March 05, 2008

Chemical Blog Aggregator ... and More!

A comment on an earlier post brought to my attention this really interesting aggregator for the Chemical Blogspace, appropriately named "Chemical Blogspace".

Chemical Blogspace: http://cb.openmolecules.net/

"Chemical blogspace collects data from tens of scientific chemistry blogs and then does useful and interesting things with it.
With Chemical blogspace, you can:
* Find, read and subscribe to new science blogs
* Find out what scientists are saying about the latest books and papers
* Read mini-reviews, conference reports or even original research
* See the buzz surrounding different websites
* Browse different subject areas - chemoinformatics, organic chemistry, ... see the 'Explore' options on the top right hand side of the page for more. "

It is the "interesting things" part of this that intrigues me. It includes molecular models, and allows you to browse the blog posts by chemical structure. Not being a chemist, I clicked on a shape that looked interesting to me. It turned out to be hydrocodone, more popularly known as Vicodan.

Chemical blogspace - Molecules: hydrocodone: http://cb.openmolecules.net/inchi.php?id=282

This pulled up two interesting posts that would normally not have been juxtaposed - one about an celebrity overdose death and the other about Chinese traditional herbal remedies. Wow! Now, tell me how else you find that there was a relationships between those dissimilar postings? Very interesting, and I could see this being a real timewaster for someone really into chemistry, biochemistry, and/or pharmacy.

Posted by pfa at 05:13 PM | Comments (1)

July 16, 2007

PostGenomic Science Blog Aggregator

For those who enjoyed our podcast on science blogs, here is a newly discovered resource to help make it easier to follow the science blogosphere -- PostGenomic.

PostGenomic is an aggregator -- a source that compiles or aggregates information from a variety of sources. In this case, PostGenomic collects information from a variety of science blogs, and repackages in a way to make them more useful. It has several very nice features, including (my favorite) the option to track your favorite blog postings and see who is talking about them. It collects science blogs across domains, so is broad in scope, but I have yet to visit their main page without finding something of interest. A marvelous resource!

PostGenomic: http://www.postgenomic.com/

Staying Current with Science Blogs & Wikis: Slides ; Podcast (zipped)

Posted by pfa at 01:16 PM | Comments (2)

May 16, 2007

New Nanotech EBook (WOWIO)

Thanks to Deena (SoD) for mentioning WOWIO, a source of free e-books on a variety of topics. WOWIO offers many books as PDFs, which work on a variety of devices from computers to PDAs. Many of the books included in WOWIO come from major publishers, with Oxford University Press as one major contributor. WOWIO makes copyrighted books available for download with registration, but free of charge, both through partnerships and as a publisher in their own right.

One title they are currently highlighting is from Eric Drexler, who might be familiar as the co-author (with Marvin Minsky) of Engines of Creation, in addition to Nanosystems and Unbounding the Future: The Nanotechnology Revolution. WOWIO has published a 20th anniversary edition of Engines of Creation with new material included.

K. Eric Drexler: http://e-drexler.com/

WOWIO: http://www.wowio.com/

Drexler, K. Eric. Engines of Creation 2.0: The Coming Era of Nanotechnology - Updated and Expanded. WOWIO Books; ISBN: DREX-00001. 646 pages (February 2007). http://www.wowio.com/users/product.asp?bookid=503

Posted by pfa at 08:33 AM | Comments (2)

May 02, 2007

Dental Nanotech in the News

Being highlighted in news reports, a new article from JDR on the use of nanocomposites in dental fillings to improve caries protection and durability.

Scientist Live: Nanocomposites Improve Dental Fillings:
http://www.scientistlive.com/17596/nanocomposites-improve-dental-fillings.thtml

"American researchers show that nanotechnology can help produce tooth restorations that are both stronger than any fillings available today, and more effective at preventing secondary decay."

H.H.K. Xu, M.D. Weir, L. Sun, S. Takagi and L.C. Chow. Effects of calcium phosphate nanoparticles on Ca-PO4 composite, The Journal of Dental Research 86(4):378-383m 2007.
http://jdr.iadrjournals.org/cgi/content/abstract/86/4/378

NOTE: If you have trouble getting into the article from off-campus, please first login to a Library service such as Mirlyn.

Posted by pfa at 12:11 PM | Comments (0)

January 08, 2007

dbGaP (database of Genotype and Phenotype)

NLM and the National Center for Biotechnology Information announce the introduction of the Database of Genotype and Phenotype (dbGaP), a new database designed to archive and distribute data from genome wide association (GWA) studies. GWA studies explore the association between specific genes (genotype information) and observable traits, such as blood pressure and weight, or the presence or absence of a disease or condition (phenotype information). See the press release for more information.

dbGaP (database of Genotype and Phenotype): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gap

Posted by pfa at 10:15 AM | Comments (0)

September 06, 2006

Staying Current: Omics Podcasts, Videocasts, Webcasts Etc (Omics Series, 24)

Another way to keep up to date with new happenings in research is to take advantage of podcasts and related offerings in your research area. Many conferences are now videotapes and made available on the web. Science news programs often feature interviews with leading researchers. Our library guide to podcasting resources describes ways to discover podcasts on a topic and some of the podcasting and vodcast (video-cast) search engines. We won't repeat that here. Instead, please find below selected examples of the types of online audio and video resources available in the omics research areas, as well as some of the better science news and radio programs that include a podcast or vodcast version of the show. (Hint: My favorite so far is Science & the City).

* GENOMICS & PROTEOMICS

Genetic Engineering News - Biotechnology from Bench to Business: http://www.genengnews.com/genCasts.aspx

Genome.gov: 2006 DNA Day Webcast and Podcast: Genomics: Towards a Healthier You: http://www.genome.gov/19016617

NIH: Functional Genomics of Critical Illness and Injury (2003): http://www.strategicresults.com/fg3/

NIH: VideoCasting: Current Topics in Genome Analysis: http://videocast.nih.gov/pastevents.asp?c=7

NIH: VideoCasting: Human Genome: http://videocast.nih.gov/pastevents.asp?c=35

NIH: VideoCasting: National Human Genome Research Institute (NHGRI): http://videocast.nih.gov/pastevents.asp?c=33

NIH: VideoCasting: Proteomics: http://videocast.nih.gov/pastevents.asp?c=36

Genomics & Proteomics Magazine: http://www.genpromag.com/
EXAMPLE:
Effective strategies for Whole Genomic Amplification of Single-Cell DNA: http://www.genpromag.com/WGADNA/

Howard Hughes Medical institute: Biointeractive: Lectures on Science Webcasts: http://www.hhmi.org/biointeractive/lectures/

Howard Hughes Medical Institute: Biointeractive: Scanning Life's Matrix, genes, proteins, and small molecules (Genomics and Chemical Genetics series): http://www.hhmi.org/biointeractive/genomics/lectures.html
Lecture 1: Reading Genes and Genomes by Eric S. Lander, Ph.D.: http://www.hhmi.org/lectures/webcast/ondemand/02webcast1/index.html
Lecture 2: Probing Genes and Genomes by Stuart L. Schreiber, Ph.D.: http://www.hhmi.org/lectures/webcast/ondemand/02webcast2/index.html
Lecture 3: Human Genetics: A New Guide for Medicine by Eric S. Lander, Ph.D.: http://www.hhmi.org/lectures/webcast/ondemand/02webcast3/index.html
Lecture 4: Chemical Genomics: New Tools for Medicine by Stuart L. Schreiber, Ph.D.: http://www.hhmi.org/lectures/webcast/ondemand/02webcast4/index.html

NHLBI: Cardiogenomics: Genomics and Genetic Epidemiology:General Principles and Application to Disease Studies: http://www.you-niversity.com/youtools/companies/viewArchives.asp?affiliateId=37


* NANOTECHNOLOGY

Institute of Nanotechnology: Webcast: Nanotechnology, Education and Training for the Future: http://www.unique-media.tv/nano_01/

Nanotech Seminar Series - Archive List: http://nano.cancer.gov/meetings_events/nanotech_seminar_series.asp

Nanotechnology Podcast Blog: http://www.nyls.blogs.com/nano/

NIH: VideoCasting: Nanotechnology: http://videocast.nih.gov/pastevents.asp?c=56

Podcast Directory: Nanotechnology: http://www.podcast.net/tag/nanotechnology


* SERIES

NIH VideoCasting: Past Events: http://videocast.nih.gov/pastevents.asp

Podfeed: Podcasts tagged with nanotechnology: http://podfeed.net/tags/nanotechnology

PodTech.net: Silicon Valley, Technology, & Media Podcast: http://www.podtech.net/

Science & the City (New York Academy of the Sciences): Podcasts: http://www.nyas.org/snc/podcasts.asp

ScienceFriday: Podcasts: http://www.sciencefriday.com/feed/

Scientific American Magazine: Podcasts: http://www.sciam.com/podcast/

TWIS (This Week In Science): http://www.twis.org/


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (podcast OR vodcast OR videocast OR webcast)

Yahoo search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (podcast OR vodcast OR videocast OR webcast)

Posted by pfa at 08:36 PM | Comments (0)

August 16, 2006

Staying Current: Omics Blogs & More (Omics Series, 23)

Assuming we already know that scientists prefer to get information from their peers, wouldn't it be great to be able to get it without even asking? Enter the blog.

Science blogs have become force to be reckoned with in the research information environment. Blogs may be from individuals (faculty, researchers, grad students) or from organizations (journals, corporations, newswires). The better science blogs define a topic they will focus on and rarely diverge from that. Many of the best blogs will also link to the other influential blogs on the same topic. These communities of bloggers are what has become known as the blogosphere.

In this blog entry, we highlight a few of the most influential or innovative blogs in several omics topics, following this with examples of sources and techniques for discovering additional blogs.

* GENOMICS

The BioTech Weblog: The -Omics Series, Part 1: Genomics: http://www.biotech-weblog.com/50226711/the_omics_series_part_1_genomics.php

DNA direct talk: Your DNA, Your Health, Your Choices: http://talk.dnadirect.com/

Genetics and Health (Hsien Hsien Lei, Ph.D.): http://www.geneticsandhealth.com/

MedBioWorld: Post-Genomics, Forging a Connection Between Research and Clinical Applications: http://www.medbioworld.com/postgenomics_blog/

Mendel's Garden: http://mendels-garden.blogspot.com/

The Personal Genome, Genomics as a medical tool and lifestyle choice: http://www.thepersonalgenome.com/

What's Next in Health: Category: Gene Research: http://www.whatsnextnetwork.com/health/index.php?cat=61


* PROTEOMICS

Comparative Proteomics: http://www.comparativeproteomics.org/

Genomics proteomics: http://genomics-proteomics.biotechnewstoday.com/

myProteome.com, The Proteomics IT Blog: http://www.myproteome.com/

Proteome Commons: http://www.proteomecommons.org/archive.jsp

Proteome Measures: http://proteomemeasures.blogspot.com/


* BIOINFORMATICS

Biological Computations: http://bifo.livejournal.com/

Biological Informatics: http://biologicalinformatics.blogspot.com/

Bionuz: Latest Bioinformatics News: http://bionuz.blogspot.com/

Flags and Lollipops - Bioinformatics & Genomics News and Views: http://www.ghastlyfop.com/blog

HubLog: http://hublog.hubmed.org/

Inforbiomatica: http://moseshohman.com/blog/

NodalPoint (A Bioinformatics Weblog): http://www.nodalpoint.org/

Notes from the Biomass: http://nftb.net/

Propellor Twist, RNA & Bioinformatics research and other interests: http://fjossinet.u-strasbg.fr/

What You're Doing is Rather Desperate: Bioinformatics: http://nsaunders.wordpress.com/tag/bioinformatics/


* NANOTECHNOLOGY

Advanced Nanotechnology (Brian Wang): http://advancednano.blogspot.com/

Foresight: Nanodot, the original nanotechnology weblog: http://www.foresight.org/nanodot/

nano | public, a weblog of nanotechnology and its impact on the public (Dietram A. Scheufele): http://nanopublic.blogspot.com/

Responsible Nanotechnology (World Care): http://crnano.typepad.com/crnblog


* OTHER RECOMMENDED SCIENCE & OMIC BLOGS

Aetiology: http://scienceblogs.com/aetiology/

The Biotech Weblog: http://www.biotech-weblog.com/

Discovering Biology in a Digital World: http://scienceblogs.com/digitalbio/

MedGadget, Internet Journal of Emerging Medical Technologies: http://www.medgadget.com/

The Omics World: http://harijay.wordpress.com/

The Scientific Activitist, Reporting from the Crossroads of Science and Politics: http://scienceblogs.com/scientificactivist/

Science Blogs: http://scienceblogs.com/

Institute for Ethics and Emerging Technologies: Ethical Technology Blog: http://ieet.org/index.php/IEET/IEETblog


* SEARCHING FOR BLOGS ON A TOPIC

Technorati Blog Finder: Genomics: http://www.technorati.com/blogs/genomics

Mendel's Garden #2: The Best of Genetics Blogging (By Hsien Hsien Lei, PhD): http://www.geneticsandhealth.com/2006/07/01/mendels-garden-2-the-best-of-genetics-blogging/#more-919

Genetics and Health: Archive for the 'Featured Genetics and Health Blogs' Category (By Hsien Hsien Lei, PhD): http://www.geneticsandhealth.com/category/genetics-blogging/featured-blogs/

Google: Blog Search: inblogtitle:"(omics OR genomics OR proteomics OR bioinformatics OR nanotechnology)"


* SEARCHING FOR BLOG ENTRIES ON A TOPIC

Feedster: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)

Google Blog Search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)

IceRocket: Blog Search Engine: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)

Technorati: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics)

More blog search engines:

Anderson, PF. "Tasks: Blogs, Blog Search & RSS Feeds." The Eight-fold Path to Right Searching: Tips, Tasks, & Tools. http://www-personal.umich.edu/~pfa/pro/8fold/taskblogs.html

Posted by pfa at 04:42 PM | Comments (0)

August 09, 2006

Omics Wikis & Community Tools (Omics Series, 22)

For many decades, research on scientific information use has shown that researchers prefer to ask their friends and colleagues and prior teachers for information they need above and beyond all other sources. The Internet has always supported communal editing of documents, and as new tools are developed to support community information sharing and communal editing, it is now making it even easier for communities (scientific or not) to share information, questions, and the process of discovery. A prime example of this is the question of human survival recently posed by Stephen Hawking to Yahoo Answers, which garnered over 25,000 responses from a diverse online community.


