Thursday, July 10, 2008



  1. Gene-Arrays mailing list (maintained by Dr. Chandi Griffin at San Francisco General Hospital/UCSF). To subscribe, Send a one line e-mail message to [email protected]; the single line message should be: subscribe Gene-Arrays your-first-name your-last-name. This is a very good place to ask all kinds of questions regarding gene chips and DNA microarrays. To post a question to the whole mailing list, send email to [email protected]. You may leave the list at any time by sending a "SIGNOFF GENE-ARRAYS" command to [email protected]
  2. A microarrays newsgroup was recently made available at (maintained by Philippe Marc).
  3. Nobel Laureate Martin L. Perl's group at the Stanford Linear Accelerator Center (SLAC) is investigating if their new drop-on-demand inkjet technology originally designed for the searching of certain hypothetical types of elementary particles would be of use in the production of DNA microarrays.
  4. Stanford University's Dr. Patrick Brown, one of the major players in this field. This group has a complete guide for researchers to build their own microarrayer
  5. DNA Microarray Protocols of Dr. Mark Schena: extremely detailed and useful information on performing DNA microarray experiments. Everyone in this field should bookmark it!
  6. Dr. Mark Schena Home Page
  7. NIST ATP Awards 1998: Tools for DNA Diagnostics (7 of the 29 proposals were awarded)  Check project manager Dr. Stanley Abramowitz's overview talk on this field
  8. CGAP (Cancer Genome Anatomy Project) at the National Cancer Institute (NCI), NIH.
  9. Microarray Project at the National Human Genome Research Institute (NHGRI), NIH
  10. Dr. John N. Weinstein at the National Cancer Institute (NCI) developed an "information-intensive" anticancer drug discovery approach that integrates chemical structure information and anticancer activity patterns of >70,000 screened compounds with gene expression (microarray) data of the 60 human cancer cell lines
  11. Gene Chips (DNA Microarrays) homepage (this site, created by Dr. Leming Shi), a good starting point, contains a lot of useful links. This site was reviewed by Science magazine.
  12. Dr. Alan Robinson's web resource on Gene Expression and Microarray Technologies, at EBI. (highly recommended)
  13. Andreas Matern's home page on DNA Microarrays
  14. Anatomy of a Comparative Gene Expression Study (by Jeremy Buhle). It's a very nice description of the microarray technology, also includes a Glossary of Microarray-related Biotechnology Terms
  15. Whitehead Institute for Biomedical Research/MIT Center for Genome Research
  16. Dr. Geoffrey Childs, Functional Genomics at AECOM, Department of Molecular Genetics, Albert Einstein College of Medicine
  17. Computational Genomics at Harvard University (Dr. George M. Church, a lot of very useful links)
  18. Human Genome Project Information at the Oak Ridge National Laboratory, U.S. Department of Energy
  19. National Human Genome Research Institute (NHGRI) is developing "Tissue Chip" to Illuminate the Cancer Development Process
  20. NIH Clinical Study: 97-C-0178: Fludarabine Treatment of Chronic Lymphocytic Leukemia: cDNA Microarray Gene Expression Analysis, and Preclinical Bone Marrow Transplant/Immunotherapy Studies
  21. Garner Lab at UTSW - Gene Networks
  22. DNA Microarray Technology to identify genes controlling spermatogenesis, Sam Ward at the University of Arizona
  23. Vivian Cheung's Lab at The Children's Hospital of Philadelphia focuses on the development of Direct Identical-by-Descent (IBD)
  24. Mapping, which is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals.
  25. University of Washington, Dr. Lee Hood,  Java-based Array Image Spot Finding and Quantification Software (CrazyQuant)
  26. Dr. Bernd Weisshaar's listing of DNA microarray links, Max-Planck-Institut für Züchtungsforschung
  27. Dr. Landers' Group at the University of Pittsburgh is developing microcolumn technology for clinical diagnostics. This capillary-based Integrated Diagnostic (ID) Chip may have great potential in clinical diagnostics.
  28. Dr. Claude Jacq's group at ENS, France. They also maintain a discussion list: [email protected]
  29. Toxicogenomics homepage at the Chemical Industry Institute of Toxicology (CIIT): discusses how the DNA microarray technology is impacting toxicological research.
  30. Dr. Willard M. Freeman's Gene Expression Technology Group at the Wake Forest University School of Medicine.
  31. The Vanderbilt University Microarray Core Facility ( offers microarray-based products and services.
  32. MRC Toxicology Unit DNA Microarray Pages maintained by Dr Timothy W. Gant.
  33. The Nylon MicroArrays site provies detailed information on the use of nylon microarrays (allowing expression profiling with small amounts of unamplified RNA) and a number of useful utilities for choosing and checking IMAGE clones representing given genes. contact: [email protected]
  34. Molecular Pattern Recognition web site at MIT's Whitehead Genome Center. Focuses on computational methodologies for the analysis and interpretation of large-scale expression datasets generated by DNA micro-array experiments.


