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Publications indexed to the term Oligonucleotide Array Sequence Analysis

FacultyTitle
4Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. (Levy H, Jia S, Pan A, Zhang X, Kaldunski M, Nugent ML, Reske M, Feliciano RA, Quintero D, Renda MM, Woods KJ, Murkowski K, Johnson K, Verbsky J, Dasu T, Ideozu JE, McColley S, Quasney MW, Dahmer MK, Avner E, Farrell PM, Cannon CL, Jacob H, Simpson PM, Hessner MJ) Physiol Genomics 2019 Jan 01;51(1):27-41       15 Citations
1Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. (Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA) Inflamm Bowel Dis 2018 Jan 18;24(2):346-360       55 Citations
2Genome-Wide Association Study to Find Modifiers for Tetralogy of Fallot in the 22q11.2 Deletion Syndrome Identifies Variants in the GPR98 Locus on 5q14.3. (Guo T, Repetto GM, McDonald McGinn DM, Chung JH, Nomaru H, Campbell CL, Blonska A, Bassett AS, Chow EWC, Mlynarski EE, Swillen A, Vermeesch J, Devriendt K, Gothelf D, Carmel M, Michaelovsky E, Schneider M, Eliez S, Antonarakis SE, Coleman K, Tomita-Mitchell A, Mitchell ME, Digilio MC, Dallapiccola B, Marino B, Philip N, Busa T, Kushan-Wells L, Bearden CE, Piotrowicz M, Hawuła W, Roberts AE, Tassone F, Simon TJ, van Duin EDA, van Amelsvoort TA, Kates WR, Zackai E, Johnston HR, Cutler DJ, Agopian AJ, Goldmuntz E, Mitchell LE, Wang T, Emanuel BS, Morrow BE, International 22q11.2 Consortium/Brain and Behavior Consortium*) Circ Cardiovasc Genet 2017 Oct;10(5):e001690       20 Citations
1Microarray Analysis of Hypertension. (Keen HL, Sigmund CD) Methods Mol Biol 2017;1527:41-52       5 Citations
1Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. (Liu C, Kraja AT, Smith JA, Brody JA, Franceschini N, Bis JC, Rice K, Morrison AC, Lu Y, Weiss S, Guo X, Palmas W, Martin LW, Chen YD, Surendran P, Drenos F, Cook JP, Auer PL, Chu AY, Giri A, Zhao W, Jakobsdottir J, Lin LA, Stafford JM, Amin N, Mei H, Yao J, Voorman A, CHD Exome+ Consortium, ExomeBP Consortium, GoT2DGenes Consortium, T2D-GENES Consortium, Larson MG, Grove ML, Smith AV, Hwang SJ, Chen H, Huan T, Kosova G, Stitziel NO, Kathiresan S, Samani N, Schunkert H, Deloukas P, Myocardial Infarction Genetics and CARDIoGRAM Exome Consortia, Li M, Fuchsberger C, Pattaro C, Gorski M, CKDGen Consortium, Kooperberg C, Papanicolaou GJ, Rossouw JE, Faul JD, Kardia SL, Bouchard C, Raffel LJ, Uitterlinden AG, Franco OH, Vasan RS, O'Donnell CJ, Taylor KD, Liu K, Bottinger EP, Gottesman O, Daw EW, Giulianini F, Ganesh S, Salfati E, Harris TB, Launer LJ, Dörr M, Felix SB, Rettig R, Völzke H, Kim E, Lee WJ, Lee IT, Sheu WH, Tsosie KS, Edwards DR, Liu Y, Correa A, Weir DR, Völker U, Ridker PM, Boerwinkle E, Gudnason V, Reiner AP, van Duijn CM, Borecki IB, Edwards TL, Chakravarti A, Rotter JI, Psaty BM, Loos RJ, Fornage M, Ehret GB, Newton-Cheh C, Levy D, Chasman DI) Nat Genet 2016 Oct;48(10):1162-70       202 Citations
1Maternal methylmercury from a wild-caught walleye diet induces developmental abnormalities in zebrafish. (Liu Q, Klingler RH, Wimpee B, Dellinger M, King-Heiden T, Grzybowski J, Gerstenberger SL, Weber DN, Carvan MJ 3rd) Reprod Toxicol 2016 Oct;65:272-282       14 Citations
2E2f8 mediates tumor suppression in postnatal liver development. (Kent LN, Rakijas JB, Pandit SK, Westendorp B, Chen HZ, Huntington JT, Tang X, Bae S, Srivastava A, Senapati S, Koivisto C, Martin CK, Cuitino MC, Perez M, Clouse JM, Chokshi V, Shinde N, Kladney R, Sun D, Perez-Castro A, Matondo RB, Nantasanti S, Mokry M, Huang K, Machiraju R, Fernandez S, Rosol TJ, Coppola V, Pohar KS, Pipas JM, Schmidt CR, de Bruin A, Leone G) J Clin Invest 2016 Aug 01;126(8):2955-69       77 Citations
1Transcription Profile in Sporadic Multiple Symmetric Lipomatosis Reveals Differential Expression at the Level of Adipose Tissue-Derived Stem Cells. (Prantl L, Schreml J, Gehmert S, Klein S, Bai X, Zeitler K, Schreml S, Alt E, Gehmert S, Felthaus O) Plast Reconstr Surg 2016 Apr;137(4):1181-1190       20 Citations
2Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease. (Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M) J Am Heart Assoc 2016 Feb 17;5(2)       46 Citations
1Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. (Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, Huang K, Sáenz-Robles MT, Cantalupo P, Pipas J, Leone G) Sci Data 2016 Feb 16;3:160008       5 Citations
1The Role of the Immune Response in the Pathogenesis of Thyroid Eye Disease: A Reassessment. (Rosenbaum JT, Choi D, Wong A, Wilson DJ, Grossniklaus HE, Harrington CA, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh PK, Harris GJ, Kazim M, Patel PJ, White VA, Dolman PJ, Edward DP, Alkatan HM, Al Hussain H, Selva D, Yeatts RP, Korn BS, Kikkawa DO, Stauffer P, Planck SR) PLoS One 2015;10(9):e0137654       16 Citations
1Genomic landscape of salivary gland tumors. (Kato S, Elkin SK, Schwaederle M, Tomson BN, Helsten T, Carter JL, Kurzrock R) Oncotarget 2015 Sep 22;6(28):25631-45       46 Citations
3Phenotypic Characterization of Mice Carrying Homozygous Deletion of KLF11, a Gene in Which Mutations Cause Human Neonatal and MODY VII Diabetes. (Mathison A, Escande C, Calvo E, Seo S, White T, Salmonson A, Faubion WA Jr, Buttar N, Iovanna J, Lomberk G, Chini EN, Urrutia R) Endocrinology 2015 Oct;156(10):3581-95       11 Citations
1Orbital pseudotumor can be a localized form of granulomatosis with polyangiitis as revealed by gene expression profiling. (Rosenbaum JT, Choi D, Wilson DJ, Grossniklaus HE, Harrington CA, Sibley CH, Dailey RA, Ng JD, Steele EA, Czyz CN, Foster JA, Tse D, Alabiad C, Dubovy S, Parekh PK, Harris GJ, Kazim M, Patel PJ, White VA, Dolman PJ, Korn BS, Kikkawa DO, Edward DP, Alkatan HM, al-Hussain H, Yeatts RP, Selva D, Stauffer P, Planck SR) Exp Mol Pathol 2015 Oct;99(2):271-8       31 Citations
