about medical profession

stop pagin me

nice articles

population-based case-control teratologic study of oral erythromycin treatment during pregnancy
hungarian authors, nice language. methods.

gwas, framingham

gwas for subclinical AS (IMT, CAC, AAI) - 100K, no genome wide significance

cf its related.
- echocardiography measurements, brachial endothelial function, stress ecgňň
- biomarkers
- hemostatic markers

matching

1. Q: to match or not to match?
A: it depends - what study design?
a) advantages
b) disadvantages

2. how to match - types of matching
a) frequency matching
b) individual

in case-control studies - Does the ratio case vs control 1:n matter? the more the better?

overmatching - cf twin studies?

terms:
counter-matching - *********counter-matching Langholz 2001, 2005
flexible matching
optimal ?
propensity score matching

matching in genetic association studies
- aim - to avoid population stratification ???
genomic control
admixture

blogtips

1. to include relevance of the link, type a number of asterisks (****) immediately in front of the link .
e.g. *********counter-matching Langholz 2001, 2005


http://kucej.blog.sme.sk/

statistics elementar courses

EPBI 431 - STATISTICAL METHODS IN BIOLOGICAL & MEDICAL SCIENCES I
ppt presentations of basic concepts

genetic epidemiology

genetic epidemiology , Khoury 1997 , book,

statistics in HLA epidemiology DORAK !!!!!!!!

cf aj recent scientific statement of AHA

genetic association, population substructure, admixture

The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases
A Geert Heidema1,4 , Jolanda MA Boer1 , Nico Nagelkerke2 , Edwin CM Mariman3 , Daphne L van der A1 and Edith JM Feskens1,4

Ethnicity, Ancestry, and Race in Molecular Epidemiologic Research
*
Genetic structure in four West African population groups
**
Genetic Admixture among Hispanics and Candidate Gene Polymorphisms: Potential for Confounding in a Breast Cancer Study?
**



nih grants, gwa
*
genetics 2006
A General Population-Genetic Model for the Production by Population Structure of Spurious Genotype–Phenotype Associations in Discrete, Admixed or Spatially Distributed Populations
*
bertram JCI 2005
The genetic epidemiology of neurodegenerative disease
*
genetic epidemiology - respiratory diseases - nice comments (from Villejuif, Paris)
*
gen epid - psychiatry - nice remarks (2000)
*
2005 Markus, Dichgans
Genetic Association Studies in Stroke
Methodological Issues and Proposed Standard Criteria
cdc
Clinical Application of Genetic Risk Assessment Strategies for Coronary Artery Disease: Genotypes, Phenotypes, and Family History

*
genetic approaches to CAD
inc. multistage design

*
artificial intelligence chapter 1

Family-Based versus Unrelated Case-Control Designs for Genetic Associations
*
1983
GUIDELINES FOR THE STUDY OF GENETIC EFFECTS IN HUMAN POPULATIONS
inchem, WHO

* 2006
International Conference on Environmental Epidemiology & Exposure
*

software, genetic association studies

PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Carlo significance testing.

observational studies, reporting

http://www.strobe-statement.org/.

Strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies.

cf article in BMJ





interpretation of observational studies BMJ 1994

case control matching, genetic association studies

role of matching in epidemiologic studies pdf

inverse sampling Keogh 2007 IJE http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxm019v1

Matching BMJ Stat notes - Bland, Altman 1994
and letter

optimal matching software - stat packages SAS, R (bipartite)

Journal of Statistical Software by Sekon - 47pp - 2007

Goldstein , Andrieu 1999 on detection of interaction GE - discusses COUNTERMATCHING method

