Nabble - Bio.net - Arrays

Most cited research reagents and kits

2009-12-01T16:53:32Z

An interactive graph showing most cited research reagents and kits
that are
currently available in the market. The data is based on recent
published journal articles, patents and patent applications. The
current research reagent/kits listings are: Transfection reagents, RT-
PCR, Real-time PCR, RNA purification, cAMP assays, Cytotoxicity assays
and Western blot reagents. Please visit:

http://www.sciclips.com/sciclips/most-cited-reagents.do?cat=TransfectionReagents\
&catId=1501

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

International qPCR 2010 Symposium & Exhibition Vienna

2009-10-25T08:33:35Z

International qPCR 2010 Symposium & Exhibition Vienna
7th – 9th April 2010 The focus of the qPCR 2010 Event will be “The
ongoing evolution of qPCR”
http://www.qpcr2010-vienna.net/
qPCR2010@...

---------------------------------------------------------------------------
qPCR 2010 in Vienna

International qPCR 2010 Symposium and Exhibition in Vienna 7th – 9th
April 2010
The focus of the qPCR 2010 Event will be “The ongoing evolution of
qPCR” representing all new and emerging techniques, applications and
data analysis methods. MIQE, HRM, microRNA, CNV, single-cell qPCR,
digital PCR, and analysis of circulating nucleic acids will be in the
focus of the conference => http://www.qpcr2010-vienna.net/

qPCR Symposium topic - “The ongoing evolution of qPCR”
The symposium focus will be on 40 lectures presented by international
recognized experts in their application fields. The emphasis will be
on unbiased, didactic information exchange. One third of the talks
will be presented by invited speakers, one third of the speakers will
be selected from the submitted abstracts and one third will be qPCR
company representatives with their newest qPCR technologies.

The focus of the qPCR 2010 Event will be “The ongoing evolution of
qPCR” representing all new and emerging techniques, applications and
data analysis methods: Symposium sessions & preliminary titles

MIQE and QM strategies in qPCR
Prof. Stephen Bustin, “The MIQE Guidelines: Minimum Information for
Publication of Quantitative Real-Time PCR Experiments”

High throughput quantitative PCR – digital PCR
Prof. Mikael Kubista, “Digital PCR and intracellular expression
profiling”
Dr. Philip Day, “High throughput droplet PCR”
Dr. Ken Livak

HRM – High Resolution Melting - Epigenetics

Prof. Carl Wittwer, "High Resolution Melting Analysis"
Prof. Claudio Orlando, “High Resolution Melting Analysis in Cancer
Diagnosis”

Circulating nucleic acids
Dr. Pamela Pinzani, “Cell free circulating DNA”
Dr. Alfred Schöller, „Targeting the human urine RNAome for tumor
diagnostics by qPCR”

Single-cell qPCR
Dr. Michael W. Pfaffl, “Quantitative expression analysis after pre-amp
in single WBCs”
Dr. Anders Stahlberg, “Single-cell gene expression

RNAi - microRNA - siRNA Applications – miRNA normalisation
Prof. Jo Vandesompele, “MicroRNA and mRNA gene expression
normalization”
Dr. Mirco Castoldi, "Expression profiling of microRNA by quantitative
real time PCR, what is available and where to go from there"

qPCR BioStatistics & BioInformatics
Dr. Ales Tichopad, “Statistical aspects of quantitative PCR experiment
design and qPCR data analysis”
Dr. Jan Hellemans, “Accurate and objective copy number profiling using
real-time quantitative PCR”
Dr. Anders Bergkvist, “Expression profiling - clusters of
possibilities”

--------------------------------------------------------

For more information:

Michael Pfaffl
BioEPS GmbH
Lise Meitner Strasse 30
85354 Freising Weihenstephan
Germany
qPCR2010@...

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

qPCR NEWS - September 2009 - key topic - circulating nucleic acids - CNA

2009-09-24T05:47:32Z

qPCR NEWS - September 2009 - key topic - circulating nucleic acids -
CNA
----------------------------------------------------------------------------------------------

Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of this newsletter issue is:

- NEW PAGE - circulating nucleic acids => http://CNA.gene-quantification.info
- a lot of updates in MIQE - media & press review =>
http://miqe.gene-quantification.info/
- New molecular diagnostics qPCR/real-time PCR discussion forum:
LinkedIN & XING
- qPCR / real-time PCR BLOG => http://real-time-pcr.blogspot.com/
- For better navigation we developed a TAG CLOUD =>
http://directory.gene-quantification.info/
- New qPCR events in autumn 2009: symposia & workshops =>
http://events.gene-quantification.info/

European wide qPCR application workshops - register now !
Course program autumn 2009 & winter 2010 =>
http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf

--------------------------------------------------------------------------------

CNA = Circulating Nucleic Acids

Most of the DNA and RNA in the body is located within cells, but a
small amount of nucleic acids can also be found circulating freely in
the blood. These DNA, RNA and small RNA molecules are thought to come
from dying cells that release their contents into the blood as they
break down. The term "Circulating Nucleic Acids = CNA" refers to
segments of DNA or RNA found in the bloodstream.

CNAs offers a non-invasive approach to a wide range in diagnostics of
clinical disorders that will allow the basic information necessary not
only for use in predictive medicine but also for direct use in acute
medicine. Further free CNAs offer unique opportunities for early
diagnosis of clinical conditions, e.g. in early cancer detection.

Although DNA was first demonstrated in human blood from healthy
donors, pregnant women and clinical patients in 1948, the structure of
DNA was still to be determined as was the elucidation of its role as
the basis of the gene. Consequently, no interest was shown in the
presence of DNA in the circulatory system until high DNA levels were
demonstrated in the blood of patients with systemic lupus
erythematosus. Similar observations were also made in acute medicine,
diabetes, oncology and fetal medicine. The presence of DNA and RNA in
plasma of patients has been recognised since the 1970s.

A range of markers have been proposed for the identification of a
particular cancer, though there is frequent conflict in the literature
as to the effectiveness of particular probes. However, recently,
hypermethylated CpG in the promotor region of tumour suppressor genes
has been suggested to trigger local gene silencing. Aberrant
methylation of the p26 tumour suppressor gene was the first to be
detected in liver, breast and lung cancer.

Nucleic acids can be found in small amounts in healthy and diseased
human plasma/serum. Higher concentrations of DNA are present in the
plasma of cancer patients sharing some characteristics with DNA of
tumor cells. Together with decreased strand stability, the presence of
specific oncogene or tumor-suppressor gene mutations, microsatellite
alterations, Ig rearrangements and hypermethylation of several genes
may be detected. Moreover, tumor-related mRNA has been found
circulating in the plasma/serum.

The results obtained in many different cancers have opened a new
research area indicating that circulating nucleic acids might
eventually be used for the development of noninvasive diagnostic,
prognostic and follow-up tests for cancer.

For more info and for some key papers about circulating nucleic acids
=> http://CNA.gene-quantification.info

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program, etc.
Please submit your qPCR event here => events@gene-
quantification.info

--------------------------------------------------------------------------------

qPCR 2010 in Vienna
international qPCR Symposium
7-9th April 2010

Main Topic “The ongoing evolution of qPCR”

download updated 2nd announcement as PDF
=> http://www.bioeps.com/qpcr2010/Vienna-qPCR-2010-2nd-announcement.pdf

Symposium sessions & preliminary title

MIQE and QM strategies in qPCR
The MIQE guidelines: minimum information for publication of
quantitative real-time PCR experiments. Following these guidelines
will encourage better experimental practice, allowing more reliable
and unequivocal interpretation of qPCR results. QM strategies in real-
time PCR to guarantee better and more valid results.
Prof. Stephen Bustin, “The MIQE Guidelines: Minimum Information for
Publication of Quantitative Real-Time PCR Experiments”

High throughput quantitative PCR – digital PCR
384 well applications, new high throughput platforms, droplet PCR,
qPCR robotics, digital PCR, gene expression real-time RT-PCR arrays
(mRNA and microRNA), quantitative multiplexing, …
Prof. Mikael Kubista, “Digital PCR and intracellular expression
profiling”
Dr. Philip Day, “High throughput droplet PCR”
Dr. Ken Livak, "title to be announced"

HRM – High Resolution Melting
SNP analysis, HRM = high resolution melt applications, Epigenetics,
methylation markers, HRM platform comparison, etc …
Prof. Carl Wittwer, "High Resolution Melting Analysis"
Prof. Claudio Orlando, “High Resolution Melting Analysis in Cancer
Diagnosis”

Circulating nucleic acids
Analysis of circulating RNAs and DNA and microRNAs as diagnostic and
prognostic marker, …
Dr. Pamela Pinzani, “Cell free circulating DNA”
Dr. Alfred Schöller, "Targeting the human urine RNAome for tumor
diagnostics by qPCR”

Single-cell qPCR
Single-cell sampling, pre-amplification techniques, laser
microdissection, sub-cellular PCR, micro-manipulation of cell
clusters, cellular micro injection, FACS spotting, single cell
handling, pre-amplification…
Dr. Michael W. Pfaffl, “Quantitative expression analysis after pre-
amp in single WBCs”
Dr. Anders Stahlberg, “Single-cell gene expression profiling”

RNAi - microRNA - siRNA Applications – miRNA normalisation
RNAi mechanism, microRNA extraction, qRT-PCR technologies to detect
microRNA, microRNA normalisation strategies, siRNA applications in
combination with qRT-PCR, microRNA targets and microRNA precursors,
new siRNA manipulation and microRNA technologies, ...
Prof. Jo Vandesompele, “MicroRNA and mRNA gene expression
normalization”
Dr. Mirco Castoldi, "Expression profiling of microRNA by quantitative
real time PCR, what is available and where to go from there"

qPCR BioStatistics & BioInformatics
software applications, data mining, calculation of relative
expression, primer and probe design on mRNA and microRNA level, real-
time PCR efficiency determination, mathematical modelling,
multivariate expression profiling, statistics in real-time PCR, data
management, multiway expression profiling, multiple regression
analysis, 3D data visualization, ...
Dr. Ales Tichopad, “Statistical aspects of quantitative PCR
experiment design and qPCR data analysis”
Dr. Jan Hellemans, “Accurate and objective copy number profiling
using real-time quantitative PCR”
Dr. Anders Bergkvist, “Expression profiling - clusters of
possibilities”

--------------------------------------------------------------------------------

qPCR WORKSHOP

BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different
prices may apply. Further customized workshops and specialized
trainings will be held as well across Europe and world-wide.
TATAA Biocenter Germany workshops are held in cooperation with BioEPS
GmbH, located at the campus of the Technical University of Munich, in
Freising-Weihenstephan, very close to the Munich Airport (MUC). For
more information and registration, please see our web page:
=> http://TATAA.gene-quantification.info/

Course Occasions 2009:

- 3-day qPCR Core Module (Mon. - Wed.)
- 2-day BioStatistics Module (Thu. - Fri.)
- 3-day single-cell qPCR Module (Mon. - Wed.)
- 3-day microRNA Module (Mon. - Wed.)

19 - 23 October 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)
26 - 28 October 2009 (E) 3-day qPCR Core Module (Mon. - Wed.)
16 - 20 November 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)
7 - 11 December 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)

=> http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf

--------------------------------------------------------------------------------

Forward Please send the qPCR NEWS to further scientists and friends
who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client,
please use following link:
http://qpcrnews.gene-quantification.info/

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl. Copyright ©
2005 - 2009 All rights reserved. Any unauthorized use, reproduction,
or transfer of this message or its contents, in any medium, is
strictly prohibited. Disclaimer & Copyrights are displayed on the
homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Handling NA's in REST 2008 software

2009-09-14T15:35:37Z

Hello,

Can any PCR data analysis experts in the forum please answer this question ?

How does one handle NA's (unknown data items) while analysing PCR data
using REST 2008 software ?

NA are not accepted by the program. While zeros are accepted, I suspect, the results are not correct if zeros are used instead of NAs.

Thanks
Suki
_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED12 - Important Information!

2009-09-01T13:29:43Z

Early registration ends Saturday!

PhD students and post-docs: This is the last week for abstract submissions to MGED12. Deadline is September 5th. Scholarship monies are still available from the EMERALD grant and the NHGRI for E.U. and American students for travel and registration expenses.

Dear Colleagues -
Our apologies if you received this notice last week, but we're pleased to announce that an additional workshop, GenePattern & IGV, has been added to MGED12, Next-gen sequencing and translational genomics in October.
Presented by members of the Cancer program at the Broad Institute of MIT and Harvard, this tutorial provides an introduction to using the integrative genomics tools GenePattern and the Integrative Genomics Viewer (IGV).
*GenePattern*, a publicly available utility ( http://genepattern.broadinstitute.org/gp <https://outlook.tgen.org/exchweb/bin/redir.asp?URL=http://genepattern.broadinstitute.org/gp> ), provides access to a broad array of over 100 computational methods used to analyze genomic data. A web-based interface provides easy access to these methods and allows the creation of analysis pipelines that enable reproducibility and sharing of /in silico /research.
The *Integrative Genomics Viewer (IGV)* is a high-performance desktop visualization tool for interactive exploration of large datasets in the context of the genome. The IGV supports integrated visualization of data from multiple sources, including next-generation sequencing and array-based platforms.
To register and/or to submit abstracts, go to www.mgedmeeting.org <https://outlook.tgen.org/exchweb/bin/redir.asp?URL=http://www.mgedmeeting.org/> .
See you in Phoenix,
The MGED Society

Denise Grusin
TGen/MGED 12 Conference Coordinator
Phone: 602-343-8628

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Early registration extended for MGED12!

2009-08-17T14:10:25Z

(Please print attached flyer and post in your departments.)

Dear Colleagues -

Due to demand, the MGED Society is extending the Early Registration deadline for MGED12, Next-gen sequencing and translational genomics. The new deadline for discounted fees is September 5th.

Recently added speaker, Mike Eisen, will present “Developmental control in Drosphila examined by ChIP-SEQ.”

