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

Detection Of Copy Number Alteration In Malignant Melanoma By Both a Panel Of 16 DNA FISH Probes and Array Comparative Genomic Hybridization: A Southwest Oncology Group Study

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 Alteration In Malignant Melanoma By Both a Panel Of 16 DNA FISH Probes and Array Comparative Genomic Hybridization: A Southwest Oncology Group Study. Clinical Cancer Research, in press.

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 A, Reis A, Rauch A (2008) 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. Eur J Med Genet, in press.

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]

TP53-mutated breast carcinomas are associated with specific array comparative hybridization (aCGH) patterns involving deletions of 3p, 4p, 4q and 5q

HKM Vollan, A Langerřd, EU Due, R Kĺresen , E Schlichting, A-L Břrresen-Dale. TP53-mutated breast carcinomas are associated with specific array comparative hybridization (aCGH) patterns involving deletions of 3p, 4p, 4q and 5q. Accepted for Poster and Oral presentation at EBBC6, Berlin, Germany, April 15-19, 2008. [Abstract] [EBBC6]

Breast cancer progression – genomic alterations in a continuum of stages

Jřrgen Aarře, Vilde D. Haakensen, Aslaug Muggerud, Vanessa Dumeaux, Fredrik Wärnberg, Anne-Lise Břrresen-Dale. “Breast cancer progression – genomic alterations in a continuum of stages.” Submitted for Poster presentation at EACR 20, Lyon, France, July 5-8, 2008. [Abstract] [EACR 20]

ImaGene and GeneDirector

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.

Zhout, Y-X., Kalocsai, P., Chen, J-Y., and Shams, S. Information Processing Issues and Solutions Associated with Microarray Technology. Microarray Biochip Technology. Schena, M. (Ed.), Eaton Publishing, BioTechniques Books,. Natick, MA, U.S.A. pp. 167-200, 2000.

Han JM, Kim JY, Kim S.
Molecular network and functional implications of macromolecular tRNA synthetase complex. Biochem Biophys Res Commun. 2003 Apr 18; 303(4): 985-93. Review.
PMID: 12684031 [PubMed - indexed for MEDLINE]

Xu SH, Qian LJ, Mou HZ, Zhu CH, Zhou XM, Liu XL, Chen Y, Bao WY. Difference of gene expression profiles between esophageal carcinoma and its pericancerous epithelium by gene chip. World J Gastroenterol. 2003 Mar; 9(3): 417-22.
PMID: 12632488 [PubMed - indexed for MEDLINE]

Xu S, Mou H, Lu G, Zhu C, Yang Z, Gao Y, Lou H, Liu X, Cheng Y, Yang W. Gene expression profile differences in high and low metastatic human ovarian cancer cell lines by gene chip. Chin Med J (Engl). 2002 Jan; 115(1): 36-41.
PMID: 11930655 [PubMed - indexed for MEDLINE]

Chen JN, Li Y, Li YL, Qin HY, Li RY, Cao HM, Xie Y, Mao YM. [Investigation of genotyping HLA DRB1 gene using oligoneucleotide arrays] Yi Chuan Xue Bao. 2001; 28(10): 887-94. Chinese.
PMID: 11695259 [PubMed - indexed for MEDLINE]

Konstantinos Boulias, Nitsa Katrakili, Krister Bamberg, Peter Underhill, Andy Greenfield, Iannis Talianidis. Regulation of hepatic metabolic pathways by the orphan nuclear receptor SHP. The EMBO Journal 24, 2624-2633 (20 Jul 2005)

Sandrine Wattel, Hortensia Mircescu, David Venet, Agnes Burniat, Brigitte Franc, Sandra Frank, Guy Andry, Jacqueline Van Sande, Pierre Rocmans, Jacques E Dumont, Vincent ... Gene expression in thyroid autonomous adenomas provides insight into their physiopathology. Oncogene , (18 Jul 2005)

Joong Sup Shim, Dong Hoon Kim, Ho Jeong Kwon. Plakoglobin is a new target gene of histone deacetylase in human fibrosarcoma HT1080 cells. Oncogene 23, 1704-1711 (04 Mar 2004)

Siew Loon Ooi, Daniel D Shoemaker, Jef D Boeke. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nature Genetics 35, 277-286 (01 Nov 2003)

Olga I Kulaeva, Sorin Draghici, Lin Tang, Janice M Kraniak, Susan J Land, Michael A Tainsky. . Epigenetic silencing of multiple interferon pathway genes after cellular immortalization. Oncogene 22, 4118-4127 (26 Jun 2003)

Ha NT, Nakayasu K, Murakami A, Ishidoh K, Kanai A. Microarray analysis identified differentially expressed genes in keratocytes from keratoconus patients. Curr Eye Res. 2004 Jun;28(6):373-9.

PMID: 15512944 [PubMed - indexed for MEDLINE]

Zhang XY, Li XP, Lai J, Feng J. Screening for ovarian cancer-associated genes with cDNA microarrays. Ai Zheng. 2003 Sep;22(9):943-7. Chinese.

PMID: 12969526 [PubMed - indexed for MEDLINE]

Andrew Whitehead, Douglas L Crawford. Variation in tissue-specific gene expression among natural populations Genome Biology 2005 6:R13
http://genomebiology.com/2005/6/2/r13

Frederic Ampe, Ernö Kiss, Frédérique Sabourdy, Jacques Batut. Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biology 2003 4:R15
http://genomebiology.com/2003/4/2/r15

Lehane MJ, Aksoy S, Gibson W, Kerhornou A, Berriman M, Hamilton J, Soares MB, Bonaldo MF, Lehane S, Hall N . Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes. Genome Biology 2003, 4(10):R63 (11 September 2003)
http://genomebiology.com/2003/4/10/R63

Stoyanova R, Clapper ML, Bellacosa A, Henske EP, Testa JR, Ross EA, Yeung AT, Nicolas E, Tsichlis N, Li YS, Linehan WM, Howard S, Campbell KS, Godwin AK, Boman BM, Crowell JA, Kopelovich L, Knudson AG. Altered gene expression in phenotypically normal renal cells from carriers of tumor suppressor gene mutations. Cancer Biol Ther. 2004 Dec;3(12):1313-21. Epub 2004 Dec 9.
PMID: 15662135 [PubMed - indexed for MEDLINE]

Junpei Hayashi, Radka Stoyanova and Christoph Seeger. The transcriptome of HCV replicon expressing cell lines in the presence of alpha interferon. Virology, Volume 335, Issue 2, 10 May 2005, Pages 264-275

Upson JJ, Stoyanova R, Cooper HS, Patriotis C, Ross EA, Boman B, Clapper ML, Knudson AG, Bellacosa A. Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection. J Cell Physiol. 2004 Dec;201(3):366-73.
PMID: 15389559 [PubMed - indexed for MEDLINE]

Stoyanova R, Upson JJ, Patriotis C, Ross EA, Henske EP, Datta K, Boman B, Clapper ML, Knudson AG, Bellacosa A. Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays. J Cell Physiol. 2004 Dec;201(3):359-65.
PMID: 15389558 [PubMed - indexed for MEDLINE]