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Loading Entrez Gene (Entire)
Too slow - < 200,000 out of 1 million+ genes loaded in > 1 week
TODO: Distribute - cut file into smaller pieces, then parse/load independently
Implementation:...
Gene Symbol/ID Converter
Presented slides on cardboard of preliminary results.
Abstract
Computational analysis of the interconnections between annotated biomedical literature data and gene databases allows the prediction...
Poster for CFRI Student Research Forum, Thursday, June 21st, 2007.
Abstract due Thursday, May 17th, 2007.
Presented the CGDN Poster
Mining Transcription Factor-Disease Relationships for Novel...
Presented at the Genetics and Bioinformatics Retreat December 5th, 2007.
Presented at Advancing Interdisciplinarity (CFIS Symposium) November 30th, 2007.
Presented at the CFRI Student Research...
Via Entrez Map Viewer
Looks like we can call the map viewer to extract what we want (and probably download it to get what we need if we need to checkpoint it…)
URLs constructed like so, where you...
Instructor
Dr. Ghassan Hamarneh
Summary
Topics in image analysis (segmentation, registration)
Advanced techniques...
To be held Nov 24, 2008 at 12:00PM noon.
Room 3027 of the CMMT
950 West 28th Avenue
Vancouver, B.C., V5Z 4H4
Canada
Comments from the Committee Meeting
Mark Wilkenson from iCapture
OMIM references...
Servers
sonoma.cmmt.ubc.ca
Databases hosted
pubmed
Pubmed 2008 Baseline load
Table pubmed: holds pubmed IDs to titles relation
Table pubmed_mesh: holds pubmed ID to mesh term relation
Table...
Please change this page according to your needs
CIHR/MSFHR Bioinformatics Training Program
Audited Courses
MEDG 520
Lorincz (Coordinator), Advances in Human Molecular Genetics
Fall 2007
Required Courses
MBB 659 / GENE 501
Ouellette and...
Indirect Gene-Disease Association via Medical Subject Term Annotation of Literature Evidence
Final poster PDF aka There Is No Step 5 - cscbc2009-poster.pdf
Abstract
Computational analysis of the...
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Table of Contents
Academic Background and Training
Work Experience
Distinctions and Credentials
Awards
Publications
Posters and Presentations
Review
Volunteer
Research Interests
Mr....
Working Title
Integrated Database Evidence Search and Evaluation System for Disease-related Transcription Factors
Lay Summary
The...
Basic Data Model
Current, we have Genes, PubMed and Diseases, for preliminary first-pass data model
PubMed MeSH Annotation
MeSH Fact Sheet (@NLM)
Principles of MeSH Subject Indexing
Medline Online Indexing Course
Changes in the Treatment of Chemical Data in MEDLINE: Details on the role of...
Preliminary Data Source Diagram
MeSH term annotate relevant
Neuronames stats
UMLS relevant sections
Brain
GENSAT
Allen Brain Atlas
proprietary interface
Disease
OMIM
downloaded (Feb 2007)
Medical Reference
Robbins...
Focus
genes
disease
genetic basis for disease
transcription factor
gene regulation
prediction of transcriptional gene regulation in disease
Data Integration
Don Swanson - speech and...
If you are allowed to edit pages in this Site, simply click on edit button at the bottom of the page. This will open an editor with a toolbar pallette with options.
To...
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Table of Contents
MySQL LOAD DATA LOCAL INFILE
Chemical Terms
Gene-MeSH and Disease-MeSH profiles
UMLS Co-occurrence loading
Entrez EUtils Data Parsing in Unicon
TODO
mesh_child
Local...
Who can join?
Open Access for all. Please edit responsibly, and note the license below.
Join!
The password is
Open Access
Instructors
Francis Ouellette
Dr. Frederic Pio
Summary
Seminar course
Recent topics in bioinformatics,...
Instructor
Dr. Dipankar Sen
Summary
Overview of techniques (digestion assays, mutation, luciferase constructs, SELEX) and role of...
Instructor
Dr. Fiona Brinkman
Summary
covers core bioinformatics concepts and tools
Presentation...
