Top 5 papers of 2010

Go and take a look at the selection made by Faculty of 1000, which includes the article describing the structure of a bacterial complex I enzyme.

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Top 25 articles in Biochemistry, Genetics and Molecular Biology

Yesterday, I twittered about Sciverse, a new "Elsevier platform that combines ScienceDirect (fulltext journal articles) and Scopus (abstract and citation database of peer-reviewed literature)" (more about it here, in @mfenner's blog).

While browsing around the ScienceDirect site, I found a new service: "Top-25 hottest articles".

Basically, Top 25 "allows you to see which articles have been downloaded the most, either from any of the 24 subject areas and/or from any of the 2,500 journals on ScienceDirect".

These reports are published quarterly and so reflect usage behavior from the prior three months.

So, which articles have been the most downloaded ones in the period between April and June 2010, in the field of "Biochemistry, Genetics and Molecular Biology"?

1. The Hallmarks of Cancer

Cell, Volume 100, Issue 1, January 2000, Pages 57-70

Hanahan, D.; Weinberg, R.A.

2. Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP Cell, Volume 141, Issue 1, April 2010, Pages 129-141

Hafner, M.; Landthaler, M.; Burger, L.; Khorshid, M.; Hausser, J.; Berninger, P.; Rothballer, A.; Ascano, M.; Jungkamp, A.C.; Munschauer, M.; Ulrich, A.; Wardle, G.S.; Dewell, S.; Zavolan, M.; Tuschl, T.

3. A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

Cell, Volume 141, Issue 1, April 2010, Pages 69-80

Sharma, S.V.; Lee, D.Y.; Li, B.; Quinlan, M.P.; Takahashi, F.; Maheswaran, S.; McDermott, U.; Azizian, N.; Zou, L.; Fischbach, M.A.; Wong, K.K.; Brandstetter, K.; Wittner, B.; Ramaswamy, S.; Classon, M.; Settleman, J.

4. Immunity, Inflammation, and Cancer

Cell, Volume 140, Issue 6, March 2010, Pages 883-899

Grivennikov, S.I.; Greten, F.R.; Karin, M.

5. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors

Cell, Volume 126, Issue 4, August 2006, Pages 663-676

Takahashi, K.; Yamanaka, S.

6. The Inflammasomes Cell, Volume 140, Issue 6, March 2010, Pages 821-832

Schroder, K.; Tschopp, J.

7. Mitochondria Supply Membranes for Autophagosome Biogenesis during Starvation

Cell, Volume 141, Issue 4, May 2010, Pages 656-667

Hailey, D.W.; Rambold, A.S.; Satpute-Krishnan, P.; Mitra, K.; Sougrat, R.; Kim, P.K.; Lippincott-Schwartz, J.

8. Pattern Recognition Receptors and Inflammation

Cell, Volume 140, Issue 6, March 2010, Pages 805-820

Takeuchi, O.; Akira, S.

9. Reconstitution of the RIG-I Pathway Reveals a Signaling Role of Unanchored Polyubiquitin Chains in Innate Immunity

Cell, Volume 141, Issue 2, April 2010, Pages 315-330

Zeng, W.; Sun, L.; Jiang, X.; Chen, X.; Hou, F.; Adhikari, A.; Xu, M.; Chen, Z.J.

10. Ragulator-Rag Complex Targets mTORC1 to the Lysosomal Surface and Is Necessary for Its Activation by Amino Acids

Cell, Volume 141, Issue 2, April 2010, Pages 290-303

Sancak, Y.; Bar-Peled, L.; Zoncu, R.; Markhard, A.L.; Nada, S.; Sabatini, D.M.

11. A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases

Cancer Cell, Volume 17, Issue 4, April 2010, Pages 348-361

Hirsch, H.A.; Iliopoulos, D.; Joshi, A.; Zhang, Y.; Jaeger, S.A.; Bulyk, M.; Tsichlis, P.N.; Shirley Liu, X.; Struhl, K.

12. NLRC5 Negatively Regulates the NF-@kB and Type I Interferon Signaling Pathways Cell, Volume 141, Issue 3, April 2010, Pages 483-496

Cui, J.; Zhu, L.; Xia, X.; Wang, H.Y.; Legras, X.; Hong, J.; Ji, J.; Shen, P.; Zheng, S.; Chen, Z.J.; Wang, R.F.

13. A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth

Cell, Volume 141, Issue 4, May 2010, Pages 583-594

Roesch, A.; Fukunaga-Kalabis, M.; Schmidt, E.C.; Zabierowski, S.E.; Brafford, P.A.; Vultur, A.; Basu, D.; Gimotty, P.; Vogt, T.; Herlyn, M.