Links About Stephen Hawking's Question: http://del.icio.us/dentlib/hawking.stephen

In today's blog entry, we will explore some of the tools being used by scientists and researchers to share research resources (including citations) and create common information tools.


* FOLKSONOMY & COMMUNITY TOOLS

Folksonomy tools are the kind described above, allowing a community of people with shared interests to share resources, citations, and information they have found, and to comment on what they or others have discovered. Three of the most popular folksonomy tools for researchers include Connotea, CiteULike and Del.icio.us.

Connotea (Nature): http://www.connotea.org/

CiteULike: http://www.citeulike.org/

Del.icio.us: http://del.icio.us/

Each of these free resources allows individuals to create their own account and track or capture information they've found, keeping the links or information handy online. This means it is accessible from home, work, school, conferences, or other places, as long as you have an Internet connection and a web browser. Connotea and CiteULike are both intended primarily for capturing citations / articles. Del.icio.us is primarily used for capturing bookmarks / webpages. With Del.icio.us you can import and export bookmarks from any computer you use, allowing you to create a master set of bookmarks available on any computer you use.

With all of these systems, people usually add descriptive comments and/or "tags". Tags are subject terms that you choose to describe the item. You can then click on a tag and see every item that shares the same tag. Some individuals have become rather well-known for their collections of resources on a specific topic. Vannevar Bush would have called these people "trailblazers." Here are two exmples of persons respected for their omics collections.

Del.icio.us: RPiquepa: Nanotechnology: http://del.icio.us/rpiquepa/Nanotechnology

CiteULike: TimyU: Genomics: http://www.citeulike.org/user/timyu/tag/genomics

Another great way to explore collections without having to know who is collecting is simply to browse by tag. All three of today's tools use similar formats for the URLs for browsing by tag (a.k.a. subject heading). You can guess what might be a tag, and then see if anyone else is using it, and what they have discovered. Items are usually displayed with the most recently added items on top, and older items toward the far end of the list. You can use these examples of URLs for browse-by-tag, and edit the end of the web address for the term you want to use. Usually capitalization doesn't make a difference, but you may want to try a word both ways just to be sure.

CiteULike: Tag: Bioinformatics: http://www.citeulike.org/tag/bioinformatics

Connotea (Nature): Tag; Proteomics: http://www.connotea.org/tag/proteomics

Del.icio.us: Tag: Genomics: http://del.icio.us/tag/genomics


When browsing by tag, if you noticed a person who seems to be collecting a lot of items or resources that interest you, you may want to browse that person's collection. You can usually do this by either clicking on the person's name or account. If accounts are not listed, you can sometimes discover who it is that collected an item by clicking on a text link that says something like "saved by 10 other people".

In any case, the various folksonomy tools can become a tool of inestimable value in staying current and discovering new resources and articles in your area of interest.


* WIKIS

The folksonomy tools like CiteULike, Connotea, and Del.icio.us all allow you personal control over your collections and information. Another approach are wikis, which are true communal efforts. In a wiki, for example Wikipedia, a community collectively edit information resources on a topic of shared interest. For Wikipedia, the community is very large, potentially open to the world. Many other wikis are less open, and may be restricted to members of an association, or to a particular research lab or other administrative unit, or however else a community defines itself. Some wikis are viewable by the world, but can only be edited by the "insiders" for that community, while others restrict both viewing and editing. Here are some examples of wikis available to persons interested in omics.

Bio-Pedia, an openfree bioinformation encyclopedia: http://biocc.ngic.re.kr/Biopedia/Biowiki/index.php/Main_Page

BioWiki: http://biowiki.org/BioWikis

BiWiki: Bingen Bioinformatics Wiki: http://biwiki.fh-bingen.de/biwiki

Evolving Code Wiki: http://www.evolvingcode.net/index.php

Fred Hutchinson Computational Proteomics Laboratory (CPL) Proteomics Repository: https://proteomics.fhcrc.org/CPAS/Project/home/home.view

GUS: The Genomics Unified Schema: http://www.gusdb.org/wiki

Molecular Station: Molecular Biology Encyclopedia: Molecular Wiki: http://wiki.molecularstation.com/

nodalpoint [nodalpoint wiki] (bioinformatics): http://wiki.nodalpoint.org/

Omics Wiki: http://biocc.ngic.re.kr/Omics/Mediawiki/index.php/Main_Page

Open Bioinformatics Foundation (OBF): http://www.open-bio.org/wiki/Main_Page

Proteomics Wiki (subscription required) [German/English]: http://elbanet.ethz.ch/wikifarm/proteomics/

Wesleyan's Genomics Wiki Web: http://twiki.wesleyan.edu/cgi-bin/view/Genomics/WebHome

Wikiomics Bioinformatics Wiki: http://wikiomics.org

Wise-Nano Project: http://wise-nano.org/w/Main_Page

Posted by pfa at 10:59 AM | Comments (0)

August 07, 2006

Staying Current: Omics Press & News Sources (Omics Series, 21)

Staying current with new developments is partly a matter of keeping abreast of the research journals (as discussed in an earlier entry), but also see what is in the recent press, nationally and globally. You can do this by looking for news from major newswire services, from the web news portals, or by going to science or omics news portals. This entry is organized from specific to general, beginning with omics and nano news sources, followed by regional science news, general science news portals, and ideas for how to find omics news in generic news portals included in our "Want More?" section.


* OMICS NEWS PORTALS & SERVICES

Bioinfo Online: http://www.bioinfo-online.net/

GeneLetter: Genetics News: http://www.geneletter.com/index.epl

Genome News Network (GNN): http://www.genomenewsnetwork.org/

GenomicsProteomics: http://www.genomicsproteomics.com

Metabolomics: http://www.metabolomics.net

Nature Omics Gateway: http://www.nature.com/omics/

ProteinCrystallography: http://www.proteincrystallography.com

Proteomics NEWS @CPRMap - Clinical Proteomics Research Map: http://www.cprmap.com/proteomics-news/

RNAi.net: http://www.RNAi.net

ScienceGenomics.org (Science Functional Genomics): News: http://www.sciencemag.org/feature/plus/sfg/

Syndicated Bioinformatics News and Biotechnology News: http://news.biohealthmatics.com/


* NANOTECHNOLOGY NEWS PORTALS & SERVICES

Nanodot: Nanotechnology News and Discussion: http://www.foresight.org/nanodot/

NanoTechnology: http://www.NanoTechnology.net

Nanotechnology.com: http://www.nanotechnology.com/

Nanotechnology News - Current Month's News: http://www.nanotech-now.com/current-months-news.htm

Nanotechnology News Network: http://www.nanonewsnet.com/

Nature: Materials science and nanotechnology: http://www.nature.com/materials/

Scientific American: Nanotechnology: http://www.sciam.com/nanotech/

Small Times: News about MEMS, Nanotechnology and Microsystems: http://www.smalltimes.com/

Yahoo! News: Nanotechnology Full Coverage: http://news.yahoo.com/fc/Tech/Nanotechnology


* REGIONAL SCIENCE NEWS

EurActiv.com: Science: http://www.euractiv.com/en/science

European Commission: Research: Fundamental Genomics: Newsletters: http://ec.europa.eu/research/health/genomics/newsletter/newsletters_en.htm

European Commission: CORDIS Express, weekly briefing on European Research and Innovation from CORDIS (Community Research and Development Information Service): http://ec.europa.eu/research/cordis-express_en.cfm

National Science Foundation (NSF): News: http://nsf.gov/news/

CBC.ca: Health & Science News: http://www.cbc.ca/science/

SciDev.net, Science and Development Network: http://www.scidev.net/


* SCIENCE NEWS PORTALS

AAAS: Eurekalert: http://www.eurekalert.org/

BrightSurf: Today's Science News and Current Science Events: http://brightsurf.com/
INCLUDES:
- Bioinformatics News
- Genomics News
- Nanotechnology News
- Omics News
- Proteomics News
- Transgenic News

FirstScience.com: http://www.firstscience.com/

NewScientist: http://www.newscientist.com/

SciCentral: http://www.scicentral.com/

ScienceDaily: http://www.sciencedaily.com/

Science News and Genomics: A Global Resource: http://science.bio.org/

Science News Online: http://www.sciencenews.org/


* WANT MORE?

Remember, you can add words to these searches to focus on an area of interest.

Google News search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified")

Yahoo News search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified")

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics OR transgenic OR "genetically modified") (news OR "press release")

Rollyo: pfa: Science News Search: http://rollyo.com/pfa/science_news/

Rollyo: robert1066: Technology & Science News Search: http://www.rollyo.com/robert1066/technology_science_news/

Posted by pfa at 04:40 PM | Comments (0)

August 04, 2006

Staying Current: Omics Journals Online (Omics Series, 20)

The omics fields have become real leaders in the idea of open access. Researchers in these cutting edge fields have found that rapid ready access to the newest research benefits them all. There is a perhaps surprising number of journals providing high quality research either completely freely online or following various models. A publication model found in omics journals that is less common among other disciplines, in my personal experience, is that of having free access for 30 days, after which access is restricted to subscribers.

Today's blog entry includes a selection of omics journals available free online, followed by selections of electronic journals available to the University of Michigan community. Last but not least, we include a structured web search for those who would like to see some of the journals we did not include today.


* OPEN ACCCESS JOURNALS

AZojono - Journal of Nanotechnology Online: http://www.azonano.com/nanotechnology.asp

BioInform (bio1nf0rm): http://www.bioinform.com/issues/

Bioinformation: http://www.bioinformation.net/

Biomarker Insights: http://www.la-press.com/bmi.htm

BMC genomics: http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=32

Comparative and Functional Genomics: http://www.hindawi.com/GetJournal.aspx?journal=CFG

EURASIP Journal on Bioinformatics and Systems Biology: http://www.hindawi.com/journals/bsb/

Genetic Engineering News: http://www.genengnews.com/
This title has an Omics skills-building tutorial article in almost every issue of the journal.

GenomeBiology.com: http://genomebiology.com/ OR http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=7

Genome informatics online (Workshop on Genome Informatics): http://www.jsbi.org/journal.html

Genome research (Cold Spring Harbor Laboratory Press): http://www.genome.org/ ($$)

Genomics and Health Weekly Update (CDC: National Office of Public Health Genomics): http://www.cdc.gov/genomics/update/current.htm

Genomics & proteomics (G&P): http://www.genpromag.com/

Genomics, Society and Policy Online Journal:http://www.gspjournal.com/

Human Genome News (National Institutes of Health: National Center for Human Genome Research): http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/hgn.shtml

Internet Electronic Journal of Molecular Design: http://www.biochempress.com/

Internet Journal of Genomics and Proteomics: http://www.ispub.com/ostia/index.php?xmlFilePath=journals/ijgp/front.xml

Molecular & cellular proteomics : MCP: http://www.mcponline.org/

Nanoscale Research Letters: http://www.springer.com/east/home/generic/search/results?SGWID=5-40109-70-173663905-0
"Nanoscale Research Letters (NRL) is the first nanotechnology journal from a major commercial publisher to publish articles with open access."

Nanotechnology: http://www.iop.org/EJ/journal/Nano
"As a service to authors, all papers published in our journals are free for 30 days from the date of online publication."

Physiological genomics: http://physiolgenomics.physiology.org/

PLoS Computational Biology: http://compbiol.plosjournals.org/perlserv/?request=index-html&issn=1553-7358


* UM ACCESS VIA MIRLYN OR SEARCHTOOLS:

This is just a small sampling of the additional electronic journals and journal archives available as a member of the University of Michigan community. These can be accessed via either Mirlyn or SearchTools. You can also browse electronic journals at the University Library Electronic Journals & Newspapers List. There are also many print journals available on the various omics topics in campus libraries.


Annual review of genomics and human genetics.
Briefings in functional genomics & proteomics
Comparative and functional genomics
Cytogenetic and genome research.
Functional & integrative genomics.
Genomics.
Human genome abstracts
IEEE transactions on nanotechnology.
Journal of biomedical nanotechnology.
Journal of structural and functional genomics
Mammalian genome : official journal of the International Mammalian Genome Society.
Microbial & comparative genomics
Molecular genetics and genomics : MGG.
Nano- and microtechnology : materials, processes, packaging and systems (SPIE--the International Society for Optical Engineering)
Nanobiotechnology : the journal at the intersection of nanotechnology, molecular biology, and biomedical sciences.
Nano letters (American Chemical Society)
Nanotechnology (SPIE--the International Society for Optical Engineering).
Omics
Pharmacogenetics and genomics.
Proteomics.
Smart structures and materials. Smart electronics, MEMS, and nanotechnology.


