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How to write scientific papers
in chemistry/biotechnology ?
Why does one actually write scientific papers?
A career in science is largely built on the (perceived) number and quality of publications
that a researcher (or a team of researchers) offers his or her colleagues.
If these publications are numerous and of high quality, they lead to a successful research
funding and employment.
The greater speed of release for journal articles when compared with books,
typically months versus years, means that those who wish to influence their field of
study need to publish in peer-reviewed journals in order to communicate quickly their
research results.
Most importantly,
- we have original and exciting results/hypotheses to share with scientific
community
- we have been asked, as an expert in the field, to prepare a review paper
or commentary on another article
Original dilemma: quantity or quality?
Impact fo the published work: impact factor and citation index
How can I find the most appropriate journal to publish a paper?
Good advice from people with experience in publishing scientific papers
Search
You can enter a few keywords that describe your paper in the Scirus SEARCH THROUGH
ARTICLES search bar, available here.
The list of results allows you to identify the Elsevier journals that publish papers on
your topic.
Browse
You can browse through our list of journals, covering all subject areas, by keyword or
subject on the Author Home Page.
Select your area(s) of research to display a list of appropriate Elsevier journal titles.
Clicking on a title will access the journal homepage.
Read the Journal Homepage
On the journal homepage you will find relevant information on the journal.
Read carefully the Aims & Scope to find out whether a journal is suitable for your
research.
If the description, scope and content align with your article, carefully view the journal
Guide for Authors, to ensure that your paper adheres to the rules and guidelines for
submission to the journal.
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Types of scientific journals: peer-reviewed and others
How to select a journal you are going to submitt the paper ?
area of research
the quality of results
whether you are ready to pay for review/page charges/color figures
open access journals/articles
submission based on pre-evaluation
required for some journals e.g. Science, Nature, etc.
PNAS – requires in track 1 submissions a paper editor
(member of USAS)
Mistakes to avoid: the time one spends to write a good quality paper is
comparable regardless of the impact factor of the target journal
Competence
An author should be competent in the area a paper he/she is about write
Story
There is no good paper without an original and exciting story supported by
good quality results
Order of co-authors
Should reflect actual contribution of each co-author to the paper.
Many journals require written confirmation as for the contribution for
each co-author.
Equal contribution (first and last authors).
Corresponding author
Usually senior researcher signing the paper (last author).
Language
It is not enough to simply have a good idea. You must be able to communicate it clearly.
First time writers are trying to sound too scientific.
Terms with everyday meanings may have different meanings for scientists.
Problem with jargon usage.
Quality of written English (style, grammar etc.)
Problem with ‘borrowing’ phrases from other articles to include them in your manuscript
(critical in review papers)
Style: wishy-washy phrases should be avoided which include words such as
‘suggests,’ ‘appears,’ ‘probably,’ ‘may be.’
Better words to use are ‘indicates,’ ‘implies,’ ‘shows,’ ‘illustrates,’ etc.
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Who is going to write a paper?
Two options:
- to work alone
to acquire these skills you can work alone, in isolation from colleagues,
and hope to learn from rejection letters and from harsh peer reviews
- or with colleagues
build an informal team of fellow scientists who are both critical and
supportive and who will read and comment on your papers.
sort out quickly who will be supportive of your aims versus who may be
less than helpful e. g. always harshly critical
Accept the rule: some people write beautifully and effortlessly while
others feel like they are sweating out each word
Problem with multi-author papers (sometimes from different research
groups)
Where to start?
Each journal has its own specific style configuration and to be accepted by a journal
you must write to its requirements, not those of another style format and not to your
own personal preferences
e.g. check for the preferred length of the paper and its abstract (no of words, characters);
gender-neutral (passive voice) or other styles of preferred language;
the maximum number, length, and style of footnotes or endnotes;
the maximum size of tables, the presentation of figures and their graphical format.
Nowadays controlled by submission portals.
