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	<title>Discovery New Media</title>
	<atom:link href="http://www.walterjessen.com/feed/" rel="self" type="application/rss+xml" />
	<link>http://www.walterjessen.com</link>
	<description>Walter Jessen</description>
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		<title>2012: The Year of Content</title>
		<link>http://www.walterjessen.com/blog/2012-the-year-of-content/</link>
		<comments>http://www.walterjessen.com/blog/2012-the-year-of-content/#comments</comments>
		<pubDate>Thu, 17 May 2012 19:19:28 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Content]]></category>
		<category><![CDATA[audience]]></category>
		<category><![CDATA[brand]]></category>
		<category><![CDATA[brand consistency]]></category>
		<category><![CDATA[brand message]]></category>
		<category><![CDATA[branded online destination]]></category>
		<category><![CDATA[content marketing]]></category>
		<category><![CDATA[content strategy]]></category>
		<category><![CDATA[niche]]></category>
		<category><![CDATA[readers]]></category>
		<category><![CDATA[self-promotion]]></category>
		<category><![CDATA[social media marketing]]></category>
		<category><![CDATA[strategy]]></category>
		<category><![CDATA[Value]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=6633</guid>
		<description><![CDATA[Forbes labeled 2012 as "The Year of Content" and outlined five strategic steps for social media marketing and content marketing success.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">L</span>ate last year, <a href="http://www.forbes.com/sites/work-in-progress/2011/12/29/cash-in-on-content-and-social-media-marketing-in-2012/">Forbes labeled 2012 as &#8220;The Year of Content&#8221;</a> and outlined five strategic steps for social media marketing and content marketing success. With almost half the year behind us, now seemed like a good time to review their strategy. </p>
<div style="width:564px;margin:auto;"><img src="http://www.walterjessen.com/wp-content/uploads/2012/05/content.jpg" alt="Content" title="Content" width="564" height="291" class="alignnone size-full wp-image-6647" /></div>
<p>Let&#8217;s start with a definition: what is content marketing? </p>
<p><strong>Content marketing</strong> is the creation and publication of original content to generate leads, enhance a brand&#8217;s visibility, and put the company&#8217;s subject matter expertise on display.</p>
<h3>1. Begin with Branding</h3>
<p>What&#8217;s your brand? How do you want to be known? Determine your niche and focus on it as your primary brand message. In today&#8217;s information-rich media environment, <a href="http://www.longtail.com/the_long_tail/2007/02/why_niche_brand.html">niche brands win</a>. Your audience needs to develop expectations for your brand to develop confidence in and loyalty to it. It&#8217;s critical to meet your audience&#8217;s expectations in every interaction. Brand consistency is key.</p>
<h3>2. Create your Branded Online Destinations</h3>
<p>Where are you directing readers? Choose one branded online destination to be your core destination. Fragmenting content and conversation across multiple destinations is risky and can confuse readers. Your branded online destination will be the central hub of your online presence and will become the go-to place for people to learn everything about your brand. It&#8217;s important that you keep your branded online destination fresh with new content that effectively represents your brand promise and invites interaction and sharing.</p>
<h3>3. Find Your Best Audience</h3>
<p>Who is your target market and what are your users&#8217; goals? Who do you want to connect with online? Use Google to search keywords your audience is likely to use to find brands, businesses, content and conversations like yours. Once you find your audience, observe and listen. What topics are important to them? What gets them excited? As you develop your branded online destination, pay attention to the content that resonates with your readers. Understanding what your audience wants and needs is a necessary step in developing a content strategy.</p>
<h3>4. Join the Conversation</h3>
<p>Interact with your audience. Avoid self-promotion. Apply the 80-20 rule, and make sure 80% of the time you are creating value to your audience. Provide a resource for readers first, then worry about enticing potential clients.</p>
<h3>5. Publish Shareworthy Content</h3>
<p>By creating content that is valuable to your audience, you create something that readers want to share with their friends, colleagues, and connections. Additionally, the Google search algorithm ranks websites with many incoming links (particularly from authoritative sites and especially from social media) higher than results with few incoming links.</p>
<p>With all of these steps, remember that content quality trumps quantity. Organic growth of readers truly interested in your brand will deliver the best long-term growth results. </p>
<p>How does your content marketing strategy measure up?</p>]]></content:encoded>
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		<title>Point-and-click: May 9th, 2012</title>
		<link>http://www.walterjessen.com/blog/point-and-click-may-9th-2012/</link>
		<comments>http://www.walterjessen.com/blog/point-and-click-may-9th-2012/#comments</comments>
		<pubDate>Thu, 10 May 2012 00:20:02 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Points of Interest]]></category>
		<category><![CDATA[AAPS]]></category>
		<category><![CDATA[Covance]]></category>
		<category><![CDATA[dinner]]></category>
		<category><![CDATA[discovery park]]></category>
		<category><![CDATA[Elsevier]]></category>
		<category><![CDATA[fortune magazine]]></category>
		<category><![CDATA[information]]></category>
		<category><![CDATA[Life]]></category>
		<category><![CDATA[life science]]></category>
		<category><![CDATA[medical meeting]]></category>
		<category><![CDATA[park]]></category>
		<category><![CDATA[point and click]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=6567</guid>
		<description><![CDATA[A digest of news and information articles, focused primarily on health and life science, shared via social media.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">A</span>ttended a really great talk from Lilly&#8217;s Jamie Dananberg on personalized medicine tonight at an #AAPS dinner: <a href="http://t.co/c80rQ3TG">http://t.co/c80rQ3TG</a> #pm101</p>
<p>Life after Elsevier: making open access to scientific knowledge a reality <a href="http://t.co/N7qDpkAL">http://t.co/N7qDpkAL</a> #OpenAcess</p>
<p>Covance Among Fortune Magazine&#8217;s &#8220;World&#8217;s Most Admired Companies&#8221; <a href="http://t.co/UknHJIsj">http://t.co/UknHJIsj</a></p>
<p>Discovery park marks milestone http://bit.ly/JgbHcI</p>
<p>Content Curators Are The New Superheros Of The Web <a href="http://t.co/x2euhqtR">http://t.co/x2euhqtR</a></p>
<p>Purdue set to start building life sciences park http://bit.ly/JVZ6ZF</p>
<p>Rebooting the medical meeting – 9 lessons from TEDMED <a href="http://t.co/Mnvzt4Op">http://t.co/Mnvzt4Op</a></p>
<p><span style="float: right;"><em>All links shared via Twitter &#8211; <a href="http://www.twitter.com/wjjessen">follow along!</a></em></span></p>]]></content:encoded>
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		<title>Point-and-click: April 16th, 2012</title>
		<link>http://www.walterjessen.com/blog/point-and-click-april-16th-2012/</link>
		<comments>http://www.walterjessen.com/blog/point-and-click-april-16th-2012/#comments</comments>
		<pubDate>Mon, 16 Apr 2012 09:00:25 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Points of Interest]]></category>
		<category><![CDATA[Apple]]></category>
		<category><![CDATA[bioinformatics and computational biology]]></category>
