Publications

The publications below provide a partial list of research citing BioDiscovery software. To add your research to the list, please contact us with the necessary information.

Nexus Copy Number | Nexus Expression | ImaGene and GeneDirector

Nexus Copy Number

NF1 Is a Tumor Suppressor in Neuroblastoma that Determines Retinoic Acid Response and Disease Outcome
Michael Hölzel, Sidong Huang, Jan Koster, Ingrid Řra, Arjan Lakeman, Huib Caron, Wouter Nijkamp, Jing Xie, Tom Callens, Shahab Asgharzadeh, Robert C. Seeger, Ludwine Messiaen, Rogier Versteeg, René Bernards. Cell - 23 July 2010

Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma.
Parris TZ, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, Möllerström E, Karlsson P, Helou K. Clin Cancer Res. 2010 Jun 15.

HDMX regulates p53 activity and confers chemoresistance to 3-Bis (2-chloroethyl)-1-nitrosoureaG
Jin G, Cook S, Cui B, Chen WC, Keir ST, Killela P, Di C, Payne CA, Gregory SG, McLendon R, Bigner DD, Yan H. Neuro Oncol. 2010 May 14. [Epub ahead of print]

Tourette disorder spectrum maps to chromosome 14q31. 1 in an Italian kindred
Breedveld GJ, Fabbrini G, Oostra BA, Berardelli A, Bonifati V. Neurogenetics. 2010 May 2. [Epub ahead of print]

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.
Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF. Nature. 2010 Apr 29;464(7293):1351-6.

High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with "stereotyped" IGHV3-21 and IGHV4-34 B cell receptors
Marincevic M, Cahill N, Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Rasmusson M, Jansson M, Ryan F, Karlsson K, Adami HO, Davi F, Jurlander J, Juliusson G, Stamatopoulus K, Rosenquist R. Haematologica. 2010 Apr 26. [Epub ahead of print]

Analysis of Segmental Duplications, Mouse Genome Synteny and Recurrent Cancer-Associated Amplicons in Human Chromosome 6p21–p12
J.W. Martin, M. Yoshimoto, O. Ludkovski, P.S. Thorner, M. Zielenska, J.A. Squire, P.A.S. Nuin. Cytogenet Genome Res 2010;128:199-213

Oligonucleotide-based array CGH analysis of diffuse large B-cell lymphomas identifies gain of 7q22 as the most common genomic alteration
Edward A. Medina, Aswani R Bolla, Rajya L Bandi and Ryan S Robetorye. FASEB J. 2010 24:954.11.

Application of Nexus Copy Number Software for CNV Detection and Analysis.
Darvishi K. Curr Protoc Hum Genet. 2010 Apr;Chapter 4:Unit4.14.

In-depth investigation of the molecular pathogenesis of bladder cancer in a unique 26-year old patient with extensive multifocal disease: a case report.
Zuiverloon TC, Abas CS, van der Keur KA, Vermeij M, Tjin SS, van Tilborg AG, Busstra M, Zwarthoff EC.BMC Urol. 2010 Feb 26;10:5.

Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression.
Andrzej B Poplawski, Michal Jankowski, Stephen W Erickson, Teresita Díaz de Stĺhl, E Christopher Partridge, Chiquito Crasto, Jingyu Guo, John Gibson, Uwe Menzel, Carl EG Bruder, et al. European Journal of Human Genetics (6 January 2010).

Genetics of uveal melanoma
Hanneke W Mensink, Dion Paridaens, Annelies de Klein Expert Review of Ophthalmology, December 2009, Vol. 4, No. 6, Pages 607-616.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.
Huang J, Wu X, Montenegro G, Price J, Wang G, Vance JM, Shy ME, Züchner S. J Neurol. 2009 Dec 1. [Epub ahead of print]

Detailed cytogenetic and array analysis of pediatric primitive sarcomas reveals a recurrent CIC-DUX4 fusion gene event.
Yoshimoto M, Graham C, Chilton-MacNeill S, Lee E, Shago M, Squire J, Zielenska M, Somers GR. Cancer Genet Cytogenet. 2009 Nov;195(1):1-11.