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (journal OR subscribe OR subscription OR "open access")

Posted by pfa at 02:34 PM | Comments (0)

August 03, 2006

Finding Omics Grants and Funding Opportunities (Omics Series, 19)

Funding is core to making it possible to have innovative and cutting edge research in the omics areas. There are a variety of resources generally available for researchers to discover grants and funding opportunities. Most UM researchers are intimately aware of the UM Research web site and what it has to offer. Please also take a look at the University Library guide on foundation and grant resources. There are in addition a number of special organizations that gather or provide grants specifically for these research areas.


* CAMPUS RESOURCES

UM Research: http://www.research.umich.edu/
INCLUDES:
Funding Opportunities: http://www.research.umich.edu/funding/funding.html
Grants.gov & the University of Michigan: http://www.research.umich.edu/era/grantsgov/index.html
Research Administrator Toolkit: http://www.research.umich.edu/ralinks/

University Library: Government Publications: Federal Government Resources on the Web/Grants and Contracts: http://www.lib.umich.edu/govdocs/fedgt.html

University Library: Government Publications: Michigan/Grants and Auctions: http://www.lib.umich.edu/govdocs/michgrt.html

University Library: Graduate Library Subject Guides: Resources on Foundations and Grants: http://www.lib.umich.edu/grad/guide/guide.php?id=84


* NATIONAL

Cancer.gov: NCI Alliance for Nanotechnology in Cancer: Funding Opportunities: http://nano.cancer.gov/resource_center/funding.asp

CDC: National Office of Public Health Genomics: Genomic Funding: http://www.cdc.gov/genomics/activities/funding.htm

genome.gov: Grants: http://www.genome.gov/10000004

National Center for Research Resources: Research Funding Opportunities: http://www.ncrr.nih.gov/rsrch_funding.asp

National Institutes of Health: Biomedical Information Science and Technology Initiative (BISTI): Bioinformatics Funding Opportunities Page: http://www.bisti.nih.gov/bistic_funding.cfm

National Institutes of Health: National Institute of Dental and Craniofacial Research: http://www.nidcr.nih.gov/Funding/CurrentFundingOpportunities/default.htm

National Nanotechnology Initiative: Funding Opportunities: http://www.nano.gov/html/funding/home_funding.html

National Science Foundation: Find Funding: http://www.nsf.gov/funding/


* INTERNATIONAL

Biotechnology and Biological Sciences Research Council (BBSRC): How to get Funding: http://www.bbsrc.ac.uk/funding/Welcome.html

Nanoforum: Funding and Support for International Nanotechnology Collaborations: http://www.nanoforum.org/nf06~modul~showmore~folder~99999~scid~351~.html?action=longview_publication&

World Health Organization (WHO): Grant Opportunites: http://www.who.int/tdr/grants/default.htm


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (grants OR contracts OR "funding opportunities") -site:edu -site:com

Posted by pfa at 11:47 AM | Comments (0)

August 02, 2006

Omics Standards (Omics Series, 18)

As with most new fields, as the discipline reaches maturity there is a call for standards and guidelines, both relating to practice as well as to terminology. The omics fields have reached that maturity with astonishing rapidity, and have had standards development efforts underway for a few years now. In thte resources listed below, you will find standards organizations at international, national, and topical levels; background information about standardization efforts in the omics fields; and much more. For University of Michigan patrons, we would like to highlight the marvelous resource from the Art, Architecture and Engineering Library on the many standards resources available to our campus. Again, we close the blog entry with a web search for those interested in finding more on this topic.


* STANDARDS, SPECIFICATIONS & GUIDELINES

Foresight Institute: Molecular Nanotechnology Guidelines: http://www.foresight.org/guidelines/


* COLLECTIONS, GUIDES AND SOURCES:

University Library: Art, Architecture and Engineering Library: Standards: http://www.lib.umich.edu/aael/division.php?divisionID=16&d=v

Georgia Tech Library: Nanoscience & Nanotechnology: Standards & Specifications: http://www.library.gatech.edu/research_help/subject/index.php?/nanoscience/standards

National Institute of Standards and Technology (NIST): Research by Subject: Nanotechnology: http://nvl.nist.gov/nvl2.cfm?dynamic=res_subj&subjectid=17

IEEE Standards Online: Nanotechnology Standards: http://standards.ieee.org/catalog/olis/nanotech.html [Requires UM login, access via AAEL page]


* STANDARDS ORGANIZATIONS:

American National Standards Institute's Nanotechnology Standards Panel (ANSI-NSP): http://www.ansi.org/standards_activities/standards_boards_panels/nsp/overview.aspx?menuid=3

Association of Biomolecular Resource Facilities (ABRF): Proteomics Standards Research Group Research Group: http://www.abrf.org/index.cfm/group.show/ProteomicsStandardsResearchGroup.47.htm

HUPO (HUman Proteome Organization): Proteomics Standards Initiative: http://psidev.sourceforge.net/
"The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification."

ISO - International Organization for Standardization: TC229, Nanotechnologies: http://www.iso.org/iso/en/stdsdevelopment/tc/tclist/TechnicalCommitteeDetailPage.TechnicalCommitteeDetail?COMMID=5932

Microarray Gene Expression Data Society: http://www.mged.org/

SOFG (Standards and Ontologies for Functional Genomics): http://www.sofg.org/


* ABOUT OMICS STANDARDIZATION EFFORTS:

Capello, Jolinda. Overview of Nanotechnology: Risks, Initiatives and Standardization. American Society of Safety Engineers: http://www.asse.org/nantechArticle.htm

European Bioinformatics Institute: Meetings: Proteomics Standards Initiative: http://www.ebi.ac.uk/Information/meetings/psi.html

European Science Foundation: Integrated Approaches for Functional Genomics: Standardisation, benchmarking and comparision of different experimental systems: http://www.functionalgenomics.org.uk/sections/programme/standardisation.htm

IEEE Standards Association: Nanotechnology Standards Initiatives at IEEE: http://standards.ieee.org/announcements/bkgnd_nanostdsinit.html

National Institute of Standards and Technology: Nanotechnology Is BIG at NIST: http://www.nist.gov/nanotech/

NIH Roadmap: Standards in Proteomics Workshop: Agenda: http://nihroadmap.nih.gov/buildingblocks/proteomics/


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (standards OR specifications OR guidelines OR standardization OR standardisation)

Posted by pfa at 09:41 PM | Comments (0)

August 01, 2006

Other Databases for Omics Researchers (Omics Series, 17)

The premiere source of omics databases is of course the collection available from NIH-NLM-NCBI (Blast, OMIM, etc). These were highlighted in a previous blog entry in this series (#9). For the current blog entry, we have selected examples of omics databases made available from various research centers, institutes and organizations around the world. We included only collections of databases, or specific databases that were free and openly available at the time of writing. There are many more that require subscription. As you can see, there are also many that do not.


* OMICS DATABASE COLLECTIONS

Kyoto University Bioinformatics Center: Genome Databases in Japan: http://www.genome.jp/genome_db/

NIH: Computational Molecular Biology: Databases: http://molbio.info.nih.gov/molbio/db.html

Proteomic World: Databases: http://www.proteomicworld.org/DatabasePage.html

* DATABASES FROM SPECIFIC PROJECTS

Baylor College of Medicine: Department of Pharmacology: Small RNA database: http://condor.bcm.tmc.edu/smallRNA/smallrna.html

BioGRID: A General Repository for Interaction Datasets: http://www.thebiogrid.org/

Bioinformatics.org, Open-Source Bioinformatics for Researchers: Online Databases: http://bioinformatics.org/
- Online Databases EST Clusters: http://bioinformatics.org/zest/
- Immigrant Genes: http://bioinformatics.org/immigrant/
- Leukemia Genes: http://bioinformatics.org/legend/
- p53 Tumor Protein Gene: http://bioinformatics.org/p53/
- Pancreatic Cancer Genes: http://bioinformatics.org/pcgdb/
- TB Drug Targets: http://bioinformatics.org/tbdtdb/
- T2K Acronym Finder: http://bioinformatics.org/textknowledge/

European Bioinformatics Institute (EMBL-EBI): IntAct Interaction Database: http://www.ebi.ac.uk/intact/index.jsp
"IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available."

European Bioinformatics Institute (EMBL-EBI): PRIDE (PRoteomics IDEntifications database): http://www.ebi.ac.uk/pride/

Georgetown University Medical Center: Protein Information Resource (Integrated Protein Informatics Resource for Genomic and Proteomic Research): http://pir.georgetown.edu/pirwww/index.shtml

Georgetown University Medical Center: Protein Information Resource: Search & Analysis Tools: http://pir.georgetown.edu/pirwww/search/

Harvard University: Dana Farber Cancer Institute: WorfDB, The C. elegans ORFeome cloning project: http://worfdb.dfci.harvard.edu/

Harvard University: Harvard Institute of Proteomics: FlexGene Database: http://kotel.harvard.edu:8080/FLEX/welcome.jsp

Kyoto University Bioinformatics Center: DBGET: Web of Molecular Biology Databases: http://www.genome.jp/dbget/

MedicalComputing.net: Search Human Gene Information Database: http://www.medicalcomputing.net/cgi-bin/query_human_gene_info

MHCPEP [A database of MHC binding peptides (v. 1.3)]: http://wehih.wehi.edu.au/mhcpep/
Entries include: " ... the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions, and publication references."

NanoWerk: NanoBank: Nanomaterials Database: http://www.nanowerk.com/phpscripts/n_dbsearch.php

Real Time Primers, validated primer sets for quantitative real time PCR: http://www.realtimeprimers.org/

RNA Interference, database of siRNA sequences and RNA inhibition studies: http://www.rnainterference.org/

Rutgers State University of New Jersey: The Nucleic Acid Database Project:
Nucleic Acid Database (NDB): http://ndbserver.rutgers.edu/

University of Texas: Bioinformatics, Proteomics, and Functional Genomics: Open Proteomics Database: http://apropos.icmb.utexas.edu/OPD/
"OPD is a public database for storing and disseminating mass spectrometry based proteomics data. The database currently contains roughly 3,000,000 spectra representing experiments from 5 different organisms."

Weizmann Institute of Science: GeneCards: http://www.genecards.org/index.shtml
"GeneCards is an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies."

World Health Organization (WHO): International Database on Craniofacial Anomalies (IDCFA): http://www.who.int/genomics/anomalies/idcfa/en/

WormBase: http://www.wormbase.org/


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (database OR dataset OR search)

Posted by pfa at 04:42 PM | Comments (0)

July 31, 2006

Resources for Omics Researchers (Omics Series, 16)

While there are a great many resources for omics researchers, both in print and online, these change rapidly and unpredictably, as do the field themselves. Today's entry includes protocols, open-source software, and a few general collections of research resources in these areas. In addition to the resources listed here (all of which were good links as of July 2006), remember to also check the website for the company that produced your equipment, as many corporations also provide detailed protocols guides.

* ONLINE RESOURCES

ApoptosisWorld, resources for studying cell death: http://www.apoptosisworld.com/

BioDAS (Biological Distributed Annotation System): http://biodas.org/
"This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data."

Bioinformatics.Org: The Open-Access Institute: http://bioinformatics.org/

CPAS: http://cpas.fhcrc.org/
"CPAS is an open source science portal offering web-based bioinformatics and collaboration tools to help scientists store, analyze, and share data from high-throughput experiments and clinical trials. The Fred Hutchinson Cancer Research Center uses CPAS to manage the Computational Proteomics Laboratory (CPL) Proteomics Repository containing over 140 million putative MS2 peptides, growing at 3 million per week. CPAS is available as free, installable software, with source code."

Drug Discovery & Development: Buyer's Guide: http://www.dddmag.com/BuyersGuide.aspx

GenomicWorld, resources for genomics and genetics: http://www.genomicworld.com/

Ion Channel Group: Bioinformatics, Databases and Software for Medicine: http://www.bio-computing.org/
Includes: "The first & only bioinformatics-specific relevancy-powered MEDLINE search." "Hint: Sort by citation score to display the highest impact articles."

Max-Planck-Institute of Immunobiology: Proteomics Protocols: http://www.immunbio.mpg.de/home/facilities/proteomics/protocols/index2.html

MicroarrayWorld, resources for microarrays and expression profiling: http://www.microarrayworld.com/

Molecular Station: Links: Proteomics Protocols: http://www.molecularstation.com/protocol-links/Proteomics_Protocols/

Molecular Station: Molecular Biology Techniques: http://www.molecularstation.com/molecular-biology-techniques/

Molecular Station: Proteomics Protocols: http://www.molecularstation.com/proteomics/proteomics-protocols/

msInspect: http://proteomics.fhcrc.org/CPL/msinspect.html
"msInspect allows you to view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration."

ProteomicWorld: http://www.proteomicworld.org/
Includes: instruments, protocols, reagents, protein arrays, software, databases and more.

Protocol Online: Index to Protocols: http://www.protocol-online.org/prot/

Sashimi: http://sashimi.sourceforge.net/
"The goal of the project is to provide the scientific community with free open source software tools for the downstream analysis of mass spectrometric data. We hope to develop and distribute analysis tools that will facilitate the ability of labs worldwide to perform proteomics experiments."


* BOOKS IN DENTISTRY LIBRARY

For additional books on this topic, we highly recommend the Science Library and Taubman Medical Library.

Cell cycle control and dysregulation protocols : cyclins, cyclin-dependent kinases, and other factors / edited by Antonio Giordano, Gaetano Romano. QH 605 .C42571 2004

Cytokine protocols / edited by Marc de Ley. QH 506 .M451 v.249

Protein purification protocols. QP 551 .P697561 2004

Recombinant gene expression : reviews and protocols / edited by Paulina Balbás and Argelia Lorence. QH 443 .R361 2004

Short protocols in cell biology : a compendium of methods from Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]. QH 585.2 .S55 2004

Bone research protocols / edited by Miep H. Helfrich, Stuart H. Ralston. QP 88.2 .B58981 2003

PCR protocols / edited by John M.S. Bartlett and David Stirling. QP 606 .D46 P35951 2003

Protein sequencing protocols / edited by Bryan John Smith. QP 625 .N89 P761 2002


* WANT MORE?

Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (instruments OR protocols OR reagents OR "open source")

Posted by pfa at 12:48 PM | Comments (0)

July 28, 2006

Nanodentistry (Omics Series, 15)

Many of the same interests and factors that have captured attention in dental proteomics also overlap with nanodentistry. Specifically, many of the proteomic sensors for biofilms and oral fluid diagnostics have underlying nanotechnology in the final implementation. For this reason, this blog entry highlights a few articles and events that focus specifically on nanotechnology, however if you are interested in this area, please also refer to our article on dental proteomics.

* RESOURCES & EVENTS

European Dental Materials Conference, September 1-2, 2005: Nanomaterials/Nanotechnology in Dentistry: http://www.ucc.ie/academic/restorative/edmc/programme.html

Foresight Institute: Recent Articles on Medical Nanomaterials, Nanobiotechnology, or "Nanomedicine" / compiled by
Robert A. Freitas Jr.: http://www.foresight.org/Nanomedicine/NanoMedArticles.html

Nature Nanotechnology [forthcoming October 2006]: http://www.nature.com/nnano/index.html

Shahed University Dental Research Center: 1st Seminar on Nanotechnology Application in Dentistry; June 15, 2006: http://www.nano.ir


* ARTICLES

Freitas Jr RA.
Nanodentistry.
J. Amer. Dent. Assoc. 131(November 2000):1559-1566.
http://www.rfreitas.com/Nano/Nanodentistry.htm
http://jada.ada.org/cgi/content/abstract/131/11/1559

Jhaveri HM, Balaji PR
Nanotechnology: The future of dentistry
J Prosthodont 2005 5(1):15-17.
http://www.jprosthodont.com/article.asp?issn=0972-4052;year=2005;volume=5;issue=1;spage=15;epage=17;aulast=Jhaveri

Kong LX, Peng Z, Li SD, Bartold PM.
Nanotechnology and its role in the management of periodontal diseases.
Periodontol 2000. 2006;40:184-96.
PMID: 16398694
http://www.ingentaconnect.com/content/mksg/pe2/2006/00000040/00000001/art00014 [UM login required]

Malamud D, Bau H, Niedbala S, Corstjens P.
Point detection of pathogens in oral samples.
Adv Dent Res. 2005 Jun;18(1):12-6.
PMID: 15998938
http://adr.iadrjournals.org/cgi/content/full/18/1/12

Schleyer TL.
Nanodentistry -- truth or fiction?
J Am Dent Assoc, Vol 131, No 11, 1567-1568.
http://jada.ada.org/cgi/content/full/131/11/1567

* WANT MORE?

Google search: nanodentistry OR ((nano OR nanotechnology OR nanobiotechnology) (dentistry OR saliva OR enamel OR periodontal OR gingival))

Google Scholar search: nanodentistry OR ((nano OR nanotechnology OR nanobiotechnology) (dentistry OR saliva OR enamel OR periodontal OR gingival))

Pubmed search: nanotechnology (dentistry OR saliva OR periodontal OR enamel)

Rollyo: pfa: Nano Search: http://rollyo.com/pfa/nano/

Posted by pfa at 09:43 PM | Comments (0)

July 27, 2006

Dentistry and Proteomics (Omics Series, 14)

Proteomics has quickly become one of the most exciting research frontiers in modern dentistry. The two primary areas in which dental proteomics has really shone are salivary diagnostics (also known as oral fluids diagnostics or oral fluid biomarkers) and proteomics of bone and mineral structures, especially dental enamel. Because these lines of research are still very much cutting edge, the bulk of the online resources are specific articles, and websites for the labs of researchers working in these areas. There are a number of meetings and working groups being initiated in these areas. Aside from research, salivary diagnostics has attracted a great deal of commercial and investor attention, making it challenging to search for information on these topics that is appropriate for the researcher or student. For those of the selected articles listed below which link to PubMed, please note that they require a University of Michigan login to retrieve the articles. Where possible, the link provided goes directly to the article on the publisher's website.


* PROTEOMICS AND ENAMEL

Hu JC. Yamakoshi Y. Yamakoshi F. Krebsbach PH. Simmer JP.
Proteomics and genetics of dental enamel.
Cells Tissues Organs. 181(3-4):219-31, 2005.
PMID: 16612087 [UM login required]

Hubbard M.
Enamel proteomics and protein interactions.
Eur J Oral Sci. 2006 May;114 Suppl 1:285-6. No abstract available.
PMID: 16674700 [UM login required]

Hubbard MJ, Kon JC.
Proteomic analysis of dental tissues.
J Chromatogr B Analyt Technol Biomed Life Sci. 2002 May 5;771(1-2):211-20.
PMID: 12016000 [UM login required]

Kim JW, Seymen F, Lin BP, Kiziltan B, Gencay K, Simmer JP, Hu JC.
ENAM mutations in autosomal-dominant amelogenesis imperfecta.
J Dent Res. 2005 Mar;84(3):278-82.
PMID: 15723871
http://jdr.iadrjournals.org/cgi/content/abstract/84/3/278

Oppenheim, Frank.
Proteomics of Human Acquired Enamel Pellicle (EP)
http://people.bu.edu/wzhang/Proteomics/proteomics.html

Simmer JP, Bartlett JD.
Kallikrein 4 is a secreted protein.
Cancer Res. 2004 Nov 15;64(22):8481-2; author reply 8482-3.
PMID: 15548723
http://cancerres.aacrjournals.org/cgi/content/full/64/22/8481

UM School of Dentistry: Biologic and Materials Science: Division of Prosthodontics: Simmer Lab: Research: Proteomics and Genetics of Enamel and Dentin: http://www.dent.umich.edu/depts/bms/research/simmerlab/research.html

Yao Y, Berg EA, Costello CE, Troxler RF, Oppenheim FG.
Identification of protein components in human acquired enamel pellicle and whole saliva using novel proteomics approaches.
J Biol Chem. 2003 Feb 14;278(7):5300-8.
PMID: 12444093
http://www.jbc.org/cgi/content/full/278/7/5300

* SALIVARY DIAGNOSTICS

Amado FML, Vitorino RMP, Domingues PMDN, Lobo MJC, Duarte JAR.
Analysis of the human saliva proteome
Expert Review of Proteomics Aug 2005 2(4):521-539
http://www.future-drugs.com/doi/abs/10.1586/14789450.2.4.521 [$$ required for article, abstract free]

Anderson JM, Oliveira F, Kamhawi S, Mans BJ, Reynoso D, Seitz AE, Lawyer P, Garfield
M, Pham M, Valenzuela JG.
Comparative salivary gland transcriptomics of sandfly vectors of visceral leishmaniasis.
BMC Genomics. 2006 Mar 15;7:52.
PMID: 16539713
http://www.biomedcentral.com/1471-2164/7/52

CPRMap: Clinical Proteomics: Fluid Proteomics: Salivary Proteomics: Salivary Proteomics Research Map:
http://www.cprmap.com/salivary-proteomics/

Li Y, Denny P, Ho CM, Montemagno C, Shi W, Qi F, Wu B, Wolinsky L, Wong DT.
The Oral Fluid MEMS/NEMS Chip (OFMNC): diagnostic and translational applications.
Adv Dent Res. 2005 Jun;18(1):3-5.
PMID: 16000263
http://adr.iadrjournals.org/cgi/content/full/18/1/3

Li Y, Zhou X, St John MA, Wong DT.
RNA profiling of cell-free saliva using microarray technology.
J Dent Res. 2004 Mar;83(3):199-203.
PMID: 14981119
http://jdr.iadrjournals.org/cgi/content/full/83/3/199

NIH: NIDCR: First Meeting of Salivary Diagnostics Group:
http://www.nidcr.nih.gov/NewsAndReports/E-Newsletters/SalivaryDiagnosticsGroup.htm

Oral-Based Diagnostics: A New York Academy of Sciences Meeting, October 10-13, 2006.
http://www.nyas.org/events/eventDetail.asp?eventID=5754&date=10/10/2006

Tabak LA
A revolution in biomedical assessment: the development of salivary diagnostics
J Dent Educ. 65(12): 1335-1339 2001
http://www.jdentaled.org/cgi/reprint/65/12/1335

Wong DT
Salivary diagnostics powered by nanotechnologies, proteomics and genomics
JADA 137 March 2006
http://www.oralcancerfoundation.org/dental/pdf/JADA%20Saliva%20Dx.pdf

Wong DT.
Towards a simple, saliva-based test for the detection of oral cancer 'oral fluid (saliva), which is the mirror of the body, is a perfect medium to be explored for health and disease surveillance'.
Expert Rev Mol Diagn. 2006 May;6(3):267-72.
PMID: 16706730
http://www.future-drugs.com/doi/abs/10.1586/14737159.6.3.267 [$$ required for article, abstract free]

Xie H, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ.
A Catalogue of Human Saliva Proteins Identified by Free Flow Electrophoresis-based Peptide Separation and Tandem Mass Spectrometry
Molecular & Cellular Proteomics 4:1826-1830, 2005.
http://www.mcponline.org/cgi/content/abstract/4/11/1826 [UM login required]


* OTHER

Barnett ML, Pihlstrom BL.
Methods for enhancing the efficiency of dental/oral health clinical trials: current status, future possibilities.
J Dent Res. 2004 Oct;83(10):744-50.
PMID: 15381712
http://jdr.iadrjournals.org/cgi/content/abstract/83/10/744

Hing KA.
Bone repair in the twenty-first century: biology, chemistry or engineering?
Philos Transact A Math Phys Eng Sci. 2004 Dec 15;362(1825):2821-50. Review.
PMID: 15539372
http://www.journals.royalsoc.ac.uk/link.asp?id=mu5xd2e1ukhn7x6m

Pappano WN, Steiglitz BM, Scott IC, Keene DR, Greenspan DS.
Use of Bmp1/Tll1 doubly homozygous null mice and proteomics to identify and validate in vivo substrates of bone morphogenetic protein 1/tolloid-like metalloproteinases.
Mol Cell Biol. 2003 Jul;23(13):4428-38.
PMID: 12808086
http://mcb.asm.org/cgi/content/full/23/13/4428?view=long&pmid=12808086

Wright JT, Hart TC.
The genome projects: implications for dental practice and education.
J Dent Educ. 2002 May;66(5):659-71.
PMID: 12056771
http://www.jdentaled.org/cgi/content/abstract/66/5/659


* WANT MORE?

Pubmed search: (proteomics OR biomarkers) (dentistry OR enamel OR pellicle OR "salivary diagnostics" OR "oral fluids")

Posted by pfa at 07:30 PM | Comments (0)

July 26, 2006

Birth Defects and Omics (Omics Series, 13)

There is perhaps an intuitive or obvious connection between dentistry and craniofacial anomalies and birth defects, as well as an intuitive connection between birth defects and genetics / genomics. Birth defects are, in some ways, one of the most significant links between genomics and both public health and dentistry. Much of the overlapping work focuses on cleft lip and palate, but definitely not all. In today's entry we will find local, national and international resources as well as articles that explore the connections between these three concepts.


* MICHIGAN

Michigan Genetics Connection: Birth Defects & Folic Acid: http://www.migeneticsconnection.org/birthdefects.shtml

Michigan Birth Defects Registry: http://www.michigan.gov/mdch/0,1607,7-132-2944_4670---,00.html

Pobojewski, Sally. "U-M scientists find genetic cause of multiple birth defects affecting kidneys, eyes and other organs." May 8, 2006. http://www.med.umich.edu/opm/newspage/2006/nphp.htm


* NATIONAL & INTERNATIONAL

CDC Birth Defects and Developmental Disabilities: http://www.cdc.gov/ncbddd/

CDC Genomics and Disease Prevention: http://www.cdc.gov/genomics/

EUROCRAN: European Collaboration on Cranial Facial Anomalies:
http://www.eurocran.org/
INCLUDES:
Directory of European Resources: http://www.eurocran.org/content.asp?contentID=6&sid=18504
Genetic Databases: http://www.eurocran.org/content.asp?contentID=10&sid=184936
Clinical Outcomes Library or Good Practice Archive (members only)
Speech Project: http://www.eurocran.org/content.asp?contentID=1213&sid=18463

Human Genome Epidemiology Network (HuGENet): http://www.cdc.gov/genomics/hugenet/

International Birth Defects Information Systems (IBIS): http://www.ibis-birthdefects.org/

International Clearinghouse for Birth Defects Monitoring Systems (ICBDMS): International Centre for Birth Defects (ICBD): http://www.icbd.org/icbd.htm

Teratology Society: http://teratology.org/

WHO: International Collaborative Research on Craniofacial Anomalies (IRCRA):
http://www.who.int/entity/genomics/anomalies/en/

WHO: International Database on Craniofacial Anomalies (IDCFA):
http://www.who.int/genomics/anomalies/idcfa/en/


* ARTICLES

Brunner HG, van Driel MA.
From syndrome families to functional genomics.
Nat Rev Genet. 2004 Jul;5(7):545-51.
http://www.nature.com/nrg/journal/v5/n7/abs/nrg1383_fs.html;jsessionid=78D5CB675EF83A5A6477FF83F14B9229

genome.gov: Genomics in Action: Lawrence C. Brody: http://www.genome.gov/13014224

Omenn GS.
Genomics and Public Health
Issues in Science and Technology, Spring 2005
"Potential benefits depend on linking genetic and environmental data in designing research, developing applications, and forging public policies."
http://www.issues.org/21.3/omenn.html

Culiat CT (Oak Ridge National Laboratory)
Modeling Human Craniofacial Birth Defects with ORNL Mouse Mutations: http://lsd.ornl.gov/highlights/culiat.pdf

Le Caignec C, Boceno M, Saugier-Veber P, Jacquemont S, Joubert M, David A, Frebourg T, Rival JM.
Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations.
J Med Genet. 2005 Feb;42(2):121-8.
http://jmg.bmjjournals.com/cgi/content/full/42/2/121

Pobojewski, Sally. "U-M scientists find genetic cause of multiple birth defects affecting kidneys, eyes and other organs." May 8, 2006. http://www.med.umich.edu/opm/newspage/2006/nphp.htm

Polifka JE, Friedman JM.
Medical genetics: 1. Clinical teratology in the age of genomics.
CMAJ August 6, 2002; 167 (3)
http://www.cmaj.ca/cgi/content/full/167/3/265


Spradling A, Ganetsky B, Hieter P, Johnston M, Olson M, Orr-Weaver T, Rossant J, Sanchez A, Waterston R.
New roles for model genetic organisms in understanding and treating human disease: report from the 2006 Genetics Society of America meeting.
Genetics. 2006 Apr;172(4):2025-32.
http://www.genetics.org/cgi/content/full/172/4/2025

Posted by pfa at 02:05 PM | Comments (0)

July 25, 2006

Dentistry and Omics In "Print" Journals (Omics Series, 12)

If you want to discover more about dentistry and the omics in the professional journal literature, then today's blog entry is for you! It is interesting to see the evolution of the field over time. Below you will find selected fulltext online journal articles both from the dental literature and other life science journals. Following the list of selected articles, are several links to other searches for locating articles in the science literature both online and in print. These will lead you to more of the articles from journals for which the University Libraries have paid subscriptions, as well as print articles held in the library itself.