  1. ACLARA BioSciences, Inc., (used to be called Soane Biosciences) Hayward, California (Plastic chips and microfluidic systems based on "Lab-On-A-Chip" microfluidics US Patent 5,750,015: "Method and device for moving molecules by the application of a plurality of electrical fields") Wins NIST ATP Award in "Tools for DNA Diagnostics" for Project: Multiplexed Sample Preparation Microsystem for DNA Diagnostics
  2. Affymetrix, Inc., Santa Clara, California (The technology leader; manufactures the widely used GeneChip?arrays, including HIV, p450, p53, Rat Toxicology U34 arrays, etc.)
  3. Alexion Pharmaceuticals Inc., New Haven, Connecticut
  4. AlphaGene, Inc., Woburn, Massachusetts (full length cDNA FLEX&S482; and MicroFLEX library construction; High Throughput Gene Expression Profiling; High Throughput DNA Sequencing; Bioinformatics)
  5. Applied Precision, Inc., ssaquah, Washington. ArrayWoRx is a wide field light source based microarray scanner, combines limitless wavelength possibilites with automation and image processing software.
  6. ArrayIt, Making DNA chip.
  7. Axon Instruments, Inc., Foster City, California (GenePix 4000 Integrated Microarray Scanner and Analysis Software, simultaneously scans microarray slides at two wavelengths using a dual laser scanning system, displays images from two wavelengths and a ratio image as they are acquired in real time; US$50,000)
  8. AxyS Pharmaceuticals, La Jolla, California: Wins NIST ATP Award in "Tools for DNA Diagnostics" Project: Liquid Array Technology Development
  9. BioChip Technologies
  10. bioDevice Partners, Cohasset, MA. Provides consulting services to the micorarraying community in the area of optics and instrumentation
  11. BioDiscovery, Inc., Los Angeles, California (ImaGene&S482;, special image processing and data extraction software)
  12. Biomedical Photometrics, Inc., (MACROscope&S482;  for reading genetic microarrays, in collaboration with Canadian Genetic Microarray Consortium)
  13. bioMerieux, in vitro diagnostics
  14. BioRobotics Ltd.,  Comberton, Cambridge, UK (MicroGrid, for arraying oligonucleotides or cDNA clones on glass slides and plastic chips)
  15. Brax, Cambridge, UK
  16. Cadus Pharmaceutical Corp., Tarrytown, New York (yeast living chip)
  17. Caliper Technologies Corp., Palo Alto, California: LabChips&S482; based on microfluidics. Awarded $2 million contract by NIST to develop high-throughput DNA diagnostic platform. Project: Reference Laboratory LabChip&S482; DNA Diagnostics System
  18. Cartesian Technologies, Inc., Irvine, CA. PixSys PA Series: for Automated liquid handling system for creating high-density arrays for genomics research. Scan Array 3000: A Fluorescent Imaging System for microarray biochips.
  19. Celera, Rockville, Maryland
  20. Cellomics, Inc., Pittsburgh, Pennsylvania (ArrayScan&S482;, cell-based "High Content Screening" (HCS) for drug discovery)
  21. Cepheid  Sunnyvale, California (microfluidics)
  22. Ciphergen Biosystems, Palo Alto, California. ProteinChip&S482; Arrays for the investigation of proteins on the femtomole scale directly from their "native" environments. Based on Surface-Enhanced Laser Desorption/Ionization (SELDI&S482;).
  23. Clinical Micro Sensors, Inc., Pasadena, California: DNA microchip-based medical diagnostics; detection of directly detect DNA via electron transfer. Wins NIST ATP Award in "Tools for DNA Diagnostics" Project: DNA Diagnostics for the Point of Care Using Electronic Nucleic Acid Detection
  24. Clontech
  25. Corning Science Products Division, Acton, MA provides the (Corning Microarray Technology) CMT-GAPS amino silane coated slides and CMT-Hybridization chamber.
  26. Corvas International, Inc., (2D gel, proteomics)
  27. CuraGen Corp., New Haven, Connecticut.  GeneCalling&S482; and Quantitative Expression Analysis (QEA&S482;), CuraMode, CuraTox
  28. diaDexus, LLC, Santa Clara, California. joint venture between SmithKline Beecham Corp. and Incyte Pharmaceuticals, Inc.. Specialized in using microarray technology for molecular diagnostics
  29. offers complete "made to order" high density DNA microarray synthesis and analysiss services. Prices, availability, and turnaround time seem impressive.
