Haplotype Assembly

GWAS Algorithms

Haplotype Phasing

Population Genetics

Spring 2021 - Advanced Algorithms in Computational Biology and Medical Bioinformatics

Welcome to CS2820 Spring 2021!

This year, due to COVID-19, we will be holding lectures online via Zoom. The link for the class is here: https://brown.zoom.us/j/92684186590 .
Please note that this meeting requires a Brown authentication. Attendance is strongly encouraged, however, lecture recordings will also be uploaded to Panopto later in the day of the lecture for your asynchronous access. If you have trouble accessing Panopto, you can also check out the video recordings of our lectures on Brown Dropbox here .

Most of the course announcements will be made on Piazza. So, please make sure to join the course Piazza via the following link as soon as you can if you are considering to take this course: piazza.com/brown/spring2021/csci2820.
Lecture Notes:
We will be uploading lecture notes (both whiteboard notes from Sorin's Zoom lectures and additional typed up notes) on this Google Drive folder every Brown student has view access to.
For additional resources, feel free to check out the Class Notes tab on this website.


Spring 2021 Course Chapters (tentative)

1.Linkage Disequilibrium (LD) and the Unification of LD Measures Problem
2. Spectral Graph Theory and Spectral Clustring
3. The Coalescent: General Theory, Polya Urn Games and Ewens Sampling Lemma
4. Genome-Wide Association Studies (GWAS): The Computational Pipeline, Genomic Common and Rare Variants, Statistical Tests of Association, Genetic Heterogeneity and the Missing Heritability Puzzle, Statistical Models of "Disease"
5. Algorithmic Problems in Haplotype Reconstruction and Tagging SNPs Selection
6. Markov Chain Monte Carlo theory and practice and the Population Genomics Substructure Problem
7. Genomic Privacy Algorithms
8. Causality and Prediction


Student Support

Academic support:
Both the instructor and the TA will hold office hours to answer students' questions. Details of office hours are listed on the left hand side of this home page. Once you join a Zoom meeting for the office hours, please wait to be admitted from the waiting room. For the TA office hours, we will use SignMeUp.We also encourage students to have discussions with their classmates on the course Piazza page.
Psychological support:
Being a student can sometimes be stressful. If you feel overwhelmed or there are psychological issues that are keeping you from performing well here, we encourage you to contact Brown’s Counseling and Psychological Services (CAPS) . They provide confidential counseling and can provide notes supporting accomodations on academic assignments.
Please talk to the instructor about accessibility accomodations if you have a disability or other condition that might require modification of the course procedures. Your confidentiality is respected and Student Accessibility Services (SAS) can provide accomodation recommendations. If you are going through a personal or medical circumstance that affect your ability to do academic work, you can generaly contact the the Deans for academic accomodations.
CSCI2820: Medical Bioinformatics