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Chien CY, Tsai HT, Su LJ, Chuang HC, Shiu LY, Huang CC, Fang FM, Yu CC, Su HT, Chen CH. Aurora-A signaling is activated in advanced stage of squamous cell carcinoma of head and neck cancer and requires osteopontin to stimulate invasive behavior. Oncotarget. 2014 Apr 30; 5(8):2243-62.

Fry CS, Lee JD, Jackson JR, Kirby TJ, Stasko SA, Liu H, Dupont-Versteegden EE, McCarthy JJ, Peterson CA. Regulation of the muscle fiber microenvironment by activated satellite cells during hypertrophy. FASEB J. 2014 Apr; 28(4):1654-65.

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Nookaew I, Thorell K, Worah K, Wang S, Hibberd ML, Sjövall H, Pettersson S, Nielsen J, Lundin SB. Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker. BMC Med Genomics. 2013 Oct 11; 6:41.

Gokulan K, Khare S, Rooney AW, Han J, Lynne AM, Foley SL. Impact of plasmids, including those encodingVirB4/D4 type IV secretion systems, on Salmonella enterica serovar Heidelberg virulence in macrophages and epithelial cells. PLoS One. 2013; 8(10):e77866.

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Wilson RA, Teng L, Bachmeyer KM, Bissonnette ML, Husain AN, Parham DM, Triche TJ, Wing MR, Gastier-Foster JM, Barr FG, Hawkins DS, Anderson JR, Skapek SX, Volchenboum SL. A novel algorithm for simplification of complex gene classifiers in cancer. Cancer Res. 2013 Sep 15; 73(18):5625-32.

Gonzalo DH, Lai KK, Shadrach B, Goldblum JR, Bennett AE, Downs-Kelly E, Liu X, Henricks W, Patil DT, Carver P, Na J, Gopalan B, Rybicki L, Pai RK. Gene expression profiling of serrated polyps identifies annexin A10 as a marker of a sessile serrated adenoma/polyp. J Pathol. 2013 Aug; 230(4):420-9.

Jernås M, Malmeström C, Axelsson M, Nookaew I, Wadenvik H, Lycke J, Olsson B. MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS). BMC Immunol. 2013 Jul 29; 14:32.

Smalling RL, Delker DA, Zhang Y, Nieto N, McGuiness MS, Liu S, Friedman SL, Hagedorn CH, Wang L. Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease. Am J Physiol Gastrointest Liver Physiol. 2013 Sep 01; 305(5):G364-74.

Xiao W, Zhu Y, Sarsour EH, Kalen AL, Aykin-Burns N, Spitz DR, Goswami PC. Selenoprotein P regulates 1-(4-Chlorophenyl)-benzo-2,5-quinone-induced oxidative stress and toxicity in human keratinocytes. Free Radic Biol Med. 2013 Dec; 65:70-7.

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Pitroda SP, Zhou T, Sweis RF, Filippo M, Labay E, Beckett MA, Mauceri HJ, Liang H, Darga TE, Perakis S, Khan SA, Sutton HG, Zhang W, Khodarev NN, Garcia JG, Weichselbaum RR. Tumor endothelial inflammation predicts clinical outcome in diverse human cancers. PLoS One. 2012; 7(10):e46104.

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Jernås M, Malmeström C, Axelsson M, Olsson C, Nookaew I, Wadenvik H, Zetterberg H, Blennow K, Lycke J, Rudemo M, Olsson B. MS risk genes are transcriptionally regulated in CSF leukocytes at relapse. Mult Scler. 2013 Apr; 19(4):403-10.

Yampolsky LY, Glazko GV, Fry JD. Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila melanogaster maintained under constant and variable ethanol stress. Mol Ecol. 2012 Sep; 21(17):4287-99.

Erickson SW, MacLeod SL, Hobbs CA. Cheek swabs, SNP chips, and CNVs: assessing the quality of copy number variant calls generated with subject-collected mail-in buccal brush DNA samples on a high-density genotyping microarray. BMC Med Genet. 2012 Jun 26; 13:51.