For more information on registration and abstract submission, go to www.mgedmeeting.org.

For hotel accommodations, go to http://www.starwoodmeeting.com/StarGroupsWeb/res?id=0903232443&key=42DE2.

We look forward to seeing you in Phoenix!

Sincerely,
The MGED Society

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED12-Deadline Extension.pdf (466K) Download Attachment

MGED12 Conference - Last week for an early registration discount!

2009-08-10T13:37:46Z

Dear Colleagues -

If you plan to attend MGED12, Next-gen sequencing and translational genomics, this is the last week to get the discounted early registration fee. (See attachment.)

Bursaries up to 1000 Euro are available for the European Union students sponsored by the EMERALD grant from the EC. Qualifying applicants will be notified by 5 September.

NHGRI has awarded a grant that will reimburse registration and travel expenses up to $2000 for American students or post-doctoral researchers. To be eligible, students or post-docs must submit an abstract for a poster or talk and be a US citizen. Reimbursed air travel must be ticketed on a US carrier.

To be entered into competition, European and American students seeking travel support should include information about their eligibility and interest in receiving support in the last field of the Abstract Submission page on the web site.

For more information on registration and abstract submission, go to www.mgedmeeting.org.

We look forward to seeing you in Phoenix!

Sincerely,
The MGED Society

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED12-Early Registration.pdf (462K) Download Attachment

Bioinformatics for Systems Biology, October 2009

2009-08-10T02:35:30Z

The online course, Bioinformatics for Systems Biology, from The
University of Manchester, will begin again in October 2009. Like all
our distance courses it is delivered in a Virtual Learning Environment,
which allows us to extend the classroom into the web. We use a range of
tools, such as bulletin boards, chat rooms and wikis, to support our
online teaching activities.

Each course, which is paced to suit those in full-time employment, runs
over 16 teaching weeks. Teaching is focussed around tutor-supported
individual and group exercises. In this course, participants discuss a
tutorial problem for each section of the course, and then submit
solutions for feedback from the course tutor.

Week 1 Introduction to the course
Installation of software for network analysis

Weeks 2 and 3 Molecular networks in biology
Group discussion of models and modelling

Weeks 4 and 5 Standards for Systems Biology
Data sources and standards for network biology
Practical exploration of a molecular network

Weeks 6 and 7 Network properties
Practical exercise on network statistics

Weeks 8 and 9 Mapping microarray data to a network

Weeks 10 and 11 Independent work on network analysis

Weeks 12 and 13 Dynamic models
Further work on modelling formalisms
Practical exercise on a metabolic model

Weeks 14 to 16 Independent research for the second assessment

You will find further information here :
http://octette.cs.man.ac.uk/bioinformatics/modules/BIOL61820.html and
the course application form is here :
https://elearn.cs.man.ac.uk/sts-tng/enrol.cgi If you have any
questions, or need advice on the other course options, please contact
Heather.Vincent@...

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED12 Conference - Early registration deadline is August 15!

2009-08-03T10:07:33Z

(Please print out attached flyer and post it in your departments.)

Dear Colleagues -

Apologies if you have already registered for MGED12, Next-gen sequencing and translational genomics. If you have yet to do so, this is a reminder that the deadline for reduced registration fees is August 15.

Bursaries up to 1000 Euro are available for the European Union students sponsored by the EMERALD grant from the EC. Qualifying applicants will be notified by 5 September.

NHGRI has awarded a grant that will reimburse registration and travel expenses up to $2000 for American students or post-doctoral researchers. To be eligible, students or post-docs must submit an abstract for a poster or talk and be a US citizen. Reimbursed air travel must be ticketed on a US carrier.

To be entered into competition, European and American students seeking travel support should include information about their eligibility and interest in receiving support in the last field of the Abstract Submission page on the web site.

For more information on registration and abstract submission, go to www.mgedmeeting.org.

We look forward to seeing you in Phoenix!

Sincerely,
The MGED Society

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED12-Early Registration.pdf (462K) Download Attachment

2nd Announcement; MGED12 Next-Gen Sequencing and Translational Genomics Conference

2009-07-15T08:33:32Z

Dear Colleagues,

This is a reminder for the 12th International meeting of the MGED society, MGED12, Next-gen sequencing and translational genomics, to be held in Phoenix, Arizona, October 6-8, 2009. The meeting will be preceded by a day of tutorials and workshops on Monday, October 5th.  

The scientific focus of the meeting will be next-gen sequencing and translational genomics and associated data handling issues and analysis techniques. With the growing demand for high throughput sequencing annotation standards and tools, this year's meeting will offer more 'hands-on' tutorials and workshops to tackle specific practical applications of these concepts. Tutorials will cover in depth data analysis and how to use BioConductor.   

We have lined up some outstanding speakers, who are leaders in their respective fields. Some of the confirmed speakers include Elaine Mardis, Hank Greely, Lynda Chin, and John Quackenbush. In addition, this year we will again select half of the plenary speakers from submitted abstracts, to encourage greater participation in the MGED community. And, as in years past, we will again be running a poster competition, with prizes for the best three posters presented by graduate and postdoctoral students.  

Early Registration is still open. Detailed program information is available at www.mged.org/Meetings.  NHGRI has awarded the MGED meeting with a grant that will reimburse registration and travel expenses up to $2000 for students or post-doctoral researchers. To be eligible, students or post-docs must submit an abstract for a poster or talk and be a US citizen. Reimbursed air travel must be ticketed on a US carrier.

A deadline of September 5th has been set for abstract submission, and those abstracts chosen for travel awards and/or selected for plenary lectures will be notified by at least 2 weeks prior to the meeting.   

We look forward to seeing you all in Phoenix.   

Sincerely,   

The MGED Society 

Register now at www.mged.org/Meetings

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

qPCR NEWS June 2009 - MIQE media & press review

2009-06-26T01:20:19Z

qPCR NEWS June 2009 - MIQE media & press review
---------------------------------------------------------------------

Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of this newsletter issue is:

- MIQE - media & press review
- For better navigation we developed a TAG CLOUD =>
http://directory.gene-quantification.info/
- NEW qPCR / real-time PCR BLOG => http://real-time-pcr.blogspot.com/
- New qPCR events in autumn 2009
- New qPCR workshop modules at the TATAA Biocenter Germany
=> http://tataa.gene-quantification.info/

European wide qPCR application workshops => register now !
=> course program spring - summer - autumn 2009
=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf
=> http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf

--------------------------------------------------------------------------------
MIQE - media & press review

=> http://www.gene-quantification.de/miqe.html#press

International Scientists Secure Quality in Molecular Diagnostics

Consensus Guideline Reached For Quantitative Polymerase Chain Reaction
Press release by TATAA Biocenter

Internationale Wissenschaftler sorgen für Qualitätssicherung in der
Molekulardiagnostik

Real-timePCR data markup language

Letter of the MIQE authors
Letter to leading journals recommending the use of MIQE for quality
control of qPCR experiments.

IBT of the Academy of Sciences of the Czech Republic

qPCR Grows Up by genome web

qPCR Assay Quality assessment on SciTopics

Quest Agrees to Pay Fine for Misbranding Tests

Advancing DNA research safely and securely

What do you hope to achieve with the guidelines?

Data that Meets the MIQE Guidelines on Canadian BioTechnologist 2.0

GLOSSARY OF REAL-TIME PCR TERMS by M.Tevfik Dorak

--------------------------------------------------------------------------------

The MIQE Guidelines Minimum Information for Publication of
Quantitative Real-Time PCR Experiments
Stephen A. Bustin, Vladimir Benes, Jeremy A. Garson, Jan Hellemans,
Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W.
Pfaffl, Gregory L. Shipley, Jo Vandesompele, & Carl T. Wittwer
Clinical Chemistry 2009, 55(4): 611-622
=> http://miqe.gene-quantification.info
=> http://www.gene-quantification.de/miqe-bustin-et-al-clin-chem-2009.pdf

RDML: structured language and reporting guidelines for real-time
quantitative PCR data
Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R,
Untergasser A, Vandesompele J; on behalf of the RDML consortium.
Center for Medical Genetics, Ghent University Hospital, Ghent,
Belgium.
Nucleic Acids Res. 2009 Apr;37(7): 2065-2069
=> http://rdml.gene-quantification.info
=> http://www.gene-quantification.de/lefever-et-al-rdml-2009.pdf

Reliability of real-time reverse-transcription PCR in clinical
diagnostics: gold standard or substandard?
Murphy J, Bustin SA.
Expert Rev Mol Diagn. 2009 9(2):187-197
=> http://www.gene-quantification.de/murphy-bustin-review-qpcr-optimization-2009.pdf

Unreliable real-time PCR analysis of human endogenous retrovirus-W
(HERV-W) RNA expression and DNA copy number in multiple sclerosis.
Garson JA, Huggett JF, Bustin SA, Pfaffl MW, Benes V, Vandesompele J,
Shipley GL.
AIDS Res Hum Retroviruses. 2009 25(3): 377-378
=> http://www.gene-quantification.de/garson-et-al-aids-research-2009.pdf

Real-time polymerasechain reaction – towardsa more reliable,
accurateand relevant assay.
SA Bustin
EUROPEAN PHARMACEUTICAL REVIEW 2008 (6): 19-27
=> http://www.gene-quantification.de/bustin-review-qpcr-optimization-2009.pdf

In-House Nucleic Acid Amplification Assays in Research:
How Much Quality ControlIs Needed before One Can Rely upon the
Results?
Petra Apfalter, UdoReischl and Margaret R. Hammerschlag
JOURNAL OF CLINICAL MICROBIOLOGY 2005 (dec): 5835–5841
=> http://www.gene-quantification.de/apfalter-review-qpcr-optimization-2005.pdf

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program, etc.
Please submit your qPCR event here => events@gene-
quantification.info

--------------------------------------------------------------------------------

qPCR WORKSHOP

BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different
prices may apply. Further customized workshops and specialized
trainings will be held as well across Europe and world-wide.
TATAA Biocenter Germany workshops are held in cooperation with BioEPS
GmbH, located at the campus of the Technical University of Munich, in
Freising-Weihenstephan, very close to the Munich Airport (MUC). For
more information and registration, please see our web page:
=> http://TATAA.gene-quantification.info/

Course Occasions 2009:

- 3-day qPCR Core Module (Mon. - Wed.)
- 2-day BioStatistics Module (Thu. - Fri.)
- 3-day single-cell qPCR Module (Mon. - Wed.)
- 3-day microRNA Module (Mon. - Wed.)

13 - 15 July 2009 (E) NEW microRNA qPCR
27 - 31 July 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)
14 - 16 September 2009 (E) NEW single-cell qPCR
19 - 23 September 2009 (E)
3-day microRNA Module (Mon. - Wed.) & 2-day BioStatistics (Thu. -
Fri.)
26 - 28 October 2009 (E) 3-day qPCR Core Module (Mon. - Wed.)
16 - 20 November 2009 (E)
3-day microRNA Module (Mon. - Wed.) & 2-day BioStatistics (Thu. -
Fri.)
7 - 11 December 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics (Thu. -
Fri.)

=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf
=> http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf

--------------------------------------------------------------------------------

Forward Please send the qPCR NEWS to further scientists and friends
who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client,
please use following link:
http://qpcrnews.gene-quantification.info/

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl. Copyright ©
2005 - 2009 All rights reserved. Any unauthorized use, reproduction,
or transfer of this message or its contents, in any medium, is
strictly prohibited. Disclaimer & Copyrights are displayed on the
homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

EMBL Events - Please subscribe

2009-06-22T03:41:32Z

Dear Colleagues,

we would like to invite you to join our mailing list to receive information about events taking place at the European Molecular Biology Laboratory.

Please use the following link to subscribe to our mailing list to receive our newsletter, event posters or e-announcements:

http://www.embl.de/training/courses_conferences/cco/contact/information/index.html

If you do not wish to receive any information from EMBL, please reply with the subject "unsubscribe".

Thanks for your interest in our events.

Best wishes,

the Team of the EMBL Course & Conference Office

.........................................................................................................
European Molecular Biology Laboratory
Course & Conference Office
Meyerhofstr. 2
69117 Heidelberg
Germany

Email: conferences@...

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Blast2GO announces: First international course in automated functional annotation and data-mining

2009-06-17T15:32:01Z

Apologies for cross-posting

Blast2GO announces: First international course in automated
functional annotation and data mining Blast2GO announces: First international course in automated
functional annotation and data mining Blast2GO announces: First international course in automated
functional annota
  
    
      

       
    
    
       

      
       

      Are you working in
sequencing projects? 

          (EST projects, Next Generation Sequencing, Microarray
design, etc... ) 
Do you have thousands of
novel sequences that need functional annotation? 
Do you need a user-friendly
tool to functionally analyze your data? 
      
      The Blast2GO Team is very pleased to
announce: 

      

      FIRST INTERNATIONAL COURSE IN 

      AUTOMATED FUNCTIONAL ANNOTATION AND DATA
MINING

      

      In this course you will learn tools and
tips for functional 

      annotation, visualization and analysis of
novel sequence data making use of Blast2GO. 

      

      The course will be offered to 35 participants at 2 locations:

      
      
        
          
            
              Valencia, Spain:
28 to 30, September 2009 
Florida, USA:
14 to 16, October, 2009 
            
          
        
      
      For more
information and registration until the 1rst of September please visit:

      http://bioinfo.cipf.es/blast2gocourse
      
       
    
    
      
       
      
      
        
          
            
            

            
            
             Bioinformatics
and Genomics Department 

Centro de Investigación Príncipe Felipe (CIPF) 

C/E.P. Avda. Autopista del Saler, 16-3

46013 Valencia, Spain

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Practical Course: Integrated Biology Microarray-based microRNA and Gene Expression profiling

2009-06-12T03:04:04Z

EMBL Course Announcement

A joint EMBL/Agilent Technologies practical course on
Integrated Biology Microarray-based microRNA and Gene Expression profiling

20 - 24 July 2009, EMBL Heidelberg, Germany

http://www.embl.de/courses/agilent/2009
Hands-On Sessions
RNA QC with Agilent Bioanalyzer and Nanodrop,
labelling and purification,
Hybridisation of labelled targets,
Washing and scanning,
Data extraction and quality assessment.