		<category><![CDATA[biomarker]]></category>
		<category><![CDATA[Biomarker Commons]]></category>
		<category><![CDATA[BYOD]]></category>
		<category><![CDATA[computational]]></category>
		<category><![CDATA[Facebook]]></category>
		<category><![CDATA[Glasses]]></category>
		<category><![CDATA[google]]></category>
		<category><![CDATA[half a million]]></category>
		<category><![CDATA[infected]]></category>
		<category><![CDATA[Kaggle]]></category>
		<category><![CDATA[mac computers]]></category>
		<category><![CDATA[malware]]></category>
		<category><![CDATA[Should]]></category>
		<category><![CDATA[Smart]]></category>
		<category><![CDATA[smart companies]]></category>
		<category><![CDATA[Target]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5908</guid>
		<description><![CDATA[A digest of news and information articles, focused primarily on health and life science, shared via social media.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">B</span>iomarker Commons releases biomarker-disease data: <a href="http://t.co/IffSe5jC">http://t.co/IffSe5jC</a> Poster: <a href="http://t.co/vVCsrdp4">http://t.co/vVCsrdp4</a></p>
<p>BYOD is unstoppable. Smart companies must build apps. <a href="http://t.co/8HnJj6NQ">http://t.co/8HnJj6NQ</a></p>
<p>Half a million Mac computers &#8216;infected with malware&#8217; <a href="http://t.co/xcuv7hwE">http://t.co/xcuv7hwE</a></p>
<p>Apple and Facebook Should Be Terrified Of Google-tinted Glasses <a href="http://t.co/7hgoIfad">http://t.co/7hgoIfad</a></p>
<p>For decades, Target has collected vast amounts of data on shoppers. How Companies Learn Your Secrets <a href="http://ow.ly/a6wzz">http://ow.ly/a6wzz</a></p>
<p>Kaggle hosts contests for data scientists: <a href="http://t.co/A01UAb5I">http://t.co/A01UAb5I</a></p>
<p>TopHat 2.0.0 released from the Center for Bioinformatics and Computational Biology at University of MD http://t.co/frIKa4J9</p>
<p>Special issue of Science focusing on Computational Biology http://t.co/X1n8XfYS</p>
<p><span style="float: right;"><em>All links shared via Twitter &#8211; <a href="http://www.twitter.com/wjjessen">follow along!</a></em></span></p>]]></content:encoded>
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		<title>A Robust Market for Computational Biologists</title>
		<link>http://www.walterjessen.com/blog/a-robust-market-for-computational-biologists/</link>
		<comments>http://www.walterjessen.com/blog/a-robust-market-for-computational-biologists/#comments</comments>
		<pubDate>Fri, 13 Apr 2012 02:46:38 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Science]]></category>
		<category><![CDATA[big data]]></category>
		<category><![CDATA[bioengineering genetics]]></category>
		<category><![CDATA[Biologists]]></category>
		<category><![CDATA[blockbuster drugs]]></category>
		<category><![CDATA[computational]]></category>
		<category><![CDATA[computational biologists]]></category>
		<category><![CDATA[computational biology]]></category>
		<category><![CDATA[disease associations]]></category>
		<category><![CDATA[genes and diseases]]></category>
		<category><![CDATA[genomic data]]></category>
		<category><![CDATA[genotypes and phenotypes]]></category>
		<category><![CDATA[pharma]]></category>
		<category><![CDATA[pharmaceutical scientists]]></category>
		<category><![CDATA[training]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=6532</guid>
		<description><![CDATA[An article discussing the burgeoning field of Computational Biology was just published on the Science Careers website. ]]></description>
			<content:encoded><![CDATA[<p><span class="drop">A</span>n article discussing the burgeoning field of Computational Biology was just published on the Science Careers website.</p>
<p>For the biopharmaceutical industry, <a href="http://www.walterjessen.com/blog/tag/big-data/">big data</a> is the abundant and ever-growing compendium of <a href="http://www.walterjessen.com/blog/tag/disease-associations/">disease associations</a> and <a href="http://www.walterjessen.com/blog/tag/genomic-data/">genomic data</a> that is (in many cases) publicly available. Instead of following the traditional pharma paradigm of systematically testing the effects of known compounds, computational biologists can now mine petabytes of data to identify linkages between <a href="http://www.walterjessen.com/blog/tag/genotypes-and-phenotypes/">genotypes and phenotypes</a>, and <a href="http://www.walterjessen.com/blog/tag/genes-and-diseases/">genes and diseases</a> to identify potential therapeutic candidates that corroborate drug screening data.</p>
<p>Indeed, I do this all the time! I&#8217;m frequently mining  and integrating data, building molecular interaction networks, and evaluating targets or indications before I ever need to &#8220;dig in&#8221; to specific drug data. From this process, I often know <em>which types of drug data</em> I need to focus on.</p>
<p>The Science Careers article highlights the growing demand for computational biologists:</p>
<blockquote><p>As the pharmaceutical industry&#8217;s blockbuster drugs fall off the patent cliff, with precious few drugs in the pipeline to replace them, there are signs that big pharma could turn more of its attention to biologically derived medicines. If that happens, computational biologists will likely play a leading role in their discovery, [says Russ Altman, a professor of bioengineering, genetics, and medicine and director of the biomedical informatics training program at Stanford University in Palo Alto, California].</p>
<p>Altman says that according to his own observations, demand for computational biologists far outstrips supply. “I was just talking to a colleague the other day from a major drug company who came in with a piece of paper with 15 bioinformatics jobs that they&#8217;re ready to hire tomorrow,” he says.</p>
<p>If there truly is a shortage of computational biologists in pharma and biotech, Altman says, the federal government should be investing more heavily in training. Three institutes at the National Institutes of Health (NIH) &#8212; the National Institute of General Medical Sciences, the National Cancer Institute, and the National Library of Medicine &#8212; fund bioinformatics training programs, he says, but that’s not enough. Altman&#8217;s training grant from NIH was renewed recently, but its funding was reduced, so he&#8217;ll have to trim three or four training slots. “I do think it&#8217;s worrisome that a field that&#8217;s exploding is seeing a reduced amount of support for training.”</p>
<p>A recently announced Obama Administration project could reverse or offset [the] trend [of reduced funding for computational biologists]. The <a href="http://blogs.sciencemag.org/sciencecareers/2012/03/new-federal-big.html">Big Data Research and Development Initiative</a> pledges $200 million for NIH, the National Science Foundation, and other federal agencies to support data collection, analysis, and dispersion. Some of that money will go toward training computational biologists. When the program comes online, it could result in some direct hiring within the agencies it supports.</p>
<p>NIH&#8217;s director, Francis Collins, seems to believe in the field&#8217;s importance. At a 29 March briefing announcing the initiative in Washington, D.C., Collins told Science Careers, &#8220;If I were a senior or first-year graduate student interested in biology, I would migrate as fast as I could into the field of computational biology. … There are vast quantities of high-quality data accessible to anybody who has the skills to find the nuggets of truth that are hiding in that information.&#8221;</p>
<p>Via <a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_04_13/caredit.a1200041">Computational Biologists: The Next Pharma Scientists?</a></p></blockquote>]]></content:encoded>