Genomic Landscape of Meningiomas.
Lee Y, Liu J, Patel S, Cloughesy T, Lai A, Farooqi H, Seligson D, Dong J, Liau L, Becker D, Mischel P, Shams S, Nelson S.Brain Pathol. 2009 Nov 20. [Epub ahead of print]

Glioblastoma Proto-oncogene SEC61-gamma Is Required for Tumor Cell Survival and Response to Endoplasmic Reticulum Stress.
Lu Z, Zhou L, Killela P, Rasheed AB, Di C, Poe WE, McLendon RE, Bigner DD, Nicchitta C, Yan H. Cancer Res. 2009 Nov 17. [Epub ahead of print]

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Hajime Matsuzaki , Pei-Hua Wang , Jing Hu , Rich Rava and Glenn K Fu, Genome Biology 2009, 9 Nov., 10:R125

CNTNAP2 and NRXN1 are mutated in autosomal-recessive Pitt-Hopkins-like mental retardation and determine the level of a common synaptic protein in Drosophila.
Zweier C, de Jong EK, Zweier M, Orrico A, Ousager LB, Collins AL, Bijlsma EK, Oortveld MA, Ekici AB, Reis A, Schenck A, Rauch A. Am J Hum Genet. 2009 Nov;85(5):655-66. Epub 2009 Nov 5.

Microarray based analysis of 3p25-p26 deletions (3p- syndrome).
Shuib S, McMullan D, Rattenberry E, Barber RM, Rahman F, Zatyka M, Chapman C, Macdonald F, Latif F, Davison V, Maher ER. Am J Med Genet A. 2009 Oct;149A(10):2099-105.

Genomic and epigenetic evidence for oxytocin receptor deficiency in autism.
Gregory SG, Connelly JJ, Towers AJ, Johnson J, Biscocho D, Markunas CA, Lintas C, Abramson RK, Wright HH, Ellis P, Langford CF, Worley G, Delong GR, Murphy SK, Cuccaro ML, Persico A, Pericak-Vance MA.
BMC Med. 2009 Oct 22;7:62.

Disruption of ST5 is associated with mental-retardation and multiple congenital anomalies.
Göhring I, Tagariello A, Endele S, Stolt CC, Ghassibé M, Fisher M, Thiel CT, Trautmann U, Vikkula M, Winterpacht A, Fitzpatrick DR, Rauch A. J Med Genet. 2009 Oct 19. [Epub ahead of print]

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.
Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Jansson M, Cahill N, Rasmussen M, Staaf J, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Juliusson G, Rosenquist R. Leukemia. 2009 Sep 10.

Array-CGH analysis indicates a high prevalence of genomic rearrangements in holoprosencephaly: an updated map of candidate loci.
Bendavid C, Rochard L, Dubourg C, Seguin J, Gicquel I, Pasquier L, Vigneron J, Laquerričre A, Marcorelles P, Jeanne-Pasquier C, Rouleau C, Jaillard S, Mosser J, Odent S, David V. Hum Mutat. 2009 Aug;30(8):1175-82.

A highly annotated whole-genome sequence of a Korean individual.
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. Nature. 2009 Jul 8.

Gene copy number and malaria biology.
Anderson TJ, Patel J, Ferdig MT. Trends Parasitol. 2009 Jul;25(7):336-43. Epub 2009 Jun 24.

DNA copy number variation and gene expression analyses reveal the implication of specific oncogenes and genes in GBM.
Margareto J, Leis O, Larrarte E, Pomposo IC, Garibi JM, Lafuente JV. Cancer Invest. 2009 Jun;27(5):541-8.

High resolution array analysis: diagnosing pregnancies with abnormal ultrasound findings.
Tyreman M, Abbott KM, Willatt LR, Nash R, Lees C, Whittaker J, Simonic I. J Med Genet. 2009 Aug;46(8):531-41. Epub 2009 May 17.

