1. Writing a Good Paper Philip Bourne & Steven Brenner pbourne@ucsd.edu brenner@compbio.berkeley.edu ISMB 2010

2. PB’s Perspective ~200 (50) papers and five books 1982-1992 only a couple of papers “Ten Rules” series + course in professional development Editor in Chief – PLoS Computational Biology Editor + reviewer for many years in different disciplines (chemistry, IT, structural biology, comp biol) ISMB 2010

3. Disclaimer Everyone is different these are just guidelines we have found useful and even these we do not necessarily agree on – consider what follows as 2 perspectives Every academic/industrial laboratory is different – alternative approaches may be more appropriate ISMB 2010

4. The Facets and Believed Importance in a US Academic Career ISMB 2010

5. Good Papers Start with Good Science (duh) – Ask Hamming … Aim to do something very significant from the outset – ie work only on the important problems (with important people) Do it when you are young You need more than brains – you need courage too Luck favors the prepared mind Time management is critical ISMB 2010 PLos Comp Biol 2007 3(10) e213

6. Good Papers Start with Good Science – Ask Hamming Work very hard and from the heart Some self doubt is a good thing Leave your door open Take time for the forest not just the trees ISMB 2010 PLos Comp Biol 2007 3(10) e213

7. Okay your work is hot you, are working around the clock, now what? ISMB 2010

8. Start Writing the Paper on Day 1 It will be easier to get it done The mere act will help focus the work, define the level of detail particularly if you choose the journal early (see discussion of scope in a minute) Much good research NEVER gets written up It is an object easily shared with colleagues ISMB 2010

9. Which means… If you hate writing – get over it If you do not write well take classes – the earlier the better ISMB 2010

10. And Remember Each Day as you Write … what you put in the literature is your scientific legacy after all else is gone ISMB 2010

11. … And Always Look From a Distance Try and see your paper as the reviewer will see it – believe me the reviewer will not see it as the best thing since sliced bread even though you do! ISMB 2010

12. A Few Obvious Ingredients of a Good Paper Novelty – figure it out for yourself – do not rely on your PI Good coverage of the literature Good data Strong statistical support Clarity of presentation Thought provoking discussion ISMB 2010

13. Avoid the Obvious Traps Don’t try and prove you are smart Avoid the kitchen sink syndrome ISMB 2010

14. How to Write a Good Paper - Pragmatically Maintain a good bibliographic database Consult a citation index (ISI, Google Scholar) and consider using that to annotate your database entries Use a tool like Mendeley to store annotations ISMB 2010

15. How to Write a Good Paper - Pragmatically Use other tools of the Web 2.0 world Have your colleagues critique your paper like object Become a reviewer early ISMB 2010

16. Become a Reviewer (Critic) Earily Work through your mentor There are way more young people than old in this field – they want you to review Approach the program committee of conferences like this Approach the editorial staff of various journals ISMB 2010

17. How to Write a Good Paper - Pragmatically Identify good and bad papers in journal club and elsewhere and study them A good paper will likely tell a story and be enjoyable to read and follow which means pitched at the right level for the intended audience ISMB 2010

18. The Work is Never Finished, but the Paper is – Now What? ISMB 2010

19. Choose the Journal Wisely Do you read that journal? Do you cite it in your work? Is it a top notch editorial board? Does it have highly accessed papers? What is the rejection rate? What is the average time to publication? Is it indexed in PubMed? Does the scope match your work! ISMB 2010

20. Understand the Publishing Process Use a presubmission inquiry if it is offered Suggest reviewers not because they might be easy, but because they will improve your work the most Understand the role of different editors, reviewers Understand the appeals process ISMB 2010

21. Consider how PLoS Computational Biology works ISMB 2010

22. Understand that the best scientists get rejected and/or have to make major revisions, they just know how to work the process better ISMB 2010

23. The Post Review Phase Get over it Do not get defensive unless it is really called for Address EVERY aspect of the reviewers concerns Make it obvious to the reviewer through the cover letter and the revised manuscript itself of the changes you have made Do not add new science unless it is called for ISMB 2010

24. Example of What I Regard As a Good Paper A beautiful story Foundation for further studies on the use of structure to study evolution Concise ISMB 2010 PNAS 2005 102(2): 373-378

25. Example of a Not So Good Paper Work not persistent Unmaintainable Good ideas but not formulated until years later ISMB 2010 Bioinformatics 2003 19(7) 897-898

26. Questions? ISMB 2010