14. Endoplasmic Reticulum Stress and the Inflammatory Basis of Metabolic Disease

Cell, Volume 140, Issue 6, March 2010, Pages 900-917

Hotamisligil, G.S.

15. 53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks Cell, Volume 141, Issue 2, April 2010, Pages 243-254

Bunting, S.F.; Callen, E.; Wong, N.; Chen, H.T.; Polato, F.; Gunn, A.; Bothmer, A.; Feldhahn, N.; Fernandez-Capetillo, O.; Cao, L.; Xu, X.; Deng, C.X.; Finkel, T.; Nussenzweig, M.; Stark, J.M.; Nussenzweig, A.

16. Molecular and Cellular Approaches for Diversifying and Extending Optogenetics Cell, Volume 141, Issue 1, April 2010, Pages 154-165

Gradinaru, V.; Zhang, F.; Ramakrishnan, C.; Mattis, J.; Prakash, R.; Diester, I.; Goshen, I.; Thompson, K.R.; Deisseroth, K.

17. Identification of the Switch in Early-to-Late Endosome Transition

Cell, Volume 141, Issue 3, April 2010, Pages 497-508

Poteryaev, D.; Datta, S.; Ackema, K.; Zerial, M.; Spang, A.

18. Matrix Metalloproteinases: Regulators of the Tumor Microenvironment

Cell, Volume 141, Issue 1, April 2010, Pages 52-67

Kessenbrock, K.; Plaks, V.; Werb, Z.

19. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation Cell, Volume 141, Issue 2, April 2010, Pages 344-354

Tuller, T.; Carmi, A.; Vestsigian, K.; Navon, S.; Dorfan, Y.; Zaborske, J.; Pan, T.; Dahan, O.; Furman, I.; Pilpel, Y.

20. 3.3 A Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry

Cell, Volume 141, Issue 3, April 2010, Pages 472-482

Zhang, X.; Jin, L.; Fang, Q.; Hui, W.H.; Zhou, Z.H.

21. A Hierarchy of Self-Renewing Tumor-Initiating Cell Types in Glioblastoma

Cancer Cell, Volume 17, Issue 4, April 2010, Pages 362-375

Chen, R.; Nishimura, M.C.; Bumbaca, S.M.; Kharbanda, S.; Forrest, W.F.; Kasman, I.M.; Greve, J.M.; Soriano, R.H.; Gilmour, L.L.; Rivers, C.S.; Modrusan, Z.; Nacu, S.; Guerrero, S.; Edgar, K.A.; Wallin, J.J.; Lamszus, K.; Westphal, M.; Heim, S.; James, C.D

22. Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity

Cell, Volume 141, Issue 4, May 2010, Pages 668-681

Dixit, E.; Boulant, S.; Zhang, Y.; Lee, A.S.Y.; Odendall, C.; Shum, B.; Hacohen, N.; Chen, Z.J.; Whelan, S.P.; Fransen, M.; Nibert, M.L.; Superti-Furga, G.; Kagan, J.C.

23. Th17 and Regulatory T Cells in Mediating and Restraining Inflammation

Cell, Volume 140, Issue 6, March 2010, Pages 845-858

Littman, D.R.; Rudensky, A.Y.

24. Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation

Cell, Volume 141, Issue 4, May 2010, Pages 632-644

Tcherkezian, J.; Brittis, P.A.; Thomas, F.; Roux, P.P.; Flanagan, J.G.

25. Persistent Telomere Damage Induces Bypass of Mitosis and Tetraploidy

Cell, Volume 141, Issue 1, April 2010, Pages 81-93

Davoli, T.; Denchi, E.L.; de Lange, T.

Well that's a very "cancer & immunology"-oriented list!

Let's take a closer look at these stats:

23 out of the 25 articles are from Cell. The other two, from Cancer Cell.

17 are review articles.

The article "The hallmarks of cancer" (2000) has been cited in 7602 documents! 

You can subscribe to the Top25 list by RSS here.

Just as a comparison, let's take a look at what the "Essential Science Indicators" tool from Web of Science has to say regarding "highly cited articles" in the field of "Molecular Biology and Genetics". This list has been updated as of July 1, 2010 to cover a ~10-year period (January 1st, 2000 to April 30th, 2010).