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		<title>Social Media Not (Yet) Widely Used for News</title>
		<link>http://www.walterjessen.com/blog/social-media-not-yet-widely-used-for-news/</link>
		<comments>http://www.walterjessen.com/blog/social-media-not-yet-widely-used-for-news/#comments</comments>
		<pubDate>Mon, 19 Mar 2012 17:12:32 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Journalism]]></category>
		<category><![CDATA[Social Media]]></category>
		<category><![CDATA[app new]]></category>
		<category><![CDATA[Facebook]]></category>
		<category><![CDATA[google]]></category>
		<category><![CDATA[Huffington Post]]></category>
		<category><![CDATA[media sectors]]></category>
		<category><![CDATA[news]]></category>
		<category><![CDATA[paidcontent]]></category>
		<category><![CDATA[PEJ]]></category>
		<category><![CDATA[percent]]></category>
		<category><![CDATA[Pew]]></category>
		<category><![CDATA[pew research center]]></category>
		<category><![CDATA[project for excellence in journalism]]></category>
		<category><![CDATA[social media]]></category>
		<category><![CDATA[story]]></category>
		<category><![CDATA[Twitter]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5886</guid>
		<description><![CDATA[Surprising data on news from social media.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">H</span>ow much news do you get from social media? I use my <a href="http://www.walterjessen.com/blog/tag/twitter/">Twitter</a> feed as a content filter &#8212; albeit not everyday &#8212; to receive curated news and information. I&#8217;ve found that &#8220;feature&#8221; to be extremely valuable compared to other social networks such as <a href="http://www.walterjessen.com/blog/tag/facebook/">Facebook</a> (it&#8217;s all about who you know).</p>
<p>Staci Kramer at <a href="http://paidcontent.org/article/419-pew-twitter-facebook-arent-moving-as-much-news-as-you-think/">paidContent</a> wrote a story this morning covering the Pew Research Center’s Project for Excellence in Journalism (PEJ) <a href="http://pewresearch.org/pubs/2222/news-media-network-television-cable-audioo-radio-digital-platforms-local-mobile-devices-tablets-smartphones-native-american-community-newspapers">2012 State of the News Media</a> report. The annual report is a comprehensive analysis on the health of journalism in America. It includes a detailed examination of eight different media sectors as well as an overview that identifies key trends and key findings of the essential statistics about news in the last year.</p>
<p>Staci&#8217;s story highlighted the PEJ finding that although social media is a great source of traffic for news outlets, it&#8217;s not as important (yet) as previously thought:</p>
<div style="float: right; margin-left: 10px;margin-bottom:15px;"><img title="Social media for news" src="http://www.walterjessen.com/wp-content/uploads/2012/03/social-media.jpg" alt="Social media for news" width="224" height="281" /></div>
<div style="margin-top: 50px;">
<blockquote><p>Nine percent of the respondents in the latest PEJ annual survey &#8220;very often&#8221; follow news recommendations from Facebook or Twitter via computer, mobile or tablet—a growing number, up 57 percent from 2009. But most digital news readers are still &#8220;very likely&#8221; using search (29 percent), web or app news aggregators (27 percent) or direct visit (38 percent). When you get granular, Facebook users are more likely to follow recommendations than those on Twitter; 27 percent follow Facebook if you combine &#8220;very likely&#8221; and &#8220;somewhat likely&#8221; for tablet and smartphone users, compared with 9 percent for Twitter.</p></blockquote>
</div>
<p>I find it surprising that digital news consumers more often follow news recommendations from Facebook than from Twitter, especially given that Twitter news is viewed as more unique (only 43% of Twitter users report that the news they get on the platform could have been gotten elsewhere, compared to 56% for Facebook). This result likely comes from the fact that <a href="http://stateofthemedia.org/2012/digital-news-gains-audience-but-loses-more-ground-in-chase-for-revenue/">people on Facebook spend a staggering 17-fold more time on the platform than on Twitter</a>!</p>
<p>Nevertheless, the report does find that Twitter is growing rapidly. The most recent estimates of U.S. Twitter users reflect a 32% increase over 2010. Given the growing role of social media, the report asks some difficult questions for news publishers:</p>
<blockquote><p>
Though far smaller than Facebook, the predominance of journalists and news organizations among its adherents has given Twitter outsized influence in the media world. It has also taken on a critical role in disseminating breaking news &#8212; as witnessed in everything from the Arab Spring to the death of Whitney Houston (announced via a Tweet sent out 55 minutes before AP posted confirmation of the news).</p>
<p>&#8220;Twitter is the new newswire,&#8221; said Chloe Sladden, the director of content and programming for the site, at a recent conference on the future of media at Stanford University.</p>
<p>One early adopter of social media strategies to considerable success is The Huffington Post. It was among the first to aggressively adopt Facebook Connect, which it credited with big traffic gains starting in 2009. The following year, HuffPo added Foursquare-style &#8220;badges&#8221; to its site, rewarding readers when they shared or commented on stories.</p>
<p>By making it something of a game &#8212; and a competition &#8212; HuffPo created one of the most active and engaged communities online. And in early 2011, it added even more tools to simplify sharing: with just one click, readers can receive updates within Facebook and Twitter on a specific story, a broader topic or a particular reporter.</p>
<p>By the fall, HuffPo was getting as many traffic referrals from Facebook as from Google, according to Hitwise.  Moreover, 7 of the top 20 political stories shared on Facebook in 2011 came from the HuffPo.</p>
<p>The growing role of social media raises difficult questions for news sites. First, does the traffic from social media lead to any broader traffic growth? In other words, do readers coming in from Facebook or Twitter develop loyalty to the news brand? Or is the increased dependence on social media another way that ties are loosening between the organizations who produce the news (and shoulder the costs of doing so) and the readers who ultimately consume it, thus making it difficult for news producers to monetize their content and develop loyalty to their brands?</p>
<p>There are few clear answers yet. But many media companies have become cognizant over the last year of the need to have a comprehensive, newsroom-wide social media strategy. And with Google&#8217;s January decision to integrate information from Google+, its own recently launched social media site, into search results, the significance of developing one will probably only grow.</p>
<p>Via <a href="http://stateofthemedia.org/2012/digital-news-gains-audience-but-loses-more-ground-in-chase-for-revenue/?src=prc-section">Digital: News Gains Audience but Loses Ground in Chase for Revenue, The State of the News Media 2012</a></p>
</blockquote>]]></content:encoded>
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		<title>Point-and-click: March 5th, 2012</title>
		<link>http://www.walterjessen.com/blog/point-and-click-march-5th-2012/</link>
		<comments>http://www.walterjessen.com/blog/point-and-click-march-5th-2012/#comments</comments>
		<pubDate>Tue, 06 Mar 2012 04:44:34 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Points of Interest]]></category>
		<category><![CDATA[BioPontis Alliance]]></category>