* 2000

Cobourne MT.
Construction for the modern head: current concepts in craniofacial development.
J Orthod. 2000 Dec;27(4):307-14.
PMID: 11099568
http://jorthod.maneyjournals.org/cgi/content/full/27/4/307


* 2001

Dionne RA.
Pharmacologic advances in orofacial pain: from molecules to medicine.
J Dent Educ. 2001 Dec;65(12):1393-403.
PMID: 11780658
http://www.jdentaled.org/cgi/content/abstract/65/12/1393

Slavkin HC.
The human genome, implications for oral health and diseases, and dental education.
J Dent Educ. 2001 May;65(5):463-79.
PMID: 11425251
http://www.jdentaled.org/cgi/content/abstract/65/5/463


* 2002

Hart TC, Ferrell RE.
Genetic testing considerations for oral medicine.
J Dent Educ. 2002 Oct;66(10):1185-202.
PMID: 12449214
http://www.jdentaled.org/cgi/content/abstract/66/10/1185

Scully C, Challacombe SJ.
Pemphigus vulgaris: update on etiopathogenesis, oral manifestations, and management.
Crit Rev Oral Biol Med. 2002;13(5):397-408.
PMID: 12393759
http://crobm.iadrjournals.org/cgi/content/full/13/5/397

Wright JT, Hart TC
The genome projects: implications for dental practice and education.
J Dent Educ. 2002 May;66(5):659-71.
PMID: 12056771
http://www.jdentaled.org/cgi/content/abstract/66/5/659


* 2003

Gettig E, Hart TC.
Genetics in dental practice: social and ethical issues surrounding genetic testing.
J Dent Educ. 2003 May;67(5):549-62.
PMID: 12809190
http://www.jdentaled.org/cgi/content/abstract/67/5/549

Kuo WP
Overview of Bioinformatics and its Application to Oral Genomics.
Adv Dent Res 17:89-94, December, 2003
PMID: 15126216
http://adr.iadrjournals.org/cgi/content/full/17/1/89

Macarthur DJ, Jacques NA.
Proteome analysis of oral pathogens.
J Dent Res. 2003 Nov;82(11):870-6.
PMID: 14578497
http://jdr.iadrjournals.org/cgi/content/full/82/11/870

Miletich I, Sharpe PT.
Normal and abnormal dental development.
Hum Mol Genet. 2003 Apr 1;12 Spec No 1:R69-73.
PMID: 12668599
http://hmg.oxfordjournals.org/cgi/content/full/12/suppl_1/R69

Nishimura I, Drake TA, Lusis AJ, Lyons KM, Nadeau JH, Zernik J.
ENU large-scale mutagenesis and quantitative trait linkage (QTL) analysis in mice: novel technologies for searching polygenetic determinants of craniofacial abnormalities.
Crit Rev Oral Biol Med. 2003;14(5):320-30.
PMID: 14530301
http://crobm.iadrjournals.org/cgi/content/full/14/5/320

Thyagarajan T, Totey S, Danton MJ, Kulkarni AB.
Genetically altered mouse models: the good, the bad, and the ugly.
Crit Rev Oral Biol Med. 2003;14(3):154-74.
PMID: 12799320
http://crobm.iadrjournals.org/cgi/content/full/14/3/154


* 2004

Collins F, Tabak L
A Call for Increased Education in Genetics for Dental Health Professionals.
(Critical Issues in Dental Education: Genetics Education for Dental Health Professionals)
J Dent Educ 68(8): 807-808 2004
http://www.jdentaled.org/cgi/content/full/68/8/807

Stanier P, Moore GE.
Genetics of cleft lip and palate: syndromic genes contribute to the incidence of non-syndromic clefts.
Hum Mol Genet. 2004 Apr 1;13 Spec No 1:R73-81. Epub 2004 Jan 13.
PMID: 14722155
http://hmg.oxfordjournals.org/cgi/content/full/13/suppl_1/R73


* 2005

Zavras AI
Post-marketing Drug Safety in the Era of Genomic Medicine.
J Dent Res 84(2):105-106, 2005
http://jdr.iadrjournals.org/cgi/content/full/84/2/105

Li Y, Denny P, Ho CM, Montemagno C, Shi W, Qi F, Wu B, Wolinsky L, Wong DT.
The Oral Fluid MEMS/NEMS Chip (OFMNC): diagnostic and translational applications.
Adv Dent Res. 2005 Jun;18(1):3-5.
PMID: 16000263
http://adr.iadrjournals.org/cgi/content/full/18/1/3

Kuratani S.
Craniofacial development and the evolution of the vertebrates: the old problems on a new background.
Zoolog Sci. 2005 Jan;22(1):1-19.
PMID: 15684579
http://www.jstage.jst.go.jp/article/zsj/22/1/22_1/_article


* 2006

Wong DT
Salivary diagnostics powered by nanotechnologies, proteomics and genomics.
J Am Dent Assoc Mar 2006
http://jada.ada.org/cgi/content/abstract/137/3/313


* WANT MORE?

Google Scholar: (genomics OR genome OR proteomics OR bioinformatics OR nanotechnology) (dentistry OR "oral health" OR craniofacial OR "oral microorganisms")

PubMed search: (genomics OR genome OR proteomics OR bioinformatics OR nanotechnology) (dentistry OR "oral health" OR craniofacial OR "oral microorganisms")

Scirus search: (genomics OR genome OR proteomics OR bioinformatics OR nanotechnology) (dentistry OR "oral health" OR craniofacial OR "oral microorganisms")

Posted by pfa at 12:04 PM | Comments (0)

July 24, 2006

Dentistry and Genomics Online (Omics Series, 11)

Much of the work to date in dental genomics has focused on oral microorganisms, an area also known as microbial genomics, oral diagnostics (especially with saliva), and forensics. Overviews of the discoveries and potential impact are available for laymen from National Coalition for Health Professional Education in Genetics (NCHPEG) and the Harris National Museum of Dentistry (NMD). NCHPEG has designed a rich Flash-based online exhibit including animations, illustrations, and a nicely selected resource list. The NMD has created the first exhibit examinig the impact of the human genome project on dentistry, with the exhibit due to be completed this year (2006).

National Coalition for Health Professional Education in Genetics (NCHPEG): Genetics, Disease and Dentistry: http://www.nchpeg.org/dental/index.html

Harris National Dental Museum (NMD): Exhibits: Your Spitting Image: http://www.dentalmuseum.umaryland.edu/exhibitions/special/detail.cfm?ID=41

The early planning from NIDCR, from 1999 through the 2002 Scientific Expert Panel, proposed that dental genomics focus on ten organisms -- nine bacteria and one yeast.

NIDCR Panel on Genomics and Proteomics Of Oral, Dental and Craniofacial Diseases -- A Scientific Expert Panel; May 22, 2002: http://www.nidcr.nih.gov/Research/LongRangeResearchOpportunities/PanelOnGenomicsAndProteomics.htm

Bacteria of periodontitis:
Porphyromonas gingivalis
Treponema denticola
Actinobacillus actinomycetemcomitans
Fusobacterium nucleatum
Bacteroides forsythus
Prevotella intermedia

Bacteria of dental caries:
Streptococcus mutans

Bacteria of dental plaque and endocarditis:
Streptococcus gordonii (in process)
Streptococcus sanguis

Yeast causing oral mucositis in the immunocompromised:
Candida albicans

Since that time, almost all of the named organisms have indeed had their genome mapped. A few of these projects have substantial websites with information about the project and organism, usually including the sequencing, assembly, and annotation of the specific genome.

Virginia Commonwealth University: Streptococcus sanguinis Genome Sequencing Project: http://www.sanguis.mic.vcu.edu/

Streptococcus mutans Genome Sequencing: http://www.genome.ou.edu/smutans.html

The Candida Genome Database (CGDTM): http://www.candidagenome.org/

NCBI: GenBank: T. denticola sequence (AE017226): http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=AE017226

Porphyromonas Gingivalis Genome Project / Dr. Robert Fleischmann et al.: http://www.pgingivalis.org/

There are a few major resources that specifically collect microbial genomes for dentristry. TIGR-CMR collects a broad range of microbial and bacterial genomes, with a collection of almost 300 bacteria alone, while ORALGEN and BROP both collect only those relevant to dentistry.

Los Alamos: Oral Pathogen Sequence Databases (ORALGEN): http://www.oralgen.lanl.gov/
INCLUDES:
* Actinobacillus actinomycetemcomitans
* Fusobacterium nucleatum
* Porphyromonas gingivalis
* Prevotella intermedia
* Streptococcus mutans
* Tannerella forsythensis
* Treponema denticola
* Human Herpesvirus 1 HSV-1
* Human Herpesvirus 2 HSV-2
* Human Herpesvirus 5 HCMV
* Human Herpesvirus 8 KSHV


Forsyth Institute: Genome Viewing, Exploring & Analysis Tools: The Bioinformatics Resources for Oral Pathogens (BROP): http://genome.brop.org/

TIGR: Comprehensive Microbial Resource (CMR):
http://www.tigr.org/CMR

Posted by pfa at 09:21 PM | Comments (0)

July 21, 2006

Omics in Michigan (Omics Series, 10)

Where do you go with a quick question or how do you find an expert partner to extend your area of inquiry? There are amazing researchers all over the world, but there are also amazing researchers right next door. Today we are looking at the range of omics resources and research centers within the state of Michigan, at academic and corporate institutions, and within the University of Michigan. Let's explore what our neighbors are doing.

* MICHIGAN GOVERNMENT, ASSOCIATIONS, & OTHER

Michigan Genetics Resource Center: http://www.migeneticsconnection.org/
INCLUDES:
- Michigan Genetics Connection: Genetic Literacy: http://www.migeneticsconnection.org/geneticliteracy.shtml
- Michigan Genetics Connection: Michigan Genetics Support Group Directory: http://www.migeneticsconnection.org/supportdirectory.shtml
- Michigan Genetics Connection: Michigan State Genetics Plan: http://www.migeneticsconnection.org/stateplan.shtml

Michigan Proteome Consortium: http://www.proteomeconsortium.org/

Michigan Public Health Genomics* Program (PHGP): http://www.michigan.gov/mdch/0,1607,7-132-2942_4911_4916-85137--,00.html

State of Michigan: Public Health Genomics Program: http://www.michigan.gov/mdch/0,1607,7-132-2942_4911_4916-85137--,00.html

Michigan SmallTech Association (MISTA): http://www.michigansmalltech.com/

Michigan.org: Life Sciences Corridor: http://www.michigan.org/medc/ttc/LifeSciences/

Nanotechnology International: Usa/Michigan: companies, profiles and links: http://www.nanovip.com/directory/International/Usa/Michigan/index.php


* MICHIGAN UNIVERSITIES & SCHOOLS

EMU: Bioinformatics@emich.edu: http://www.emich.edu/bioinformatics/

MSU: Bioinformatics Services: http://genomics.msu.edu/bioinformatics/Bioinformatics.html

MSU: Genomics: Research Technology Support Facility (RTSF): http://genomics.msu.edu/index.html

MSU: Nanoscale Interdisciplinary Research Team (NIRT): http://nirt.pa.msu.edu/

MSU: Proteomics Database: http://genomics.msu.edu/cgi-bin/proteomics/login.cgi

MSU: Proteomics: http://proteomics.msu.edu/

MSU: The Nanotechnology Site: http://www.pa.msu.edu/cmp/csc/nanotech/

Michigan Technological University (MTU): Nanotechnology: http://nano.mtu.edu/

UM: Bioinformatics: http://www.bioinformatics.med.umich.edu/

UM: Center for Computational Medicine and Biology: http://www.ccmb.med.umich.edu/

UM: Center for Integrative Genomics: http://www.med.umich.edu/cig/index.html

UM: Center for Proteome Studies: http://www.proteomecenter.med.umich.edu/

UM: Michigan Center for Genomics & Public Health: http://www.sph.umich.edu/genomics/

UM: Michigan Nanofabrication Facility: http://www.mnf.umich.edu/

UM: Michigan Nanotechnology Institute for Medicine and Biological Sciences (M-NIMBS): http://nano.med.umich.edu/

UM: Microbial Genomics: http://sitemaker.umich.edu/microbial_genomics

UM: National Nanotechnology Infrastructure Network (Nanotech at UM): http://www.mnf.umich.edu/NNIN/


* WANT MORE?