Flexible Matching Strategies to Increase Power and Efficiency to Detect and Estimate Gene-Environment Interactions in Case-Control Studies.
Original Contributions American Journal of Epidemiology. 155(7):593-602, April 1, 2002.Sturmer, Til 1,2; Brenner, Hermann 1,2
Abstract: Lack of power is a pertinent problem in many case-control studies of gene-environment interactions. The authors recently introduced the concept of flexible matching strategies with varying proportions of a matching factor among selected controls (degree of matching) to increase the power and efficiency of case-control studies. In this study, they extended the concept of flexible matching strategies to the field of gene-environment interactions. They assessed the power and efficiency of such studies to detect and estimate gene-environment interactions under a variety of assumptions regarding the prevalence and effects of the environmental exposure and the genetic susceptibility as well as their association in the population. For each set of parameters, 10,000 case-control studies were simulated using varying degrees of matching. Traditional frequency matching increased the power and precision in most scenarios, but even greater gains were often obtained by increasing the prevalence of the environmental exposure in controls above the one in cases. The authors concluded that flexible matching strategies can increase the power and efficiency of case-control studies to detect and estimate gene-environment interactions compared with traditional frequency matching and therefore might help to alleviate the notorious lack of power of these studies in specific situations.
Flexible Matching in Case-Control Studies of Gene-Environment Interactions
2004 AJE, Saunders, Barrett


Multivariate and Propensity Score Matching
Software with Automated Balance Optimization:
The Matching package for R

reducing selection bias by propensity score matching (PPT) Bo Lu 2007
in SAS - MACRO

matching software" in R - matchbalance, match, genmatch

SPSS - XXXXX

SPSS - propensity score macro

matching for ethnicity using a panel of SNPs (pdf)





An Introduction to Matching and its Application using SAS®














The use and misuse of matching in case-control studies: the example of PCOS




Fertil Steril 2007









part of paper on "degree of matching and gain in power and efficiency of case control studies" in Epidemiology 2001




(terms frequency matching, ...)









cf counter matching - (counterintuitive matching) to increase informative pairs




example - countermatching on radiation exposure from IJE 2004




advanced ??









file:///C:/Documents%20and%20Settings/Javorsky/Local%20Settings/Temporary%20Internet%20Files/Content.IE5/K1UJG9UN/256,1,Reducing Selection Bias via Propensity Score Approach









optimal case control multivariate matching









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HILDA australian data - social survey

regular expressions resources

library of regexps

some intro McCook 2003

Finnish !

to your attention
starter Helsinki uni (yliopisto)

morphological analyzer (parser) from xerox.
cf for "Minun mieheni nimi on Timo." (meaning Mon mari s’appelle Timo.) gives:
Result of Finnish Morphological Analysis :
Minun minä +PRO+GEN
mieheni mies +N+PL+NOM+PSG+PSF1
mieheni mies +N+SG+GEN+PSG+PSF1
mieheni mies +N+SG+NOM+PSG+PSF1
nimi nimi +N+SG+NOM
on olla +V+ACT+IND+PR+SG+PER3
Timo. Timo. +?

CONJUGATOR from verbix

at verbix.com there is also a list of 10000 most common used Finnish words

statistics resources

from DISCOVER ô long list of resources on regression etc etc .........

comparison of statistical packages Stata, SAS, SPSS,
technical reports at UCLA 2007


from australian page for statistics course/exam in radiation oncology training (PDF)

statistics page by Dallal from Tufts - nice basic concepts, up to regression analysis (not so good logistic reg)

BUT involves treatise on estimation of CI for transformed data (eg log) !!!!!!!

LernSTATS - german/english - sociology-psychology - java examples


- up to factor analysis, some examples intuitive







lisrel online kurs - SEM - structural equation modelling - german FU Berlin

kuopio PhD, finnish resources

RESOURCES on FINNISH language

blog on fremdsprachen und neue medien (podcast etc) by german teacher (unfortunately no link to finnish)

On Finland and Finnish

suomi-info.de - XXX very nice site in german, includes links to Finnish culture, short course on Finnish language and resources (eg how to subscribe to YLE podcast)

finnish

finnish grammar

- book Finnish: Essential Grammar, by Karlsson /1st ed 1999, 2nd edition end Nov 2007)

sites - to be used as complementary resources for novices XXX

0. a very short finnish grammar - nice brief "one webpage" overview

1. Kimberli Mäkäräinen

2. Panu Mäkinen - English, german, structured, but some grammar concepts just given as bulky examples without explanation (eg. consonant gradation)