		<category><![CDATA[Cost]]></category>
		<category><![CDATA[Covance]]></category>
		<category><![CDATA[CR-V]]></category>
		<category><![CDATA[development gap]]></category>
		<category><![CDATA[diabetes]]></category>
		<category><![CDATA[diabetes risk]]></category>
		<category><![CDATA[drug development]]></category>
		<category><![CDATA[drugs]]></category>
		<category><![CDATA[ferris bueller]]></category>
		<category><![CDATA[Ferris Bueller's Day Off]]></category>
		<category><![CDATA[google]]></category>
		<category><![CDATA[Staggering]]></category>
		<category><![CDATA[statin]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5873</guid>
		<description><![CDATA[A digest of news and information articles, focused primarily on health and life science, shared via social media.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">C</span>ovance looking to win biz from competitors busy integrating recent acquisitions <a href="http://t.co/GvCCE6AE">http://t.co/GvCCE6AE</a></p>
<p>The Truly Staggering Cost Of Inventing New Drugs ($4-11 billion per drug) <a href="http://t.co/0sTxP1rT">http://t.co/0sTxP1rT</a></p>
<p>How cool! Ferris Bueller&#8217;s latest day off (in a CR-V), Super Bowl commercial: <a href="http://t.co/gQscJoJN">http://t.co/gQscJoJN</a></p>
<p>Covance and BioPontis Alliance Collaborate to Bridge Drug Development Gap <a href="http://t.co/AZWsgmXD">http://t.co/AZWsgmXD</a></p>
<p>Selventa Receives Patent for Method to Identify Biomarker Profiles <a href="http://t.co/oFvXrHek">http://t.co/oFvXrHek</a></p>
<p>Top Cardiologist Argues We Should Dial Back On Statins Because Of Diabetes Risk <a href="http://ow.ly/9rP5e">http://ow.ly/9rP5e</a></p>
<p>Scientists release project aimed at creating the cellular equivalent of Google Earth <a href="http://bit.ly/xrRj4l">http://bit.ly/xrRj4l</a></p>
<p><span style="float:right"><em>All links shared via Twitter &#8211; <a href="http://www.twitter.com/wjjessen">follow along!</a></em></span></p>]]></content:encoded>
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		</item>
		<item>
		<title>Reflecting on the 2012 Molecular Med Tri-Con</title>
		<link>http://www.walterjessen.com/blog/reflecting-on-the-2012-molecular-med-tri-con/</link>
		<comments>http://www.walterjessen.com/blog/reflecting-on-the-2012-molecular-med-tri-con/#comments</comments>
		<pubDate>Tue, 28 Feb 2012 04:45:47 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Research]]></category>
		<category><![CDATA[Broad]]></category>
		<category><![CDATA[cambridge healthtech institute]]></category>
		<category><![CDATA[drug discovery and development]]></category>
		<category><![CDATA[informatics]]></category>
		<category><![CDATA[information]]></category>
		<category><![CDATA[Integrated]]></category>
		<category><![CDATA[knowledge management]]></category>
		<category><![CDATA[merck]]></category>
		<category><![CDATA[merck research laboratories]]></category>
		<category><![CDATA[molecular med]]></category>
		<category><![CDATA[Molecular Med Tri-Con]]></category>
		<category><![CDATA[san francisco]]></category>
		<category><![CDATA[speaker]]></category>
		<category><![CDATA[tag cloud]]></category>
		<category><![CDATA[tricon]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5825</guid>
		<description><![CDATA[The 2012 Molecular Med Tri-Con (MMTC) tag cloud and my notes from the conference.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">I</span> had the opportunity to attend the <a href="http://biomarkercommons.org/biomarker-news/covance-scientists-to-present-at-the-molecular-med-tri-con">2012 Molecular Med Tri-Con (MMTC)</a> in San Francisco last week (<a href="http://www.walterjessen.com/blog/traveling-to-the-molecular-med-tri-con-wrinkle-free/">wrinkle-free</a>, I might add). The Molecular Med Tri-Con meeting brings together the therapeutic and diagnostic aspects of the life sciences industry for lectures, discussions, exhibits and various receptions on diagnostics, drug discovery and development, informatics and cancer. It&#8217;s an interesting mix of research and commercial science.</p>
<p>It was my first year attending the MMTC and it was <em>really</em> a lot of fun. I caught up with <a href="http://www.collabchem.com/">Sean Ekins</a>, whom I met last month at <a href="http://www.walterjessen.com/blog/selecting-scienceonline2012-sessions/">ScienceOnline2012</a> and whose work on GeneGo MetaCore and MetaDrug, surprisingly enough, I had unknowingly referenced on my poster <a href="http://www.walterjessen.com/blog/poster-mining-pubmed-for-biomarker-disease-associations-to-guide-discovery/">Mining PubMed for Biomarker-Disease Associations to Guide Discovery</a>. We brainstormed an exciting path forward for the work.</p>
<h3>Live Tweeting a Science Conference</h3>
<p>It was especially exciting for me to find several people live tweeting the conference. Besides, Sean (<a href="http://twitter.com/collabchem">@collabchem</a>) and myself (<a href="http://twitter.com/wjjessen">@wjjessen</a>), Ingrid Akerblom (<a href="http://twitter.com/ingridbio">@ingridbio</a>), Executive Director, Merck Research Laboratories (MRL) Clinical IT, was very active on Twitter. Additional contributors included <a href="http://www.martinleach.com">Martin Leach</a> (<a href="http://twitter.com/mdleach">@mdleach</a>), Chief Information Officer at the Broad Institute; <a href="http://kdbio.inesc-id.pt/~jcarrico/">João André Carriço</a> (<a href="http://twitter.com/jacarrico">@jacarrico</a>), a researcher in the <a href="http://www.inesc-id.pt/intranet/laboratoriogrupo/kdbio/kdbio.php">Knowledge Discovery and Bioinformatics group of INESC-ID</a> (Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa); and Kate Skaare (<a href="https://twitter.com/#!/kateskaare">@kateskaare</a>), Conference Producer for Cambridge Healthtech Institute (CHI).</p>
<p>Last month, I created a <a href="http://www.walterjessen.com/blog/scienceonline2012-tag-cloud/">tag cloud of tweets from the ScienceOnline2012 conference</a>. With an established workflow, it didn&#8217;t take much time over the weekend to create a 2012 Molecular Med Tri-Con tag cloud. The cloud covers tweets from Wednesday, February 15th to Saturday, February 25th. In total, there were 491 tweets comprised of 8,762 words.</p>
<p>From 8,762 words, 2,275 were unique. I calculated the frequency of all 2,275 words and then curated the data set, removing all words less than 4 characters, numbers, and words that were either common words (such as &#8220;with&#8221;, &#8220;this&#8221; or &#8220;your&#8221;) or gibberish (consisting principally of url strings from shared links). I also reduced the frequency of the top term &#8212; tricon &#8212; from 429 to 125, so that it was easier to see the other terms. The top 250 terms were used to generate a weighted tag cloud. Feel free to download any of the files below and reshare.</p>
<div style="width: 564px; margin: auto;"><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/2012mmtc-tagcloud.png"><img class="alignnone size-full wp-image-5830" title="2012 MMTC tagcloud" src="http://www.walterjessen.com/wp-content/uploads/2012/02/2012mmtc-small-tagcloud.jpg" alt="2012 MMTC tagcloud" width="564" height="362" /></a></div>
<p>Here&#8217;s the top 10 terms from the cloud above:</p>
<table>
<tbody>
<tr>
<td><strong>Term</strong></td>
<td><strong>Frequency</strong></td>
</tr>
<tr>
<td>tricon</td>
<td>429 (125)</td>
</tr>
<tr>
<td>data</td>
<td>72</td>
</tr>
<tr>
<td>informatics</td>
<td>65</td>
</tr>
<tr>
<td>talk</td>
<td>41</td>
</tr>
<tr>
<td>Molecular</td>
<td>35</td>
</tr>
<tr>
<td>TriCon</td>
<td>35</td>
</tr>
<tr>
<td>booth</td>
<td>27</td>
</tr>
<tr>
<td>@wjjessen</td>
<td>26</td>
</tr>
<tr>
<td>@TriConference</td>
<td>25</td>
</tr>
<tr>
<td>medicine</td>
<td>24</td>
</tr>
</tbody>
