PLOS ONE’s New Look: Redesigned for Discovery

The PLOS Product and Development teams are constantly working to enhance the web experience for authors, editors, and readers. Today, we’re unveiling the latest update to PLOS ONE. Here’s an overview of what’s new:

Navigate Faster with Figures
The PLOS ONE home page now features a new way to discover and explore the latest research. Instead of seeing a list of articles, you’ll see a grid of articles each presented with a key figure. Hover over the figure for one-click access to the article’s abstract, figures, or full text.
home Subject Area Browsing
We’ve introduced a brand new way to navigate the research that PLOS ONE publishes across the entire spectrum of subject areas. Dive in by clicking “Subject Areas” at the top of every page. Once you find your preferred topic, click “View all articles” to get to one of our new subject-specific browse pages.
browseThese new pages feature a grid just like the home page, sortable by most recent or most popular allowing you to easily navigate all of PLOS ONE’s research articles. If you prefer, you can switch to a more traditional list of articles. If the subject area you’re browsing isn’t quite what you’re looking for, click the arrow to the left of the subject header to navigate one level up or down our taxonomy.
navIf you’ve found the right subject area for your research, you can click the mail icon to sign up for a weekly email alert for that subject area, or the RSS icon to subscribe to that feed.
feed

As always, the article page gives you one-click access to the Article Level Metrics (ALMs), author information, comments, and related content.

More to Come
You can expect ongoing improvements to the PLOS ONE web experience. As always, we’ll be looking to the community for feedback and suggestions. Feel free to leave a us a comment below.

PLOS ONE – Measuring Article Impact

citation counts2

A common misconception of PLOS ONE is that just because we don’t consider perceived impact or novelty when deciding what to publish, doesn’t mean we don’t care about the impact of articles we publish. We of course understand that some papers are more impactful than others. That’s why we’re committed to developing new tools that realistically and unbiasedly evaluate how our papers shape their fields.

The number of citations an article collects offers one perspective on how the work has influenced its field, and is one of the many diverse measures that PLOS Article-Level Metrics provide to help the community measure article impact (others include usage and social sharing).

We recently plotted all citations to every PLOS ONE paper published in 2010 (thanks to our ALM guru Martin Fenner, and to Scopus for the data in the graph above)

The graph tells an interesting story about the range of papers published in PLOS ONE, showing that, from ground-breaking, highly-cited research to small studies that appeal to niche audiences, the journal really is for all of science. But another important thing that arose from this analysis was how much the variability in citations came from the range of subjects we publish. Fields like cell biology are huge and well-funded, with thousands of research groups around the world publishing tens of thousands of papers, while others such as ophthalmology are quite small, with only a few groups actively publishing research. All those extra cell biology papers mean lots of extra citations for the whole field, so papers in this area receive many more citations overall compared to ophthalmology, where only a few hundred papers are published each year.

The catch-all nature of journal metrics, such as the Impact Factor, means that PLOS ONE is considered a ‘top journal’ in the field of ophthalmology, as its Impact Factor is higher than any specialist journal in that field, whereas in the cell biology world we are ‘mid-level’. To address this discrepancy between fields, PLOS now includes relative metrics on all our papers, so readers can see the activity around a paper (just page views so far) relative to others in its field. As a result, you can see at the article level the impact of specific research on its field.

My feeling is that PLOS ONE has a wider citation distribution than most other journals, although I haven´t seen their data to say for certain (I would love for more journals to start displaying their full citation data!). But while it’s great to see a good number of PLOS ONE papers receiving very high numbers of citations, I think the more notable achievement is that we really are publishing all kinds of research, regardless of its estimated impact, and letting the community decide what is worthy of citation. With the usual flurry of Impact Factor announcements due to start any day now, it’s a good time to remember that it is the papers, not the journals they´re published in, that make the impact.