Special case: review papers
Review papers are most commonly written by invitation only
If ou want to write a review paper
-it is advisable to contact your chosen journal with a draft title and abstract,
- ask if your paper is of interest and relevant to the journal's mandate
Beginning researchers are expected to make it clear to the editor and reader what is
the original contribution of a paper
- describe the originality of your research analyses in your initial letter to the editor
- your original contribution(s) should be clear from the Title (if possible),
mentioned in the Abstract, and described in the Introduction and in the Discussion
(and/or Conclusion).
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Writing process
Contents of the manuscript
Title
Author name(s) and address(es)
Abstract
Introduction
Main body of manuscript
Conclusion/Summary
Acknowledgments
References Cited
Illustrations and Figure captions
Tables
+graphical/video abstract
Title: You should be aware that overall number of articles published each year is so big
that it is critical for the visibility of your work to come up with a ‘flashy’ title but
well enough to be suitable for the journal of your choice.
The title should be short and unambiguous, yet be an adequate description of the
work.
A general rule-of-thumb is that the title should contain the key words describing the
work presented. Remember that the title becomes the basis for most on-line computer
searches - if your title is insufficient, few people will find or read your paper.
If in doubt:
(a)read the 'Table of contents' of several issues to get a feel for their style of titles
(b)make up a couple of possible titles and ask for reactions from colleagues
who know this journal well.
Mistakes to avoid: trendy and ‘cute’ titles may soon look trivial and outdated
Abstract: The abstract summarizes how you carried out your research and what you
learned. It usually requires a short description of objectives, design, setting, participants,
interventions, main outcome measures, results, and conclusions.
· the question(s) you investigated (or purpose), (from Introduction)
state the purpose very clearly in the first or second sentence.
· the experimental design and methods used, (from Methods)
clearly express the basic design of the study.
Name or briefly describe the basic methodology used without going into
excessive
detail - be sure to indicate the key techniques used.
· the major findings including key quantitative results, or trends (from Results)
report those results which answer the questions you were asking
identify trends, relative change or differences, etc.
· a brief summary of your interpretations and conclusions. (from Discussion)
clearly state the implications of the answers your results gave you.
Mistakes to avoid:
- do not go beyond what is established in your paper: offer no non-significant
results, no speculation;
- do not use telegraphic style (i.e., omitting articles and other parts of speech to achieve
brevity) unless allowed by the journal;
- do not go over the abstract size limit set by the journal (usually 150-250 words).
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Keywords
Introduction: A good introduction tells the reader why the paper is important in terms
of the problems to be investigated, the context for the research question, what place this
research question has in understanding addictions, and what is original about the
endeavour.
Introduction must answer the questions: "What was I studying? Why was it an
important question? What did we know about it before I did this study? How will this
study advance our knowledge?„
Style: Use the active voice as much as possible. Some use of first person is okay, but do
not overdo it.
Structure: an inverted triangle (the most general information and focusing down to the
specific problem you studied)
Mistakes to avoid: Do not simply describe the substance under study as it is not always
implies what research is needed. Synthesis f new compounds must be justified by a clear
hypothesis, not just because compounds are new chemical entities (never synthesized
before).
Materials and Methods: describe all methods, with particular attention to new
experimental procedures.
Function: In this section you explain clearly how you carried out your study:
· the the organism(s) studied (plant, animal, human, etc.) and their pre-experiment
handling and care, and when and where the study was carried out (only if location and
time are important factors); note that the term "subject" is used ONLY for human studies.
· if a field study, a description of the study site, including the significant physical and
biological features, and precise location (latitude and longitude, map, etc);
· the experimental OR sampling design. For example, controls, treatments, the variable(s)
measured, how many samples were collected, replication, etc.);
· the protocol for collecting data, i.e., how the experimental procedures were carried out,
· how the data were analyzed (qualitiative analyses and/or statistical procedures used).
