trinity college dublin, the university of dublin ge3m25: bioinformatics karsten hokamp, phd genetics...
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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
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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'
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Google Scholar vs other Resources
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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 [email protected] 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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