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Posts from the ‘Open Access’ Category

First Step in a PhD: Peripheral Blood Genomics

After graduating from medical school last year, I started PhD in the field of clinical genomics in October of 2009. My first paper (Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets) just came out in BMC Medical Genomics. Publishing our results in an open access journal was a real priority for me. The provisional pdf is now available. The hardest task was to visualize the findings.

Your comments, as always, are most welcome!


Chronic inflammatory diseases including inflammatory bowel disease (IBD; Crohn’s disease and ulcerative colitis), psoriasis and rheumatoid arthritis (RA) afflict millions of people worldwide, but their pathogenesis is still not well understood. It is also not well known if distinct changes in gene expression characterize these diseases and if these patterns can discriminate between diseased and control patients and/or stratify the disease. The main focus of our work was the identification of novel markers that overlap among the 3 diseases or discriminate them from each other.


Diseased (n=13, n=15 and n=12 in IBD, psoriasis and RA respectively) and healthy patients (n=18) were recruited based on strict inclusion and exclusion criteria; peripheral blood samples were collected by clinicians (30 ml) in Venous Blood Vacuum Collection Tubes containing EDTA and peripheral blood mononuclear cells were separated by Ficoll gradient centrifugation. RNA was extracted using Trizol reagent. Gene expression data was obtained using TaqMan Low Density Array (TLDA) containing 96 genes that were selected by an algorithm and the statistical analyses were performed in Prism by using non-parametric Mann-Whitney U test (P-values < 0.05).


Here we show that using a panel of 96 disease associated genes and measuring mRNA expression levels in peripheral blood derived mononuclear cells; we could identify disease-specific gene panels that separate each disease from healthy controls. In addition, a panel of five genes such as ADM, AQP9, CXCL2, IL10 and NAMPT discriminates between all samples from patients with chronic inflammation and healthy controls. We also found genes that stratify the diseases and separate different subtypes or different states of prognosis in each condition.


These findings and the identification of five universal markers of chronic inflammation suggest that these diseases have a common background in pathomechanism, but still can be separated by peripheral blood gene expression. Importantly, the identified genes can be associated with overlapping biological processes including changed inflammatory response. Gene panels based on such markers can play a major role in the development of personalized medicine, in monitoring disease progression and can lead to the identification of new potential drug targets in chronic inflammation.

Science and Social Media News: Nature comments and Wikipedia books

  • Content rules: Nature opens up content for comments and discussions.

‘Conversation is king’, according to a mantra frequently repeated by enthusiasts of online social media. But we editors and writers tend to give our first allegiance to content — not least because of our labours to research, commission, select, create and otherwise add value to content, and to do so in a way that informs and stimulates our readers: the people who pay for it.

But, unquestionably, conversation can add value to such efforts. Therefore, this week we introduce an online commenting facility that will allow readers to respond directly to any of our content.

Existing metrics have known flaws
A reliable, open, joined-up data infrastructure is needed
Data should be collected on the full range of scientists’ work
Social scientists and economists should be involved

Peer Review 2.0

I’m really angry when I want to access a paper and has to pay for that. I totally understand that journals have to make money somehow but I don’t believe they cannot come up with a better business model in 2010.

Obviously open science is not just about open access but also making scientific processes automatic with online tools. Jean-Claude Bradley has always been a pioneer in this field:

Best Slideshow about Open Access

Have you ever wondered what the problems of publishing science are, how to solve these and what exactly open access means? Martin Fenner will answer all of your questions:

Describing PLoS Medicine through Videos

Ginny Barbour, Chief Editor for PLoS Medicine talks about the beginnings and day to day operation of an online open access medical journal.

Cameron Neylon discusses how article-level metrics can make online research easier (I’ve recently covered – (HONcode certified)this issue):

Other videos were also published:

Huge Steps in Changing Science

Even if I will have the last exam in medical school in August, I’ve already started PhD in genetics and I’m about to finish my first manuscript so I have to face some scientific publishing issues nowadays.  Here are 3 things that might change the future of scientific publishing.

  • Journal Finder: It’s extremely hard to determine which journal you should send your manuscript to. ResearchGATE just came up with a solution, the Journal Finder. You insert keywords or your entire abstract and it gives you some tips on which journal to contact.

journal finder

  • Article of the Future by The Cell: A new structure for scientific articles with integrated audio and video interview; real-time reference analyses, clickable areas on figures, etc.

cell future article

  • Article-Level Metrics at PLoS: The metric should be the article (new concept at PLoS), and not the source (Impact factors work like that) as scientists want their work to be judged by the quality of the publication and not by the journal it was published in. Real-time incoming link and citations.

plos metric

Nature’s role in e-Science: Second Life conference LIVE

Another day with live blogging, but this time from the Scifoo lives on Second Life conference session, where we’ll talk about‘s role in e-Science. Enjoy and join us here!