Getting Database Size
echo "SELECT TABLE STATUS" | mysql-dbrc //database// | awk '{sum=sum+$7+$9;} END {print sum/1024/1024 "M"}'
Add an Index
ALTER TABLE table_name ADD INDEX (fields to...
Cited by
http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4563023
http://en.wikipedia.org/wiki/Netflix_Prize
Given the 1 to 5 star grade of some films by a set of users <user, movie, date of grade, grade> [training set]
Predict the star grade of other...
Requirements
A bioinformatics thesis is:
computational analysis of biological sequences or other associated biological data, to investigate a biological question
derivation of new algorithmic...
TiGER: a database for tissue-specific gene expression and regulation
http://www.biomedcentral.com/1471-2105/9/271/abstract
Whole genome oPossum co-occurrence analysis - look for overrepresented...
Continuing work on the n-dimensional Scale Invariant Feature Transform Filter for ITK
Things to Add/Change
Adding a Noise filter (itkGaussianNoise ?)
Update/more verbosity on the multimodality...
Guiding Statement
I propose a system for discovery and evaluation of evidence-supported relationships between genes and diseases. The focus of this research will be on linking human transcription...
module "wiki/pagestagcloud/PagesListByTagModule"
More content as I actually think of something to add.
Swing Dancing
Mining Brain-Related Transcription Factor-Disease Relationships for Novel Linkages
Overview of PhD Research
PhD Research Proposal - Summer 2007
Committee Meeting - Fall 2008
Blog and Meeting...
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Table of Contents
Abstract
Introduction
Motivation
Goals
Open Access
Integrated, Unified Repository
Efficient Programmatic Framework
Exploration of Gene-Disease Relationships
Example...
Ph.D. Comprehensive Qualifying Exam - Passed August 9 2007
Final Release to Committee July 31, 2007
Current
Warren-Proposal-Mining-TF-Genes-Disease-2007-08-13Corrected.doc: Minor corrections...
Details on gene-profile to disease profile comparisons will go here.
For now, here's the a pdf slideshow with sample results: WIP-2008-06-05.pdf
For the terms in common between the gene profile...
Author Information in PubMed
authors are listed in order as per article (au field)
Last (or last few) authors are likely the primary investigators
limits (et al.) were used for articles during a...
Flags and Lollipops Open Lab...
Research Interests
I am interested in computer science techniques for biological knowledge discovery in large datasets, particularly theoretical aspects of algorithm design and optimization. More...
Implementation Details
GeneRIF vs Gene2Pubmed
watson
302091 GeneRIFs, 12453338 Gene2Pubmed
Overlap is 301690 (missing 401 GeneRIFs)
chickenwire wcdb
189629 GeneRIFs, 3223895...
Running in batch mode
For an R script file plot.R, session output put into output.txt
R CMD BATCH plot.R output.txt
Labelling Graphs
the parameters main="main title", xlab="x-axis label",...
Alzheimer Disease (MeSH profile) (disease BG)
Acetylcholine , Acetylcholinesterase , Acetyltransferases , Acridines , Activities of Daily Living , Acyltransferases , Adult , Age Groups , Age of...
Gene ID 1 A1BG alpha-1-B glycoprotein
1|Amino Acids, Peptides, and Proteins|1|1|4140771|12738681|0
1|Animals|1|1|13088183|3791269|0
1|Biochemical Phenomena|1|1|1663930|15215522|0
1|Biochemical...
Profiles
Sample Disease Profiles
Sample Gene Profiles
Validation Results with NEJM articles
Other numbers
38605 Human Genes
10180 MeSH Disease terms
Data Sources
MeSH 2008
PubMed...
Indirect Gene-Disease Association via Medical Subject Term Annotation of Literature Evidence
Warren A Cheung, BF Francis Ouellette, Wyeth W Wasserman
Bioinformatics Program, University of British...
Current
NSERC Postgraduate Scholarship D - 3 years (PGS D3)
Previously Held
NSERC Undergraduate Student Research Award (Summer 2002)
Previously Offered
Applications Completed - 2008...
