BIOL2254 - Assessment 3 Semester 2, 2021
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RMIT Classification: Trusted
Bioinformatics Tutorial 3: Article Analysis and Press Release
Overview:
An important skill as a scientist is being able to effectively communicate complex topics to a general
audience. In this assignment, you will read and analyse a journal article that covers a recent advance
in a bioinformatics-related field (Part 1). Using the knowledge gained from this analysis and
associated background reading, you will write a short scientific press release that explains the
importance and
oader context for your selected paper (Part 2). This should be aimed towards a
general scientific audience.
Part 1 (50 points):
With your selected research paper, answer the following questions:
• What is the fundamental research question or bioinformatics problem that this paper is
trying to address? (100 words) (10 points)
• What data has been used to answer the research question? In the case of a new
tool/technique, what data is used to validate the tool/technique being presented? (100
words) (10 points)
• Describe one main bioinformatics technique used in this paper. How does this technique
work, and how does it help the researchers answer their question? (150 words) (10 points)
• Describe the controls used in this study. Are these controls appropriate? Are there
additional controls (or control experiments) you would use? (150 words) (10 points)
• What alternative bioinformatics technique could be used to tackle the question/problem
addressed in this paper? Describe how the suggested technique helps address the research
question/problem (100 words) (10 points)
Part 2 (50 points):
Using your selected paper, write a short scientific press release that highlights the importance and
oader context of your chosen paper to a general scientific audience. This should be 400 words in
length (+/-10%, excluding reference list and in-text citations), and could cover:
• The relevant background to the chosen paper: In what context has this work been done?
What knowledge are they building on? What important concepts does the reader need to
understand in order to understand the chosen paper?
• Major results/conclusions/contributions for the chosen paper: What new knowledge has
this paper added to the field? Have they introduced a new tool or analysis technique? Have
they used existing bioinformatics techniques to answer a fundamental biological question?
• Future directions for this research: What impact is this research likely to have on future
work? Are there obvious follow-up studies that lead on from this research? Are there
additional studies that need to be done to validate this research? This is a chance for you to
express your scientific opinion.
Note that you will need to be selective with what information you include within your press release,
as you will not have enough space to cover every result in the article. While many press release do
not include in-text citations, you will need to provide in-text citations and a reference list.
To help guide you in this task, we have provided an example original research paper (Jumper et al.,
2021) and associated scientific press release, as well as some hints for writing for a non-specialist
https:
microbiomejournal.biomedcentral.com/articles/10.1186/s XXXXXXXXXX
https:
microbiomejournal.biomedcentral.com/articles/10.1186/s XXXXXXXXXX
https:
www.biomedcentral.com/about/press-centre/science-press-releases/ XXXXXXXXXX
BIOL2254 - Assessment 3 Semester 2, 2021
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RMIT Classification: Trusted
audience below. While many press releases contain direct quotes from the authors, this will
generally not be possible for your selected articles.
Topics/Articles:
Choose one paper from any of the following topics (PDFs of these papers are available on Canvas):
Single-cell RNA-Seq
• Liu Y, Wang T, Zhou B, Zheng D. Robust integration of multiple single-cell RNA sequencing
datasets using a single reference space. Nat Biotechnol. 2021;39: 877–884.
• Che
y C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, et al. Computational
econstruction of the signalling networks su
ounding implanted biomaterials from single-
cell transcriptomics. Nat Biomed Eng XXXXXXXXXXdoi:10.1038/s XXXXXXXXXX
Genome Assembly:
• Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. HASLR: Fast Hy
id Assembly of Long
Reads. iScience. 2020;23: 101389.
Machine Learning
• Elnaggar A, Heinzinger M, Dallago C, Rehawi G, Yu W, Jones L, et al. ProtTrans: Towards
Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High
Performance Computing. IEEE Trans Pattern Anal Mach Intell. 2021;PP.
doi:10.1109/TPAMI XXXXXXXXXX
Protein structure, function and modelling
• Necci M, Piovesan D, CAID Predictors, DisProt Curators, Tosatto SCE. Critical assessment of
protein intrinsic disorder prediction. Nat Methods. 2021;18: 472–481.
Submission and Grading
This assignment is worth 11.4% of the final marks for the course.
Both Part 1 and Part 2 are to be submitted as either a Microsoft Word or PDF document and will be
eviewed for plagiarism using Turnitin.
