 No. 2 February 2008, pp. 364-371; doi:10.1634/stemcells.2007-0440

Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data.

Duane C. Hassane, Monica L. Guzman, Cheryl Corbett, Xiaojie Li, Ramzi Abboud, Fay Young, Jane L. Liesveld, Martin Carroll, and Craig T.Jordan; Blood, 2008 Jun 15;111(12):5654-62. Epub 2008 Feb 27.

Heterogeneity of Human Macrophages in Culture and in Atherosclerotic Plaques

Stephen W. Waldo, Yifu Li, Chiara Buono, Bin Zhao, Eric M. Billings, Janet Chang and Howard S. Kruth American Journal of Pathology. 2008;172:1112-1126. doi:10.2353/ajpath.2008.070513 on March 5, 2008

In Vitro Proliferation Of Cells Derived From Adult Human Beta Cells Revealed By Cell-lineage Tracing.

Holger A. Russ, Yael Bar, Philippe Ravassard, Shimon Efrat; Diabetes, 2008 Jun; 57(6):1575-83. Epub 2008 Mar 3.

Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays

Sylvain Pradervand, Alexandra Paillusson, Jerome Thomas, Johann Weber, Pratyaksha Wirapati, Otto Hagenbuchle, and Keith Harshman  BioTechniques May 2008 Volume 44, Number 6: pp 759-762

Gene expression profiling reveals that the regulation of estrogen-responsive element-independent genes by 17beta-estradiol-estrogen receptor beta is uncoupled from the induction of phenotypic changes in cell models.

Xiaodong Li, Stephanie L Nott, Yanfang Huang, Russell Hilf, Robert A Bambara, Xing Qiu, Andrei Yakovlev, Stephen Welle, and Mesut Muyan; Journal of Molecular Endocrinology, 2008 May; 40(5):211-29.

Kruppel-like factor 5 is required for perinatal lung morphogenesis and function.

Huajing Wan, Fengming Luo, Susan E. Wert, Liqian Zhang, Yan Xu, Machiko Ikegami, Yutaka Maeda, Sheila M. Bell and Jeffrey A. Whitsett; Development. 2008 Aug;135(15):2563-72. Epub 2008 Jul 3.

Transcriptomic Biomarkers for Individual Risk Assessment in New-Onset Heart Failure.

Bettina Heidecker, MD, Edward K. Kasper, MD, Ilan S. Wittstein, MD, Hunter C. Champion, MD, PhD, Elayne Breton, RN, Stuart D. Russell, MD, Michelle M. Kittleson, MD, PhD, Kenneth L. Baughman, MD, Joshua M. Hare, MD, Circulation, 2008 Jul 15;118(3):238-46. Epub 2008 Jun 30.

Discovery and Implementation of Transcriptional Biomarkers of Synthetic LXR Agonists in Peripheral Blood Cells.

Elizabeth A DiBlasio-Smith, Maya Arai, Elaine M Quinet, Mark J Evans, Tad Kornaga, Michael D Basso, Liang Chen, Irene Feingold, Anita R Halpern, Qiang-Yuan Liu, Ponnal Nambi, Dawn Savio, Shuguang Wang, William M Mounts, Jennifer A Isler, Anna M Slager, Michael E Burczynski, Andrew J Dorner, and Edward R LaVallie; Journal of Translational Medicine 2008 Oct 16; 6:59.

Delineation of VEGF-regulated genes and functions in the cervix of pregnant rodents by DNA microarray analysis.

Chishimba N Mowa, Tianbo Li, Subrina Jesmin, Hans G Folkesson, Sharon E Usip, Raymond E Papka, and Guichuan Hou; Reproductive Biology and Endocrinology 2008; 2008 Dec 16; 6:64.

LXR ligand lowers LDL cholesterol in primates, is lipid neutral in hamster, and reduces atherosclerosis in mouse

Elaine M. Quinet, Michael D. Basso, Anita R. Halpern, David W. Yates, Robert J. Sheffan, Valerie Clerin, Christine Resmini, James C. Keith, Thomas J. Berrodin, Irene Feingold, Wenyan Zhong, Helen B. Hartman, Mark J. Evans, Stephen J. Gardell, Elizabeth DiBlasio-Smith, William M. Mounts, Edward R. LaVallie, Jay Wrobel, Ponnal Nambi, and George P. Vlasuk; Journal of Lipid Research. 2009 Mar 24.

