​Few weeks after your initial submission of the paper, your journey to publish academic paper will face the first pivotal moment – sent out for an external review or desk rejected. In this post, I wish to describe this first editorial decision with my experience with possible suggestions or tips that you might find helpful.

It might be different in each journal, but the first editorial decision to send out for external review or desk reject (or screened) is mostly made by the editor (often with help of the editorial/advisory board of the journal) without in-depth review. Hence, this first editorial decision might reflect various factors such as the journal’s coverage, timeliness of topic, and potential overlap with works under review in the journal on top of the paper’s quality and scientific rigor. As curating appropriate papers to fill the limited space in the journal is the editor’s job, it is something we have to respect not dispute.

As this is the first editorial decision without in-depth review, the possible outcomes are also very simple. Let’s think about good case first – your paper is sent out for an external review! Your paper is one step closer to the publication. In this case, you need to wait until the external referees return their comments and suggestions, based on which the editor would make the next editorial decision. This decision often happens silently without informing the authors although some journals do notify the corresponding author if the editor decides to send out for external review (for example, Nature and its family journals). More commonly, you might be able to see the status change in the manuscript tracking system of each journal (but don’t check too often! Not good for mental health – advice from my experience).

Another possibility is bad news – your paper is desk rejected. Well, this might be quite bitter moment with disappointment. But it should not be taken too badly – the desk rejection is probably the most frequently encountering moment in publication journeys sadly. Some highly competitive journals desk rejects very high fraction of the submitted papers (for example, Science screens 80 % of the submitted papers). But life is going on, so you have to decide the next step picking up your sad mind. One important aspect about the desk rejection is that there are not really many things you can do other than trying other journal in most of cases because it is the editor’s editorial decision, and we have to respect it. Hence, I wish to share my experience with very rough category (which is definitely personal not generalizable):

Category I – Desk rejection without any specific reason/detail
In this case, the rejection decision email contains only common phrases without any specific reason/detail from the editor as the basis of desk rejection. This is probably the hardest type to decipher as there is no clue on what can be improved. However, it is pretty common and there can be myriad editorial reasons behind it. It’s time to search another journal to submit.

Category II – Desk rejection with specific reason/detail
In this case, the rejection decision email may contain some specific reasons/details that the editor considered as the basis of desk rejection. It’s very thankful that the editor spent time to share their thought on the work as you might be able to reflect them when you submit to another journal.

Category III – Desk rejection with erroneous specific reason/detail
In this super rare case, the rejection decision email may contain some specific reasons/details that the editor considered as the basis of desk rejection but with error (for example, concerns on the lack of certain detail/data which are actually included in the submitted work). Importantly, the error should be really error not disagreement on subjective evaluation of the work. In this case, you can potentially consider to politely remind the editor about the error although it is again totally up to the editor whether the correction of error would change the editorial decision.

Well, this is it. But I have something more to share. When I did not have much experience on the paper publication, the desk rejection without review was one of the most stressful and saddened moment, probably because the disappointment you would feel might be proportional to the care and love you gave to your paper. It’s your baby, so seeing your baby being rejected even without careful look breaks your heart. I wish to share some perspectives that helped me to deal with it over time. Hopefully these would be helpful for you as well:

Its editorial decision not rejection on the value of your work. Yes, it’s editorial decision that the editor has to make for various reasons beyond the quality of each paper – so let’s don’t take it personal. In some sense, it’s just routine business in academia.

Take it as another chance to improve your work more. Showing your work to peer reviewers is nervous process and you would love to be perfect before it. Seeing a bit differently, you got another chance to improve your work more. It’s not a bad thing!

Share the feeling with your co-authors and colleagues. Human is social and emotional animals. It is totally natural to be disappointed sometimes and it is great thing to share it with your co-authors and colleagues. It’s something everybody in academia can be whole heartedly sympathetic to you, sharing their own tearful stories and eventual happy ending.

What’s next is the return of reviewer’s comments and suggestions after review along with the editor’s decision to whether take revision or reject. We may cover the revision case in the next post.

Part I: Overview 
Part II: Presubmission Inquiry & Initial Submission
Part III: Desk Rejected, What Can be Next Step? (this post)
Part IV: Revision, Art of Rebuttal
Part V: Rejected After Review, End of World?
Part VI: Acceptance & Post-Acceptance Jobs

Disclaimer. The contents are my personal opinion and do not represent the view of any institution or company I am affiliated/employed. If you find any incorrect information, please feel free to let me know via my email.