Style: the active voice to a certain extent, although this section requires more use
of third person, passive constructions than others. Avoid use of the first person in this
section. Use past tenses throughout - the work being reported is done, and was
performed in the past, not the future.
In some journals it is required that you provide specialty materials (custom antibodies,
DNA vectors etc.) on request from readers.
Mistakes in the description of experimental procedures: copy-paste problem,
never ending ‘chain of references’, intentional mistakes?
Results: to objectively present your key results, without interpretation, in an orderly and
logical sequence using both text and illustrative materials.
Important negative results should be reported, too. Authors usually write the text of the
results section based upon the sequence of Tables and Figures.
The text should guide the reader through your results stressing the key results which
provide the answers to the question(s) investigated.
Style: The text of the Results section should be concise and objective. The passive voice
will likely dominate here, but use the active voice as much as possible. Use the past
tense. Avoid repetitive paragraph structures.
Mistakes to avoid: Do not interpret your data here!
This section especially lends itself either to over-writing (excessive detail beyond what is
needed for analysis, excessive weight given to non-significant results) or to under-writing
(cursory attention to important aspects and variables).
Beginning researchers often take up too much of their paper with non-significant results;
be ready to drop a result which colleagues or reviewers suggest is unimportant, even
though it seems like a wondrous and magical thing to you.
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Discussion and Conclusions: The function of the Discussion is to interpret your results
in light of what was already known about the subject of the investigation, and to explain
our new understanding of the problem after taking your results into consideration.
· Do your results provide answers to your testable hypotheses? If so, how do you interpret
your findings?
· Do your findings agree with what others have shown? If not, do they suggest an
alternative explanation or perhaps a unforseen design flaw in your experiment (or theirs?)
· Given your conclusions, what is our new understanding of the problem you investigated
and outlined in the Introduction?
· If warranted, what would be the next step in your study, e.g., what experiments would
you do next? Present a model, if possible.
Style: Use the active voice whenever possible in this section. Watch out for wordy phrases;
be concise and make your points clearly. Use of the first person is okay, but too much use
of the first person may actually distract the reader from the main points.
Mistakes to avoid: A little speculation is allowed, but limit it and ask your supportive
colleagues what they think. Do not introduce new results.
Restrict your discussion of your future research plans to a line or two. Some authors like to
end with the trite conclusion "More research is needed.
Literature review
The literature review is a crucial portion of your paper. In particular when writing
a thorough review paper, not advised as a start for beginnig authors!
Remember: peer reviewers will likely be much more familiar with the literature
than you are, and so your literature review needs to be as informative and critical
as possible, not naïve and accepting of all that is published.
- all of the relevant literature needed to establish the theory and/or hypothesis that
you will examine. It will help to outline your paper and to see what background or
literature reviews you need for each section.
- all relevant literature for each of the measures that you have used (the initial paper
describing each measure, crucial papers describing challenges, alterations,
refinements, including statistics on validity, reliability, and all other relevant
attributes).
- all of the data needed for your Methods, Procedures, and Results sections. A good
way to assess if you need more literature for a given section is to ask yourself, "If
I were challenged to support why I chose this [measure, method, statistic], what
literature supports my choice?”
Mistakes to avoid: do not forget that the function of references is to allow any reader to
retrace the evidence that you cite.
Proper reference style for your chosen journal is very important. Too many errors tell
the editor that an author has been careless, probably not only in References section.
Preparation of graphical data: Experimental data put in the graphical form (graphs,
figures, pictures).
“a picture is worth a thousand words”
Problem with different formats which are acceptable by particular journals
Busy, multicomponent graphs - limitation of graphics, supplementary data
‘Improving’ graphical data by graphical software: sometimes original pictures are required
by reviewers
Very often experimental data can be presented directly in the text!
Preparation of figure captions: clear and concise. Each figure and caption should be
provide enough information to explain the data without reading the results section, i.e., it
must be able to stand alone and be interpretable.
