Hello, First of all, apologies for this lengthy post. If it is found to be inappropriate, kindly remove it. I have learnt my bioinformatics from this community and hope to get some valuable suggestions from here.
This year, we had sent our manuscript to a reputed plant science journal. Our 1.5 yrs work mostly comprised of large-scale data mining using on publicly available transcriptomics data on rice. We used network-based approach along with protein-protein interactions and gene-association information to construct the networks. Finally we used clustering approaches and extensive manual curation to analyse and validate the various processes indicated by the data.
Rice has more than 50K genes and only a small percentage have known functions associated with them. Moreover, the GO annotations assigned are very generic and pathway-based information is even less. Hence we felt that network-based topological analysis of important nodes (genes) in our network can provide important cues to identify potential biomarkers for the particular condition we studied, which can be further validated by the scientific community
We submitted in April, 2017 and after several delays and mess-ups by the journal, they rejected it few days back. Two reviewers were assigned and they endorsed the manuscript and the handling editor provisionally accepted it after which it went for a technical validation. To our surprise, the review was re-activated and it went to a third reviewer who basically had a problem with bioinformatics itself and insilico analysis. We performed additional analysis to validate our work and after we responded to him, the reviewer withdrew without giving any replies or further comments. Our paper was stuck in this state for 2 months. Then after repeated mails to the journal, the specialty editor (who seems to be above the handling editor) made a comment in the portal that the manuscript seems fine and comments of the reviewers are based on their respective backgrounds. The consensus is in favor of the MS and it should be accepted. After this, the paper again went for a technical validation for a month! We then receive a mail from the chief editor, that the MS is rejected based on the comments of the third reviewer. We were shocked, as it was seen from the portal, the third reviewer had 'withdrawn' . So how a paper can be accepted once and rejected again (on the basis of a reviewer who left the review process) is what we fail to understand. Moreover, they held up our paper for so long, and none of the editors or the other two reviewers had demanded for a wet-lab validation.
So basically, I am in a frustrated state of mind, and would like to have suggestions from this community as to where we can submit the MS again and expect to have a fair and transparent review-process. It need not be a plant-based journal.