When you are nearly completing your initial submission package of paper, it is time to think about paths toward paper publication. For me, this is the most exciting moment throughout the whole life cycle of academic paper. Full of potential like a child, allowing us to do colorful and unbounded imagination of upcoming glory! But hold on your bumping heart and wild dream – academic paper publication process is not a sprint but more like doing marathon in an uncharted area, but with many supporters and waypoints we can take a look along the way. I wish to share my experience on the journey to academic paper publication step-by-step as planned in Part I: Overview. As I find each journey is all different and refreshingly frustrating, these would only serve as helpful tips than solid guidelines. But, looking back my initial attempts full of confusion, I hope these tips would still be very helpful. Let us start with the very beginning of the journey: Submission of the paper.

Pre-prints
Pre-prints are a relatively modern invention but have become a major route to publicly share academic outcomes early in their form before formal publications in journals/proceedings. There are many pre-print servers for various research areas (for example, arXiv for physical science, bioRxiv for biological science, etc) and new pre-print servers are keep adding up as academic journals start to embrace them as part of their publication process.

Submitting your initial version of manuscript to pre-print server can be a very nice choice before starting the formal publication process. In my personal opinion, there are several key benefits of the pre-print publication. First, it allows you to share your work publicly early on with academically traceable record (as pre-prints are citable references in most journals nowadays). Second, it allows you to openly communicate with your colleagues or collaborators to get feedbacks with less worry on scooping of idea (as pre-prints are citable references that can protect your novelty). Third, it can potentially lower the vicious competitive pressure among researchers/groups by disclosing the work early on (as the lack of openness until the ultimate journal publication with long-time process is easy setting to push researchers into the Prisoner’s dilemma).

Presubmission inquiry
Presubmission inquiry is the first thing available in the journal paper publication process, but not frequently used or well-known. I learned about the presubmission inquiry as Nature Publishing Group started to make it part of their manuscript tracking system with dedicated instruction for it in their journal websites. Essentially, the presubmission inquiry is a brief communication with the editor to inquire basic feedbacks ahead of the formal paper submission. As mentioned earlier, Nature Publishing Group journals offers the presubmission inquiry as a selectable option in their submission system (for example, the manuscript tracking system for Nature). However, many journals do not have dedicated option for the presubmission inquiry in their submission system, but rather adopt direct email communications to editors for such purpose.

One important thing about the presubmission inquiry is that it is not always necessary or recommended. Unless journals have dedicated option for it, some journals or editors might not be available for the presubmission inquiry ahead of the formal submission of manuscript (especially given flood of works they are already swamped). Also, there are relatively limited purposes/merits of the presubmission inquiry, and you would better to do it only when necessary. The purpose and the scope of expectable feedbacks from the presubmission inquiry are the following based on my experience:

1) Purpose. There are two major purposes of the presubmission inquiry: Checking the work’s fit with the journal’s coverage & learning the editor’s opinion on the work. Sometimes, you are not certain whether your work falls within the coverage of the journal of interest, especially when the work is multidisciplinary. In this case, the presubmission inquiry can be a quick way to hear the editor’s input to avoid waste by submitting without knowing mismatch in coverage. The presubmission inquiry can also be a less formal way to hear the editor’s quick impression/opinion/concern on the work ahead of the formal submission. In many cases, the coverage fit with a target journal can be pretty straightforward and the presubmission inquiry is not particularly necessary or helpful.

2) Expectable feedbacks. Typically, the editor’s response to the presubmission inquiry is very brief. While it would vary a lot depending on the editor, the editor’s response to the presubmission inquiry may contain three key information:  First, the coverage fit with the journal; Second, overall interest (often with the encouragement to formally submit); Third, specific aspects/concerns that they expect/want to check detail in the formal submission.

The presubmission inquiry can be done in many forms including a short cover letter, email communication, etc. I most prefer a short cover letter as it is probably the most familiar format of communication to the editor and can contain needed information in an organized manner. While there can be many ways to prepare a presubmission inquiry cover letter, here is a template for presubmission inquiry cover letter that I use frequently (also below image):

If the editor informs you that your work is not fit with or not under the coverage of the journal, then it is very helpful information to search for other possible journals. It’s not a bad thing at all – you can save 2+ weeks of waiting time to learn the exactly same information from the initial decision letter (in more frustrating manner)!