Late submission will be penalised at 10% of the total available marks for this assignment per day.
BIOL2254 - Assessment 3 Semester 2, 2021
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RMIT Classification: Trusted
Tips for writing for a non-specialist audience
Writing about complex scientific research can be challenging and presenting research for a general
scientific audience is no exception. Here are a few tips to keep in mind that may make the process a
it easier (although these are just suggestions - and you may not have space to adequately cover all
of these in your press release!).
• Remember that your audience does not have the knowledge that you do (imagine your
audience is from the Physics or Geology department!). It is your job to cover the important
ackground concepts that will help them understand the research you are writing about.
There may be 2-3 key concepts that need to be explained before the reader can understand
the importance of your chosen research article.
• Avoid excessive use of acronyms or complex domain-specific terms. If possible, limit yourself
to 3-4 complex terms/acronyms, and make sure you explain each of these when they are
introduced.
• You don’t need to cover all the results presented in the primary research article. Choose
what you think are the 1 or 2 most important results or advances and discuss these.
• A well-chosen diagram or figure can help to reinforce key ideas or concepts for the reader.
This might be a diagram or figure modified from the original article (with appropriate
attribution) or it may be a figure you have created yourself.
• Start with the big picture, and slowly na
ow down till you get to the problem that your
esearch article is tackling. This can be an effective way of structuring your introduction and
initial discussion of the research article.
• End with a big-picture view of the research area – where is it going and what might it lead
to?
• Try to identify the knowledge gap that your research article is trying to fill. Make sure you
clearly explain to the reader what this knowledge gap is, and how the research article helps
to fill this gap.
• There may be potential flaws in your chosen research article. It can be helpful to discuss
alternative approaches, or potential issues with the research. If there are conflicting studies,
you may want to
iefly discuss these (making sure to reference appropriately).
• You will likely need to read beyond the original research article to understand the context
for the research. There may be recent review articles that could help you get an overview of
the
oader subject area (try a PubMed or Google Scholar search).
BIOL2254 Tutorial 3 Assessment Ru
ic Semester 2, 2021
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RMIT Classification: Trusted
Part 1 Ru
ic:
High Distinction Distinction Credit Pass Not satisfactory Total Marks
All questions There is an advanced and
thorough understanding of
the bioinformatics
approaches used in the
chosen research article,
including an understanding
of data
sources/controls/similar
techniques.
There is a strong
understanding of the
ioinformatics approaches
used in the chosen
esearch article, including
an understanding of data
sources/controls/similar
techniques. There may be
minor omissions or e
ors.
There is a reasonable
understanding of the
ioinformatics
approaches used in
the chosen research
article. There may be
omissions or e
ors.
There is limited
understanding of the
ioinformatics
approaches used in the
chosen research
article. There are major
omissions or e
ors.
There is an
inadequate
understanding of
the bioinformatics
approaches used in
the chosen research
article.
50 points
Total: /50
BIOL2254 Tutorial 3 Assessment Ru
ic Semester 2, 2021
Page 2 of 4
RMIT Classification: Trusted
Part 2 Ru
ic:
High Distinction Distinction Credit Pass Not satisfactory Total Marks
Introduction Introduction clearly
introduces the topic and
oader context,
demonstrating an
advanced understanding
of the
oader research
field. Key bioinformatics
terms are defined clearly
and simply.
Introduction includes an
appropriate level of
detail to enable a general
scientific audience to
understand the research
eing discussed.
Introduction clearly
introduces the topic
and
oader context,
demonstrating a good
understanding of the
oader research field.
Key bioinformatics
terms are defined.
Introduction includes
an appropriate level of
detail to enable a
general scientific
audience to
understand the
esearch being
discussed. There may
e minor e
ors in
understanding.
Introduction introduces
the topic and
oader
context, demonstrating a
easonable understanding
of the
oader research
field. Key bioinformatics
terms may be defined but
are difficult to understand
from the description.
There may be e
ors in
understanding.
Introduction adequately
describes the topic,
demonstrating an
acceptable
understanding of the
oader research field.
Key bioinformatics
terms are either defined
poorly or otherwise
missing.
There are major e
ors
in understanding.
Introduction does not
adequately describe the
topic. Key bioinformatics
terms are not defined.
There are major e
ors in
understanding.
10 points
Body Discussion of chosen
esearch article is clear
and articulate,
demonstrating an
advanced understanding
of the chosen research