</table>
<p>All data and images are available for download: <a href="http://www.walterjessen.com/wp-content/uploads/2012/02/2012mmtc-small-tagcloud.jpg">low-resolution image</a>, <a href="http://www.walterjessen.com/wp-content/uploads/2012/02/2012mmtc-tagcloud.png">high-resolution image</a> or <a href="http://www.walterjessen.com/wp-content/uploads/2012/02/2012mmtc-word-frequencies.txt">raw data set of 250 words with frequencies</a>.</p>
<h3>Light on Data</h3>
<p>Unfortunately, most of the informatics sessions were light on data; a few were simply marketing. With twelve parallel sessions, I should have left the track more often. I heard there were several good talks in the <a href="http://www.triconference.com/Bioinformatics-Cancerinformatics/">Bioinformatics and Cancerinformatics track</a>, which unfortunately I never made it to. A good point to remember for next year&#8217;s meeting: track hop.</p>
<h3>Notes from the Conference</h3>
<p>Below are my notes from the conference. Most of them were taken in the <a href="http://www.triconference.com/Discovery-Informatics/">Integrated R&amp;D Informatics &amp; Knowledge Management track</a>.</p>
<div style="border-top:1px dotted #87BCD2;">&nbsp;</div>
<div style="height: 60px;">At the airport, catching a flight to San Francisco to attend the @TriConference #tricon #mmtc</div>
<div style="height: 60px;">@mndoci Flying in tonight for the #tricon Attending most of the Integrated R&amp;D Informatics &amp; Knowledge Mngmnt talks.</div>
<div style="height: 60px;">@mndoci Disappointed I missed your #tricon #mmtc talk. Checking out your #datascience #genomics slides now: <a href="http://t.co/eZXaZ7yX">http://t.co/eZXaZ7yX</a></div>
<div style="height: 60px;">Looking forward to catching the rest of #cloud #computing talks this morning. #tricon #mmtc</div>
<div style="height: 60px;">Bummer. Track hopping at the #tricon doesn&#8217;t include symposia. I&#8217;m not allowed to attend the #cloud #computing sessions today. Disappointed.</div>
<div style="height: 60px;">Covance Scientists to Present at the Molecular Med Tri-Con | Biomarker Commons <a href="http://t.co/cjZ596S5">http://t.co/cjZ596S5</a> #tricon</div>
<div style="height: 60px;">Covance Scientists to Discuss R&amp;D Capabilities, Talent and Technologies at the Molecular Med #TriCon <a href="http://t.co/YNK7rE1Z">http://t.co/YNK7rE1Z</a></div>
<div style="height: 60px;">At the #TriCon keynote. Wish the wifi worked! Plenary keynote speaker: Rick Guidotti, Director, Positive Exposure</div>
<div style="height: 60px;">Positive Exposure is an arts organization working with individuals living with genetic difference: <a href="http://t.co/RVz5y2S0">http://t.co/RVz5y2S0</a> #tricon</div>
<div style="height: 60px;">Rick Guidotti from Positive Exposure is showing fantastic photos of people around the world with albinoism. #tricon</div>
<div style="height: 60px;">Rick Guidotti starts almost every photo/story of albino individuals with the phrase &#8220;this is my friend&#8221; #tricon</div>
<div style="height: 60px;">Pearls Project invites students to learn about peers living with genetic, physical, behavioral differences: <a href="http://t.co/W0YHkHQT">http://t.co/W0YHkHQT</a> #tricon</div>
<div style="height: 60px;">RT @bkmacy: Empowerment equation for those with genetic disease: Self acceptance = self esteem = self advocacy, #tricon</div>
<div style="height: 60px;">Inspiring keynote from Rick Guidotti of Positive Exposure, amazing stories, photos and videos. #tricon</div>
<div style="height: 60px;">Comment from the audience: as scientists, we should be taking the stand that genetic diversity is beautiful. #tricon</div>
<div style="height: 60px;">Attending sessions this morning on Integrated R&amp;D Informatics &amp; Knowledge Management #tricon #informatics #km</div>
<div style="height: 60px;">You know you have a #data problem if you know the difference between curate, harmonize, rationalize and normalize. #tricon #informatics #km</div>
<div style="height: 60px;">First up, Ingrid Akerblom from Merck: New Frontiers for Research, Integrating the Virtual R&amp;D Lab #tricon #informatics #km</div>
<div style="height: 60px;">Ingrid Akerblom: Industry is very focused on informed decision making #tricon #informatics #km</div>
<div style="height: 60px;">@ingridbio: informed decision-making depends on access to accurate and timely information #tricon #informatics #km</div>
<div style="height: 60px;">Pistoia Alliance: collaboration across the life sciences ecosystem <a href="http://t.co/JOSIZuSN">http://t.co/JOSIZuSN</a> #tricon #informatics #km</div>
<div style="height: 60px;">@ingridbio Merck strategy for simplifying collaboration experience: single portal for access and services. #tricon #informatics #km</div>
<div style="height: 60px;">@ingridbio closes w/shots of TechCrunch and Guardian articles <a href="http://t.co/nTc5RJK8">http://t.co/nTc5RJK8</a> and <a href="http://t.co/Qj6a7Bcn">http://t.co/Qj6a7Bcn</a> #tricon #informatics #km</div>
<div style="height: 60px;">Agreed! RT @collabchem: #tricon attendees should be allowed to tweet images to drive traffic they also need wireless for attendees</div>
<div style="height: 60px;">Comment from audience: economic crisis will pale in comparison to coming healthcare crisis (huge # of patients, volumes of data) #tricon&#8230;</div>
<div style="height: 60px;">Next talk: Daniel Robertson from Lilly. #tricon #informatics #km</div>
<div style="height: 60px;">Robertson&#8217;s talk: Breaking through walls of traditional pharma to access &amp; generate info and enable innovation #tricon #informatics #km</div>
<div style="height: 60px;">Dan Robertson talking about early chemogenomics at Lilly. One key learning: extend knowledge through external data #tricon #informatics #km</div>
<div style="height: 60px;">Lilly&#8217;s strategy as a FIPNet company: fully integrated pharmaceutical network. Leverage external competencies, primary driver collab #tricon</div>
<div style="height: 60px;">Robertson talking about Lilly Open Innovation Drug Discovery. Lilly doesn&#8217;t own the data, but has first right to collab #tricon&#8230;</div>
<div style="height: 60px;">Swan Project: Semantic Web Apps in Neuromedicine. Dev knowledge bases for the neurodegen research communities <a href="http://t.co/SrbXJTu0">http://t.co/SrbXJTu0</a> #tricon</div>
<div style="height: 60px;">Robertson: future approach to use improved semantic integration. #tricon #informatics #km</div>
<div style="height: 60px;">Robertson: competing in biopharma R&amp;D requires new approaches to manage, analyze, interact with data #tricon #informatics #km</div>
<div style="height: 60px;">Molecular Med Tri-Con conference exhibit hall #tricon <a href="http://t.co/kmaYTbXQ">http://t.co/kmaYTbXQ</a></div>
<div style="height: 60px;">Attending #tricon sessions discussing the integration of biomarker, clinical and personalized medicine data.</div>
<div style="height: 60px;">Speaker: Shawn Murphy from Partners HealthCare. Talk: Secondary Use of Healthcare Data for the study of Genomics and Pharmacology #tricon</div>
<div style="height: 60px;">Next speaker: Carol Hill from Duke. Talk: Clinical Research Informatics, Challenges &amp; Efforts in Translational Research #tricon</div>
<div style="height: 60px;">Next speaker: Gary Kennedy from REMEDY Informatics. Talk: &#8220;Big Data&#8221; Problem or Opportunity? #tricon</div>
<div style="height: 60px;">#tricon #informatics #kb Yang showing MedHelp: <a href="http://t.co/CfVz48in">http://t.co/CfVz48in</a></div>
<div style="height: 60px;">#tricon #informatics Yang showing complex social network analysis; content &amp; network similarity analysis, implicit relationship extraction.</div>
<div style="height: 60px;">Kennedy prefers registry-centric architecture. Common repository (federated), master ontology. #tricon</div>
