Professional Development Course 1 – Molecular Medicine June 06, 2013
description
Transcript of Professional Development Course 1 – Molecular Medicine June 06, 2013
![Page 1: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/1.jpg)
Professional Development Course 1 –Molecular Medicine
June 06, 2013
Ansuman Chattopadhyay, PhDHead, Molecular Biology Information ServicesHealth Sciences Library SystemUniversity of [email protected]
http://www.hsls.pitt.edu/guides/genetics
![Page 2: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/2.jpg)
http://www.hsls.pitt.edu/molbio
HSLS Molecular Biology Information Service
![Page 3: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/3.jpg)
• 1990-1996University of Nebraska-LincolnPhD. in BiochemistryProtein synthesis initiation in eukaryotic system
• 1997-2001Vanderbilt University School of Medicine, NashvilleResearch FellowEpidermal Growth Factor (EGF) mediated signal transduction
• 2001-2002Cellomics Inc., PittsburghKnowledge Engineer
• 2002- 2006Information Specialist in Molecular Biology and GeneticsHSLS, University of Pittsburgh
Ansuman Chattopadhyay, [email protected]
• 2006- PresentHead, Molecular Biology Information ServiceHSLS, University of Pittsburgh
http://www.hsls.pitt.edu/molbio
![Page 4: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/4.jpg)
HSLS Molecular Biology Information Service
Workshops
Website
Software Licensing
Bioinformatics Consultations
http://www.hsls.pitt.edu/molbio
![Page 5: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/5.jpg)
June 06:Literature InformaticsBioinformatics Search Engines
June 13:Genome Browsers
http://www.hsls.pitt.edu/molbio
![Page 6: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/6.jpg)
ED Green et al. Nature 470, 204-213 (2011) doi:10.1038/nature09764
Genomic achievements since the Human Genome Project
![Page 7: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/7.jpg)
Genome Sequencing Cost
$0.40
![Page 9: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/9.jpg)
Growth of PubMed Citations
Lu et al. Database (Oxford). 2011: baq036
240 K
• Breast Cancer
97K • Schizophrenia
8.7K • BRCA1
61K. p53
Feb 28th 2012
http://www.hsls.pitt.edu/molbio
![Page 10: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/10.jpg)
Literature Informatics
http://www.hsls.pitt.edu/guides/genetics
![Page 11: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/11.jpg)
Literature Informatics
Learn how to
.. find the most appropriate literature
.. mine the literature
.. manage your collected information
.. browse the scientific papers
http://www.hsls.pitt.edu/molbio
![Page 12: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/12.jpg)
Literature Informatics
Comprehensive search: MESH term based PubMed Search PubMed special topics query
Next-generation literature search tools: GoPubMed, eTBlast Quertle HuGE Navigator
http://www.hsls.pitt.edu/molbio
![Page 13: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/13.jpg)
Literature Informatics
Find published literature with statistical and numerical data on DENGUE OUTBREAKS in India.
What genes are reported to be associated with the disease SCHIZOPHRENIA?
http://www.hsls.pitt.edu/molbio
![Page 14: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/14.jpg)
Searching PubMed
http://www.hsls.pitt.edu/molbio
![Page 15: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/15.jpg)
Literature Informatics
Citations: 20 millionJournals: 5200
Schizophrenia: 103,512Schizophrenia gene: 8341
Dengue outbreaks in India: 381 Dengue outbreaks statistics India: 27
http://www.hsls.pitt.edu/molbio
![Page 16: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/16.jpg)
Challenges
Am I getting everything / the right things?
How to digest this?
http://www.hsls.pitt.edu/guides/genetics
![Page 17: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/17.jpg)
PubMed Search
Am I getting the right things?
