How to read papersA biologist’s perspective Holly H. Ganz, UC Davis

Journals publishing papers in microbial phylogenomics

• Considerations that authors make when choosing where to publish

• Impact Factor

• Audience

• open access

Learn to read critically, so you don’t just judge a book by its cover• Don’t just assume that a paper

in Science is correct.

• Important to learn how to judge each paper on its own merits.

• And to identify what else there is to be done. What are the unanswered questions?

• This is a lot of what we learn how to do in graduate school.

Article structure

• What is the format for scientific papers?

Article structure• Title

• Authors and Affiliations

• Abstract

• (Author summary)

• Introduction

• Materials and Methods

• Results

• Discussion

• Literature Cited

• Figures and Tables

• Supplementary Files

Start by reading the introduction, not the abstract

• The abstract contains the authors’ summary and overall conclusions of their study.

• When I write a paper, I write the abstract last.

• Read it last.

x

As you read the introduction, ask: What big question is being asked here?

As you read the introduction, ask: What question is being asked here?

Why should we care?

What is the ecology of buildings? Do buildings affect human health through the microbiome?

What is the ecology of buildings? !

Environmental selection (such as …) Dispersal of microbes from a source (such as …)

Other factors (such as …)

Effects of building design on the indoor microbiome !

function, form and organization

What work has been done in this field already? What were the limitations of prior work?

What needs to be done next?

How design choices influence the biogeography of indoor bacterial communities

!What specific question(s) are the authors trying to answer?

Were they testing a null hypothesis? What is it?

What are they going to do? Why?

The methods section• How did they attempt to

answer the specific questions?

• What did they do?

• How/where did they collect samples? How many?

• How samples stored, DNA extracted, PCR methods, sample processing, data analysis

• Be sure to read supplementary info

Methods!Where? The study site

The results section

• Try to summarize the results

• Focus on figures and tables

• Be sure to read any supplementary results

• Do they provide statistical analyses, significance values? Do graphs have error bars? Pay attention to sample sizes.

• Do the results answer the specific questions?

• What do you think the results mean?

• Do the authors refer to their questions/hypotheses?

• How do they interpret their results?

• Can you think of any alternative interpretations?

• Do the authors identify weaknesses or limitations of their study? What do you see as limitations?

• What do the authors propose to do next?

• What would you do next?

The discussion section

Finish by reading the abstract• The abstract contains the authors’ summary and overall conclusions of their

study.

• Does the abstract match what was said in the paper?

• Does it fit with your interpretation of their results?

• Can also read comments (if any) from other people in the field.