Copy Number Variation in African Americans.
Joseph P. McElroy, Matthew R. Nelson, Stacy J. Caillier, Jorge, R. Oksenberg. BMC Genetics 2009, 10:15.

Genomic aberrations in squamous cell lung carcinoma related to lymph node or distant metastasis.
Boelens MC, Kok K, van der Vlies P, van der Vries G, Sietsma H, Timens W, Postma DS, Groen HJ, van den Berg A. Lung Cancer. 2009 Mar 24. [Epub ahead of print].

Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic lymphocytic leukemia
Sargent R, Jones D, Abruzzo LV, Yao H, Bonderover J, Cisneros M, Wierda WG, Keating MJ, Luthra R. J Mol Diagn. 2009 Jan;11(1):25-34. Epub 2008 Dec 12.

6.7 Mb interstitial duplication in chromosome band 11q24.2q25 associated with infertility, minor dysmorphic features and normal psychomotor development
Göhring Ina; Blümlein Hans-Martin; Hoyer Juliane; Ekici Arif B; Trautmann Udo; Rauch Anita. Eur J Med Genet. 2008 Nov-Dec;51(6):666-71. Epub 2008 Aug 12. [PubMed]

Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis
Khorashad JS, De Melo VA, Fiegler H, Gerrard G, Marin D, Apperley JF, Goldman JM, Foroni L, Reid AG. Leukemia. 2008 Sep;22(9):1806-7. Epub 2008 Jul 31. [Abstract] [PubMed]

3.8 MB Deletion of Chromosome 5q in a Newborn Tracheal Agenesis Patient
Elisabeth de Jong, Hannie Douben, Bert Eussen, Dick Tibboel and Annelies de Klein. Poster presentation at ASHG 2008, Philadelphia, PA [Poster]

DNA Copy Number Stratification of Breast Cancer Samples Identifies Distinct Biological Mechanisms
S. Shams, R. Davis, B. Poirier, J. Gregg. Poster presentation at AACR Translational Cancer Medicine Conference, July 2008, San Diego, CA. [Poster]

Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431)
Moore SR, Persons DL, Sosman JA, Bobadilla D, Bedell V, Smith DD, Wolman SR, Tuthill RJ, Moon J, Sondak VK, Slovak ML. Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431). Clin Cancer Res. 2008 May 15;14(10):2927-35. [PubMed]

A de-novo 7.6 Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay
Thiel CT, Dörr HG, Trautmann U, Hoyer J, Hofmann K, Kraus C, Ekici AB, Reis A, Rauch A. A de novo 7.6Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay. Eur J Med Genet. 2008 Jul-Aug; 51(4):362-7. Epub 2008 Mar 20. [PubMed]

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia
Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjene M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra, Abishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg , Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 27 March 2008. (10.1126/science.1155174). [Abstract]

Challenges In Array CGH For the Analysis Of Cancer Samples
Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mwahech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML. Challenges In Array CGH For the Analysis Of Cancer Samples. Genetics in Medicine, 9(9): 585-595, 2007. [PubMed]

Nexus Expression

Clinical Implications of Gene Dosage and Gene Expression Patterns in Diploid Breast Carcinoma.
Parris TZ, Danielsson A, Nemes S, Kovács A, Delle U, Fallenius G, Möllerström E, Karlsson P, Helou K. Clin Cancer Res. 2010 Jun 15.

Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype.
Crispín JC, Tsokos GC. J Immunol. 2009 Oct 1;183(7):4675-81. Epub 2009 Sep 4. [PubMed]

ImaGene and GeneDirector

New methods to analyse microarray data that partially lack a reference signal.
Carpaij N, Fluit AC, Lindsay JA, Bonten MJ, Willems RJ. BMC Genomics. 2009 Nov 13;10:522. [PubMed]

Identification of a novel microRNA cluster miR-193b-365 in multiple myeloma.
Unno K, Zhou Y, Zimmerman T, Platanias LC, Wickrema A. Leuk Lymphoma. 2009 Nov;50(11):1865-71. [PubMed]

Loading-related regulation of gene expression in bone in the contexts of estrogen deficiency, lack of estrogen receptor alpha and disuse.
Zaman G, Saxon LK, Sunters A, Hilton H, Underhill P, Williams D, Price JS, Lanyon LE. Bone. 2009 Oct 24. [Epub ahead of print] [PubMed]

Anti-carbohydrate antibodies of normal sera: findings, surprises and challenges.
Huflejt ME, Vuskovic M, Vasiliu D, Xu H, Obukhova P, Shilova N, Tuzikov A, Galanina O, Arun B, Lu K, Bovin N. Mol Immunol. 2009 Sep;46(15):3037-49. Epub 2009 Jul 15. [PubMed]

Dicer-dependent microRNA pathway controls invariant NKT cell development.
Fedeli M, Napolitano A, Wong MP, Marcais A, de Lalla C, Colucci F, Merkenschlager M, Dellabona P, Casorati G. J Immunol. 2009 Aug 15;183(4):2506-12. Epub 2009 Jul 22. [PubMed]

FOXP3 inhibits activation-induced NFAT2 expression in T cells thereby limiting effector cytokine expression.
Torgerson TR, Genin A, Chen C, Zhang M, Zhou B, Ańover-Sombke S, Frank MB, Dozmorov I, Ocheltree E, Kulmala P, Centola M, Ochs HD, Wells AD, Cron RQ. J Immunol. 2009 Jul 15;183(2):907-15. Epub 2009 Jun 29. [PubMed]

Use of spermatozoal mRNA profiles to study gene-environment interactions in human germ cells.
Linschooten JO, Van Schooten FJ, Baumgartner A, Cemeli E, Van Delft J, Anderson D, Godschalk RW. Mutat Res. 2009 Jul 10;667(1-2):70-6. [PubMed]

Consequences of perinatal treatment with L-arginine and antioxidants for the renal transcriptome in spontaneously hypertensive rats.
Wesseling S, Koeners MP, Kantouh F, Joles JA, Braam B. Pflugers Arch. 2009 Jul;458(3):513-24. Epub 2009 Feb 3. [PubMed]

Genome-wide identification of long noncoding RNAs in CD8+ T cells.
Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS. J Immunol. 2009 Jun 15;182(12):7738-48. [PubMed]

Transcriptomic analysis of aorta from a short-term high-fat diet fed mouse reveals changes in the expression of vessel structure genes.
Dejeans N, Auclair S, Chauvet S, Milenkovic D, Mazur A. J Physiol Pharmacol. 2009 May;60 Suppl 1:37-45. [PubMed]

In vivo knockdown of the androgen receptor results in growth inhibition and regression of well-established, castration-resistant prostate tumors.
Snoek R, Cheng H, Margiotti K, Wafa LA, Wong CA, Wong EC, Fazli L, Nelson CC, Gleave ME, Rennie PS. Clin Cancer Res. 2009 Jan 1;15(1):39-47. [PubMed]

Charričre, G., Cousin, B., Arnaud, E., André, M., Bacou, F., Pénicaud, L., and Casteilla, L. . Preadipocyte Conversion to Macrophage. EVIDENCE OF PLASTICITY. J. Biol. Chem., Mar 2003; 278: 9850 - 9855.

Draghici S, Kulaeva O, Hoff B, Petrov A, Shams S, Tainsky MA (2003) Noise Sampling Method: an ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays, Bioinformatics, 2003 Jul 22;19(11):1348-59

Draghici, S. Data Analysis and Visualization in DNA Microarrays,Introduction to Bioinformatics, S.Krawetz and D. Womble (Eds.), Humana Press, 2002.

