Changes

== Objective ==

== Objective ==

Gene mapping studies aim to study the relationship between genetic variation and susceptibility to human disease. These studies can be used to elucidate the biochemical basis of medically interesting traits leading to knowledge that will, ultimately, help us improve treatment and management of human disease. Biostatistics 666 is a Masters level course that introduces many of the concepts, statistical models and numerical methods useful for studies.

Gene mapping studies study the relationship between genetic variation and susceptibility to human disease. These studies can be used to elucidate the biochemical basis of medically interesting traits leading to knowledge that will, ultimately, help us improve treatment and management of human disease. Biostatistics 666 is a Masters level course that introduces many of the concepts, statistical models and numerical methods useful for studies.

For additional information, see also [[Biostatistics 666: Core Competencies|Core Competencies in Biostatistics Program covered by this course]].

For additional information, see also [[Biostatistics 666: Core Competencies|Core Competencies in Biostatistics Program covered by this course]].

== Target Audience ==

== Target Audience ==

Students in Biostatistics 666 should be confortable with simple algebra and, ideally, have previous exposure to maximum likelihood. Previous knowledge of Genetics is helpful, but not required. Most students registering for the course are Master or Doctoral students in Human Genetics, Bioinformatics, Statistics or Biostatistics.

Students in Biostatistics 666 should be comfortable with simple algebra and, ideally, have previous exposure to maximum likelihood. Previous knowledge of Genetics is helpful, but not required. Most students registering for the course are Master or Doctoral students in Human Genetics, Bioinformatics, Statistics or Biostatistics.

== Scheduling ==

== Scheduling ==

For Fall 2012, classes are scheduled for Mondays and Wednesdays, 8:30 - 10:00 am. Classes will start at 8:30 am sharp. Goncalo will be avaialble for weekly office hours in the SPH Tower, 4th floor at a mutually convenient time (to be determined).

Final grades will take into account performance in written in-class assessments, take home problem sets, as well as participation in class and any class projects.

The final grade will take into account your performance in written in-class assessments, take home problem sets, as well as your participation in class and any class projects.

 

 

 

 

[[Biostatistics 666: Introduction to the Coalescent]] - [[Media:666.04 - The Coalescent.pdf|PDF]]

 

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.2017.05_-_Coalescent_and_Allele_Counts.pdf|PDF]]

 

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.2017.06_-_More_Advanced_Coalescent_Models.pdf|PDF]]

 

 

 

 

[[Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium]] - [[Media:2011.666.01.pdf|PDF]]

Biostatistics 666: Kinship Coefficients and Relatedness - [[Media:666.2017.12_-_Kinship_Coefficients.pdf|PDF]]

[[Biostatistics 666: Linkage Disequilibrium]] - [[Media:666.03.pdf|PDF]]

[[Biostatistics 666: Variance Component Analyses]] - [[Media:666.2017.13_-_Variance_Component_Models.pdf|PDF]]

[[Biostatistics 666: Introduction to the Coalescent]] - [[Media:666.04.pdf|PDF]]

[[Biostatistics 666: Linkage Analysis in Sibling Pairs]] - [[Media:666.2017.14_-_Affected_Sibling_Pairs.pdf|PDF]]

[[Biostatistics 666: Modeling Variation in the Coalescent]] - [[Media:666.05.pdf|PDF]]

[[Biostatistics 666: Genotype Imputation]] - [[Media:666.2017.15_-_Genotype_Imputation.pdf|PDF]]

[[Biostatistics 666: Modeling Recombination and Migration in the Coalescent]] - [[Media:666.06.pdf|PDF]]

[[Biostatistics 666: Whole Genome Sequencing]] - [[Media:666.2017.16_-_Introduction_to_Sequencing.pdf|PDF]]

[[Biostatistics 666: Maximum Likelihood Allele Frequency Estimation]] - [[Media:666.09.pdf|PDF]]

[[Biostatistics 666: Functional Genomics (Guest lecture)]] - [[Media:Biostat666FunctionalGenomics_v4(2017).pdf|PDF]]

[[Biostatistics 666: Introduction to the E-M Algorithm]] - [[Media:666.10.pdf|PDF]]

[[Biostatistics 666: Introduction to De Novo Assembly]] - [[Media:666.2012.01_-_De_Novo_Assembly.pdf|PDF]]

[[Biostatistics 666: Haplotype Estimation]] - [[Media:666.11.pdf|PDF]]

Lectures below have not yet been updated for 2017.

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Haplotype Association Tests]] - [[Media:666.12.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Association Tests in Structured Populations]] - [[Media:666.13.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Multipoint Analysis in Sibling Pairs]] - [[Media:666.16.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Relationship Checking]] - [[Media:666.17.pdf|PDF]]

[[Biostatistics 666: Analysis of Low Pass Sequence Data]] - [[Media:666.2010.05.pdf|PDF]]

[[Biostatistics 666: Analysis of Low Pass Sequence Data]] - [[Media:666.2010.05.pdf|PDF]]

[[Biostatistics 666: Analysis of Copy Number Using Sequence Data]] - [[Media:666.2011.02.pdf|PDF]]

[[Biostatistics 666: Analysis of Copy Number Using Sequence Data]] - [[Media:666.2011.02.pdf|PDF]]

[[Biostatistics 666: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]]

[[Biostatistics 666: Rare Variant Burden Tests]] - [[Media:666.2011.01.pdf|PDF]]

[[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|PDF]]

[[Biostatistics 666: Likelihood Calculations for Large Pedigrees]] - [[Media:666.24.pdf|PDF]]

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[Biostatistics 666: Introductory Lecture]] - [[Media:666.01.pdf|PDF]]

[[Biostatistics 666: Hardy-Weinberg Equilibrium]] - [[Media:666.02.pdf|PDF]]

[[Biostatistics 666: Course Introduction and Hardy Weinberg Equilibrium]] - [[Media:2011.666.01.pdf|PDF]]

[[Biostatistics 666: Advanced Coalescent, Changing Population Size]] - [[Media:666.07.pdf|PDF]]

[[Biostatistics 666: Advanced Coalescent, Changing Population Size]] - [[Media:666.07.pdf|PDF]]

[[Biostatistics 666: Applications of the Lander-Green Algorithm]] - [[Media:666.19.pdf|PDF]]

[[Biostatistics 666: Applications of the Lander-Green Algorithm]] - [[Media:666.19.pdf|PDF]]

== Office Hours ==

== Office Hours ==

For the 2012 Fall Term, office hours will take place in office 4614 in the School of Public Health Tower. I will provide free coffee to anyone who turns up.

For the 2017 Fall Term, office hours are tentatively schedule for Friday afternoons at 3pm. I will provide free coffee to anyone who turns up.

== Standards of Academic Conduct ==

== Standards of Academic Conduct ==

* 2011/2012

* 2011/2012

* 2012/2013

* 2012/2013

He is currently teaching it in the 2012/2013 academic year. For previous course notes, see [[http://www.sph.umich.edu/csg/abecasis/class Goncalo's older class notes]].

He last taught it in the 2017/2018 academic year. For previous course notes, see [[http://csg.sph.umich.edu/abecasis/class Goncalo's older class notes]].