Initial submission
Initial submission is the formal start point of the academic publication process (and prelude of long and bumpy road ahead). In the initial submission package, you may likely need to prepare the following items ready:

• Cover letter
• Manuscript (follows the format requirements of the journal)
• Supplementary information (texts, figures, tables, videos, etc)
• Other journal-required submission item (reporting summary, etc)

Since the focus of this post is for the publication process, I may focus only on the cover letter here. The cover letter is probably one of the most important items in the initial submission as it greatly influences the first pivotal editorial decision made by your handling editor – sending out for external review or desk rejected. The importance of cover letter is really well discussed in the recent editorial by the chief editor of Matter, Dr. Cranford, reflecting the editor’s view.

The cover letter is basically a professional & moderately technical advertisement of your paper to the editor. Therefore, your cover letter should have contents to act as a concise yet sharply convincing sales pitch of your work to the editor, or as Dr. Cranford aptly described, something similar to an elevator pitch for startups. There can be very broad range of cover letter styles, but I wish to share a template for initial submission cover letter that I frequently use (also below image):

If you tried the presubmission inquiry, the editor might encourage you to submit formally. If the editor did not share specific questions/concerns in their response, you may need to prepare your initial submission package and cover letter without big difference from the case without presubmission inquiry (but try to avoid overly duplicating the contents of your presubmission inquiry cover letter in your initial submission cover letter).

If the editor provided some specific aspects/concerns in their response, there can be more things you can do in the initial submission (and kind of positive sign as the editor was interested/intrigued enough to spend their busy schedule to think and write some details about your work!). In this case, the initial submission cover letter can be a better targeted advertisement of your work as the presubmission inquiry served as a sort of customer survey. So, you may wish to address the editor’s question/concern on specific aspects of the work in your initial submission cover letter. While it is hard to say whether it increases your chance to convince the editor to send your paper out for external review, but better targeted pitch is not a bad thing anyway (otherwise why Google charges so high for its targeted advert service?). Here is a template for initial submission cover letter after presubmission inquiry that I use frequently (also below image):

What’s next after the initial submission? As mentioned earlier, you have to wait for the first pivotal editorial decision in the publication process – decision to whether send out for external review or not by your handling editor. We may cover this in the next post.

Part I: Overview 
Part II: Presubmission Inquiry & Initial Submission (this post)
Part III: Desk Rejected, What Can be Next Step?
Part IV: Revision, Art of Rebuttal
Part V: Rejected After Review, End of World?
Part VI: Acceptance & Post-Acceptance Jobs

Disclaimer. The contents are my personal opinion and do not represent the view of any institution or company I am affiliated/employed. If you find any incorrect information, please feel free to let me know via my email.

Publishing academic papers - the job located at the heart of most researchers' work life - is the major source of spectrum of emotions researchers face in our academic life including anxiety, hope, destress, anger, frustration, satisfaction, and happiness. It is also an integral part of our research career and arguably the thing cultivated somehow toxic over-competitive culture in the academia. Well, whatever love-hatred relationships we have with paper publication, it is a cold fact that we have to write paper and make sure it is published as it is our key way to communicate with our peers and the world to share our findings and cherished science out of our lab notes and laboratories.

In the recent decade, non-traditional pre-print publications have become a welcoming trend for expedited and free early destination of manuscripts (for example, arXiv, bioRxiv, etc). I also recently fall into love with pre-print publications and found lots of benefits. But, the pre-print publication has some limitations due to the lack of peer-review and filtering mechanisms of quality and other issues. Hence, despite some ongoing debate on the problems of traditional publication practices, the majority of academic papers still be published through the formal editor-curated & peer-reviewed academic journals. So, more or less, knowing how to publish your work to those journals is something similar to learning how to speak for baby in the academic world. In short, it is important and likely one of the governing factors in your academic life/career (sadly...).

When I started writing my first papers around 10 years ago, it seemed like just a bit slower version of term paper I submit for undergrad courses. After few years spent in graduate schools, I realized that it is pretty naive view. It's complicated and stressful like a hell! One major source of all problems is a pretty realistic aspect of our academic life - it is highly competitive to publish in prestigious journals. In other words, it is inevitable to face lots of rejections, tepid responses, and crushing of hope (especially after sleepless nights while waiting the initial editorial decision) that all require stone-cold reality checks on questions like what was wrong? and what should be the next step?