Construct PubMed queries with MeSH terms using MeSH browser
http://www.hsls.pitt.edu/guides/genetics
![Page 18: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/18.jpg)
Medical Subject Headings (MeSH)
http://www.hsls.pitt.edu/guides/genetics
The U.S. National Library of Medicine's controlled vocabulary (thesaurus)
Arranged in a hierarchical manner called the MeSH Tree Structures
Updated annually
http://www.nlm.nih.gov/mesh/meshhome.html
![Page 19: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/19.jpg)
MeSH Vocabulary Headings
over 24,000 representing concepts found in the biomedical literature (Body Weight, Kidney, Radioactive Waste)
Subheadings attached to headings to describe a specific aspect of a
concept (adverse effects , metabolism, diagnosis, therapy)
Supplementary Concept Records over 172,000 terms in a separate chemical thesaurus -
updated weekly (cordycepin , valspodar , tacrolimus binding protein 4)
Publication Types(Letter, Review, Randomized Controlled Trial)
http://www.hsls.pitt.edu/guides/genetics
![Page 20: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/20.jpg)
MeSH Tree Structure A. Anatomy
B. OrganismsC. DiseasesD. Chemical and DrugsE. Analytical, Diagnostic and
Therapeutic Techniques and EquipmentF. Psychiatry and PsychologyG. Biological SciencesH. Physical SciencesI. Anthropology, Education,
Sociology and Social PhenomenaJ. Technology and Food and BeveragesK. Humanities L. Information Science M. Persons N. Health CareV. Publication Characteristics Z. Geographic Locations
http://www.hsls.pitt.edu/guides/genetics
![Page 21: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/21.jpg)
MeSH Indexing
http://www.hsls.pitt.edu/guides/genetics
Source: NLM
![Page 24: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/24.jpg)
PubMed Search
Retrieve published articles
on Dengue outbreaks in India
including Statistical and numerical data on dengue
outbreaks
http://www.hsls.pitt.edu/guides/genetics
![Page 25: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/25.jpg)
PubMed Query Using MeSH http://www.ncbi.nlm.nih.gov/mesh
http://www.hsls.pitt.edu/molbio
![Page 26: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/26.jpg)
http://www.hsls.pitt.edu/molbio
Find articles on “Dengue outbreaks in India” by searching PubMed using MeSH terms
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/mesh.swf
Resources
• Mesh Browser : http://www.ncbi.nlm.nih.gov/mesh• PubMed: http://www.ncbi.nlm.nih.gov/pubmed
![Page 27: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/27.jpg)
PubMed Query Using MeSH
http://www.hsls.pitt.edu/guides/genetics
![Page 28: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/28.jpg)
PubMed Query Using MeSH
http://www.hsls.pitt.edu/guides/genetics
![Page 29: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/29.jpg)
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
![Page 30: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/30.jpg)
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
![Page 31: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/31.jpg)
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
![Page 32: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/32.jpg)
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
![Page 33: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/33.jpg)
Building a PubMed Query
http://www.hsls.pitt.edu/guides/genetics
![Page 34: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/34.jpg)
Building PubMed QueriesTerm Boolean Term Boolean Term # papers
Dengue AND Outbreaks 823
Dengue * AND Outbreaks 746
Dengue AND Outbreaks AND India 123
Dengue* AND Outbreaks AND India 116
Dengue AND Outbreaks/statistics and numerical data
AND India 7
Dengue* AND Outbreaks/statistics and numerical data
AND India 7
http://www.hsls.pitt.edu/guides/genetics
![Page 35: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/35.jpg)
Useful Links for MeSH
MESH Browser: http://www.ncbi.nlm.nih.gov/mesh
18 ways to improve your Pubmed searches by Carrie Iwema http://bitesizebio.com/2008/03/05/18-ways-to-improve-your-pubmed-s
earches/
Searching by using the MeSH Database. NCBI Handbook : http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part
=pubmedhelp#pubmedhelp.Searching_by_using_t
http://www.hsls.pitt.edu/guides/genetics
![Page 36: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/36.jpg)
PubMed Query
What genes are reported to be associated with the disease SCHIZOPHRENIA ?
Topic-Specific PubMed Queries
http://www.hsls.pitt.edu/guides/genetics
![Page 37: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/37.jpg)
Topic-Specific PubMed Querieshttp://www.nlm.nih.gov/bsd/special_queries.html
http://www.hsls.pitt.edu/guides/genetics
![Page 38: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/38.jpg)
http://www.hsls.pitt.edu/molbio
Find genes that are reported to be associated with the disease SCHIZOPHRENIA by searching PubMed
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/scz.swf
Resources
• PubMed Clinical Queries: http://www.ncbi.nlm.nih.gov/pubmed/clinical
![Page 39: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/39.jpg)
Research on Optimal Search Strategies
http://www.hsls.pitt.edu/molbio
![Page 40: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/40.jpg)
PubMed Special Topic Queries
http://www.hsls.pitt.edu/molbio
![Page 42: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/42.jpg)
PubMed Search Filter: Medical Genetics ("schizophrenia"[MeSH Terms] OR
"schizophrenia"[All Fields]) AND (("genetics, medical"[MeSH Terms] OR ("genetics"[All Fields] AND "medical"[All Fields]) OR "medical genetics"[All Fields] OR ("medical"[All Fields] AND "genetics"[All Fields])) OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR "genetics"[Subheading] AND ("genetics"[Subheading] OR "genetics"[All Fields] OR "genetics"[MeSH Terms]))
http://www.hsls.pitt.edu/molbio
![Page 43: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/43.jpg)
Topic-Specific PubMed Queries
![Page 44: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/44.jpg)
PubMed Search Result Display
http://www.hsls.pitt.edu/molbio
How to digestthis?