1Microarray Determination of the Expression of Drug Transporters in Humans and Animal Species Used for the Investigation of Nasal Absorption. (Al-Ghabeish M, Scheetz T, Assem M, Donovan MD) Mol Pharm 2015 Aug 03;12(8):2742-54       21 Citations
1Calcium/calmodulin-dependent kinase II inhibition in smooth muscle reduces angiotensin II-induced hypertension by controlling aortic remodeling and baroreceptor function. (Prasad AM, Morgan DA, Nuno DW, Ketsawatsomkron P, Bair TB, Venema AN, Dibbern ME, Kutschke WJ, Weiss RM, Lamping KG, Chapleau MW, Sigmund CD, Rahmouni K, Grumbach IM) J Am Heart Assoc 2015 Jun 15;4(6):e001949       36 Citations
1Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations. (Hu YJ, Li Y, Auer PL, Lin DY) Proc Natl Acad Sci U S A 2015 Jan 27;112(4):1019-24       12 Citations
1NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases. (Nalls MA, Bras J, Hernandez DG, Keller MF, Majounie E, Renton AE, Saad M, Jansen I, Guerreiro R, Lubbe S, Plagnol V, Gibbs JR, Schulte C, Pankratz N, Sutherland M, Bertram L, Lill CM, DeStefano AL, Faroud T, Eriksson N, Tung JY, Edsall C, Nichols N, Brooks J, Arepalli S, Pliner H, Letson C, Heutink P, Martinez M, Gasser T, Traynor BJ, Wood N, Hardy J, Singleton AB, International Parkinson's Disease Genomics Consortium (IPDGC), Parkinson's Disease meta-analysis consortium) Neurobiol Aging 2015 Mar;36(3):1605.e7-12       85 Citations
1NEK2 mediates ALDH1A1-dependent drug resistance in multiple myeloma. (Yang Y, Zhou W, Xia J, Gu Z, Wendlandt E, Zhan X, Janz S, Tricot G, Zhan F) Oncotarget 2014 Dec 15;5(23):11986-97       62 Citations
1Histopathologic alterations associated with global gene expression due to chronic dietary TCDD exposure in juvenile zebrafish. (Liu Q, Spitsbergen JM, Cariou R, Huang CY, Jiang N, Goetz G, Hutz RJ, Tonellato PJ, Carvan MJ 3rd) PLoS One 2014;9(7):e100910       16 Citations
1Notch3 pathway alterations in ovarian cancer. (Hu W, Liu T, Ivan C, Sun Y, Huang J, Mangala LS, Miyake T, Dalton HJ, Pradeep S, Rupaimoole R, Previs RA, Han HD, Bottsford-Miller J, Zand B, Kang Y, Pecot CV, Nick AM, Wu SY, Lee JS, Sehgal V, Ram P, Liu J, Tucker SL, Lopez-Berestein G, Baggerly KA, Coleman RL, Sood AK) Cancer Res 2014 Jun 15;74(12):3282-93       59 Citations
1Expression profiling of the RPE in zebrafish smarca4 mutant revealed altered signals that potentially affect RPE and retinal differentiation. (Zhang L, Ma P, Collery R, Trowbridge S, Zhang M, Zhong W, Leung YF) Mol Vis 2014;20:56-72       5 Citations
1Antagonistic regulation by the transcription factors C/EBPα and MITF specifies basophil and mast cell fates. (Qi X, Hong J, Chaves L, Zhuang Y, Chen Y, Wang D, Chabon J, Graham B, Ohmori K, Li Y, Huang H) Immunity 2013 Jul 25;39(1):97-110       119 Citations
1Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans. (Ahn SH, Tsalik EL, Cyr DD, Zhang Y, van Velkinburgh JC, Langley RJ, Glickman SW, Cairns CB, Zaas AK, Rivers EP, Otero RM, Veldman T, Kingsmore SF, Lucas J, Woods CW, Ginsburg GS, Fowler VG Jr) PLoS One 2013;8(1):e48979       51 Citations
1Increased dietary intake of vitamin A promotes aortic valve calcification in vivo. (Huk DJ, Hammond HL, Kegechika H, Lincoln J) Arterioscler Thromb Vasc Biol 2013 Feb;33(2):285-93       30 Citations
1Hierarchical modularity in ERα transcriptional network is associated with distinct functions and implicates clinical outcomes. (Tang B, Hsu HK, Hsu PY, Bonneville R, Chen SS, Huang TH, Jin VX) Sci Rep 2012;2:875       25 Citations
1Concordance of DMET plus genotyping results with those of orthogonal genotyping methods. (Fernandez CA, Smith C, Yang W, Lorier R, Crews KR, Kornegay N, Hicks JK, Stewart CF, Kawedia JD, Ramsey LB, Liu C, Evans WE, Relling MV, Broeckel U) Clin Pharmacol Ther 2012 Sep;92(3):360-5       38 Citations
1Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data. (Cai J, Keen HL, Sigmund CD, Casavant TL) J Integr Bioinform 2012 Jul 30;9(1):208       3 Citations
1The feed-forward loop between YB-1 and MYC is essential for multiple myeloma cell survival. (Bommert KS, Effenberger M, Leich E, Küspert M, Murphy D, Langer C, Moll R, Janz S, Mottok A, Weissbach S, Rosenwald A, Bargou R, Bommert K) Leukemia 2013 Feb;27(2):441-50       45 Citations
1Clinical phenotype and candidate genes for the 5q31.3 microdeletion syndrome. (Hosoki K, Ohta T, Natsume J, Imai S, Okumura A, Matsui T, Harada N, Bacino CA, Scaglia F, Jones JY, Niikawa N, Saitoh S) Am J Med Genet A 2012 Aug;158A(8):1891-6       26 Citations
3Role of genetic modifiers in an orthologous rat model of ARPKD. (O'Meara CC, Hoffman M, Sweeney WE Jr, Tsaih SW, Xiao B, Jacob HJ, Avner ED, Moreno C) Physiol Genomics 2012 Aug 01;44(15):741-53       23 Citations
1Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects. (Sung YJ, Gu CC, Tiwari HK, Arnett DK, Broeckel U, Rao DC) Genet Epidemiol 2012 Jul;36(5):508-16       12 Citations
3Requirements for growth and IL-10 expression of highly purified human T regulatory cells. (Bonacci B, Edwards B, Jia S, Williams CB, Hessner MJ, Gauld SB, Verbsky JW) J Clin Immunol 2012 Oct;32(5):1118-28       11 Citations
1Collaborative Ocular Oncology Group report number 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. (Onken MD, Worley LA, Char DH, Augsburger JJ, Correa ZM, Nudleman E, Aaberg TM Jr, Altaweel MM, Bardenstein DS, Finger PT, Gallie BL, Harocopos GJ, Hovland PG, McGowan HD, Milman T, Mruthyunjaya P, Simpson ER, Smith ME, Wilson DJ, Wirostko WJ, Harbour JW) Ophthalmology 2012 Aug;119(8):1596-603       426 Citations
