Session Started

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Some example Keywords you might find listed:

Bioinformatics, Companies (services, consumables and instrumentation), Data (public Domain)/Data Analysis, Databases, Data Standards, General Information, Languages (MAML GEML and others), Link Collections and Resource Pages, Labs European/North American/Rest of the World, News Groups/News and Veiws, Software, Statistcal Analysis, Organisations using or developing Microarrays, Shared/Core facilities, Pathways (regulatory networks), Protocols, QC, References and Reveiws

B

Bioinformatics

see also Statistical Analysis

• Bioinformatics resource listings on the WWW compiled at SGUL

• Alan Robinson's home page at the EBI, Links to web pages for the "Microarray XML Working Group", "The Second International Meeting on Microarray Data Standards, Annotations, Ontologies and Databases", The links included are biased towards the development and application of informatics and bioinformatics.
• Alvis Brazma's home page, links to other pages both at the EBI and external including gene regulation networks,  data annotation, public repository for microarray based gene expression, data mining the yeast genome expression, pattern discovery in biosequences, data mining.
• Bioinformatics at UCLA
• BioInformatics & Molecular Analysis Section (BIMAS), Computational Bioscience and Engineering Lab (CBEL), Center for Information Technology (CIT), National Institutes of Health (NIH)
• Center for Computational and Experimental Genomics University of Southern California contains links to interesting publications Heyer et al. Exploring Expression Data: ...Genome Research 2000
• Jacques van Helden's home page contains links to regulatory sequence analysis tools a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. In addition there are links to the biochemical network database PFMB.
• The Institut Curie Bioinformatics Group home, has a nice range of tools and associated publications mainly relating to transcriptomics and aCGH
• Mike Eisen's home page, links to his publications list, supplemental data and software.
• For XML, GEML and other inforamtion on computer languages and their usage in gene expression analysis see Languages below
• The computational biology laboratory in the School of Computer Science and Engineering. Research in the lab applies methods from machine learning, theory of computer science, combinatorial optimization, information theory and applied statistics for a wide range of problems in computational molecular biology. This includes projects on Using Bayesian Networks to Analyze Gene Expression Data
• The Analytical Biostatistics Section is part of the Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health.

Bioinformatics Papers

This listing is by no means comprehensive and is meant to wet the appetite you might also try below

• Patrik D'haeseleer at University of New Mexico: Gene Network Inference from Large-Scale Gene Expression  interesting discussion with linked articles.
• On-line papers presented at Pacific Symposium on Biocomputing 1996-2000 available as pdf files
• Michael P. S. Brown, William Noble Grundy, David Lin, Nello Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr., David Haussler, paper on "Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines", at the Baskin Center for Computational Biology University of California.
• On-line paper "Knowledge Mining With VxInsight: Discovery Through Interaction" GEORGE S. DAVIDSON, BRUCE HENDRICKSON, DAVID K.JOHNSON, CHARLES E. MEYERS AND BRIAN N.WYLIE , Sandia National Laboratories.
• Singular value decomposition for genome-wide expression data processing and modeling. Orly Alter, Patrick O. Brown, and David Botstein Proceedings of the National Academy of Sciences 97 (18), pp. 10101–10106 (August 29, 2000), supplement to paper
• Tibshirani, R., Hastie, T. Eisen, M., Ross, D. , Botstein, D. and Brown, P. (compressed postscript file) "Clustering methods for the analysis of DNA microarray data". (postscript 4.8mb) Compressed postscript. Tech. report Oct. 1999, see also statistical analysis for other reports and publications from this lab
• Lazzeroni, L. and Owen, A.B (2000) "Plaid Models for Gene Expression Data"
• Papers and talks on Baysian Networks from the computational biology laborartory, Hebrew University
• Abstracts from ISMB 2001. Networks and Modeling and Gene expression
• Breifing in Bioinformatics 2 (4) 1467-5463 this is a special issue on Gene Expression Studies
• Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains.  Soumya Raychaudhuri, Joshua M. Stuart, Xuemin Liu, Peter M. Small & Russ B. Altman. (pdf) Paper presented at ISMB 2000

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CGH (Comparative Genome Hybridisation)

• The Molecular Cytogenetics Group Department for Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin work on the characterization of chromosomal aberrations in patients with congenital diseases and in solid tumours. One focus is the search for chromosomal changes responsible for the disruption of brain development and function. One of the main techniques used in this goup is arrayCGH Currently we are focusing on the generation of a genome wide tiling path array of 32450 BAC clones providing a resolution of about 70kb. Their protocols page from

Cluster Analysis
For Other articles or sites on Cluster Analysis see also: Bioinformatics, Statistical Analysis or Data Analysis

• Cluster Analysis and Display of Genome-wide Expression Patterns. Eisen et al. (1998) Proc. Natl. Acad. Sci. (USA) 95:14863
• Coupled two-way clustering analysis of gene microarray data.Gad Getz, Erel Levine, and Eytan Domany.  PNAS 2000 97: 12079-12084
• Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Grotkjaer et al.  Bioinformatics 2005 doi:10.1093/bioinformatics/bti746
• A range of free-ware is available for cluster analysis by heirachical, k-means, SOM & SOTA
  • CNIO server - Spanish National Cancer Center
  • Cluster & Tree Veiw - University of California
  • CAGED - Harvard Medical Scool for temporal gene expression analysis using Baysian Clustering
  • GeneMaths - commercial
  • Genesis - Institue of BioMedical Engineering