Google: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (site:umich.edu OR site:msu.edu OR site:michigan.gov)

Google: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) michigan -site:umich.edu -site:msu.edu -site:michigan.gov

Posted by pfa at 02:41 PM | Comments (0)

July 20, 2006

Genetic and Genomic Information from NLM and the Genetics Home Reference (GHR) (Omics Series, 9)

The United States government, in general, and the National Library of Medicine, in particular, have taken leading roles in providing information, tools, resources, and training for biomedical and life sciences researchers and clinicians, including omics researchers. Very few people make use of the full range of resources they provide. Today, we will survey a few of the broad omics resources available, and then spend a little more time on a specific resource that tends to have information for both dental researchers and clinicians.

This is probably a good time to again mention the forthcoming short course on campus about NCBI resources.

National Center for Biotechnology Information: Short Course, September 7,2006 (Hosted by the Program in Bioinformatics, Department of Human Genetics & Taubman Medical Library): http://www.hg.med.umich.edu/ncbi/

In this course, you will see overviews and demonstrations of how to use many of the databases listed below. NLM and NCBI provide an astonishing number of databases. From their main databases page, you can browse a list of many of their offerings in this area.

NLM: NCBI: Entrez: All Databases: http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?itool=toolbar

Here are a few of the specific databases, just to give you an idea of what you might find.

3D Domains: domains from Entrez Structure: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Domains

BLAST (Basic Local Alignment Search Tool finds regions of local similarity between sequences): http://www.ncbi.nlm.nih.gov/BLAST/

Cancer Chromosomes: cytogenetic databases: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=CancerChromosomes

CDD: conserved protein domain database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd

Gene: gene-centered information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Genome Project: genome project information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj

Genome: whole genome sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

GENSAT: gene expression atlas of mouse central nervous system: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat

GEO DataSets: experimental sets of GEO data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds

GEO Profiles: expression and molecular abundance profiles: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo

HomoloGene: eukaryotic homology groups: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene

Nucleotide: sequence database (GenBank): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide

OMIA: online Mendelian Inheritance in Animals: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia

OMIM: online Mendelian Inheritance in Man: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

PopSet: population study data sets: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PopSet

Probe: sequence-specific reagents: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe

Protein: sequence database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

PubChem BioAssay: bioactivity screens of chemical substances: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcassay

PubChem Compound: unique small molecule chemical structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound

PubChem Substance: deposited chemical substance records: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance

SNP: single nucleotide polymorphism: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp

Structure: three-dimensional macromolecular structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

Taxonomy: organisms in GenBank: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy

UniGene: gene-oriented clusters of transcript sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene

UniSTS: markers and mapping data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists

Another source they provide is the Human Genome. This resource contains an entirely different list of great tools and resources. I encourage you to explore the Human Genome more on your own.

Human Genome (an integrated, one-stop, genomic information infrastructure for biomedical researchers): http://www.ncbi.nlm.nih.gov/genome/guide/

Last, for today, but not least, is the Genetics Home Reference (GHR). The GHR serves as a bridge between the technical information for researchers and the consumer or general public. It includes information on the correspondence between specific genes and diseases, diagnostic signs/symptoms, an much more. Although the information is for consumers, it can still be fairly technical. It includes a handbook and glossary, which helps, and provides information at a level that can also be useful for the clinician. In addition, they include a list of resources about genetic conditions specifically for clinicians.

NLM: Genetics Home Reference: http://ghr.nlm.nih.gov/

GHR: Genetics Resources for Clinicians and Health Professionals: http://ghr.nlm.nih.gov/ghr/resource/clinicians

Among their newest topics on conditions, you'll find Dentinogenesis Imperfecta and Amelogenesis Imperfecta. Among their new pages on specific genes, you'll find amelogenin (amelogenesis imperfecta 1, X-linked), dentin sialophosphoprotein (DSPP), enamelin, and matrix metallopeptidase 20 (MMP20 or enamelysin). They have also recently added information on a number of specific genes that are associated with the Charcot Marie Tooth Disease. Here is a sampling of pages on dental-related conditions and genes.

CONDITIONS:

Condition: Achondrogenesis: http://ghr.nlm.nih.gov/condition=achondrogenesis

Condition: Amelogenesis Imperfecta: http://ghr.nlm.nih.gov/condition=amelogenesisimperfecta

Condition: Dentinogensis imperfecta: http://ghr.nlm.nih.gov/condition=dentinogenesisimperfecta

Condition: Fibrodysplasia ossificans progressiva: http://ghr.nlm.nih.gov/condition=fibrodysplasiaossificansprogressiva

Condition: Greig cephalopolysyndactyly syndrome: http://ghr.nlm.nih.gov/condition=greigcephalopolysyndactylysyndrome

Condition: Platyspondylic lethal skeletal dysplasia, Torrance type: http://ghr.nlm.nih.gov/condition=platyspondyliclethalskeletaldysplasiatorrancetype

Condition: Sotos syndrome: http://ghr.nlm.nih.gov/condition=sotossyndrome

GENES:

Gene: DNM2: dynamin 2: http://ghr.nlm.nih.gov/gene=dnm2

Gene: MMP20: matrix metallopeptidase 20 (enamelysin): http://ghr.nlm.nih.gov/gene=mmp20

Gene: SH3TC2: SH3 domain and tetratricopeptide repeats 2: http://ghr.nlm.nih.gov/gene=sh3tc2

Gene: YARS: tyrosyl-tRNA synthetase: http://ghr.nlm.nih.gov/gene=yars

Posted by pfa at 02:16 PM | Comments (0)

July 19, 2006

Omics E-Books (Omics Series, 8)

Genomics, as a discipline or research field, is more mature than either proteomics or nanotechnology. This, combined with the observation that books usually represent a later stage in the life of an idea, justifies why most of the online or free e-books are about genomics. For this reason, today's selections are not organized in the three groups we have used in the other blog entries of this series. Instead, you will find a list of selected recent electronic books on a variety of Omics topics and other matters of interest to Omics researchers. As this is a small sampling, at the end of this entry are suggested tools and techniques for discovering additional books available online.


Ensuring an Infectious Disease Workforce: Education and Training Needs for the 21st Century - Workshop Summary. 2006. http://www.nap.edu/books/0309100100/html/51.html

GeneReviews. Pagon, Roberta A., Editor-in-chief; Cassidy, Suzanne B.; Bird, Thomas C.; Dinulos, Mary Beth; Feldman, Gerald L.; Smith, Richard J.H.; Dolan, Cynthia R.; Associate editors; Baskin, Patricia K., Technical editor. Seattle (WA): University of Washington; c1993-2006. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gene.TOC

Genes and Disease. Bethesda (MD): National Library of Medicine (US), NCBI. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2

Genetic Landscape of Diabetes. Dean, Laura; McEntyre, J.R. Bethesda (MD): National Library of Medicine (US), NCBI; 2004 Jun. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=diabetes.TOC&depth=1

Genomes 2nd ed. Brown, T.A. New York and London: Garland Science; c2002. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=genomes.TOC&depth=2

Genomic Signal Processing and Statistics. Edited by: Edward R. Dougherty, Ilya Shmulevich, Jie Chen, and Z. Jane Wang. 2005. http://books.google.com/books?vid=ISBN9775945070&id=0YGlW6Oo2kMC&printsec=frontcover

Globalization, Biosecurity, and the Future of the Life Sciences. 2006. http://www.nap.edu/openbook/0309100321/html/index.html

Human ATP-Binding Cassette (ABC) Transporter Superfamily. Dean, Michael. Bethesda (MD): National Library of Medicine (US), NCBI; 2002 Nov. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mono_001.TOC&depth=2

Human Molecular Genetics 2, 2nd ed. Strachan, Tom and Read, Andrew P. New York and London: Garland Science; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=hmg.TOC&depth=2

Implications of Nanotechnology for Environmental Health Research. 2005. http://www.nap.edu/openbook/0309095778/html/index.html

Informing the Future: Critical Issues in Health, Third Edition. 2005. http://www.nap.edu/catalog/11469.html

Introduction to Genetic Analysis, 7th ed. Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. New York: W. H. Freeman & Co.; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=iga.TOC

KEGG: Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/

KEGG2: Kyoto Encyclopedia of Genes and Genomes, 2nd edition. http://www.genome.jp/kegg/kegg2.html

KIR Gene Cluster. Carrington, Mary; Norman, Paul. Bethesda (MD): National Library of Medicine (US), NCBI; 2003. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mono_003.TOC&depth=2

Making Babies: reproductive decisions and genetic technologies, 31 January 2006. http://www.hgc.gov.uk/Client/document.asp?DocId=112&CAtegoryId=8

Mapping Protein/DNA Interactions by Cross-Linking. Paris: Institut National de la Santé et de la Recherche Médicale (INSERM); c2001. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=inserm.TOC

Medical Biotechnology: Achievements, Prospects and Perceptions. By Albert Sasson. http://books.google.com/books?vid=ISBN9280811142&id=WjC_e27xgUEC&printsec=titlepage

Modern Genetic Analysis. Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C. New York: W. H. Freeman & Co.; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mga.TOC

Molecular Imaging and Contrast Agent Database. Bethesda (MD): National Library of Medicine (US), NCBI; 2004-2005. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=micad.TOC

Nanotechnology for the Intelligence Community. 2005. http://www.nap.edu/openbook/0309096650/html/index.html

National Academies: Keck Futures Initiative. Designing Nanostructures at the Interface between Biomedical and Physical Systems: Conference Focus Group Summaries. 2005. http://www.nap.edu/openbook/0309096685/html/index.html

National Academies: Keck Futures Initiative. The Genomic Revolution -- Implications for Treatment and Control of Infectious Disease: Working Group Summaries. 2006. http://www.nap.edu/openbook/0309101093/html/index.html

Proceedings from the Workshop on Biomedical Materials at the Edge: Challenges in the Convergence of Technologies. 2006. http://www.nap.edu/openbook/030910209X/html/index.html

Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health. 2006. Board on Science, Technology, and Economic Policy (STEP); Science, Technology, and Law (STL). http://www.nap.edu/openbook/0309100674/html/index.html

Regenerative Medicine (Sackler NAS Colloquium). PNAS September 30, 2003; 100 (Suppl. 1). http://www.pnas.org/content/vol100/suppl_1/

Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. Koonin, Eugene V; Galperin, Michael Y. Norwell (MA): Kluwer Academic Publishers; c2003. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=sef.TOC&depth=1

Small Wonders, Endless Frontiers: A Review of the National Nanotechnology Initiative. 2002. http://www.nap.edu/openbook/0309084547/html/index.html

Utilization of genomic information for tropical disease drug and vaccine discovery. Report of a WHO/TDR Scientific Working Group, Geneva, 18-20 February 1998. http://www.who.int/tdr/publications/publications/genomic.htm

* WANT MORE?

Today's selections primarily highlight resources available free to the world via the Internet. There are many other excellent electronic books that are included in the collections of our libraries. To discover these, go into Mirlyn, click on "Command Language", then copy and paste in the following search string.

( WRD=( omics OR genomics OR proteomics OR nanotechnology ) ) and WTP=( CF | CE ) and WTP=BK


To discover additional free electronic books, try first browsing the collections available via the National Academies Press and the PubMed Bookshelf. Those include only peer-reviewed materials, usually of exceptional quality. It is also possible to search Google or WikiBooks to discover fulltext books online in various topics. Example searches are included below.

National Academies Press: http://www.nap.edu/

NCBI: PubMed: Bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books&itool=toolbar

Google Books: Genomics: http://books.google.com/books?q=genomics&btnG=Search+Books&as_brr=1

Google Books: Proteomics: http://books.google.com/books?q=proteomics&btnG=Search+Books&as_brr=1

WikiBooks: Proteomics: http://en.wikibooks.org/wiki/Proteomics

WikiBooks: Proteomics and Drug Discovery: http://en.wikibooks.org/wiki/Proteomics/Proteomics_and_Drug_Discovery

Google Books: Nanotechnology: http://books.google.com/books?q=nanotechnology&btnG=Search+Books&as_brr=1

Wikibooks: Nanotechnology: http://en.wikibooks.org/wiki/Nanotechnology

Posted by pfa at 08:23 AM | Comments (1)

July 18, 2006

Other International Omics Resources (Omics Series, 7)

The resources for today were selected to illustrate the range of resources and activities happening around the globe. These may represent initiatives at the level of a single country, or collaborative efforts involving a region. Just as with the United States governmental resources, these sites often provide a range of information including both education for the general public and indepth detailed resources for researchers. Researcher resources begin with publications and presentations continuing on to databases and datasets. The resources are usually available in English, although sometimes they are provided in multiple languages.