Top-10

THE HALLMARKS OF CANCER
CELL 100 (1): 57-70 JAN 7 2000

INITIAL SEQUENCING AND ANALYSIS OF THE HUMAN GENOME
NATURE 409 (6822): 860-921 FEB 15 2001

THE SEQUENCE OF THE HUMAN GENOME
SCIENCE 291 (5507): 1304-+ FEB 16 2001

INFERENCE OF POPULATION STRUCTURE USING MULTILOCUS GENOTYPE DATA
GENETICS 155 (2): 945-959 JUN 2000

TRANSLATING THE HISTONE CODE
SCIENCE 293 (5532): 1074-1080 AUG 10 2001

MICRORNAS: GENOMICS, BIOGENESIS, MECHANISM, AND FUNCTION
CELL 116 (2): 281-297 JAN 23 2004

THE GENOME SEQUENCE OF DROSOPHILA MELANOGASTER
SCIENCE 287 (5461): 2185-2195 MAR 24 2000

THE LANGUAGE OF COVALENT HISTONE MODIFICATIONS
NATURE 403 (6765): 41-45 JAN 6 2000

INITIAL SEQUENCING AND COMPARATIVE ANALYSIS OF THE MOUSE GENOME
NATURE 420 (6915): 520-562 DEC 5 2002

A NEW STATISTICAL METHOD FOR HAPLOTYPE RECONSTRUCTION FROM POPULATION DATA
AMER J HUM GENET 68 (4): 978-989 APR 2001

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The 2009 Journal Citation Report is in!

The 2009 Journal Citation Report has just been published!

Just as last year [See The 2008 Journal Citation Report is in! ], there are not many surprises on the top (considering ALL journals), with some medical (CA-CANCER J CLIN, NEW ENGL J MED) and review journals holding on to most of the top 10 positions (including biology related review journals like NAT REV MOL CELL BIO -with an amazing 42.198, which ranks it 4th overall- and NAT REV IMMUNOL).

Also in the top 10, we find Nature (34.480, compared to its 2008 IF of 31.434) and Nature Genetics (34.284, compared to its 2008 IF of 30.259).

Cell, which last year was among the top 10, is now ranked 12th, with 31.152, compared to its 2008 IF of 31.253.

Science, the other glam journal, is now at the 15th position overall, with 29.747, compared to its 2008 IF of 28.103.

Note that, just as I said last year...

you know how I feel about the IF [for example see here] and I've talked about the special care one has to have with it before, so I don't want you to get the impression that just because I'm posting the news I think we should all live our lives around the IF (which of course, I don't... don't be silly). The list, however, is a highlight so we are bringing some details right to your RSS reader (if you follow us through one of those).

Now let's get down to business: who made the Top-20 in the Biochemistry & Molecular Biology category?

In descending order: CELL, ANNU REV BIOCHEM¹, NAT MED, ANNU REV BIOPH BIOM¹, NAT CHEM BIOL, MOL PSYCHIATR, MOL CELL, PLOS BIOL, NAT STRUCT MOL BIOL, MOL SYST BIOL, BBA-REV CANCER¹, TRENDS BIOCHEM SCI¹, GENOME RES, TRENDS MOL MED¹, CURR BIOL, CRIT REV BIOCHEM MOL, MOL BIOL EVOL, CURR OPIN STRUC BIOL¹, PLANT CELL, NAT PROD REP.

¹ Review journals

Here's the 2008 top-20 list in the field, for comparison:

CELL, ANNU REV BIOCHEM¹, NAT MED, ANNU REV BIOPH BIOM¹, NAT CHEM BIOL,TRENDS BIOCHEM SCI¹, MOL CELL, PLOS BIOL, MOL PSYCHIATR, MOL SYST BIOL, PROG LIPID RES, NAT STRUCT MOL BIOL, CURR BIOL, BBA-REV CANCER¹, GENOME RES, TRENDS MOL MED¹, PLANT CELL, CURR OPIN STRUC BIOL¹, CRIT REV BIOCHEM MOL¹, EMBO J

Just as last year, let's take a look at how some of the PLoS journals are doing (why? because we love PLoS and what it represents, see here and here)

First, the heavily criticized PLoS ONE shows that their novel strategy is working, with a great 4.351!.

PLoS Medicine now leads the way for the PLoS journals with 13.050 (last year PLoS Biology held the top position)

Also, PLoS Biology 12.916 (close second!), PLoS Pathogens 8.978, PLoS Genetics 9.532, PLoS Computational Biology 5.759, PLoS Neglected Tropical Diseases 4.693.