Companies

• Listings are also available on some of the Links pages suggested (found under L)
• A company listing of Microarray technology suppliers (Nature technology feature)
• Companies supplying off-the-shelf and custom array services 

• Companies supplying Instumentation, allied Software & Consumables

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Data (Public Domain)

Various Organisms

• A page giving a comprehensive list of published public domain data at SMD 

Eukaryotic Data Sets

• LymphoChip Database Gateway. Tissue-Enriched Unigene Build #61 Clusters, Interactive Selection of Hs (Human) Clusters from individual Tonsil Libraries, Interactive Selection of Hs (Human) Clusters from Lymphoid Libraries
• Lymphoma/Leukemia Molecular Profiling Project a suppliment to Alizadeh et al. Nature 403: 2000, includes primary data download
• The transcriptional program in the repsonse of human fibroblasts to serum stimulation, a supplement to Iyer et al. Science 283: 1999 data download entry page
• Data supplement to:Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, Somogyi R (1998) Large-Scale Temporal Gene Expression Mapping of CNS Development. Proc Natl Acad Sci USA, 95:334-339. pdf file data download site.
• Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum. R. E. Hayward, J. DeRisi, S. Alfadhli, D. C. Kaslow, P. O. Brown & P. K. Rathod Molecular Microbiology (2000) Vol. 35, pp 6-14.
• Molecular Portraits of Human Breast Tumors Perou et al. Nature(2000) 406 : 747-752, The data from this project is freely available to academic researchers.
• Functional Discovery via a Compendium of Expression Profiles. Cell 102, 109-126 (2000) & Widespread aneuploidy revealed by DNA microarray expression profiling. Nature Genetics 25, 333-337 (2000).. Hughes et al. have constructed a reference database or 'compendium' of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. Data download page.
• Cancer Microarray project web supplement Ross et al. (2000) Nat Genet., 24 (3) 227-234 . Collaboration between Brown/Botstein labs and Weinsteins group

Yeast Data Sets

• Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. A web companion including data sets to all time points of the diauxic shift time course. Data for the Tup1 deletion strain versus wild type. Yap1 Data for the Yap1 over expression strain versus wild type. Additional Figures and data and the array scans, download the complete data sets. Sporulation: Gene expression time course DeRisi et al. (1997) Science 278: 680
• Eisen MB, Spellman PT, Brown PO and Botstein D. (1998). Cluster Analysis and Display of Genome-Wide Expression Patterns. Proc Natl Acad Sci U S A 95, 14863-8. pdf and On-line suppl. to paper
• Provides access to genome-wide expression levels in yeast, the complete characterization of mRNA transcript levels during the cell cycle of the budding yeast Saccharomyces cerevisiae. Cho et al.(1998) Mol Cell 2(1):65-73 .
• Yulei Wang, Chih Long Liu, John D. Storey, Robert J. Tibshirani, Daniel Herschlag, and Patrick O. Brown. Precision and functional specificity in mRNA decay (2002) PNAS Vol. 99:5860-5865. pdf and web suppl.

Prokaryotic Data Sets

• Sherman et al. (2001) PNAS 98 7534-7539 Regulation of Mycobacterium tuberculosis hypoxic response gene encoding alpha-crystalin data. On-line Supplement
• E.coli K12 gene expression. Both microarray and HDG data sets for heat shock and IPTG induction as well as a searchable database from Blattner, et al. 1997
• A supplement to Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, Rane S, Small PM. Comparative Genomics of BCG Vaccines by Whole-Genome DNA Microarray. Science 1999 May 28; 284, download page
• Jianqiang Huang, Chih-Jian Lih, Kuang-Hung Pan, and Stanley N. Cohen. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes and Development 15 3183-3192, December 1, 2001. web suppl.
• Arkady Khodursky et al. DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc.Natl.Acad.Sci.(2000) pdf and web suppl.
• Salama N et al.(2000) A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains Proc Natl Acad Sci U S A 97:14668-14673. pdf and web suppl. at SMD with public download availability
• Min-Kyu Oh, Lars Rohlin, Katy C. Kao, and James C. Liao (2002) Global Expression Profiling of Acetate-grown Escherichia coli. JBC Vol. 277, No. 15, 13175–13183, suppl data, pdf
• Laub, M.T., McAdams, H.H., Feldblyum, T., Fraser, C. M., Shapiro, L. "Global Analysis of the Genetic Network Controlling a Bacterial Cell Cycle" Science 2000 Dec 15; vol. 290, p. 2144-2148.

Data Analysis

• CAMDA: Critical Assessment of Microarray Data Analysis. CAMDA1 was founded to provide a forum to critically assess different techniques used in microarray data mining. It aims to establish the state-of-the-art in microarray data mining, as well as identify progress and highlight the direction for future effort. To achieve these goals, CAMDA adopted the approach of community-wide experiment by letting the whole scientific community to analyze the same standard data sets. See abstracts and presentations from CAMDA01

Databases (Expression Data)

For a comprehensive survey of microarray databases see Gardiner-Garden and Littlejohn (2001) Breifings in Bioinformatics vol 2 no 2 143-153.

