Special BiB issue on "Orthology and Applications"

 An special issue on "Orthology and Applications"  is out in the journal Briefings in Bioinformatics.

 This special issue has been edited by Christophe Dessimoz and comprises a number of interesting papers including several comprehensive reviews and also original research articles. Some of the papers emerge from efforts on orthology benchmarking and standardization of datasets that were initiated during the first "Quest for Orthologs meeting" in 2009. See this letter reporting from that meeting. We contributed with an article reporting on the comparison of expression patterns between across-species orthologs and paralogs of a similar evolutionary age.

Article collection on the Tree Of Life in Biology Direct

The journal Biology Direct has initiated an article collection entitled "Beyond the tree of Life". The main focus of this series seems to be the challenges posed by evolutionary mechanisms, such as Horizontal Gene Transfer, that may blur or completely destroy the classical view of a bifurcating tree of life representing the evolutionary relationships of organisms, specially prokaryotes.

 The issue is not new, but the current wealth of genomic data and the availability of new methodological approaches to measure and compare the evolutionary signals of thousands of protein families has prompted a revival of the debate on how strong are tree-like and network-like signals in the different domains of life.

The series started last June and is being updated regularly. There are already interesting articles from various authors including William Martin, Eric Bateste, and Eugene Koonin.

A nice add-on, which is one of the features I lke the most about Biology Direct, is that reviewer's reports can be read along with the paper, thus having a complementary view of the author's interpretation of the data.

A new journal for "big" Science

 I have a mixed feeling for the current proliferation of scientific journals. On the one hand I feel that it is a natural response to the increase in the number of researchers in the world and the growing specialization of science. Moreover, it serves to open up the publication system to the wider community and sometimes breaks up dangerous closed circles that monopolize the access to publication in certain areas. On the other hand, as a researcher with broad interests and one who wants to follow the progress of my field, I feel overwhelmed. Times when browsing the table of contents (TOCs) of a handful of journals was enough to identify almost all relevant papers are definitely over. Nowadays one needs complex literature-mining strategies to try to cope with the flow. It seems one also needs to search for potential new Journals that may become the forum for papers relevant to your research. I'm keen to use this blog to spread the word of new Journals that are relevant to my field, as I did in the past. Now I am doing it again.


When I recently heard about the new BMC-based journal Giga Science Journal I felt it will be worth to keep an eye. As they say, "GigaScience aims to revolutionize data dissemination, organization, understanding, and use. An on-line open-access open-data journal, we publish 'big-data' studies from the entire spectrum of life and biomedical sciences."

 
 The original idea of this journal is that it links standard publication with a database to store and search all asociated data. I personally think this journal will fill and important gap and seems perfectly prepared to do so, as judged by the The editorial board, which includes many researchers from centres that are at the forefront of massive data production such as BGI, Wellcome Trust, EBI, JCVI, 

I am looking forward to the first articles to see direct examples of how effective this system is and how the database fits the needs of inherently diverse types of data, but at a first glance it seems that this journal may meet the needs of upcoming studies on massive data such as those coming from genomics or systems biology.

A PLoS currents for the Tree of Life

 I recently discovered that PLoS Currents has opened a new track for the Tree of Life: PLoS Currents: Tree Of Life.

 PLoS currents is yet another form of publishing scientific results. A small group of editors and reviewers reviews every paper to check that it is t is " a legitimate work of science and does not contain any obvious methodological, ethical or legal violations." If that's the case papers are published immediately (and indexed in Pubmed). Another novelty is that all the publication procedure is based on a web-based tool called google-knol.

 So far there are only 4 articles (or "knols"?) and they all seem pertinent to the topic, one of them was very useful to me, since it described a compilation of benchmark datasets for phylogeny. 

 It looks worth to keep an eye.