Syllabus 2021

Please post questions on Piazza if you have any questions on class, assignments, exams etc.

 

Date  Day Lecture/Lab Lecturer Assignment due (policies)
1/25/21 Mon Introduction I

Bio5488_Introduction_2021.pdf

Reading Materials:

Genomics is failing on diversity

Shendure et al. 2017

Gibbs 2020

Green et al. 2020

Astley et al. 2009

1_s41586-020-2547-7.pdf

Wang
1/27/21 Wed Introduction II Wang
1/29/21 Fri LAB 1: Introduction of statistical models and Python programming

LAB_1 slide

LAB 1 review slide

TAs
2/1/21 Mon Sequencing technology I

Bio5488_NGS Technologies_2021

Mitra
2/3/21 Wed Sequencing technology II

Bio5488_NGS Technologies_2_2021

Mitra
2/5/21 Fri LAB 2: Sequence technology

LAB 2 slide

LAB 1: Introduction of statistical models and Python programming
2/8/21 Mon Homology I

Bio5488_homology_2021

Reading Materials:

4_HomologyReading_1_STATISTICAL-ERRORS 4_HomologyReading_2_Designing-comparative-experiments 4_HomologyReading_3_Stormo_HomologySearch 4_HomologyReading_4_Eddy_HMM 4_HomologyReading_5_Eddy_DynamicProgramming 4_HomologyReading_6_Eddy_BLOSUM62 4_HomologyReading_7_Eddy_Bayesian

Wang
2/10/21 Wed Homology II Wang
2/12/21 Fri LAB 3: Sequence comparison

2021_Assignment3

2021 Lab 3 Slides

LAB 2: Sequence technology
2/15/21 Mon Gene expression I

Bio5488_Lawson2021_lecture1

Lawson
2/17/21 Wed Gene expression II

Bio5488_Lawson2021_lecture2

Lawson
2/19/21 Fri LAB 4: Gene expression

Assignment4-2021_Gene_Expression

2021 Lab4 slides

LAB 3: Sequence comparison
2/22/21 Mon Epigenomics I

Lecture Slides

Precision Medicine Pathway

Reading Materials:

Paper 1, Paper 2, Paper 3, Paper 4, Paper 5

Wang
2/24/21 Wed Epigenomics II Wang
2/26/21 Fri LAB 5: Epigenomics

2021 Lab5 slides

LAB 4: Gene expression
3/1/21 Mon 4D genome

Reading materials:

Paper 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

Wang
3/3/21 Wed Wellness day No class
3/5/21 Fri LAB 6: Long range interaction

2021 Lab6 slides

3/8/21 Mon Single cell genomics I

single_cell_gen_partI_2021

Morris LAB 5: Epigenomics
3/10/21 Wed Single cell genomics II

single_cell_gen_partII_2021

single_cell_gen_partII_2021_modified

Morris
3/12/21 Fri Lab 7: Single cell analysis

2021_Lab7_assignment

2021 Lab7 Slides

3/13/21 Sat LAB 6: Long range interaction
3/15/21 Mon Genetic variation I

Bio5488_Genetic-Variation-I_2021

Reading material:

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Structural variation in the sequencing era

Jin
3/17/21 Wed Genetic variation II

Bio5488_Genetic-Variation-II_2021

Jin
3/19/21 Fri MIDTERM EXAM
Lab 8: Genetic variation

2021_Assignment_8

lab8_slides

No Spring Break
3/22/21 Mon Population genetics I

Bio5488_Population_Genetics_I_2021

Bio5488_Population_Genetics_I_2021_updated

Jin
3/24/21 Wed Population genetics II

Bio5488_Population_Genetics_II_2021

Jin
3/26/21 Fri LAB 9: Wright-Fisher Model

StudentAssignment 9_2021

Assignment9_slides_spring2021

3/27/21 Sat LAB 7: Single cell analysis
LAB 8: Genetic variation
3/29/21 Mon Metagenomics I

Metagenomics Lecture I

Clinical_metagenomics_review_2019

Baldridge
3/31/21 Wed Metagenomics II

Metagenomics Lecture II

Baldridge
4/2/21 Fri LAB 10: Metagenomics
4/3/21 Sat LAB 9: Wright-Fisher Model
4/5/21 Mon Functional assays I

FunctionalAssays_I

Reading1_mpra; Reading2_perturb-seq; Reading3_vamp-seq

White
4/7/21 Wed Functional assays II

FunctionalAssays_II

White
4/9/21 Fri LAB 11: Identify Expression-Modulating Variants
4/10/21 Sat  Assignment10_Spring2021.docx

Assignment_10_slides

LAB 10: Metagenomics
4/12/21 Mon Wellness day No class
4/14/21 Wed Variant effect analysis

Variant_effects

White
4/16/21 Fri LAB 12: Synthetic gene assembly
4/17/21 Sat LAB 11: Identify Expression-Modulating Variants
4/19/21 Mon Comparative genomics I

Updated Prezi

Buchser
4/21/21 Wed Comparative genomics II

Resources:
SCA talk by Kim Reynolds
Fire Prot
Raptor Structure
SCA tool
Another Comparative Genomics Lecture

Reading:
HMM
Improved measures for evolutionary conservation that exploit taxonomy distances
Initial sequencing and comparative analysis of the mouse genome (Figure 23, 28)
Morpheus Family
Homo Sapien compared to Chimp
FoxP2
Human Sub clusters

Buchser
4/23/21 Fri LAB 13: Cis-regulatory evolution

Assignment 13

4/24/21 Sat LAB 12: Synthetic gene assembly
4/26/21 Mon Review No class
4/28/21 Wed Review

Review | GeneticsVariation&FunctionalAssay

No class
4/30/21 Fri FINAL EXAM
5/1/21 Sat
5/3/21 Mon LAB 13: Cis-regulatory evolution
(Due at 11:59pm)