<div style="height: 60px;">Next speaker: Jill Hagenkord Talk: Breaking the Mold, Whole Genome Sequencing as a Diagnostic Assay #tricon</div>
<div style="height: 60px;">Hagenkord: Complete Genomics is a genome information company. Focused only humans, whole genome seq. #tricon</div>
<div style="height: 60px;">Hagenkord: P4 Medicine = Genomic Medicine #tricon</div>
<div style="height: 60px;">First #tricon #informatics #km speaker Martin Leach: Surfing the Petabyte Waves &#8211; IT Partnering for Informatics and Comp Bio at the Broad</div>
<div style="height: 60px;">#tricon #informatics #kb Martin Leach thinks the term &#8220;big data&#8221; is phooey. Have to agree the term is overused today.</div>
<div style="height: 60px;">#tricon #informatics #kb @mdleach describing how Broad deals with big data challenges. Automation, gigabit networking, limited metadata.</div>
<div style="height: 60px;">#tricon #informatics #kb Broad has 4-5 tiers of storage ~12PB (10,000+ spinning disks). A disk fails every 36 hours.</div>
<div style="height: 60px;">#tricon #informatics #kb Broad doesn&#8217;t really leverage the cloud for computing. Takes too many hours to move huge amounts of data to Amazon.</div>
<div style="height: 60px;">#tricon #informatics #kb Network connections between buildings at the Broad are 60-80gbits &#8211; 12,000x the bandwidth your home tv/internet.</div>
<div style="height: 60px;">#tricon #informatics #kb Broad uses BASS to search data, bringing I-RODS online. Wonder how easy/difficult it is to find a dataset.</div>
<div style="height: 60px;">#tricon #informatics #kb How to work with a #bigdata org? Communicate, educate (see video <a href="http://t.co/TdxiFNp4">http://t.co/TdxiFNp4</a> ). Have patience.</div>
<div style="height: 60px;">#tricon #informatics #kb Really nice overview by @mdleach from @broadinstitute.</div>
<div style="height: 60px;">Next speaker, Juergen Hammer from Roche. Talk: Disease &amp; Translational Informatics: From Bioinformatics Playground to Critical Path #tricon</div>
<div style="height: 60px;">#tricon #kb Hammer describing Roche&#8217;s Biological Data System (BDS). Big investment in #informatics analysis tools.</div>
<div style="height: 60px;">#tricon #informatics #kb Hammer: Traditional informatics portals, simplistic viewers have only moderate value for drug discovery.</div>
<div style="height: 60px;">#tricon #informatics #kb Next speaker: Anastasia M. Khoury Christianson from AstraZeneca. Talk: New approaches for Better Decisions</div>
<div style="height: 60px;">#tricon #informatics #kb Most important decision for drug dev: deliver right treatment to right patient, right dose at right (first) time.</div>
<div style="height: 60px;">#tricon #informatics #kb If the goal is informed decisions, that requires right target, compound, trial design, disease, patient, dose.</div>
<div style="height: 60px;">#tricon #informatics #kb People make 2,500 &#8211; 15,000 decisions daily, requires many needs.</div>
<div style="height: 60px;">#tricon #informatics #kb Are we stuck in information overload? Christianson believes there&#8217;s gap between data/info, knowledge and decisions.</div>
<div style="height: 60px;">#tricon #informatics #kb Christianson describing a drug tox signaling path (DTSP) detection algorithm. Very cool.</div>
<div style="height: 60px;">#tricon Checking out Ingenuity talk &#8220;Efficiently unlocking biological meaning from complex &#8216;omics data&#8221;</div>
<div style="height: 60px;">#tricon IPA from @ING_SYS has a new visualization tool for alt splicing. Nice.</div>
<div style="height: 60px;">#tricon With one click, you can highlight biomarkers in an IPA network. @ING_SYS What criteria is met for a gene to be called a biomarker?</div>
<div style="height: 60px;">#tricon #kb Christopher Yang from Drexel talking about social media analytics for health #informatics.</div>
<div style="height: 60px;">#tricon #informatcis #kb Yang introducing the concept of an e-patients.</div>
<div style="height: 60px;">#tricon #kb 41% of e-patients read patient blog, health newsgroup or health website. 39% use social networking. 12% share or view updates.</div>
<div style="height: 60px;">#tricon #informatics #kb Who says scientists don&#8217;t use social media? Yang just asked who uses and many in the room raised their hand!</div>
<div style="height: 60px;">#tricon #informatics #kb Yang showing MedHelp: medhelp.org</div>
<div style="height: 60px;">#tricon #informatics #kb Social media analysis and mining; Yang explores 3 dimensions: people, time, content.</div>
<div style="height: 60px;">#tricon #informatics Yang showing complex social network analysis; content &amp; network similarity analysis, implicit relationship extraction.</div>
<div style="height: 60px;">MT @collabchem: If Google Docs host Genentech docs, will other pharmas do the same? #collab tools key for global interactions w/CROs #tricon</div>
<div style="height: 60px;">Other recommendations for @triconference: provide fast, free WiFi to encourage tweeting, blogging of #tricon.</div>
<div style="height: 60px;">Other recommendations for @triconference: twitter wall in the lobby showing real time #tricon stream helps involve those who don&#8217;t tweet.</div>
<div style="height: 60px;">Just landed in Indy. Passed through three time zones today. It&#8217;s 8pm .. or 10. Not sure. Thankfully the airport #Starbucks is open.</div>]]></content:encoded>
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		<item>
		<title>Poster: Mining PubMed for Biomarker-Disease Associations to Guide Discovery</title>
		<link>http://www.walterjessen.com/blog/poster-mining-pubmed-for-biomarker-disease-associations-to-guide-discovery/</link>
		<comments>http://www.walterjessen.com/blog/poster-mining-pubmed-for-biomarker-disease-associations-to-guide-discovery/#comments</comments>
		<pubDate>Sun, 26 Feb 2012 18:12:10 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Research]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[biomarkers]]></category>
		<category><![CDATA[BioPathways]]></category>
		<category><![CDATA[Covance]]></category>
		<category><![CDATA[data mining]]></category>
		<category><![CDATA[Disease]]></category>
		<category><![CDATA[disease ontology]]></category>
		<category><![CDATA[Interaction]]></category>
		<category><![CDATA[life science journals]]></category>
		<category><![CDATA[medical subject headings]]></category>
		<category><![CDATA[mesh browser]]></category>
		<category><![CDATA[meta knowledge]]></category>
		<category><![CDATA[molecular med]]></category>
		<category><![CDATA[ontology]]></category>
		<category><![CDATA[PubMed]]></category>
		<category><![CDATA[text mining]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5346</guid>
		<description><![CDATA[My poster that I presented at the 2012 Molecular Med Tri-Con (MMTC) in San Francisco last week.]]></description>
			<content:encoded><![CDATA[<p><span class="drop">B</span>elow is the poster I presented at the <a href="http://biomarkercommons.org/biomarker-news/covance-scientists-to-present-at-the-molecular-med-tri-con">2012 Molecular Med Tri-Con (MMTC)</a> in San Francisco last week. A copy has also been deposited at <a href="http://f1000.com/posters/browse/summary/1089905">F1000 Posters</a>, <a href="http://precedings.nature.com/documents/6941/version/1">Nature Precedings</a> and <a href="http://figshare.com/articles/Mining_PubMed_for_Biomarker-Disease_Associations_to_Guide_Discovery/91250">FigShare</a>; you can also <a href="http://www.walterjessen.com/wp-content/uploads/2012/02/jessen-2012-mmtc-poster.pdf">download a PDF of the poster</a>. </p>
