1. Bin Liu ( 刘滨 ), PhD, Associate Professor Intelligent Computing Research Center Homepage: http://bioinformatics.hitsz.edu.cn/ Homepage: http://bioinformatics.hitsz.edu.cn/ Email: bliu@insun.hit.edu.cnEmail: bliu@insun.hit.edu.cn or binliu@hitsz.edu.cn binliu@hitsz.edu.cn Email: bliu@insun.hit.edu.cnbinliu@hitsz.edu.cn About the papers

2. Course web site http://bioinformatics.hitsz.edu.cn/course/ http://bioinformatics.hitsz.edu.cn/course/ http://bioinformatics.hitsz.edu.cn/course/ Course information, PPT, papers, books, project information can be found on this web site. Course information, PPT, papers, books, project information can be found on this web site.

3. Thank Junjie Chen for constructing this web site http://bioinformatics.hitsz.edu.cn/course/

4. As a master, when you do research on a given topic, you would ask….

5. What should I do? What did other researchers do? How did they do?

6. Medical Literature retrieval Importance ： Literature is an important tool for storing techniques and knowledge, which is very important for research Literature is an important tool for storing techniques and knowledge, which is very important for research Literature is a measure of researchers. Literature is a measure of researchers.

7. 1 、 retrieval methods ： （ 1 ） trace back （ 1 ） trace back （ 2 ） search engine （ 2 ） search engine （ 3 ） Journal website （ 3 ） Journal website

8. PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. PubMed is NCBI gateway to MEDLINE PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. PubMed is NCBI gateway to MEDLINE including more than 4600 medical journals including more than 4600 medical journals Pubmed

9. http://www.ncbi.nlm.nih.gov/pubmed

10. Alcoholic AND disease

11. Advanced search

13. history

17. "Liu Bin" AND ("Harbin Institute of Technology Shenzhen Graduate School”)

20. Other database Elsevier 、 Springer 、 Wiley InterScience 、 BMC 、 Plos 、 WorldSciNet 、 Bentham Science 、 Oxford 、 Nature 、 Physical Review 、 Blackwell Synergy 、 Libertas Academica 、 CNKI 、万方、维普 Elsevier 、 Springer 、 Wiley InterScience 、 BMC 、 Plos 、 WorldSciNet 、 Bentham Science 、 Oxford 、 Nature 、 Physical Review 、 Blackwell Synergy 、 Libertas Academica 、 CNKI 、万方、维普

21. 1. Elsevier Elsevier publishes 250,000 articles a year in 2,000 journals. [1] Its archives contain seven million publications. Total yearly downloads amount to 240 million. Elsevier publishes 250,000 articles a year in 2,000 journals. [1] Its archives contain seven million publications. Total yearly downloads amount to 240 million. [1] http://www.sciencedirect.com/

22. Bioinformatics journals in Elsevier JournalIF Cell31.253 Trends in Genetics 8.659 Journal of Molecular Biology 4.146 Biochemical and Biophysical Research Communications 2.648 FEBS Letters 3.264 Journal of Theoretical Biology 2.454 Gene2.578 Computational Biology and Chemistry 1.837 Biophysical Journal 4.683

23. Bioinformatics journals in Springer JournalIF Amino Acids4.132 Journal of Human Genetics 2.431 Mammalian Genome 2.35 Acta Biotheoretica 0.735 Journal of Mathematical Biology 1.577 Journal of Biosciences 1.703 Chromosome Research 3.405 Journal of Molecular Modeling 2.018

24. http://scholar.google.com/

25. 3. 中国知网 http://edu.cnki.net/ 目前期刊总计 9357 种， 1157300 期，共计文章 36753208 篇。

26. http://www.dlib.cnki.net/kns50/

27. 尧德中

28. Wiley InterScience: Wiley InterScience: http://www3.interscience.wiley.com/cgi- bin/home BMC: open access (OA) BMC: open access (OA)http://www.biomedcentral.com/home/ PloS: (OA) PloS: (OA)http://www.plos.org/ WorldSciNet: WorldSciNet:http://www.worldscinet.com/ Bentham Science: Bentham Science:http://www.bentham.org/ Oxford: Oxford:http://www.oxfordjournals.org/ Nature: Nature:http://www.nature.com/