![Page 45: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/45.jpg)
Data Mining-Knowledge Discovery
http://www.hsls.pitt.edu/molbiohttp://www.hsls.pitt.edu/molbio
![Page 46: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/46.jpg)
Next-Generation Literature Search Tools
![Page 47: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/47.jpg)
PubMed based Tools
http://www.hsls.pitt.edu/molbio
Lu et al. Database (Oxford). 2011; 2011: baq036
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/
![Page 48: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/48.jpg)
Latest Innovations in Literature Searching
GoPubMed Display search results sorted into meaningful topics and subtopics
http://www.hsls.pitt.edu/molbio
![Page 49: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/49.jpg)
GoPubMed
http://www.hsls.pitt.edu/molbio
www.gopubmed.com
![Page 50: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/50.jpg)
http://www.hsls.pitt.edu/molbio
Find genes that are reported to be associated with the disease SCHIZOPHRENIA by using GoPubMed
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/gopubmed.swf
Resources
• GoPubMed: http://www.gopubmed.org/web/gopubmed/2?WEB10O00h00100090000
![Page 52: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/52.jpg)
GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/molbio
![Page 53: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/53.jpg)
GoPubMed Search Result Analysis
http://www.hsls.pitt.edu/molbio
![Page 54: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/54.jpg)
Latest Innovations in Literature Searching
http://www.hsls.pitt.edu/molbio
![Page 55: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/55.jpg)
GoPubMed
Noteworthy links
GoPubMed: exploring PubMed with the Gene Ontology. Doms A,Schroeder M., Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue):W783-6. http://www.ncbi.nlm.nih.gov/pubmed/15980585
http://www.hsls.pitt.edu/molbio
![Page 56: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/56.jpg)
PubMed driven Web Tools
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/
http://www.hsls.pitt.edu/molbio
![Page 57: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/57.jpg)
PubMed based Tools
http://www.hsls.pitt.edu/molbio
Lu et al. Database (Oxford). 2011; 2011: baq036
http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search/
![Page 58: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/58.jpg)
Extract gene list from Literature
http://www.hsls.pitt.edu/molbio
http://www.quertle.info/
![Page 59: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/59.jpg)
Questions for Quertle
What genes cause Asthma? What cell lines are used in diabetes research? Which cell types are known to express EGFR? What animals are used in studies for diabetes? Which protein kinases activate TP53?
http://www.hsls.pitt.edu/molbio
![Page 60: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/60.jpg)
http://www.hsls.pitt.edu/molbio
A short video on Quertle
Link to the video tutorial:http://media.hsls.pitt.edu/media/molbiovideos/quertle-ac0212.swf
Resources
• Quertle: www.quertle.info
![Page 61: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/61.jpg)
Search Engine for NIH funded research http://projectreporter.nih.gov/reporter.cfm
http://www.hsls.pitt.edu/molbio
![Page 62: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/62.jpg)
NIH Grant Applications to Gene List
http://www.hsls.pitt.edu/molbio
![Page 63: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/63.jpg)
MESH GoPubMed Quertle
![Page 64: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/64.jpg)
Search Engine for finding
Disease Causing Genes
![Page 65: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/65.jpg)
Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/molbio
![Page 66: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/66.jpg)
http://www.hsls.pitt.edu/molbio
Find human genes reported to be associated with Asthma
Find human SNPs reported to be associated with Asthma
Link to the video tutorial:http://media.hsls.pitt.edu/media/clres2705/asthma.swf
Resources
• HugeNavigator:
http://hugenavigator.net/HuGENavigator/home.do
![Page 67: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/67.jpg)
GWAS Catalog http://www.ebi.ac.uk/fgpt/gwas/#timeseriestab
http://www.hsls.pitt.edu/molbio
![Page 68: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/68.jpg)
Search Engine Just for Human Genetics
http://www.hsls.pitt.edu/molbio
![Page 69: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/69.jpg)
Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/molbio
![Page 70: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/70.jpg)
Search Engine Just for Human Geneticshttp://hugenavigator.net/HuGENavigator/huGEPedia.do
http://www.hsls.pitt.edu/molbio
![Page 71: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/71.jpg)
Search Engine Just for Human GeneticsCDC HuGENavigator : http://hugenavigator.net/
http://www.hsls.pitt.edu/molbio
![Page 72: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/72.jpg)
Find Disease Causing SNPs
What SNPs are associated with “Schizophrenia”?
