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Beall's list of Predatory Journals and Publishers taken down

Unfortunately, the Scholarly Open Access website was recently taken down (On 15 January 2017, according to this Wiki page that explains more). This Scholarly Open Access website contained "Beall's list" that alerted scientists to the increasing problem of predatory journals and publishers. It also explained this new trend, and contained discussions and articles with specific examples. This website, as well as the list itself, played an important role in putting the spotlight on an increasing problem: Publishing for profit, with (too) fast, fee-based online publishing, without the scientific rigor that proper peer review is supposed to provide. Some "journals" are clear scam, while others are grey-zone, with some solid science mixed with weaker articles that never benefited from proper scientific peer review. There were also examples of self-promotion of journals, by editor- or reviewer-requested references, to drive up "impact factor" of the journal. It is unfortunate that the host, Jeffrey Beall, decided to take down the website. But thanks to his efforts and the information previosuly provided on his website, the problem has receved attention, and we can hope that the efforts results in more careful and critical evaluation of journals - both in regards to where to publish, where to accept invites to be reviewer or on editorial board, and how to evaluate the papers published within these journals.   

Recent Publication in Genes & Development: 

Arenzana T, Schjerven H, and Smale ST. (2015) Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor. Genes Dev., Published online: August 27th, 2015.

With the use of the Ikaros-ZnF-specific mutant mice (Schjerven et al, 2013), this work analyzed the roles of Ikaros in five sequential stages of thymocyte development. Strikingly, the results revealed a role of Ikaros to set a dynamic range of gene expression changes during development.

Published online: August 27th, 2015, in Genes & Development.

Congratulations to Linn and Ida! 

Ida Lindeman and Linn Eggesbø successfully defended their M.Sc. thesis work at University of Oslo (UiO), Norway on Tuesday Sept. 1st, 2015. They did a great job, and are now ready to start their Ph.D. studies, with Prof. Ludig M Sollid at Univ of Oslo, Norway. Congratulations and good luck with the next few years of Ph.D. studies!

Recent Publication in Journal of Immunology: 

Heller J, Schjerven H*, Li S, Lee A, Qiu J, Chen ZE, Smale ST and Zhou L*. (2014) Restriction of IL-22- producing T Cell Responses and Differential Regulation of Regulatory T Cell Compartments by Zinc Finger Transcription Factor Ikaros. J Immunol., Vol 193 (8): 3934-46. Published online: September 5th, 2014.  (*) Co-corresponding authors

Published online: September 5th, 2014, in Journal of Immunology.

WikiGenes - Public Authored Open Access Sharing of Scientific Knowledge

Although not a new concept, as "WikiGenes" was published already in 2008 in Nature Genetics, this website that is designed for sharing of scientific knowledge in a non-anonymous way, is beneficial for both author and reader. It provides credit to the author, as well as accountability, and gives the reader a chance to evaluate the source (author). Open access and easy interface to write, link and insert the correct references (via PubMed search), makes this website attractive to both contributors as well as readers, and most likely, we can all contribute within our area of expertise, and benefit as readers in others topics. A 5 minute video will give you the quick introduction to the website and how to edit, and contribute with your knowledge to the open access scientific community. 

There are other similar websites with different focus, based on the concept of community sharing of knowledge, some of these are listed here, and discussed in this article.

Interestingly, UCSF is teaching students how to edit and contribute to the general wikipedia (with a focus on medical content articles), and encouraging this by offering the students credits for doing so.

Research Highlight in Nature Reviews Immunology:  

Two versions of the Ikaros tale

Maria Papatriantafyllou 

Published: Nature Reviews Immunology, October 2013 | DOI:10.1038/nri3550

"Members of the Ikaros protein family are important transcriptional regulators: studies in Ikaros-deficient mice have indicated a role for Ikaros (encoded by IKZF1) in lymphopoiesis, and genetic analyses in humans have linked mutations at the IKZF1 locus with B cell acute lymphoblastic leukaemia (B-ALL). Now, Schjerven et al. investigate the involvement of individual zinc fingers...…"
(Research Highlight of Schjerven et al., Nature Immunology, 2013, see below)

News & Views in Nature Immunology:  

Fingerprinting Ikaros

Fotini Gounari & Barbare L Kee

Published: Nature Immunology, October 2013 | DOI: 10.1038/ni.2709

"Zinc fingers 1 and 4 of Ikaros have unique functions in the selection of Ikaros target genes, lymphocyte development and the suppression of leukemogenesis."
(Commentary on Schjerven et al., Nature Immunology, 2013, see below)

Advance Online Publication in Nature Immunology:  