Sadly, no one might be able to give a miraculous tip to cope with all stressing situations around paper publications. But, at least it would be helpful to know the rather tortuous (often hidden) steps in academic publications toward the ultimate acceptance with some checkable examples for each step. While my research experience is not something comprehensive enough to give deep wisdom, but I was lucky (or unlucky) enough to experience various situations of publication processes to share some tips and experience. As this is a topic worthy of detailed touches and examples, I wish to divide this tip post into several sub-posts in the coming weeks. But, wait, I prepared a starting gift for you!

​A flowchart for paper publication process (drawn by Lucidchart):

I plan to discuss each step in the above flowchart with some personal examples & templates (for example, cover letter I used for each case, etc).

Part I: Overview (this post)
Part II: Presubmission Inquiry & Initial Submission
Part III: Desk Rejected, What Can be Next Step?
Part IV: Revision, Art of Rebuttal
Part V: Rejected After Review, End of World?
Part VI: Acceptance & Post-Acceptance Jobs
​
Disclaimer. The contents are my personal opinion and do not represent the view of any institution or company I am affiliated/employed. If you find any incorrect information, please feel free to let me know via my email.

This is the first post - Yay! Research is a fun but sophisticated job (at least to me), so there will be lots of tips to share over many many posts. So, I wish to keep each relatively short & concise yet informative.

Literature review is one of the most important things in research. Why it is so important? Let me explain in this way. When we do research, write manuscript, and submit to a certain journal to persuade the editor and peers how important and suitable the work is for it, one word always bugs us - Novelty. Alas, just typing it already makes me stressed out! In modern research (especially in science and engineering), the novelty of work has been so emphasized in paper publication and how well to assess novelty of your work & make persuasive argument about it will likely be deterministic factors in successful defense of your work.

How literature review is related to novelty? Simple - the literature review provides the basis to evaluate novelty. Novelty is a comparative quality, so the knowledge of prior works in your research field/topic is essentially determine what's novel or not. The thorough and up-to-date literature review can empower  you to 1) quickly filter and assess the novelty of your and others ideas, 2) formulate well-versed and -supported arguments to the editor and your peer reviewers, and most importantly 3) focus your limited time and resources to new, meaningful, and impactful ideas to best contribute in your field instead of repetitive or redundant addition (which are oftentimes the hallmark of bad research).

There can be many ways to do literature review nicely. Here are few methods I personally find useful and effective:

Curated literature review
​Each research field has own wide and deep sea of literatures which are too much to digest all when we start our research career or dive into a new field. For such cases, curated literature reviews can be very nice mode to select. There are various forms of curated literature reviews.

1) Review papers
Review papers are the most traditional form of curated literature review, often written by the authors who are familiar with a certain research topic. But, I wish to add some caveats - there are too many review papers, often with ever overlapping contents (especially during COVID-19 pandemic), so selection of few good review papers can be a wise choice than being overwhelmed by reading reviews. My advice is to go for the most prestigious and highly selective journals of your field. Nature Publishing Group has developed a pretty comprehensive set of review journals (journals named Nature Reviews XXX) which are pretty helpful with relatively concise format with the copyedited stylish figures. In my fields, there are some traditional review journals like Chemical Reviews and Chemical Society Reviews which are in longer and detailed formats. Each field may have equivalent of these type of journals.

2) News collections
As research findings become broadly reaching to the general public, there are many news collection websites and their SNS accounts (Twitter, Facebook, etc) that cover various research areas. While this is not as professionally formatted or written as academic review papers, it is often very handy way to keep up-to-date on the latest research articles in your field (or at least make SNS time feels less guilty). In my fields, I follow Phys.org for physical sciences and engineering, Medical Xpress for biomedicine, and Science News for broad topic.

Daily crawling literature review
This is the main dish of tip I wish to cover - my favorite & arguably the most powerful mode of literature review, but with much higher difficulty. It is for advanced users who may take research as their long-term career, mostly because this approach is more like a making a habit than a quick-use tip. Let me explain more about this.

In each field (or fields if you work on multidisciplinary topics), new papers appear almost daily (or weekly/monthly depending on journals - but any field has more than one journal to cover, so virtually daily). If you could check most of newly appearing papers daily & keep track what's new and key contents (for works closely relevant to your research topic/interest) continuously over years, you will surely undergo an amazing process of becoming something wonderful - a walking review paper - the status that I think ideal & beautiful. I understand this sounds like a crazy approach, but I could do this for the last 7 years and I really guarantee that this is truly powerful. The key is efficiency and making a habit.