• ACTuDB array CGH database housed at the Institute Curie allows meta analysis of CGH data on cancer genomics (see Hupé, et al. Oncogene. ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors. 2007 Oct 11;26(46):6641-52.)
• ArrayDB Integrating cDNA Microarray Gene Expression Data with Distributed Biological Resources, NHGRI/NIEHS/NIH
• ArrayExpress, developed at the EBI, is a public repository for microarray based gene expression data based at the EBI Establishing a Public Repository for DNA Microarray-Based Gene Expression Data, European Bioinformatics Institute
• BASE is an open source web-based comprehensive database server to manage the massive amounts of data generated by microarray
  analysis
• ExpressDB a relational yeast expression database at Harvard
• Geo Gene Expression Omnibus at the NCBI, "GEO is our effort to build a gene expression data repository and online resource"
• GeneX is an open source a public repository database with integrated tools being developed at the NCGR
• Gene Expression Database (GXD) is to store and integrate the many types of public gene expression data on the laboratory mouse, has been developed by and housed at the Jackson Laboratory. See also MGI gene expression pages
• GNF DB (Genomics Institute of the Novartis Research Foundation Expression databse for affymetrix chip data,San Diego,USA) 
• KEGG microarray expression database: a web link to flat file download
• Lymphochip Database Gateway at the NIH-CIT
• NOMAD is currently being developed at UCSF for local installation
• NHGRI are developing a Sybase (relational) database schema this is an introductory page to ArrayDB and mArray database
• CIT/BIMAS is collaborating with NCI/CCR in the development of mAdb to manage, access and analyze cDNA µArray data generated by the NCI/CCR mArray Center. NIH-CIT (center for information technology)
• maxdSQL is a local data warehouse and visualisation environment for microarray expression data being developed by the Microarray Group at Manchester Bioinformatics using java.
• MAT at ASCOM uses Sybase
• ChipDB: A Genome Expression Monitoring Database System from the Whitehead Institute for biomedical research/MIT Center for Biotechnology allowing public queries
• RAD  (RNA Abundance Database) is a gene expression database designed to hold data from array-based (e.g., microarray, high-density oligo array, and macroarray) and non-array-based (e.g., SAGE) experiments. Close integration with the DoTS gene index will eventually allow the comparative analysis of experiments performed by different laboratories using different platforms and investigating different biological systems. Version 2.0, is available to the public for queries, and a future version of the database will support direct third-party data entry at University of Pennsylvania.
• Microarray Expression Profiling of Rodent Models of Human Disease .Our goal is to begin an exploration of these interactions of genes with their environments, including the genetic background in which the genes are expressed using rodent models of human disease and cDNA microarray assays to elucidate patterns of gene expression. 
• Stanford Microarray Database SMD is an oracle database.
• A Gene Expression Database for theMolecular Pharmacology of Cancer. Scherf et al. Nature Genetics, volume 24, no 3 March 1st, 2000 pp:236-244. This is purportedly the first study to integrate large databases on gene expression and molecular pharmacology.
• The IGMS is a comprehensive information system that combines the knowledge from genomic sequence, genetic map and genetic disorders databases. This system is updated weekly and focuses on the analysis of EST data. The IGMS identifies UniGene clusters that are differentially expressed in different types of cancer with respect to different reference tissues
• The recently established web site EcoReg is designed to be a repository of primary data (analogous to Genbank) for E. coli transcriptional control processes. It will be a bioinformatics database project to facilitate improved understanding and modeling of the transcriptional control of E. coli gene expression.

Commercial databases

• GeNet Silicon Genetics, "GeNet^TM is the first public web database that allows scientists working with any organism to freely distribute and visualize gene expression data from micro-arrays, Affymetrix chips, and related technologies"

Secondary Databases utilizing expression data

• Experimental Database of functioal networks in organisms Protein Function and Biochemical Pathways (PFBP) Project

Datamining: For Other artcles or sites on Datamining see also: Bioinformatics, Statistical Analysis, Data Analysis or Database

• Hughes et al. Cell 102, 109-126 (2000) (Functional Discovery via a Compendium of Expression Profiles) constructed a reference database or 'compendium' of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae and is a good example of how datamining may be used in conjunction with microarray analysis in the future.
• COMPUTATIONAL ANALYSIS OF MICROARRAY DATA. An excellent review article by John Quackenbush in Nature Reviews Genetics 2, 418 -427 (2001).

Data Standardization:

• The goal of MGED is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalization methods.
• MGED Normalization working group, which is charged with developing standards for normalization of microarray data. Includes links to presentations on the subject given at the MGED IV meeting held in Boston, February 13th-16th, 2002
• MIAME aims to outline the minimum information required to unambiguously interpret microarray data and to subsequently allow independent verification of this data. Nature Genetics, vol 29, no. 4, pp 365-371
• MAGE : standard for the representation of microarray expression data that would facilitate the exchange of microarray information. see also MAGE-ML Languages
• MicroArray Quality Control Project (MAQC) The MicroArray Quality Control (MAQC) project involves six FDA Centers, major providers of microarray platforms and RNA reference samples, EPA, NIST, academic laboratories, and other stakeholders. The MAQC project aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods. The first publications coming from this project recently appeared available online see: Nature Biotechnology. Data sets are also available for download from the MAQC project home pages (MAQC)

Discussion Forums: 

• see News Groups & Electronic Forums

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General Information

• See also News and veiws (listed under N) and/or other Links page (listed under L)

See also News and veiws (listed under N) and/or other Links page (listed under L)

• Gene Chip technology, Affymetrix (DNA chip manufacturer) - includes QuickTime demo 
• Gene Genie: Two biotech greats uncork DNA semiconductors, Red Herring Online 31 March 1997
• Please pass the DNA chips, NIST TechBeat, November 1997 
• Everything's Great When It Sits on a Chip: A bright future for DNA arrays, 24 May 1999, The Scientist