2Atypical E2F repressors and activators coordinate placental development. (Ouseph MM, Li J, Chen HZ, Pécot T, Wenzel P, Thompson JC, Comstock G, Chokshi V, Byrne M, Forde B, Chong JL, Huang K, Machiraju R, de Bruin A, Leone G) Dev Cell 2012 Apr 17;22(4):849-62       83 Citations
2Intestinal microbiota as novel biomarkers of prior radiation exposure. (Lam V, Moulder JE, Salzman NH, Dubinsky EA, Andersen GL, Baker JE) Radiat Res 2012 May;177(5):573-83       68 Citations
1Identification of vascular and hematopoietic genes downstream of etsrp by deep sequencing in zebrafish. (Gomez G, Lee JH, Veldman MB, Lu J, Xiao X, Lin S) PLoS One 2012;7(3):e31658       25 Citations
5Human gene copy number spectra analysis in congenital heart malformations. (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) Physiol Genomics 2012 May 01;44(9):518-41       89 Citations
2Reprogramming of the tumour microenvironment by stromal PTEN-regulated miR-320. (Bronisz A, Godlewski J, Wallace JA, Merchant AS, Nowicki MO, Mathsyaraja H, Srinivasan R, Trimboli AJ, Martin CK, Li F, Yu L, Fernandez SA, Pécot T, Rosol TJ, Cory S, Hallett M, Park M, Piper MG, Marsh CB, Yee LD, Jimenez RE, Nuovo G, Lawler SE, Chiocca EA, Leone G, Ostrowski MC) Nat Cell Biol 2011 Dec 18;14(2):159-67       251 Citations
1S100A7 enhances mammary tumorigenesis through upregulation of inflammatory pathways. (Nasser MW, Qamri Z, Deol YS, Ravi J, Powell CA, Trikha P, Schwendener RA, Bai XF, Shilo K, Zou X, Leone G, Wolf R, Yuspa SH, Ganju RK) Cancer Res 2012 Feb 01;72(3):604-15       104 Citations
1Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells reveals potential intervention targets for plasma cell neoplasia. (LeGrand J, Park ES, Wang H, Gupta S, Owens JD Jr, Nelson PJ, DuBois W, Bair T, Janz S, Mushinski JF) Blood 2012 Jan 26;119(4):1018-28       6 Citations
1Microdeletions and microduplications in patients with congenital heart disease and multiple congenital anomalies. (Goldmuntz E, Paluru P, Glessner J, Hakonarson H, Biegel JA, White PS, Gai X, Shaikh TH) Congenit Heart Dis 2011;6(6):592-602       90 Citations
2Mechanochemical control of mesenchymal condensation and embryonic tooth organ formation. (Mammoto T, Mammoto A, Torisawa YS, Tat T, Gibbs A, Derda R, Mannix R, de Bruijn M, Yung CW, Huh D, Ingber DE) Dev Cell 2011 Oct 18;21(4):758-69       167 Citations
2Evaluation of a microarray-based genotyping assay for the rapid detection of cytochrome P450 2C19 *2 and *3 polymorphisms from whole blood using nanoparticle probes. (Buchan BW, Peterson JF, Cogbill CH, Anderson DK, Ledford JS, White MN, Quigley NB, Jannetto PJ, Ledeboer NA) Am J Clin Pathol 2011 Oct;136(4):604-8       21 Citations
1PITX2 is involved in stress response in cultured human trabecular meshwork cells through regulation of SLC13A3. (Strungaru MH, Footz T, Liu Y, Berry FB, Belleau P, Semina EV, Raymond V, Walter MA) Invest Ophthalmol Vis Sci 2011 Sep 29;52(10):7625-33       25 Citations
2Sox factors transcriptionally regulate ROBO4 gene expression in developing vasculature in zebrafish. (Samant GV, Schupp MO, François M, Moleri S, Kothinti RK, Chun CZ, Sinha I, Sellars S, Leigh N, Pramanik K, Horswill MA, Remadevi I, Li K, Wilkinson GA, Tabatabai NM, Beltrame M, Koopman P, Ramchandran R) J Biol Chem 2011 Sep 02;286(35):30740-30747       14 Citations
1Transformation of human mesenchymal cells and skin fibroblasts into hematopoietic cells. (Harris DM, Hazan-Haley I, Coombes K, Bueso-Ramos C, Liu J, Liu Z, Li P, Ravoori M, Abruzzo L, Han L, Singh S, Sun M, Kundra V, Kurzrock R, Estrov Z) PLoS One 2011;6(6):e21250       31 Citations
1Regulation of glycosyltransferase genes in apoptotic breast cancer cells induced by L: -PPMP and cisplatin. (Ma R, Hopp EA, Decker NM, Loucks A, Johnson JR, Moskal J, Basu M, Banerjee S, Basu S) Adv Exp Med Biol 2011;705:621-42       4 Citations
1SAQC: SNP array quality control. (Yang HC, Lin HC, Kang M, Chen CH, Lin CW, Li LH, Wu JY, Chen YT, Pan WH) BMC Bioinformatics 2011 Apr 18;12:100       6 Citations
1The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. (Liu Y, Bauer SC, Imlay JA) J Bacteriol 2011 May;193(9):2186-96       63 Citations
1Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with hematologic malignancies. (Dougherty MJ, Wilmoth DM, Tooke LS, Shaikh TH, Gai X, Hakonarson H, Biegel JA) Cancer Genet 2011 Jan;204(1):26-38       29 Citations
1A gene expression signature from human breast cancer cells with acquired hormone independence identifies MYC as a mediator of antiestrogen resistance. (Miller TW, Balko JM, Ghazoui Z, Dunbier A, Anderson H, Dowsett M, González-Angulo AM, Mills GB, Miller WR, Wu H, Shyr Y, Arteaga CL) Clin Cancer Res 2011 Apr 01;17(7):2024-34       85 Citations
1Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer. (Zuo T, Liu TM, Lan X, Weng YI, Shen R, Gu F, Huang YW, Liyanarachchi S, Deatherage DE, Hsu PY, Taslim C, Ramaswamy B, Shapiro CL, Lin HJ, Cheng AS, Jin VX, Huang TH) Cancer Res 2011 Mar 01;71(5):1752-62       54 Citations
1W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. (Lan X, Bonneville R, Apostolos J, Wu W, Jin VX) Bioinformatics 2011 Feb 01;27(3):428-30       45 Citations
1Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina. (Natoli R, Zhu Y, Valter K, Bisti S, Eells J, Stone J) Mol Vis 2010 Sep 03;16:1801-22       116 Citations
1Identification of genetic determinants of IGF-1 levels and longevity among mouse inbred strains. (Leduc MS, Hageman RS, Meng Q, Verdugo RA, Tsaih SW, Churchill GA, Paigen B, Yuan R) Aging Cell 2010 Oct;9(5):823-36       32 Citations
1Tumor antigen analysis in neuroblastoma by serological interrogation of bioinformatic data. (Kohler ME, Johnson BD, Palen K, Chen QR, Khan J, Orentas RJ) Cancer Sci 2010 Nov;101(11):2316-24       6 Citations
1Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles. (Meadows SK, Dressman HK, Daher P, Himburg H, Russell JL, Doan P, Chao NJ, Lucas J, Nevins JR, Chute JP) PLoS One 2010 Jul 12;5(7):e11535       51 Citations
1Early differential expression of oncostatin M in obstructive nephropathy. (Elbjeirami WM, Truong LD, Tawil A, Wang W, Dawson S, Lan HY, Zhang P, Garcia GE, Wayne Smith C) J Interferon Cytokine Res 2010 Jul;30(7):513-23       16 Citations
1Use of cross species genomic profiling identifies pathways and genes differentially regulated in prostate cancer cells treated with soy protein isolates or purified genistein. (Liss MA, Schlicht M, Degueme A, Hessner M, Datta MW) Cancer Genomics Proteomics 2010;7(3):111-28       5 Citations
1Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. (Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, Bennett LB, Shi H, Davis JW, Arthur GL, Shanafelt TD, Kay NE, Wooldridge JE, Caldwell CW) Epigenomics 2009 Oct;1(1):39-61       49 Citations
1Ectopic expression of wild-type FGFR3 cooperates with MYC to accelerate development of B-cell lineage neoplasms. (Zingone A, Cultraro CM, Shin DM, Bean CM, Morse HC 3rd, Janz S, Kuehl WM) Leukemia 2010 Jun;24(6):1171-8       21 Citations
1Elevated PIN1 expression by C/EBPalpha-p30 blocks C/EBPalpha-induced granulocytic differentiation through c-Jun in AML. (Pulikkan JA, Dengler V, Peer Zada AA, Kawasaki A, Geletu M, Pasalic Z, Bohlander SK, Ryo A, Tenen DG, Behre G) Leukemia 2010 May;24(5):914-23       47 Citations
1Functional muscle analysis of the Tcap knockout mouse. (Markert CD, Meaney MP, Voelker KA, Grange RW, Dalley HW, Cann JK, Ahmed M, Bishwokarma B, Walker SJ, Yu SX, Brown M, Lawlor MW, Beggs AH, Childers MK) Hum Mol Genet 2010 Jun 01;19(11):2268-83       40 Citations
1Emerging regulatory paradigms for control of gene expression by 1,25-dihydroxyvitamin D3. (Pike JW, Meyer MB, Martowicz ML, Bishop KA, Lee SM, Nerenz RD, Goetsch PD) J Steroid Biochem Mol Biol 2010 Jul;121(1-2):130-5       51 Citations
1An ets2-driven transcriptional program in tumor-associated macrophages promotes tumor metastasis. (Zabuawala T, Taffany DA, Sharma SM, Merchant A, Adair B, Srinivasan R, Rosol TJ, Fernandez S, Huang K, Leone G, Ostrowski MC) Cancer Res 2010 Feb 15;70(4):1323-33       110 Citations
1CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. (Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS) BMC Bioinformatics 2010 Feb 04;11:74       45 Citations
1A microRNA expression signature for cervical cancer prognosis. (Hu X, Schwarz JK, Lewis JS Jr, Huettner PC, Rader JS, Deasy JO, Grigsby PW, Wang X) Cancer Res 2010 Feb 15;70(4):1441-8       280 Citations
1PepD participates in the mycobacterial stress response mediated through MprAB and SigE. (White MJ, He H, Penoske RM, Twining SS, Zahrt TC) J Bacteriol 2010 Mar;192(6):1498-510       56 Citations
1Brucella melitensis, B. neotomae and B. ovis elicit common and distinctive macrophage defense transcriptional responses. (Covert J, Mathison AJ, Eskra L, Banai M, Splitter G) Exp Biol Med (Maywood) 2009 Dec;234(12):1450-67       33 Citations
1Chromosome 7 and 19 trisomy in cultured human neural progenitor cells. (Sareen D, McMillan E, Ebert AD, Shelley BC, Johnson JA, Meisner LF, Svendsen CN) PLoS One 2009 Oct 29;4(10):e7630       59 Citations
1W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. (Jin VX, Apostolos J, Nagisetty NS, Farnham PJ) Bioinformatics 2009 Dec 01;25(23):3191-3       41 Citations
1High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. (Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, Murphy K, O'Hara R, Casalunovo T, Conlin LK, D'Arcy M, Frackelton EC, Geiger EA, Haldeman-Englert C, Imielinski M, Kim CE, Medne L, Annaiah K, Bradfield JP, Dabaghyan E, Eckert A, Onyiah CC, Ostapenko S, Otieno FG, Santa E, Shaner JL, Skraban R, Smith RM, Elia J, Goldmuntz E, Spinner NB, Zackai EH, Chiavacci RM, Grundmeier R, Rappaport EF, Grant SF, White PS, Hakonarson H) Genome Res 2009 Sep;19(9):1682-90       307 Citations
4An autoinflammatory disease due to homozygous deletion of the IL1RN locus. (Reddy S, Jia S, Geoffrey R, Lorier R, Suchi M, Broeckel U, Hessner MJ, Verbsky J) N Engl J Med 2009 Jun 04;360(23):2438-44       360 Citations
1Involvement of a membrane-bound class III adenylate cyclase in regulation of anaerobic respiration in Shewanella oneidensis MR-1. (Charania MA, Brockman KL, Zhang Y, Banerjee A, Pinchuk GE, Fredrickson JK, Beliaev AS, Saffarini DA) J Bacteriol 2009 Jul;191(13):4298-306       65 Citations
1Genomic analysis using high-density single nucleotide polymorphism-based oligonucleotide arrays and multiplex ligation-dependent probe amplification provides a comprehensive analysis of INI1/SMARCB1 in malignant rhabdoid tumors. (Jackson EM, Sievert AJ, Gai X, Hakonarson H, Judkins AR, Tooke L, Perin JC, Xie H, Shaikh TH, Biegel JA) Clin Cancer Res 2009 Mar 15;15(6):1923-30       174 Citations
1Chemical genomics of cancer chemopreventive dithiolethiones. (Tran QT, Xu L, Phan V, Goodwin SB, Rahman M, Jin VX, Sutter CH, Roebuck BD, Kensler TW, George EO, Sutter TR) Carcinogenesis 2009 Mar;30(3):480-6       22 Citations
1A 3.1-Mb microdeletion of 3p21.31 associated with cortical blindness, cleft lip, CNS abnormalities, and developmental delay. (Haldeman-Englert CR, Gai X, Perin JC, Ciano M, Halbach SS, Geiger EA, McDonald-McGinn DM, Hakonarson H, Zackai EH, Shaikh TH) Eur J Med Genet 2009;52(4):265-8       19 Citations
1N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. (Cotterman R, Jin VX, Krig SR, Lemen JM, Wey A, Farnham PJ, Knoepfler PS) Cancer Res 2008 Dec 01;68(23):9654-62       112 Citations
1Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. (Sievert AJ, Jackson EM, Gai X, Hakonarson H, Judkins AR, Resnick AC, Sutton LN, Storm PB, Shaikh TH, Biegel JA) Brain Pathol 2009 Jul;19(3):449-58       210 Citations
1E2f3a and E2f3b contribute to the control of cell proliferation and mouse development. (Chong JL, Tsai SY, Sharma N, Opavsky R, Price R, Wu L, Fernandez SA, Leone G) Mol Cell Biol 2009 Jan;29(2):414-24       70 Citations
1Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. (Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA) PLoS One 2008;3(10):e3583       325 Citations
1Quorum sensing primes the oxidative stress response in the insect endosymbiont, Sodalis glossinidius. (Pontes MH, Babst M, Lochhead R, Oakeson K, Smith K, Dale C) PLoS One 2008;3(10):e3541       38 Citations
1The effects of acute 17beta-estradiol treatment on gene expression in the young female mouse hippocampus. (Pechenino AS, Frick KM) Neurobiol Learn Mem 2009 Mar;91(3):315-22       35 Citations
1E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. (Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ) Genome Res 2008 Nov;18(11):1763-77       116 Citations
2Snrk-1 is involved in multiple steps of angioblast development and acts via notch signaling pathway in artery-vein specification in vertebrates. (Chun CZ, Kaur S, Samant GV, Wang L, Pramanik K, Garnaas MK, Li K, Field L, Mukhopadhyay D, Ramchandran R) Blood 2009 Jan 29;113(5):1192-9       29 Citations
1Zebrafish as a developmental model organism for pediatric research. (Veldman MB, Lin S) Pediatr Res 2008 Nov;64(5):470-6       155 Citations
2Detection of 11 common viral and bacterial pathogens causing community-acquired pneumonia or sepsis in asymptomatic patients by using a multiplex reverse transcription-PCR assay with manual (enzyme hybridization) or automated (electronic microarray) detection. (Kumar S, Wang L, Fan J, Kraft A, Bose ME, Tiwari S, Van Dyke M, Haigis R, Luo T, Ghosh M, Tang H, Haghnia M, Mather EL, Weisburg WG, Henrickson KJ) J Clin Microbiol 2008 Sep;46(9):3063-72       89 Citations
1Global expression profiling identifies a novel biosignature for protein aggregation R120GCryAB cardiomyopathy in mice. (Rajasekaran NS, Firpo MA, Milash BA, Weiss RB, Benjamin IJ) Physiol Genomics 2008 Oct 08;35(2):165-72       26 Citations
2Molecular networks in Dahl salt-sensitive hypertension based on transcriptome analysis of a panel of consomic rats. (Liang M, Lee NH, Wang H, Greene AS, Kwitek AE, Kaldunski ML, Luu TV, Frank BC, Bugenhagen S, Jacob HJ, Cowley AW Jr) Physiol Genomics 2008 Jun 12;34(1):54-64       43 Citations
1Type IV pili in Francisella tularensis: roles of pilF and pilT in fiber assembly, host cell adherence, and virulence. (Chakraborty S, Monfett M, Maier TM, Benach JL, Frank DW, Thanassi DG) Infect Immun 2008 Jul;76(7):2852-61       68 Citations
1High perfusion pressure accelerates renal injury in salt-sensitive hypertension. (Mori T, Polichnowski A, Glocka P, Kaldunski M, Ohsaki Y, Liang M, Cowley AW Jr) J Am Soc Nephrol 2008 Aug;19(8):1472-82       92 Citations
1Targeted deletion of Prkar1a reveals a role for protein kinase A in mesenchymal-to-epithelial transition. (Nadella KS, Jones GN, Trimboli A, Stratakis CA, Leone G, Kirschner LS) Cancer Res 2008 Apr 15;68(8):2671-7       34 Citations
1Genetic analysis of congenital cystic adenomatoid malformation reveals a novel pulmonary gene: fatty acid binding protein-7 (brain type). (Wagner AJ, Stumbaugh A, Tigue Z, Edmondson J, Paquet AC, Farmer DL, Hawgood S) Pediatr Res 2008 Jul;64(1):11-6       41 Citations
1Genotyping platforms for mass-throughput genotyping with SNPs, including human genome-wide scans. (Maresso K, Broeckel U) Adv Genet 2008;60:107-39       29 Citations
1Identification of novel susceptibility genes in childhood-onset systemic lupus erythematosus using a uniquely designed candidate gene pathway platform. (Jacob CO, Reiff A, Armstrong DL, Myones BL, Silverman E, Klein-Gitelman M, McCurdy D, Wagner-Weiner L, Nocton JJ, Solomon A, Zidovetzki R) Arthritis Rheum 2007 Dec;56(12):4164-73       73 Citations
1Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. (Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McK Bird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ) Genome Biol 2007;8(10):R211       43 Citations
1Microarray analysis reveals distinctive signaling between the bed nucleus of the stria terminalis, nucleus accumbens, and dorsal striatum. (Olsen CM, Huang Y, Goodwin S, Ciobanu DC, Lu L, Sutter TR, Winder DG) Physiol Genomics 2008 Feb 19;32(3):283-98       18 Citations
2Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. (Heiden TC, Struble CA, Rise ML, Hessner MJ, Hutz RJ, Carvan MJ 3rd) Reprod Toxicol 2008 Jan;25(1):47-57       55 Citations
1Quantitative measurement of pathogen-specific human memory T cell repertoire diversity using a CDR3 beta-specific microarray. (Wang X, Jia S, Meyer L, Yassai MB, Naumov YN, Gorski J, Hessner MJ) BMC Genomics 2007 Sep 19;8:329       5 Citations
1Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates. (Gius D, Funk MC, Chuang EY, Feng S, Huettner PC, Nguyen L, Bradbury CM, Mishra M, Gao S, Buttin BM, Cohn DE, Powell MA, Horowitz NS, Whitcomb BP, Rader JS) Cancer Res 2007 Aug 01;67(15):7113-23       79 Citations
2Distinct profiles of endothelial gene expression in hyperpermeable regions of the porcine aortic arch and thoracic aorta. (LaMack JA, Himburg HA, Friedman MH) Atherosclerosis 2007 Dec;195(2):e35-41       11 Citations
1Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. (Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ) Genome Res 2007 Jun;17(6):807-17       50 Citations
1Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissues. (Mullins M, Perreard L, Quackenbush JF, Gauthier N, Bayer S, Ellis M, Parker J, Perou CM, Szabo A, Bernard PS) Clin Chem 2007 Jul;53(7):1273-9       61 Citations
1Unique requirement for Rb/E2F3 in neuronal migration: evidence for cell cycle-independent functions. (McClellan KA, Ruzhynsky VA, Douda DN, Vanderluit JL, Ferguson KL, Chen D, Bremner R, Park DS, Leone G, Slack RS) Mol Cell Biol 2007 Jul;27(13):4825-43       75 Citations
1Serum from mice immunized in the context of Treg inhibition identifies DEK as a neuroblastoma tumor antigen. (Zheng J, Kohler ME, Chen Q, Weber J, Khan J, Johnson BD, Orentas RJ) BMC Immunol 2007 Mar 30;8:4       11 Citations
1Gene expression analysis of gallium-resistant and gallium-sensitive lymphoma cells reveals a role for metal-responsive transcription factor-1, metallothionein-2A, and zinc transporter-1 in modulating the antineoplastic activity of gallium nitrate. (Yang M, Kroft SH, Chitambar CR) Mol Cancer Ther 2007 Feb;6(2):633-43       35 Citations
1N-{3-[2-(4-alkoxyphenoxy)thiazol-5-yl]-1-methylprop-2-ynyl}carboxy derivatives as acetyl-coA carboxylase inhibitors--improvement of cardiovascular and neurological liabilities via structural modifications. (Gu YG, Weitzberg M, Clark RF, Xu X, Li Q, Lubbers NL, Yang Y, Beno DW, Widomski DL, Zhang T, Hansen TM, Keyes RF, Waring JF, Carroll SL, Wang X, Wang R, Healan-Greenberg CH, Blomme EA, Beutel BA, Sham HL, Camp HS) J Med Chem 2007 Mar 08;50(5):1078-82       35 Citations
1Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. (Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ) J Biol Chem 2007 Mar 30;282(13):9703-9712       71 Citations
1Microarray and real-time PCR analysis of adrenal gland gene expression in the 7-day-old rat: effects of hypoxia from birth. (Bruder ED, Lee JJ, Widmaier EP, Raff H) Physiol Genomics 2007 Apr 24;29(2):193-200       17 Citations
1The interaction of adenovirus E1A with p300 family members modulates cellular gene expression to reduce tumorigenicity. (Miura TA, Cook JL, Potter TA, Ryan S, Routes JM) J Cell Biochem 2007 Mar 01;100(4):929-40       5 Citations
1Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. (Elnitski L, Jin VX, Farnham PJ, Jones SJ) Genome Res 2006 Dec;16(12):1455-64       188 Citations
1A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. (Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ) Genome Res 2006 Dec;16(12):1585-95       59 Citations
1Identification of genes regulated by Wnt/beta-catenin pathway and involved in apoptosis via microarray analysis. (Huang M, Wang Y, Sun D, Zhu H, Yin Y, Zhang W, Yang S, Quan L, Bai J, Wang S, Chen Q, Li S, Xu N) BMC Cancer 2006 Sep 07;6:221       47 Citations
1Potential role of Jun activation domain-binding protein 1 as a negative regulator of p27kip1 in pancreatic adenocarcinoma. (Kouvaraki MA, Korapati AL, Rassidakis GZ, Tian L, Zhang Q, Chiao P, Ho L, Evans DB, Claret FX) Cancer Res 2006 Sep 01;66(17):8581-9       55 Citations
1Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays. (Wang X, Jia S, Meyer L, Xiang B, Chen LY, Jiang N, Moreno C, Jacob HJ, Ghosh S, Hessner MJ) BMC Bioinformatics 2006 Aug 14;7:378       8 Citations
1Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior. (Rahmatpanah FB, Carstens S, Guo J, Sjahputera O, Taylor KH, Duff D, Shi H, Davis JW, Hooshmand SI, Chitma-Matsiga R, Caldwell CW) Leukemia 2006 Oct;20(10):1855-62       67 Citations
1Microarray analysis of differentially expressed genes in mouse bone marrow tissues after ionizing radiation. (Dai JM, Sun DC, Lin RX, Yang J, Lou S, Wang SQ) Int J Radiat Biol 2006 Jul;82(7):511-21       19 Citations
1Dickkopf homologs in squamous mucosa of esophagitis patients are overexpressed compared with Barrett's patients and healthy controls. (Ali I, Rafiee P, Hogan WJ, Jacob HJ, Komorowski RA, Haasler GB, Shaker R) Am J Gastroenterol 2006 Jul;101(7):1437-48       19 Citations
1CDDO-Imidazolide inhibits growth and survival of c-Myc-induced mouse B cell and plasma cell neoplasms. (Han SS, Peng L, Chung ST, DuBois W, Maeng SH, Shaffer AL, Sporn MB, Janz S) Mol Cancer 2006 Jun 07;5:22       15 Citations
1Suz12 binds to silenced regions of the genome in a cell-type-specific manner. (Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ) Genome Res 2006 Jul;16(7):890-900       275 Citations
1Assessing the reliability of amplified RNA used in microarrays: a DUMB table approach. (Bearden ED, Simpson PM, Peterson CA, Beggs ML) Appl Bioinformatics 2006;5(2):67-76       2 Citations
1Gene expression patterns in advanced human cervical cancer. (Grigsby PW, Watson M, Powell MA, Zhang Z, Rader JS) Int J Gynecol Cancer 2006;16(2):562-7       28 Citations
1Identification of chromosomal alterations important in the development of cervical intraepithelial neoplasia and invasive carcinoma using alignment of DNA microarray data. (Fitzpatrick MA, Funk MC, Gius D, Huettner PC, Zhang Z, Bidder M, Ma D, Powell MA, Rader JS) Gynecol Oncol 2006 Nov;103(2):458-62       18 Citations
1Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region. (Riehle MM, Markianos K, Niaré O, Xu J, Li J, Touré AM, Podiougou B, Oduol F, Diawara S, Diallo M, Coulibaly B, Ouatara A, Kruglyak L, Traoré SF, Vernick KD) Science 2006 Apr 28;312(5773):577-9       229 Citations
1Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay. (Perreard L, Fan C, Quackenbush JF, Mullins M, Gauthier NP, Nelson E, Mone M, Hansen H, Buys SS, Rasmussen K, Orrico AR, Dreher D, Walters R, Parker J, Hu Z, He X, Palazzo JP, Olopade OI, Szabo A, Perou CM, Bernard PS) Breast Cancer Res 2006;8(2):R23       167 Citations