29. Other Bioinformatics Journals JournalIF Bioinformatics4.328 Nucleic Acids Research 6.878 Briefings in Bioinformatics 4.627 Molecular Biology and Evolution 7.28 DNA Research 3.612 BMC Genomics 3.926 BMC Bioinformatics 3.781 Genome Biology 6.153 PLoS Computational Biology 5.895 PLoS ONE 4.092

30. JournalIF Journal of Computational Biology1.563 Genome Research 10.176 P NATL ACAD SCI USA （ PNAS ） 9.38 Proteins3.419 Journal of Computational Chemistry 3.39 Biopolymers2.823 Nature42.351 Science31.477 生物化学与生物物理进展SCIE 生物物理学报核心 生物信息学核心

31. Biology Letters Comparative and Functional Genomics Genes & Development Journal of biomolecular structure and dynamics Molecular BioSystems Molecular & Cellular Proteomics Journal of Proteome Research The European Physical Journal E Protein & Peptide Letters Molecular Microbiology Current Bioinformatics BMC Systems Biology Current Protein & Peptide Science Analytical Biochemistry proteomics Physical Review E

32. How to access papers Pubmed Pubmed Journal website Journal website Google Google VPN VPN BBS BBS Friends Friends authors authors

33. Reference management

34. Reference management software Reference Manager Reference Manager Endnote Endnote ProCite ProCite BibTeX BibTeX RefWorks RefWorks

35. advantages? as a database as a database Format Format easy insert and delete easy insert and delete

38. How to measure the quality of journal Impact factor Impact factor The impact factor (IF) of an academic journal is a measure reflecting the average number of citations to recent articles published in that journal. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. The impact factor was devised by Eugene Garfield, the founder of the Institute for Scientific Information. Impact factors are calculated yearly starting from 1975 for those journals that are indexed in the Journal Citation Reports. The impact factor (IF) of an academic journal is a measure reflecting the average number of citations to recent articles published in that journal. It is frequently used as a proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. The impact factor was devised by Eugene Garfield, the founder of the Institute for Scientific Information. Impact factors are calculated yearly starting from 1975 for those journals that are indexed in the Journal Citation Reports.

39. How to rate a researcher h-index h-index The h-index is an index that attempts to measure both the productivity and impact of the published work of a scientist or scholar. The index is based on the set of the scientist's most cited papers and the number of citations that they have received in other publications. The h-index is an index that attempts to measure both the productivity and impact of the published work of a scientist or scholar. The index is based on the set of the scientist's most cited papers and the number of citations that they have received in other publications.

40. h-index in Google Scholar

41. How to Read a Scientific Paper

42. Key Topics Types of scientific papers Types of scientific papers Organization of a paper Organization of a paper Actions to take – to properly read a paper Actions to take – to properly read a paper Difficulties in reading scientific papers Difficulties in reading scientific papers

43. Types of Scientific Papers Original article – information based on original research Original article – information based on original research Application notes - describe a specific technique or procedure Application notes - describe a specific technique or procedure Review – detailed analysis of recent research on a specific topic Review – detailed analysis of recent research on a specific topic Editorial – often short review or critique of original articles Editorial – often short review or critique of original articles Letter to the Editor – short & on subject of interest to readers Letter to the Editor – short & on subject of interest to readers Effective Medical Writing. Peh WCG &, NG K H Singapore Medical Journal 2008 49(7) 522 smj.sma.org.sg/4907/4907emw1.pdf (accessed 05 November 2013) smj.sma.org.sg/4907/4907emw1.pdf

44. Organization of a Paper Abstract Abstract Introduction Introduction Methods Methods Results Results Discussion/Conclusions Discussion/Conclusions Acknowledgements Acknowledgements References References Note: most scientific journals follow the format of the Structured Abstract. Occasionally, the Results and Discussion are combined – when the data need extensive discussion to allow the reader to follow the train of logic of the research. Note: most scientific journals follow the format of the Structured Abstract. Occasionally, the Results and Discussion are combined – when the data need extensive discussion to allow the reader to follow the train of logic of the research.