3. ressources pour le finnois - from forum at Inalco - dept for languages of northern and eastern europe .....

http://virtual.finland.fi/netcomm/news/showarticle.asp?intNWSAID=25831
http://www.cs.tut.fi/~jkorpela/Finnish.html

absolute starter on finnish - SUPERB - with embeded audio.:.
http://donnerwetter.kielikeskus.helsinki.fi/FinnishForForeigners/parts-index.htm
http://donnerwetter.kielikeskus.helsinki.fi/FinnishForForeigners/parts-index.htm
quiz - finnish english vocabulary

DICTIONARY + resources XXXXX

finnish in finnish

YLE radio, tv podcast !!!!XXXX how to subscribe see - suomi-info.de

maybe some resources can be found here

PhD in Kuopio

http://www.uku.fi/laake/english/forms.shtml http://www.uku.fi/laake/english/studies.shtml http://www.uku.fi/intl/english/prospective/applying.shtml#PG IMPIT cf International Master´s Program in Information Technology research at Dept of Computer science and applied mathematics Structured Documents

databases, intro, relational, Access tutorial

some INTRO resources on databases (database management systems, DMBS) especially the so called relational databases
- tutorial-like resources

1. databasics from scratch - instructional, very understandable (at geekgirls.com ....???)

2. types of databases -
flat spreadsheet / hierarchical / relational / object oriented
- a brief (minimal) theoretical intro with examples of structure and questions/queries - also (Funnel 2007, McGill Uni)

3. intro to Access - (basic relational db available as part of MS Office)
very instructional TUTORIAL - really click-by-click intro into designing creating, viewing, querying a relational database. (holowczak from Baruch College CUNY) with multiple screenshots.

4. designing and creating relational database - course/tutorial - looks comprehensible with multiple figures to describe problems with designing db, however some links broken (Newcastle 2004)
also some useful guides on software by administrators at Newcastle
eg access, excel, word, spss.
check using ACCESS and SPSS

5. Dilip´s brief intro to relationdal db (1998), schemes, screenshots + some syntax.

perl, intro, resources

perl
- program - originally developed to transform various dataformats
- useful for data manipulation
- esp. text manipulation by means of regular expressions
- web pages (amazon.com etc)
- cf data manipulation for Human Genome Project
-
- Bioperl - (manipulation and evaluation of genome sequence data)

can be downloaded free from activestate.com as ActivePerl

intro at perl.com, perl.org, where also a library with online books can be found
eg. beginning Perl by S. Cozens
at CPAN - official Perl site with comprehensive documentation-

intro text also here, helps to get first glimpse on the structure of perl + one gets acquainted with some terminology (variable types-scalar, array, hashes, references, subroutines, regular expressions), but not many "aha" feelings so far. however - nicely organized.

PERL INTRO + links to other INTROs and more
Broman´s page - reads very well

Perl code editors - syntax color coding, ....
FREE:
Perl Express - looks trustworthy - last update 2005?
Open Perl IDE looks like OptiPerl - from 2003+patch for Perl 5.8
Perl code editor - basic, webpage rather shabby

shareware
OPTIPERL intergrated environment - looks interesting
DZSoft Perl Editor

ER stress

2007 - Ind J Med Res

ER stress and diabetes. Sundar Rajan



2006 - Science - Hotamisligil.

chemical chaperones reduce ER stress and restore glucose homeostatis in mouse model of T2DM

XXXX - 4-phenylbutyric acid, taurine-conjugated ursodeoxycholic acid

cf XXXXX treatment of ER stressss, cf cited bys



2006 - Phys Reviews
Marinciak S. Endoplasmic Reticulum Stress Signaling in Disease

2005 - JCI
Xu, Bailly-Maitre, Reed. Endoplasmic reticulum stress: cell life and death decisionsJ. Clin. Invest., Oct 2005; 115: 2656 - 2664.


