How To Writea Paper10

Writing a Good Paper Philip Bourne & Steven Brenner [email_address] [email_address] ISMB 2010

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

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

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

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

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

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

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

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

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

… 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

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

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

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
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Use other tools of the Web 2.0 world
Have your colleagues critique your paper like object
Become a reviewer early
ISMB 2010

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

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

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

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

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

Consider how PLoS Computational Biology works ISMB 2010

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

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

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

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

Questions? ISMB 2010

How To Writea Paper10

by Philip Bourne

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