Bartpho T, Wongsurawat T, Wongratanacheewin S, Talaat AM, Karoonuthaisiri N, Sermswan RW. Genomic islands as a marker to differentiate between clinical and environmental Burkholderia pseudomallei. PLoS One. 2012; 7(6):e37762.

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Zhang J, Lazarenko OP, Wu X, Tong Y, Blackburn ML, Gomez-Acevedo H, Shankar K, Badger TM, Ronis MJ, Chen JR. Differential effects of short term feeding of a soy protein isolate diet and estrogen treatment on bone in the pre-pubertal rat. PLoS One. 2012; 7(4):e35736.

Rangani G, Khodakovskaya M, Alimohammadi M, Hoecker U, Srivastava V. Site-specific methylation in gene coding region underlies transcriptional silencing of the Phytochrome A epiallele in Arabidopsis thaliana. Plant Mol Biol. 2012 May; 79(1-2):191-202.

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Cheng BY, Zhi J, Santana A, Khan S, Salinas E, Forrest JC, Zheng Y, Jaggi S, Leatherwood J, Krug LT. Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection. J Virol. 2012 Apr; 86(8):4340-57.

Tomita-Mitchell A, Mahnke DK, Struble CA, Tuffnell ME, Stamm KD, Hidestrand M, Harris SE, Goetsch MA, Simpson PM, Bick DP, Broeckel U, Pelech AN, Tweddell JS, Mitchell ME. Human gene copy number spectra analysis in congenital heart malformations. Physiol Genomics. 2012 May 01; 44(9):518-41.

Markello TC, Carlson-Donohoe H, Sincan M, Adams D, Bodine DM, Farrar JE, Vlachos A, Lipton JM, Auerbach AD, Ostrander EA, Chandrasekharappa SC, Boerkoel CF, Gahl WA. Sensitive quantification of mosaicism using high density SNP arrays and the cumulative distribution function. Mol Genet Metab. 2012 Apr; 105(4):665-71.

Chen JR, Zhang J, Lazarenko OP, Kang P, Blackburn ML, Ronis MJ, Badger TM, Shankar K. Inhibition of fetal bone development through epigenetic down-regulation of HoxA10 in obese rats fed high-fat diet. FASEB J. 2012 Mar; 26(3):1131-41.

Farrar JE, Vlachos A, Atsidaftos E, Carlson-Donohoe H, Markello TC, Arceci RJ, Ellis SR, Lipton JM, Bodine DM. Ribosomal protein gene deletions in Diamond-Blackfan anemia. Blood. 2011 Dec 22; 118(26):6943-51.

Boyd KD, Ross FM, Walker BA, Wardell CP, Tapper WJ, Chiecchio L, Dagrada G, Konn ZJ, Gregory WM, Jackson GH, Child JA, Davies FE, Morgan GJ. Mapping of chromosome 1p deletions in myeloma identifies FAM46C at 1p12 and CDKN2C at 1p32.3 as being genes in regions associated with adverse survival. Clin Cancer Res. 2011 Dec 15; 17(24):7776-84.

Agnelli L, Forcato M, Ferrari F, Tuana G, Todoerti K, Walker BA, Morgan GJ, Lombardi L, Bicciato S, Neri A. The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma. Clin Cancer Res. 2011 Dec 01; 17(23):7402-12.

Matsuo K, Nishimura M, Bottsford-Miller JN, Huang J, Komurov K, Armaiz-Pena GN, Shahzad MM, Stone RL, Roh JW, Sanguino AM, Lu C, Im DD, Rosenshien NB, Sakakibara A, Nagano T, Yamasaki M, Enomoto T, Kimura T, Ram PT, Schmeler KM, Gallick GE, Wong KK, Frumovitz M, Sood AK. Targeting SRC in mucinous ovarian carcinoma. Clin Cancer Res. 2011 Aug 15; 17(16):5367-78.