2005 - JBC
Nakatami. Involvement of Endoplasmic Reticulum Stress in Insulin Resistance and Diabetes*

2002 - JCI
David Ron - Translational control in the endoplasmic reticulum stress response J. Clin. Invest., Nov 2002; 110: 1383 - 1388.

quantitative genetics veterinary

quantitative genetics in veterinary medicine - a booklet

http://www.kursus.kvl.dk/shares/vetgen/_Popgen/genetics/genetik.htm

statistics genetics "a must see"

http://www.dorak.info/genetics/notes05.html

European Genetics Foundation
http://www.charite.de/ch/medgen/eumedis/statistics05/genetic-epidemiology.html

article by Kruglyak, Nickerson on the effect of SNP frequency on the LD and a measure of frequency matched SNP correlation.

linear trend ordinal variables

linear trend test for dichotomous(binary) with categorical-ordinal variables
e.g. linear trend of risk (OR) of some disease across genotypes

Cochran-Armitage - in SPSS can be done as - sort of - CROSSTABS - linear-by-linear association

more theory + statsdirect software

statistics resources

statistics resources + accompanying SPSS syntax
as recommended by Marta Garcia-Granero

at www.nabble.com

The book: http://www.bmj.com/collections/statsbk/
The SPSS syntax: http://www.kingdouglasconsulting.com/SPSS/DiverseCultures/Marta/Code/BMJ%20-%20Stats%20Square%20One.txt

statistics resources

XXXXXX
the well known series by dr Bland et ???? that appeared in BMJ
statistics at square one

XXXXXX
very instructive resource (maryland biology) by McDonald

measures of central tendency (location)

1. mean (arithmetic, geometric, harmonic)
2. median
3. mode

anova POST HOCS EG:

http://www.uwsp.edu/psych/cw/statmanual/posthocs.html

statistics resources, tutorials, SPSS, other

resources on statistics
1. xxxxx - comprehensive at onlinetutorialsstatistics. ... as of 2000?

okstate.edu - also other tutorials
http://home.okstate.edu/homepages.nsf/toc/onlinetutorials

R resources

graphics:

1. addictedtoR

intro - multiple tips: Using R for psychological research:



fora (pl. forum)

nabble seems nice
cf thread - regular expressions ..... "solution to my problems?"

ANOVA, permutation test, in R

while searching for a code in R to run a permutation test on ANOVA (eg. genotype - continuous variable association, adaptation of p values etc.) I found the following resources valuable:

some resources on ANOVA calculation in R and permutation test when comparing multiple groups (more than two)

mrpp function in vegan package seems to be appropiate (as an alternative to permutation test and comparison of F-values), cf measures of distance (euclidian, delta etc.)
MRPP stands for
Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities

certainly a comprehensive resource on ANOVA in R is
Faraway´s: Practical Regression and Anova using R (pdf) 200+ pages

very nice intro in ANOVA 3pp (pdf)

site by the Dutch Guido W to accompany some textbook by neter (1996), but nevertheless seems informative/instructive

(((((((( what is this about?????))))))
voila: fast introduction to the concept of resampling, randomization (and permutation) tests, bootstrapping can be found on pages of David Howell. david also provides a free software, which is very easy to install, use and understand. However, it may not be used for publications, as the algorithms is not clear etc. Anyway, a very nice site and software.
check david howell´s site here.
other resource is the freely available book (pdf) of Simon´s book - e.g. on statistics.com



les examples utiles de code en R pour les analyses simples je trouvait sur la site de Christian Jost dans le cadre de ses courses
Données pour les TP du module 3L3B03M 'Traitement des données en biologie' (http://cognition.ups-tlse.fr/_christian/L2-BopeStat/index.html)

e.g. intro pdf

ANOVA ici XXXXXXXXXXXXXXXXX

aussi en Francais est le contribution de Mr Pallier
les exemples d´ ANOVA - (pdf)
montre les differentes designs d´ANOVA (one/two-way, factorial, repeated measures, nested, hierarchical etc)

forum francais (groupe d´utilisateur du logiciel R)