Data Analysis Lectures
Introduction to the Agilent microarray platform,
Quality control of total RNA using the Bioanalyzer,
Data generation and data extraction with Feature Extraction software and GeneSpring GX .
Please circulate this announcement to interested members and groups within your institute.

We are looking forward to welcoming you at EMBL Heidelberg.

If you do not wish to receive further event announcements of EMBL, please reply with "unsubscribe" in the subject.

Best wishes,
Bettina Schaefer

Head of Course and Conference Office
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8836
Fax: +49-6221-387 8158
Email: schaefer@...

For full event listings please visit our website: www.embl.org/events

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

qPCR NEWS May 2009 - focus on RNA integrity

2009-05-28T04:02:16Z

qPCR NEWS May 2009 - focus on RNA integrity
------------------------------------------------------------

Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of this newsletter issue is:

- The MIQE Guidelines Minimum Information for Publication of
Quantitative Real-Time PCR Experiments
- RNA integrity - latest papers
- PowerNest - illuminating error in qPCR experiment design
- new TAG CLOUD for better navigation => http://directory.gene-quantification.info/
- New qPCR workshop modules at the TATAA Biocenter Germany =>
http://tataa.gene-quantification.info/
- European wide qPCR application workshops => register now !

--------------------------------------------------------------------------------

The MIQE Guidelines Minimum Information for Publication of
Quantitative Real-Time PCR Experiments

Stephen A. Bustin, Vladimir Benes, Jeremy A. Garson, Jan Hellemans,
Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W.
Pfaffl, Gregory L. Shipley, Jo Vandesompele, & Carl T. Wittwer
Clinical Chemistry 2009, 55(4): 611-622

=> http://www.gene-quantification.de/miqe-bustin-et-al-clin-chem-2009.pdf

BACKGROUND: Currently, a lack of consensus exists on how best to
perform and interpret quantitative real-time PCR (qPCR) experiments.
The problem is exacerbated by a lack of sufficient experimental detail
in many publications, which impedes a reader's ability to evaluate
critically the quality of the results presented or to repeat the
experiments.

CONTENT: The Minimum Information for Publication of Quantitative Real-
Time PCR Experiments (MIQE) guidelines target the reliability of
results to help ensure the integrity of the scientific literature,
promote consistency between laboratories, and increase experimental
transparency. MIQE is a set of guidelines that describe the minimum
information necessary for evaluating qPCR experiments. Included is a
checklist to accompany the initial submission of a manuscript to the
publisher. By providing all relevant experimental conditions and assay
characteristics, reviewers can assess the validity of the protocols
used. Full disclosure of all reagents, sequences, and analysis methods
is necessary to enable other investigators to reproduce results. MIQE
details should be published either in abbreviated form or as an online
supplement.

SUMMARY: Following these guidelines will encourage better
experimental practice, allowing more reliable and unequivocal
interpretation of qPCR results.

=> http://miqe.gene-quantification.info/

--------------------------------------------------------------------------------

As part of the MIQE guidelines - chapter 5.1 - the RNA quality control
is an essential step in the quantification process.

5. Nucleic acid quality control
5.1. RNA samples
Since it is advisable to use approximately the same amount of RNA for
cDNA synthesis when comparing different samples, quantification of RNA
in extracted samples is important. However, there are several
procedures in common use, including spectrophotometry (Nanodrop),
microfluidic analysis (Agilent BioAnalyser, BioRad Experion),
capillary gel electrophoresis (Qiagen QIAexcel) or fluorescent dye
detection (Ribogreen); all produce different results making it unwise
to compare data obtained using the different methods. The preferred
method for RNA quantity determination uses fluorescent RNA binding
dyes, for example RiboGreen, which are best for the detection of low
target concentrations. In any case, it is advisable to measure all
samples using one method only and to report this
information. ... ... ...

latest papers => http://www.gene-quantification.de/rna-integrity2.html

- Reverse transcription-quantitative polymerase chain reaction:
description of a RIN-based algorithm for accurate data normalization.
- Time course analysis of RNA stability in human placenta.
- Evaluation of isolation methods and RNA integrity for bacterial RNA
quantitation.
- A comparison and evaluation of RNA quantification methods using
viral, prokaryotic, and eukaryotic RNA over a 10(4) concentration
range.
- Validation of lab-on-chip capillary electrophoresis systems for
total RNA quality and quantity control.
- Improved RNA quality and TaqMan Pre-amplification method (PreAmp) to
enhance expression analysis from formalin fixed paraffin embedded
(FFPE) materials.
- Optimization of the method of RNA isolation from paraffin blocks to
assess gene expression in breast cancer.
- Measuring microRNAs: comparisons of microarray and quantitative PCR
measurements, and of different total RNA prep methods.
- Focus on RNA isolation: obtaining RNA for microRNA (miRNA)
expression profiling analyses of neural tissue.
- Systematic analysis of microRNA expression of RNA extracted from
fresh frozen and formalin-fixed paraffin-embedded samples.
- Stability of RNA isolated from post-mortem tissues of Atlantic
salmon (Salmo salar L.)
- Prediction of qualitative outcome of oligonucleotide microarray
hybridization by measurement of RNA integrity using the 2100
Bioanalyzer capillary electrophoresis system.
- Removal of contaminating DNA from commercial nucleic acid extraction
kit reagents.

--------------------------------------------------------------------------------

PowerNest - illuminating error in qPCR experiment design

PowerNest is a software tool enabling experimenters to explore the
effect of sampling on noise propagation throughout qPCR assays. The
sampling process is assumed to be comprised of a number of levels; the
acquisition of a sample and the preparation of extracted material,
reverse-transcription of the mRNA, and the qPCR itself. Given a small
set of data, representative of a larger assay, the error at each stage
of the experiment is profiled using a nested-ANOVA.
Armed with this information, PowerNest allows the experimenter to
explore the effects of modifications to the experimental design on the
expected total error of the assay. When given the financial cost of
replicates at each level, PowerNest will calculate a cost-optimal
sampling-plan, delivering an experiment design that will minimise
processing error and maximise the statistical resolution of the assay.
The software is temporarily undergoing final testing, during which
time it has been made available as a free download =>
http://www.gene-quantification.de/main-bioinf.shtml#powernest

PowerNest Poster => http://www.gene-quantification.de/powernest-poster.pdf

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program, etc.
Please submit your qPCR event here => events@gene-
quantification.info

--------------------------------------------------------------------------------

qPCR WORKSHOP

BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different
prices may apply. Further customized workshops and specialized
trainings will be held as well across Europe and world-wide.
TATAA Biocenter Germany workshops are held in cooperation with BioEPS
GmbH, located at the campus of the Technical University of Munich, in
Freising-Weihenstephan, very close to the Munich Airport (MUC). For
more information and registration, please see our web page:
=> http://TATAA.gene-quantification.info/

Course Occasions 2009:

3-day qPCR Core Module (Mon. - Wed.)
2-day BioStatistics Module (Thu. - Fri.)
3-day single-cell qPCR Module (Mon. - Wed.)
3-day microRNA Module (Mon. - Wed.)

15 - 19 Juni 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) & 2-day
BioStatistics (Thu. - Fri.)
13 - 15 Juli 2009 (E) NEW microRNA qPCR (in cooperation with
Qiagen)
27 - 31 Juli 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) & 2-day
BioStatistics (Thu. - Fri.)
14 - 16 September 2009 (E) NEW single-cell qPCR
19 - 23 September 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)
26 - 28 October 2009 (E) 3-day qPCR Core Module (Mon. - Wed.)
16 - 20 November 2009 (E) 3-day microRNA Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)
7 - 11 December 2009 (E) 3-day qPCR Core Module (Mon. - Wed.) & 2-
day BioStatistics (Thu. - Fri.)

=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf
=> http://www.gene-quantification.de/bioeps-courses-autumn-2009.pdf
=> http://www.gene-quantification.de/single-cell-qpcr-course-sept-2009.pdf

--------------------------------------------------------------------------------

Forward Please send the qPCR NEWS to further scientists and friends
who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client,
please use following link:
http://qpcrnews.gene-quantification.info/

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl. Copyright ©
2005 - 2009 All rights reserved. Any unauthorized use, reproduction,
or transfer of this message or its contents, in any medium, is
strictly prohibited. Disclaimer & Copyrights are displayed on the
homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Forest Tree Microarray Workshop

2009-05-22T06:24:48Z

Good Day!

My name is Kate from School of Forestry and Natural Resources, University of Georgia. Our department is holding a Microarray Workshop this August specifically for the Forestry major scholars. Could you please help us to distribute this announcement plus two attachments to the forestry/natural resources list or any other mailing lists that might be interested or beneficial?

Thank you so much and have a nice day!

Regards,
Kate

*********************************************************************************************

Greetings from the School of Forestry and Natural Resources @ University of Georgia!

We are pleased to announce the "Forest Tree Microarray Workshop" to be held at the University of Georgia on August 3-7, 2009. Please post and forward the attached workshop flyer and pre-registration form to your faculty, staff and graduate students as appropriate.

Postdocs and advanced graduate students who have no prior hands-on experience with microarray technology are particularly encouraged to attend. The 5-day workshop will guide the participants through the wet-lab as well as data analysis processes, using the Agilent poplar whole-genome arrays. Spaces are limited to 12 and the registration fees are $700 per person (excluding lodging). Download pre-registration form & submit ASAP (seats will be filled on a first-come-first-serve basis).

August 3-7, 2009 Forest Tree Microarray Workshop @ University of Georgia

Workshop topics:

* Overview of microarray expression profiling
* Hands-on target amplification and Cy-dye labeling
* Microarray hybridization using Agilent Poplar array
* Array scanning and image analysis
* Data analysis, clustering, and more

Who should attend?

Participants who have no prior hands-on experience in microarray technology. Postdocs and graduate students are
particularly encouraged to attend.

What is the cost?

Registration fee is $700 per person.
Space is limited to 12.

How to register?

* Download pre-registration form & submit ASAP (seats will be filled on a first-come-first-serve basis).
* Selected participants must register by June 15.

Accommodation:

A block of rooms have been reserved at the Georgia Center.
Participants must make their hotel reservations by July 1 to enjoy the special rates.

* Single occupancy: $89 plus tax
* Double occupancy: $109 plus tax
* Please reference "Microarray Workshop" for the special rates.
* If you are interested in sharing a room with another workshop participant, please contact Kate for assistance.

Workshop Instructors:

* Juan Cui (Ph.D.), Institute of Bioinformatics
* Prof. CJ Tsai, Department of Genetics & Warnell School of Forestry and Natural Resources
* Scott Harding (Ph.D.), Warnell School of Forestry and Natural Resources
* Kate Tay (M.S.), Warnell School of Forestry and Natural Resources

For more information, please visit http://aspenDB.uga.edu/workshop

or contact Kate Tay (ktay@...) or Professor CJ Tsai (cjtsai@...).

We are looking forward to seeing you soon!

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Pre_RegForm_UGA_array_worshop.pdf (148K) Download Attachment

The joint EMBL/Affymetrix workshop on whole transcript microarray data analysis

2009-04-09T01:01:16Z

EMBL Course Announcement
Dear Colleagues,

We are writing to announce the The joint EMBL/Affymetrix workshop on whole transcript microarray data analysis at the European Molecular Biology Laboratory (Heidelberg, Germany) from 4 - 7 May 2009.
Please visit the web site for full conference details: www.embl.de/courses/affymetrix/2009
Registration deadline: 19 April 2009

Please circulate this announcement to interested members and groups within your institute.

We are looking forward to welcoming you at EMBL Heidelberg.

Best wishes,
Bettina Schäfer

Conference Officer
Course and Conference Office
European Molecular Biology Laboratory
Meyerhofstr. 1
D-69117 Heidelberg
Tel: +49-6221-387 8397
Fax: +49-6221-387 8836
Email: schaefer@...

For full event listings please visit our website: www.embl.org/events
If you do not wish to receive any further event announcements, please reply with "unsubscribe".

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

qPCR NEWS March 2009 - focus on HRM & HRM dyes

2009-03-26T03:30:14Z

qPCR NEWS March 2009 - focus on HRM & HRM dyes
---------------------------------------------------------------------

Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of this newsletter issue is:

- HRM page updated with new papers
- NEW page - HRM dyes
- Online translation service of the Gene Quantification
- New qPCR events in autumn 2009
- New qPCR workshop modules at the TATAA Biocenter Germany
- Online translation service of the Gene Quantification =>
http://translation.gene-quantification.info/

New qPCR workshop modules at the TATAA Biocenter Germany =>
http://tataa.gene-quantification.info/
European wide qPCR application workshops => register now !
=> course program spring - summer 2009
=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf

--------------------------------------------------------------------------------

High Resolution Melting (HRM) is a novel, homogeneous, close-tube,
post-PCR method, enabling genomic researchers to analyze genetic
variations (SNPs, mutations, methylations) in PCR amplicons. It goes
beyond the power of classical melting curve analysis by allowing to
study the thermal denaturation of a double-stranded DNA in much more
detail and with much higher information yield than ever before. HRM
characterizes nucleic acid samples based on their disassociation
(melting) behavior. Samples can be discriminated according to their
sequence, length, GC content or strand complementarity. Even single
base changes such as SNPs (single nucleotide polymorphisms) can be
readily identified.

http://hrm.gene-quantification.info/

The most important High Resolution Melting application is gene
scanning - the search for the presence of unknown variations in PCR
amplicons prior to or as an alternative to sequencing. Mutations in
PCR products are detectable by High Resolution Melting because they
change the shape of DNA melting curves. A combination of new-
generation DNA dyes, high-end instrumentation and sophisticated
analysis software allows to detect these changes and to derive
information about the underlying sequence constellation.