Graphical abstract: more and more popular in scientific journals
Video Abstract: proposed by e. g. ACS for JACS articles
Acknowledgements: funding institutions, colleagues who provided materials, advisers
etc.
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
First draft: You have written this first version and now you allow to circulate it
to selected colleagues whom you can trust to read and offer prompt and fair critiques.
Once you have their feedback, consider if their assessments warrant rewriting before
submitting it to your chosen journal.
Advice: It is always better to get comments from your colleagues than harsh criticism
from reviewers!
Submitting the paper
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Specific steps in the submission process (Elsevier):
Select Article Type
Enter Article Title
Add/Edit/Remove Authors
Submit Abstract
Enter Keywords
Select Section/Category
Submit Classifications
Enter EES Comments
Suggest Reviewers
Oppose Reviewers
Attach Files
Upload Figures
Submit Figure Captions
Approve the PDF
Experimental process
Section of Paper
What did I do in a nutshell?
What is the problem?
How did I solve the problem?
What did I find out?
What does it mean?
Who helped me out?
Whose work did I refer to?
Extra Information
Abstract
Introduction
Materials and Methods
Results
Discussion
Acknowledgments (optional)
Literature Cited
Appendices/Supplementary Data (optional)
Evaluation process
- quality check (format, references etc.)
- meritorious evaluation
The role of the editor
Coordinate and control the revision process and to decide whether another
reviewer should be asked for opinion (conflicting opinions).
The role of reviewers
Evaluation of:
- originality of work
- clarity of presentation
- if sufficient exeprimental data are prvided to support conclusions
- quality of language, misspellings, errors etc.
Comments for authors and at the discretion of the editor only
Acceptance ratio: top journals usually well below 10% of all manuscripts are accepted
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
First submission: Submit your paper to the editor.
Importance of letter to the editor!
Two possible outcomes:
1. Paper has been rejected.
If your paper is rejected then carefully read the critiques and see if you feel that
submitting it to another journal seems a wise step.
If you decide the referees' criticisms are too severe for you to answer, then write
the editor a rebuttal letter to tell her so along with your precise reasons for re-revision
of your paper.
This may work for your benefit:
(a) it labels you as someone who takes editing a journal seriously, who knows her goals,
and does not let work slide;
(b) it signals to the editor how serious the criticisms were and may lead her to discuss
options with you, and (c) she will remember you as someone who didn't leave her
hanging and wondering if that paper was ever coming back.
Mistakes to avoid: re-submitting the paper to lower-ranked journals.
The quality of reviewers tends to go follow the quality of journals!
It is always an emotional blow to anybody to get negative comments. If it happens
to you, it is best to set the manuscript aside for a week or more in order to get some
emotional distance. Then go back through the review comments and tweak your
manuscript to improve it according to the comments. Your manuscript will be better
for it.
2. Paper has been accepted as such (rare), or has been provisionally accepted but minimal
or extensive revision is expected according to the reviewers' and the editor's comments.
If you decide to revise your paper:
Be aware that authors should not see themselves as helpless in front of their reviewers
and a reviewer's comments are not orders that have to be carried out.
To the contrary, for each point that a reviewer has made an author has these three
options:
i) discuss/debate/refute a reviewer's comment(s), or
ii) rewrite the text in response to a comment(s), or
iii) a combination of these so that an author both discusses/debates/refutes a
reviewer's comment(s) and rewrites to accommodate some comments by a
reviewer.
Be crystal clear in accounting for how you responded to each point made by each
reviewer. An efficient way to do this is to follow each reviewer's comment with an
explanation of how you respond and to key this up in a contrasting and easily read
colour within the manuscript.
Mistakes to avoid: do not consider that after revision your revised paper is accepted!
Check the timing of your submission of the revised paper (usually 60 days).
Important if you are asked to provide more experimental data!
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Once your paper is accepted you may have little more involvement until the publisher
sends you the proofs to check. The proofs of the accepted paper are sent to the
corresponding author within 3 to 5 weeks of receipt of the accepted manuscript by the
production department.