1Aberrant promoter methylation and silencing of the POU2F3 gene in cervical cancer. (Zhang Z, Huettner PC, Nguyen L, Bidder M, Funk MC, Li J, Rader JS) Oncogene 2006 Aug 31;25(39):5436-45       34 Citations
1Combinatorial analysis of transcription factor partners reveals recruitment of c-MYC to estrogen receptor-alpha responsive promoters. (Cheng AS, Jin VX, Fan M, Smith LT, Liyanarachchi S, Yan PS, Leu YW, Chan MW, Plass C, Nephew KP, Davuluri RV, Huang TH) Mol Cell 2006 Feb 03;21(3):393-404       157 Citations
1Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. (Hessner MJ, Xiang B, Jia S, Geoffrey R, Holmes S, Meyer L, Muheisen S, Wang X) Physiol Genomics 2006 Mar 13;25(1):166-78       5 Citations
1MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. (Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV) Nucleic Acids Res 2006 Jan 01;34(Database issue):D98-103       35 Citations
2Fetomaternal cross talk in the placental vascular bed: control of coagulation by trophoblast cells. (Sood R, Kalloway S, Mast AE, Hillard CJ, Weiler H) Blood 2006 Apr 15;107(8):3173-80       89 Citations
1Role of the serum response factor in regulating contractile apparatus gene expression and sarcomeric integrity in cardiomyocytes. (Balza RO Jr, Misra RP) J Biol Chem 2006 Mar 10;281(10):6498-510       86 Citations
1Molecular and cytological features of the mouse B-cell lymphoma line iMycEmu-1. (Han SS, Shaffer AL, Peng L, Chung ST, Lim JH, Maeng S, Kim JS, McNeil N, Ried T, Staudt LM, Janz S) Mol Cancer 2005 Nov 09;4:40       6 Citations
1ERTargetDB: an integral information resource of transcription regulation of estrogen receptor target genes. (Jin VX, Sun H, Pohar TT, Liyanarachchi S, Palaniswamy SK, Huang TH, Davuluri RV) J Mol Endocrinol 2005 Oct;35(2):225-30       27 Citations
1Specific pharmacological dimerization of KDR in lentivirally transduced human hematopoietic cells activates anti-apoptotic and proliferative mechanisms. (Siatskas C, Underwood J, Ramezani A, Hawley RG, Medin JA) FASEB J 2005 Oct;19(12):1752-4       10 Citations
1Tumor-associated alterations in caspase-14 expression in epithelial malignancies. (Krajewska M, Kim H, Shin E, Kennedy S, Duffy MJ, Wong YF, Marr D, Mikolajczyk J, Shabaik A, Meinhold-Heerlein I, Huang X, Banares S, Hedayat H, Reed JC, Krajewski S) Clin Cancer Res 2005 Aug 01;11(15):5462-71       60 Citations
1Changes in gene expression following high-temperature adaptation in experimentally evolved populations of E. coli. (Riehle MM, Bennett AF, Long AD) Physiol Biochem Zool 2005;78(3):299-315       21 Citations
2Transcriptome analysis and kidney research: toward systems biology. (Liang M, Cowley AW Jr, Hessner MJ, Lazar J, Basile DP, Pietrusz JL) Kidney Int 2005 Jun;67(6):2114-22       23 Citations
1Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. (Liu H, Tarima S, Borders AS, Getchell TV, Getchell ML, Stromberg AJ) BMC Bioinformatics 2005 Apr 25;6:106       44 Citations
1Overexpression of tropomysin-related kinase B in metastatic human pancreatic cancer cells. (Sclabas GM, Fujioka S, Schmidt C, Li Z, Frederick WA, Yang W, Yokoi K, Evans DB, Abbruzzese JL, Hess KR, Zhang W, Fidler IJ, Chiao PJ) Clin Cancer Res 2005 Jan 15;11(2 Pt 1):440-9       122 Citations
1Identification of persistently altered gene expression in the kidney after functional recovery from ischemic acute renal failure. (Basile DP, Fredrich K, Alausa M, Vio CP, Liang M, Rieder MR, Greene AS, Cowley AW Jr) Am J Physiol Renal Physiol 2005 May;288(5):F953-63       89 Citations
1Discriminate gene lists derived from cDNA microarray profiles of limited samples permit distinguishing mesenchymal neoplasia ex vivo. (Joyner DE, Wade ML, Szabo A, Bastar J, Coffin CM, Albritton KH, Bernard PS, Randall RL) J Cancer Res Clin Oncol 2005 Mar;131(3):137-46       5 Citations
1Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray. (Jin VX, Leu YW, Liyanarachchi S, Sun H, Fan M, Nephew KP, Huang TH, Davuluri RV) Nucleic Acids Res 2004;32(22):6627-35       64 Citations
1Regulation and function of trefoil factor family 3 expression in the biliary tree. (Nozaki I, Lunz JG 3rd, Specht S, Park JI, Giraud AS, Murase N, Demetris AJ) Am J Pathol 2004 Dec;165(6):1907-20       47 Citations
1IFI16 is an essential mediator of growth inhibition, but not differentiation, induced by the leukemia inhibitory factor/JAK/STAT pathway in medullary thyroid carcinoma cells. (Kim EJ, Park JI, Nelkin BD) J Biol Chem 2005 Feb 11;280(6):4913-20       49 Citations
1Involvement of eotaxin, eosinophils, and pancreatic predisposition in development of type 1 diabetes mellitus in the BioBreeding rat. (Hessner MJ, Wang X, Meyer L, Geoffrey R, Jia S, Fuller J, Lernmark A, Ghosh S) J Immunol 2004 Dec 01;173(11):6993-7002       52 Citations
1A novel approach for high-quality microarray processing using third-dye array visualization technology. (Wang X, Jiang N, Feng X, Xie Y, Tonellato PJ, Ghosh S, Hessner MJ) IEEE Trans Nanobioscience 2003 Dec;2(4):193-201       15 Citations
1Sinusoidal length oscillation- and receptor-mediated mRNA expression of myosin isoforms and alpha-SM actin in airway smooth muscle. (Wahl M, Eddinger TJ, Hai CM) Am J Physiol Cell Physiol 2004 Dec;287(6):C1697-708       12 Citations
1Immobilized probe and glass surface chemistry as variables in microarray fabrication. (Hessner MJ, Meyer L, Tackes J, Muheisen S, Wang X) BMC Genomics 2004 Aug 04;5(1):53       38 Citations
1Statistical modeling for selecting housekeeper genes. (Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS) Genome Biol 2004;5(8):R59       164 Citations
2Identification of a low affinity mannose 6-phosphate-binding site in domain 5 of the cation-independent mannose 6-phosphate receptor. (Reddy ST, Chai W, Childs RA, Page JD, Feizi T, Dahms NM) J Biol Chem 2004 Sep 10;279(37):38658-67       60 Citations