HRM Applications => new papers
The introduction of HRM has renewed interest in the utility of DNA
melting for a wide range of uses, including:
Mutation discovery (gene scanning)
Screening for loss of heterozygosity
DNA fingerprinting
SNP genotyping
Characterization of haplotype blocks
DNA methylation analysis
DNA mapping
Species identification
Somatic acquired mutation ratios
HLA compatibility typing
Association (case/control) studies
Allelic prevalence in a population
Identification of candidate predisposition genes

http://hrm.gene-quantification.info/

--------------------------------------------------------------------------------

High Resolution Melting Dyes & probes

http://hrm-dyes.gene-quantification.info/

The secret of High Resolution Meling (HRM) analysis is to monitor this
process happening in real-time. This is achieved by using saturating
fluorescent dye. HRM dyes are known as intercalating dyes bind
specifically and in high amount (= saturating dye, except SYBR Green)
to double-stranded DNA and when they are bound they fluoresce
brightly. In the absence of double-stranded DNA they have nothing to
bind to and they only fluoresce at a low level (estimations are
between 1-4% false positive fluorescence). At the beginning of the HRM
analysis, after complete PCR amplification, there is a high level of
fluorescence in the sample because of the millions of copies of the
amplicon. But as the sample DNA is heated up and the two strands of
the DNA denaturate there is no longer any double stranded DNA present
and thus fluorescence is reduced => http://hrm-dyes.gene-quantification.info/

* LC Green * SYTO9 * Eva Green * BEBO * SYBR Green

--------------------------------------------------------------------------------
online translation

Since October 2008 we provide an online translation service of the
Gene Quantification pages to several languages. Please recognize this
is an automatic and robotic based translation service, and therefore
we can give NO guarantee about the generated content. It should help
to understand the "rough" content of the Gene Quantification pages,
but still the original is the ENGLISH version:

http://translation.gene-quantification.info/

--------------------------------------------------------------------------------

With the new qPCR INFO PORTAL and all the presented tools we will help
you with to find the right information about qPCR and related topics
in Molecular Biology in the literature and in the World Wide Web.
=> Papers / Protocols / Methods / Databases / Alets / Feeds / Books /
Forums / E-mail / Directory

http://infoportal.gene-quantification.info/

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program, etc.
Please submit your qPCR event here => events@gene-
quantification.info

--------------------------------------------------------------------------------

qPCR WORKSHOP

BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different
prices may apply. Further customized workshops and specialized
trainings will be held as well across Europe and world-wide.
TATAA Biocenter Germany workshops are held in cooperation with BioEPS
GmbH, located at the campus of the Technical University of Munich, in
Freising-Weihenstephan, very close to the Munich Airport (MUC). For
more information and registration, please see our web page:
=> http://TATAA.gene-quantification.info/

Course Occasions 2009:

3-day qPCR Core Module (Mon. - Wed.)
2-day BioStatistics Module (Thu. - Fri.)
3-day single-cell qPCR Module (Mon. - Wed.)
3-day microRNA Module (Mon. - Wed.)

20 - 22 April 2009 (E) NEW microRNA qPCR

11 - 15 May 2009 (Deutsch)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

15 - 19 Juni 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

13 - 15 Juli 2009 (E) NEW microRNA qPCR

27 - 31 Juli 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf

--------------------------------------------------------------------------------

Forward Please send the qPCR NEWS to further scientists and friends
who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client,
please use following link:
http://qpcrnews.gene-quantification.info/

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl. Copyright ©
2005 - 2009 All rights reserved. Any unauthorized use, reproduction,
or transfer of this message or its contents, in any medium, is
strictly prohibited. Disclaimer & Copyrights are displayed on the
homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Introduction to microarray data analysis - deadline reminder

2009-02-02T13:18:37Z

This is a reminder for those people considering taking our online
course, which begins again in March 2009.

The application deadline is 13 February. However, it is advisable to
apply before the deadline to allow time for any questions in processing
your application.

I have included the course outline below; the full details are on our
website
(http://octette.cs.man.ac.uk/bioinformatics/modules/BIOL61010.html). If
you have any questions, or need advice on the module options, please
contact Heather.Vincent@...

This course focuses on microarray analysis in the context of modelling
for a systems approach to biology. Course participants will work through
practical examples using maxdview, a visualisation environment for
microarray data from The University of Manchester, and/or Bioconductor.

The course is designed to be taken either as a stand-alone course for
those already working with microarrays, or as a final module for those
working towards a formal qualification in bioinformatics. In the context
of the full programme in bioinformatics, the module builds on the
methods covered in the earlier module, Introduction to Bioinformatics
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6061.html).

Week 1 Introductions and software setup

Weeks 2 and 3 Microarrays and experimental design

Weeks 4 and 5 Data capture and preliminary checks

Weeks 6 and 7 Data analysis

Weeks 8 and 9 2-channel data

Weeks 10 and 11 Independent research and work on the first assessment

Weeks 12 and 13 Gene Class Tests

Weeks 14 to 16 Independent research and work on the second assessment

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

qPCR NEWS January 2009 - Lab-on-Chip special edition

2009-01-26T00:28:11Z

qPCR NEWS January 2009 - Lab-on-Chip special edition
--------------------------------------------------------------------------------

Dear researcher,
dear Gene Quantification page reader,

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of this newsletter issue is:

- qPCR 2009 Event => http://www.qPCR2009.net
- we are proud to present 230 scientific contributions (86 talks & 144
posters) have a look on the preliminary online agenda
- http://online-AGENDA.qpcr2009.net/
- Lab on Chip application papers
- PCR efficiency page updated with the newest papers in the field
- Online translation service of the Gene Quantification
=> http://translation.gene-quantification.info/

- European wide qPCR application workshops => register now !
=> qPCR course program spring - summer 2009
=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf

--------------------------------------------------------------------------------

Lab-on-a-chip (LOC) is a term for devices that integrate (multiple)
laboratory functions on a single chip of only millimeters to a few
square centimeters in size and that are capable of handling extremely
small fluid volumes down to less than pico liters. Lab-on-a-chip
devices are a subset of MEMS devices and often indicated by "Micro
Total Analysis Systems" (µTAS) as well. Microfluidics is a broader
term that describes also mechanical flow control devices like pumps
and valves or sensors like flowmeters and viscometers. However,
strictly regarded "Lab-on-a-Chip" indicates generally the scaling of
single or multiple lab processes down to chip-format, whereas "µTAS"
is dedicated to the integration of the total sequence of lab processes
to perform chemical analysis. The term "Lab-on-a-Chip" was introduced
later on when it turned out that µTAS technologies were more widely
applicable than only for analysis purposes.
Microfluidics deals with the behavior, precise control and
manipulation of fluids that are geometrically constrained to a small,
typically sub-milimeter, scale. It is a multidisciplinary field
intersecting engineering, physics, chemistry, microtechnology and
biotechnology, with practical applications to the design of systems in
which such small volumes of fluids will be used. Microfluidics has
emerged in the beginning of the 1980s and is used in the development
of inkjet printheads, DNA chips, lab-on-a-chip technology, micro-
propulsion, and micro-thermal technologies.

http://lab-on-chip.gene-quantification.info/

--------------------------------------------------------------------------------

- Nanodroplet real-time PCR system with laser assisted heating
- A polymer lab-on-a-chip for reverse transcription (RT)-PCR based
point-of-care clinical diagnostics
- Microchip-based one step DNA extraction and real-time PCR in one
chamber for rapid pathogen identification
- PCR thermal management in an integrated Lab on Chip
- Rapid PCR in a continuous flow device
- Single-molecule DNA amplification and analysis in an integrated
microfluidic device
- Microfabricated PCR-electrochemical device for simultaneous DNA
amplification and detection
- Miniaturized flow-through PCR with different template types in a
silicon chip thermocycler
- Coordinating Multiple Droplets in Planar Array Digital Microfluidic
Systems
- Microcontact Printing of DNA Molecules
- Ultra fast miniaturized real-time PCR: 40 cycles in less than six
minutes
- ITO-coated glass/polydimethylsiloxane continuous-flow PCR chip
- and much more here http://lab-on-chip.gene-quantification.info/

--------------------------------------------------------------------------------

LOC technology for total RNA and microRNA quality & quantity control
- Bioanlyzer 2100
- Experion
- RNA integrity measurements
- RIN and RQI algorithms
- find more information and papers here
=> http://rna-integrity.gene-quantification.info/

--------------------------------------------------------------------------------
online translation

Since October 2008 we provide an online translation service of the
Gene Quantification pages to several languages. Please recognize this
is an automatic and robotic based translation service, and therefore
we can give NO guarantee about the generated content. It should help
to understand the "rough" content of the Gene Quantification pages,
but still the original is the ENGLISH version:

http://translation.gene-quantification.info/

http://www.gene-quantification.asia
http://chinese.gene-quantification.asia/
http://dutch.gene-quantification.info/
http://french.gene-quantification.info/
http://german.gene-quantification.info/
http://greek.gene-quantification.info/
http://italian.gene-quantification.info/
http://japanese.gene-quantification.asia/
http://korean.gene-quantification.asia/
http://portuguese.gene-quantification.info/
http://russian.gene-quantification.asia/
http://spanish.gene-quantification.info/

--------------------------------------------------------------------------------

With the new qPCR INFO PORTAL and all the presented tools we will help
you with to find the right information about qPCR and related topics
in Molecular Biology in the literature and in the World Wide Web.
=> Papers / Protocols / Methods / Databases / Alets / Feeds / Books /
Forums / E-mail / Directory

http://infoportal.gene-quantification.info/

--------------------------------------------------------------------------------

Upcoming Events World-wide academic and commercial qPCR Events
http://events.gene-quantification.info/

Symposia, Meetings, Conferences, Workshops, Seminars, Online-Seminars,
qPCR Education Program, etc.
Please submit your qPCR event here => events@gene-
quantification.info

--------------------------------------------------------------------------------

qPCR 2009 EVENT - 9 - 13 March 2009

more news here => http://www.qPCR2009.net
download event FLYER => http://www.bioeps.com/qpcr2009/qPCR-2009-3rd-announcement.pdf

We are proud to present 230 scientific contributions (86 talks & 144
posters) have a look on the preliminary online agenda =>
http://online-AGENDA.qpcr2009.net/

It is a pleasure to announce the Nobel Prize Laureate Kary Mullis at
the qPCR 2009 event in an own session “25th Anniversary of PCR”

List of confirmed speakers => http://speakers.qpcr2009.net/
An industrial exhibition with the 30 world leading companies will be
held during the qPCR Symposium March 9-11 => http://exhibition.qpcr2009.net/

Our sponsors => http://sponsors.qpcr2009.net/

Please register until 31st December to get the early registartion fee
=> http://registration.qpcr2009.net/

Keynote lectures

The Pioneer in PCR Kary B. Mullis 1993 Nobel Prize in Chemistry
- 25th Anniversary of PCR

Stephen A. Bustin
Professor of Molecular Science, Institute of Cell and Molecular
Science, Queen Mary's School of Medicine and Dentistry, University of
London, UK

- A new qPCR assay for the detection of Clostridium difficile
- MIQE- guidelines for publication of qPCR data

Ken Livak
Senior Scientific Fellow, Fluidigm Corporation,San Francisco, CA, US
- Moving from qPCR Assays to qPCR Arrays.

--------------------------------------------------------------------------------

qPCR WORKSHOP

BioEPS GmbH / TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
Depending on the occasion the workshop language and the different
prices may apply. Further customized workshops and specialized
trainings will be held as well across Europe and world-wide.
TATAA Biocenter Germany workshops are held in cooperation with BioEPS
GmbH, located at the campus of the Technical University of Munich, in
Freising-Weihenstephan, very close to the Munich Airport (MUC). For
more information and registration, please see our web page:
=> http://TATAA.gene-quantification.info/

Course Occasions 2009:

3-day qPCR Core Module (Mon. - Wed.)
2-day BioStatistics Module (Thu. - Fri.)
3-day single-cell qPCR Module (Mon. - Wed.)
3-day microRNA Module (Mon. - Wed.)

26 - 30th January 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

20 - 22 April 2009 (E) NEW microRNA qPCR

20 - 22 April 2009 (E) NEW singel-cell qPCR Application Workshop

11 - 15 May 2009 (Deutsch)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

15 - 19 Juni 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

13 - 15 Juli 2009 (E) NEW microRNA qPCR

27 - 31 Juli 2009 (E)
3-day qPCR Core Module (Mon. - Wed.) & 2-day BioStatistics Module
(Thu. - Fri.)

=> http://www.gene-quantification.de/bioeps-courses-spring-summer-2009.pdf

--------------------------------------------------------------------------------

Forward Please send the qPCR NEWS to further scientists and friends
who are interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.gene-quantification.info

--------------------------------------------------------------------------------

If this newsletter is not displayed correctly by your email client,
please use following link:
http://qpcrnews.gene-quantification.info/

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl.
Copyright © 2005 - 2009 All rights reserved. Any unauthorized use,
reproduction, or transfer of this message or its contents, in any
medium, is strictly prohibited. Disclaimer & Copyrights are displayed
on the homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Introduction to Microarray Data Analysis, March 2009

2008-12-29T08:18:16Z

Introduction to Microarray Data Analysis is one of a number of online
courses from The University of Manchester. It is suitable for anyone
beginning work with microarrays, or for those needing to extend their
skills in data analysis.

There are now many tools available for microarray data analysis. In
this course, instructions for the practical exercises are given for
maxdview or for Bioconductor, so participants can choose which tool to
use.

maxdview, from The University of Manchester, has a graphical user
interface, providing an excellent learning environment for those new to
work with microarrays.

Many new methods for the analysis of genomic data are now written in the
R programming language, and then contributed to the BioConductor
project. The packages are called from the command line, so the
Bioconductor exercises are more suitable for those with some experience
of programming.

Our distance courses are delivered in a Virtual Learning Environment,
which allows us to extend the classroom into the web. We use a range of
tools to support our online teaching activities.