A novel method of amplification of FFPET-derived RNA enables accurate disease classification with microarrays

Williams PM, Li R, Johnson NA, Wright G, Heath JD, Gascoyne RD. J Mol Diagn. 2010 Sep;12(5):680-6. Epub 2010 Aug 5

Microfluidics-based capture of human neutrophils for expression analysis in blood and bronchoalveolar lavage

Akinori Muto, Toshihide Mizoguchi, Nobuyuki Udagawa, Susumu Ito, Ichiro Kawahara, Yoshimitsu Abiko, Atsushi Arai, Suguru Harada, Yasuhiro Kobayashi, Yuko Nakamichi, Josef M Penninger, Toshihide Noguchi, Naoyuki Takahashi PhD, Article first published online: 21 NOV 2011DOI: 10.1002/jbmr.490

A multi-site feasibility study for personalized medicine in canines with Osteosarcoma

Noel R Monks, David M Cherba1, Steven G Kamerling, Heather Simpson, Anthony W Rusk, Derrick Carter, Emily Eugster, Marie Mooney, Robert Sigler, Matthew Steensma, Tessa Grabinski, Keith R Marotti and Craig P Webb doi:10.1186/1479-5876-11-158

A New Resource for Arabidopsis Transcriptome Profiling

Rehrauer, H, Hennig, L, Plant Physiology 152:487-499 (2010)

A pathobiological role of the insulin receptor in chronic lymphocytic leukemia.

Saiya-Cork K, Malek S, Clin Cancer Res. 2011 Feb 17. [Epub ahead of print]

MicroRNAs regulate the timing of embryo maturation in Arabidopsis

Willmann M, Jenik P, Plant Physiol. 2011 Apr;155(4):1871-84. Epub 2011 Feb 17.

The Absence of ER-β Results in Altered Gene Expression in Ovarian Granulosa Cells Isolated From In Vivo Preovulatory Follicles

April K. Binder, Karina F. Rodriguez, Katherine J. Hamilton, Patricia S. Stockton, Casey E. Reed and Kenneth S. Korach, Endocrinology June 1, 2013 vol. 154 no. 6 2174-2187

Transcriptional Profiling of mRNAs and microRNAs in Human Bone Marrow Precursor B Cells Identifies Subset- and Age-Specific Variations

Jensen K, Brusletto BS, Aass HCD, Olstad OK, Kierulf P, et al. (2013) Transcriptional Profiling of mRNAs and microRNAs in Human Bone Marrow Precursor B Cells Identifies Subset- and Age-Specific Variations. PLoS ONE 8(7): e70721. doi:10.1371/journal.pone.0070721

Airway basal stem cells: a perspective on their roles in epithelial homeostasis and remodeling

JR Rock, BL Hogan Dis Model Mech. 2010 Sep-Oct;3(9-10):545-56. doi: 10.1242/dmm.006031. Epub 2010 Aug 10. PMID:20699479

Microarray analysis of thyroid nodule fine-needle aspirates accurately classifies benign and malignant lesions

Lubitz CC, Ugras SK, Kazam JJ, Zhu B, Scognamiglio T, Chen YT, Fahey TJ 3rd. November 2006, Journal of Molecular Diagnostics. 2006; 8: 490-498

TAT-BH4 and TAT-Bcl-xL Peptides Protect against Sepsis-Induced Lymphocyte Apoptosis In Vivo1

Richard S. Hotchkiss, Kevin W. McConnell, Kristin Bullok, Christopher G. Davis, Katherine C. Chang, Steven J. Schwulst, Jeffrey C. Dunne, Gunnar P. H. Dietz, Mathias Bähr, Jonathan E. McDunn, Irene E. Karl, Tracey H. Wagner, J. Perren Cobb, Craig M. Coopersmith and David Piwnica-Worms February 2006, The Journal of Immunology, 2006, 176: 5471-54770

Gene Expression Profiling of Peripheral Blood From Patients With Untreated New-Onset Systemic Juvenile Idiopathic Arthritis Reveals Molecular Heterogeneity That May Predict Macrophage Activation Syndrome

