Publications
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Genetic Engineering News: Sample Preparation for RNA Expression Analysis
Nurith Kurn, Ph.D. and Joe Don Heath, Feb 2004, Genetic Engineering News, Volume 24, Number 3
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
Microarray-based comparison of three amplification methods for nanogram amounts of total RNA
Ruchira Singh, Rajanikanth J. Maganti, Sairam V. Jabba, Martin Wang, Glenn Deng, Joe Don Heath, Nurith Kurn, and Philine Wangemann. May 2005, Am J Physiol Cell Physiol 288: C1179-C1189
NovaChip Evanescent Resonator Technology
Dieter Neuschafer, Estelle Marrer and Wolfgang Budach at Novartis Pharma AG, September 2005, Innovations in Pharmaceutical Technology 78-82
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
Central Nervous System Drug Development: An Integrative Biomarker Approach toward Individualized Medicine
B. Gomez-Mancilla, E. Marrer, J. Kehren, A. Kinnunen, G. Imbert, R. Hillebrand, M. Bergstrom and M. E. Schmidt. October 2005, NeuroRx: J American Society for Experimental NeuroTheraputics Vol 2: 683-695
Functional genomic methodologies
Stephen D. Ginsberg and Karoly Mirnics. 2006, Progress in Brain Research, Vol. 158; 15-40. PMID: 17027690
Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome
Carol A Gilchrist, Eric Houpt, Nino Trapaidze, Zhangjun Fei, Oswald Crasta, Amon Asgharpour, Clive Evans, Susan Martino-Catt, Duza J Baba, Suzanne Stroup, Shinjiro Hamano, Gretchen Ehrenkaufer, Mami Okada, Upinder Singh, Tomoyoshi Nozaki, Barbara J Mann, William A Petri Jr. June 2006, Molecular and Biochemical Parasitology, 147:163-176
Automated Solutions for Total RNA Isolation from Diverse Sample Types.
Paula Selley, Jimmy Bruner, Fiona Kelly, Frank Maurio, Michelle Waters and Jay Strum. Oct 2006, Journal of the Association for Laboratory Automation, Volume 11, Issue 5, 309-313
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
Whole Genome Oligonucleotide-Based Array Comparative Genomic Hybridization Analysis Identified Fibroblast Growth Factor As a Prognostic Marker for Advanced-Stage Serous Ovarian Adenocarcinomas
Michael J. Birrer, Michael E. Johnson, Ke Hao, Kwong-Kwok Wong, William R. Welch, Ross S. Berkowitz, Samuel C. Mok; Journal of Clinical Oncology, Vol. 25, No. 16, June 1, 2007.
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
Gene Expression Profiles as Markers of Aggressive Disease-EGFR as a Factor
Christine H. Chung, Joel Parker, Shawn Levy, Robbert J. Slebos, Adam P. Dicker, Ulrich Rodeck International Journal of Radiation Oncology * Biology * Physics Volume 69, Issue 2, Supplement, October 2007, Inaugural Multidisciplinary Head and Neck Cancer Symposium
The Transcriptome and Metabolic Gene Signature of Protoplasmic Astrocytes in the Adult Murine Cortex
Ditte Lovatt, Ursula Sonnewald, Helle S. Waagepetersen, Arne Schousboe, Wei He, Jane H.-C. Lin, Xiaoning Han, Takahiro Takano, Su Wang, Fraser J. Sim, Steven A. Goldman, and Maiken Nedergaard, The Journal of Neuroscience, November 7, 2007, 27(45):12255-12266; doi:10.1523/JNEUROSCI.3404-07.2007
Homer1a is a core brain molecular correlate of sleep loss
Stephanie Maret, Stephane Dorsaz, Laure Gurce, Sylvain Pradervand, Brice Petit, Corinne Pfiste, Otto Hagenbuchle, Bruce F. O'Hara, Paul Franken, Mehdi Tafti; Proc Natl Acad Scence USA. 2007 Dec 11;104(50):20090-5. Epub 2007 Dec 6.
Effects of dietary energy restriction on gene regulation in mammary epithelial cells
Zongjian Zhu, Weiqin Jiang, John N. McGinley, Jennifer M. Price, Bifeng Gao, Henry J. Thompson; Cancer Research, 2007 Dec 15; 67(24):12018-25.