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Folkers ME, Delker DA, Maxwell CI, Nelson CA, Schwartz JJ, Nix DA, Hagedorn CH. ENCODE tiling array analysis identifies differentially expressed annotated and novel 5' capped RNAs in hepatitis C infected liver. PLoS One. 2011 Feb 16; 6(2):e14697.

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O'Connell CM, AbdelRahman YM, Green E, Darville HK, Saira K, Smith B, Darville T, Scurlock AM, Meyer CR, Belland RJ. Toll-like receptor 2 activation by Chlamydia trachomatis is plasmid dependent, and plasmid-responsive chromosomal loci are coordinately regulated in response to glucose limitation by C. trachomatis but not by C. muridarum. Infect Immun. 2011 Mar; 79(3):1044-56.

Arlt VM, Zuo J, Trenz K, Roufosse CA, Lord GM, Nortier JL, Schmeiser HH, Hollstein M, Phillips DH. Gene expression changes induced by the human carcinogen aristolochic acid I in renal and hepatic tissue of mice. Int J Cancer. 2011 Jan 01; 128(1):21-32.

Bradford BU, Lock EF, Kosyk O, Kim S, Uehara T, Harbourt D, DeSimone M, Threadgill DW, Tryndyak V, Pogribny IP, Bleyle L, Koop DR, Rusyn I. Interstrain differences in the liver effects of trichloroethylene in a multistrain panel of inbred mice. Toxicol Sci. 2011 Mar; 120(1):206-17.

Bahl A, Davis PH, Behnke M, Dzierszinski F, Jagalur M, Chen F, Shanmugam D, White MW, Kulp D, Roos DS. A novel multifunctional oligonucleotide microarray for Toxoplasma gondii. BMC Genomics. 2010 Oct 25; 11:603.

Pogribny IP, Filkowski JN, Tryndyak VP, Golubov A, Shpyleva SI, Kovalchuk O. Alterations of microRNAs and their targets are associated with acquired resistance of MCF-7 breast cancer cells to cisplatin. Int J Cancer. 2010 Oct 15; 127(8):1785-94.

Tryndyak VP, Han T, Muskhelishvili L, Fuscoe JC, Ross SA, Beland FA, Pogribny IP. Coupling global methylation and gene expression profiles reveal key pathophysiological events in liver injury induced by a methyl-deficient diet. Mol Nutr Food Res. 2011 Mar; 55(3):411-8.

Hassane DC, Sen S, Minhajuddin M, Rossi RM, Corbett CA, Balys M, Wei L, Crooks PA, Guzman ML, Jordan CT. Chemical genomic screening reveals synergism between parthenolide and inhibitors of the PI-3 kinase and mTOR pathways. Blood. 2010 Dec 23; 116(26):5983-90.

Papini M, Nookaew I, Scalcinati G, Siewers V, Nielsen J. Phosphoglycerate mutase knock-out mutant Saccharomyces cerevisiae: physiological investigation and transcriptome analysis. Biotechnol J. 2010 Oct; 5(10):1016-27.

Singh S, Vinson C, Gurley CM, Nolen GT, Beggs ML, Nagarajan R, Wagner EF, Parham DM, Peterson CA. Impaired Wnt signaling in embryonal rhabdomyosarcoma cells from p53/c-fos double mutant mice. Am J Pathol. 2010 Oct; 177(4):2055-66.

Sharma A, Bartell SM, Baile CA, Chen B, Podolsky RH, McIndoe RA, She JX. Hepatic gene expression profiling reveals key pathways involved in leptin-mediated weight loss in ob/ob mice. PLoS One. 2010 Aug 16; 5(8):e12147.

Nagarajan R, Upreti M. Granger causality analysis of human cell-cycle gene expression profiles. Stat Appl Genet Mol Biol. 2010; 9:Article31.

Wongsurawat T, Leelatanawit R, Thamniemdee N, Uawisetwathana U, Karoonuthaisiri N, Menasveta P, Klinbunga S. Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). BMC Mol Biol. 2010 Aug 09; 11:55.