1) Efficient daily crawling - RSS feeds are your friend
Simplest way to keep up-to-date is just visiting all key journals in your fields every day or publishing day (every Wed around 1 PM ET for Nature, every Thu around 2 PM ET for Science, etc - I hate myself that I know these...). But, it will be overly tiresome processes as you may have a long list of journals to keep track - such inefficiency is the major source of difficulty to keep this powerful daily crawling not sustainable for long time. When I first tried to do this, I imagined that it would be wonderful if I have personal assistant who can collect all new papers in every key journals I selected and bring them on top of my desk every morning... and surprisingly there is a widely used technology doing exactly that - RSS Feed.

Most journals have RSS Feed link in their website that forward their new articles to the linked RSS Feed account (as an example, see Nature website below).

So, with your RSS Feed account to link from all journals of your interest, it can serve as a nexus of forwarded new article alarms you can check every day! There are various RSS Feed account services, but I personally recommend Feedly due to its intuitive and nice user interface & no cost (most basic functions are freely available). Also, many journal RSS Feed page provides option to directly link to your Feedly account (like the above Nature website). Feedly also supports search function where you can search your interested journal name directly and add​ if it appears in the search result. You also can easily categorize journals for easier tracking.

Feedly is an online service, so you may need to open web browser. In my case, I find it is more convenient to have a desktop app that are connected to Feedly. There are several good RSS Feed apps for Mac and Windows - I recommend Leaf (the above image) which has very nice user interface!

​2) Habitual literature review - Potential morning routine to add
Even with nice tools to make this process efficient, still the most important thing is making it into daily routine or habit. Reading papers every day can feel like a torturous way to live a life. But, I have done this everyday for the last 7 years, the first thing I do as a morning routine together with drinking a cup of coffee after wake up & wash without pain or pressure. How? Maybe I am an abnormal crazy research nerd. Or maybe the same reason why I and you love and do research. We are curious about things we do not know & eager to learn and understand better - now you have efficient tools to know and learn new stuffs every day in your beloved research fields/topics, why not do it with fun and joy? Make a habit & have fun. After few years, you will find yourself of being a proud walking review paper in your field (and surely be loved by your colleagues and collaborators).

Let me finish this tip by adding few more recent thoughts on potential advantages of the daily crawling literature review. Curated literature review, especially through prestigious review papers in each field is efficient and effective, but also come with some danger of being biased or affected by the existing academic power structure. As nicely summarized in recent articles including the one in Nature Review Materials, there is a tendency that papers from well-known and prestigious research groups/journals/institutions are being more frequently cited due to their higher visibility. I think that the daily crawling literature review practice can potentially overcome this danger by directly be exposed to new works in up-to-date manner with minimal curation, and therefore, empowering researchers to truly choose and cite the most relevant papers for each context based on their contents.

Let's all be walking review papers!
​
Disclaimer. The contents are my personal opinion and do not represent the view of any institution or company I am affiliated/employed. If you find any incorrect information, please feel free to let me know via my email.

Research is fun but definitely not an easy job to do. But, it is lovely and exciting enough for many people to dive into including myself around 10 years ago. Yes, whether you just begun or are experienced guru of your topic, we all in the same fun ride of boat named science!

We all have to self-train and grow ourselves to become seasoned researchers - well, life is a such thing. But, it doesn't mean that everyone has to repeat the same trials and error & endless search and try loops for everything in research. Maybe some good tips can save hurtles and offer more time to think innovative ideas! Despite we see the increasing trend of saddening politicization of science to promote certain political ideas, self-promotions, damaging competitions, etc, we all have to strive to share good things with others under the shared goal - doing good and quality science & having fun.

Being the first member of the lab where I did my Master and Ph.D. degrees, I have been (although not intentional) in the position of training new members for many things, including basic research skills. As this job becomes repeated more than 6 years, I found many of the contents is repeating again and again for different members. With this obvious observation, one simple idea hits me - maybe it would be helpful to gather those in more sharable form for everyone beyond certain labs I work in - and here I wish to start TechRabbit's Note.

Maybe my note will be a bit ecliptic collection of many things - tips for literature review, paper publication, figure drawing, collaboration formation, idea/project formation, etc - but will be fun as I will try my best to share the best practices and tips I have learned with some downloadable examples I can share. Hope this small rabbit effort would be helpful for the fellow science lovers.