A study of 17 beta-estradiol-regulated genes in the vagina of postmenopausal women with vaginal atrophy
A study of 17 beta-estradiol-regulated genes in the vagina of postmenopausal women with vaginal atrophy Cotreau MM, Chennathukuzhi VM, Zakaria M, Strahs AL, Crabtree JS, Winneker RC, Jelinsky SA., Maturitas. 2007 Dec 20;58(4):366-76. Epub 2007 Nov 9
Transcriptional profiling of the megabladder mouse: A unique model of bladder dysmorphogenesis
Singh S, Robinson M, Ismail I, Saha M, Auer H, Kornacker K, Robinson ML, Bates CM, McHugh KM. January 2008, Developmental Dynamics , Volume 237, issue 1, 170-186
Lrig3 regulates neural crest formation in Xenopus by modulating Fgf and Wnt signaling pathways
Hui Zhao, Kosuke Tanegashima, Hyunju Ro, Igor B. Dawid; Development, 2008 Apr; 135(7):1283-93. Epub 2008 Feb 20.
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
Plasticity in Tumor-Promoting Inflammation: Impairment of Macrophage Recruitment Evokes a Compensatory Neutrophil Response
Jessica C Pahler, Simon Tazzyman, Neta Erez, Yung-Yi Chen, Craig Murdoch, Hiroaki Nozawa, Claire E Lewis, and Douglas Hanahan 2008 April, Neoplasia, 10(4): 329-339
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
Phenotypic Analysis of Prostate-Infiltrating Lymphocytes Reveals TH17 and Treg Skewing
Karen Sandell Sfanos, Tullia C. Bruno, Charles H.Maris, Lauren Xu, Christopher J. Thoburn, Angelo M. DeMarzo, Alan K. Meeker, William B. Isaacs, and Charles G. Drake Clinical Cancer Research, June 2008;14(11):3254-3261
GATA4 is a direct transcriptional activator of Cyclin D2 and Cdk4 and is required for cardiomyocyte proliferation in anterior heart field-derived myocardium
Anabel Rojas, Sek Won Kong, Pooja Agarwal, Brian Gilliss, William T. Pu, and Brian L. Black; Mol Cell Biol. Molecular and Cellular Biology, September 2008, p. 5420-5431, Vol. 28, No. 17. Epub 2008 Jun 30.
Tlymphocytes potentiate endogenous neuroprotective inflammation in a mouse model of ALS.
Isaac M. Chiu, Adam Chen, Yi Zheng, Bela Kosaras, Stefanos A. Tsiftsoglou, Timothy K. Vartanian, Robert H. Brown, Jr., Michael C. Carroll; Proc National Academy Science USA. 2008 Nov 18;105(46):17913-8. Epub 2008 Nov 7.
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
Expression profiling using Affymetrix GeneChip microarrays
Herbert Auer, Karl Kornacker, Methods of Molecular Biology, February 12, 2009
Skeletal muscle gene expression after myostatin knockout in mature mice
Stephen Welle, Rabi Tawil, Physiological Genomics, June 1, 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, Martin Grumet, Journal of Neurotrauma, July 26, 2009
Biomarkers of Dietary Energy Restriction in Women at Increased Risk of Breast Cancer
Kai Ren Ong, Anthony Howell, Cancer Prevention Research, August 2, 2009
Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease
Andrew M. Smith, Anthony W. Segal, The Journal of Experimental Medicine, August 31, 2009
Culture-induced changes in blood-brain barrier transcriptome: implications for amino-acid transporters in vivo
Ruth Lych, Francois Verrey, Journal of Cerebral Blood Flow & Metabolism, September 2009
Reproductive Aging is Associated With Altered Gene Expression in Human Luteinized Granulosa Cells
JM Hurwitz, D. Berger, Reproductive Sciences, October 5, 2009
Molecular, Anatomical, Physiological, and Behavioral Studies of Rats Treated with Buprenorphine after Spinal Cord Injury
Jose M. Santiago, Jorge D. Miranda, Journal of Neurotrauma, October 15, 2009
RNA Pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts
Joelle Vermeulen, Stefaan Derveaux, Steve Lefever, Els De Smet, Katleen De Preter, Nurten Yigit, Anne De Paepe, Filip Pattyn, Frank Speleman and Jo Vandesople; BMC Research Notes November 25 2009, 2:235