That's it for the moment.
I have to get back to my bacterial transformations and to watch some World Cup games ;-)


--
[Image credit: The NAD group]

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Cell launches a new format for the presentation of research articles online

Just a heads up for those who don't follow me on twitter, where I've promoted this more extensively.
Remember that a few months ago I discussed Cell Press' "Article of the Future"?

At the time I wrote

"As a collaborative effort to redefine the way a scientific article is presented online, integrating the tools and capabilities of the online environment, Cell Press and Elsevier have launched a project called Article of the Future at its Beta Prototype site."

So now, they've relaunched it, integrating some of the changes the community suggested. Check it out here!

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The most cited biology articles of 2009

These are the 5 papers in biology, published in the last two years, which received the most citations during 2009, according to Thomson Reuters (thanks to TheScientist.com for the info!)

5. A M. Wernig, et al., "In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state," Nature 448: 318-24, 2007.

4. E. Birney, et al., "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, "Nature, 447: 799-816, 2007.

3. A. Barski, et al., "High-resolution profiling of histone methylations in the human genome," Cell, 129: 823-37, 2007.

2. K.A. Frazer, et al., "A second generation human haplotype map of over 3.1 million SNPs," Nature, 449: 854-61, 2007.

1. K. Takahashi, et al., "Induction of pluripotent stem cells from adult human fibroblasts by defined factors," Cell, 131: 861-72, 2007.

Three Nature articles and two Cell ones... well, I guess there's no surprise there.

Here's a cartoon from Jorge Cham's Piled Higher and Deeper series.

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The most-cited institutions and Journals

ScienceWatch.com has released a ranking of the top 20 institutions (out of over 4,000) which have attracted the highest total citations to their papers published in Thomson Reuters-indexed journals over 22 fields. This has been done using the data from Essential Science Indicators since January 1, 1999 to April 30, 2009 [The Most-Cited Institutions Overall, 1999-2009].

This includes the "Molecular Biology & Genetics" field, so we checked it out and bring it to you.

The top 20 institutions over all fields include 14 US-based universities, 3 UK-based universities, and one each in Canada, Japan, and Germany.

Considering all 22 fields, the 20 most-cited institutions are:

01 HARVARD UNIV
02 MAX PLANCK SOCIETY
03 JOHNS HOPKINS UNIV
04 UNIV WASHINGTON
05 STANFORD UNIV
06 UNIV CALIF LOS ANGELES
07 UNIV MICHIGAN
08 UNIV CALIF BERKELEY
09 UNIV CALIF SAN FRANCISCO
10 UNIV PENN
11 UNIV TOKYO
12 UNIV CALIF SAN DIEGO
13 UNIV TORONTO
14 UCL
15 COLUMBIA UNIV
16 YALE UNIV
17 MIT
18 UNIV CAMBRIDGE
19 UNIV OXFORD
20 UNIV WISCONSIN

Interestingly, Harvard leads in 9 of the 22 fields, including "Molecular Biology & Genetics".

Harvard's citation strengths lie in biological and health sciences: the top five fields in their the citation record are Clinical Medicine, Molecular Biology & Genetics, Biology & Biochemistry, Neuroscience & Behavior, and Immunology.

The Max Planck Society ranks #2 overall and #2 in the "Molecular Biology & Genetics" and also in the "Biology & Biochemistry" sub-categories.

And on a personal note... Wisconsin rules!

Now, regarding journals, the top 10 most-cited (during the same period, 1999-2009) in all fields are:

1 Journal of Biological Chemistry
2 Proc. Natl. Acad. Sci. USA (PNAS)
3 Nature
4 Science
5 Physical Review Letters
6 J. American Chemical Society
7 Physical Review B
8 Astrophysical Journal
9 New England Journal of Medicine
10 Applied Physics Letters

[Source: Top Ten Most-Cited Journals (All Fields), 1999-2009]

Note that this has not been normalized in any way, and just reflects the total number of citations.

If you divide the total number of citations by the number of articles published in those journals, you get the following ranking:

01. New England Journal of Medicine
02. Science
03. Nature
04. PNAS
05. JBC
06. J. American Chemical Society
07. Physical Review Letters
08. Astrophysical Journal
09. Applied Physics Letters
10. Physical Review B

[Image credit: The NAD group]

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JANE: Journal and Author Name Estimator

I've just read over at Scienceroll about two tools that “help you determine which journal you should choose for publication”, based on your abstract or keywords [See Journal and Author Name Estimator and Huge Steps in Changing Science].

The first one is part of ResearchGATE (a “scientific network that connects researchers”) and the second one (which has been around for some time, since early 2008) comes as a standalone web application called "Journal and Author Name Estimator" (JANE). Note that to use the tool at ResearchGATE you must sign in.