P-values for significance of terms
For a given term and disease: Given that there are n articles cited by the gene and N articles in PubMed, and given that k of the cited articles have the disease...
Loop through lines of a file
while read line ; do
echo $line
done < infile
Put a program into background, do not terminate even if logged out
nohup nice program &
Recent posts
Forum
Contents
Welcome page
Research
PhD-Research
Blogs
DNAHelix (Research Log)
TwinRAM.com (Personal)
Admin
How to join this site?
Site members
Recent changes
List all...
Members:
Moderators
Admins
Instructor
Dr. Raphael Gottardo
From the Syllabus
Administrative Information
Times: MW 1:30-3:00
Place: LSK...
Using Hypergeometric Distribution to compute P-values
Using R statistical package, phyper()
Hypergeometric Distribution Model
white balls = pmids marked with a particular MeSH term (m)
black...
Abbreviations
NLM: National Library of Medicine
NCBI: National Center for Biotechnology Information
NIH: National Institutes of Health
Disease
Disease:
abnormality of the human body or...
People of Swing
Because I can't remember names for the life of...
Winter 2009 (Jan-Apr) - CPSC 445 (Algorithms in Bioinformatics)
Summer 2005 (June-July) - CPSC 304 (Introduction to Databases)
Summer 2005 (May-June) - CPSC 314 (Introduction to Computer...
Lots of different data sources, with lots of different formats. Common formats being dealt with are delimited text and XML.
Delimited text
can use piped shell commands (or KNIME)
Piped Shell...
Gene ID
Last Name
Gene2PubmedReferences (2003 or more recent)
Gene2Pubmed Links
AHR (196)
Perdew
2
ER alpha-AHR-ARNT protein-protein interactions mediate estradiol-dependent transrepression of...
Gene ID
Last Name
Gene2PubmedReferences (2003 or more recent)
Gene2Pubmed Links
CEBPE (1053)
Koeffler
3
C/EBPepsilon interacts with retinoblastoma and E2F1 during granulopoiesis.(Cedars-Sinai...
Gene ID
Last Name
Gene2PubmedReferences (2003 or more recent)
Gene2Pubmed Links
NR1I3 (9970)
Goldstein
2
The nuclear receptors constitutive androstane receptor and pregnane X receptor...
First 250 Results - TF Author - Next 210 Results
TF Author - AHR to NR1I2 - TF Author - NR1I3 to ZHX1
Gene ID
Last Name
Gene2PubmedReferences (2003 or more recent)
Gene2Pubmed Links
TP53...
Notes:
CART1 = ALX1
CHX10 = VSX2
CREG = CREG1
CUTL1 = CUX1
CUTL2 = CUX2
DACH = DACH1
DLX7 = DLX4
E2FS = ???
EHOX = ???
FALZ = BPTF
FOXE2 = FOXE1
FOXF1A = Mouse?
FOXG1B = FOXG1
Gene EntrezGene
AHR...
May 2: Committee Meeting at the CMMT
Mid-May: Draft of the Proposal
End-May: Release Candidate, Proposal
August 9th: Qualifying Exam (!!)
Research
Curriculum Vitae
Courses
Teaching Assistant
Scholarships
DNAHelix Blog
Personal
Twinram.com Blog
contact
Use cumulative gains chart as per http://www2.cs.uregina.ca/~hamilton/courses/831/notes/lift_chart/lift_chart.html
y axis - percentage of positive responses == TP / TP+FN == true positive rate
x...
Gene
MeSH Disease Term
Score
gene2pubmed
APOE (348)
Amino Acid Metabolism, Inborn Errors
-13320.2132268
11844848 Plasma homocysteine as a risk factor for dementia and Alzheimer's...
Welcome to DNAHelix.org, wiki publishing platform for Warren Cheung. My blog will continue to be available at Twinram.com
Warren Cheung is a PhD Student at the University of British Columbia, in...
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A Wiki ([ˈwiː.kiː] <wee-kee> or [ˈwɪ.kiː] <wick-ey>) is a type of website that allows...