* GENERAL / MULTIDISCIPLINARY

Australian Research Council Centre in Bioinformatics (ACB): http://bioinformatics.org.au/

Bioinformatics Canada: http://bioinformatics.ca/

Canadian Bioinformatics Help Desk: http://gchelpdesk.ualberta.ca/servers/servers.php

European Bioinformatics Institute: http://www.ebi.ac.uk/

Hong Kong Bioinformatics Centre: http://www.hkbic.bch.cuhk.edu.hk/

Hong Kong Bioinformatics Centre: Biotechnology Dictionary: http://www.hkbic.bch.cuhk.edu.hk/BioTechDict/

National Research Council Canada: Molecular Sciences: Steacie Institute for Molecular Sciences (NRC-SIMS): http://steacie.nrc-cnrc.gc.ca/

UK: York Structural Biology Laboratory: http://www.ysbl.york.ac.uk/


* GENOMICS

Australia: Human Genetics Advisory Commission: http://www.nhmrc.gov.au/about/committees/hgac/index.htm

Australian National Genomic Information Service (ANGIS): http://www.angis.org.au/

Canada's Michael Smith Genome Sciences Center: http://www.bcgsc.ca/

Canadian Genetic Disease Network (CGDN): http://www.cgdn.ca/

Canadian Genome Education Centre: Centre d'éducation sur le génome: http://www.genomeeducation.ca/

Centre for Integrated Genomics: http://www.cigenomics.bc.ca/

Chinese Academy of Sciences: Beijing Genomics Institute: http://www.genomics.org.cn/bgi/english/index.htm

European Science Foundation Programme: Functional Genomics: http://www.functionalgenomics.org.uk/

Genome Canada: http://www.genomecanada.ca/

Karolinska Institutet: Center for Genomics & Bioinformatics (CGB): http://www.cgb.ki.se/

Kyoto University: Institute for Chemical Research: Bioinformatics Center: GenomeNet: http://www.genome.jp/

Medical Research Council (MRC): Toxicology Unit: Microarray and Bioinformatics: http://www.le.ac.uk/mrctox/microarray_lab

Netherlands Genomics Initiative: http://www.genomics.nl/

Sanger Institute: Genomics and Genetics at the Sanger Institute: http://www.sanger.ac.uk/genetics/

UK Human Genetics Advisory Commission (HGC): http://www.hgc.gov.uk/


* PROTEOMICS

Australian Proteome Analysis Facility: http://www.proteome.org.au/

Canada: Protein Engineering Network of Centres of Excellence (PENCE): http://www.pence.ca/
INCLUDES:
PENCE: Proteomics Resources: Directory of Proteomics in Canada

Canadian Proteomics Initiative: http://cpicanada.org/

Ontario Centre for Structural Proteomics: http://www.uhnres.utoronto.ca/proteomics

SPINE, Structural Proteomics in Europe: http://www.spineurope.org/


* NANOTECHNOLOGY

Canada: EthicsWeb: Ethical Issues in Nanotechnology: http://www.ethicsweb.ca/nanotechnology/

European Union: Thematic Network: Nanoforum.org (European Nanotechnology Gateway): http://www.nanoforum.org/

Institute of Nanotechnology (IoN) (UK): http://www.nano.org.uk/

Japan: National Institute of Advanced Industrial Science and Technology: Nanotechnology Research Institute (NRI): http://unit.aist.go.jp/nanotech/

National Institute for Nanotechnology / Institut national de nanotechnologie: http://nint-innt.nrc-cnrc.gc.ca/home/index_e.html

National Research Council Canada: Nanotechnology: http://www.nrc-cnrc.gc.ca/randd/areas/nanotechnology_e.html

Royal Society / Royal Academy of Engineering: Nanotechnology and Nanoscience: http://www.nanotec.org.uk/

Posted by pfa at 02:59 PM | Comments (0)

July 17, 2006

Genomics and the World Health Organization (Omics Series, 6)

The World Health Organization is a non-governmental organization that is a rich resource for information in global and public health. In this role, it has made available a number of resources on genetics and genomics, particularly with respect to birth defects and genetically modified foods. Here are the two most significant collections of resources and activities relevant to Omics from the WHO.

World Health Organization (WHO): Human Genetics Programme: http://www.who.int/genomics/
Publications: http://www.who.int/genomics/publications/en/index.html
INCLUDES:
* Genetics, genomics and the patenting of DNA: Review of potential implications for health in developing countries (2005)
* Global registry and database on craniofacial anomalies (2003)
* World Atlas of Birth Defects (2003)
* Global Strategies to Reduce the Health Care Burden of Craniofacial Anomalies (2001)

World Health Organization (WHO): Genomic Resource Centre: http://www.who.int/genomics/anomalies/cfaproject/en/
INCLUDES:
"Ask the expert"
"Send your questions about genomics to members of a judiciously selected group of health professionals in genetics and related disciplines, who are committed to the development of genomics, public health systems and public engagement in the development of science and technology."


Here is a sampling of some of the additional resources they have made available in this area of enquiry.


Biotechnology (GM Foods): http://www.who.int/foodsafety/biotech/en/

Craniofacial Anomalies Directory of Resources: http://www.who.int/genomics/anomalies/cfadirectory/en/
INCLUDES: Patient support groups; Epidemiological and Genetic databases; Organizations & institutes; Articles.

Diagnostics for the Developing World [PDF: 236KB]:
http://www.who.int/std_diagnostics/publications/Diagnostics%20for%20the%20developing%20world.pdf

Executive course on genomics and public health policy: http://www.emro.who.int/rpc/pdf/GenomicsCourse-2003.pdf

Food Standards (Codex Alimentarius): http://www.who.int/foodsafety/codex/en/

International Collaborative Research on Craniofacial Anomalies: http://www.who.int/genomics/anomalies/en/

International Database on Craniofacial Anomalies (IDCFA): http://www.who.int/genomics/anomalies/idcfa/en/

Introduction to biotechnology: http://whqlibdoc.who.int/publications/2004/9241546506_partV.pdf

Public Health: Innovation and Intellectual Property Rights ... April 2006: http://www.who.int/intellectualproperty/en/

20 questions on genetically modified foods: http://www.who.int/foodsafety/publications/biotech/20questions/en/

Workshop on Application of Proteomics and Transcriptomics in EMF Research (30 October - 1 November 2005 / Helsinki, Finland): http://www.who.int/peh-emf/meetings/proteomics_helsinki05/en/

Posted by pfa at 09:50 AM | Comments (0)

July 14, 2006

National Governmental Omics Resources (Omics Series, 5)

As in so many other ways, the United States government has taken a leading role in providing information resources in leading edge topics, such as omics. There are a number of national initiatives and research centers that provide educational support, research resources, funding opportunities, technical information, and much more. This is a small sampling, including only the major sources in these topics from the US goverment.

* CROSS-DISCIPLINARY

Oak Ridge National Laboratory: Life Sciences Division: http://lsd.ornl.gov [See: Research Tools: http://lsd.ornl.gov/tools.html]

NIH: Roadmap for Medical Research: http://nihroadmap.nih.gov/

President's Council on Bioethics: http://www.bioethics.gov/


* GENOMICS

Argonne National Laboratory (ANL): Midwest Center for Structural Genomics: http://www.mcsg.anl.gov/

Brookhaven National Laboratory (BNL): Genome Group: http://www.genome.bnl.gov/

CDC: Genomics and Disease Prevention: http://www.cdc.gov/genomics/

DOE: Human Genome Project: Genomics Primers: Genomics and Its Impact on Science and Society: The Human Genome Project and Beyond (2003): http://www.ornl.gov/sci/techresources/Human_Genome/publicat/primer/index.shtml

DOE: Joint Genome Institute: http://www.jgi.doe.gov/

Lawrence Berkeley National Laboratory: Arkin Laboratory for Dynamical Genomics: http://genomics.lbl.gov/

Lawrence Livermore National Laboratory: Biosciences Directorate: Human Genome Center: http://bbrp.llnl.gov/genome/genome.html

Library of Congress: Selected Internet Resources: Molecular Biology and Bioinformatics: http://www.loc.gov/rr/scitech/selected-internet/molecular.html

National Human Genome Research Institute: http://www.genome.gov/

National Institute of Allergy and Infectious Diseases (NIAID): Pathogen Functional Genomics Resource Center (PFGRC): http://pfgrc.tigr.org/

NIH: Computational Molecular Biology: http://molbio.info.nih.gov/

NIH: NCBI: What Is a Genome: http://www.ncbi.nih.gov/About/primer/genetics_genome.html

NIH: NCI: The Genomics and Bioinformatics Group: http://discover.nci.nih.gov/


* PROTEOMICS

Argonne National Laboratory (ANL): Proteomics: http://gelbank.anl.gov/

FDA: National Center for Toxicological Research (NCTR): Center for Proteomics: http://www.fda.gov/nctr/science/centers/proteomics/index.htm

National Center for Research Resources (NCRR): Proteomics: Proteomics Research Resource for Integrative Biology at PNNL: http://ncrr.pnl.gov/

NIH: NCI: Clinical Proteomic Technologies for Cancer: http://proteomics.cancer.gov/


* NANOTECHNOLOGY

CDC: NIOSH Safety and Health Topic: Nanotechnology: http://www.cdc.gov/niosh/topics/nanotech/

FDA: Nanotechnology: http://www.fda.gov/nanotechnology/

Library of Congress: Nanotechnology: Science Tracer Bullets - Research Finding Aids from the Library of Congress, Science Reference Services: http://www.loc.gov/rr/scitech/tracer-bullets/nanotechnologytb.html

Library of Congress: Nanotechnology: Selected Internet Resources in Nanotechnology: http://www.loc.gov/rr/scitech/selected-internet/nanotechnology.html

NASA: Center for Nanotechnology: http://www.ipt.arc.nasa.gov/

National Nanotechnology Initiative: http://www.nano.gov/

NIH: NCI: Alliance for Nanotechnology in Cancer: http://nano.cancer.gov/

NIH: NCI: Nanotechnology Characterization Lab (NCL): http://ncl.cancer.gov/

NIST: Center for Nanoscale Science and Technology: http://cnst.nist.gov/

NSF: National Nanotechnology Initiative (NNI): http://www.nsf.gov/crssprgm/nano/

Sandia National Labs: Nanotechnology: http://nano.sandia.gov/


* WANT MORE?

Google: (omics OR genomics OR proteomics OR nanotechnology) site:.gov

Science.gov: Applied Science & Technologies: Nanotechnology: http://www.science.gov/browse/w_113P.htm

Posted by pfa at 01:51 PM | Comments (0)

July 13, 2006

Omics Institutes and Research Centers (Omics Series, 4)

Research centers and institutes are excellent sources not jsut of training but also cutting edge research, recent publications, innovative techniques, custom databases and software tools, and links to core resources. If you are trying to discover more about any of the omics areas or are seeking partners for collaboration, these are great resources. There are many research centers and institutes around the world in these areas, ranging from those embedded in educational or government organizations, independent organizations, and commercial research entities. The following list highlights a few of the leaders in all these areas. At the end of this entry there is a web search if you want to discover more like these.

* GENOMICS

Institute of Genomics and Integrative Biology: http://www.igib.res.in/

North Carolina Center for Genomics and Public Health: http://www.sph.unc.edu/nccgph/

Novartis Research Foundation: Genomics Institute: http://www.gnf.org/

Pennsylvania State University: Center for Nanotechnology Education and Utilization: http://www.cneu.psu.edu/

The Genomics and Bioinformatics Group: http://discover.nci.nih.gov/

The Genomics Institute: http://www.wadsworth.org/genomics/

The Institute for Genomic Research (TIGR): http://www.tigr.org/

University of Michigan Center for Genomics and Public Health: http://www.sph.umich.edu/genomics

University of Washington Center for Genomics and Public Health: http://depts.washington.edu/cgph


* PROTEOMICS

Harvard Institute of Proteomics: http://www.hip.harvard.edu/

Johns Hopkins: NHLBI Proteomics Center: http://www.proteomics.jhu.edu/

Yale: NHLBI Proteomics Center: http://info.med.yale.edu/nhlbi-proteomics/


* NANOTECHNOLOGY

Center for Responsible Nanotechnology: http://www.crnano.org/

Foresight Institute: Nanotechnology: http://www.foresight.org/

Institute for Nanotechnology: http://www.ctn.northwestern.edu/

Institute of Nanotechnology (UK): http://www.nano.org.uk/

NanoTechnology Institute: http://www.nanotechinstitute.org/

NASA: Center for Nanotechnology: http://www.ipt.arc.nasa.gov/

University of Wisconsin: Center for NanoTechnology (CNTech): http://www.nanotech.wisc.edu/

Washington University: The Center for Nanotechnology: http://www.nano.washington.edu/


* WANT MORE?

Google: (institute OR center) (genomics OR proteomics OR nanotechnology) -site:.com

Posted by pfa at 12:20 PM | Comments (0)

July 12, 2006

Omics Tutorials and Training (Omics Series, 3)

So, where can you go to learn more about Omics? There are a variety of both online tutorials for specific tasks, as well as training programs and "boot camp" tutorials that require registration and personal attendance. We'll start with local resources, and then go on to a sampling of online resources in the specific topics.


* MICHIGAN

- Hot off the press! Just announced today, you might want to register for the upcoming short course on information resources in bioinformatics and omics.