Browsing around its site, I noticed that JANE was described in an article published in Bioinformatics in 2008¹, so I read the article and gave it a little try.

Here’s JANE’s description from its website:

Have you recently written a paper, but you're not sure to which journal you should submit it? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Jane can help!
Just enter the title and/or abstract of the paper in the box, and click on 'Find journals', 'Find authors' or 'Find Articles'. Jane will then compare your document to millions of documents in Medline to find the best matching journals, authors or articles

Also, here’s how it works (again, according to the info on its website -more details in the article-):

How does Jane work?

Jane first searches for the 50 articles that are most similar to your input*. For each of these articles, a similarity score between that article and your input is calculated. The similarity scores of all the articles belonging to a certain journal or author are summed to calculate the confidence score for that journal or author. The results are ranked by confidence score.

* For the computer geeks: we use the open source search engine Lucene. Queries using keywords are parsed with the QueryParser class, titles and abstracts are parsed using the MoreLikeThis parser class.

It’s hard for me to picture a submitting scientist SO lost that he/she  has absolutely no idea which journal publishes articles related to the work he/she is doing and with no clue whatsoever where to submit his/her work, to the extent that he/she would have to rely on a web-based application to enlighten him/her. I mean, surely he/she must have read an article or two for his/her own research and then have some sense of where he/she could submit. I agree that selecting a particular journal to submit your work is not a decision to be taken lightly, and in our case, after putting some thought into it, we generally narrow it down to 2-3 journals, but surely we know what journals have published work related (even remotely) to our own research in the past, from which we can pick our top 3.

In my opinion, using JANE for this is definitely not the way to go. I think it’s wiser to talk to colleagues at your department or at conferences. Their input will be more valuable and practical; some may have even submitted to some of the journals in your area and know a little about the inner workings of that particular journal. Also, at some conferences you can meet with journal’s representatives and discuss if your work would be suitable for their journal, or if you are lucky, they will approach you!

I tried JANE with several abstracts as query and it was kinda hit or miss: it generally gave the correct journal where the manuscript was originally published (not surprisingly, though) but some of the other journals in the list of “recommended journals” were not particularly related to the query as a whole, but to some particular words. This led JANE to propose journals (and this proposal was based on certain articles supposedly related to the query, published in those journals) that were way off.

Nevertheless, you will generally find journals that are indeed related to your input. The good thing is that you can check which articles JANE used to recommend the journals listed, so you can see if they are related as a whole or just because of a particular keyword in the abstract used as a query.

Furthermore, I fail to see an improvement large enough to justify not using directly Pubmed for this. If you put your keywords (although not whole abstracts) into Pubmed, you’ll get a series of articles with their respective journals and also, related papers. The way the authors justify using JANE over Pubmed is in no way satisfactory.

Despite all this, I think this tool can be useful for two things.

The first one is to discover “new” journals or to become aware of other journals (not from your typical selection) that have published related work in the past, so you can have a larger pool where to choose from. Also, you can narrow down your search to find Open Access journals, which is always good.

The second one is directed to editors or grant-awarding institutions: due to its “Find Authors” tool, it can help in finding reviewers for a particular article or grant.

Nevertheless, journals typically have a database with reviewers they generally use, but maybe a new journal (or editor) can benefit from this. I tried it with several articles in the different research areas I’ve been involved, and it generally turned up with a list of relevant researchers who would be appropriate for reviewing them. In my opinion, this is the best use for this tool.

In conclusion, I think that using this tool for “finding the most appropriate journal for publishing your results”¹ is definitely not the way to go, but I see some potential in using it to find related alternatives and, more importantly, as a tool for editors to find potential reviewers.

¹Schuemie, M., & Kors, J. (2008). Jane: suggesting journals, finding experts Bioinformatics, 24 (5), 727-728 DOI: 10.1093/bioinformatics/btn006

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The Scientific article of the future

Cell Press has always been innovative [See Another one from Cell Press: free symposia! and references therein]. As a collaborative effort to redefine the way a scientific article is presented online, integrating the tools and capabilities of the online environment, Cell Press and Elsevier have launched a project called Article of the Future at its Beta Prototype site.

Together, they've compiled two prototypes with several features.
Some of them are:

A graphical abstract allows readers to quickly gain an understanding of the main take-home message of the paper. The graphical abstract is intended to encourage browsing, promote interdisciplinary scholarship and help readers identify more quickly which papers are most relevant to their research interests.

This is great as it helps you get the idea of the paper and its implications graphically. Note that this does not replace the written abstract; it's just an addition.

Research highlights provide a bulleted list of the key results of the article.

A figure that contains clickable areas so that it can be used as a navigation mechanism to directly access specific sub-sections of the results and figures.

And many others.

You can check the prototypes here. I particularly liked Prototype #1.

I think that taking full advantage of the most important platform used nowadays to search for and read articles (that is, online), is a great idea. As some have stated in the past (including my former PI) the print version of journals is inevitably heading towards disappearance unless it can find a way to compete with the complete set of tools provided by the Internet (commenting, sharing, rating, audio and video, etc) that enhances the reading (and science communicating) experience. Although I like my print version of Nature, as it allows me to read the News & Views section and editorials during my daily commute, I hardly use it to read the articles related to my research. I'd rather download them, file them, attach comments, etc and save them for good, without worrying about spilling my coffee over them or leaving them behind somewhere. Also, there's some great reference-managing software around nowadays to help you cope with the increasing amounts of articles being published so you can find a particular article in seconds, leaving the old days of diving into piles of photocopied articles to find the right one or visiting the library, behind.

But what about reading the articles online? Is it the same as downloading the article and reading it offline? This new approach by Cell Press and Elsevier, says no. The idea is to take advantage of the capabilities the online environment provides and to "allow readers individualized entry points and routes through the content, while using the latest advances in visualization techniques". Something not available in a simple PDF file.

You can download it just to have it backed up and organized and read it offline if you want to (although, who works offline nowadays?), but the idea behind the project is to enhance the reading experience by taking advantage of what the Internet has to offer.

I think that journals integrating and taking advantage of all the tools the online environment provides, benefits us all and can lead to better science communication.

Be sure to provide feedback to this project.

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New journal from CSHL Press

A new review journal, covering all aspects of molecular biology, has recently been launched.

Cold Spring Harbor Perspectives in Biology (CSH Perspectives) is a monthly online publication from CSHL Press, with an outstanding editorial board (featuring renowned scientists like Tom Cech, Mark Estelle, Peter Lawrence, Tom Misteli, Paolo Sassone-Corsi and David Spector just to name a few), analyzing progress in emerging areas of molecular, cell, and developmental biology, genetics, evolutionary biology, neuroscience, cancer biology, and molecular pathology.

Interestingly, articles will be organized as "Subject Collections", which will "gradually accumulate articles as new issues of the journal are published and, when complete, each will represent a comprehensive survey of the field it covers".

This is a very attractive feature and I'm confident, considering its board, that the journal will keep up with the rapidly advancing pace of molecular biology.

Also you can follow the journal on twitter (http://twitter.com/cshperspectives) which is always a great addition.

We'll keep our eyes open.

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The 2008 Journal Citation Report is in!

The 2008 release of Journal Citation Reports is in (the IF report for a certain year, is released the following year). If it weren't for twitter I would have never known, mainly because every journal is promoting themselves through it. Score for twitter! (Please note: the image on the left will make sense in a second).

Anyway, you know how I feel about the IF [for example see here] and I've talked about the special care one has to have with it before, so I don't want you to get the impression that just because I'm posting the news I think we should all live our lives around the IF (which of course, I don't... don't be silly). The list, however, is a highlight so we are bringing some details right to your RSS reader (if you follow us through one of those).

Not many surprises on the top (considering ALL journals), with some medical (CA-CANCER J CLIN, NEW ENGL J MED) and review journals holding on to most of the top 10 positions (including some biology related journals like NAT REV MOL CELL BIO, ANNU REV IMMUNOL) but also of interest is Nature with an amazing 31.434 and Cell with a 31.253 (8th and 9th, respectively) way over Science at 28.103. Also, I didn't know Nature Genetics was doing so well (30.259!).

Now let's get down to business: who made the Top-20 in the Biochemistry & Molecular Biology category? (I feel like I'm on E! at the Oscars... yes.. now the image should make sense. OK maybe it wasn't funny at all).

In descending order: CELL, ANNU REV BIOCHEM¹, NAT MED, ANNU REV BIOPH BIOM¹, NAT CHEM BIOL,TRENDS BIOCHEM SCI¹, MOL CELL, PLOS BIOL, MOL PSYCHIATR, MOL SYST BIOL, PROG LIPID RES, NAT STRUCT MOL BIOL, CURR BIOL, BBA-REV CANCER¹, GENOME RES², TRENDS MOL MED¹, PLANT CELL, CURR OPIN STRUC BIOL¹, CRIT REV BIOCHEM MOL¹, EMBO J

¹ Review journals
²This journal keeps going up in the rankings, as a reflection of the way we are approaching science at present, making use of several bioinformatics tools to mine the increasing amounts of genomic data being generated, to ask and answer important biological questions. Also, to report such data!

