About PCI Genomics

What is Peer Community in Genomics?

Peer Community in Genomics (PCI Genomics) has been launched in October 2019. The scope of this PCI encompasses all aspects of genomics (structural genomics, functional genomics, epigenomics, evolutionary genomics, population genomics, proteomics, bioinformatics) dealing with every type of organisms (viruses, bacteria, fungi, plants, animals,...) as well as metagenomes. PCI Genomics is a community of recommenders who recommend your unpublished articles (mainly preprints) based on peer-reviews to make them complete, reliable and citable articles, without the need for publication in ‘traditional’ journals. Evaluation and recommendation by PCI Genomics are free of charge. When an recommender decides to recommend an article, he/she writes a recommendation text that is published along with all the editorial correspondence (reviews, recommender's decisions, authors’ replies) by PCI Genomics. The article itself is not published by PCI Genomics; it remains in the preprint server where it has been posted by the authors. PCI Genomics recommenders can also recommend, but to a lesser extent, postprints.

 

PCI Genomics is a community of the parent project Peer Community In, an original idea of Denis Bourguet, Benoit Facon and Thomas Guillemaud.

PCI Genomics is not designed to be a free peer-reviewing service for authors aiming to improve their articles before submission to a journal. It is, of course, possible, for authors to then submit their recommended article to a traditional journal, but this is not the goal of PCI Genomics.

PCI Genomics is stimulating: it recommends remarkable articles.

PCI Genomics is free: there are no fees associated with the evaluation process, and no charge for access to the comments and recommendations. The website is freely accessible.

PCI Genomics is transparent: Reviews and recommendations (for unpublished articles) and recommendations (for published articles) are freely available for consultation. Recommendations are signed by the recommenders. Reviews may also be signed if the reviewers agree to do so.

PCI Genomics is not exclusive: An article may be recommended by different Peer Communities in X (a feature of particular interest for articles relating to multidisciplinary studies) and may even be published in a traditional journal (although this is not the goal of PCI Genomics).


Editorial Criteria

 

PCI Genomics recommends preprints addressing genomics questions about all types of organisms. We cover all fields of biology, provided that the context of the study and the key question addressed relate to genomics. The preprint or the preregistration must not be published or under consideration for evaluation elsewhere at the time of its submission to PCI Genomics.
 

The preprints or preregistrations recommended may describe empirical or theoretical studies, and be based on observations from experiments or nature, or previously acquired data. They may also report the results of verbal, computer or mathematical models. Studies of methodologies for genomics are also appreciated. Perspectives, reviews and opinions, as well as comments on previously published articles are also welcome. Data papers (preprints) presenting a new genome are also possible to submit, by first contacting the managing board.  

PCI Genomics recommends only preprints of high scientific quality that are methodologically and ethically sound. To this end, PCI Genomics:
- Requires data, computer codes and mathematical and statistical analysis scripts to be made available to reviewers and recommenders at the time of submission and to readers after recommendation.
- Welcomes reproductions of studies.
- Welcomes preregistration submissions and preprint submissions based on preregistrations (whether or not reviewed)
- Welcomes preprints reporting negative results, provided that the questions addressed and the methodology are sound. - Welcomes data papers but please contact the managing board prior submission. - Does not accept submissions of preprints presenting financial conflicts of interest. Other conflicts of interest must be minimal and declared.
- Ensures that, as far as possible, the reviewers and referees have no conflict of interest with the content or authors of the study being evaluated.
 

PCI Genomics does not guarantee the evaluation or recommendation of all submitted preprints. Only preprints or preregirstrations considered interesting by at least one competent recommender (equivalent to an associate editor in a classical journal) will be peer-reviewed. The interest of the preprint or preregistration, as determined by the recommender, can relate to its context, the scientific question addressed, the methodology, or the results. PCI Genomics has a large number of recommenders, ensuring a considerable diversity of interests. The recommendations published by PCI Genomics are designed to draw the attention of the research community to the qualities of the article, including the subjective reasons for the recommender’s interest in it.
 


Why submit your preprint to PCI Genomics?

 

 


Which manuscripts can be recommended?