<p>The project began with two simple questions: (1) Which therapeutic areas are seeing the most research for the discovery, refinement or application of biomarkers? (2) Which diseases are most frequently associated with the term &#8220;biomarker&#8221;? I hope to expand upon this work in a collaboration later this year.</p>
<h3>Introduction</h3>
<p>Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to describe both known and potential biomarkers as well as disease-associated genes/proteins for select diseases. This approach identifies therapeutic areas with candidate or validated biomarkers, and highlights those areas where a paucity of biomarkers exists.</p>
<h3>Materials and Methods</h3>
<p>Text mining was performed using PolySearch, a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites [1]. The MeSH Browser (2012 MeSH) was used to map disease associations to MeSH IDs. Once MeSH IDs were assigned, the Disease Ontology was used to map DOIDs [2]. Interaction networks were constructed in GeneGo MetaCore [3] using the Auto expand algorithm, which gradually expands sub-networks around every object from the seed object list based on interactions identified in the literature. At every step, preference is given to objects with more connectivity to the initial object, and expansion halts when the sub-networks intersect, or when the overall network size reaches a predefined limit. Genes/proteins for which validated commercial assays exist were identified using Covance BioPathways at <a href="http://www.Covance.com/BioPathways">http://www.Covance.com/BioPathways</a> and are indicated with a red dot. These genes/proteins can be considered potential biomarkers.</p>
<h3>Results</h3>
<p><strong>Data Extraction and Curation</strong></p>
<p>In June 2011, we mined PubMed for term(&#8216;biomarker&#8217;)-disease associations and identified a total of 1,181 disease associations (Table 1). We then curated the top 100 disease associations from the list, mapping each result to both medical subject (MeSH) ID and Disease Ontology ID (DOID), and then subsequently queried the GeneGo diseases ontology for associated biomarkers (Table 2). Of 100 results, 62 map to both MeSH ID and DOID and are shown below.</p>
<p><strong>Table 1.</strong> A representative list of term(&#8216;biomarker&#8217;)-disease associations mined from PubMed in June 2011. The top 100 disease associations were ranked by Z Score. The Z-score indicates the number of standard deviations that the relevancy score is above the mean; larger Z-scores denote stronger associations. The top 100 data set is available under the Open Data Commons Attribution License at <a href="http://biomarkercommons.org/biomarker-disease-associations">http://BiomarkerCommons.org</a></p>
<p><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/table1.jpg"><img class="alignnone size-full wp-image-5407" title="Table 1" src="http://www.walterjessen.com/wp-content/uploads/2012/02/table1.jpg" alt="Table 1" width="654" height="397" /></a></p>
<p><strong>Table 2.</strong> The curated list of disease associations minded from PubMed and organized by high-level Disease Ontology. Each specific disease association has a unique MeSH ID, DOID and number of associated genes as defined in the GeneGo MetaCore knowledgebase.</p>
<p><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/table2.jpg"><img class="alignnone size-full wp-image-5408" title="Table 2" src="http://www.walterjessen.com/wp-content/uploads/2012/02/table2.jpg" alt="Table 2" width="654" height="645" /></a></p>
<p><strong>Disease Interaction Network and Biomarker Assay Identification</strong></p>
<p>For illustrative purposes, we constructed an interaction network around disease-associated genes for two diseases – one with few associated genes (atherosclerosis) and one with many associated genes (asthma) – using a network building algorithm in GeneGo MetaCore. For each interaction network gene set, we then queried Covance BioPathways, a publicly accessible, web-based data source that integrates biological and disease pathway maps with validated Covance assays and antibody products, to identify commercially available biomarker assays.</p>
<p><strong>Figure 1.</strong> Atherosclerosis interaction network. Disease-associated genes are indicated with blue halos; genes without a halo were included by the network building algorithm.  Biomarkers that have commercially validated assays are indicated with a red dot; they either are known or can be considered potential atherosclerosis biomarkers.</p>
<p><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/figure1.jpg"><img class="alignnone size-full wp-image-5409" title="Figure 1" src="http://www.walterjessen.com/wp-content/uploads/2012/02/figure1.jpg" alt="Figure 1" width="654" height="300" /></a></p>
<p><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/legend.jpg"><img class="alignnone size-full wp-image-5410" title="Legend" src="http://www.walterjessen.com/wp-content/uploads/2012/02/legend.jpg" alt="Legend" width="654" height="202" /></a></p>
<p><strong>Figure 2.</strong> Asthma interaction network. All nodes shown are disease-associated genes. Biomarkers that have commercially validated assays are indicated with a red dot; they are either known or can be considered potential asthma biomarkers.</p>
<p><a href="http://www.walterjessen.com/wp-content/uploads/2012/02/figure2.jpg"><img class="alignnone size-full wp-image-5411" title="Figure 2" src="http://www.walterjessen.com/wp-content/uploads/2012/02/figure2.jpg" alt="Figure 2" width="654" height="292" /></a></p>
<h3>Discussion</h3>
<p>Given the molecular interdependencies within a cell, a disease is rarely a consequence of a single gene abnormality but instead reflects the perturbation of a complex network of biological and signaling pathways. The approach described here describes the detection and ranking of human disease based on research/clinical activity surrounding biomarkers. It also enables the identification of therapeutic areas with candidate or validated biomarkers. The strategy takes an integrative approach to identify candidate disease biomarkers by combining disease-associated genes/proteins with commercially validated assays for known biomarkers. We first constructed a system-level model of disease that incorporates molecular interactions across biological and signaling pathways. We then identified each gene/protein in the model that has an existing commercially validated assay. This research offers an alternative, comprehensive view of key relationships and pathway perturbations that may identify biomarkers of disease emergence or progression.</p>
<h3>References</h3>
<ol>
<li>
Cheng et al. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. Epub 2008 May 16.<br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed/18487273">View abstract</a>
</li>
<li>
Schriml et al. Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6. Epub 2011 Nov 12.<br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed/22080554">View abstract</a>
</li>
<li>
Ekins et al. Pathway mapping tools for analysis of high content data. Methods Mol Biol. 2007;356:319-50.<br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed/16988414">View abstract</a>
</li>
</ol>]]></content:encoded>
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		<title>Traveling to the Molecular Med Tri-Con Wrinkle-Free</title>
		<link>http://www.walterjessen.com/blog/traveling-to-the-molecular-med-tri-con-wrinkle-free/</link>
		<comments>http://www.walterjessen.com/blog/traveling-to-the-molecular-med-tri-con-wrinkle-free/#comments</comments>
		<pubDate>Sat, 18 Feb 2012 03:21:53 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Business]]></category>
		<category><![CDATA[dress]]></category>
		<category><![CDATA[dress clothes]]></category>
		<category><![CDATA[informatics]]></category>
		<category><![CDATA[knowledge management]]></category>