Gene Ontology

• see Ontology

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L

• XML working group, appears to have currently, as of 2001, two proposals that of NCGR GEXML and Paul Spellman's
• Gene Expression Markup Language (GEML™), an Extensible Markup Language (XML)-based tag set, was developed by Rosetta Inpharmatics and others in the GEML community to provide a standard method of exchanging gene expression data along with the associated gene and experiment annotation. The GEML White Paper from Rosetta is available in PDF. GEML, although still supported by Rosetta software has been superseded by the Microarray and Gene Expression Data (MAGE) UML model and DTDs.
• Rosetta's link page for those interested in XML, includes links to BioPerl and EBI XML as well as other internet resource pages
• The data exchange model (MAGE-OM: Microarray Gene Expression - Object Model) and data exchange format (MAGE-ML:Microarray Gene Expression - Markup Language) for microarray expression experiments. MAGE-OM has been modelled using the Unified Modelling Language (UML) and MAGE-ML has been implemented using XML (eXtensible Markup Language).
• Microarray Markup Language (MAML) is a data format for describing information about DNA-array based experiments. MAML is based on the Extensible Markup Language (XML). MAML primer
• OPEN-BIO ORG The Open Bioinformatics Foundation is an umbrella group for the various bio*.org projects that grew out of the original BioPerl project.

Link Collections and Resource Pages

• Andreas Matern's Web page DNA Microarrays a comprehensive links page at Cornell, also has a good list of references for the new comer
• Entry Page to ADIS (Automatische DNA Isolierung und Sequenzierung / Zentrale Analytik) plant DNA arrays
• Ruth Alscher's Grid-it Links and resource page North Carolina State University
• Large-Scale Gene Expression and Microarray Links and Resources, European Bioinformatics Institute
• Lab-on-a-Chip.com provides focused information on all Lab-on-a-Chip technologies. It includes published papers, news, events, new products , suppliers, research links, jobs and discussion forums.
• Alan Robinson's Web Page at the European Bioinformatics Institute
• Gene-Chips (DNAMicroarray), Liming Shi comprehensive Technology and Links page at Gene-chips.com
• BioPlanet Bioinformatics links page.
• Wentian Li at Rockefeller University maintains a collection of papers with emphasis on  microarray data analysis 
• Y F Leungs Functional Genomics pages these include comprehensive listings of web links to pages of interest to the Microarray community with an especially good page on software
• Bioinformatics.net provides links to microarray and other resources including software
• ProteomicsSurf links pages for functional genomics
• Bugarrays is a collection of information for scientists using DNA microarray technology for bacteriology. The Bugarrays community originated in the San Francisco Bay Area with members from Stanford, UC Berkeley, and UCSF

Research Labs

please also see below : Organisations using or developing Microarray Shared/Core facilities

European based Labs
	The MRC Cooperative at St Georges is a multi-disciplinary collaborative group studying various intracellular pathogens. Our research interests cover areas such as host-pathogen interactions, bacterial gene expression, molecular and cellular biology, cellular immunology, microbiology and vaccine research
	The microarray facility at the Iinstitute of Food Research is part of a robust genomic approach to the study of food and health related issues and is part of Jay Hinton's group at the IFR
	Created as a result of increasing technological developments within the field of genomics and in particular microarrays. Set up at the LSHTM around Brendan Wren's group.
	Richard Wooster at The Institute of Cancer Research UK
	The Toxicogenomics resources in the MRC Toxicology Unit were first set up in 1999 and primarily service the need of in house research programmes.
	The CSC/ICSM Microarray Centre forms an integral part of the new Genomics, Proteomics and Informatics Research Laboratories (GPIRL) on the Hammersmith Campus
	Tim Gant MRC Toxicology Unit DNA Microarray Pages at the University of Leicester UK.
	Jürg Bähler's group at the Sanger Centre is working on various post-genomics projects using the fission yeast Schizosaccharomyces pombe as a model organism
	The Genomics Laboratory at the University Medical Center Utrecht ( UMC Utrecht) has been set up to implement technology and resources generated through whole genome sequencing projects.
	Jörg Hoheisel's group at DKFZ (Deutsches Krebsforschungszentrum). The Division of Functional Genome Analysis is involved in the development of technologies for the analysis of large genomic areas to entire genomes with respect to the encoded functions and their regulation
	The Molecular Cytogenetics Group Department for Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin work on the characterization of chromosomal aberrations in patients with congenital diseases and in solid tumours. One focus is the search for chromosomal changes responsible for the disruption of brain development and function.  using arrayCGH along with other Cytogentic techniques.
US/Canadian based Labs
	The MGuide : The Brown Lab's complete guide to microarraying for the molecular biologist, Stanford University
	Vivian Chung's Lab.  Direct IBD Mapping is a DNA microarray-based mapping technique that allows isolation and mapping of DNA fragments shared IBD between individuals.
	Geoffrey Childs lab at Albert Einstein College of Medicine
	Michael Eisen's lab at the Lawrence Berkeley National Lab (LBNL) and the University of California at Berkeley (UCB).
	The Washington University microarray core facility offers a variety of services to meet the needs of researchers who wish to utilize spotted microarrays. Our lab has been in existence since June of 2001.
	Ron Davies Stanford DNA sequencing and technology development center, Stanford University
	Stanley Falkow's Lab at Stanford. The primary focus of our research is to understand how bacterial agents cause infection and disease
	Technology, Software and Methods for Biology, Genetics, and Medicine  The Garner Lab at University of Texas South Western linked to Microarrays at UTSW
	Leroy Hood at Molecular Oncology and Development in the Department of Molecular Biotechnology at the University of Washington
	Welcome to the website of the DeRisi Lab, Biochemistry & Biophysics Department, U.C. San Francisco.
	Kim Lab Home Page, (C. elegans Microarray), Department of Developmental Biology, Stanford University
	Staudt Lab at the NIH home page
	Stanford Center for Tuberculosis research
	DNA microarray technology to identify genes controlling spermatogenesis from the Ward Lab, University of Arizona
	The Wallace lab are developing DNA microarrays to study changes in mitochondrial gene expression at the EMROY University School of Medicine, Atlanta
	John Weinstein's Laboratory at The National Cancer Institute are to better understand the complex molecular pharmacology of cancer cells and to find new agents for treatment of cancer
	White Lab: The home of Drosophila DNA Microarrays, Homepage at the Stanford University School of Medicine
	The Young lab at the Whitehead Institute for Biomedical Research working with high-density oligonucleotide arrays to gain insights into the transcriptional regulatory circuitry of eukaryotic cells during infection by HIV and M.tuberculosis
Rest of the World
	SRC hosted by University of Queensland Austrailia