Each course, which is paced to suit those in full-time employment, runs
over 16 teaching weeks.

Teaching and learning are focussed around tutor-supported exercises. In
this course, participants are encouraged to discuss their work, before
submitting exercises for feedback from the course tutor. Participants
who wish to be assessed for credits at Masters level should complete
additional independent research for assessment

Week 1 Introductions and software setup

Weeks 2 and 3 Microarrays and experimental design

Weeks 4 and 5 Data capture and preliminary checks

Weeks 6 and 7 Data analysis

Weeks 8 and 9 2-channel data

Weeks 10 and 11 Independent research and work on the first assessment

Weeks 12 and 13 Gene Class Tests

Weeks 14 to 16 Independent research and work on the second assessment

You will find information on all our courses, including fees and a link
to the online application form, here :
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the module options, please contact
Heather.Vincent@...

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

ANNOUNCEMENT. V International Course on Microarray Data Analysis, CIPF, Valencia, SPAIN

2008-11-05T01:03:10Z

Dear colleague,

Would you be so kind of giving diffusion to this course on microarray
data analysis that we are organizing here, in Valencia (Spain).
Find below details. Apologies for possible multiple posting

Thanks

V International Course on Microarray Data Analysis

Valencia, Spain. 9th- 13th March, 2009

http://bioinfo.cipf.es/courses/mda09/

Joaquin Dopazo, David Montaner and Ana Conesa

Department of Bioinformatics and Genomic & Functional Genomics Node (INB)

Centro de Investigación Príncipe Felipe (CIPF)

46012, Valencia, Spain

http://bioinfo.cipf.es

http://www.gepas.org

http://www.babelomics.org

http://www.blast2go.org/

---------

DNA microarrays constitute, no doubt, a paradigm among post-genomic
technologies, which are characterised for producing large amounts of
data, whose analysis and interpretation is not trivial. Microarray
technologies allows querying living systems in a completely new way, but
at the same time present new challenges in the way hypotheses must be
tested and our results ought to be analysed.

Since the first papers published in the latest nineties the number of
questions that have been addressed through this technique have both
increased and diversified. Initial interest was focused on genes
co-expressing across sets of experimental conditions, implying
essentially the use of clustering techniques. More recently, however,
the interest has switched to find genes differentially expressed among
distinct classes of experiments, or correlated to diverse parameters.
There is also much interest in robust methods for building predictors of
clinical outcomes. Also, CGH-arrays (Albertson and Pinkel, 2003) are
recently becoming an alternative for studying the relationship between
chromosomal alterations affecting to copy number (which are behind many
diseases) and gene expression. In addition, there is also a clear demand
for methods that allow automatic transfer of biological information to
the results of microarray experiments and to interpret them at the light
of the biological knowledge. Recently, new methods of analysis have been
proposed that directly address hypothesis on modules of genes
functionally related that have demonstrated to be superior to the
classical one-gene-at-a-time approaches (Mootha et al., 2003;
Al-Shahrour et al., 2005, 2007). New high throughput sequencing methods
will increase the availability of transcriptomic and genomic data in a
different format but with the same scientific questions behind.

This course covers the state-of-the-art in the above mentioned topics,
which are of major relevance in today’s gene expression data analysis.
Through sessions of theory and practical examples, the students will
acquire the experience necessary to address scientific questions to gene
expression array datasets and solve them. Special attention will be
devoted to important (although not always took into account) aspects in
microarray data analysis, such as multiple testing or functional
profiling. In addition, some theoretical lessons on basic statistics
will be included as part of the programme. Finally, for the bravest and
those who want to go in more depth into analysis possibilities, the last
day a short course on Bioconductor (Gentleman et al., 2004) will be taught.

The course is designed to be a mixture of theoretical and practical
sessions. The latter will require some familiarity with the use of
web-based tools and knowledge of basics notions of statistics.

Practical sessions will be carried out using the GEPAS (Herrero et al.,
2003, 2004, Vaquerizas et al., 2005; Montaner et al., 2006) environment,
an integrated web tool for microarray data analysis, and the Babelomics
suite (Al-Shahrour et al., 2005b, 2006, 2007) for functional profiling
of genome-scale experiments, and the Blast2GO suite (Conesa et al.,
2005), a set of tools for the high-throughput functional annotation and
analysis of uncharacterized sequences.

The course will be held the week before fallas, one of the most popular
and impressing folkloric festivals in Spain which ends the 19th March
when all the fallas are burnt in an apotheosis of fireworks. So you can
use this opportunity to enjoy one of the most exceptional holiday
festival in the world. See more in:
http://www.fallas.com/contenido.asp?seccion=museo&tema=historia&bandera=en

See information on the Bioinformatics Department courses in:
http://bioinfo.cipf.es/docus/courses/courses.html

Programme

Day 1

--------

9.30 – 11.30. Introduction

Structure of the course. Why microarrays? Pre- and post-genomics
hypothesis testing: a note of caution. Design of experiments. Data
preprocessing and normalization. Unsupervised analysis (clustering).
Supervised analysis (gene selection, predictors). Functional profiling.

12.00–13.30. Normalization (theory and practical exercises)

Getting rid of unwanted variability from sources other than the
experimental conditions assayed. Methods for Affymetrix, two-colour and
one-colour microarrays

13.30-14.30 Lunch

14.30-16.00 Gene selection (theory)

Methods for selecting genes differentially expressed among two or more
experimental conditions, correlated to a continuous variable or
correlated to survival. How to deal with the multiple-testing problem.

16.30-18.00 Gene selection (practical exercises)

Day 2

-------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-13.30 Predictors (theory and practical exercises)

Gene selection in the context of class prediction. How to deal with the
selection bias problem. Different methods for class prediction.
Estimating the error of classification. Interpretation of confusion
matrices.

13.30-14.30 Lunch

14.30-16.00 Clustering (theory)

Different clustering methods: hierarchical clustering, SOM, SOTA and
k-means. Pros and cons. Measures of cluster quality. Cluster visualisation.

16.30-18.00 Clustering (practical exercises)

Day 3

--------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-13.30 Functional profiling of experiments

Understanding the biological roles played by the genes in the
experiments. Using different types of information for the functional
profiling of microarray experiments: gene ontology, InterPro motifs,
transcription factor binding sites, gene expression in other
experiments, text-mining, etc. New trends in the analysis of microarray
data: testing pathway-based or function-based hypothesis.

13.30-14.30 Lunch

10.30-12.30 Functional profiling. The Babelomics suite

Different methods for functional profiling of experiments from the
Babelomics suite: FatiGO/FatiGO+, Marmite (using text-mining) or TMT
(pre-tabulated gene expression results). Methods for finding blocs of
functionally-related genes differentially expressed (GSEA, FatiScan).

Day 4

--------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-12.00 Array-CGH

Estimation of copy number in chromosomal aberrations. Joint study of
copy number, gene expression and functional profiling.

12.00-13.30 Introduction to the programmable GEPAS interface

Using the visual programming interface of GEPAS to build up pipelines of
analysis.

13.30-14.30 Lunch

14.30-17.30 Exercises

Do a complete practical exercise using the tools you learned.

17.30-18.00 Concluding remarks and final questions

Day 5

--------

9.30-13.30 A primer on automatic annotation of sequences.

13.30-14.30 Lunch

14.30-18.00 Blast2GO

References

Albertson, D.G. and Pinkel, D. Genomic microarrays in human genetic
disease and cancer. Hum Mol Genet, 2003 12 Spec No 2, R145-52

Al-Shahrour, F., Diaz-Uriarte, R. & Dopazo, J. Discovering molecular
functions significantly related to phenotypes by combining gene
expression data and biological information. Bioinformatics. 2005;21:
2988-2993

Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J: BABELOMICS:
a suite of web tools for functional annotation and analysis of groups of
genes in high-throughput experiments. Nucleic Acids Res 2005b, 33:W460-464

Al-Shahrour F., Minguez P., Tárraga J., Montaner D., Alloza E.,
Vaquerizas J.M., Conde L., Blaschke C., Vera J. and Dopazo J.
BABELOMICS: a systems biology perspective in the functional annotation
of genome-scale experiments Nucl Acids Res., 2006, 34: W472-W476

Al-Shahrour F, Arbiza L, Dopazo H, Huerta J, Minguez P, Montaner D,
Dopazo J. From genes to functional classes in the study of biological
systems. 2007 BMC Bioinformatics 8:114

Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO:
a universal tool for annotation, visualization and analysis in
functional genomics research. 2005 Bioinformatics, 21(18), 3674-3676.

Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M.,
Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al.
Bioconductor: open software development for computational biology and
bioinformatics. Genome Biol, 2004, 5, R80

Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM,
Santoyo J, Dopazo J: GEPAS: A web-based resource for microarray gene
expression data analysis. Nucleic Acids Res 2003, 31:3461-3467.

Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Diaz-Uriarte
JS, Dopazo J: New challenges in gene expression data analysis and the
extended GEPAS. Nucleic Acids Res 2004, 32:W485-491

Montaner D., Tárraga J., Huerta-Cepas J., Burguet J., Vaquerizas J.M.,
Conde L., Minguez P., Vera J., Mukherjee S., Valls J., Pujana M., Alloza
E., Herrero J., Al-Shahrour F., Dopazo J. Next station in microarray
data analysis: GEPAS Nucl Acids Res., 2006, 34: W486-W491

Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J,
Puigserver P, Carlsson E, Ridderstrale M, Laurila E et al:
PGC-1alpha-responsive genes involved in oxidative phosphorylation are
coordinately downregulated in human diabetes. Nat Genet 2003, 34(3):267-273.

Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P,
Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J: GEPAS, an
experiment-oriented pipeline for the analysis of microarray gene
expression data. Nucleic Acids Res 2005, 33:W616-620

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

posting of our systems biology webinar

2008-10-22T16:04:48Z

I wanted to bring this to your attention and would appreciate your consideration of posting this event on your message board.

Systems Biology: New Approaches, New Tools, and Implications for Human Health Care

Presenters will include worldclass scientists at the cutting edge of systems biology:
• Dr. Leroy Hood (Institute for Systems Biology) will discuss the implications of the systems approach in healthcare.
• Dr. Akhilesh Pandey (Johns Hopkins University) will describe the systems approach and its benefits relative to more straightforward, individual omics approaches.
• Dr. Rudolf Grimm (Agilent Technologies), will discuss the analytical tools for systems biology research and novel translational technologies to support large-scale studies.

This webinar makes the case for a "systems" approach, specifically to better understand how biological systems interact and the profound implications for human healthcare. In addition, attendees will learn about the latest tools and techniques used in systems biology research, particularly how these tools serve each omics discipline while simultaneously drawing them together to the advantage of biomedical research.

Register today at www.genengnews.com/systemsbiology

Thank you for your consideration.

Best regards,

Joan Boyce

Group Publisher

_______________________________________

Genetic Engineering & Biotechnology News

E: jboyce@...

T: 914-740-2211

F: 914-740-2201

www.genengnews.com

Mary Ann Liebert, Inc. is recognized as a Certified Woman-Owned Business by the Women's Business Enterprise National Council (WBENC).

This e-mail message, and any attachments to it, are for the sole use of the intended recipients, and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution of this email message or its attachments is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, while the company uses virus protection, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email.

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

CAMDA08 Announcement. Deadline extension

2008-10-15T00:07:53Z

Dear Colleagues,

Because of the fairly late release of the second contest data set
we have had many requests for a deadline extension. We have thus
decided to push back the deadline for all papers by two more weeks
to 22 October.

For fairness towards already submitted manuscripts, past submissions
can also be revised and resubmitted until that date.

We are looking forward to a lively contest
and hope to see you at the conference!

Kind regards,
David Kreil.

CAMDA'08, Vienna, Austria, 4-6 December 2008 --
http://camda.bioinfo.cipf.es/

News: ** Emerald calibration data set released!
Contest deadline extended to 22 Oct. **

News: ** CAMDA is featured in the August Nature Methods editorial! **

Dear colleague!

We cordially invite you to attend this year's conference on

Critical Assessment of Microarray Data Analysis (CAMDA) .

CAMDA was founded to provide a forum for the critical assessment
of the many different techniques used in microarray data mining
(Nature 411, 885, Nature 424, 610). It aims to establish the state of
the art in microarray data analysis, as well as highlight progress and
identify directions of future efforts.
In order to achieve these goals, CAMDA adopted the approach of a
community-wide experiment, letting the scientific community analyse
the same contest data sets.
Researchers worldwide are invited to take the CAMDA challenge.
Accepted submissions will be asked to give an oral presentation.
Results of analysis are discussed and compared at the CAMDA
conference.
As a special opportunity, this year, a selection of analysis predictions
will also be verified experimentally by the laboratory collecting the
original contest data set. CAMDA provides a unique environment for
testing and demonstrating your latest analysis methods.
In addition, the Emerald project has just provided fresh data from
an experiment dissecting technical and biological variance in
known mixture samples on three different platforms, now also available
via ArrayExpress.

CAMDA, which began in 2000, was initiated by Simon Lin and Kimberly
Johnson from the Duke University Bioinformatics Shared Resource
(www.camda.duke.edu <http://www.camda.duke.edu>). CAMDA has since become
an internationally
roving conference, with the first such meeting held 2007 at CIPF in
Valencia, Spain.
This year, CAMDA is hosted by Boku University Vienna in Austria.

Your participation is critical for making this year's CAMDA meeting
again a great event.

Please do distribute this announcement to other colleagues who might
be interested.

We look forward to seeing you in Vienna!

