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======Navigating the publication process======
Beyond the manuscript and reviews.

=====Picking a journal======
Some considerations when selecting a journal in which to publish your work:

//Open access vs. “closed”//. eLife is an example of an publishing platform that is open source, and adopts a number of author-friendly innovations.

//General vs. specialty audience//. Journals vary in the specificity of their topic area. In the old days, the most general scientific journals (Science, Nature, Current Biology) were the most prestigious. In recent years, the advent of broad, open-access, on-line only journals has changed this (PLoS One, Frontiers, Scientific Reports).

//Where to find your audience//. It is still the case that some journals are seen and considered by your particular target audience (e.g., the green journal).

//Prestige//. Sadly, this matters.
  * Impact factor is a metric of how often articles in a journal are cited over the last 2-3 years. The calculation for 2020 would be: In calendar year 2020, the number of citations of articles published in 2018 and 2019, divided by the total number of papers during that time.
  * It is a highly manipulated (and negotiated!) metric that varies substantially between fields of study
  * Review journals tend to have elevated impact factors (e.g., Nature Reviews …)
  * Although it is (in my opinion) a lousy metric, departmental and promotions committees prefer higher IF journals, and some have a threshold preference for IF > 6.
  * IFs of relevant journals: NEJM 91, JAMA 56, Nature Medicine 53, Nature 50, Science 47, Lancet Neurology 44, Cell 42, Nature Neuroscience 25, Alzheimer’s & Dementia 22, Science Translational Medicine 18, Neuron 17, Nature Communications 15, Journal of Clinical Investigation 15, Brain 14, PNAS 11, PLoS Medicine 11, Current Biology 11, Annals of Neurology 10, Movement Disorders 10, Neurology (Green journal) 10, eLife 8, Neuroimage 7, Journal of Neuroscience 6, Scientific Reports 4, PLoS One 3, Frontiers (several options) 2-3.

//Other considerations//: reputation for the speed of the review process, tendency to post pre-prints quickly, reputation for promoting the work, quality of the journal website. On the last point: Scientific Reports is the Nature publishing group’s answer to PLoS One. In my opinion, it has moved ahead of PLoS One because the URL for the published paper begins “nature.com”

=====Cultivating a relationship with the journal personnel======
The organization of a journal typically includes an editor-in-chief, a set of associate editors, and a set of editorial board members. Often, you will be asked to identify an associate editor, who will then select an editorial board member who will handle your submission. The board member will invite anonymous reviewers, consider their advice, and make decisions regarding publication (sometimes in concert with the associate editors). This information can be found on the journal website. 

These are actual human beings who run journals. As a matter of basic decency, you should be nice to them. Also, you may better position your paper if these people know you, your work, potential reviewers, or the area of your study.

Journal editors often have a booth in the vendor section of scientific meetings. Say hello! You can pitch ideas for papers, and get some informal feedback on manuscripts you are preparing.

=====The cover letter======
A hold-over from the days of paper publishing is the “cover letter” that you submit with a manuscript. For some journals, this cover letter needs to contain specific types of information, such as a declaration regarding conflicts of interest or the role of the authors. For some higher-prestige journals, the cover letter is where you provide a brief pitch for the exciting qualities of the study using non-specialist language. There are reasons to criticize this practice, including the fact that one may be tempted to go beyond the provable results and conclusions from a study in this non-peer-reviewed setting. Nonetheless, the odds of having your paper sent for review at a high-prestige journal can be strongly influenced by the description that you provide of the impact of the work.

=====Selecting reviewers to include or exclude======
If you are given the opportunity to suggest reviewers for your work, you should do so. As an ethical matter, the onus is on you to avoid suggesting people for whom there is a conflict. That said, it is acceptable to suggest people who you suspect view the area of research favorably. 

You are also given the opportunity to exclude reviewers. I suggest that you use this opportunity sparingly. Over a career, having a long list of enemies starts to reflect more upon you than it does upon your enemies. 

=====Appealing editorial decisions======
Sometimes a journal will decline to send your manuscript for review. Sometimes your manuscript will be rejected based upon reviewer comments. Perhaps surprisingly, this may not be the end. If you feel you have a compelling case that the decision was in error, you can appeal to the editor. Sometimes this is by email, sometimes by picking up the phone. Your case is obviously strengthened if you have a specific grounds for reversal, and if you don’t make an appeal as a routine matter.
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