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Microarray Gene Expression Data Society-MGED

The Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.

The current focus is on establishing standards for microarray data annotation and exchange, facilitating the creation of microarray databases and related software implementing these standards, and promoting the sharing of high quality, well annotated data within the life sciences community. A long-term goal for the future is to extend the mission to other functional genomics and proteomics high throughput technologies.

• The goal of MGED is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalization methods.
• MGED Normalization working group, which is charged with developing standards for normalization of microarray data. Includes links to presentations on the subject given at the MGED IV meeting held in Boston, February 13th-16th, 2002
• OWG ontology working group for the MGED project, which is charged with developing an ontology for describing samples used in microarray experiments.

Meetings/ Conferences/Symposia

• SmallTalk2002, The Microfluidics, Microarrays and BioMEMS Conference July 28-31, 2002 USA. microtechnology conference dedicated to microfluidics, microarrays, and bioMEMSmicrofluidics, microarrays, and bioMEMS technologies and their applications
• MGEDIV The goals of MGED IV are to present the results of the standards developed so far and engage the microarray community in the continued development of these standards. The underlying goal is to facilitate the establishment of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software.
• ISMB 2001. Abstracts from Networks and Modeling and Gene expression
• ISMB 2000.The ISMB Conference provides a general forum for disseminating the latest developments in bioinformatics. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. Its scope includes the development and application of advanced computational methods for biological problems.
• The Second International Meeting on Microarray Data Standards, Annotations, Ontologies and Databases. May 25 - 27, 2000, DKFZ and EMBL, Heidelberg,Germany
• Integrated Bioinformatics
• 7th Conference on Small Genomes The meeting was held November 13-17, 1999
• ABRF99 Bioinformatics and Biomolecular Technologies:Linking Genomes, Proteomes and Biochemistry
• Mathematical and Statistical Aspects of Molecular Biology workshops (MSAMB)

General listings of Meetings/Conferences/Symposia

• Agricultural Conferences, Meetings, Seminars Calendar
• http://www.faseb.org/meetings/ listings of meetings including ABRF2000
• Lab Chips and Microarrays

N

News and Veiws In the Field

News Groups & Electronic Forums or BLOGS 

• Microarray Users Group site at the NIH, a newsgroup 
• electonic news group at eGroups: Microarray  Yahoo Microarrays Group (includes messages from Gene Arrays Listserv)
• Gene Arrays Listserv -- For anyone interested in arrays
• Todd Martinsky BLOG on microarrays http://arrayit.blogspot.com/

  Past entries include:

  • Simple antigen microarray protocol is listed today
  • High Throughput SNP genotyping
  • Pathogen detection
  • Oligos microarray data shown to be more sensitive than qPCR
  • Spotted CGH microarrays using BACs compared to in-situ microarrays
  • Luminex versus microarray

Normalisation

• MGED Data transformation and normalisation working group, includes an extensive reference listing

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Ontology

An ontology is an explicit specification of some topic....provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary

• MGED Ontology working group
• Department of Computer Science, Wayne State University hosts a collection of GO tools which are free tools to academics and includes Onto-Express (OE) as a novel tool able to automatically translate gene lists of differentially regulated genes into functional profiles.
• Gene Ontology for Significant Collection of Annotations: GO-Scan  is a tool that selects and presents relevant Gene Ontology (GO) annotations for a gene "hit" list from an Affymetrix microarray experiment
• GENETOOLS is a collection of web-based tools on top of a database that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0

Organisations using or developing Microarray Shared/Core facilities

• TIGR and microarray resource pages at TIGR
• E.coli genome project University of Wisconsin-Madison
• Sanger Center Microarray Facility Hinxton UK
• EMBL
• MRC Human Genome Mapping Project Resource Centre is now closed spring 2005 and no longer provides arrays, Harwell Microarray Facility.
• The Toxicogenomics resources in the MRC Toxicology Unit were first set up in 1999 and primarily service the need of in house research programmes.
• EBI
• Paterson Institute for Cancer Research (PICR) CRUK affymetrix gene chip service