David Kreil &
Joaquin Dopazo

(chairs)

CAMDA'08 Conference, Vienna, Austria, 4-6 December 2008

Conference home http://camda.bioinfo.cipf.es/
Contest data set at http://camda.bioinfo.cipf.es/contest_dataset

Important Dates:
2008-06-01 Public release of Contest Data Set
2008-10-22 Extended Abstract Proposals due
2008-11-01 Acceptance notification for session speakers
2008-11-01 Acceptance notification for poster presenters
2008-11-03 Early registration closes
2008-12-04 Conference opens (later p.m.)
2008-12-06 Conference closes
2009-01-31 Full paper submission

(--- for technical reasons, you may receive this announcement more
than once ---)

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

CAMDA08 Announcement

2008-09-09T04:25:33Z

CAMDA'08, Vienna, Austria, 4-6 December 2008 --
http://camda.bioinfo.cipf.es/

News: ** Emerald calibration data set released! **

News: ** CAMDA is featured in the August Nature Methods editorial! **

Dear colleague!

We cordially invite you to attend this year's conference on

Critical Assessment of Microarray Data Analysis (CAMDA) .

CAMDA was founded to provide a forum for the critical assessment
of the many different techniques used in microarray data mining
(Nature 411, 885, Nature 424, 610). It aims to establish the state of
the art in microarray data analysis, as well as highlight progress and
identify directions of future efforts.
In order to achieve these goals, CAMDA adopted the approach of a
community-wide experiment, letting the scientific community analyse
the same contest data sets.
Researchers worldwide are invited to take the CAMDA challenge.
Accepted submissions will be asked to give an oral presentation.
Results of analysis are discussed and compared at the CAMDA
conference.
As a special opportunity, this year, a selection of analysis predictions
will also be verified experimentally by the laboratory collecting the
original contest data set. CAMDA provides a unique environment for
testing and demonstrating your latest analysis methods.
In addition, the Emerald project has just provided fresh data from
an experiment dissecting technical and biological variance in
known mixture samples on three different platforms.

CAMDA, which began in 2000, was initiated by Simon Lin and Kimberly
Johnson from the Duke University Bioinformatics Shared Resource
(www.camda.duke.edu
<http://www.camda.duke.edu>). CAMDA has since become an internationally
roving conference, with the first such meeting held 2007 at CIPF in
Valencia, Spain.
This year, CAMDA is hosted by Boku University Vienna in Austria.

Your participation is critical for making this year's CAMDA meeting
again a great event.

Please do distribute this announcement to other colleagues who might
be interested.

We look forward to seeing you in Vienna!

David Kreil &
Joaquin Dopazo

(chairs)

CAMDA'08 Conference, Vienna, Austria, 4-6 December 2008

Conference home http://camda.bioinfo.cipf.es/
Contest data set at http://camda.bioinfo.cipf.es/contest_dataset

Important Dates:
2008-06-01 Public release of Contest Data Set
*2008-10-06 * Extended Abstract Proposals due
2008-11-01 Acceptance notification for session speakers
2008-11-01 Acceptance notification for poster presenters
2008-11-03 Early registration closes
2008-12-04 Conference opens (later p.m.)
2008-12-06 Conference closes
2009-01-31 Full paper submission

(--- for technical reasons, you may receive this announcement more
than once ---)

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED 11 : Additional tutorial on Analysis of Short Reads from High-Throughput Sequencing

2008-08-01T04:50:59Z

Dear Colleagues,

Apologies if you receive this more than once (and sorry for the second
email in a week).

We are pleased to announce the addition of a new tutorial/workshop,
run by Martin Morgan from the FHCRC in Seattle, that will take place
at MGED 11 on September 4th:

Analysis of Short Reads from High-Throughput Sequencing using R and
Bioconductor

DESCRIPTION: Short reads are DNA sequences derived from ultra-high
throughput sequencing technologies. Data can consist of millions of
reads, ranging from 10's to 100's of nucleotides each. This hands-on
presentation and workshop introduces BioConductor tools for initial
exploration of short read data. Participants will learn how to import
and manipulate reads, visualize and assess read quality, work with
genome-sized sequences, and perform fast matching or flexible
alignment. Available tools provide effective ways to explore short
read data, and form the foundation for creative methodologies for
downstream statistical analysis.

Participants excited by next-generation sequencing technologies and
eager to engage R's scripting language will get the most out of this
workshop if they come with a laptop with the 'development' version of
R and software installed by the commands "source('http://bioconductor.org/biocLite.R')
; biocLite('ShortRead')".

If you have already registered for MGED 11, you can enroll in this
tutorial/workshop by sending an email to mged11@...
Please put into the Subject line: "Registration to Short Reads
Tutorial"; and provide your Name, Surname, and affiliation.
For payment: we will send a reply document with details for a bank
transfer before Aug 29 2008, or by credit card or cash on site in Riva
del Garda.

If you have yet to register for the conference, you can sign up for
the workshop during the registration process.
Acceptance into the workshop is on a first come, first served basis.

Finally, a reminder that the abstract submission deadline is next
Tuesday, August 5th. Registration will stay open until the meeting
begins.

More information about the meeting is available at http://www.mgedmeeting.org/

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

----------------------------------------------------------------------------------
MGED 11 Program

Sunday 31st Aug.

15:00 - Registration and Exhibit Area are open

Monday 1st Sept.

07:30 Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert, Cesare Furlanello

ENCODE Session
09:00-10:00 Keynote Lecture: Piero Carninci
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:15 Geoffrey Faulkner

Short sequence tags reveal global transcription of repetitive elements
in mammalian genomes

12:15-12:30 Alessandro Coppe

Motif Discovery In Promoters Of Genes Co-Expressed And Co-Localized In
Myelopoiesis By A Novel Computational Framework

12:30-14:00 Lunch (Palameeting)

PARALLEL EVENT in President Room (floor1):
talk-and-lunch sponsored by TECAN
"Microarray experiment quality: on direct route to reliable data"
(register at mged11@...)

Wine and Yeast Genomics Session

14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:00 Dan Riordan

Uncovering RNA Regulatory Information in the Yeast Genome

15:00-15:15 Gavin Sherlock

Molecular Characterization of Clonal Interference during Adaptive
Evolution in Asexual Populations of Saccharomyces cerevisiae

15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer

18:00-20:00 Welcome cocktail

Tuesday 2nd Sept.

Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:00 Adam Butler

Mining Affymetrix SNP6.0 Copy Number Data In Human Cancer

12.00-12.15 Alistair Chalk

An integrated transcriptome analysis approach to characterise adult
neural stem cells and study complex disease

12.15-12.30 Silvio Bicciato

A Computational Procedure To Identify Significant Overlap Of
Differentially Expressed And Genomic Imbalanced Regions In Cancer
Datasets

12:30-14:00 Lunch

PARALLEL EVENT:
talk-and-lunch sponsored by Molecular Stamping (register at mged11@...
)

Quality and Standards in Action

14:00-14:15 Introduction and update on MGED Standards: Chris
Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta
Sansone/Philippe Rocca-Serra
14:45-15:30 Semantic Web and Gene Expression: Alan Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I

19:00-21:00 Conference Dinner

Wednesday 3rd Sept.

Learning from Microarray Data

09:00-10:00 Keynote Lecture: Naama Barkai
10:00-10:45 Plenary Talk: Atul Butte
10:45-11:00 Break
11:00-11:45 Plenary Talk: Rainer Spang
11:45-12:00 Misha Kapushesky

A cross-study and platform meta-analysis of condition-specificity of
gene expression in 20,000+ assays in ArrayExpress

12:00-12:15 Peter Murakami

Evaluation of Metrics for the Assessment of Microarray Data Quality

12:15-12:30 Paul Boutros

Systematic evaluation of the microarray analysis pipeline

12:30-14:00 Lunch

PARALLEL EVENT:
talk-and-lunch sponsored by INTEGROMICS
"Microarray Gene Expression Data Analysis: Avoiding Pitfalls"
(register at mged11@...)

Functional Genomics and Systems Biology

14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:45 Break
15:45-16:00 Josselin Noirel

Network-based integration of transcriptomic and proteomic data

16:00-16:15 Christine Wells

Diversification of inflammatory outcomes in human macrophages via
alternate transcription in the Toll-like Receptor signalling

16:15-17:00 Keynote Lecture: Ewan Birney
17:00-19:00 Poster Session II

20.45 Public Science Conference

Thursday 4th Sept.

Workshops
8:00 - 11:00 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment:
Audrey Kauffmann and Wolfgang Huber
11:00 - 14:30 Mid Morning Parallel Sessions
• Gene Pattern tutorial: Ted Liefeld
• Analysis of Short Reads from High-Throughput Sequencing using R
and Bioconductor: M. Morgan
15:00 - 18:00 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici and Misha
Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods:
Marc Salit and Wolfgang Huber

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED 11 Meeting, Trentino, Italy : Final abstract submission deadline is August 5th

2008-07-28T23:00:09Z

Dear Colleagues,

Apologies if you receive this more than once.

The MGED 11 final abstract submission deadline is next Tuesday,
August 5th.

Further information on MGED 11 is available at http://www.mgedmeeting.org/

Registration will stay open up until the meeting begins.

The scientific focus of the meeting will be high throughput
technologies - in particular microarrays and ultra high throughput
sequencing - and associated data handling issues, analysis techniques
and standards. We have lined up some outstanding speakers who will be
giving talks on these topics.

Continuing from last year, we will again be running a poster
competition, with prizes for the best posters presented by graduate
and postdoctoral students.

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

----------------------------------------------------------------------------------
MGED 11 Program

Sunday 31st Aug.

15:00 - Registration and Exhibit Area are open

Monday 1st Sept.

07:30- Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert, Catherine Ball, Cesare Furlanello

ENCODE Session
09:00-10:00 Keynote Lecture: Piero Carninci
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:30 Talks from Submitted abstracts (2)

12:30-14:00 Lunch

Wine Genomics Session
14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:30 Talks from Submitted abstracts (2)
15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer

18:00-20:00 Welcome cocktail
21.00 Public Science Conference I

Tuesday 2nd Sept.

Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:30 Talks from Submitted abstracts (3)

12:30-14:00 Lunch

Quality and Standards in Action
14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone
14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan
Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I

19:00-21:00 Conference Dinner

Wednesday 3rd Sept.

Learning from Microarray Data
09:00-10:00 Keynote Lecture: Naama Barkai
09:45-10:30 Plenary Talk: Rainer Spang
10:30-11:00 Break
11:00-11:45 Plenary Talk: Atul Butte
11:45-12:30 Talks from Submitted Abstracts (3)

12:30-14:00 Lunch

Functional Genomics and Systems Biology
14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:30 Break
15:30-16:15 Talks from Submitted Abstracts (3)
16:15-17:00 Keynote Lecture: Ewan Birney
17:00-19:00 Poster Session II
Close of Meeting, Final Announcements, Award of Poster Prizes

20.15 Public Science Conference 2

Thursday 4th Sept.

Workshops
8:00 - 11:00 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment: Audrey
Kauffmann and Wolfgang Huber
11:00 - 14:30 Gene Pattern tutorial: Ted Liefeld
15:00 - 18:00 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods: Marc Salit
and Wolfgang Huber

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED 11 Meeting, Trentino, Italy : Early Registration deadline is June 30th

2008-06-24T11:31:49Z

Dear Colleagues,

Apologies if you receive this more than once.

The MGED 11 early registration deadline is next Monday, June 30th,
after which registration fees increase by € 100.

Further information on MGED 11 is available at http://www.mgedmeeting.org/

Abstract for poster presentations will be accepted until August 5th.

The scientific focus of the meeting will be high throughput
technologies - in particular microarrays and ultra high throughput
sequencing - and associated data handling issues, analysis techniques
and standards. We have lined up some outstanding speakers who will be
giving talks on these topics.

This year we will again be selecting half of the plenary speakers from
submitted abstracts, to encourage greater participation in the MGED
community. Continuing from last year, we will also be running a
poster competition, with prizes for the best posters presented by
graduate and postdoctoral students. Finally, we will be awarding up
to seven $1500 travel grants to graduate or postdoctoral students who
are US citizens traveling from the US.

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

----------------------------------------------------------------------------------
MGED 11 Program

Sunday 31st Aug.

15:00 - Registration and Exhibit Area are open

Monday 1st Sept.

07:30- Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert Catherine Ball, Cesare Furlanello

ENCODE Session
09:00-10:00 Keynote Lecture: Piero Carninci
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:30 Talks from Submitted abstracts (1)

12:30-14:00 Lunch

Wine Genomics Session
14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:30 Talks from Submitted abstracts (2)
15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer

18:00-20:00 Welcome cocktail
21.00 Public Science Conference I

Tuesday 2nd Sept.

Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:30 Talks from Submitted abstracts (3)

12:30-14:00 Lunch

Quality and Standards in Action
14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone
14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan
Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I

19:00-21:00 Conference Dinner

Wednesday 3rd Sept.

Learning from Microarray Data
09:00-10:00 Keynote Lecture: Naama Barkai
09:45-10:30 Plenary Talk: Rainer Spang
10:30-11:00 Break
11:00-11:45 Plenary Talk: Atul Butte
11:45-12:30 Talks from Submitted Abstracts (3)

12:30-14:00 Lunch

Functional Genomics and Systems Biology
14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:30 Break
15:30-16:15 Talks from Submitted Abstracts (3)
16:15-17:00 Keynote Lecture: Ewan Birney
17:00-19:00 Poster Session II
Close of Meeting, Final Announcements, Award of Poster Prizes

20.15 Public Science Conference 2

Thursday 4th Sept.

Workshops
8:30 - 11:30 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment: Audrey
Kauffmann and Wolfgang Huber
11:30 - 14:30 Gene Pattern tutorial: Ted Liefeld
14:30 - 17:30 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods: Marc Salit
and Wolfgang Huber

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

MGED 11 Meeting, Trentino, Italy : Abstract Submission deadline for oral presentations is June 10th

2008-06-05T14:53:55Z

Dear Colleagues,

Apologies if you receive this more than once.

The MGED 11 abstract submission deadline for consideration for an oral
presentation is next Tuesday, June 10th.

Further information on MGED 11 is available at http://www.mgedmeeting.org/
and other key dates are:

Notice of acceptance: June 25th
Early registration ends: June 30th
All abstract submission closes: August 5th

The scientific focus of the meeting will be high throughput
technologies - in particular microarrays and ultra high throughput
sequencing - and associated data handling issues, analysis techniques
and standards. We have lined up some outstanding speakers who will be
giving talks on these topics.