http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do
http://www.hsls.pitt.edu/molbio
![Page 73: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/73.jpg)
Hands On
Search PubMed and retrieve a list of genes that can serve as biomarkers for Alzheimer Disease
![Page 74: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/74.jpg)
Software for Finding Similar Texts in Published Literature
![Page 75: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/75.jpg)
Text-based Similarity Search Tools
Search Box:
http://www.hsls.pitt.edu/molbio
![Page 76: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/76.jpg)
Text Similarity Search Tools
eTBLASThttp://etest.vbi.vt.edu/etblast3/
http://www.hsls.pitt.edu/molbio
![Page 77: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/77.jpg)
Text Similarity Search Tools
eTBLAST
http://www.hsls.pitt.edu/molbio
![Page 78: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/78.jpg)
Text Similarity Search Tools
http://www.hsls.pitt.edu/molbio
![Page 79: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/79.jpg)
Déjà Vu: a Database of Highly Similar Citationshttp://dejavu.vbi.vt.edu/dejavu/duplicate/
http://www.hsls.pitt.edu/molbio
![Page 81: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/81.jpg)
Automated email Notification Tool
http://www.ncbi.nlm.nih.gov/sites/myncbi/
Save your searches at My NCBI and set up an email notification on new publication based on your search query
http://www.hsls.pitt.edu/molbio
![Page 85: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/85.jpg)
Reference Management Tools
Connotea
CiteULike
Mendaley
Zotero
online
downloadable
Scientific Research Papers
Web pages
EndNoteRefworks
http://www.hsls.pitt.edu/molbio
![Page 86: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/86.jpg)
PDF Reader
http://www.hsls.pitt.edu/molbio
![Page 87: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/87.jpg)
HTML Vs PDF
![Page 88: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/88.jpg)
ReadCube
Utopia Docs
![Page 90: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/90.jpg)
NextGen PDF Reader: Utopia docs
http://www.hsls.pitt.edu/molbio
![Page 91: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/91.jpg)
Utopia DocsPMID: 22683712
![Page 92: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/92.jpg)
READCUBE
READCUBE MEDIA FILE
MendeleyEndNote
Utopia Docs
![Page 93: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/93.jpg)
Search Engine for Life Scientists
http://www.hsls.pitt.edu/molbio
![Page 94: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/94.jpg)
Search Engine
Horizontal Vertical
![Page 96: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/96.jpg)
Molecular Databases
Nucleic Acids Research : Annual databases Issue NAR: Annual Web Server Issue Oxford Journal : Bioinformatics BioMedCentral: BMC Bioinformatics
http://www.hsls.pitt.edu/molbio
Growth of bioinformatics tools
![Page 97: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/97.jpg)
Biomedical & Life Sciences Search Engines
OBRC : University of Pittsburgh
http://www.hsls.pitt.edu/molbio/obrc
Bioinformatics.cahttp://bioinformatics.ca/links_directory/
OReFil : University of Tokyo
http://orefil.dbcls.jp/
http://www.hsls.pitt.edu/molbio
![Page 98: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/98.jpg)
Peptide Sequence >nxp|NX_P00533-1|EGFR|Epidermal growth factor receptor|Iso 1
MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC TGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV
APQSSEFIGA
P P P P? ? ? ? ?
S Y Y T S
P
![Page 99: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/99.jpg)
http://www.hsls.pitt.edu/molbio
Search for bioinformatics ResourcesLocate online tools that predict phosphorylation sites in a protein sequence.
Link to the video tutorial:http://media.hsls.pitt.edu/media/Search%20Bioinfo%20Resoursec.swf
Resources
• Search.HSLS.MolBio :
![Page 100: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/100.jpg)
Life Sciences Search Enginehttp://www.hsls.pitt.edu/molbio/
http://www.hsls.pitt.edu/molbio
![Page 101: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/101.jpg)
Hands on
(a) Locate two online databases on microRNA targets, and report their URLs.
(b) Identify one database that store all HIV inhibiting siRNA data and cite its URL.
(c) Cite a paper offering a step-by-step guide
for analyzing ChIP-seq data.
![Page 102: Professional Development Course 1 – Molecular Medicine June 06, 2013](https://reader034.fdocuments.in/reader034/viewer/2022051316/56815a4e550346895dc78145/html5/thumbnails/102.jpg)
Thank you!Any questions?
http://www.hsls.pitt.edu/molbio