UK Facilities
	The Bacterial Microarray Group at St George's Hospital Medical School (BµG@S) has been funded by The Wellcome Trust to generate whole genome microarrays for twelve bacterial pathogens. The arrays will be made available for collaborative research with groups around the UK and the rest of Europe. .....
	The Functional Genomics Laboratory is a central facility within the Microbial Sciences Group, University of Surrey & houses the Streptomyces coelicolor Microarray Resource headed by Colin Smith is part of a coordinated UK program of Streptomyces coelicolor functional genomics funded by the BBSRC.
	The FlyChip project is a publicly funded resource and its principal aim is to provide a non-profit microarray resource for the UK Drosophila research community. Department of Genetics, Cambridge
	GARNet microarray pages, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for genomics research on Arabidopsis thaliana.
	ARK-Genomics is a collaborative centre for functional genomics in farm animals (i.e. chickens, pigs, cattle and sheep) funded by the BBSRC.
European Facilities
	Nylon based arrays made in house at the TAGC :Macroarrays are Nylon (or other) membranes that carry PCR products (or bacterial colonies) with typical diameter of 0.5 to 1 mm and a pitch (center to center spacing) of approximately 2 mm
	The Netherlands Cancer Institute (NKI / AvL) started a DNA microarray facility in January 1999 The CMF is one of the largest microarray facilities in The Netherlands. Providing oligo arrays printed with the Operon v3 library (35K Human, 32K Mouse) along with  18K Human, 15K Mouse cDNA arrays, BAC and barcode arrays.
	Norwegian Microarray Consortium, A consortium, consisting of groups from three centers DNR, NTNU, UiB collaboarting on the establishment of microarray resources  for production of human gene resources, and provides arrays. Now runs the National Microarray Platform under the FUGE program
	Department of Human and clinical Genetics - Leiden University Medical Center Leiden Genome Technology Centre (LGTC) Director: Dr. Johan T. den Dunnen. Providing a non-profit service
	The National Institute of Environmental Health Sciences has established a cDNA microarray center which provides access to this technology for the intramural and extramural community
	Ecole Normale Superieure, Paris Contains a nice links page to sites containing information about DNA microarrays and a whole host of other goodies . Includes a microarray newsgroup

US/Canadian Facilities
	The Microarray Centre at The Ontario Cancer Institute, University Health Network is a leader in Canadian microarray technology. We are dedicated to providing high quality microarrays, technical support and service to Canadian researchers
	The Corning/Whitehead Institute Center for MicroArray Technology is a state-of-the-art, full service microarray facility. Located at the Whitehead Institute
	Microarray Core Facility previously hosted by Vanderbilt University currently a new web under construction
	Microarrays.org is a public source for microarray protocols and software. This site is built and maintained by the DeRisi Lab, Dept. of Biochemistry & Biophysics, Univ. of California at San Francisco.
	The DNA microarray core facility for the Genomics and Proteomics Core Labs of the University of Pittsburgh
	The Biomedical Genomics Microarray (BIOGEM) Core Facility at UCSD
	Microarray Project, National Human Genome Research Institute
	Vanderbilt Microarray Shared Resource VMSR, mouse and human arrays
	The Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes 70-mer glass slide DNA microarrays for pathogens and biodefense related organisms.  In 2008 39 microarrays were currently supported by the PFGRC.

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Pathways

• Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Kurt W. Kohn Molec. Biol. Cell 1999 Aug;10(8):2703-34
  • The BioCyc Knowledge Library is a collection of Pathway/Genome Databases. Each database describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc.
    • EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli.
    • MetaCyc metabolic pathway database contains pathways from over 150 different organisms
    • Amongst the Pathway Tools available at BioCyc is Expression Viewer (Omics Viewer) this paints expression data onto the Metabolic Overview diagram for an organism
  • Kyoto Encyclopedia of Genes and Genomes, KEGG integrates the information about genes and proteins generated by genome sequencing, functional genomics and proteomics with metabolic pathways
  • The Reactome knowledgebase relies on collaborations with research biologists to construct expert consensus views of key biological processes
    • Skypainter is a tool to determine which events (reactions and/or pathways) are statistically overrepresented in a set of genes as specified by submitted list of identifiers. In other words, given a list of genes, Skypainter can identify common events for these genes
  • Database for Annotation, Visualization and Integrated Discovery (DAVID)is a web-based tool that provides integrated solutions for the annotation and analysis of genome-scale datasets derived from high-throughput technologies such as microarray and proteomic platforms. Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.
• ~

Platform Cross Comparability

• Nature Biotechnology Sept 2006 presented the first formal results of the MicroArray Quality Control (MAQC) project, an unprecedented, community-wide effort, under the auspices of the FDA, with the goal of experimentally addressing the key issues surrounding the reliability of DNA microarray data and establishing operational metrics to objectively assess the performance of seven microarray platforms. includes research papers on:
  • Evaluation of DNA microarray results with quantitative gene expression platforms
  • Using RNA sample titrations to assess microarray platform performance and normalization techniques
  • Evaluation of external RNA controls for the assessment of microarray performance
  • Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project
  • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
  • Rat toxicogenomic study reveals analytical consistency across microarray platforms
• RESOURCERER ( Genome Biology 2001 PDF ) provides annotation based on the TIGR Gene Indices (TGI) for commonly available microarray resources, including widely used clone sets and Affymetrix GeneChip Arrays.