Ndate Fall, Michael Barnes, Sherry Thornton, Lorie Luyrink, Judyann Olson, Norman T. Ilowite, Beth S. Gottlieb, Thomas Griffin, David D. Sherry, Susan Thompson, David N. Glass, Robert A. Colbert, and Alexei A. Grom Arthritis & Rheumatis, Vol. 56, No. 11, November 2007, pp 3793-3804, DOI 10.1002/art.22981

Cross-Species Translocation of mRNA from Host Plants into the Parasitic Plant Dodder

Jeannine K. Roney, Piyum A. Khatibi, and James H. Westwood. Plant Physiology, February 2007, Vol. 143, pp. 1037-1043

Regulatory hotspots in the malaria parasite genome dictate transcriptional variation.

Gonzales JM, Patel JJ, Ponmee N, Jiang L, Tan A, et al. (2008) Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation. PLoS Biol 6(9): e238. doi:10.1371/journal.pbio.0060238

Renal ischemia reperfusion inhibits VEGF expression and induces ADAMTS-1, a novel VEGF inhibitor.

David P. Basile, Katherine Fredrich, Bhadrani Chelladurai, Ellen C. Leonard, and Alan R. Parrish; American Journal of Physiology Renal Physiology. 2008 Apr;294(4):F928-36. Epub 2008 Feb 13.

The DM domain protein DMRT1 is a dose-sensitive regulator of fetal germ cell proliferation and pluripotency

Anthony D. Krentz, Mark W. Murphy Shinseog Kim , Matthew S. Cook, Blanche Capel\, Rui Zhu,Angabin Matin, Aaron L. Sarver, Keith L. Parker, Michael D. Griswold ,Leendert H. J. Looijenga ,Vivian J. Bardwell and David Zarkower PNAS, vol. 106 no. 52 December 29, 2009

Infragranular gene expression disturbances in the prefrontal cortex in schizophrenia: Signature of altered neural development?

Dominique Arion, Szatmár Horváth, David A. Lewis, Károly Mirnics Neurobiology of Disease, December 23, 2009

Gene Expression Profiling of Formalin-Fixed, Pariffin-Embedded (FFPE) Tissues from Triple-Negative (TN) Breast Cancer (BC) Patients.

L. Baumbach, J. Yan, M. Ahearn, C. Gomez, M. Jorda, T. Halsey, A. Mejias, K. Ellilson, K. Mulligan, S. Gluck and M. Pegram Cancer Research: December 15, 2009; Volume 69, Issue 24, Supplement 3 doi: 10.1158/0008-5472.SABCS-09-6125

Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study

Daniel A Enquobahrie, Michelle A Williams, Chunfang Qiu, Seid Y Muhie,Kimberly Slentz-Kesler, Zhaoping Ge and Tanya Sorenson , BMC Pregnancy and Childbirth, December 10, 2009

Generation of pluripotent stem cells from eggs of aging mice

Junjiu Huang, Maja Okuka, Fang Wang, Bingfeng Zuo, Ping Liang,Keri Kalmbach, Lin Liu, David L. Keefe , Aging Cell, December 8, 2009

Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

Jay E. Johnson, Kajia Cao, Paul Ryvkin, Li-San Wang and F. Brad Johnson , Nucleic Acid Research, November 9, 2009

Age-associated Changes in Cardiac Gene Expression after Preconditioning

Liu, Lixin M.D., Ph.D.; Zhu, Jiang M.D.; Glass, Peter S. A. M.B., Ch.B.; Brink, Peter R. Ph.D.; Rampil, Ira J. M.D., M.S.; Rebecchi, Mario J. Ph.D. , Anesthesiology, November 2009

Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology

Stuart J. Rabin, Jae Mun ‘Hugo’ Kim, Michael Baughn, Ryan T. Libby,Young Joo Kim, Yuxin Fan, Randell T. Libby, Albert La Spada, Brad Stone and John Ravits, Human Molecular Genetics, October 26, 2009

Genomic Profiling of MicroRNAs and Messenger RNAs Reveals Hormonal Regulation in MicroRNA expression in Human Endometrium