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Walker BA, Leone PE, Chiecchio L, Dickens NJ, Jenner MW, Boyd KD, Johnson DC, Gonzalez D, Dagrada GP, Protheroe RK, Konn ZJ, Stockley DM, Gregory WM, Davies FE, Ross FM, Morgan GJ. A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value. Blood. 2010 Oct 14; 116(15):e56-65.

Zhang J, Dhakal IB, Lang NP, Kadlubar FF. Polymorphisms in inflammatory genes, plasma antioxidants, and prostate cancer risk. Cancer Causes Control. 2010 Sep; 21(9):1437-44.

Zhou Y, Chen L, Barlogie B, Stephens O, Wu X, Williams DR, Cartron MA, van Rhee F, Nair B, Waheed S, Pineda-Roman M, Alsayed Y, Anaissie E, Shaughnessy JD. High-risk myeloma is associated with global elevation of miRNAs and overexpression of EIF2C2/AGO2. Proc Natl Acad Sci U S A. 2010 Apr 27; 107(17):7904-9.

Vongsangnak W, Nookaew I, Salazar M, Nielsen J. Analysis of genome-wide coexpression and coevolution of Aspergillus oryzae and Aspergillus niger. OMICS. 2010 Apr; 14(2):165-75.

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Kang BY, Hu C, Ryu S, Khan JA, Biancolella M, Prayaga S, Seung KB, Novelli G, Mehta P, Mehta JL. Genomics of cardiac remodeling in angiotensin II-treated wild-type and LOX-1-deficient mice. Physiol Genomics. 2010 Jun; 42(1):42-54.

Dickens NJ, Walker BA, Leone PE, Johnson DC, Brito JL, Zeisig A, Jenner MW, Boyd KD, Gonzalez D, Gregory WM, Ross FM, Davies FE, Morgan GJ. Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome. Clin Cancer Res. 2010 Mar 15; 16(6):1856-64.

Hu X, Schwarz JK, Lewis JS, Huettner PC, Rader JS, Deasy JO, Grigsby PW, Wang X. A microRNA expression signature for cervical cancer prognosis. Cancer Res. 2010 Feb 15; 70(4):1441-8.

Dai Y, Pierson SE, Dudney WC, Stack BC. Extraribosomal function of metallopanstimulin-1: reducing paxillin in head and neck squamous cell carcinoma and inhibiting tumor growth. Int J Cancer. 2010 Feb 01; 126(3):611-9.

Poplawski AB, Jankowski M, Erickson SW, Díaz de Ståhl T, Partridge EC, Crasto C, Guo J, Gibson J, Menzel U, Bruder CE, Kaczmarczyk A, Benetkiewicz M, Andersson R, Sandgren J, Zegarska B, Bala D, Srutek E, Allison DB, Piotrowski A, Zegarski W, Dumanski JP. Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression. Eur J Hum Genet. 2010 May; 18(5):560-8.

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Lee T, Desai VG, Velasco C, Reis RJ, Delongchamp RR. Testing for treatment effects on gene ontology. BMC Bioinformatics. 2008 Aug 12; 9 Suppl 9:S20.

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Tan X, Yuan Y, Zeng G, Apte U, Thompson MD, Cieply B, Stolz DB, Michalopoulos GK, Kaestner KH, Monga SP. Beta-catenin deletion in hepatoblasts disrupts hepatic morphogenesis and survival during mouse development. Hepatology. 2008 May; 47(5):1667-79.

Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P. Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol Genet Genomics. 2008 May; 279(5):523-34.

Stojadinovic O, Pastar I, Vukelic S, Mahoney MG, Brennan D, Krzyzanowska A, Golinko M, Brem H, Tomic-Canic M. Deregulation of keratinocyte differentiation and activation: a hallmark of venous ulcers. J Cell Mol Med. 2008 Dec; 12(6B):2675-90.

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