Here are some interesting web sites and papers which will introduce you to one of the more exciting technological beakthroughs in genomics -- DNA microarrays. This site is far from a comprehensive listing, but it may be a good place to start. This page started in 1999 and now that I have a real job, its a little harder to keep it up to date. However, I'm going to give it the old 'college try'. If you know of any sites which belong here or have any additional information please let me know. - Andreas
The Genetic Science Learning Center has recently completed a very cool interactive online DNA microarray biotechniques lab here
Stanford has some PowerPoint presentations from a recent meeting
Please check out:
The ABRF Microarray Survey at Cornell University.
The following links will give you a brief overview of DNA microarrays, they are mostly papers in the (somewhat) popular press:
An article at Cold Spring Harbor labs gives a nice overview
An article entitled "MicroArrays in the New Millenium, Part I" from Bioresearch online which is a brief review of the types of technologies used in making DNA chips.
Here's an article in The Scientist by Bob Sinclair which is a nice introduction to the technologies used in creating arrays and some of the commercial products available to analyze the data.
Another article in The Scientist which focuses on measuring expression.
A third article from The Scientist discusses using Mathcad to analyze microarray data.
Here's an article on the NIH Microarray User Group Mini-Symposium from biomednet.
This page is a homepage of a Stanford University Med Student involved with microarrays
Here's an article from SCIENCE NEWS DIGEST FOR PHYSICIANS AND SCIENTISTS
Here's an article from The American Institute of Physics Bulletin of Physics News
Here's another article, this one explains how DNA is attached to the chips
The following are mostly homepages of laboratories which have built succcessful MicroArrays:
The Brown lab at Stanford University has extensive information on expression array chip design and use. They even have a forum whre people who are trying to make their own microarrays can look for help.
The Functional Genomics site at the Albert Einstein College of Medicine has information on their printer and scanner
The National Human Genome Research Institute at NIH has their own Microarray Project
The Ward Lab at the University of Arizona uses microarrays for the analysis of C. elegans sperm gene expression.
The Leroy Hood lab at the University of Washington, Seattle
An Introduction to DNA Microarray Technology -- an online talk by Alan J. Robinson
Vivian Cheung's Lab at the Children's Hospital of Philadelphia
Drosophila DNA Microarray Homepage at Stanford Medical
The Microarray Centre at the Ontario Cancer Institute.
DNA Microarray Services at Yale Med.
Gene Expression Technology Group at Wake Forest School of Medicine
The Center for Gene Expression Profiling at the Boyce Thompson Institute for Plant Research at Cornell University -- includes some protocols.
The Xenopus Microarray Team at The Rockefeller University
As a computational biologist who enjoys sitting in front of the computer more than sitting in the lab, I am interested in seeing how people tackle the very difficult problem of analyzing the large amount of data that microarray experiments produce. Here are some groups that I know of who are tackling this problem:
DRAGON at Johns Hopkins
TIGR ArrayViewer from The Institute for Genomic Research
Michael Eisen's software at Stanford -- includes ScanAlyze, Cluster and TreeView.
NHGRI's ArrayViewer Java Applet
NHGRI's database design for microarray data
Art Owen's Plaid model software at Stanford.
AMADA (Analyzing Microarray Data) from Dr. Xuhua Xia, University of Hong Kong
Statistical Methods and Analysis at the Arabidopsis Functional Genomics Consortium
DNA Array Analysis Tools at the CNIO Bioinformatics Unit
The following sites have links to other array information
WWW Virtual Library: (Botany) Plant-Arrays
The PlantArrays e-mail message archive at Stanford
Genemachines' links page
Nanogen's links page
Dr. Bernd Weisshaar's links page at the Max-Planck-Institut für Züchtungsforschung in Köln, Germany
Large-Scale Gene Expression and Microarray Links and Resources by Alan Robinson
Information about the "Gene-Array" listserv
NIH's microarray project's list of links
This page has Japanese Links to microarray projects
Gene Chip Microarray Protocol Websites
Resources for microarray technology maintained by Ruth Alscher at Virginia Tech
biocompare.com - The Consumer Guide for the Life Scientist
Microarrays Horizon Press' page for microarrays.