Draghici, S., Kuklin A., Hoff, B., Shams S. Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays, Current Opinion in Drug Discovery & Development, vol. 4, no. 3, 2001.

Draghici, S. DNA Arrays: The Steam Engine of the 21st Century?, ACM SIGBIO Newsletter, vol. 21, no. 1, pp. 2-9, April, 2001.

Draghici, S., Kulaeva, O., Hoff, B., Petrov, A., Shams, S., Tainsky, M. A. , Computational Methods for Selection of Differentially Regulated Genes in Cell Immortalization, Bioinformatics, September 2003

Erlander, M. Using Laser Capture Microdissection and cDNA Microarrays to Profile Expression Neuronal Subtypes. DNA Microarrays. The New Frontier in Gene Discovery and Gene Expression Analysis. Short Course Syllabus. Society for Neuroscience, Miami Beach, FL. pp. 67- 71, 1999.

Fathallah-Shaykh, Hassan M., He, Bin, Zhao, Li-Juan, Engelhard, Herbert H., Cerullo, Leonard, Lichtor, Terry, Byrne, Richard, Munoz, Lorenzo, Von Roenn, Kelvin, Rosseau, Gail L., Glick, Roberta, Sherman, Chen, and Farooq, Khan . Genomic Expression Discovery Predicts Pathways and Opposing Functions behind Phenotypes. J. Biol. Chem., Jun 2003; 278: 23830 - 23833.

Grimmond S, Van Hateren N, Siggers P, Arkell R, Larder R, Soares MB, de Fatima Bonaldo M, Smith L, Tymowska-Lalanne Z, Wells C, Greenfield A. Hum Mol Genet. 2000 Jun 12;9(10):1553-60.

Groch, K., Kuklin A. Query Tools for Microarray Data Mining Applications. Lab Technology. PharmaGenomics pp 53-55, August, 2001.

Heyer, L.J., Kruglyak, S., and Yooseph, S. Exploring Expression Data: Identification and Analysis of Co-Expressed Genes. Genome Research 9:1106-1115. 1999.

Hihara Y, Kamei A, Kanehisa M, Kaplan A, Ikeuchi M. Dna microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell. 2001 Apr;13(4):793-806.

Hoff B, Significance Testing Among Groups using GeneSight, in Data Analysis Tools for Microarrays, S. Draghici ed., Chapman and Hall/CRC Press, 2003.

Hoff, B., Shams, S., Kuklin, A. Gene Expression-Based Tumor Classification with GeneSight from BioDiscovery, Inc., Dispatches from the Forefront of Array BioInformatics Vol. 1, No.,

Hoff B., Kuklin, A., Shams, A. Gene Expression Pattern Analysis with Clustering in the Data Mining System GeneSight. BIOforum, International Life Sciences and Technology, February, 2001, Advanced Publication.

Holzberg, David , C. Graham Knight, Oliver Dittrich-Breiholz, Heike Schneider, Anneke Dörrie, Elke Hoffmann, Klaus Resch, and Michael Kracht. Disruption of the c-JUN-JNK Complex by a Cell-permeable Peptide Containing the c-JUN Domain Induces Apoptosis and Affects a Distinct Set of Interleukin-1-induced Inflammatory Genes. J. Biol. Chem., Oct 2003; 278: 40213 - 40223.

Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K. Differential gene expression between chronic hepatitis B and C hepatic lesion. Gastroenterology ;120(4):955-66, March 2001.

Inaba, Masami , Iwane Suzuki, Balázs Szalontai, Yu Kanesaki, Dmitry A. Los, Hidenori Hayashi, and Norio Murata. Gene-engineered Rigidification of Membrane Lipids Enhances the Cold Inducibility of Gene Expression in Synechocystis. J. Biol. Chem., Mar 2003; 278: 12191 - 12198.

Kaloscai, P. and Shams, S. Visualization and Analysis of Gene Expression Data. JALA Vol 4, No. 5:pp17-21. 1999.

