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Trinity College Dublin, The University of Dublin

GE3M25:Bioinformatics

Karsten Hokamp, PhDGenetics

TCD, 05/11/2015

Trinity College Dublin, The University of Dublin

GE3M25 Data Handling Module Content

PythonProgramming

Bioinformatics

ChIP-Seq analysis

Trinity College Dublin, The University of Dublin

GE3M25 Data Handling Module Content

PythonProgramming

Bioinformatics

ChIP-Seq analysis

Evaluation:

1. Weekly tasks

2. Project report

Trinity College Dublin, The University of Dublin

Overview

• PubMed

• Google Scholar

• Comparative search

• Extra features

• Weekly task

http://bioinf.gen.tcd.ie/GE3M25/

Trinity College Dublin, The University of Dublin

PubMed

Web-based search and retrieval system for MEDLINE

MEDLINE: biomedical journal citations and abstracts

Citations: 2014: 22,376,811

2013: 21,508,439

2012: 20,494,848

2011: 19,569,568

2010: 18,502,916

Trinity College Dublin, The University of Dublin

PubMed

Part of Entrez Search System at NCBI

Trinity College Dublin, The University of Dublin

PubMed Search

Trinity College Dublin, The University of Dublin

PubMed Search

Explore menu options and filters!

Trinity College Dublin, The University of Dublin

PubMed Search, Refinement

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

Medline Tags

https://www.nlm.nih.gov/bsd/mms/medlineelements.html

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

Medline Tags

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

EXERCISE: Search for retractions

Tip:- General search for retraction- Look at Medline format- Check for publication type

Extra tasks:Look for retractions in- high-profile journals (Nature, Science, Cell, PNAS)- specific fields (bioinformatics, population genomics)- specific countries, e.g. Ireland

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

EXERCISES

1. Using quotes:colon cancer vs "colon cancer" – what's the difference?

2. Bioinformatics: which is the first publication using this word?

3. Find out how many reviews on 'tuberculosis vaccine' were published in the last five years.How many of them were not written in English?

4. Can you tell from the results by year display when research into AIDS started to ramp up?

5. What would be a good search strategy to find all publications that came from the Genetics department in 2015?

Trinity College Dublin, The University of Dublin

Kavanagh TBracken ABradley DCampbell MDevine KFares MFarrar JHumphries PLabrador JMartin SMcConnell DMcLysaght AMitchell KRamaswami MWellmer FDeArce MHokamp KMcDermott P

"Trinity College Dublin" [Affiliation]+ combine with () OR ()

AND ("2015/01/01"[PDAT] : "2015/12/31"[PDAT])

range operator

PubMed Search, Genetics Department 2015

Trinity College Dublin, The University of Dublin

PubMed Search, Genetics Department 2015

(Kavanagh T AND "Trinity College Dublin" [Affiliation]) OR (Bracken A AND "Trinity College Dublin" [Affiliation]) OR (Bradley D AND "Trinity College Dublin" [Affiliation]) OR (Campbell M AND "Trinity College Dublin" [Affiliation]) OR (Devine K AND "Trinity College Dublin" [Affiliation]) OR (Fares M AND "Trinity College Dublin" [Affiliation]) OR (Farrar J AND "Trinity College Dublin" [Affiliation]) OR (Humphries P AND "Trinity College Dublin" [Affiliation]) OR (Labrador J AND "Trinity College Dublin" [Affiliation]) OR (Martin S AND "Trinity College Dublin" [Affiliation]) OR (McConnell D AND "Trinity College Dublin" [Affiliation]) OR (McLysaght A AND "Trinity College Dublin" [Affiliation]) OR (Mitchell K AND "Trinity College Dublin" [Affiliation]) OR (Ramaswami M AND "Trinity College Dublin" [Affiliation]) OR (Wellmer F AND "Trinity College Dublin" [Affiliation]) OR (Hokamp K AND "Trinity College Dublin" [Affiliation]) OR (DeArce M AND "Trinity College Dublin" [Affiliation]) OR (McDermott P AND "Trinity College Dublin" [Affiliation]) AND ("2015/01/01"[PDAT] : "2015/12/31"[PDAT])

Trinity College Dublin, The University of Dublin

Google Scholar Search

https://scholar.google.com

Trinity College Dublin, The University of Dublin

Google Scholar Search

Trinity College Dublin, The University of Dublin

Google Scholar Search

How are documents ranked?Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature.

Trinity College Dublin, The University of Dublin

Google Scholar – Author Profiles

Trinity College Dublin, The University of Dublin

Google Scholar – Advanced Search

Click arrow in search box

Trinity College Dublin, The University of Dublin

Google Scholar – EXERCISE

Find recently developed phylogenetic footprinting tools (similar to FootPrinter).

Find authors with a very high h-index.

Pick a scientist of your choice and try to find his or her h-index.

Trinity College Dublin, The University of Dublin

Searching for the origin of 'ohnologues'

Trinity College Dublin, The University of Dublin

Searching for the origin of 'ohnologues'

23 hits in PubMedCentral (only 3.5M articles but full-text available)

Trinity College Dublin, The University of Dublin

Searching for the origin of 'ohnologues'

Trinity College Dublin, The University of Dublin

Programming Concepts

Search for Ohnologues

Trinity College Dublin, The University of Dublin

Programming Concepts

Search for Ohnologues

Trinity College Dublin, The University of Dublin

Programming Concepts

Search for Ohnologues

Trinity College Dublin, The University of Dublin

Searching for the origin of 'ohnologues'

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

Google Scholar vs other Resources

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

Other resources

Scholarometerhttp://scholarometer.indiana.edu

Web of Sciencehttps://apps.webofknowledge.com

Scopus:http://www.scopus.com

PubCrawlerhttp://www.pubcrawler.ie

Trinity College Dublin, The University of DublinTrinity College Dublin, The University of Dublin

Weekly task

Scenario:You have just joined the bioinformatics support team and your first job is to analyse some yeast ChIP-seq data that is due to arrive from the microbiology department within the next two weeks. That gives you a bit of time to prepare.

In PubMed, Google Scholar or both,- find the first study that uses ChIP-Seq- find a recent study that used ChIP-Seq in yeast and has a data set in GEO- find an article that reviews methods for ChIP-Seq analysis and was not published in 'Methods in Molecular Biology'.List the step(s) that led to your finding of this last article.Report studies with the following information:Author(s), Title, Journal, Year of publication, Volume and page numbers

To be submitted latest by Monday, 16th Nov, 10 am to kahokamp@tcd.ie as plain text, Word or PDF document. Please include your name and student number!

Trinity College Dublin, The University of Dublin

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