Satu Kuokkanen, Bo Chen, Laureen Ojalvo, Lumie Benard, Nanette Santoro and Jeffrey W. Pollard Biology of Reproduction, October 28, 2009

Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastatic head and neck squamous cell

C. H. Chung,J. Aulino,N. J. Muldowney, H. Hatakeyama, J. Baumann,B. Burkey, J. Netterville, R. Sinard, W. G. Yarbrough, A. J. Cmelak, R. J. Slebos, Y. Shyr, J. Parker, J. Gilbert1 and B. A. Murphy1, Annals of Oncology, October 22, 2009

Unique biomechanical interactions between myeloma cells and bone marrow stroma cells

Yongdong Feng, Gidon Ofek,  Dong Soon Choi,  Jianguo Wen,  Jerry Hu,  Hong Zhao,  Youli Zu, Kyriacos A. Athanasiou, Chung-Che Chang, Progress in Biophysics and Molecular Biology, October 17, 2009

Dysregulation of gene expression within the peroxisome proliferator activated receptor pathway in morbidly obese patients

A. Katharine Hindle,  Jadd Koury, Tim McCaffrey, Sidney W. Fu, Fred Brody, Surgical Endoscopy, October 15, 2009

Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

Elizabeth H Robison, Tony S Mondala, Adam R Williams, Steven R Head, Daniel R Salomon and Sunil M Kurian , BMC Genomics, October 5, 2009

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity

Weiyin Zhou, Margaret A Calciano, Heather Jordan, Michael Brenner, Seth Johnson, Darong Wu, Lin Lei, Diego Pallares, Pascale Beurdeley, Fabien Rouet,Pritmohinder S Gill, Laurent Bracco, Cyril Soucaille and Richard Einstein, BMC Genetics, October 5, 2009

Imprinting of the Polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis

Aleksandra Erilova, Lynette Brownfield, Vivien Exner, Marisa Rosa, David Twell, Ortrun Mittelsten Scheid, Lars Hennig, and Claudia Köhler,PLoS Genetics, September 25, 2009

Brief focal cerebral ischemia that simulates transient ischemic attacks in humans regulates geneexpression in rat peripheral blood

Xinhua Zhan, Bradley P Ander, Glen Jickling, Renée Turner, Boryana Stamova, Huichun Xu, Dazhi Liu, Ryan R Davis and Frank R Sharp, Journal of Cerebral Blood Flow & Metabolism, September 9,2009

Molecular clock is involved in predictive circadian adjustment of renal function

Annie Mercier, ZuberGabriel Centeno, Sylvain Praderv, Svetlana Nikolaeva,Lionel Maquelin,Léonard Cardinaux,Olivier Bonnyand Dmitri Firsov , PNAS, September 9, 2009

PML-RARα Initiates Leukemia by Conferring Properties of Self-Renewal to Committed Promyelocytic Progenitors

S Wojiski, F C Guibal, T Kindler,B H Lee, J L Jesneck, A Fabian, D G Tenen, and D G Gilliland, Leukemia, August 23, 2009

Developmental delays consistent with cochlear hypothyroidism contribute to failure to develop hearing in mice lacking Slc26a4/pendrin expression

Philine Wangemann, Hyoung-Mi Kim, Sara Billings, Kazuhiro Nakaya, Xiangming Li, Ruchira Singh, David S. Sharlin, Douglas Forrest, Daniel C. Marcus, Peying FongAmerican Journal of Physiology – Renal PhysiologyPublished 19 August 2009Vol. no. DOI: 10.1152/ajprenal.00011.2009

Rapid induction of genes associated with tissue protection and neural development in contused adult spinal cord after radial glial cell transplantation

Yu-Wen Chang, Loyal A. Goff, Hedong Li, Noriko Kane-Goldsmith, Evangeline Tzatzalos, Ronald P. Hart, Wise Young, and Martin Grumet, Journal of Neurotrauma, July 26, 2009

A regulatory pathway involving Notch1/beta-catenin/lsl1 determines cardiac progenitor cell fate.