Kawai H, Kaneko S. DNA chip; recent advances and applications in gene expression profiling. Tanpakushitsu Kakusan Koso ;45(11):1841-7. Review. Japanese. No abstract available, August 2000.

Kawai HF, Kaneko S, Honda M, Shirota Y, Kobayashi K. alpha-fetoprotein-producing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis. Hepatology ;33(3):676-91, March 2001.

Kiguchi T, Niiya K, Shibakura M, Miyazono T, Shinagawa K, Ishimaru F, Kiura K, Ikeda K, Nakata Y, Harada M. Int J Cancer 2001 Sep15;93(6):792-7 Related Articles, Books, LinkOut.

Kiyoko AF, Petrov, A., A Comprehensive Microarray Data Management Approach in Microarrays Methods and Applications: Nuts & Bolts, G. Hardimann (ed.), DNA Press (2003)

Kuklin A., Shams S., Shah S. Automation in Microarray Image Analysis with AutoGene Technical Report, JALA Vol 5, No. 5, pp. 67-70, November, 2000.

Kuklin, A., S. Shah, B. Hoff, and S. Shams. (2001) Data management in Microarray Fabrication, Image Processing, and Data Mining. In: Grigorenko (Ed.) DNA Arrays - Technologies and Experimental Strategies. CRC Press, Boca Raton pp. 115-128.

Kuklin, A. Automation In Microarray Image Processing and Data Mining. High Throughput Screening Supplement, BioMedical Products 1:4-8. 2000.

Kuklin, A. Laboratory Automation in Microarray Image Processing. International Laboratory pp 36-40. May, 2000.

Kuklin, A. Spot Checks. Modern Drug Discovery pp 52-54. May, 2000.

Kuklin, A., Shah, S., Hoff, B, Shams, S., Information Processing Issues and Solutions Associated with Microarray Technology. LRA, Vol 12,pp.317-327, September 2000.

Kuklin, A. DNA Microarray Production, Virtual Experimental Design, Databasing and Clone Tracking with CloneTracker. SC&I Technology Notes, January 2001.

Kuklin, A., Petrov A., Shams, S. Quality Control in Mircroarray Image Analysis. Imaging & Microscopy Research, Development, Production. GIT Volume 1, April, 2001.

Luo, L., Salunga, R., Guo, H. et al. Gene Expression Profiles of Laser-Captured Adjacent Neuronal Subtypes. Nature Medicine, Vol. 5 No.1: pp117-122. 1999.

Mansourian, R., Mutch, D., Antille, N., Aubert, J., Fogel, P., Goff, J., Moulin, J., Petrov, A., Rytz, A., Voegel, J., Roberts, M., The Global Error Assessment Model for the Selection of Differentially Expressed Genes in Microarray Data, scheduled to appear in Bioinformatics in September 2004.

Nagasako, Tomokazu , Toshiro Sugiyama, Takuji Mizushima, Yosuke Miura, Mototsugu Kato, and Masahiro Asaka. Up-regulated Smad5 Mediates Apoptosis of Gastric Epithelial Cells Induced by Helicobacter pylori Infection. J. Biol. Chem., Feb 2003; 278: 4821 - 4825.

Oh, Min-Kyu , Lars Rohlin, Katy C. Kao, and James C. Liao. Global Expression Profiling of Acetate-grown Escherichia coli. J. Biol. Chem., Apr 2002; 277: 13175 - 13183.

Petrov, A., Shams, S., Microarray Image Processing and Quality Control, The Journal of VLSI Signal Processing, scheduled to appear in special Microarray issue (October, 2004).

Petrov, A., Shams, S., Image Analysis Issues and Solutions for High-Density Arrays in Protein Microarray Technology, Dev Kambhampati (ed.), Wiley Publishers (2003)

Petrov, A., Shah, S., Draghici, S.,Shams, S. , Microarray Image Processing and Quality Control, in DNA Array Image Analysis Nuts & Bolts, G. Kamberova, S. Shah (ed.), Ch. 6, DNA Press (2002)

Posas, Francesc , James R. Chambers, John A. Heyman, James P. Hoeffler, Eulalia de Nadal, and Joaquín Arińo. The Transcriptional Response of Yeast to Saline Stress. J. Biol. Chem., Jun 2000; 275: 17249 - 17255.

