Publications associated with the Covance Genomics Laboratory*

2012 Publications

Novel Tissue Types for the Development of Genomic Biomarkers

Zinaida Sergueeva, Heather Collins, Sally Dow, Mollie McWhorter and Mark L. Parrish (2012). Novel Tissue Types for the Development of Genomic Biomarkers, Biomarker, Prof. Tapan Khan (Ed.), ISBN: 978-953-51-0577-0, InTech.

Transcriptional architecture of the primate neocortex.
Neuron. 2012 Mar 22;73(6):1083-99. Epub 2012 Mar 21.

Bernard A, Lubbers LS, Tanis KQ, Luo R, Podtelezhnikov AA, Finney EM, McWhorter MM, Serikawa K, Lemon T, Morgan R, Copeland C, Smith K, Cullen V, Davis-Turak J, Lee CK, Sunkin SM, Loboda AP, Levine DM, Stone DJ, Hawrylycz MJ, Roberts CJ, Jones AR, Geschwind DH, Lein ES.

 

2011 Publications

A gene expression signature that classifies human atherosclerotic plaque by relative inflammation status.
Circ Cardiovasc Genet. Dec 1;4(6):595-604. Epub 2011 Oct 18.

Puig O, Yuan J, Stepaniants S, Zieba R, Zycband E, Morris M, Coulter S, Yu X, Menke J, Woods J, Chen F, Ramey DR, He X, O'Neill EA, Hailman E, Johns DG, Hubbard BK, Yee Lum P, Wright SD, Desouza MM, Plump A, Reiser V. 

2010 Publications

Identification and validation of genes affecting aortic lesions in mice.
J Clin Invest 2010 July 1; 120(7): 2414-2422.

Xia Yang, Larry Peterson, Rolf Thieringer, Joshua L. Deignan, Xuping Wang, Jun Zhu, Susanna Wang, Hua Zhong, Serguei Stepaniants, John Beaulaurier, I-Ming Wang, Ray Rosa, Anne-Marie Cumiskey, Jane Ming-Juan Luo, Qi Luo, Kashmira Shah, Jianying Xiao, David Nickle, Andrew Plump, Eric E. Schadt, Aldons J. Lusis, and Pek Yee Lum
 

2009 Publications

Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
Genome Biology 2009, 10:R55.

Radu Dobrin, Jun Zhu, Cliona Molony, Carmen Argman, Mark L Parrish, Sonia Carlson, Mark F Allan, Daniel Pomp and Eric E Schadt

Refined anatomical isolation of functional sleep circuits exhibits distinctive regional and circadian gene transcriptional profiles
Brain Res.2009 May 19;1271:1-17.

Christopher J. Winrow, Keith Q. Tanis, Alison M. Rigbya, Rhonda R. Taylora, Kyle Serikawa, Mollie McWhorter, George Y. Tokiwa, Matthew J. Marton, David J. Stone, Kenneth S. Koblan and John J. Renger

 

2008 Publications

Selection of housekeeping genes for real-time PCR in atopic human bronchial epithelial cells
Eur Respir J 2008 Sep;32(3):755-62. Epub 2008 Apr 16.

He JQ, Sandford AJ, Wang IM, Stepaniants S, Knight DA, Kicic A, Stick SM, Pare PD.

Characterization of Globin RNA Interference in Gene Expression Profiling of Whole-Blood Samples
Clinical Chemistry. 2008 54(2):396-405.

Christopher Wright, Donald Bergstrom, Hongyue Dai, Matthew Marton, Mark Morris, George Tokiwa, Yanqun Wang, and Thomas Fare

Improved high-throughput ultrafiltration process enables cRNA purification for gene expression profiling. 
ASSAY and Drug Development Technologies. 2008 6(3):421-32.

Morris MD, Meyer MR, Painchaud G, Marlowe J, Tokiwa GY, Fare TL.

2007 Publications

Reagent Preparation and Storage for Amplification of Microarray Hybridization Targets with a Fully Automated System
ASSAY and Drug Development Technologies. 2007 5(4):551-58.

Mingjie Zhou, Jon Marlowe, Jaime Graves, Jason Dahl, Zackery Riley, Lena Tian, Sven Duenwald, George Tokiwa, and Thomas L. Fare

2005 Publications

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.
Nucleic Acids Res. 2005 Dec 23;33(22):187.

Thompson KL, Rosenzweig BA, Pine PS, Retief J, Turpaz Y, Afshari CA, Hamadeh HK, Damore MA, Boedigheimer M, Blomme E, Ciurlionis R, Waring JF, Fuscoe JC, Paules R, Tucker CJ, Fare T, Coffey EM, He Y, Collins PJ, Jarnagin K, Fujimoto S, Ganter B, Kiser G, Kaysser-Kranich T, Sina J, Sistare FD.

Regulation of gene expression by lithium and depletion of inositol in slices of adult rat cortex.
Neuron. 2005 Mar 24;45(6):861-72.

Philip E. Brandish, Ming Su, Daniel J. Holder, Paul Hodor, John Szumiloski, Robert R. Kleinhanz, Jaime E. Forbes, Mollie E. McWhorter, Sven J. Duenwald, Mark L. Parrish, Sang Na, Yuan Liu, Robert L. Phillips, John J. Renger, Sethu Sankaranarayanan, Adam J. Simon and Edward M. Scolnick

Publications from 2004 and earlier

A microarray platform comparison for neuroscience applications.
J Neurosci Methods. 2004 Jan 15;132(1):57-68.

Parrish ML, Wei N, Duenwald S, Tokiwa GY, Wang Y, Holder D, Dai H, Zhang X, Wright C, Hodor P, Cavet G, Phillips RL, Sun BI, Fare TL.

Effects of atmospheric ozone on microarray data quality.
Anal Chem. 2003 Sep 1;75(17):4672-5.

Fare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y.

Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.
Bioinformatics. 2003 May 22;19(8):956-65.

He YD, Dai H, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB.

Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol. 2003;4(10):R66. Epub 2003 Sep 19.

Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM.

A gene-expression signature as a predictor of survival in breast cancer.
N Engl J Med. 2002 Dec 19;347(25):1999-2009.

van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R.

Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays.
Nucleic Acids Res. 2002 Aug 15;30(16):e86.

Dai H, Stepaniants S, Ziman M, Stoughton R.

Identification of genes over-expressed in small cell lung carcinoma using suppression subtractive hybridization and cDNA microarray expression analysis.
Oncogene. 2002 May 23;21(23):3814-25.

Bangur CS, Switzer A, Fan L, Marton MJ, Meyer MR, Wang T.

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer.
Nat Biotechnol. 2001 Apr;19(4):342-7.

Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS.

Experimental annotation of the human genome using microarray technology.
Nature. 2001 Feb 15;409(6822):922-7.

Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS.

Signalizing and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles.
Science. 2000 Feb 4;287(5454):873-80.

Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH.

*Some publications date back to when the Covance Genomics Laboratory was Rosetta Inphamatics, owned by Merck & Co., Inc.