Cancer gene profiling in prostate cancer
Grutzmann, R, Pilarsky, C, Methods in Molecular Biology, 2010, Volume 576, 293-326
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 Profiling of Blood for the Prediction of Ischemic Stroke
Stamova, B, Sharp, FR, Stroke 2010;41:2171-2177
Pancreatic [beta] Cells Require NeuroD to Achieve and Maintain Functional Maturity
Gu, C, Lee, JE, Cell Metabolism, Volume 11, Issue 4, 298-310, 7 April 2010
State-of-the-art genomics approaches in toxicology
Van Hummelen, P, Sasaki, J, Mutation Research 11 May 2010
Providing a stable methodological basis for comparing transcript abundance of developing embryos using microarrays
Gilbert, I, Robert, C, Molecular Human Reproduction, May 17, 2010
The Netherlands Twin Register Biobank: a resource for genetic epidemiological studies
Willemsen, G, Boomsma, DI, Twin Research and Human Genetics 13 Issue 3 June 2010 231-245
Peripheral blood gene expression in alopecia areata reveals molecular pathways distinguishing heritability, disease and severity
Coda, AB, Sinha, AA, Genes and Immunity, (10 June 2010)
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation
Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE. BMC Genomics. 2010 Aug 13;11:473.
Bcl9-Bcl9l Are Critical for Wnt-Mediated Regulation of Stem Cell Traits in Colon Epithelium and Adenocarcinomas
Deka J, Aguet M, Cancer Research August 15, 2010 70; 6619
The endocytic adaptor Numb regulates thymus size by modulating pre-TCR signaling during asymmetric division
Aguardo A, Blood, Vol. 116, Issue 10, 1705-1714, September 9, 2010
Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling
Peng X, Gralinski L, Armour CD, Ferris MT, Thomas MJ, Proll S, Bradel-Tretheway BG, Korth MJ, Castle JC, Biery MC, Bouzek HK, Haynor DR, Frieman MB, Heise M, Raymond CK, Baric RS, Katze MG. MBio. 2010 Oct 26;1(5). pii: e00206-10.
Acquiring genome_wide gene expression profiles in Guthrie card blood spots using microarrays
Khoo S, Resau J, Pathology International, Volume 61, Issue 1, pages 1-6, January 2011
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
FOXL2 and BMP2 Act Cooperatively to Regulate Follistatin Gene Expression during Ovarian Development
Kashimada K, Koopman P, Endocrinology. 2011 Jan;152(1):272-80. Epub 2010 Nov 17.
Fusion between Intestinal Epithelial Cells and Macrophages in a Cancer Context Results in Nuclear Reprogramming
Powell A, Wong M, Cancer Res. 2011 Feb 15;71(4):1497-505. Epub 2011 Feb 8.
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]
GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells
Yu S, Xue H, Blood. 2011 Feb 17;117(7):2166-78. Epub 2010 Dec 7.
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.
Transient receptor potential ion channel Trpm7 regulates exocrine pancreatic epithelial proliferation by Mg2+-sensitive Socs3a signaling in development and
Yee N, Liang I, Dis Model Mech. 2011 Mar;4(2):240-54. Epub 2010 Dec 23
Genetic mosaic analysis reveals a major role for frizzled 4 and frizzled 8 in controlling ureteric growth in the developing kidney
Ye X, Nathans J, Development. 2011 Mar;138(6):1161-72.
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]
Clonal B cells in patients with hepatitis C virus-associated mixed cryoglobulinemia contain an expanded anergic CD21low B cell subset
Marks K, Dustin L, Blood. 2011 Mar 18. [Epub ahead of print]
Transcriptomic Biomarkers for the Accurate Diagnosis of Myocarditis
Heidecker B, Hare J, Circulation. 2011 Mar 22;123(11):1174-84. Epub 2011 Mar 7
Non-Invasive Genomic Detection of Melanoma
Wachsman W, Chang S, British Journal of Dermatology Volume 164, Issue 4, pages 797-806, April 2011
Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma
Howell G, John S, J Clin Invest. 2011 April 1; 121(4): 1429-1444