Live Coverage starts (Second Life time):

  • 8:25: Everything seems to be ready! We’ll start exactly at 9:00 (or 17:00 GMT). Here is a funny welcome image with Adastar Galsworthy:


  • 8:40: You may remember our first Scifoo lives on session that took place on the 20th of August. Emile Petrone talked about, a knowledge community for researchers to connect, communicate and collaborate. Now Emile told us they closed the site and started a new project. It’s good to be informed.
  • 8:45: Joanna Scott, the owner of the Second Nature island is with us as well. More and more people are coming…


  • 8:58: About a dozen attendees are here. We should start the session in some minutes. Come and join!
  • 9:02: Kick-off! Matt Brown will be the first speaker and he focuses on Nature Network. He has a weird avatar:


  • 9:07: I’ve always wanted to know why Nature Network is better (if it is) than WordPress or Blogger. “They’re getting about 1000 new scientists a month signing up on NN, but tens of thousands more regularly browse it.”
  • 9:09: Emile Pintens: Are you looking to move into other disciplines? Outside of the life sciences? … Matt: Really, we’re trying to cover the whole of science from physics to maths to biology.
  • 9:10: Richard Akerman asked a great question: say a research organisation … a research council wanted to subscribe all of it’s members – any cost? something to discuss offline?
  • 9:11: The answer is they’re working on it…
  • 9:14: The next speaker is Ian Mulvany from


  • 9:20: Connotea “is is somewhere between being an online social bookmark manager and an online social reference manager. The goal is to create a tool that allows the researcher to stay on top of the literature.”
  • 9:24: Connotea is going to be integrated into Nature Network. Wow! As Emile pointed out we all have to follow the guideline 1 site to rule them all.
  • 9:26: They have “a little over 60,000 people request an account, but less than that use it regularly”. What a number!
  • 9:28: According to Ian Mulvany, they have something in the region of 300,000 bookmarks with citation data, and more if you roll in non citation bookmarks… + 1.2 million tags!
  • 9:30: I asked him what he thinks about the recently launched 2collab. And the answer of the day is: i don’t think any one service is going to capture the market, and as a result i think it’s important for all of these services to find a way to share data and api calls, otherwise we will do a disservice to our useres
  • 9:32: Here is the page for Medicine 2.0 tag on Connotea.

A panorama image of us:


  • 9:36: We move on to Hilary Spencer from Nature Precedings. She talked about her project back in August, in the first sesison. Nature Precedings is a site for “Pre-publication research and preliminary findings”.
  • 9:40: I remember that last time we tried to find out where is the border between review and peer-review.


  • 9:46: Hilary: Nature Precedings is a place to store pieces of scientific communication in a way that allows them to be easily shared, referenced, and found by other researchers. We accept submissions in biology, medicine, chemistry and the earth sciences (except for clinical medicine).
  • 9:49: They also include collaborative “web 2.0”-like features. Like commenting directly on papers; a feature called “vote to promote” (kind of like the voting on Digg); tag-based classification; RSS feeds and e-mail alerts.
  • 9:53: Ricardo Vidal always has a great question: By using nature precedings does it bind the documents in any way to Nature? The answer is No, papers in Precedings receive a Creative Commons 3.0 license.
  • 9:56: I just subscribed to the Genetics channel of Precedings. It’s going to be useful to follow.
  • 9:58: I’m a bit surprised. They “only” have about 240 documents on the site. I thought they had many more.
  • 10:03: It’s not peer-reviewed, but moderated to keep things within guidelines.
  • 10:06: Helen Jaques is here on behalf of Nature Clinical Practice. Helen King couldn’t make it. She talks about Dissect Medicine.


  • 10:11: 642 users in total in 2006. I asked her how Dissect Medicine is different from Biowizard.
  • 10:14: Now some words about Nature Clinical Practice. As it seems to be involved in medical education, I’m curious whether they’d be interested in organizing medical educational exercises in Second Life.
  • 10:23: That’s all folks! It’s been great to hear the thoughts of the guys at I hope we got closer to understand Nature’s role in e-Science.

See you next time! Check out the transcript at the official page.

Live Coverage Ends

Read more!


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