  30. Gel biochip
  31. Gene Logic, Inc., Columbia, Maryland (Flow-thru ChipTM: has hundreds of thousands of discrete microscopic channels that pass completely through it. Probe molecules are attached to the inner surface of these channels, and target molecules flow through the channels, coming into close proximity to the probes. This proximity facilitates hybridization. READS&S482;, Restriction Enzyme Analysis of Differentially-expressed Sequences, for capturing and analyzing the overall gene expression profile of a given cell or tissue type to identify drug targets)
  32. GeneData AG (Basel, Switzerland), analysis of genomics and proteomics data: GeneData WorkBench, GeneData Expressionist.
  33. Genemachines Genomic Instrumentation Services, Inc., Menlo Park, California (OmniGrid, glass slides or nylon membranes, similar to Dr. Pat Brown's)
  34. General Scanning Inc., Watertown, Massachusetts (laser scanning and micropositioning, manufactures MicroArray Biochip Scanning System: ScanArrayTM). Now called GSI Lumonics
  35. GeneScreen, Inc.,  The Genetics Profiling Company
  36. GeneTrace Systems
  37. Genetic Analysis Technology Consortium (GATC)
  38. Genetic MicroSystems Inc., Woburn, Massachusetts (instrumentation for DNA microarray-based analysis)
  39. Genetix Ltd., Christchurch, Dorset, UK (Q-Bot, Q-Pix)
  40. Genome Systems Inc., St. Louis, MO, a wholly owned subsidiary of Incyte Pharmaceuticals, Inc., GDA: Gene Discovery Array
  41. Genometrix Inc., The Woodlands, Texas (Bioscanner&S482;, GeneView?, Universal Arrays&S482;, Risk-Tox)
  42. Genomic Solutions, Ann Arbor, Michigan (Flexys&S482; modular robotic system, GeneTAC&S482; and Genomic Integrator&S482; array analysis products automates the imaging and analysis of gene microarrays.)
  43. Genosys Biotechnologies, Inc., The Woodlands, Texas (Panorama&S482;E. coli Gene Arrays, 4,290 genes per array)
  44. GENSET, Paris, France (specialized in pharmacogenomics)
  45. Genzyme Molecular Oncology (SAGE?: Serial Analysis of Gene Expression)
  46. HP GeneArray Scanner (used by Affymetrix and others)
  47. Hyseq Inc., Sunnyvale, California (Sequencing By Hybridization. HyX platform and Gene Discovery, HyGnostics, and HyChip&S482; modules)
  48. Illumina, Inc., San Diego, California. utilizes fiber optics, microfabrication, and advanced information processing to create arrays where 250,000 discrete sensors fit on a probe the diameter of the head of a pin.
  49. I.M.A.G.E. Consortium: "Sharing resources to achieve a common goal - the discovery of all genes"
  50. Imaging Research, Inc., St. Catharines, Ontario, Canada. The company writes software, develops detection technologies, and integrates systems for image analysis. Its PC-based ArrayVisionTMsystem has been widely used for rapid and automated analysis of genome arrays.
  51. Incyte Pharmaceuticals, Inc., Palo Alto, California (GEM Microarrays, GeneJetTM array, LifeSeq? Database with estimated 100,000 genes, and LifeArray Microarray Software)
  52. Intelligent Bio-Instruments, Cambridge, Massachusetts
  53. JMAR's Precision Systems, Inc., Chatsworth, CA. Designer and manufacturer of UV exposure and mask aligner systems specifically designed for bio-chip manufacturers. Also produces custom micropositioning systems for micro-spotting equipment and high resolution dimensional metrology and defect inspection systems for quality assurance of bio-chips and DNA micro-arrays.
  54. Labman AutomationLtd., North Yorkshire, TS9 5JY, UK (HDMS: Labman High-Density Microarray Spotter)
  55. Lifecodes Corp., Stamford, Connecticut (Lifecodes MicroArray System: LMAS)
  56. Micronics, Inc., Redmond, Washington. microfluidics based systems for application to clinical laboratory diagnostics: Microcytometer&S482;, H-Filter&S482;, T-Sensor&S482;, and O.R.C.A. μFluidics.
  57. Molecular Applications Group, Palo Alto, CA. Stingray&S482; is integrated software and database products for gene expression, gene function, and gene sequence analysis from microarray data. It is integrated with and dependent upon the use of Affymetrix's  GeneChip? system and its Expression Data Mining Tool (EDMT) software.