This year we will again be selecting half of the plenary speakers from
submitted abstracts, to encourage greater participation in the MGED
community. Continuing from last year, we will also be running a
poster competition, with prizes for the best posters presented by
graduate and postdoctoral students. Finally, we will be awarding up
to seven $1500 travel grants to graduate or postdoctoral students who
are US citizens traveling from the US.

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

----------------------------------------------------------------------------------
MGED 11 Program

Sunday 31st Aug.

15:00 - Registration and Exhibit Area are open

Monday 1st Sept.

07:30- Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert Catherine Ball, Cesare Furlanello

ENCODE Session
09:00-10:00 Keynote Lecture: Ewan Birney
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:30 Talks from Submitted abstracts (1)

12:30-14:00 Lunch

Wine Genomics Session
14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:30 Talks from Submitted abstracts (2)
15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer

18:00-20:00 Welcome cocktail
21.00 Public Science Conference I

Tuesday 2nd Sept.

Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:30 Talks from Submitted abstracts (3)

12:30-14:00 Lunch

Quality and Standards in Action
14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone
14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan
Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I

19:00-21:00 Conference Dinner

Wednesday 3rd Sept.

Learning from Microarray Data
09:00-10:00 Keynote Lecture: Naama Barkai
09:45-10:30 Plenary Talk: Rainer Spang
10:30-11:00 Break
11:00-11:45 Plenary Talk: Atul Butte
11:45-12:30 Talks from Submitted Abstracts (3)

12:30-14:00 Lunch

Functional Genomics and Systems Biology
14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:30 Break
15:30-16:15 Talks from Submitted Abstracts (3)
16:15-17:00 Plenary Lecture TBA
17:00-19:00 Poster Session II
Close of Meeting, Final Announcements, Award of Poster Prizes

20.15 Public Science Conference 2

Thursday 4th Sept.

Workshops
8:30 - 11:30 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment: Audrey
Kauffmann and Wolfgang Huber
11:30 - 14:30 Gene Pattern tutorial: Ted Liefeld
14:30 - 17:30 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods: Marc Salit
and Wolfgang Huber

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

CAMDA'08 Challenge -- Contest data set release, Call for Papers, and Conference Announcement

2008-05-29T17:19:44Z

CAMDA'08, Vienna, Austria, 4-6 December 2008 --
http://camda.bioinfo.cipf.es/

Dear colleague!

We cordially invite you to attend this year's conference on

Critical Assessment of Microarray Data Analysis (CAMDA) .

CAMDA was founded to provide a forum for the critical assessment of
the many different techniques
used in microarray data mining (Nature 411, 885, Nature 424, 610). It
aims to establish the state of the
art in microarray data analysis, as well as highlight progress and
identify directions of future efforts.
In order to achieve these goals, CAMDA adopted the approach of a
community-wide experiment,
letting the scientific community analyse the same contest data sets.
Researchers worldwide are invited to take the CAMDA challenge.
Accepted submissions will be asked
to give an oral presentation. Results of analysis are discussed and
compared at the CAMDA conference.
As a special opportunity, this year, a selection of analysis
predictions will also be verified experimentally
by the laboratory collecting the original contest data set. CAMDA
provides a unique environment for
testing and demonstrating your latest analysis methods.

CAMDA, which began in 2000, was initiated by Simon Lin and Kimberly
Johnson from the Duke University
Bioinformatics Shared Resource (www.camda.duke.edu). CAMDA has since
become an internationally
roving conference, with the first such meeting held 2007 at CIPF in
Valencia, Spain.
This year, CAMDA is hosted by Boku University Vienna in Austria.

Your participation is critical for making this year's CAMDA meeting
again a great event.

Please do distribute this announcement to other colleagues who might
be interested.

We look forward to seeing you in Vienna!

David Kreil &
Joaquin Dopazo

(chairs)

CAMDA'08 Conference, Vienna, Austria, 4-6 December 2008

Conference home http://camda.bioinfo.cipf.es/
Contest data set at http://camda.bioinfo.cipf.es/contest_dataset

Important Dates:
2008-06-01 Public release of Contest Data Set
2008-09-28 Extended Abstract Proposals due
2008-11-01 Acceptance notification for session speakers
2008-11-01 Acceptance notification for poster presenters
2008-11-03 Early registration closes
2008-12-04 Conference opens (later p.m.)
2008-12-06 Conference closes
2009-01-31 Full paper submission

(--- for technical reasons, you may receive this announcement more
than once ---)

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

Registration and Abstract Submission now open for MGED 11 Meeting, Trentino, Italy

2008-05-09T16:06:22Z

Dear Colleagues,

Apologies if you receive this more than once.

It is the pleasure of the Microarray Gene Expression and Data (MGED)
society to announce that registration and abstract submission is now
open for the MGED11 meeting in Trentino, Italy, Monday September 1st -
> Wednesday September 3rd, 2008. In addition, there will be a day of
optional tutorials and workshops following the meeting on September 4th.

Further information is available at http://www.mgedmeeting.org/ and
key dates are:

Deadline for Abstract submission for consideration as an oral
presentation : June 10th
Notice of acceptance: June 25th
Early registration ends: June 30th
Abstract submission closes: August 5th

The scientific focus of the meeting will be high throughput
technologies - in particular microarrays and ultra high throughput
sequencing - and associated data handling issues and analysis
techniques. We have lined up some outstanding speakers who will be
giving talks on these topics.

This year we will again be selecting half of the plenary speakers from
submitted abstracts, to encourage greater participation in the MGED
community. Continuing from last year, we will again be running a
poster competition, with prizes for the best posters presented by
graduate and postdoctoral students. Finally, we will be awarding up
to seven $1500 travel grants to graduate or postdoctoral students who
are US citizens traveling from the US.

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

----------------------------------------------------------------------------------
MGED 11 Program

Sunday 31st Aug.

15:00 - Registration and Exhibit Area are open

Monday 1st Sept.

07:30- Registration opens
08:30- 09:00 Welcome, Introduction and organization details: Chris
Stoeckert Catherine Ball, Cesare Furlanello

ENCODE Session
09:00-10:00 Keynote Lecture: Ewan Birney
10:00-10:45 Plenary Lecture: Barbara Wold
10:45-11:15 Break
11:15-12:00 Plenary Lecture: Shirley Liu
12:00-12:30 Talks from Submitted abstracts (1)

12:30-14:00 Lunch

Wine Genomics Session
14:00-14:45 Plenary Talk: Claudio Moser
14:45-15:30 Talks from Submitted abstracts (2)
15:30-16:00 Break
16:00-16:45 Plenary Talk: Duccio Cavalieri
16:45-17:45 Keynote Talk: Grant Cramer

18:00-20:00 Welcome cocktail
21.00 Public Science Conference I

Tuesday 2nd Sept.

Human Disease Session
09:00-10:00 Keynote Lecture: Joe Gray
10:00-10:45 Plenary Lecture: Mike Bittner
10:45-11:00 Break
11:00-11:45 Plenary Lecture: Nigel Carter
11:45-12:30 Talks from Submitted abstracts (3)

12:30-14:00 Lunch

Quality and Standards in Action
14:00-14:15 Introduction and update on MGED Standards: Chris Stoeckert
14:15-14:30 MAGE-TAB Tools: Helen Parkinson/Tim Rayner
14:30-14:45 ISA-TAB and integrative standards: Susanna-Assunta Sansone
14:45-15:30 Title TBA (Semantic Web and Gene Expression): Alan
Ruttenberg
15:30-16:00 Break
16:00-18:00 Poster Session I

19:00-21:00 Conference Dinner

Wednesday 3rd Sept.

Learning from Microarray Data
09:00-10:00 Keynote Lecture: Naama Barkai
09:45-10:30 Plenary Talk: Rainer Spang
10:30-11:00 Break
11:00-11:45 Plenary Talk: Atul Butte
11:45-12:30 Talks from Submitted Abstracts (3)

12:30-14:00 Lunch

Functional Genomics and Systems Biology
14:00-15:00 Keynote Lecture : Stephen Oliver
15:00-15:30 Break
15:30-16:15 Talks from Submitted Abstracts (3)
16:15-17:00 Plenary Lecture TBA
17:00-19:00 Poster Session II
Close of Meeting, Final Announcements, Award of Poster Prizes

20.15 Public Science Conference 2

Thursday 4th Sept.

Workshops
8:30 - 11:30 Morning Parallel Sessions
• Data Analysis Tutorial: John Quackenbush and Roger Bumgarner
• Tutorial on using Bioconductor for Array Quality Assessment: Audrey
Kauffmann and Wolfgang Huber
11:30 - 14:30 Gene Pattern tutorial: Ted Liefeld
14:30 - 17:30 Afternoon Parallel Sessions
• Using ArrayExpress Tutorial: Gabriella Rustici andMisha Kapushesky
• EMERALD Workshop on Array Quality Assessment Methods: Marc Salit
and Wolfgang Huber

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

The Reference in qPCR - Academic & Industrial Information Platform

2008-01-20T23:30:51Z

The Reference in qPCR - Academic & Industrial Information Platform

Dear researcher,
dear Gene Quantification page reader,

The Gene Quantification page - www.Gene-Quantification.info -
describes and summarises all technical aspects involved in
quantitative gene expression analysis using real-time qPCR & qRT-PCR.
It presents a lot of applications, chemistries, methods, algorithms,
cyclers, kits, dyes, analysis methods, meetings, workshops, and
services involved. Commercial and academic institutions can present
their qPCR tools right here

=> http://qpcrplatform.gene-quantification.info/

--------------------------------------------------------------------------------

The quantification strategy in real-time RT-PCR is the principal
marker in gene quantification. Generally two strategies can be
performed in real-time RT-PCR. The levels of expressed genes may be
measured by absolute quantification or relative quantitative real-time
RT-PCR.
Absolute quantification relates the PCR signal to input copy number
using a calibration curve, while relative quantification measures the
relative change in mRNA expression levels. The reliability of an
absolute real-time RT-PCR assay depends on the condition of
'identical' amplification efficiencies for both the native target and
the calibration curve in RT reaction and in following kinetic PCR.
Relative quantification is easier to perform than absolute
quantification because a calibration curve is not necessary. It is
based on the expression levels of a target gene versus a housekeeping
gene (reference or control gene) and in theory is adequate for most
purposes to investigate physiological changes in gene expression
levels. The units used to express relative quantities are irrelevant,
and the relative quantities can be compared across multiple real-time
RT-PCR experiments.

=> http://strategy.gene-quantification.info/

--------------------------------------------------------------------------------

With this page and all the presented tools we will help you with to
find the right information about qPCR and related topics in Molecular
Biology in the literature and in the World Wide Web:
New Papers / Protocols / Methods / Databases / Alets / Feeds / Books /
Forums / E-mail / Directory

=> http://infoportal.gene-quantification.info/

--------------------------------------------------------------------------------

Our newsletter informs about the latest news in quantitative real-time
PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene
Quantification homepage. The focus of the December newsletter issue
was:

=> Copy Number Variation
=> new webinars online
=> new application workshops in 2008
...........

http://qpcrnews.gene-quantification.info/

--------------------------------------------------------------------------------

The gene copy number (also "copy number variants" or CNVs) is the
number of copies of a particular gene in the genotype of an
individual. Recent evidence shows that the gene copy number can be
elevated in cancer cells.

=> Why are CNVs important?

Differences in the DNA sequence of our genomes contribute to our
uniqueness. These changes influence most traits including
susceptibility to disease. It was thought that single nucleotide
changes (called SNPs) in DNA were the most prevalent and important
form of genetic variation. The current studies reveal that CNVs
comprise at least three times the total nucleotide content of SNPs.
Since CNVs often encompass genes, they may have important roles both
in human disease and drug response. Understanding the mechanisms of
CNV formation may also help us better understand human genome
evolution.

http://cnv.gene-quantification.info/

--------------------------------------------------------------------------------

Data Analysis and BioInformatics in real-time qPCR

Bioinformatics is a multidisciplinary approach to discribe, model and
understand biological processes on basis of information on genes,
proteins and metabolism. It uses computers, data bases and algorythms
to link information and translate it back into biology, physiology or
pathophysiology.

BioInformatics => Database Management Systems, Data Mining, Sample
Tracking, Information Management, Data Acquisition, Data Analysis,
Statistics, Pattern Recognition & Classification, Simulation &
Modeling

Bioinformatics initially centered on sequence and genome analysis but
now the extensive use of microarrays, mass spectrometry, qPCR and qRT-
PCR, has stimulated bioinformatic work in data acquisition, signal
processing, and data mining. Also, simulation and modeling are
becoming increasingly important areas of focus in bioinformatics which
finally will lead to a new level of understanding the networks in the
metabolism: Genomics, Transcriptomics, Splicomics, Proteomics,
Metabolomics, etc.

http://bioinformatics.gene-quantification.info/

--------------------------------------------------------------------------------

TATAA Biocenter Germany - qPCR Application workshops

At the TATAA Biocenter Germany we offer qPCR application workshops, a
3-day qPCR Core Module and a 2-day qPCR Biostatistics Module. All
courses are held regularly in Göteborg, Sweden, in English and in
Freising-Weihenstephan, Germany, in German and English, and in Prague,
Czech Republic in English and Czech.
http://tataa.gene-quantification.info/

Course Occasions 2007 and 2008:
3-day qPCR Core Module (Mon. - Wed.) and 2-day BioStatistics
Module (Thu. - Fri.)

=> 3rd - 7th March 2008 (in Freising, Germany, English language)
=> 5 - 9th May 2008 (in Freising, Germany, Kurs wird in DEUTSCH
gehalten, German language)
=> 7 - 11th July 2008 (in Freising, Germany, English language)

=> Please register here => http://www.tataa.com/Courses/Courses.html

--------------------------------------------------------------------------------

Forward Please send the mail to further scientists and friends who are
interested in qPCR !