Graph: This is a kernel density estimation of citation distribution rather than actual numbers, hence the fact that it looks like some papers have received fewer than zero citations (credit Martin Fenner)

 

 

PLOS ONE Papers of 2012

As we start off the New Year, we wanted to take a quick moment and highlight a few noteworthy papers published in 2012. Of the 23,468 papers published last year, five are already in the top 12 most viewed PLOS papers to date. Although they may not have gotten the press coverage of those listed in our 2012 Media Round-Up, Article Level Metrics reveal they’ve certainly received a lot of attention.

Published just over three months ago, a study showing that withdrawal symptoms of marijuana can be similar to those of tobacco is the third most highly viewed article published by any PLOS journal. With 227,928 total article views since publication on September 26, 2012 it’s only a few thousand views short of the top two articles published in 2008 and 2009. Other highly viewed ONE articles from 2012 include a study of genetic alterations in a line of flies reared in the dark (197,150 views since publication in March), the ecosystem implications of an invasive species (174,742 total article views, published September), an experiment depicted in Figure 3 to the right in immersive virtual reality between rats and humans (139,683 total article views, published in October), and a comparison of Westerners energetics with those of a hunter-gatherer society (102,167 total article views, published in July).

2012 also brought several papers describing new species, one of which was recognized as the “Best new species that was hiding in plain sight” by Jason G. Goldman of Scientific American. Other papers of note questioned beliefs about the limitations of alternative agriculture and challenged trusted measurements such as the Body Mass Index, commonly used to determine obesity rates.

Several more papers could even help support or inspire your New Year’s Resolutions. Whether it is to spend more time outdoors, watch what you eat, lose weight or conquer your fears, ONE has published research to help motivate those resolutions.

2012 was a year of growth and innovation for PLOS ONE, here’s looking forward to another great year!

Great Genetics: PLOS ONE at ASHG

For the 2012 American Society for Human Genetics conference in San Francisco, we are highlighting a selection of recently published articles in the area.  In the last two years, PLOS ONE has published over 700 articles on human genetics; the eight summarized below are among the top 5% with regard to post-publication citations, HTML views, PDF downloads, and bookmarking.

Two of these papers address the genetic underpinnings of Alzheimer disease.  By mining genetic data, Jones et al. linked two physiological processes, cholesterol metabolism and the innate immune response, to late-onset Alzheimer disease development.  In a paper published in September of this year, Jun et al. discovered a correlation between the presence of cataracts and Alzheimer disease, and identified genetic variations in the gene encoding for the ?-catenin protein that may be the link between these two conditions.

Looking at another eye disorder, Nakano et al. investigated the genetic component of glaucoma.  Their research identified genetic variations among people of Japanese ancestry that are associated with certain types of glaucoma.

Another paper looked at the potential role of epigenetic modification in type 2 diabetes. Specifically, Bell et al. compared DNA from healthy women and women with type 2 diabetes and examined variations in DNA methylation, a chemical modification to the DNA that affects gene expression.  The analysis revealed significant methylation differences in regions of DNA previously associated with type 2 diabetes, suggesting that variations in DNA methylation may play a role in the disease.

Two studies considered variations in the number of repeats of specific DNA sequences, which can affect disease pathology and even drive evolution.  Valsesia et al. investigated DNA copy number variations and their effect on gene expression in seven different melanoma cell lines.  Their research identified candidate genes and molecular pathways involved in metastatic melanoma.  Zhang et al. compared the performance of four software programs in detecting copy number variations in DNA sequences longer than 1,000 bases.  The authors found inconsistency even among the most established programs, emphasizing the work that still needs to be done in this area.

Another paper addressed the issue of chromosome translocation, or the abnormal rearrangement of parts of chromosomes.  In a collaboration between biologists and physicists, Engreitz et al. showed that the three-dimensional organization of DNA in the cell nucleus may help explain certain chromosomal translocations linked to human disease.