  58. Molecular Dynamics, Inc., Sunnyvale, California (Storm? and FluorImager?)
  59. Molecular Tool, Inc., Baltimore, Maryland. Genetic Bit Analysis, GBA?, Genomatic&S482;. Acquired by Orchid Biocomputer on September 14, 1998.
  60. Nanogen, San Diego, California (Electronic Addressing, Concentration, and Hybridization)
  61. NEN Life Science Products, Boston, MA (MICROMAX&S482; Human cDNA Microarray System I for differential gene expression analysis)
  62. Oncormed Inc., (acquired by Gene Logic in July, 1998) characterizes genes to establish their clinical relevancy and provides molecular profiling of patients for pharmacogenomic and therapeutic purposes
  63. Orchid Biocomputer, Inc., Princeton, New Jersey (a Sarnoff company) microfluidic chips; applying microfabrication processes in glass, silicon, and other materials to create three dimensional structures.  Contained within these devices are small capillary channels less than a millimeter wide. Wins NIST ATP Award in "Tools for DNA Diagnostics" Project: Polymerase Signaling Assay for DNA Variation Detection on Universal Processor Arrays It also has a Web site on single nucleotide polymorphisms (SNPs).
  64. Packard Instrument Company, Meriden, Connecticut. (BioChip Arrayer)
  65. Partek, Inc., St. Peters, Missouri. Provider of pattern recognition and data visualization software for science and engineering. Its Partek Pro 2000 system has been used by companies to analyze microarray gene expression data.
  66. PE Applied Biosystems, Wins NIST ATP Award in "Tools for DNA Diagnostics" for project: Integrated, Micro-Sample Preparation System for Genetic Analysis
  67. PharmaSeq, Inc., Monmouth Junction (near Princeton), NJ. Developer of microtransponder-based technology for DNA diagnostic assays. Wins NIST ATP Award in "Tools for DNA Diagnostics" for project: Multiplex DNA Diagnostic Assay Based on Microtransponders
  68. Phase-1 Molecular Toxicology, Inc., Santa Fe, New Mexico. Molecular and high throughput toxicology using gene chips (Licensed from Xenometrix)
  69. Proteome, Inc.
  70. Protogene Laboratories, Palo Alto, California (Surface tension array on glass substrate; "Printing" reagents using drop-on-demand technology)
  71. Radius Biosciences, Medfield, Massachusetts
  72. Research Genetics, Huntsville, Alabama (GeneFilter)
  73. Rosetta Inpharmatics, Kirkland, Washington.
  74. Scanalytics, Inc. , Fairfax, VA. Its MicroArray Suite enables researchers to acquire, visualize, process, and analyze gene expression microarray data. Developed by scientists at the NIH's National Human Genome Research Institute.
  75. Sequana Therapeutics (merged with Arris Pharmaceutical to become AxyS Pharmaceuticals), La Jolla, California
  76. Sequenom, Hamburg, Germany, and San Diego, California (DNA MassArray, BiomassPROBE, Biomass SIZE, BiomassSEQUENCE, BiomassSCAN, BiomassINDEX, and SpectroChip)
  77. Silicon Genetics, Redwood City, California (GeneSpring workbench for analyzing experiments based upon genomic expression experiments)
  78. Spotfire, Inc., Cambridge, Massachusetts. Offers advanced data visualization capabilities including the ability to perform gene cluster analysis and metabolic pathway mapping. The Spotfire Array Explorer is ideal for any researcher performing microarray analysis.
  79. Synomics Ltd., Cambridge, UK  (bioinformatics)
  80. Synteni, Inc., Fremont, California (acquired by Incyte Pharmaceuticals, Inc. in January 1998) (UniGEM&S482; Gene Expression Microarray)
  81. TeleChem International, Sunnyvale, California (offers whole system parts: ChipMaker, SmartChips, ArrayIt, Hybridization Cassette, ScanArray 3000, ImaGene Quantification Software)
  82. Virtek Vision International Inc. (Ontario, Canada) ChipReader&S482; is a high-sensitivity laser confocal system for rapid imaging of the DNA microarrays.
  83. Vysis, Inc., Downers Grove, Illinois (CGH-Comparative Genomic Hybridization)
  84. Xanthon, Research Triangle Park, North Carolina. develops microplate based mini-arrays for high throughput screening of compounds for their effects on gene expression.
  85. Xenometrix, Inc., Boulder, CO (Gene Profile Assay and bioinformatics for gene induction profile analysis; a demo is available)

Powered by Blogger Skins. Theme: TheBuckmaker | Free Wordpress Templates. Presents HD TV Futurama Streaming. Featured on Wedding Dresses.