

AdministriviaSchedule 
Date  Lecture Topic(s)  Sections Covered  Slides  Assignments 
WJanuary 15  Introduction  Chapter 1  slides  Getting to Know You Survey (link on Moodle)  due by 1/17 Read the following 2 articles: Life and Its Molecules A Brief Introduction Molecular Biology for Computer Scientists 
FJanuary 17  DNA Sequencing Technologies  Chapter 3  slides  Reading Assignment/Questions (paper on Moodle) (due 1/22) 
MJanuary 20  No Class  Holiday  
WJanuary 22  Exact Pattern Matching  Sections 9.19.4  slides  
FJanuary 24  Suffix Trees  Section 9.5  slides  Problem Set 1 
MJanuary 27  KnuthMorrisPratt MotifFinding Problem 
Sections 4.44.9  slides  
WJanuary 29  Motif Finding Algorithms  Sections 4.44.9  slides  
FJanuary 31  Greedy Motif Search Lab  
MFebruary 3  Genome Rearrangements  Section 5.35.5  slides  Problem Set 2 CodingsequenceofthehumanCFTRgene.txt 
WFebruary 5  More on Genome Rearrangements  Section 5.35.5  
FFebruary 7  Dynamic Programming Intro  Section 6.16.3  
MFebruary 10  DP: Edit Distance  Section 6.4  
WFebruary 12  DP: LCS & Sequence Alignment  Section 6.56.8  slides  Problem Set 3 
FFebruary 14  Sequence Alignment Lab  
MFebruary 17  Global & Local Alignment  Section 6.46.8  
WFebruary 19  Fitting Alignment & Intro to Affine Gap Penalties  Section 6.9  slides  
FFebruary 21  Multiple Sequence Alignment Lab  Section 6.10  
MFebruary 24  Alignment with Gap Penalties  Section 6.9  
WFebruary 26  Exam 1  
FFebruary 28  SpaceEfficient Global Alignment & Multiple Alignment  Section 7.2 and 6.10  slides  
MMarch 2  Assembling a Genome  Section 8.18.4  slides  
WMarch 4  Overlap Graphs for SCS, Assembly terms and evaluation metrics  Section 8.5  slides  
FMarch 6  OverlapLayoutConsensus Framework for Assembly
Assembly Worksheet Eulerian Cycles and Paths 
Section 8.78.9  slides  
MMarch 9  Spring Break  No Class  
W March 11  Spring Break  No Class  
FMarch 13  Spring Break  No Class  
MMarch 16  Classes Suspended  COVID19  
WMarch 18  Classes Suspended  COVID19  
FMarch 20  Classes Suspended  COVID19  
MMarch 23  Meet via Zoom, final project details, link to recorded Zoom meeting on Moodle  Read Ch. 3 (online book), Sect. 3.13.3  Problem Set 4  due Friday 3/27 Final Project Information Watch the following video lectures, which should be review: Ch. 3: String Reconstruction as a Hamiltonian Path Ch. 3: String Reconstruction as a Eulerian Path Problem Ch. 3: Similar Problems with Different Fates 

WMarch 25  De Bruijn Graphs Worksheet Solutions for De Bruijn Worksheet 
Read Sect. 3.43.6 (online book)  Watch these videos: Ch.3: De Bruijn Graphs Ch.3: Euler's Theorem 

FMarch 27  Realities of Genome Assembly  Read Sect. 3.73.9 
Homework 5  due Monday 4/6 Watch these videos: Ch.3: Assembling ReadPairs Ch.3: De Bruijn Graphs Face Harsh Realities of Assembly Ch.3: Konigsberg 3 

MMarch 30  Which Animal Gave us SARS?  Read Sect. 7.17.2 
Watch these videos: Ch. 7: The Fastest Outbreak Ch. 7: Transforming Distance Matrices into Evolutionary Trees 

WApril 1  Phylogeny Trees  Read Sect. 7.37.4  Project Proposal due by 11:55pm  upload to Moodle Watch these videos: Ch. 7: Towards An Algorithm for DistanceBased Phylogeny Reconstruction Ch. 7: Additive Phylogeny 

FApril 3  Phylogeny Trees II Additive Phylogeny Worksheet (Solution) 
Read Sect. 7.57.6 
Watch these videos: Ch. 7: Using Least Squares to Construct Approximate Phylogenies Ch. 7: Ultrametric Evolutionary Trees 

MApril 6  Phylogeny Trees III Large Additive Phylogeny Worksheet (Solution) Neighbor Joining Worksheet (Solution) 
Read Sect. 7.77.8 
Homework 6  due Watch these videos: Ch. 7: The NeighborJoining Algorithm Ch. 7: CharacterBased Tree Reconstruction 

WApril 8  The Parsimony Problem Notes for Sankoff and Fitch Algorithms 
Read Sect. 7.97.10 & Epilogue 
Watch these videos: Ch. 7: The Small Parsimony Problem Ch. 7: The Large Parsimony Problem 

FApril 10  Easter Break  No Class  
MApril 13  Clustering  Watch these videos: Ch. 8: Clustering as an Optimization Problem Ch. 8: The Lloyd Algorithm for kmeans Clustering Ch. 8: Hierarchical Clustering Note: all other Ch. 8 videos are optional, but recommended 

WApril 15  Work on HW and Projects  Homework 7  due Wed, 4/22 at 2pm  
FApril 17  Work on HW and Projects  
MApril 20  Work on HW and Projects  
WApril 22  Optional Review Session for Exam 2 Study Guide for Exam 2 
Presentation Details Presentation Grading Rubric 

FApril 24  Exam 2  
MApril 27  Project Presentations Fill out Course Evaluations 
Ben Chris & Reese Trang Presentation Worksheet  due 5/1 by 11:55pm 

WApril 29  Project Presentations  Aubrey & Madi Marisa Henry, Matthew & Addison John & Tim 

FMay 8  Final Project Papers due by 5:30pm  upload to Moodle  