Finally, using data from the Human Genome Diversity Project, Kirin et al. profiled the lengths and frequencies of DNA sequences that are identical on maternal and paternal chromosomes.  This large-scale analysis allowed the authors to make conclusions about historic and contemporary patterns of intra-communal parentage in different human populations.

If you are at the ASHG, we hope that you stop by the PLOS booth and meet some of the PLOS staff.  We will be at booth # 1606.  Also, if you have published in PLOS ONE, we have a stylish PLOS ONE author t-shirt to give you.  We look forward to seeing you there.

Acknowledgments:  Thank you to Martin Fenner for helping us with the article-level metrics analysis.  Thank you to Eric Martens and Matt Hodgkinson for designing the literature search and helping analyze the final results.  Finally, thank you to Camron Assadi for coordinating our efforts.

Image:  Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, et al. (2011) Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma. PLoS ONE 6(4): e18369. doi:10.1371/journal.pone.0018369

Citations:

Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, et al. (2010) Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus. PLoS ONE 5(11): e14040. doi:10.1371/journal.pone.0014040

Engreitz JM, Agarwala V, Mirny LA (2012) Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease. PLoS ONE 7(9): e44196. doi:10.1371/journal.pone.0044196

Jones L, Holmans PA, Hamshere ML, Harold D, Moskvina V, et al. (2010) Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer’s Disease. PLoS ONE 5(11): e13950. doi:10.1371/journal.pone.0013950

Jun G, Moncaster JA, Koutras C, Seshadri S, Buros J, et al. (2012) ?-Catenin Is Genetically and Biologically Associated with Cortical Cataract and Future Alzheimer-Related Structural and Functional Brain Changes. PLoS ONE 7(9): e43728. doi:10.1371/journal.pone.0043728

Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, et al. (2010) Genomic Runs of Homozygosity Record Population History and Consanguinity. PLoS ONE 5(11): e13996. doi:10.1371/journal.pone.0013996

Nakano M, Ikeda Y, Tokuda Y, Fuwa M, Omi N, et al. (2012) Common Variants in CDKN2B-AS1 Associated with Optic-Nerve Vulnerability of Glaucoma Identified by Genome-Wide Association Studies in Japanese. PLoS ONE 7(3): e33389. doi:10.1371/journal.pone.0033389

Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, et al. (2011) Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma. PLoS ONE 6(4): e18369. doi:10.1371/journal.pone.0018369

Zhang D, Qian Y, Akula N, Alliey-Rodriguez N, Tang J, et al. (2011) Accuracy of CNV Detection from GWAS Data. PLoS ONE 6(1): e14511. doi:10.1371/journal.pone.0014511

Announcing the Altmetrics Collection

With the increasing use of Web 2.0 tools in scientific publishing and discussion, there is growing concern that scholarly output may be swamping traditional mechanisms for filtering scientific impact, such as peer review (pre-publication filtering) or the journal impact factor (post-publication). In response to this concern, it has become clear that “altmetrics” based on a diverse set of social sources are increasingly likely to provide deeper, richer, and real-time assessments of current and potential scholarly impact.

Today, PLOS ONE, in collaboration with altmetrics.org is pleased to announce the launch of the PLOS ONE Altmetrics Collection, a body of research that aims to provide a forum for the dissemination of innovative research on these metrics.

The growing field of altmetrics uses online activity to collect fine-grained data, including viewership, discussion, saving, and recommendation along with traditional citation. This allows   researchers, funders, institutions and policy makers to create a higher resolution picture of the reach and impact of academic research and track its effects on diverse audiences. The PLOS ONE Altmetrics Collection gathers an emerging body of research for the further study and use of altmetrics. As an on-going collection, it aims to continually cover a range of subjects including statistical analysis of altmetrics data sources; metric validation, and identification of biases in measurements; validation of models of scientific discovery or recommendation based on altmetrics; qualitative research describing the scholarly use of online tools and environments; empirically-supported theory guiding altmetrics use; and other research relating to scholarly impact in online tools and environments.