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros

Hilde Schjerven, Jami McLaughlin, Teresita L Arenzana, Seth Frietze, Donghui Cheng, Sarah E Wadsworth, Gregory W Lawson, Steven J Bensinger, Peggy J Farnham, Owen N Witte & Stephen T Smale

Published online: 08 September 2013 | DOI: 10.1038/ni.2707

"C2H2 zinc fingers are found in several key transcriptional regulators in the immune system. However, these proteins usually contain more fingers than are needed for sequence-specific DNA binding, which suggests that different fingers regulate different genes and functions. Here we found that mice lacking finger 1 or finger 4 of Ikaros exhibited distinct subsets of the hematological defects of Ikaros-null mice. Most notably, the two fingers controlled different stages of lymphopoiesis, and finger 4 was selectively required for tumor suppression. The distinct defects support the hypothesis that only a small number of genes that are targets of Ikaros are critical for each of its biological functions. The subcategorization of functions and target genes by mutagenesis of individual zinc fingers will facilitate efforts to understand how zinc-finger transcription factors regulate development, immunity and disease."

The eLife Journal: Starting a New Trend in Scientific Publishing? 

Whether you are looking to publish your first scientific paper, or you have several years of experience in publishing, we all can benefit and learn from the new scientific journal, eLife, published in collaboration between HHMI, Max Planck Society and Welcome Trust. Their review process is changing the way scientific work is peer reviewed and presented. In addition to a fast turn-around time and quick initial response from editors after submission (which is also implemented by many other journals), the eLife journal has a unique approach to the peer review process: First, the reviewers meet and discuss the paper, and coordinates their comments and evaluation into ONE constructive review, with one voice and a clear decision. Second, they will be realistic in what they ask upon invited re-submission. If they do not think the authors can revise the manuscript within a reasonable time, to reach the standard described in the scope of the journal, they will reject it. However, if they think the required revisions are within the expertise of the laboratory, they will ask for key points to be addressed, with the anticipation of acceptance upon requested revisions. Thirdly, they publish both the reviewers comments, as well as the authors response, together with the paper. This last point provides an excellent resource for the scientific community by providing transparency in the peer review process, as well as providing an educational resource, where both new, as well as more experienced scientists, can learn from the review process of published work.

In addition, the journal is Open Access, and for an initial time period, there is no fee for the authors to submit or publish.

Journal Impact Factors: 2012 update

The 2012 Impact Factors were published this summer, and the discussions in regards to the use and interpretation of this re-surfaced. Some of the concerns in regards to the common use of Impact Factors are described in DORA, and also discussed by an article in the Guardian. The Journal Impact Factor of a journal is based on average number of citation pr article published (or total number of citations divided by total number of articles published), as explained in this article published at the Web of Knowledge website. Online, the number of citations can often be found linked to each individual paper, and as such, is a better indicator of what impact an individual paper has had to date. 

The journals listed in table below (for 2011 impact factor) has been updated with the 2012 Impact Factors, for comparison. In addition, below are some links to publishers websites, listing the Impact Factors of the journals they publish:

Nature Publishing Groups (NPG).

Cell Press.

Annual Reviews.

The Icefish movie won the STEAM award  

"The Making of the Fittest: The Birth and Death of Genes", directed by Sarah Holt and Kirk Wolfinger, and produced by Sean Carroll and HHMI won the STEAM award at the 4th Annual New Media Film Festival held in Los Angeles (see more below). The two-day long film festival "honored stories worth telling" and screened a wide variety of short films to an engaged audience. The shortfilm about the discovery of the Icefish received the STEAM award (Science, Technology, Engineering, Art & Math), as well as great interest and feedback from the audience. The list of winners are given on this page (currently under construction/uploading ongoing), and video from the event is available here thru July 10th, 2013. 

Winner STEAM award New Media Film Festival 2013

The educational shortfilm about the discovery of the Icefish is nominated for the STEAM award

"The Making of the Fittest: The Birth and Death of Genes", directed by Sarah Holt and Kirk Wolfinger, and produced by Sean Carroll and HHMI, has been nominated in the STEAM category (Science, Technology, Engineering, Art and Math) at the 4th Annual New Media Film Festival. The festival is held in Los Angeles, on June 11-12th, and the film will be screened in the STEAM session between 1 pm and 4 pm. This short educational movie describes the stunning discovery of the Icefish by scientist Ditlef Rustad during an expedition to the antarctic waters in 1927: A fish that had colorless blood! For vertebrates to be able to survive without the red blood cells was a stunning discovery, and only recently, after development of the technology of DNA sequencing, have researchers been able to find out what happened, and explain this incredible example of evolution.  