Respect timing of the proof submission, usually proofs are expected within two working
days.
Carefully follow all the changes introduced by editors, check for:
mispellings, formatting, omissions etc.
Mistakes to avoid: Proofs are sent by e-mail as PDFs. If you have problems with your
mailbox/server, you can expect delays with publication of your paper.
It is advisable to track the progress of your accepted paper through the publication
process.
Is it really possible to publish well ?
Molecular Pharmacology/Chemistry (35.957)
Skladanowski A, Bozko P, Sabisz M.
DNA structure and integrity checkpoints during the cell cycle and their role
in drug targeting and sensitivity of tumor cells to anticancer treatment.
Chem. Rev. 109 (2009), 2951-2973.
Analytical Chemistry (20.086)
Tobiszewski M, Mechlińska A, Namieśnik J.
Green analytical chemistry: theory and practice.
Chem. Soc. Rev., 39 (2010), 2869-2878
Inorganic Chemistry (11.225)
Dolega A.
Alcohol dehydrogenase and its simple inorganic models.
Coordin. Chem. Rev. (2010) 25: 916-937.
Biophysics/Chemistry (8.580)
Neumann A, Baginski M, Czub J.
How do sterols determine the antifungal activity of amphotericin B? Free energy
of binding between the drug and its membrane targets.
J. Am. Chem. Soc. (2010) 132: 18266-18272.
Organic Chemistry (4.802)
Kukowska-Kaszuba M, Dzierzbicka K, Serocki M, Skladanowski A.
Solid phase synthesis and biological activity of tuftsin conjugates.
J Med Chem. (2011) 54: 2447-2454
Molecular Pharmacology (4.531)
Bram EE, Adar Y, Mesika N, Sabisz M, Skladanowski A, Assaraf YG.
Structural determinants of imidazoacridinones facilitating antitumor activity are
crucial for substrate recognition by ABCG2.
Mol. Pharmacol. (2009) 75: 1149-1159.
Chemical Technology (5.836)
Łuczak J, Jungnickel C, Łącka I, Stolle S, Hupka J.
Antimicrobial and surface activity of 1-alkyl-3-methylimidazolium derivatives.
Green Chem. (2010) 12: 593-601.
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Microbiology (3.556)
Sachadyn P.
Conservation and diversity of MutS proteins.
Mutat. Res. (2010) 694: 20-30.
Chemical Engineering (3.480)
Boczkaj G, Przyjazny A, Kaminski M.
A new procedure for the determination of distillation temperature distribution of
high-boiling petroleum products and fractions.
Anal. Bioanal. Chem. (2011) 339: 3253-3260.
Corrosion Science (3.325)
Arutunow A, Darowicki K, Zielinski A.
Atomic force microscopy based approach to local impedance measurements of
grain interiors and grain boundaries of sensitized AISI 304 stainless steel.
Elecrochim. Acta (2011) 56: 2372-2377.
Physical Chemistry (3.093)
Kuffel A, Zielkiewicz J.
The hydrogen bond network structure within the hydration shell around simple
osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated
using both a fixed charge and a polarizable water model.
J. Chem. Physics (2010) 133: 035102.
What about your next publication record ?
A. Skladanowski, P. Bożko and A.K. Larsen
G2 arrest following treatment with DNA damaging agents
is accompanied by antiapoptotic signaling which can be overcome
by UCN-01: how to Akt to avoid Bad influence
94th ANNUAL AACR MEETING, Washington, USA, 13-16 July 2003
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.
Prepare a tentative title of your current/future publication
as well as its abstract
so we can discuss your specific problems together
Friday April 15th
Group 1: 16.15-17.00
Group 2: 17.15-18.00
Projekt „Rozwój interdyscyplinarnych studiów doktoranckich na Politechnice Gdańskiej w zakresie nowoczesnych technologii” jest
współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego.