Muscular Dystrophy Inheritance Patterns

Students will write a minimum 10-page (double-spaced, 12pt font, 1in margins) term paper on any topic of their choosing within the field of genomics in the style of a review article. Graduate students involved in research are encouraged to write on a topic close to their field of research (this can also be based on original research and include analysis of unpublished or publicly available data if possible; see Gendreau et al. 2017 paper as example of such an effort)
Please make sure it is full 10 page.
Agenda Item 1 – What is a review paper and expectations for writing review paper (or alternative primary research paper) for graduate students
By now you are aware of the term paper assignment for this class and you have already selected a topic. Your assignment is to write a review paper in a topic in Genomics. A review paper is a summary of a body of literature, in your case a minimum of eight references, which mostly should consist of primary scientific articles, more articles is of course acceptable. [Make sure you know the difference between a primary article and a review article – see below]. The articles you select should be cutting-edge and relate to each other in some way, as is appropriate for your topic. They should be published in reputable peer-reviewed scientific journals, ideally within the last 5-10 years. Accordingly, you will want to select your references carefully, making sure they are not especially old (if newer and better articles exist on your topic) and are highly relevant to your topic and clearly relate to each other in a way that will allow you to write a cohesive review.
Overview of the draft
Your draft should as closely resemble the final paper as possible. You are expected to turn in a draft of high quality. Remember that good writing is the result of repeated editing in response to feedback. In the same way, your final paper will benefit from comments from the instructor and another student you will be partnered with.
Your paper should have the following sections:
1. Title
2. Abstract (short ~200-300 word paragraph summarizing paper)
3. Introduction (present background to topic)
4. Rest of text broken into subsections, you decide how to organize each subsection and the header (subtitle) for each
5. References (list all cited references in scientific format: author names, year of publication, article title, journal name, volume, pages


Your paper should be about 10 double-spaced pages excluding references.

On the day it is due you will provide one copy of your draft to your professor and one to another grad student, who will be selected to provide you with additional feedback. You will also receive the draft of another student and you will review their paper and complete a critique assignment of their paper. You will also be required to submit the draft to turnitin.com – I will provide the needed course ID and password to do this shortly.

Exceptions – those students that have received approval to write up their paper as an original research article (rather than a review article) should format their paper to include the following sections: (1) Title (2) Abstract, (3) Introduction, (4) Methods, (5) Results, and (6) Discussion, (7) References, along with potential figures and tables to illustrate the results or other aspects of the study. It is also allowable to combine the Results and Discussion into one section as is sometimes seen in scientific articles. These students should *not* submit to Turnitin.com to protect the information in the paper.

Expectations for the draft

Your papers should fulfill the following criteria below, as reviewers of another student’s work you will also be critiquing your partner’s draft using the same criteria.

Scientific content
1. Is the paper clearly related to Genomics?
2. Does the paper have a central theme or topic and do all of the sections clearly relate to this topic and address it?
3. Does the paper present scientifically sound writing?
4. Has the author provided citations where appropriate and using standard scientific format (author, year)?
5. Are all of the citations listed in the references section?
6. Does the writing suggest the author understands the papers reviewed?
7. Does the paper present a cohesive overview of the topic? Does the author bring the articles together (relate them to each other) in a way that makes sense?
8. Does it seem as if the author has identified essential articles for the topic and are they relatively recent articles?

Grammar and Style
1. Are there spelling errors or grammatical errors?
2. Does the writing make sense, is it clear to read (check this by reading aloud to yourself)
3. Does the writing flow? Do sentences follow from one to the next seamlessly or do they jump around?

General
1. Are all sections present (i.e., title, abstract, introduction, other sections, references)?
2. Is the paper 10 double-spaced pages excluding references?
3. Are the references formatted properly in the text and in the references section?
4. Did the author use at least 8 references, mostly citing primary scientific articles?

How to write the paper (suggestions)
1. Think about your organization – how will you organize it into section so that the text flows from one paragraph to the next in a sensible way.
2. Once you’ve decided your organization, write like crazy without thought to perfect grammar or sentence structure.
3. Once you have written everything, edit very carefully, read sentences aloud, do they make sense when read out-loud? Print out and read carefully, make notes on hard copy.
4. Correct your edits, print and edit at least one last time.
5. Proofread your paper pretending to be someone unfamiliar to the topic – does the writing make sense to you"

This is the expectation for your draft. It will be difficult to make comments on the scientific content of your paper if the instructor or your partner cannot read your writing to start with and is spending all of their time editing grammar and spelling mistakes. If you do this your final paper will be even better.



Agenda Item 2: Graduate students next assignment – the preliminary list of references
Undergrads – you can use this information for any paper for which you need to provide a list of references – this is the standard practice for citing information in the sciences

Grad students - For Oct 18 provide a list of at least eight references, which mostly should consist of primary scientific articles related to your chosen term paper topic. For each reference indicate whether it is a primary scientific article or a review article and a brief 1-2 sentence explanation of why it is relevant to your topic.

A primary scientific article is one that reports the results of an original scientific study, written by the scientists that conducted the study. This contrast with a review article which is an article that summarizes many different studies related to a particular topic. You are permitted to read and reference review articles for your term paper, but the majority of your references should be primary articles.

Preparing list of references:

To find your articles, I suggest two search engines of scholarly research: Google Scholar (www(dot)scholar(dot)google(dot)com) and PubMed (http://www(dot)ncbi(dot)nlm(dot)nih(dot)gov/pubmed). For each reference in your list make sure each is formatted properly using standard scientific reference formatting (see example below).

Generic example of how to format reference:

Paper Authors (last name, first name (or initial) of first author, followed by other author names); year of publication; article title; journal name; volume; pages numbers

Specific example, following above guide (how each of the minimum 8 references should be formatted for your list and don’t forget to indicate whether it is a primary or review article and the 1-2 explanation of how it relates to your paper topic):

Garb JE, DiMauro T, Lewis RV, Hayashi CY. (2007) Expansion and intragenic homogenization of spider silk genes since the Triassic: evidence from Mygalomorphae (tarantulas and their kin) spidroins. Molecular Biology and Evolution, 24:2454-2464.

*This is an example of a primary article because it reports on the results of original research.
* My topic is on the evolution of spider silk and I plan to use this article because it is one of a small number that discuss the ancient origin of spider silk genes and how it related to the ecological uses of silk.


In this example, the Authors are Garb, DiMauro, Lewis and Hayashi, the article was published in 2007, with the title “Expansion and intragenic homogenization of spider silk genes since the Triassic: evidence from Mygalomorphae (tarantulas and their kin) spidroins.” In the journal “Molecular Biology and Evolution”, in volume 24 of this journal, on pages 2454-2464.




Agenda Item 3: Effectively searching the literature, google scholar (recommended), pubmed, identifying difference between primary articles and review articles in scientific journals

• Brief example on how to use scholar.google.com

Example: I am interested in the evolution of spider silk proteins, demo going to www(dot)scholar(dot)google(dot)com, and enter the terms “spider silk protein evolution”
You will see the following (or something very similar):

Note below each article there is often text that says “Cited by” this is a useful link to a page that will list all of the papers that cited the paper in its list of references. Thus this is a good way to find papers on a related topic and you can sort them by date of publication to find more recently published papers. Also note that papers that have been cited many times are often important in the field.

This is how you can also obtain a pdf of the paper itself, often the link to the right directly links to the pdf that can be downloaded. However, some journals articles are behind “paywalls” and cannot be obtained unless you are going through the university subscription. Often by searching the literature via web browsers on vlabs you can access those articles behind paywalls if UML has a subscription to the journal. If you are not using vlabs and are using your computer at home (e.g., not on eduoroam network) another option is to use the uml library website (https://www(dot)uml(dot)edu/library/). Often putting the title in the search field for the EBSCO’s discovery service can retrieve papers that may be behind paywalls. A last resort is interlibrary loan, or asking me (Dr. Garb for help), because you should never have to pay for one of these articles.


Difference between primary article and review article – primary articles report the findings of novel research and will have methods and results section, an exception is articles in the journals Science and Nature which often do not have standard Introduction, Methods, Results and Discussion sections, however, they often have Methods reported somewhere in the article. Review articles do not report new results, they summarize results from multiple primary articles and will never have “Methods” or “Results” section.

Let’s inspect one example of each kind of article.

First this article – what kind of article is this – primary or review?

CY Hayashi, RV Lewis. 2000 Molecular architecture and evolution of a modular spider silk protein gene. Science. Vol. 287, Issue 5457, pp. 1477-1479
https://science(dot)sciencemag(dot)org/content/sci/287/5457/1477.full.pdf?casa_token=wkqmwGw8CGcAAAAA:xWW1ZxzrmEkvexassJQaO3DabrYMK9UGtBPi7tQCeR69gFgmL0gqDlGoMZRLEtO7k__Imz5AIVu1oA



Here is an example of a primary article with standard sections:
JE Garb, NA Ayoub, CY Hayashi. 2010. Untangling spider silk evolution with spidroin terminal domains. BMC evolutionary biology 10:243
https://link(dot)springer(dot)com/article/10.1186/1471-2148-10-243

Here is a review article:
JE Garb, PP Sharma, NA Ayoub. 2018. Recent progress and prospects for advancing arachnid genomics. Current opinion in insect science. 25:51–57
https://doi(dot)org/10.1016/j.cois.2017.11.005

Let’s notice how they are different to be able to detect the difference in primary and review articles as you come across them for your own research


Agenda Item 4: Reference management: Zotero tutorial, building a library of references, using the Zotero connector, adding references to your Zotero library

Dr. Garb will demo her Zotero library, the Connector extension in the web browser and how to add new references into the library by selecting two recently published articles to add to her library.