There are many efforts to make DNA microarrays by industry:
Monsanto's Arabidopsis EST Microarray-DNA Chip Plant Biology Research proposals
Affymetrix, Inc., Santa Clara, California
Agilent Technologies, Palo Alto, California
Applied Precision, Inc., Issaquah, Washington
Axon Instruments, Inc. Foster City, California
Biochip Technologies Freiburg, Germany
BioDiscovery, Inc., Los Angeles, California
BioRobotics, Ltd., Cambridge, England
Biospace Mesures, Paris, France
Clinical Microsensors, Pasadena, California
Clontech, Palo Alto, California
Corning Microarray Technology, Corning, NY
DNAmicroarray.com, ???, California
Exiqon, Vedbaek, Denmark
Gene Logic, Inc., Columbia, Maryland
Gene Machines Menlo Park, California
General Scanning Inc., Watertown, Massachusetts
Genetic MicroSystems Inc., Woburn, Massachusetts
Genometrix Inc., The Woodlands, Texas
Genomic Solutions, Ann Arbor, Michigan
Genpak Ltd., Brighton, UK
Incyte Genomics, Inc. Palo Alto, California
Lab-on-a-Chip.com, Suffolk, UK
Molecular Dynamics, Inc., Sunnyvale, California
Nanogen San Diego, California
NEN Life Science Boston, MA
Packard Instrument Company Meriden, Connecticut
PHASE-1 Molecular Toxicology, Inc. Santa Fe, NM
Point Technologies, Inc. Boulder, CO
Radius Biosciences, Medfield, Massachusetts
Research Genetics, Huntsville, Alabama
SciMatrix, Durham, North Carolina
Silicon Genetics San Carlos, California
Super Array, Inc., Bethesda, Maryland
Synteni, Fremont, CA
TeleChem International, Inc. Sunnyvale, CA -- includes some protocols
V & P Scientific Inc. San Diego, California
Vysis Inc., Downers Grove, Ill.
Click here to do a PubMed search for "DNA Microarray"
This list is by no means complete, it is merely a selection of articles which I found interesting and informative re: DNA microarrays. However if you know of an article that isn't here, please Let me know:
Nature Genetics has a recent issue devoted to DNA Chips.
Beier M, et al. 2000. Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays. Nucleic Acids Res. 28(4):E11
Bertucci, F., Bernard, K., Loriod, B., Chang, Y.-C., Granjeaud, S., Birnbaum, D., Nguyen, C., Peck, K., Jordan, B. R. 1999. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples Hum Mol Genet 1999 8: p. 1715-1722
Bowtell DD. 1999. Options available--from start to finish--for obtaining expression data by microarray. Nat Genet 1999 Jan;21(1 Suppl):25-32
Brown, MP, et al. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. PNAS 97(1):262-267.
Brown PO, Botstein D. 1999. Exploring the new world of the genome with DNA microarrays. Nat Genet 1999 Jan;21(1 Suppl):33-7
Mark Chee, Robert Yang, Earl Hubbell, Anthony Berno, Xiaohua C. Huang, David Stern, Jim Winkler, David J. Lockhart, Macdonald S. Morris, Stephen P. A. Fodor. 1996. Accessing Genetic Information with High-Density DNA Arrays.Science 274: 610-614.
Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. 1999. Making and reading microarrays. Nat Genet 1999 Jan;21(1 Suppl):15-9
Cheung VG, Gregg JP, Gogolin-Ewens KJ, Bandong J, Stanley CA, Baker L, Higgins MJ, Nowak NJ, Shows TB, Ewens WJ, Spielman RS. 1998. Linkage-disequilibrium mapping without genotyping. NATURE GENETICS 18: (3) 225-230 MAR 1998
Cheung VG, Nelson SF. 1998. Genomic mismatch scanning identifies human genomic DNA shared identical by descent. Genomics 1998 Jan 1;47(1):1-6
Claverie, J.-M. 1999. Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet 1999 8: p. 1821-1832.
Debouck C, Goodfellow PN. 1999. DNA microarrays in drug discovery and development. Nat Genet 1999 Jan;21(1 Suppl):48-50
DeRisi JL, Iyer VR. 1999. Genomics and array technology. Curr Opin Oncol 1999 Jan;11(1):76-9
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. 1996. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996 Dec;14(4):457-460
J. L. DeRisi, V. R. Iyer, P. O. Brown. 1997. Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 1997 October 24; 278 (5338):680
Desprez T, Amselem J, Caboche M, Hofte H. 1998. Differential gene expression in Arabidopsis monitored using cDNA arrays. PLANT JOURNAL 14: (5) 643-652 JUN 1998
Drobyshev A, Mologina N, Shik V, Pobedimskaya D, Yershov G, Mirzabekov A. 1997. Sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations. Gene 1997 Mar 25;188(1):45-52
Dubiley S, Kirillov E, Lysov Y, Mirzabekov A. 1997. Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization. Nucleic Acids Res 1997 Jun 15;25(12):2259-2265
Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. 1999. Expression profiling using cDNA microarrays. Nat Genet 1999 Jan;21(1 Suppl):10-4
Eisen MB, Spellman, PT, Brown, PO and D Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863-14868
Favis, R., Day, JP, Gerry, NP, Phelan, C., Narod, S., and Barany, F. 2000. Universal DNA array detection of small insertions and deletions in BRCA1 and BRCA2 Nat Biotechnol May; 18(5):561-564.
Ferguson JA, Boles TC, Adams CP, Walt DR. 1996. A fiber-optic DNA biosensor microarray for the analysis of gene expression. NATURE BIOTECHNOLOGY 14: (13) 1681-1684 DEC 1996
Fodor, S. A. 1997. Massively Parallel Genomics. Science 277:393-395.
Forozan F, Karhu R, Kononen J, Kallioniemi A, Kallioniemi OP. 1997. Genome screening by comparative genomic hybridization. TRENDS IN GENETICS 13: (10) 405-409 OCT 1997
Gerry NP, et al. 1999. Universal DNA microarray method for multiplex detection of low abundance point mutations. J. Mol. Biol. 292(2):251-62
Ginot F. 1997. Oligonucleotide micro-arrays for identification of unknown mutations: how far from reality? Hum Mutat 1997;10(1):1-10
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gassenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., and E. S. Lander. 1999. Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science 1999 286: 531-537.
Gunderson KL, Huang XC, Morris MS, Lipshutz RJ, Lockhart DJ, Chee MS. 1998. Mutation detection by ligation to complete n-mer DNA arrays. Genome Res 1998 Nov;8(11):1142-53
Guschin D, Yershov G, Zaslavsky A, Gemmell A, Shick V, Proudnikov D, Arenkov P, Mirzabekov A. 1997. Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal Biochem 1997 Aug 1;250(2):203-211
Hacia JG, Woski SA, Fidanza J, Edgemon K, Hunt N, McGall G, Fodor SP, Collins FS. 1998. Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res 1998 Nov 1;26(21):4975-82
Joseph G. Hacia, Bryan Sun, Nathaniel Hunt, Keith Edgemon, Deborah Mosbrook, Christiane Robbins, Stephen P.A. Fodor, Danilo A. Tagle, and Francis S. Collins. 1998. Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays. Genome Res. 1998 December 1; 8(12): p. 1245-1258
Hacia JG. 1999. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 1999 Jan;21(1 Suppl):42-7
Hayward RE, et al. 2000. Shotgun DNA microarrays and stage-specific expression in plasmodium falciparum malaria. Mol Microbiol 35(1)6-14
Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW. 1997. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A 1997 Mar 18;94(6):2150-2155
Hoheisel JD. 1997. Oligomer-chip technology. TRENDS IN BIOTECHNOLOGY 15: (11) 465-469 NOV 1997
Johannes G, et al. 1999. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci USA 96(23):13118-23.
Johnston M. 1998. Gene chips: Array of hope for understanding gene regulation. CURRENT BIOLOGY 8: (5) R171-+ FEB 26 1998
Kal, A. J., van Zonneveld, A. J., Benes, V., van den Berg, M., Koerkamp, M. G., Albermann, K., Strack, N., Ruijter, J. M., Richter, A., Dujon, B., Ansorge, W., Tabak, H. F. 1999. Dynamics of Gene Expression Revealed by Comparison of Serial Analysis of Gene Expression Transcript Profiles from Yeast Grown on Two Different Carbon Sources. Mol. Biol. Cell. 10:1859-1872
Khan J, et al. 1999. cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene. Proc Natl Acad Sci USA 96(23):13264-9
Khrapko KR, Lysov YuP, Khorlyn AA, Shick VV, Florentiev VL, Mirzabekov AD. 1989. An oligonucleotide hybridization approach to DNA sequencing. FEBS Lett 1989 Oct 9;256(1-2):118-122
Kononen J, Bubendorf L, Kallioniemi A, Barlund M, Schraml P, Leighton S, Torhorst J, Mihatsch MJ, Sauter G, Kallioniemi OP. 1998. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 1998 Jul;4(7):844-847
Kruglyak L, McAllister L. 1998. Who needs genetic markers? NATURE GENETICS18: (3) 200-202 MAR 1998
Lander ES. 1999. Array of hope. Nat Genet 1999 Jan;21(1 Suppl):3-4
Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 94: (24) 13057-13062 NOV 25 1997
Lee PS, Lee KH. 2000. Genomic analysis. Curr Opin Biotechnol Apr; 11(2):171-175
Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. 1999. High density synthetic oligonucleotide arrays. Nat Genet 1999 Jan;21(1 Suppl):20-4
David J. Lockhart, Helin Dong, Michael C. Byrne1, Maximillian T. Follettie, Michael V. Gallo, Mark S. Chee, Michael Mittmann, Chunwei Wang, Michiko Kobayashi, Heidi Horton, and Eugene L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays, NATURE BIOTECHNOLOGY 14: (12) 1675-1680 DEC 1996
Marshall A, Hodgson J. 1998. DNA chips: an array of possibilities. Nat Biotechnol 1998 Jan;16(1):27-31
Matsumura H, et al. 1999. Technical Advance: Transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE). Plant J. 20(6):719-726.
Lucito R, Nakimura M, West JA, Ying H, Chin K, Jensen K, McCombie R, Gray JW, Wigler M. 1998. Genetic analysis using genomic representations. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 95: (8) 4487-4492 APR 14 1998
Noble D. 1995. DNA sequencing on a chip. Anal Chem 1995 Mar 1;67(5):201A-204A
Pappalardo PA, Bonner R, Krizman DB, Emmert-Buck MR, Liotta LA. 1998. Microdissection, Microchip Arrays, and Molecular Analysis of Tumor Cells (Primary and Metastases). Semin Radiat Oncol 1998 Jul;8(3):217-223
Pennisi E. 1999. DNA chips give new view of classic test. Science 1999 Jan 1;283(5398):17-8
Proudnikov D, Timofeev E, Mirzabekov A. 1998. Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA-oligonucleotide microchips. ANALYTICAL BIOCHEMISTRY 259: (1) 34-41 MAY 15 1998
Radtkey, R., Feng, L., Muralhidar, M., Duhon, M., Canter, D., DiPerro, D., Fallon, S., Tu, E., McElfresh, K., Nerenber, M., and R. Sosnowski. 2000. Rapid high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Research Methods 28(7) April 1.
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Richmod T and S Somerville. 2000. Chasing the dream: plant EST microarrays. Curr Opin Plant Biol Apr;3(2):108-116.
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SCHENA M, SHALON D, DAVIS RW, BROWN PO. 1995. Quantitative Monitoring Of Gene-expression Patterns With A Complementary-DNA Microarray. SCIENCE 270: (5235) 467-470 OCT 20 1995
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Stimpson DI, Cooley PW, Knepper SM, Wallace DB. 1998. Parallel production of oligonucleotide arrays using membranes and reagent jet printing. Biotechniques 1998 Nov;25(5):886-90
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Elizabeth A. Winzeler, Dan R. Richards, Andrew R. Conway, Alan L. Goldstein, Sue Kalman, Michael J. McCullough, John H. McCusker, David A. Stevens, Lisa Wodicka, David J. Lockhart, Ronald W. Davis. 1998. Direct Allelic Variation Scanning of the Yeast Genome. Volume 281, Number 5380 Issue of 21 Aug 1998, pp. 1194 - 1197
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Zanders, ED et al. 2000. Analysis of immune system gene expression in small rheumatoid arthritis biopsies using a combination of subtractive hybridization and high-density cDNA arrays. J Imminol Methods. 233(1-2):131-140.
You can search for more recent references here: ISI Citation Database
And PubMed is also an invaluable reference tool.
Affymetrix's list of publications.
There is some more information about bioinformatics at the main science section. And if you're curious, please feel free to check out deathstarinc
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(C) 1998-2005 Andreas Matern.
Last modified: February 22, 2005