So how are some of the PLoS Journals doing? PLoS Biology 12,683 (and still the best ranked, and let's face it, best overall PLoS Journal), PLoS Medicine 12.185 (close second!), PLoS Pathogens 9.125, PLoS Genetics 8.883, PLoS Computational Biology 5.895, PLoS Neglected Tropical Diseases 4.172.

It is pretty awesome if you ask me. Great for PLoS and OA publishing!

We'll have to keep our eyes open in case someone gets down to do the analysis of how the OA journals did this year in the IF report. I'd be very interested in knowing if OA journals are going up in the rankings as some have suggested. Let us know shall you find such an analysis in the days to come.

The list is available through institutional subscription at Web of Science.


PS. For my plant biologists readers: Plant Cell 9.296 (and top 20 in B&MB!), The Plant Journal 6.493, Plant Physiology 6.110. Plant Physiology is getting closer!!

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The Top 100 Journals in Biology and Medicine

I've just learned about this (although the list has been around for a while):

In conjunction with SLA’s Centennial, the BioMedical & Life Sciences Division conducted a poll among its 686 members, to identify the 100 most influential journals of Biology & Medicine over the last 100 years.

Wow, that's a hard task. Lot's of journals come to mind... but let's continue with the news..

Interestingly, there was an entire section devoted to "Molecular and Cellular Biology journals, which also included Journals in Biotechnology and the Leading Multiscience Publications".

You can check the whole list here.

The "DBIO Top 10" journals were announced yesterday at the DBIO Annual Business luncheon during the Centennial Conference in Washington, DC, where Nature was awarded the first place. (OK, so maybe I made a good decision to renew my print subscription for the third year in a row). Anyway, this sounds OK to me. [You can check more details about it here: Nature wins 'journal of the century' award!]

Other journals which also made the list (and if they hadn't made it, it would have been, IMHO, a somewhat misleading poll) include Science, Cell and PNAS.

To some of my readers, it would interesting to know that Plant Physiology (but not The Plant Journal or Plant Cell) made the cut (although this may be related to their different "ages" and the fact that the scope in the early days of Plant Physiology also included fungi research).

On the other hand, I was surprised to see the EMBO Journal and the FASEB journal in the list. Not that I think they are not important journals in their fields, but I hardly consider them to be among the "most influential journals in the last 100 years".

Anyway, I'm not sure I see the point on doing such a poll, but good for Nature.
Also, I hardly think that a scientist will be influenced by this list at all, in a similar way that scientists are not (or should not) be influenced by the impact factor, when analyzing papers, but then again, I don't think this was the purpose behind making this list... so, why was this poll put together? Any thoughts?

Are the most influential journals in your field represented in this list? Check it out here.

Image credit: Copyright © 2009, American College of Chest Physicians

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On PLoS' article-level metrics

As some of you may know, since March this year, PLoS has started an "article-level metrics" campaign [See Article redesign on PLoS Journals]. This is a very interesting topic and I'll try to break it down to you here.

This discussion is centered around a webinar recently gave by Pete Binfield, the Managing Editor of PLoS ONE [Article-Level Metrics (at PLoS and beyond)], so if you want more info, do not hesitate to listen to it. [Hat Tip at A Blog Around The Clock for the link].

An increasing problem put forward by many people is that there are simply too many articles being published and basically it's impossible for us to read them all. Imagine you work in colorectal cancer. Of course you'll have to read some of the new articles arising on that topic, as they may be useful for your research. But what about new findings in other types of cancer? OK, so you start adding thousands of RSS to your Google Reader, trying to incorporate journals where cancer articles may be published. Now you have >1000 new items in your Google Reader each morning and little time.

Do you see my point?

One approach to this problem (if you want to call it that), and is the idea behind, for example F1000, is to read (or read more thoroughly) only the papers that are actually worth your while. For this, you'll have to be able to asses if the article you've just found through your weekly (daily?) Pubmed search fits within this category.

If you are anything like me, you'll read the abstract and, if you are still interested, download the article and flip through the figures and Discussion to “evaluate” if you are going to read this thing completely: you've just made your own analysis of the article.
However, it may still be interesting (as complementary info) to know, for example, how many times the article has been downloaded, of if it has been extensively commented on the blogosphere. That may mean something, or at least suggest that, if it’s getting reviewed a lot, maybe you should read it soon.