Schenk PM, Kazan K, Wilson I, Anderson JP, Richmond T, Somerville SC, Manners JM. Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11655-60.

Schwenk,Jochen M., Stroll, Dieter, Templin, Markus F., And Joos, Thomas O. Cell Microarrays : An Emerging Technology for the Characterization of Antibodies Biotechniques 33:S54-61 December 2002.

Shah, S., Kuklin, A., Shams, S. High Throughput Screening of Gene Expression Signatures. Genetica 108: 41-46, 2000.

Shams, S., Kuklin, A. Data Mining in the Exploration of Genomic Expression. Bio/Medical Synergies. 22: 4-5 Summer 2000.

Shams, S., Park, J.D., Chen, J.Y., Kalocsai, P. and Zhou, Y.X. Image Analysis and Data Management Issues Associated with Microarray Technology. DNA Microarrays - The New Frontier in Gene Discovery and Gene Expression Analysis. Short Course Syllabus. Society for Neuroscience, Miami Beach, FL. pp. 43-56, 1999.

Shirota Y, Kaneko S, Honda M, Kawai HF, Kobayashi K. Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology ;33(4):832-40, April 2001.

Smedberg, Jennifer L., Smith, Elizabeth R., Capo-chichi, Callinice D., Frolov, Andrey, Yang, Dong-Hua, Godwin, Andrew K., and Xu, Xiang-Xi Ras/MAPK Pathway Confers Basement Membrane Dependence upon Endoderm Differentiation of Embryonic Carcinoma Cells. J. Biol. Chem., Oct 2002; 277: 40911 - 40918.

Stears, R.L., Getts, R.C., and Gullans, S.R. A Novel, Sensitive Detection System for High- Density Microarrays Using Dendrimer Technology. Physiol. Genomics 3:93-99, 2000.

Stöver, Axel G. , Jean Da Silva Correia, Jay T. Evans, Christopher W. Cluff, Mark W. Elliott, Eric W. Jeffery, David A. Johnson, Michael J. Lacy, Jory R. Baldridge, Peter Probst, Richard J. Ulevitch, David H. Persing, and Robert M. Hershberg. Structure-activity relationship of synthetic toll-like receptor 4 agonists. J. Biol. Chem., Oct 2003; 10.1074/jbc.M310760200

Suzuki, Mika , Hiroshi Kobayashi, Yoshiko Tanaka, Yasuyuki Hirashima, Naohiro Kanayama, Yuji Takei, Yasushi Saga, Mitsuaki Suzuki, Hiroshi Itoh, and Toshihiko Terao. Bikunin Target Genes in Ovarian Cancer Cells Identified by Microarray Analysis. J. Biol. Chem., Apr 2003; 278: 14640 - 14646.

Taniguchi M, Miura K, Iwao H, Yamanaka S. Quantitative assessment of DNA microarrays--comparison with Northern blot analyses. Genomics. 2001 Jan 1;71(1):34-9.

Tan ZJ, Hu XG, Cao GS, Tang Y. Analysis of Gene Expression Profile of Pancreatic Carcinoma using cDNA Microarray. World J Gastroenterol. 2003 Apr;9(4):818-23.

That's The Spot! The Scientist, Lab Consumer, Vol 14:5 March 6, 2000.

Yamada M, Yamada M, Yamazaki S, Takahashi K, Nishioka G, Kudo K, Ozawa H, Yamada S, Kiuchi Y, Kamijima K, Higuchi T, Momose K. Biochem Biophys Res Commun. 2000 Nov 11;278(1):150-7.

Yoshida K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y. Nucleic Acids Res. 2001 Feb 1;29(3):683-92.

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