Protein Arrays

• Introductory web page from ArrayIt.com describing prtein microarrays and their use
• Todd Martinsky's article on protein array manufacture in pharmaGenomics March/April 2004

Protocols

• TeleChemInternational DNA-Microarray Protocols
• Resources at Vanderbilt University MCF
• Current Protocols at NHGRI
• Brown Lab's at Standford Protocols page
• Protocols used in three papers coming out of MIT
• Geoffrey Child's Lab at ASCOM Protocols page
• Childs / Kucherlapati Lab Protocol cDNA-Microarray Hybridization 
• Protocols used in Vivian Chung's lab, has protocols for both Genomic Mismatch Scanning and Microarrays
• NIH-CIT reference page including some protocols
• Jeremy Buhler's Protocol web page for Comparative Gene Expression Studies
• Leroy Hood's Lab protocols page at MOD a mix of protocols for DNA/microcolonys on membranes as well as protocols for microarrays
• cDNA membrane array (methods page), University of  Delaware's Center for Agricultural Biotechnology 
•  Richmond et al. NAR (2000) Genome-wide expression profiling in E.coli pdf, a comparative methods paper from Fred Blattner's Lab University of Wisconsin.
• UTSW basic microarray protocols page
• TIGR Protocols page includes Biotechniques (2000)  A concise guide to microarray analysis. Available as text or pdf from the TIGR web site
• LGTC (Netherlands) Protocol last update is limited to protocols for amplification, processing and printing arrays
• Protocols currently in use at the Ontario Cancer Institue microarray center
• Chris Seidel's general  protocols page. Includes a link page for incorporation of amino-allyl modified nucleotide for esterification of the Cyanine dyes and hybridisation of labelled random nano-mer.

• Commercial Protocols
  • Atlas^Tm glass slide array user manual pdf, membrane array user manual pdf, generic product page with links to various manuals and FAQs
  • Detailed protocols for indirect labeling can be found Microarrays.Org. Alternatively, fluorescent labeling kits can be purchased from Stratagene , Clontech or Molecular Probes.

Primer/Probe design software

• WWW programs for primer design :
  • Primer3 at MIT: http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi 
  • Xprimer: http://alces.med.umn.edu/xprimerinfo.html 
  • Primers for the WWW: http://www.williamstone.com/primers/index.html
• Array Designer (Premier Biosoft)- windows application designs primer pairs for PCR or oligonucleotide probes in batch mode. Amplicons or probes are tested for specificity by accessing the NCBI blast server and designed to standardised hybrisation PCR conditions.HMS Beagal review
• GAP (Genome- wide Automated Primer finder servers) - Originally written to design primer pairs to upstream regions of the E.coli genome but will also now also finds genome-wide primers given the ORF coordinates. GAP allows primers to be designed to the regions chosen with some degree of freedom. GAP (Genome-wide Automated Primer finder) has two interfaces PIORF (Primer InterORFinder) and PORF (Primer ORFinder)
• ArrayOligoSelector from the DeRisi Lab systematically designs gene specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3'end of the gene.
• OligoArray2.1 - An Oligo nucleotide probe design based on three major criteria: melting temperature, specificity and absence of stable secondary structure at the hybridization temperature. OligoArray: genome-scale oligonucleotide design for microarrays Rouillard et al. (2002). Bioinformatics 18 (3) 486-487
• ProbeSelect: They have described algorithms to optimize the selection of specific probes for each gene in an entire genome.
• Featurama / ProbePicker: The Featurama software is intended as a tool to aid biological researchers employing custom designed oligonucleotide microarrays with oligonucleotide design for their experiments.
• OligoPicker: This program is to help selecting one 70-mer oligo for each of the DNA sequences you provided for microarray experiments.
• ROSO: optimizing oligonucleotide probes for microarrays Bioinformatics 2004.ROSO is software to design optimal oligonucleotideprobe sets for microarrays. "Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set".
• YODA: selecting signature oligonucleotides Bioinformatics 2005 21(8):1365-1370. YODA is an application for assisting biological researchersin selecting signature sequences. It incorporates a custom sequencesimilarity search to find potential cross-hybridizing non-targetsequences. For this task, most oligo design tools rely on BLAST,which is ill suited for it due to an unacceptable risk of false negatives. YODA supports multiple probe design goals including single-genome, multiple-genome, pathogen-host and species/strain-identification.
• Oligodb -a batch web-based system for interactive design of oligonucleotides  for transcription profiling (hybridization) of human genes based on the ENSEMBL database. Mrowka et al. Oligodb-interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics. 2002 Dec;18(12):1686-7. (pdf). Criteria for selecting oligos are:
  •  low similarity to all other known human transcripts or genes
  •  positive minimum folding energy to avoid formation of secondary structures
  •  the length of the oligo
  •  the exclusion of low complexity regions.

  Furthermore, the user may select oligos according to information on:

  •  the position in the 5'-3' direction of the transcript and the melting temperature Tm. 
    
• PRIMEGENS (PRIMEr Design Using GEN Specific Fragments) is program to select gene-specific fragments and then design primer pairs for PCR amplifications. Xu D, Li G, Wu L, Zhou J, Xu Y. Bioinformatics 2002 Nov;18(11):1432-7
• ProbeWiz Server - The CBS ProbeWiz WWW server predicts optimal PCR primer pairs for generation of amplicon based probes for cDNA arrays. see Avoiding cross hybridization by choosing nonredundant targets on cDNA arraysH. B. Nielsen and S. Knudsen.  Bioinformatics ( 2002) 18: 321-322 
• Primer3 - download page at MIT probably the most commonly used software for designing primers for PCR.