Best regards,

Michael W. Pfaffl
responsible Editor of the Gene Quantification Pages
http://www.Gene-Quantification.info

The qPCR NEWS and the Gene Quantification Pages are educational sites
with the only purpose of facilitating access to qPCR related
information on the internet. The qPCR NEWS and the Gene
Quantification Pages are edited by Michael W. Pfaffl and powered by
BioScience Events. Copyright (c) 2005 - 2008 All rights reserved. Any
unauthorized use, reproduction, or transfer of this message or its
contents, in any medium, is strictly prohibited. Disclaimer &
Copyrights are displayed on the homepage www.gene-quantification.com
To subscribe or change your e-mail address in qPCR NEWS, and if you
would like to receive future issues FREE of charge, please send an e-
mail with the subject SUBSCRIBE to mailto:newsletter@gene-
quantification.info?subject=SUBSCRIBE

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

SECOND ANNOUNCEMENT: IV International Course on Microarray Data Analysis

2008-01-17T06:51:55Z

Dear Colleague,

We are pleased to announce the IV International Course on Microarray
Data Analysis to be held at the CIPF (Valencia) in March 2008.

The course provides theoretical and practical lectures on the use of
user-friendly web tools for the analysis and interpretation of
microarray experiments.
See below for detailed information.

Please forward this message to other colleagues who might be interested.
Our apologies is this mail reaches you several times.

Best regards,

Joaquin Dopazo, Fatima Al-Shahrour, David Montaner and Ana Conesa

Department of Bioinformatics and Functional Genomics Node (INB)

Centro de Investigación Príncipe Felipe (CIPF)

46013, Valencia, Spain

http://bioinfo.cipf.es

http://www.gepas.org

http://www.babelomics.org

http://www.blast2go.org

*******************************************************************************

IV International Course on Microarray Data Analysis

Centro de Investigaciones Príncipe Felipe

Valencia, Spain. 10th- 14th March, 2008

http://bioinfo.cipf.es/docus/courses/coursesCIPF/MDA2008.html

********************************************************************************

DNA microarrays constitute, no doubt, a paradigm among post-genomic
technologies, which are characterised for producing large amounts of
data, whose analysis and interpretation is not trivial. Microarray
technologies allows querying living systems in a completely new way, but
at the same time present new challenges in the way hypotheses must be
tested and our results ought to be analysed.

Since the first papers published in the latest nineties the number of
questions that have been addressed through this technique have both
increased and diversified. Initial interest was focused on genes
co-expressing across sets of experimental conditions, implying
essentially the use of clustering techniques. More recently, however,
the interest has switched to find genes differentially expressed among
distinct classes of experiments, or correlated to diverse parameters.
There is also much interest in robust methods for building predictors of
clinical outcomes. Also, CGH-arrays (Albertson and Pinkel, 2003) are
recently becoming an alternative for studying the relationship between
chromosomal alterations affecting to copy number (which are behind many
diseases) and gene expression. In addition, there is also a clear demand
for methods that allow automatic transfer of biological information to
the results of microarray experiments and to interpret them at the light
of the biological knowledge. Recently, new methods of analysis have been
proposed that directly address hypothesis on modules of genes
functionally related that have demonstrated to be superior to the
classical one-gene-at-a-time approaches (Mootha et al., 2003;
Al-Shahrour et al., 2005, 2007)

This course covers the state-of-the-art in the above mentioned topics,
which are of major relevance in today’s gene expression data analysis.
Through sessions of theory and practical examples, the students will
acquire the experience necessary to address scientific questions to gene
expression array datasets and solve them. Special attention will be
devoted to important (although not always took into account) aspects in
microarray data analysis, such as multiple testing or functional
profiling. In addition, some theoretical lessons on basic statistics
will be included as part of the programme. Finally, for the bravest and
those who want to go in more depth into analysis possibilities, the last
day a short course on Bioconductor (Gentleman et al., 2004) will be taught.

The course is designed to be a mixture of theoretical and practical
sessions. The latter will require some familiarity with the use of
web-based tools and knowledge of basics notions of statistics.

Practical sessions will be carried out using the GEPAS (Herrero et al.,
2003, 2004, Vaquerizas et al., 2005; Montaner et al., 2006) environment,
an integrated web tool for microarray data analysis, and the Babelomics
suite (Al-Shahrour et al., 2005b, 2006, 2007) for functional profiling
of genome-scale experiments. and the Blast2GO suite (Conesa et al.,
2005), a set of tools for the high-throughput functional annotation and
analysis of uncharacterized sequences.

The course will be held the week before fallas, one of the most popular
and impressing folkloric festivals in Spain which ends the 19th March
when all the fallas are burnt in an apotheosis of fireworks. So you can
use this opportunity to enjoy one of the most exceptional holiday
festival in the world. See more in:
http://www.fallas.com/contenido.asp?seccion=museo&tema=historia&bandera=en

See information on the Bioinformatics Department courses in:
http://bioinfo.cipf.es/docus/courses/courses.html

*Programme*

*Day 1 *

--------

9.30 – 11.30. Introduction

Structure of the course. Why microarrays? Pre- and post-genomics
hypothesis testing: a note of caution. Design of experiments. Data
preprocessing and normalization. Unsupervised analysis (clustering).
Supervised analysis (gene selection, predictors). Functional profiling.

12.00–13.30. Normalization (theory and practical exercises)

Getting rid of unwanted variability from sources other than the
experimental conditions assayed. Methods for Affymetrix, two-colour and
one-colour microarrays

13.30-14.30 Lunch

14.30-16.00 Gene selection (theory)

Methods for selecting genes differentially expressed among two or more
experimental conditions, correlated to a continuous variable or
correlated to survival. How to deal with the multiple-testing problem.

16.30-18.00 Gene selection (practical exercises)

*Day 2*

-------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-13.30 Predictors (theory and practical exercises)

Gene selection in the context of class prediction. How to deal with the
selection bias problem. Different methods for class prediction.
Estimating the error of classification. Interpretation of confusion
matrices.

13.30-14.30 Lunch

14.30-16.00 Clustering (theory)

Different clustering methods: hierarchical clustering, SOM, SOTA and
k-means. Pros and cons. Measures of cluster quality. Cluster visualisation.

16.30-18.00 Clustering (practical exercises)

*Day 3*

--------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-13.30 Functional profiling of experiments

Understanding the biological roles played by the genes in the
experiments. Using different types of information for the functional
profiling of microarray experiments: gene ontology, InterPro motifs,
transcription factor binding sites, gene expression in other
experiments, text-mining, etc. New trends in the analysis of microarray
data: testing pathway-based or function-based hypothesis.

13.30-14.30 Lunch

10.30-12.30 Functional profiling. The Babelomics suite

Different methods for functional profiling of experiments from the
Babelomics suite: FatiGO/FatiGO+, Marmite (using text-mining) or TMT
(pre-tabulated gene expression results). Methods for finding blocs of
functionally-related genes differentially expressed (GSEA, FatiScan).

*Day 4*

--------

9.30-10.30 Basic statistical methods

Some theory on basic statistical methods.

11.00-12.00 Array-CGH

Estimation of copy number in chromosomal aberrations. Joint study of
copy number, gene expression and functional profiling.

12.00-13.30 Introduction to the programmable GEPAS interface

Using the visual programming interface of GEPAS to build up pipelines of
analysis.

13.30-14.30 Lunch

14.30-17.30 Exercises

Do a complete practical exercise using the tools you learned.

17.30-18.00 Concluding remarks and final questions

*Day 5*

--------

9.30-13.30 A primer on automatic annotation of unknown sequences.

13.30-14.30 Lunch

14.30-18.00 Blast2GO

-------------------------------------------------------------------------------------------------------------------------------

*/References/*

· Albertson, D.G. and Pinkel, D. Genomic microarrays in human genetic
disease and cancer. Hum Mol Genet, 2003 12 Spec No 2, R145-52

· Al-Shahrour, F., Diaz-Uriarte, R. & Dopazo, J. Discovering molecular
functions significantly related to phenotypes by combining gene
expression data and biological information. Bioinformatics. 2005;21:
2988-2993

· Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J:
BABELOMICS: a suite of web tools for functional annotation and analysis
of groups of genes in high-throughput experiments. Nucleic Acids Res
2005b, 33:W460-464

· Al-Shahrour F., Minguez P., Tárraga J., Montaner D., Alloza E.,
Vaquerizas J.M., Conde L., Blaschke C., Vera J. and Dopazo J.
BABELOMICS: a systems biology perspective in the functional annotation
of genome-scale experiments Nucl Acids Res., 2006, 34: W472-W476

· Al-Shahrour F, Arbiza L, Dopazo H, Huerta J, Minguez P, Montaner D,
Dopazo J. From genes to functional classes in the study of biological
systems. 2007 BMC Bioinformatics 8:114

· Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M.
Blast2GO: a universal tool for annotation, visualization and analysis in
functional genomics research. 2005 Bioinformatics, 21(18), 3674-3676.

· Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M.,
Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al.
Bioconductor: open software development for computational biology and
bioinformatics. Genome Biol, 2004, 5, R80

· Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM,
Santoyo J, Dopazo J: GEPAS: A web-based resource for microarray gene
expression data analysis. Nucleic Acids Res 2003, 31:3461-3467.

· Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A,
Diaz-Uriarte JS, Dopazo J: New challenges in gene expression data
analysis and the extended GEPAS. Nucleic Acids Res 2004, 32:W485-491

· Montaner D., Tárraga J., Huerta-Cepas J., Burguet J., Vaquerizas J.M.,
Conde L., Minguez P., Vera J., Mukherjee S., Valls J., Pujana M., Alloza
E., Herrero J., Al-Shahrour F., Dopazo J. Next station in microarray
data analysis: GEPAS Nucl Acids Res., 2006, 34: W486-W491

· Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J,
Puigserver P, Carlsson E, Ridderstrale M, Laurila E et al:
PGC-1alpha-responsive genes involved in oxidative phosphorylation are
coordinately downregulated in human diabetes. Nat Genet 2003, 34(3):267-273.

· Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P,
Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J: GEPAS, an
experiment-oriented pipeline for the analysis of microarray gene
expression data. Nucleic Acids Res 2005, 33:W616-620

--
------------------------------------------
Ana Conesa, PhD
Bioinformatics Department
Centro de Investigación Príncipe Felipe
Avda. Autopista Saler, 16
46013 Valencia Spain
http://bioinfo.cipf.es/aconesa
==========================================

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

First Announcement for MGED 11 Meeting, Trentino, Italy

2007-12-06T18:26:04Z

Dear Colleagues,

Apologies if you receive this more than once.

It is the pleasure of the Microarray Gene Expression and Data (MGED)
society to announce the MGED11 meeting in Trentino, Italy, Monday
September 1st -> Wednesday September 3rd, 2008. In addition, there
will be two days of optional tutorials and workshops following the
meeting on September 4th and 5th.

Further information is available at http://mgedmeeting.org/ and key
dates are:

Registration and Abstract Submission Opens: March 1st
Deadline for Abstract submission for consideration as an oral
presentation : June 10th
Notice of acceptance: June 25th
Early registration ends: June 30th
Abstract submission closes: August 5th

The scientific focus of the meeting will be high throughput
technologies - in particular microarrays and ultra high throughput
sequencing - and associated data handling issues and analysis
techniques. With the continued maturation of microarray annotation
standards and tools, this year's meeting will offer more 'hands-on'
tutorials and workshops to tackle specific practical applications of
these concepts. Tutorials are expected to cover in depth data
analysis and how to use Bioconductor.

We have already lined up the following outstanding international
keynote speakers:

Naama Barkai - Weizmann Institute of Science
Ewan Birney - EMBL-EBI
Joe Gray - UCSF/ Lawrence Berkeley Nat'l Laboratory
Steve Oliver - Cambridge University

and will announce invited plenary speakers in the near future. In
addition, this year we will again be selecting half of the plenary
speakers from submitted abstracts, to encourage greater participation
in the MGED community. Continuing from last year, we will again be
running a poster competition, with prizes for the best posters
presented by graduate and postdoctoral students.

We look forward to seeing you all in Trentino,

Sincerely,

The Microarray and Gene Expression Data (MGED) Society

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays

CAMDA07 Conference at Valencia. Agenda is now available

2007-11-26T04:15:22Z

=============================================================
CAMDA07 --- December 13 - 14, 2007 ---- CIPF, Valencia, Spain
PreConference Seminar December 12
=============================================================

Dear colleague,

We kindly remind your our invitation to the new edition of CAMDA
CAMDA07 agenda is now available at:

http://camda.bioinfo.cipf.es

YOU CAN STILL REGISTER till 7th December 2007.
Your participation would be of utmost importance in order to make CAMDA
2007 a great event.

Joaquin Dopazo
And the CAMDA07 local organizing committee
Fatima Al-Shahrour, Ana Conesa and David Montaner

===================
CAMDA07 HIGHLIGHTS
===================

PRECONFERENCE SEMINAR
=====================

Dr. Benjamin Blencowe
Professor, Banting and Best Department of Medical Research
Department of Molecular and Medical Genetics
University of Toronto, Canada
"Global insights from microarray profiling of mammalian alternative
splicing""

KEYNOTE SPEAKERS
================

Dr. Sandrine Dudoit
Associate Professor of Biostatistics and Statistics
Chair, Graduate Group in Biostatistics
University of California, Berkley, USA
"Statistical challenges in microarray data analysis: past, present and future"

Dr. Wei Pan
Professor, Division of Biostatistics
School of Public Health
University of Minnesota, USA
"Incorporating biological knowledge of genes into statistical analysis of genomic data"

Dr. John Quackenbush
Professor of Computational Biology and Bioinformatics
Department of Biostatistics
Dana-Farber Cancer Institute, USA
"Stochasticity and Networks in Genomic Data"

_______________________________________________
Arrays mailing list
Arrays@...
http://www.bio.net/biomail/listinfo/arrays