1. Trinity College Dublin, The University of Dublin GE3M25: Bioinformatics Karsten Hokamp, PhD Genetics TCD, 05/11/2015

2. Trinity College Dublin, The University of Dublin GE3M25 Data Handling Module Content Python Programming Bioinformatics ChIP-Seq analysis

3. Trinity College Dublin, The University of Dublin GE3M25 Data Handling Module Content Python Programming Bioinformatics ChIP-Seq analysis Evaluation: 1.Weekly tasks 2.Project report

4. Trinity College Dublin, The University of Dublin Overview PubMed Google Scholar Comparative search Extra features Weekly task http://bioinf.gen.tcd.ie/GE3M25/

5. 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

6. Trinity College Dublin, The University of Dublin PubMed  Part of Entrez Search System at NCBI

7. Trinity College Dublin, The University of Dublin PubMed Search

8. Trinity College Dublin, The University of Dublin PubMed Search Explore menu options and filters!

9. Trinity College Dublin, The University of Dublin PubMed Search, Refinement

10. Trinity College Dublin, The University of Dublin Medline Tags https://www.nlm.nih.gov/bsd/mms/medlineelements.html

11. Trinity College Dublin, The University of Dublin Medline Tags

12. Trinity 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

13. Trinity 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?

14. Trinity College Dublin, The University of Dublin Kavanagh T Bracken A Bradley D Campbell M Devine K Fares M Farrar J Humphries P Labrador J Martin S McConnell D McLysaght A Mitchell K Ramaswami M Wellmer F DeArce M Hokamp K McDermott P "Trinity College Dublin" [Affiliation] + combine with () OR () AND ("2015/01/01"[PDAT] : "2015/12/31"[PDAT]) range operator PubMed Search, Genetics Department 2015

15. 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])

16. Trinity College Dublin, The University of Dublin Google Scholar Search https://scholar.google.com

17. Trinity College Dublin, The University of Dublin Google Scholar Search

18. 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.

19. Trinity College Dublin, The University of Dublin Google Scholar – Author Profiles

20. Trinity College Dublin, The University of Dublin Google Scholar – Advanced Search Click arrow in search box

21. 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.

22. Trinity College Dublin, The University of Dublin Searching for the origin of 'ohnologues'

23. 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)

24. Trinity College Dublin, The University of Dublin Searching for the origin of 'ohnologues'

25. Trinity College Dublin, The University of Dublin Programming Concepts Search for Ohnologues

26. Trinity College Dublin, The University of Dublin Programming Concepts Search for Ohnologues

27. Trinity College Dublin, The University of Dublin Programming Concepts Search for Ohnologues

28. Trinity College Dublin, The University of Dublin Searching for the origin of 'ohnologues'

29. Trinity College Dublin, The University of Dublin Google Scholar vs other Resources

30. Trinity College Dublin, The University of Dublin Other resources Scholarometer http://scholarometer.indiana.edu Web of Science https://apps.webofknowledge.com Scopus: http://www.scopus.com PubCrawler http://www.pubcrawler.ie

31. Trinity 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!

32. Trinity College Dublin, The University of Dublin Don't forget to log out!