Chulan Kwon, Li Qian, Paul Cheng, Vishal Nigam, Joshua Arnold & Deepak Srivastava, Nature Cell Biology, July 20, 2009

Regulation of Adult Hematopoietic Stem Cells Fate for Enhanced Tissue-specific Repair

Nilanjana Sengupta, Sergio Caballero, Sean M Sullivan, Lung-Ji Chang, Aqeela Afzal, Sergio Li Calzi, Jennifer L Kielczewski, Sabrina Prabarakan, E Ann Ellis, Leni Moldovan, Nicanor I Moldovan, Michael E Boulton and Maria B Grant, Molecular Therapy, July 7, 2009

Foxl 2 functions in sex determination and histogenesis throughout mouse ovary development

José Elias Garcia-Ortiz, Emanuele Pelosi, Shakib Omari, Timur Nedorezov, Yulan Piao, Jesse Karmazin ,Manuela Uda, Antonio Cao, Steve W Cole, Antonino Forabosco, David Schlessinger, and Chris Ottolenghi, BMC Developmental Biology, June 18, 2009

Interesting times for microarray expression profiling

Yvonne Hey, Stuart D. Pepper, Briefings in Functional Genomics, May 27, 2009

Genome-wide analysis of gene expression in primate taste buds reveals links to diverse processes

Peter Hevezi, Bryan D. Moyer, Min Lu, Na Gao, Evan White, Fernando Echeverri, Dalia Kalabat, Hortensia Soto ,Bianca Laita, Cherry Li, Shaoyang Anthony Yeh, Mark Zoller, and Albert Zlotnik, PLoS One, May 27, 2009

Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses

Donna K. Slonim, Keiko Koide, Kirby L. Johnson, Umadevi Tantravahi, Janet M. Cowan, Zina Jarrah and Diana W. Bianchi, PNAS, May 27, 2009

Gene Expression Analysis Of Peripheral Blood Following Resistance Exercise: 2964: Board# 111 May 30 9: 30 AM-11: 00 AM

Carlson, Lara A., Westcott, Nicholas W., Martell, Travis J., Carter, Vanessa L., Marelli, Blair S., Tighe, Scott W, Medicine & Science in Sports & Exercise, May 2009

Hypothesis: Sarcoidosis is a STAT1-mediated disease

James T. Rosenbaum, M.D., Sirichai Pasadhika, M.D.,Elliott D. Crouser, M.D., Dongseok Choi, Ph.D., Christina A. Harrington, Ph.D., Jinnell A. Lewis, B.A., Carrie R. Austin, B.A., Tessa N. Diebel, B.A., Emily E. Vance, B.S., Rita M. Braziel, M.D., Justine R. Smith, M.B.B.S., Ph.D., and Stephen R. Planck, Ph.D. , Clinical Immunology, May 2009

P06: Gene expression profiling in toxicological studies using FFPE tissues

C. Schmitt, A. Walijew, P. Hewitt, J.H. Harleman, Experimental and Toxicological Pathology, April 29, 2009

Genomic strategy for targeting therapy in castration-resistant prostate cancer

Prateek Mendiratta, Elahe Mostaghel, Justin Guinney, Alok K. Tewari,Alessandro Porrello, William T. Barry, Peter S. Nelson and Phillip G. Febbo, Journal of Clinical Oncology, April 20, 2009

MicroRNA Expression Profiling Outperforms mRNA Expression Profiling in Formalin-fixed Paraffin-embedded Tissues

Aihua Liu, Michael T. Tetzlaff, Pat VanBelle, David Elder, Michael Feldman, John W. Tobias, Antonia R. Sepulveda, Xiaowei Xu , International Journal of Clinical and Experimental Pathology, March 20, 2009

Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device

AmirAli H. Talasaz, Ashley A. Powell, David E. Huber , James G. Berbee, Kyung-Ho Roh, Wong Yu , Wenzhong Xiao, Mark M. Davis, R. Fabian Pease , Michael N. Mindrinos, Stefanie S. Jeffrey and Ronald W. Davis, PNAS, March 10, 2009

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris

Mooney M, Bond J, Monks N, Eugster E, Cherba D, et al. (2013) PLoS ONE 8(4): e61088. doi:10.1371/journal.pone.0061088

Characterizing the Molecular Spatial and Temporal Field of Injury in Early-Stage Smoker Non–Small Cell Lung Cancer Patients after Definitive Surgery by Expression Profiling

Humam Kadara, Li Shen, Junya Fujimoto, Pierre Saintigny, Chi-Wan Chow, Wenhua Lang, Zuoming Chu, Melinda Garcia, Mohamed Kabbout, You-Hong Fan, Carmen Behrens, Diane A. Liu, Li Mao, J. Jack Lee, Kathryn A. Gold, Jing Wang, Kevin R. Coombes, Edward S. Kim, Waun Ki Hong, and Ignacio I. Wistuba, Cancer Prev Res January 2013 6; 8, doi: 10.1158/1940-6207.CAPR-12-0290

An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples

Marlene Thomas, Manuela Poignée-Heger, Martin Weisser, Stephanie Wessner and Anton Belousov, Journal of Clinical Bioinformatics 2013, 3:10

Increased ID2 Levels in Adult Precursor B Cells as Compared with Children Is Associated with Impaired Ig Locus Contraction and Decreased Bone Marrow Output

Kristin Jensen, Magdalena B. Rother, Berit Sletbakk Brusletto, Ole K. Olstad, Hans Christian Dalsbotten Aass, Menno C. van Zelm, Peter Kierulf and Kaare M. Gautvik, The Journal of Immunology, August 1, 2013, vol. 191 no. 3 1210-1219,nbsp; doi: 10.4049/jimmunol.1203462

Progressive morphological changes and impaired retinal function associated with temporal regulation of gene expression after retinal ischemia/reperfusion injury in mice

Byung-Jin Kim, Terry A Braun, Robert J Wordinger and Abbot F Clark, Molecular Neurodegeneration 2013, 8:21 doi:10.1186/1750-1326-8-21

Endothelial Cell Whole Genome Expression Analysis in a Mouse Model of Early-Onset Fuchs' Endothelial Corneal Dystrophy

Mario Matthaei, Jianfei Hu, Huan Meng, Eva-Maria Lackner, Charles G. Eberhart, Jiang Qian, Haiping Hao and Albert S. Jun, Invest. Ophthalmol. Vis. Sci. March 15, 2013 vol. 54 no. 3 1931-1940, doi: 10.1167/iovs.12-10898

Patients with activated B-cell like diffuse large B-cell lymphoma in high and low infectious disease areas have different inflammatory gene signatures

Hogfeldt T, Bahnassy AA, Kwiecinska A, Osterborg A, Tamm KP, Porwit A, Zekri AR, Lundahl J, Khaled HM, Mellstedt H, Moshfegh A., Leuk Lymphoma. 2013 May;54(5):996-1003. doi: 10.3109/10428194.2012.738365. Epub 2012 Nov 8

Genomic Signatures of Pregnancy-Associated Breast Cancer Epithelia and Stroma and their Regulation by Estrogens and Progesterone

Djuana M. E. Harvell, Jihye Kim, Jenean Orsquo Brien, Aik-Choon Tan, Virginia F. Borges, Pepper Schedin, Britta M. Jacobsen, Kathryn B. Horwitz, Hormones and Cancer June 2013, Volume 4, Issue 3, pp 140-153

The epigenetic modifier Ubiquitin Specific Protease 22 (Usp22) regulates embryonic stem cell differentiation via transcriptional repression of Sex determining region Y-box 2 (Sox2)

Robyn T. Sussman, Timothy J. Stanek, Paul Esteso, John D. Gearhart, Karen E. Knudsen and Steven B. McMahon, jbc.M113.469783 doi: 10.1074/jbc.M113.469783

MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP)

Margareta Jernas, Intawat Nookaew, Hans Wadenvik, and Bob Olsson, Blood March 14, 2013 vol. 121 no. 11 2095-2098, doi: 10.1182/blood-2012-12-471250

Clonal progression of prostate cancers from Gleason grade 3 to grade 4

Adam G. Sowalsky, Huihui Ye, Glenn J. Bubley, and Steven P. Balk, Cancer Res February 1, 2013 73; 1050, doi: 10.1158/0008-5472.CAN-12-2799

Genomic Signatures of a Global Fitness Index in a Multi-Ethnic Cohort of Women

Rampersaud E, Nathanson L, Farmer J, Meshbane K, Belton RL, Dressen A, Cuccaro M, Musto A, Daunert S, Deo S, Hudson N, Vance JM, Seo D, Mendez A, Dykxhoorn DM, Pericak-Vance MA, Goldschmidt-Clermont PJ, Ann Hum Genet. 2013 Mar;77(2):147-57. doi: 10.1111/ahg.12006

Butyrophilin-like 2 Modulates B7 Costimulation To Induce Foxp3 Expression and Regulatory T Cell Development in Mature T Cells

Swanson RM, Gavin MA, Escobar SS, Rottman JB, Lipsky BP, Dube S, Li L, Bigler J, Wolfson M, Arnett HA, Viney JL, J Immunol. 2013 Mar 1;190(5):2027-35. doi: 10.4049/jimmunol.1201760

Differential expression of T-cell genes in blood and bone marrow be-tween ITP patients and controls

Jernas M, Nookaew I, Wadenvik H, Olsson B, Thromb Haemost. 2013 Jan;109(1):112-7. doi: 10.1160/TH12-07-0468

Genome wide differences of gene expression associated with HLA-DRB1 genotype in multiple sclerosis: A pilot study

Apperson ML, Tian Y, Stamova B, Ander BP, Jickling GC, Agius MA, Sharp FR, J Neuroimmunol. 2013 Apr 15;257(1-2):90-6. doi: 10.1016/j.jneuroim.2013.02.004

Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders

Boryana S Stamova, Yingfang Tian, Christine W Nordahl, Mark D Shen, Sally Rogers, David G Amaral and Frank R Sharp; Stamova et al. Molecular Autism 2013, 4:30 doi:10.1186/2040-2392-4-30

Downstream Signaling Pathways in Mouse Adipose Tissues Following Acute In Vivo Administration of Fibroblast Growth Factor 21

Muise ES, Souza S, Chi A, Tan Y, Zhao X, et al. PLoS ONE 8(9): e73011. doi:10.1371/journal.pone.0073011

Sex-specific control of CNS autoimmunity by p38 MAPK signaling in myeloid cells

Krementsov, Dimitry N., Noubade, Rajkumar, Dragon, Julie A., Otsu, Kinya, Rincon, Mercedes, Teuscher, Cory; Ann Neurol.1531-8249 10.1002/ana.24020

Chordoma Low-Template Microarray Analysis

Julia Feichtinger, Amin El-Heliebi, Thomas Kroneis, Karin Wagner, Bernadette Liegl-Atzwanger, Andreas Leithner, Gerhard G. Thallinger, and Beate Rinner; Biomedical Engineering / Biomedizinische Technik. Pages 1862-278X, ISSN (Print) 0013-5585, DOI:10.1515/bmt-2013-4310, September 2013

A transcriptional and metabolic signature of primary aneuploidy is present in chromosomally-unstable cancer cells and informs clinical prognosis

Jason M. Sheltzer; Published Online First September 16, 2013; doi: 10.1158/0008-5472.CAN-13-0749

Nfix is a novel regulator of murine hematopoietic stem and progenitor cell survival

Per Holmfeldt, Jennifer Pardieck, Anjelica C. Saulsberry, Satish Kumar Nandakumar, David Finkelstein, John T. Gray, Derek A. Persons, and Shannon McKinney-Freeman; Blood First Edition Paper, prepublished online September 16, 2013; DOI 10.1182/blood-2013-04-493973

