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Posts from the ‘Open Access’ Category

What is open access about?

Fellow genomic blogger, Jonathan Eisen, created a great video that describes what open access publishing is about. I’ve always tried to publish in open access journals.

Access2Research: Global Petition!

I’ve been a supporter of open access research for a long time (Just 2 examples why: My Open Access Success Story and Open access social media guide for pharma) and it was a pleasure to see the announcement coming from the OA community about signing a global petition today.

Sign the petition to require free access over the Internet to journal articles arising from taxpayer-funded research. This will require you to create an account at the White House petition website, confirm the account by clicking on a link in your email, and then sign the petition itself.

Please sign the petition and follow the movement on Facebook.

My Open Access Success Story

An interview with me focusing on how open access changed the way I conduct my research in genomics was published on Open Access Success Stories. An excerpt:

So what happened when he published his first paper? Naturally, Dr Mesko chose to publish it in an open access journal and to use his expertise with social media to share it as widely as possible.

“As I’ve been a medical blogger for years, it was clear to me I would like to get as much feedback as possible for my work so we decided to publish the paper in an open access journal. I wanted to get suggestions, I wanted to hear the opinion of respected scientists, some of whom were also bloggers,” explains Dr Mesko.

Open-Access Social Media Guide for Pharma: Want to join?

I’ve been planning to launch this project for some time but before launching it officially I wanted to get feedback from some companies I spoke at about this important topic. So here is the deal. I would like to create collaboratively an open-access set of guidelines that pharma companies could use for free and personalize for their own needs and preferences. I believe we (medical professionals and patients) have to know how the pharma sector do and should not use social media and vica versa.

Let’s get together and please let me know if you think you would like to contribute to that. Myself, I would cover the Wikipedia usage section but I would need participants focusing on pharma and Twitter, blogs or Facebook, etc.

Please let me know what you think! If there are enough participants, would happily host the platform on which we can create this guide.

An excerpt from one of my recent Prezis:

British Medical Journal Open!

I was a bit surprised but at the same time glad to see the details about the upcoming (autumn, 2010) BMJ Open, an open access journal of the BMJ Group.

BMJ Open is an open access journal for general medical research.

Not only will the journal publish traditional full research reports, including small or low-impact studies, but we intend to shed light on all stages of the research process by publishing study protocols, pilot studies and pre-protocols. The journal will also place great emphasis on the importance of data sharing; raw data will be linked to at its repository or hosted online as supplementary material wherever possible.

Authors will be asked to pay article-processing charges on acceptance, although waivers will be available on request. The ability to pay will not influence editorial decisions; payment requests will be made on acceptance.

How Science 2.0 and Open Access Really Work

Last week, I wrote about publishing my first paper in PhD (Peripheral blood gene expression patterns discriminate among chronic inflammatory diseases and healthy controls and identify novel targets) and I said publishing in an open access journal was a real priority for us because we really wanted to get feedback from the scientific communities. So let’s see where I shared that paper:

  1. and also my Hungarian medical blog (
  2. Twitter and Friendfeed
  3. ResearchGATE

And let’s see what happened after that:

  • The paper now is the most viewed one in the last 30 days in BMC Medical Genomics.
  • It received the “Highly accessed” badge
  • I received many e-mails with relevant questions and I had interesting discussions on Twitter (actually found some collegues who work in the same field)
  • I got invitations for collaboration from several international labs.

Before you’d ask, yes, I think it’s because we chose an open access journal. It costs a lot but is really worth it.

What is your story?

BioLit: Open-access articles in a semantic database

I just published my first paper in PhD and publishing in an open-access journal was a real priority for us so I’m glad I just found the BioLit Project which is a semantic database of over 140,000 open-access articles.

The establishment of open access literature makes it possible for knowledge to be extracted from scholarly articles and included in other resources. BioLit aims to extract database identifiers and rich meta-data from open access articles in the life sciences and integrate that information with existing biological databases. We have begun prototyping this effort using a clone of the RCSB Protein Data Bank, a database of macromolecular structures.

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:


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