		<category><![CDATA[management track]]></category>
		<category><![CDATA[MMTC]]></category>
		<category><![CDATA[molecular med]]></category>
		<category><![CDATA[packing]]></category>
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		<category><![CDATA[Travel]]></category>
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		<description><![CDATA[I'll be at the Molecular Med Tri-Con (MMTC) next week in San Francisco, so I thought it was fortuitous that I stumbled across this video today. ]]></description>
			<content:encoded><![CDATA[<p><span class="drop">I</span>f you&#8217;ve ever had to travel for business, packing a dress shirt, sport coat and slacks so that they don&#8217;t wrinkle too much can be challenging. I&#8217;ll be at the <a href="http://biomarkercommons.org/biomarker-news/covance-scientists-to-present-at-the-molecular-med-tri-con">Molecular Med Tri-Con (MMTC)</a> next week in San Francisco, so I thought it was fortuitous that I stumbled across this video today. </p>
<p>If you&#8217;re also attending the MMTC, you can catch me at most of the sessions in the <a href="http://www.triconference.com/Discovery-Informatics/">Integrated R&#038;D Informatics &#038; Knowledge Management</a> track on Tuesday and Wednesday. I&#8217;ll also be at the Covance booth during the day both days demoing <a href="http://www.walterjessen.com/blog/covance-biopathways-adapt-congress-presentation/">BioPathways</a>.</p>
<p>Most hotels provide irons and ironing boards, but who wants to spend time ironing when you could be enjoying a new place instead? As the dry cleaner in the video below demonstrates, with proper folding techniques you can ensure that your dress clothes arrive at your destination relatively wrinkle-free.</p>
<div style=margin-top:20px;margin-bottom:10px;">
<iframe width="654" height="473" src="http://www.youtube.com/embed/VDGWW7_O2sI?rel=0" frameborder="0" allowfullscreen></iframe>
</div>
<p>HT: <a href="http://lifehacker.com/5885879/fold-and-pack-your-suits-like-a-dry-cleaner-for-wrinkle+free-portability">Lifehacker</a></p>]]></content:encoded>
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		<title>Apple: The First $1 Trillion Company?</title>
		<link>http://www.walterjessen.com/blog/apple-the-first-1-trillion-company/</link>
		<comments>http://www.walterjessen.com/blog/apple-the-first-1-trillion-company/#comments</comments>
		<pubDate>Tue, 14 Feb 2012 02:52:46 +0000</pubDate>
		<dc:creator>Walter</dc:creator>
				<category><![CDATA[Apple]]></category>
		<category><![CDATA[Business]]></category>
		<category><![CDATA[apple stock]]></category>
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		<category><![CDATA[Economix]]></category>
		<category><![CDATA[Fortune]]></category>
		<category><![CDATA[General]]></category>
		<category><![CDATA[goldman sachs]]></category>
		<category><![CDATA[iPad3]]></category>
		<category><![CDATA[iPhone5]]></category>
		<category><![CDATA[medco health]]></category>
		<category><![CDATA[medco health solutions]]></category>
		<category><![CDATA[price target]]></category>
		<category><![CDATA[record]]></category>
		<category><![CDATA[revenue]]></category>
		<category><![CDATA[Starbucks]]></category>
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		<category><![CDATA[Value]]></category>

		<guid isPermaLink="false">http://www.walterjessen.com/?p=5347</guid>
		<description><![CDATA[Today, a single share of Apple reached a record new high: $500. In October 2010, shares of Apple closed above $300. Less than a year [...]]]></description>
			<content:encoded><![CDATA[<p><span class="drop">T</span>oday, a single share of Apple reached a record new high: $500. In October 2010, shares of Apple closed above $300. Less than a year later (July 2011), they hit $400.</p>
<div style="width: 564px; margin: auto;"><img class="alignnone size-full wp-image-5380" title="Apple campus" src="http://www.walterjessen.com/wp-content/uploads/2012/02/apple-campus.jpg" alt="Apple campus" width="564" height="355" /></div>
<p>An Economix article last week put the company&#8217;s value in perspective:</p>
<blockquote><p>Here are a few other comparisons:</p>
<ul>
<li>With a market value of about $460 billion, Apple is worth more than Google, Goldman Sachs, General Motors, Ford, Starbucks and Boeing combined.</li>
<li>Apple is now worth almost twice as much as Microsoft (about $258 billion) and more than twice as much as Google ($198 billion).</li>
<li>It is also worth more than twice as much as General Electric (about $202 billion), I.B.M. (about $224 billion) or Wal-Mart ($212 billion).</li>
<li>Apple &#8212; ranked 35th in the <a href="http://money.cnn.com/magazines/fortune/fortune500/2011/full_list/">Fortune 500</a>, which is based on annual sales &#8212; is worth eight times as much as the company just below it on the Fortune list (Boeing, at about $56.5 billion). Its value is 20 times as much as the company just above it (Medco Health Solutions, about $23.4 billion).</li>
</ul>
<p>via <a href="http://economix.blogs.nytimes.com/2012/02/09/apple-stocks-lofty-heights-in-context/">Apple Stock&#8217;s Lofty Heights, in Context: Economix [2012-02-09]</a>.</p></blockquote>
<p>That first bullet point bears repeating: Apple is worth more than Google, Goldman Sachs, General Motors, Ford, Starbucks and Boeing <em>combined</em>.</p>
<p>And the company is still growing.</p>
<p>Given the trajectory of Apple stock, there&#8217;s a chance the company could hit the $1 trillion mark this decade, making it the most valued company in history.</p>
<p>How likely is the possibility? Consider this:</p>
<p>In 2006, Apple stock rose 18%. In 2007, it jumped 133%. The stock price fell 56% in 2008, but bounced back 147% in 2009. In 2010, it rose 53%. If the company&#8217;s five year average 59% annual growth rate continues, Apple could be worth $1 trillion in as little as three years [1]. Using a more conservative annual growth rate of 23%, Apple will hit $1 trillion by 2017.</p>
<p>In a <a href="http://www.marketplace.org/topics/business/apple-breaks-through-500-share">Marketplace report today</a>, Panos Mourdoukoutas, professor of Economics at Long Island University, contended that only market rookies look just at a stock&#8217;s price.</p>
<blockquote><p>This idea that the stock is cheap or expensive, it&#8217;s actually useless. [Even at $502], Apple is a very inexpensive stock.</p></blockquote>
<p>Besides share value, you also have to look at a company&#8217;s earnings.</p>
<p>And Apple&#8217;s earnings are impressive. Last month, the company announced financial results for its fiscal 2012 first quarter, posting a record quarterly revenue of $46.33 billion and record quarterly net profit of $13.06 billion [2]. Compared to 2011, Apple revenues increased by 73% and profits by 117%.</p>
<p>And why stop at $1 trillion? Last year, James Altucher at MarketWatch maintained that <a>Apple is going to be the world&#8217;s first $2 trillion company</a>. Or is it $3 trillion?</p>
<p>All these financial numbers aside, I think there are several really good (and as-of-yet unreleased) reasons to own Apple stock: iPad3, iPhone5 and Apple TV. Nevertheless (and yes, you can call me a market rookie), $500 bucks is still a lot to spend for a single share of stock, even if it is for stock in a $1 trillion company.</p>
<h2>References</h2>
<ol>
<li><a href="http://www.usatoday.com/money/perfi/columnist/krantz/2011-04-13-can-apple-hit-trillion-market-value.htm">Can Apple reach $1 trillion in market value? It&#8217;s possible</a>. USA Today. 2011 Apr 18.</li>
<li><a href="http://www.apple.com/pr/library/2012/01/24Apple-Reports-First-Quarter-Results.html">Apple Reports First Quarter Results</a>. Apple. 2012 Jan 24.</li>
</ol>]]></content:encoded>
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