Just to repeat what is ANOVA about
and link to some other basic statistical concepts can be found on Stattrek.com

causality, complex genetic disease

"Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits. by Page GP et al, Am J Hum Gen 2003
back in 2003 was published nice overview of the causality concept of complex multifactorial polygenic diseases. author mentions Hill´s criteria for causality in epidemiological research, as well as those of Koch´s postulates, along with the review of causality concepts from the scientific to philosophical standpoint. Page discusses the common problem of causality vs association, and gives a step-by-step detailed treatise of what can be cause of a positive genetic association.

here you can read article in AJHG 2003

sample size, general, genetic association, SW

discussion of/ and practical guide on sample size determination - in general
by Lenth, Effective sample size determination
Lenth is author of Java based software for sample size/ power estimation. it is very intuitive
classical web-based calculators of power and sample size for GENETIC ASSOCIATION studies are:
Purcell´s site:
Genetic power calculator

and Derek Gordon´s calculator, allowing researchers to take into account possible genotypic error and/or misclassification errror:

PAWE - Power for Association With Errors

also see Gordon´s article on factors affecting statistical power in the detection of genetic association which was published as part of the JCI review series on genetics of complex diseases.

primer of allelic association

základy genetických asociačných štúdií - vysvetlené na príkladoch spred éry HUGO project.
includes TDT analysis and GE interactions, case-only designs (Khoury)

a primer of allelic association

interakcia, viacrozmerná lineárna regresia

prehľad testovania interakcií v multivariatnom linearnom regresnom modeli.
formou častých otázok (FAQ - pýtate sa).

interakcia, MLR

interakcie gény, gén prostredie, epistáza, software MDR

pre záujemcov o genetiku a interakcie medzi génmi, génmi a faktormi prostredia odporúčam blog Jasona Moore-a z Vanderbildtovej Uni. Jason je spoluautorom jednej z metód na testovanie interakcií medzi génmi (epistázy) ako aj príslušného softwéru - multifactor dimensionality reduction, MDR.
epistasis blog

Moore JH. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered. 2003;56(1-3):73-82. pubmed
There is increasing awareness that epistasis or gene-gene interaction plays a role in susceptibility to common human diseases. In this paper, we formulate a working hypothesis that epistasis is a ubiquitous component of the genetic architecture of common human diseases and that complex interactions are more important than the independent main effects of any one susceptibility gene. This working hypothesis is based on several bodies of evidence. First, the idea that epistasis is important is not new. In fact, the recognition that deviations from Mendelian ratios are due to interactions between genes has been around for nearly 100 years. Second, the ubiquity of biomolecular interactions in gene regulation and biochemical and metabolic systems suggest that relationship between DNA sequence variations and clinical endpoints is likely to involve gene-gene interactions. Third, positive results from studies of single polymorphisms typically do not replicate across independent samples. This is true for both linkage and association studies. Fourth, gene-gene interactions are commonly found when properly investigated. We review each of these points and then review an analytical strategy called multifactor dimensionality reduction for detecting epistasis. We end with ideas of how hypotheses about biological epistasis can be generated from statistical evidence using biochemical systems models. If this working hypothesis is true, it suggests that we need a research strategy for identifying common disease susceptibility genes that embraces, rather than ignores, the complexity of the genotype to phenotype relationship.

tu je odkaz na článok o metóde MDR
Hahn
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions.Bioinformatics. 2003 Feb 12;19(3):376-82.

v tomto článku nájdete prehľad používaných metód na štúdium interakcií predovšetkým medzi génmi.

Heidema
The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases.BMC Genet. 2006 Apr 21;7:23.