A SALL4/MLL/HOXA9 pathway in murine and human myeloid leukemogenesis
Ailing Li, Youyang Yang, Chong Gao, Jiayun Lu, Ha-Won Jeong, Bee H. Liu, Ping Tang, Xiaopan Yao, Donna Neuberg, Gang Huang, Daniel G. Tenen and Li Chai; J Clin Invest. 2013;123(10):4195;4207. doi:10.1172/JCI62891
F11R Is a Novel Monocyte Prognostic Biomarker for Malignant Glioma
Winnie W. Pong, Jason Walker, Todd Wylie, Vincent Magrini, Jingqin Luo, Ryan J. Emnett, Jaebok Choi, Matthew L. Cooper, Malachi Griffith, Obi L. Griffith, Joshua B. Rubin, Gregory N. Fuller, David Piwnica-Worms, Xi Feng, Dolores Hambardzumyan, John F. DiPersio, Elaine R. Mardis,David H. Gutmann;DOI:10.1371/journal.pone.0077571
Identification of Candidate B-Lymphoma Genes by Cross-Species Gene Expression Profiling
Van S.Tompkins, Seong-Su Han, Alicia Olivier, Sergei Syrbu, Thomas Bair, Anna Button, Laura Jacobus, Zebin Wang, Samuel Lifton, Pradip Raychaudhuri, Herbert C. Morse III, George Weiner, Brian Link, Brian J. Smith, Siegfried Janz; DOI: 10.1371/journal.pone.0076889
The Ets transcription factor EHF as a regulator of cornea epithelial cell identity
Denise N. Stephens, Rachel Herndon Klein, Michael L. Salmans, William Gordon, Hsiang Ho and Bogi Andersen; First Published on October 18, 2013, doi: 10.1074/jbc.M113.504399 jbc.M113.504399.
Complement Activation and Intraventricular Rituximab Distribution in Recurrent Central Nervous System Lymphoma
Cigall Kadoch, Jing Li, Valerie S. Wong, Lingjing Chen, Soonmee Cha, Pamela N. Munster, Clifford A. Lowell, Marc A Shuman, and James Rubenstein; November 4, 2013; doi: 10.1158/1078-0432.CCR-13-0474
Early B-Cell Factor-1 (Ebf1) is a key regulator of metabolic and inflammatory signaling pathways in mature adipocytes
Michael J. Griffin, Yiming Zhou, Sona Kang, Xiaolan Zhang, Tarjei S. Mikkelsen and Evan D. Rosen; October 30, 2013, doi: 10.1074/jbc.M113.491936 jbc.M113.491936.
Myc is required for B-catenin-mediated mammary stem cell amplification and tumorigenesis
Mejdi Moumen, Aurelie Chiche, Charles Decraene, Valerie Petit, Alberto Gandarillas, Marie-Ange Deugnier, Marina A Glukhova,and Marisa M Faraldo; Molecular Cancer 2013,12:132
Molecular Profiling of the Lateral Habenula in a Rat Model of Depression
Trine Christensen, Line Jensen, Elena V. Bouzinova, Ove Wiborg; DOI: 10.1371/journal.pone.0080666
Toward a therapeutic reduction of imatinib refractory myeloproliferative neoplasm-initiating cells

S T Philips, Z L Hildenbrand, K I Oravecz-Wilson, S B Foley, V E Mgbemena and T S Ross; Oncogene , (18 November 2013) | doi:10.1038/onc.2013.484

Defining pancreatic endocrine precursors and their descendants.

Peter White, Ph.D., Catherine Lee May, Ph.D., Rodrigo N. Lamounier, M.D., John E. Brestelli, M.S., Klaus H. Kaestner, Ph.D.; Diabetes, 2008 March; 57(3):654-68. Epub 2007 Dec 10.

Skeletal muscle gene expression after myostatin knockout in mature mice

Stephen Welle, Andrew Cardillo, Michelle Zanche and Rabi Tawil, Physiological Genomics, June 1, 2009

Differential gene expression in chronic inflammatory demyelinating polyneuropathy (CIDP) skin biopsies

Grace Lee, Zhaoying Xiang,Thomas H. Brannagan , Russell L. Chin, Norman Latov , Journal of the Neurological Sciences, October 7, 2009

The function of FGF signaling in the lens placode

Garcia C, Beebe D, Dev Biol. 2011 Mar 1;351(1):176-85. Epub 2011 Jan 9.

Ketones and lactate increase cancer cell stemness, driving recurrence, metastasis and poor clinical outcome in breast cancer

Ubaldo E Martinez-Outschoorn, Marco Prisco, Adam Ertel, Aristotelis Tsirigos, Zhao Lin, Stephanos Pavlides, Chengwang Wang, Neal Flomenberg, Erik S Knudsen, Anthony Howell, Richard G Pestell, Federica Sotgia, and Michael P Lisanti. Cell Cycle 2011 April 15; 10(8): 1271-1286. doi:  10.4161/cc.10.8.15330. Published online 2011 April 15. PMCID: PMC3117136

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