45. Abstract - a summary (~ 150-200 words) of the Abstract - a summary (~ 150-200 words) of the problem, the method, the results and the problem, the method, the results and the conclusions; the reader can decide whether or conclusions; the reader can decide whether or not to read the whole article not to read the whole article Introduction - clearly states the problem being investigated & reasons for the research; summarizes relevant research to provide context; identifies the questions being answered; briefly describes the experiment, hypothesis(es), research question(s) & general experimental design or method Introduction - clearly states the problem being investigated & reasons for the research; summarizes relevant research to provide context; identifies the questions being answered; briefly describes the experiment, hypothesis(es), research question(s) & general experimental design or method

46. Methods - provides the reader enough details so they can understand and replicate the research; explains how the problem was studied; identifies the procedures followed; explains new methodology in detail; includes the frequency of observations, what types of data were recorded, etc. Methods - provides the reader enough details so they can understand and replicate the research; explains how the problem was studied; identifies the procedures followed; explains new methodology in detail; includes the frequency of observations, what types of data were recorded, etc. Results - presents the findings, and explains what was found; shows how the new results are contributing to the body of scientific knowledge; follows a logical sequence based on the tables and figures presenting the findings to answer the question or hypothesis(es) Results - presents the findings, and explains what was found; shows how the new results are contributing to the body of scientific knowledge; follows a logical sequence based on the tables and figures presenting the findings to answer the question or hypothesis(es)

47. Discussion/Conclusions - describes what the results mean regarding what was already known about the subject; indicates how the results relate to expectations and to the literature previously cited; explains how the research has moved the body of scientific knowledge forward; outlines the next steps for further study Discussion/Conclusions - describes what the results mean regarding what was already known about the subject; indicates how the results relate to expectations and to the literature previously cited; explains how the research has moved the body of scientific knowledge forward; outlines the next steps for further study Acknowledgements – recognize various contributions of other workers Acknowledgements – recognize various contributions of other workers References - the sources of previously References - the sources of previously published work; includes information not from published work; includes information not from the experiment and not ‘common knowledge’ the experiment and not ‘common knowledge’

48. Actions to Take Skim the article without taking notes: Skim the article without taking notes: Read the abstract; it will tell you the major findings of the article and why they matter Read the abstract; it will tell you the major findings of the article and why they matter Read first for the ‘big picture’ Read first for the ‘big picture’ Note any terms or techniques you need to define Note any terms or techniques you need to define Jot down any questions or parts you don’t understand Jot down any questions or parts you don’t understand If you are unfamiliar with any of the key concepts in the article, look them up in a textbook If you are unfamiliar with any of the key concepts in the article, look them up in a textbook

49. Re-read the article more carefully especially the ‘methods’ and ‘results/conclusions’ sections: Re-read the article more carefully especially the ‘methods’ and ‘results/conclusions’ sections: Carefully examine the graphs, tables, and diagrams Carefully examine the graphs, tables, and diagrams Try to interpret the data first before reading the captions and details Try to interpret the data first before reading the captions and details Make sure you understand the article fully Make sure you understand the article fully Ask yourself questions about the study, such as: Ask yourself questions about the study, such as: What problems does the study address? Why is it important? Is the method good? Are the findings supported by evidence? Are they unique and supported by other work in the field? What problems does the study address? Why is it important? Is the method good? Are the findings supported by evidence? Are they unique and supported by other work in the field?

