Writing a Good Paper
Philip Bourne & Steven Brenner
pbourne@ucsd.edu
brenner@compbio.berkeley.edu
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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)
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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
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The Facets and Believed Importance in
a US Academic Career
Teaching /
Mentoring
Grants
Community
Service
Good
Talks/Networking
Good Papers
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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
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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
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PLos Comp Biol 2007 3(10) e213
Okay your work is hot you, are
working around the clock, now
what?
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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
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Which means…
If you hate writing – get over it
If you do not write well take
classes – the earlier the better
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And Remember Each Day as you
Write …
what you put in the literature is
your scientific legacy after all else
is gone
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… 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!
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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
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Avoid the Obvious Traps
• Don’t try and prove you are smart
• Avoid the kitchen sink syndrome
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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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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
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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
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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
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The Work is Never Finished,
but the Paper is – Now What?
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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!
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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
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Consider how PLoS
Computational Biology works
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Understand that the best
scientists get rejected and/or
have to make major revisions,
they just know how to work the
process better
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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
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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
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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
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Bioinformatics 2003 19(7) 897-898
Questions?
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