1Coordinate expression of regulatory genes differentiates embryonic and perinatal forms of biliary atresia. (Zhang DY, Sabla G, Shivakumar P, Tiao G, Sokol RJ, Mack C, Shneider BL, Aronow B, Bezerra JA) Hepatology 2004 Apr;39(4):954-62       75 Citations
1Gene expression profiling of potential PPARgamma target genes in mouse aorta. (Keen HL, Ryan MJ, Beyer A, Mathur S, Scheetz TE, Gackle BD, Faraci FM, Casavant TL, Sigmund CD) Physiol Genomics 2004 Jun 17;18(1):33-42       44 Citations
1Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. (Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC) BMC Genomics 2004 Feb 09;5(1):12       33 Citations
1Interactions between hepatic Mrp4 and Sult2a as revealed by the constitutive androstane receptor and Mrp4 knockout mice. (Assem M, Schuetz EG, Leggas M, Sun D, Yasuda K, Reid G, Zelcer N, Adachi M, Strom S, Evans RM, Moore DD, Borst P, Schuetz JD) J Biol Chem 2004 May 21;279(21):22250-7       219 Citations
1Difference in gene expression profiles between human CD4+CD25+ and CD4+CD25- T cells. (Pati N, Ghosh S, Hessner MJ, Khoo HJ, Wang X) Ann N Y Acad Sci 2003 Nov;1005:279-83       6 Citations
1The design of a gene chip for functional immunological studies on a high-quality control platform. (Waukau J, Jailwala P, Wang Y, Khoo HJ, Ghosh S, Wang X, Hessner MJ) Ann N Y Acad Sci 2003 Nov;1005:284-7       3 Citations
1Multivariate exploratory tools for microarray data analysis. (Szabo A, Boucher K, Jones D, Tsodikov AD, Klebanov LB, Yakovlev AY) Biostatistics 2003 Oct;4(4):555-67       35 Citations
1COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations. (Hausmann M, Winkler R, Hildenbrand G, Finsterle J, Weisel A, Rapp A, Schmitt E, Janz S, Cremer C) Biotechniques 2003 Sep;35(3):564-70, 572-7       48 Citations
1Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. (Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S) Bioinformatics 2003 Jul 22;19(11):1341-7       68 Citations
2Consomic rats for the identification of genes and pathways underlying cardiovascular disease. (Roman RJ, Cowley AW Jr, Greene A, Kwitek AE, Tonellato PJ, Jacob HJ) Cold Spring Harb Symp Quant Biol 2002;67:309-15       20 Citations
1DNA expression analysis: serial analysis of gene expression, microarrays and kidney disease. (Hayden PS, El-Meanawy A, Schelling JR, Sedor JR) Curr Opin Nephrol Hypertens 2003 Jul;12(4):407-14       15 Citations
1Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies. (Liang M, Briggs AG, Rute E, Greene AS, Cowley AW Jr) Physiol Genomics 2003 Aug 15;14(3):199-207       35 Citations
1Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. (Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta MW, Jacob HJ, Ghosh S) Nucleic Acids Res 2003 Jun 01;31(11):e60       43 Citations
1Gene expression reveals vulnerability to oxidative stress and interstitial fibrosis of renal outer medulla to nonhypertensive elevations of ANG II. (Yuan B, Liang M, Yang Z, Rute E, Taylor N, Olivier M, Cowley AW Jr) Am J Physiol Regul Integr Comp Physiol 2003 May;284(5):R1219-30       27 Citations
1Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature. (Riehle MM, Bennett AF, Lenski RE, Long AD) Physiol Genomics 2003 Jun 24;14(1):47-58       78 Citations
1Microarray analysis of mRNA levels from RAW264.7 macrophages infected with Brucella abortus. (Eskra L, Mathison A, Splitter G) Infect Immun 2003 Mar;71(3):1125-33       96 Citations
1Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. (Hessner MJ, Wang X, Hulse K, Meyer L, Wu Y, Nye S, Guo SW, Ghosh S) Nucleic Acids Res 2003 Feb 15;31(4):e14       53 Citations
1Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. (Wang HY, Malek RL, Kwitek AE, Greene AS, Luu TV, Behbahani B, Frank B, Quackenbush J, Lee NH) Genome Biol 2003;4(1):R5       122 Citations
1Insights into Dahl salt-sensitive hypertension revealed by temporal patterns of renal medullary gene expression. (Liang M, Yuan B, Rute E, Greene AS, Olivier M, Cowley AW Jr) Physiol Genomics 2003 Feb 06;12(3):229-37       54 Citations
1Identification of gene expression profiles that segregate patients with childhood leukemia. (Moos PJ, Raetz EA, Carlson MA, Szabo A, Smith FE, Willman C, Wei Q, Hunger SP, Carroll WL) Clin Cancer Res 2002 Oct;8(10):3118-30       85 Citations
1Regulation of MDR-1 (P-glycoprotein) by cyclooxygenase-2. (Patel VA, Dunn MJ, Sorokin A) J Biol Chem 2002 Oct 11;277(41):38915-20       192 Citations
1Radiation hybrid mapping of 70 rat genes from a data set of differentially expressed genes. (Wallace CA, Ali S, Glazier AM, Norsworthy PJ, Carlos DC, Scott J, Freeman TC, Stanton LW, Kwitek AE, Aitman TJ) Mamm Genome 2002 Apr;13(4):194-7       7 Citations
1Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization. (Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai RP, Galbraith DW, Pierson EA, Walbot V) Plant Physiol 2002 Mar;128(3):896-910       88 Citations
1Renal medullary genes in salt-sensitive hypertension: a chromosomal substitution and cDNA microarray study. (Liang M, Yuan B, Rute E, Greene AS, Zou AP, Soares P, MCQuestion GD, Slocum GR, Jacob HJ, Cowley AW Jr) Physiol Genomics 2002 Feb 28;8(2):139-49       47 Citations
1Induction of chondrocyte growth arrest by FGF: transcriptional and cytoskeletal alterations. (Rozenblatt-Rosen O, Mosonego-Ornan E, Sadot E, Madar-Shapiro L, Sheinin Y, Ginsberg D, Yayon A) J Cell Sci 2002 Feb 01;115(Pt 3):553-62       56 Citations
1Multivariate approach for selecting sets of differentially expressed genes. (Chilingaryan A, Gevorgyan N, Vardanyan A, Jones D, Szabo A) Math Biosci 2002 Mar;176(1):59-69       34 Citations
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