The Collection is open to all authors to submit research in these areas. Articles are presented in order of publication date and new articles will be added to the Collection as they are published.

To read more about this collection, please visit: PLOS Collections: Altmetrics Collection (2012)

 

A selection of influential PLOS ONE papers on tropical medicine and malaria

For the XVIII International Congress for Tropical Medicine and Malaria Conference in Rio de Janeiro, PLOS ONE is highlighting eight recent articles.  Since January 2011, PLOS ONE has published almost 700 articles in the areas of tropical neglected diseases, tropical medicine, and malaria.  We’re sharing with you some of the papers that have received the most attention.  The authors on these papers come from across the globe, representing Brazil, Colombia, Ethiopia, France, the Netherlands, Papua New Guinea, Spain, Sri Lanka, Switzerland, the United Kingdom, and the United States.

One paper in particular has stood out.  Researchers found a novel therapy that could revolutionize the treatment of viral infections from the common cold to Ebola.  The therapy eliminates cells that contain viral RNA while leaving uninfected cells unharmed.  In the study, the therapy was effective against 15 different viruses, including dengue flavivirus, rhinoviruses, and H1N1 influenza virus.

An article published last month reported that malaria incidence in Sri Lanka has declined by 99.9% since 1999, despite ongoing conflict in the country.  The success of the malaria program could be explained in part by effective prevention measures, early detection, and maintaining the program in conflict zones.  In less than a month, the paper has received over 1,000 views.

Bacteria on people’s skin can affect how attractive they seem to malaria-transmitting mosquitoes.  Research published last December found that malaria mosquitoes preferred people whose skin had an increased number of bacteria but fewer overall types.  The article received significant press coverage and has been viewed almost 10,000 times.

Although a vaccine that blocks malaria transmission is theoretically possible, several obstacles have prevented its development, including producing Plasmodium parasite antigens in a cost-effective manner.  A paper published in May 2012 showed algae can make Plasmodium proteins that can elicit an antibody response.  This approach could bring down overall costs of a vaccine.  Since publication this paper has been viewed over 3,500 times.

A different approach to combatting malaria is to increase the mosquito’s defenses against the parasite.  A paper published in January 2011 showed that it is possible to insert an anti-malarial gene into a specific location in the Anopheles gambiae genome.  This technique decreased infections of Plasmodium yoelii nigeriensis and could be effective against other Plasmodium parasites.  Since publication this paper has received over 2,000 views.

The results from a World Health Organization-led effort to estimate the global incidence of leishmaniasis, a parasitic disease spread by sandflies, published in May 2012.  To obtain an accurate estimate of the disease burden, the authors collected data from 98 countries and 3 territories.  The authors stressed the importance of this in-depth assessment in helping policy makers and aid organizations determine funding priorities for this underreported disease.  The paper has been viewed over 5,000 times.

One strategy parasites use to evade the host’s immune system, initiate infection, and even manipulate host behavior is to imitate the host’s proteins.  A study published in March 2011 presented a method for scanning entire parasite genomes to identify proteins that are mimicking host proteins.  The paper received over 4,000 views and was featured on the This Week in Parasitism podcast.

Finally, a new method for diagnosing infection by Schistosoma mansoni, the parasite that causes schistosomiasis, was published in June 2012.  This method, which is based on detecting the parasite’s DNA, provides greater sensitivity than the most routinely used diagnostic approach, requires only a urine sample, and has a relatively low cost.

If you are at the ICTMM, we hope that you have had a chance to stop by the PLOS booth, pick up one of the PLOS ONE postcards, and meet staff from PLOS Pathogens and PLOS Neglected Tropical Diseases.

Acknowledgment:  Thank you to Martin Fenner for helping us use the PLOS Article Level Metrics to identify influential PLOS ONE papers in the areas of tropical neglected diseases, tropical medicine, and malaria.