PCI Genomics will evaluate preprints or preregistrations, and to a lesser extent articles published in journals, dealing with all fields of Genomics. The articles recommended may have diverse formats: reviews, comments, opinion papers, research articles, data papers, technical notes, computer notes, movies, etc. No editing, formatting or proofing of the recommended papers is required but we provide the authors with a template if they want to format their article. We also ask the authors of recommended article to add a sentence in the acknowledgements stating that their article has been recommended by PCI Genomics.  
PCI Genomics welcomes anonymous submissions (see details).


PCI Genomics friendly journals

 

The Editors-in-Chief of the following journals have indicated (or have been asked by their scientific Society) they will consider submissions of articles recommended by PCI Genomics and that they may use PCI Genomics reviews and recommendations for their own review processes, if appropriate:.
 

BMC Evolutionary Biology

Genetica

Journal of Evolutionary Biology

Molecular Ecology

Molecular Ecology Resources

PeerJ


PCI Genomics is indexed by

 

Preprints

Preprints

Preprints

Preprints

Preprints

Preprints

Preprints  


Peer Community In is member of

 

COPE

Crossref

Clockss

Similarity Check  


Peer Community In promotes the repeatability of science

PCI wants to promote scientific repeatability to improve the overall robustness and integrity of our scientific conclusions. To this aim, PCI has set up 3 mandatory rules and made 2 suggestions to authors:

Mandatory rules:

Articles recommended by PCI must provide the readers:
-Raw data by making them available either in the text or through an open data repository such as Zenodo, Dryad or some other institutional repositories (see Directory of Open Access Repositories). Data must be reusable, thus metadata and accompanying text must carefully describe the data.
-Details on the quantitative analyses (e.g., data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and details concerning simulations (scripts, codes) in the text, as appendices, or through an open data repository, such as Zenodo, Dryad or some other institutional repositories (see Directory of Open Access Repositories). The scripts or codes must be carefully described such that another researcher can run them.
-Details on experimental procedures. These details must be given in the text or as appendices at the end of the article.

Suggestions to authors:

-PCI encourages authors to use preregistrations: Authors may post their research questions and analysis plan to an independent registry before observing the research outcomes, and thus before writing and submitting their article. This provides a way for them to clarify their hypotheses, avoid confusing “postdictions” and predictions, and carefully plan appropriate statistical treatment of the data (eg see 10.1073/pnas.1708274114).
-PCI also welcomes submissions of preregistrations. Authors can submit their preregistrations to a PCI before beginning their study, and thus before acquiring the data. Preregistrations are then evaluated by recommenders based on independent reviews, in exactly the same way as preprint articles. Preregistrations can thus be rejected or undergo revisions, improving the quality and robustness of the experimental design. When a preregistration is accepted, the subsequent article submitted to the corresponding PCI would be recommended provided the study has been conducted as described in the preregistration (or with any modifications clearly justified). In this way, an article cannot be rejected due to the outcome of the study only. Details on preregistration submissions can be found for example here.


Managing board of PCI Genomics

Pierre Capy (Gif-sur-Yvette, EGCE, France)

Rosa Fernandez (Barcelona, IRB, Spain)

Jean-François Flot (Bruxelles, Evolutionary Biology & Ecology, Univ Libre de Bruxelle, Belgium)

Denis Tagu (Rennes, Inrae, IGEPP, France)

To contact the Managing Board please send a message to managing-board@genomics.peercommunityin.org


PCI Genomics recommenders

Recommenders manage the evaluation of preprints or preregistrations (and, to a lesser extent, published articles), which they may choose to recommend. Recommenders have a role similar to that of a journal editor (finding reviewers, collecting reviews, and taking an editorial decision based on reviews), and they may eventually recommend the article after several rounds of reviews. If they decide to recommend an article, they write a “recommendation” that has its own DOI and is published in the PCI Genomics electronic journal.

PCI Genomics Recommenders can recommend up to five articles per year. They are expected to comply with the code of conduct of PCI Genomics, are eligible for selection as a member of the Managing Board for a period of two years, and they can propose the nomination of new recommenders to the Managing Board. The current list of recommenders can be found here.

New recommenders are nominated by current recommenders, with the approval of the Managing Board. If you are interested in becoming an recommender, please contact a current recommender in your field.


Why be a recommender for a PCI?