Primer design reference papers and notes

• A "manual" on primer design: http://www.hgmp.mrc.ac.uk/MANUAL/faq/faq-primers.html 
• A review of some on-line primer design packages, with links. http://www.alkami.com/reviews/rvwdsgn3.htm 
• A GNU/Linux-based system, called DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools from other authors: Clustalw, CODEHOP, and EMBOSS, for an easy to read overview see the O'Rielly Network page.
• Genome-directed primer for selective labelling of bacterial transcripts for DNA microarray analysis. Talaat AM, Hunter P, Johnston SA  Nature Biotech 18 June 2000. A brief description of the process used to obtain the minimal primer set for M.tuberculosis.
• FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis. Robert J. Blick, Andrew T. Revel and Eric J. Hansen (2003). A program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames in a genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences.
• Raddatz G, Dehio M, Meyer TF, Dehio C.(2000) Bioinformatics 17: 98-99. PrimeArray: genome-scale primer design for DNA-microarray construction. PDF version
• Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001 Dec;2(4):329-40. [PubMed]
  

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QC: Quality control

• The Ecole Normale SupErieure microarray platform team released Doelan 1.0.1 late in 2005. Doelan is designed as an tool to monitor the array quality for production QC ( see Jourdren & Le Crom Bioinformatics 2005). The software executes a series of quality control tests on hybridizations carried out on batches of arrays. The reports generated by Doelan aim at providing quality certification such as ISO 9001. The Doelan application is written in Java and works with a plug-in system that allows everyone to add custom validation tests.
• MicroArray Quality Control Project (MAQC) The MicroArray Quality Control (MAQC) project involves six FDA Centers, major providers of microarray platforms and RNA reference samples, EPA, NIST, academic laboratories, and other stakeholders. The MAQC project aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods. The first publications coming from this project recently appeared available online see: Nature Biotechnology. Data sets are also available for download from the MAQC project home pages (MAQC)

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References and Review Articles on Microarrays

• This list is not meant to be comprehensive but provides a taster for people new to the technology. For microarray papers try Arrayit.com/e-library/ an excellent  free service
• Bibliography of Microarray Data analysis: A useful collection of papers (so far, ~1440 as of 2006) with emphasis on analysis of microarray expression data which uses a google search engine. The focus of the bibliography is methodology papers, not on applications
• For Affymetrix a free searchable library of papers using their gene-chip technology is accessable.
• A collection of papers compiled by Wentian Li of North Shore LIJ Research Institute with emphasis on analysis of microarray (a.k.a. DNA chip) data. General reviews on microarray may be included along with those on analysis of gene networks, microarray-related databases, some papers on results of microarray expriments , Affymetrix and Protein chips.
• Standford Microarray Database (SMD) also maintains a publication listing with public domain data, web suppl. and papers. For more specialized articles try the appropriate section e.g. bioinformatics papers  or statistical papers
• GeneSpring citation pages at Silicon Genetics
• MicroArray Quality Control Project (MAQC) The MicroArray Quality Control (MAQC) project involves six FDA Centers, major providers of microarray platforms and RNA reference samples, EPA, NIST, academic laboratories, and other stakeholders. The MAQC project aims to establish QC metrics and thresholds for objectively assessing the performance achievable by various microarray platforms and evaluating the advantages and disadvantages of various data analysis methods. The first publications coming from this project recently appeared available online see: Nature Biotechnology. Data sets are also available for download from the MAQC project home pages (MAQC)

General Articles

• This supplement to Nature Genetics 2002 (suppl) analyzes the last several years of progress in the exciting field of microarrays and is available free online, The Chipping Forecast II  explores how this breakthrough technology has had an impact on basic and clinical research. 
• Genomics, gene expression and DNA arrays. Lockhart & Winzeler (2000) Nature 405: 827-836 
• Special Microarray Issue, Nature Genetics, Microarray Site
• Chipping Forcast Natrure Genetics 1999 Jan 21(Suppl: Table of contents and access to articles subcrition is required for full articles)
• Getting Hip to the Chip Nature Genetics 1998 Jan 8 (full article)
• Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Haab, B.B., Dunham M.J., and Brown, P.O. Genome Biology 2001 2(2): research0004.1-0004.13

Lab Publication Pages or Listings of other labs publications

• George Church's Lab publications page
•  Eisens publication page including Cluster Analysis and Display of Genome-wide Expression Patterns. Eisen et al. (1998) Proc. Natl. Acad. Sci. (USA) 95:14863 and many more seminal papers on microarray data analysis.
• Wentian Li at Rockefeller University maintains a collection of papers with emphasis on  microarray data analysis. 
• A good general review focused on bacterial array construction and their uses. Applications of DNA microarrays in microbial systems. Rick W. Ye , Tao Wang, Laura Bedzyk, Kevin M. Croker (2001) Journal of Microbiological Methods 47
• Publications page of the Yeast Microarray group at Ecole Normale Superieure Paris, Director Claude Jacq.
• RosettaBiosoftware publications page.

Important or Early publications

• Spellman et al., (1998). Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell 9, 3273-3297. Supplement to the paper with on-line data
• Distinct Types of Diffuse Large B-Cell Lymphoma Identified by Gene Expression Profiling. Alizadeh, A., et al. (2000) Nature 403:503-511.
• Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Spellman et al. (1998) Mol. Biol. Cell 9: 3273
• A supplemental page with links Molecular Portraits  of Human Breast Tumors Perou et al. Nature(2000) 406 : 747-752, The data from this proje