50. Write a ‘summary’ of the article Write a ‘summary’ of the article Describe the article in your own words, write down the sentences can be used in your own papers in the future (important for Chinese students) Describe the article in your own words, write down the sentences can be used in your own papers in the future (important for Chinese students) Note the ‘key points’ - purpose of the study/questions asked, assumptions, major findings & conclusions, questions unanswered & any surprises Note the ‘key points’ - purpose of the study/questions asked, assumptions, major findings & conclusions, questions unanswered & any surprises How to Read and Review a Scientific Journal Article Duke University Writing Studio twp.duke.edu/uploads/media_items/scientificarticlereview.original.pdf (accessed 05 November 2013) twp.duke.edu/uploads/media_items/scientificarticlereview.original.pdf

51. Other Useful Hints Draw inferences (a conclusion reached on the basis of evidence and reasoning): Draw inferences (a conclusion reached on the basis of evidence and reasoning): not everything in an article is stated explicitly; rely on your prior knowledge/experience and the background in the article, to draw inferences from the material not everything in an article is stated explicitly; rely on your prior knowledge/experience and the background in the article, to draw inferences from the material Distinguish main points: Distinguish main points: Document level: in title, abstract and keywords Document level: in title, abstract and keywords Paragraph level: look for words/phrases like unexpected, in contrast to previous work, hypothesize that, propose, introduce, data suggests Paragraph level: look for words/phrases like unexpected, in contrast to previous work, hypothesize that, propose, introduce, data suggests

52. Take notes as you read: Take notes as you read: this improves recall and comprehension; you may think you’ll remember everything but details will slip away this improves recall and comprehension; you may think you’ll remember everything but details will slip away develop a template for recording notes on articles develop a template for recording notes on articles can use the structured abstract format (abstract, introduction, methods, results, discussion & conclusions, references) can use the structured abstract format (abstract, introduction, methods, results, discussion & conclusions, references) How to read a scientific article: Mary Purugganan & Jan Hewitt, Rice University www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pd f (accessed 05 November 2013) www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pd f www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pd f

53. Difficulties in Reading Papers Papers can be poorly written Papers can be poorly written Bad writing has consequences for the reader Bad writing has consequences for the reader The reader cannot easily understand what the experiment was The reader cannot easily understand what the experiment was Lack background information or training Lack background information or training

54. Additional Resources Effective Medical Writing. Peh WCG &, NG K H Singapore Medical Journal 2008 49(7) 522 smj.sma.org.sg/4907/4907emw1.pdf Effective Medical Writing. Peh WCG &, NG K H Singapore Medical Journal 2008 49(7) 522 smj.sma.org.sg/4907/4907emw1.pdf smj.sma.org.sg/4907/4907emw1.pdf How to read a scientific article. Mary Purugganan & Jan Hewitt, Rice University www.owlnet.rice.edu/~cainproj/courses/HowToReadSciAr ticle.pdf How to read a scientific article. Mary Purugganan & Jan Hewitt, Rice University www.owlnet.rice.edu/~cainproj/courses/HowToReadSciAr ticle.pdf www.owlnet.rice.edu/~cainproj/courses/HowToReadSciAr ticle.pdf www.owlnet.rice.edu/~cainproj/courses/HowToReadSciAr ticle.pdf How to read a scientific paper. John W. Little & Roy Parker--University of Arizona www.biochem.arizona.edu/classes/bioc568/papers.htm How to read a scientific paper. John W. Little & Roy Parker--University of Arizona www.biochem.arizona.edu/classes/bioc568/papers.htm www.biochem.arizona.edu/classes/bioc568/papers.htm How to read and review a scientific journal article. Duke University Writing Studio twp.duke.edu/uploads/media_items/scientificarticlereview. original.pdf How to read and review a scientific journal article. Duke University Writing Studio twp.duke.edu/uploads/media_items/scientificarticlereview. original.pdf twp.duke.edu/uploads/media_items/scientificarticlereview. original.pdf twp.duke.edu/uploads/media_items/scientificarticlereview. original.pdf