An article about the discovery of the Icefish published in "The Scientist" 

The popular science magazine "The Scientist" published an article in regards to the discovery of the Icefish (see more info in my article under Educational).

Journal Impact Factors 2011 - with 2012 update

Although Impact factor is not a "say all" and cannot always be directly compared between journals (since for instance journals that contain reviews will in general be cited more often, and thus get increased Impact Factor), it is still an estimate of the impact of a journal and can be a quick way to estimate the potential impact of papers published in that journal. Who and how many people have read a paper is indirectly indicated by how many times the paper has been cited. This information is now more accessible, and it is becoming increasingly more common to link citations directly to the individual papers. However, this information is also used to calculate the impact factor of the journal - which then reflects an average of how often a paper in that journal is cited.

This is only a partial list, of some of the journals relevant for immunology and molecular biology.

Primary Research Journals

Full Journal name Abbreviated journal name
2011 Impact Factor 2012 Impact Factor
Nature Immunology Nat. Immunol. 26.008 26.199
Immunity Immunity 21.637 19.795
Journal of Experimental Medicine J. Exp. Med. 14.510 13.853
Molecular Cell Mol. Cell
Genes & Development G&D
Proc. Natl. Acad. Sci. U S A PNAS
Journal of Molecular Cell Biology JMCB 7.667
Journal of Immunology
J. Immunol.
Mol Cell Biol
European Journal of Immunology
Eur. J. Immunol.
5.100 4.970
J Biol Chem
Scandinavian Journal of Immunology
Scand.J. Immunol.

Review journals:

Full Journal name Abbreviated journal name 2011 Impact factor 2012 Impact factor
Nature Reviews in Cancer Nat. Rev. Cancer 37.55
Nature Reviews in Immunology Nat. Rev. Immmunol. 33.29
Trends in Immunology Trends Immunol.



Latest Updates:

1/28-2017: News: Beall's list of Predatory Journals and Publishers taken down. 

1/17-2017: Danielle, Johanne and Marit arrived in lab: Master students performing their laboratory project work in lab at UCSF. Welcome!

9/23-9/25-2016: UCSF/UCB Immunology Retreat at Asilomar, CA

8/26-2015: Etapong Fonabei Ayongaba (Eta) successfully defended his M.Sc. thesis work at UiO, Norway. Congratulations! Well done!

5/18-2016: Karissa Hansen joins the group. Welcome!

5/13-5/17-2016: AAI Immunology 2016 meeting in Seattle, WA 

2/15-2016: Tara Kheiri joins the group. Welcome! 

1/11-2016: Biniam Tesfai and Bryan K.Wong join the group. Welcome!

9/25-9/27-2015: UCSF/UCB Immunology Retreat at Asilomar, CA.

9/1-2015: Published: "Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor" by T. Arenzana, H. Schjerven and ST Smale published in Genes & Development

9/1-2015: Linn Eggesbø and Ida Lindeman successfully defended their M.Sc. thesis work at UiO, Norway. Congratulations! Well done!

1/30-2015: Buchner et al.; "Identification of FOXM1 as therapeutic target in B cell lineage acute lymphoblastic leukemia" accepted in Nature Communications.

Published: Heller et al.; "Restriction of IL-22- producing T Cell Responses and Differential Regulation of Regulatory T Cell Compartments by Zinc Finger Transcription Factor Ikaros" published online in Journal of Immunology.

4/20-2014: News & Views: Contribute with your knowledge in "WikiGenes" by "Collaborative Publishing".

10/27-2013: News & Views: Research Highlight in Nature Reviews Immunology of Schjerven et al., 2013, NI paper: "Two versions of the Ikaros tale" by Maria Papatriantafyllou.

9/21-2013: News & Views: "Fingerprinting Ikaros" by Fotini Gounari & Barbara L Kee (Commentary on Schjerven et al., 2013, NI), doi:10.1038/ni.2709  

9/8-2013: Published: Schjerven et al.; Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros, Nat Immunol, 2013, DOI:10.1038/ni.2707 

8/18-2013: eLife Journal: New Trend in Scientific Publishing? 

8/18-2013: Update on Journal Impact Factors (2012).

6/16-2013: News: The Icefish movie won the STEAM award at the 4th Annual New Media Film Festival.

6/9-2013: News: The educational movie about the Icefish is nominated in the STEAM category at the 4th Annual New Media Film Festival. 

4/1-2013: News: "The Scientist" publish an article on the Icefish.

10/14-2012: Journal Impact Factors.


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