National Center for Biotechnology Information: Short Course, September 2006 (Hosted by the Program in Bioinformatics, Department of Human Genetics & Taubman Medical Library): http://www.hg.med.umich.edu/ncbi/

- Michigan (General)

Michigan Proteome Consortium: Training: http://www.proteomeconsortium.org/training.html


- University of Michigan

Center for Computational Medicine and Biology: http://www.ccmb.med.umich.edu/

Center for Proteomics Training (requires UM login): http://sitemaker.umich.edu/gannon

Michigan Nanotechnology Institute for Medicine and Biological Sciences: http://nano.med.umich.edu/

School of Public Health: Michigan Public Health Training Center: Six Weeks to Genomic Awareness: https://www.sph.umich.edu/iscr/mphtc/courses/one-online-course.cfm?id=108


- Michigan State University

MSU Proteomics: http://proteomics.msu.edu/

MSU Genomics: Research Technology Support Facility: http://genomics.msu.edu/

Nanoscale Interdisciplinary Research Team (NIRT): http://nirt.pa.msu.edu/


* OMICS (General)

Genetic Engineering News has an Omics skills-building tutorial article in almost every issue of the journal. Here are a few example of past tutorial articles, but you may want to browse the journal for more.

Genetic Engineering News: http://www.genengnews.com/

Tutorial: Omics: Next-Generation RNA Interference: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1321

Tutorial: Omics: Assay: Parallel Approaches to Target Identification: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1708

Tutorial: Omics: Barcoding and Automated Electophoresis: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1769


* GENOMICS

Genomic Awareness: http://www.genomicawareness.org/

Genome Biology: Tutorials: http://genomebiology.com/tutorials/

Keck-UNM Genomics Resource: A Primer for Using Microarrays in Biomedical Applications: http://hsc.unm.edu/som/micro/Genomics/newbies.html

M.D. Anderson: Bioinformatics: Tutorials (microarrays): http://bioinformatics.mdanderson.org/tutorial.html

United States: CDC: Genomics: Training: Six Weeks To Genomics Awareness: http://www.cdc.gov/genomics/training/sixwks.htm


* PROTEOMICS

National Center for Research Resources: Proteomics: Training and Protocols: http://ncrr.pnl.gov/training/

Proteome Software: Tutorials on Proteomics For Scientists: http://www.proteomesoftware.com/Proteome_software_link_tutorials.html

Proteomics: 2D electrophoresis for proteomics tutorial / by James R. Jeffries: http://www.aber.ac.uk/~mpgwww/Proteome/Tut_2D.html

Proteomics: Protein identification (PMF) tutorial / by James R. Jeffries: http://www.aber.ac.uk/~mpgwww/Proteome/MS_Tut.html

Spot the Difference: Analysing Gel Images for Proteomics (Roland Wilson): http://www.dcs.warwick.ac.uk/~rgw/spot/index.html


* NANOTECHNOLOGY

Nanotechnology Characterization Lab (NCL): Education & Training: http://ncl.cancer.gov/working_education-training.asp

Nanotechnology Industries: Education and Career: http://www.nanoindustries.com/edu.html

National Nanotechnology Infrastructure Network (NNIN): Education Portal: Nanotechnology: http://www.nnin.org/nnin_edu.html

Pacific Nanotechnology: Atomic Force Microscopes - Tutorial Page: http://www.pacificnanotech.com/afm-tutorial.html


* WANT MORE?

Google Search: (training OR tutorial) (genomics OR proteomics OR nanotechnology) -site:.com

Posted by pfa at 03:48 PM | Comments (0)

July 11, 2006

General Resources about Genomics, Proteomics and Nanotechnology (Omics Series, 2)

Yesterday's blog focused on introductory resources describing a few core omics concepts. Today we are providing resources that are more technical, as well as a couple of sources that list the over 300 different types of "omics" research areas. Each section includes web resources, searches for more information and collections of general articles on these topics.

* OMICS

- Books (Dentistry Library)

Bioinformatics : a practical guide to the analysis of genes and proteins / edited by Andreas D. Baxevanis, B.F. Francis Ouellette. 2005. Dentistry - Books - In the Book Stacks | QH 324.2 .B5471 2005

The dictionary of gene technology : genomics, transcriptomics, proteomics / Günter Kahl. 2001. Dentistry - Reference - Main Floor | QH 506 .K3331 2001

Redei, G. P. Encyclopedic dictionary of genetics, genomics, and proteomics / George P. Rédei. 2003. Dentistry - Reference - Main Floor | QH 430 .R432 2003

- Terms, Citations, Searches

Argus Biotech: Current topics in biotechnology: X-omes & X-omics: http://www.argosbiotech.de/700/omics/Xomics.htm

Biodirectory: Omics: http://www.biodirectory.com/directory/Top/Omics_274.html

CiteULike: Tag: Omics: http://www.citeulike.org/tag/omics

Connotea: Tag: Omics: http://www.connotea.org/tag/omics

Google Scholar: Omics

- Resources

Nature: Omics Gateway: http://www.nature.com/omics/index.html

OmicsWorld: http://www.omicsworld.com/

Omics Wiki: http://omics.org/


* GENOMICS

- Books (Dentistry Library)

Brown, Stuart M. Essentials of medical genomics / Stuart M. Brown ; with contributions by John G. Hay and Harry Ostrer. 2003. Dentistry - Books - In the Book Stacks | RB 155 .B6741 2003

Human genome epidemiology : a scientific foundation for using genetic information to improve health and prevent disease / edited by Muin J. Khoury, Julian Little, Wylie Burke. 2004. Dentistry - Books - In the Book Stacks | RB 155.5 .H861 2004

Recombinant gene expression : reviews and protocols / edited by Paulina Balbás and Argelia Lorence. 2004. Dentistry - Books - In the Book Stacks | QH 443 .R361 2004


- Terms, Citations, Searches

Google Scholar: Genomics

Wikipedia: Genomics: http://en.wikipedia.org/wiki/Genomics

- Resources

PLoS Primer: Comparative Genomics: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000058

Functional Genome Analysis / by Dr Jörg Hoheisel: http://www.dkfz-heidelberg.de/funct_genome/index.html

Functional Genomics / by Y.F. Leung: http://ihome.cuhk.edu.hk/~b400559/

Functional Genomics Experiment (FuGE): http://fuge.sourceforge.net/
NOTE: "Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards."

Human Genome Project: http://www.doegenomes.org/

The Institute for Genomic Research (TIGR): http://www.tigr.org/

Translational Genomics Research Institute: http://www.tgen.org/

International Genomics Consortium: http://www.intgen.org/


* PROTEOMICS

- Books (Dentistry Library)

Protein arrays, biochips and proteomics : the next phase of genomic discovery / edited by Joanna S. Albala, Ian Humphery-Smith. 2003. Dentistry - Books - In the Book Stacks | QP 551 .P6957 2003

Proteomics of microorganisms : fundamental aspects and application / volume editors, M. Hecker, S. Müllner. 2003. Dentistry - Books - In the Book Stacks | TP 248.3 .P76 2003

Westermeier, Reiner. Proteomics in practice : a laboratory manual of proteome analysis / Reiner Westermeier, Tom Naven. 2002. Dentistry - Books - In the Book Stacks | QP 551 .W47 2002

- Terms, Citations, Searches

Google Scholar: Proteomics

Wikipedia: Proteomics: http://en.wikipedia.org/wiki/Proteomics

- Resources

ExPASy Proteomics Server: http://www.expasy.org/

Nature: Focus on Proteomics: http://www.nature.com/reviews/focus/proteomics/index.html

Protein Society: http://www.proteinsociety.org

PROWL - a resource for protein chemistry and mass spectrometry: http://prowl.rockefeller.edu/

Science: Functional Genomics Resources: Proteomics: http://www.sciencemag.org/feature/plus/sfg/resources/res_proteomics.dtl


* NANO

- Books (Dentistry Library)

Luo, Jiazhong. Inorganic-organic nanocomposites formed using porous ceramic particles. 1998. Dentistry - Books - In the Book Stacks | RK 655 .L86 1998a

Mann AB, Dickinson ME. "Nanomechanics, chemistry and structure at the enamel surface." IN: The teeth and their environment : physical, chemical and biochemical influences / volume editor, Ralph M. Duckworth. 2006. Dentistry - Books - In the Book Stacks | RK 305 .T441 2006

- Terms, Citations, Searches

Google Scholar: Nano

Wikipedia: Nanotechnology: http://en.wikipedia.org/wiki/Nanotechnology

- Resources

NanoWerk: Introduction to Nanomaterials: http://www.nanowerk.com/n_nanomaterials_1.html

NanotechWeb.org: http://nanotechweb.org/
INCLUDES: News, events, press releases, the journal Nanotechnology, opinions / editorials, features, jobs, "nano & society" article archive, resources and links

Ralph Merkle's Nanotechnology Homepage: http://www.zyvex.com/nano/
INCLUDES: articles, awards, FAQs, groups / organizations,

National Nanotechnology Initiative: http://www.nano.gov/

Nanotechnology Now: http://www.nanotech-now.com/

Nanotechnology - Foresight Institute: http://www.foresight.org/

Scientific American Magazine (April 2004): The First Nanochips

Posted by pfa at 12:53 PM | Comments (0)

July 10, 2006

Background Information about Omics (Omics Series, 1)

To start our series off, we'd like to some definitions and background information about Omics for people who are new to the topic. The resources listed below also include a number of glossaries and terminology tools that may be useful for researchers.

Glossaries

This first resource (from ColorBasePair) is a nice, relatively simple, one-page overview of just the primary concepts -- what are genomics, proteomics, and nanotechnology. A useful starting place.

ColorBasePair: What is Bioinformatics: Bioinformatics Definitions
http://www.colorbasepair.com/what_is_bioinformatics.html

Here are two glossaries from reputable sources, both moderately sized -- bigger than a loaf of bread and smaller than a building, to describe it colloquially.

Genomics & Proteomics Magazine: Glossary:
http://www.genpromag.com/Glossary.html

National Cancer Institute: Clinical Proteomic Technologies for Cancer: Glossary:
http://proteomics.cancer.gov/resource_room/glossary.asp

This next glossary is a motherlode of technical jargon and definitions, with over 5,000+ definitions compiled & edited by Mary Chitty, the head librarian for Cambridge Healthtech Institute. Truly a masterful and comprehensive resource, frequently updated, so always current and at the cutting edge. The place to go when you aren't sure about a new term.

Genomic Glossaries (BioPharmaceutical Glossary, Taxonomies and guide to 21st century therapeutics, technologies and trends):
http://www.genomicglossaries.com/
INCLUDES:
* Molecular Diagnostics & Molecular Medicine glossary:
http://www.genomicglossaries.com/CONTENT/clinical_genomics_email.asp
* Biology: Basic genetics & genomics: Basic biopharmaceutical genetics & genomics:
http://www.genomicglossaries.com/CONTENT/Basic_Genetic_Glossaries.asp


What is Genomics?

The following resources describe what genomics is for a variety of audiences, from children and the general public (NOVA and the DoE) to resources for a more advanced audience.

Canada: BioPortal: BioBasics: Genomics: http://biobasics.gc.ca/english/View.asp?x=738

Comparative Genomics Tutorial (Phillipe Gautier): http://rsat.scmbb.ulb.ac.be/rsat/Comparative_Genomics/tutorial/

United States: Department of Energy (DoE): Joint Genomics Institute: Education: http://www.jgi.doe.gov/education/index.html
Includes: An Introduction to Genomics; How Sequencing is Done; Historical Timeline

NOVA: Sequence for Yourself: http://www.pbs.org/wgbh/nova/genome/sequencer.html


What is Proteomics?

This group of resources about what is proteomics tends to focus on resources appropriate for persons and high school and older.

Annenberg/CPB: Rediscovering Biology: Unit 2, Proteins and Proteomics: What is Proteomics?:
http://www.learner.org/channel/courses/biology/textbook/proteo/proteo_1.html

Children's Hospital Boston: Introduction to Proteomics: http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
INCLUDES:
Guide to Sequencing and Identifying Proteins:
http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
The Basics: http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P1.html

United States: National Cancer Institute: Explore Proteomic Technologies and Cancer:
http://proteomics.cancer.gov/resource_room/animation.asp


What is Nanotechnology?

NanoWord: Introduction to Nanotechnology / by Steve Lenhert, Quanteq, LLC:
http://www.nanoword.net/pages/intro.htm
INCLUDES: A Brief History of Nanotechnology

MITRE: Introduction to Nanotechnology and Nanocomputers (Tutorial):
http://www.mitre.org/tech/nanotech/intronano.html

Nanotechnology Now: Nanotechnology Introduction:
http://www.nanotech-now.com/introduction.htm

Harper, Tim. What is Nanotechnology? (Institute of Physics)
2003 Nanotechnology 14: http://www.iop.org/EJ/abstract/0957-4484/14/1/001

Institute of Nanotechnology (UK): Glossary: http://www.nano.org.uk/nano/glossary.htm


Want More?

Want to know more or explore on your own? Here are some web searches to find materials similar to those above.

Google (for web pages only): (genomics proteomics (nanotech OR ~nanotechnology)) ("what is" OR definitions OR glossary OR dictionary)

a9 (finds books and more, in addition to web pages): (genomics proteomics nanotechnology) (definitions OR glossary OR dictionary)

Posted by pfa at 01:58 PM | Comments (1)

Introducing our Omics Blog Series

This time of year, new graduate students are flooding into the School and faculty are intensely working on their research projects while the teaching course load is somewhat lighter than during September through May.

While there are a variety of research areas and interests, the University of Michigan and the School of Dentistry have a committed interest in the research areas that have come to be known popularly as "Omics" (genomics, proteomics, nanotechnology, and related bioinformatics concepts).

In the interests of providing useful information for those working in these areas and those who would like to know more about what their colleagues might be doing, the Dentistry Library today begins a roughly two week series of blog entries on OMICS.

The entire collection of entries will be collected at this location, with more added periodically in the future:

http://mblog.lib.umich.edu/dentlib/archives/resources/research/omics/index.html

Posted by pfa at 01:40 PM | Comments (1)