These last measurements are “article-level metrics” –ALMs- (as opposed to “journal metrics”, such as the IF) as they refer specifically to certain article and not to the journal where it was published.
Generally (or up to now, maybe), I’ve been comfortable with one ALM: article citation. I don’t actually use it nor it has any influence on my decision of reading a certain article, but “I’m comfortable” with it in the sense that people that are actually interested in the “impact” (in its classical ISI meaning) of a particular article could just take a look at this little number. You can get this through Web of Science. However, this may not be very useful with a new article, as its citation count will be zero.

Interestingly, there are several other useful pieces of data that can be added to compile a whole list of an article’s related metrics, which can give a more complete view of the article’s “social impact”.

For example, article usage. This generally refers to the number of downloads of a particular article, or the number of views. I’m not sure if there is a strong correlation between downloads and citations (I know I’ve downloaded hundreds of articles I’ve never read), but many journals are now implementing these sort of metrics (although some just list the “most read” or “most downloaded” articles, without numbers).

And what about media coverage? Or blog coverage? As I mentioned, it may be interesting to know that a particular article has been commented many times in the blogosphere, for example at Researchblogging.org (of which we are members).

PLoS has started the article-level metrics program to include all these “types of measures” for its articles to “implement new approaches to the evaluation and filtering of journal articles”, which they hope other publishers will follow.

The idea is to integrate info on citations, usage, media coverage, blog coverage, expert ratings (for example F1000), social bookmarking activity (for example Connotea), etc., and display it right in the article’s web page!

Indeed, in every PLoS article you’ll find a new tab entitled “Related content”, where some of this info can be found. The idea is to have a complete picture of the article’s impact and not just its citation numbers. As we now have the technology to follow these other numbers and include them in the article’s web page, I think it’s a great idea to put them up there. Also, as is now typical at PLoS, you can rate the articles and leave comments, completing the scene.

The expert’s rating I was talking about hasn’t been implemented yet, and it “could be” coupled to F1000 some day (in the sense that if a particular PLoS paper has been reviewed at F1000, it will be displayed at the article's web page), but this hasn’t been settled yet. Anyway, for some, it would be nice to know that the particular article on which they are deciding to read or not, has been reviewed at F1000.

In conclusion, ALMs can be very useful and they are a great addition to the “classic” assessment tools we’ve been using. This is a great idea by PLoS, which is always trying new things to improve scholar communication.

And who knows? It may also be used as a not-so-serious tool: maybe down the line we’ll be compulsively looking at the stats of our own articles and betting a beer over who got more downloads during a particular week.

Mmm…actually, that’s not a bad idea…

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Science metrics: the h-index

Nick Oswald at BiteSize Bio has recently published a post explaining the basic pros and cons of the H-index (or Hirsch number, named after his creator Jorge E. Hirsch), one of the many metrics developed to asses the apparent scientific impact of a scientist [Does Your h-index Measure Up?]. Although no single number can "give more than a rough approximation to an individual’s multifaceted profile" (as Jorge Hirsch wisely puts it¹), the H-index has been gaining adepts worldwide and it's increasingly being used as the metric of choice for many committees (I'm not saying that I agree with using such numbers for giving grants or for tenure evaluation, though).

Briefly, the advantage of the h-index is that it combines productivity and impact in a single number.

Nick's article is very interesting and enlighting in the sense of explaining the advantages, but also pointing out the limitations, of the h-index.

I encourage everyone to read it.

--
¹Hirsch JE(2005)An index to quantify an individual's scientific research output. PNAS 102 (46): 16569–16572.

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SNPs in the human genome: Hot paper in biology

The article "A second generation human haplotype map of over 3.1 million SNPs," by the International HapMap Consortium (K.A. Frazer, et al.), Nature, 449(7164): 854-61, 18 October 2007, has made it to the Hot Papers Database in the area of Biology due to its high citation rate during November-December 2008. The paper was cited 61 times in current journal articles indexed by Thomson Reuters in those months. Notably, during that period, only two other biology papers published in the last two years (aside from reviews) attracted higher citation totals.

[Source: ScienceWatch]

I normally do not encourage "excitement" about citations and journal statistics such as the Impact Factor, but I did a lot of reading on SNPs and the HapMap last year, and I thought it was interesting to highlight this article as the HapMap has important implications for the prevention, diagnosis, and treatment of human diseases.

Do you know what the HapMap is? If you don't, take a look at this site [What is the HapMap?]
It's a short (~2 pages) and very illustrative article explaining the basics about the whole project.

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