Date/Topic
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Reading
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Faculty
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Monday, January 27
Course Overview and Introduction to Genome Sequencing
|
Genome Sequencing Lecture
Background:
Resources:
Next-generation Sequencing Review:
-
Goodwin S.
Coming of age: ten years of next- generation sequencing technologies.
Nat Rev Genet 2016.
|
MB |
Wednesday, January 29
Transcriptome I
|
Transcriptional Profiling and Clustering Lecture
Required:
Resources:
-
Jain AK.
Data Clustering: 50 years beyond K-means.
Pattern Recognition Letters. 2010; 31(8):651-666.
|
MB |
Monday, February 3
Transcriptome II
|
Required:
Resources:
-
Harrow J et al.
GENCODE: the reference human genome annotation for The ENCODE Project.
Genome Research. 2012; 22:1760-74.
|
MB |
Wednesday, February 5
Genome Analysis
|
Genome Analysis Lecture
Required:
Background:
-
Zhang MQ.
Computational prediction of eukaryotic protein-coding genes.
Nat Rev Genet. 2002; 3(9):698-709.
-
Durbin R et al.
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids.
(On reserve at Countway and available in the Biophysics office)
Chapters 1 and 3.
|
SS |
Monday, February 10
Comparative Genomics and Metagenomics
|
Required:
-
Sackton TB et al.
Convergent regulatory evolution and loss of flight in paleognathous birds.
Science. 2019; 364:74-78.
Supplementary Materials
-
Donia M et al.
A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics.
Cell. 2014; 158:1402-1414.
-
Pachiadaki MG et al.
Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.
Cell. 2019; 169:1623-1635.
Background:
Resources:
- Altschul
SF, Boguski MS, Gish W, Wootton JC.
Issues in searching molecular sequence databases.
Nat Genet. 1994 Feb; 6(2):119-29. Review.
- Altschul
SF and Koonin EV
Iterated profile searches with PSI-BLAST: a tool for discovery in protein databases.
Trends Biochem Sci. 1998 Nov;23(11):444-7. Review.
- Eddy
SR.
Profile hidden Markov models.
Bioinformatics. 1998; 14(9): 755-83.
- Durbin et al. Biological Sequence Analysis
Chapter 5
|
SS |
Wednesday, February 12
Genomics and Protein Structures
|
Required:
Resources:
-
Marks DS et al.
Protein structure prediction from sequence variation.
Nat Biotechnol. 2012; 30:1072-80.
|
SS |
Monday, February 17
|
No class - President's Day
|
|
Wednesday, February 19
Noncoding RNAomics
|
Required:
Background:
-
Lindberg J et al.
The plasticity of the mammalian transcriptome.
Genomics. 2010; 95:1-6.
-
Ulitsky I and Bartel DP.
lincRNAs: Genomics, Evolution, and Mechanisms.
Cell. 2013; 154:26-46.
-
Krol J et al.
The widespread regulation of microRNA biogenesis, function and decay.
Nat Rev Gen. 2010; 11:597-610.
|
MB |
Monday, February 24
Genetic Variation I
|
Genetic Variation Lecture
Required:
Resources:
|
SS |
Wednesday, February 26
Metabolome
|
Required:
|
MV |
Monday, March 2
Hi-C, DHS, and Histone Modifications
|
Histone Modifications Mini-Lecture
Required:
Resources:
-
Bell O et al.
Determinants and dynamics of genome accessibility.
Nat Rev Genet. 2011; 12:554-64.
-
Dekker J, Marti-Renom MA, and Mirny LA.
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Nat Rev Genet. 2013; 14:390-403.
|
MB |
Wednesday, March 4
Sequence Motifs
|
Required:
|
MB |
Monday, March 9
Regulome
|
Required:
-
Schmidt D et al.
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Science. 2010; 328(5981):1036-40.
-
Osterwalder M et al.
Enhancer redundancy provides phenotypic robustness in mammalian development.
Nature. 2018; 554:239-43.
-
Fulco CP et al.
Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Nat Genet. 2019; 51:1664-1669.
Supplementary Materials
Background:
Resources:
|
MB |
Wednesday, March 11
Phenome
|
Required:
-
Alexandrov V et al.
Large-scale phenome analysis defines a behavioral signature for Huntington's disease genotype in mice.
Nat Biotechnol. 2016;34(8):838-44.
Supplementary Data
-
Roederer M et al.
The Genetic Architecture of the Human Immune System: A Bioresource for Autoimmunity and Disease Pathogenesis.
Cell. 2015; 161(2):387-403.
-
Plata G et al.
Long-term phenotypic evolution of bacteria.
Nature. 2015; 517(7534):369-72.
Supplementary Data
Background:
-
Houle D et al.
Phenomics: the next challenge.
Nat Rev Genet. 2010; 11:855-66.
Resources:
-
Bogue MA et al.
Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice.
Nucleic Acids Res. 2018; 46:D843-50.
|
MV |
Monday, March 16
|
No class - Spring Break
|
|
Wednesday, March 18
|
No class - Spring Break
|
|
Monday, March 23
Epigenomes and Epitranscriptomes
|
Required:
-
Mueller B et al.
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.
Genes & Dev. 2017; 31:451-62.
Supplementary Materials
-
Tan MH et al.
Dynamic landscape and regulation of RNA editing in mammals.
Nature. 2017; 550(7675):249-254.
Supplementary Materials
-
Shen SY et al.
Sensitive tumour detection and classification using plasma cell-free DNA methylomes.
Nature. 2018; 563:579-583.
Resources:
-
Stricker SH et al.
From profiles to function in epigenomics.
Nat Rev Gen. 2017; 18:51-66.
-
Skvortsova K et al.
Functions and mechanisms of epigenetic inheritance in animals.
Nat Rev Mol Cell Biol. 2018; 19:774-90.
|
MB |
Wednesday, March 25
Proteomics and Mass Spectrometry
|
Proteomics Lecture
Required:
Resources:
-
Aebersol R and Mann M.
Mass-spectrometric exploration of proteome structure and function.
Nature. 2016; 537(7620):347-55.
|
PS |
Monday, March 30
Genetic Variation II
|
Required:
|
SS |
Wednesday, April 1
|
No class - NHGRI Conference (BIG Trainees)
|
|
Monday, April 6
RNA Stability and Translation Regulation
|
DUE @ 11:59PM: 1-page description of proposal idea
Required:
-
Jens M and Rajewsky N.
Competition between target sites of regulators shapes post-transcriptional gene regulation.
Nat Rev Genet. 2015; 16(2):113-26.
-
Taggart and Li.
Production of Protein-Complex Components is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes.
Cell Systems. 2018; 7(6):580-9.
Supplementary Materials
Resources:
|
PS |
Wednesday, April 8
Genetic Variation III
|
Required:
Resources:
-
Blair DR et al.
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.
Cell. 2013; 155(1):70-80.
-
Lek M et al.
Analysis of protein-coding genetic variation in 60,706 humans.
Nature. 2016; 536(7616):285-91.
Supplementary Materials
|
SS |
Monday, April 13
Protein Interactions, Modifications, and Networks
|
Required:
-
Garzón et al.
A computational interactome and functional annotation for the human proteome.
eLife 2016; 5.
-
Kastritis PL et al.
Capturing protein communities by structural proteomics in a thermophilic eukaryote.
Mol Sys Biol. 2017; 13:936.
Resources:
|
PS |
Wednesday, April 15
Network Analysis
|
Required:
Background:
-
Cowen L et al.
Network propagation: a universal amplifier of genetic associations.
Nat Rev Gen. 2017; 18:551-62.
Resources:
-
Heo M, Maslov S, and Shakhnovich E.
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.
PNAS. 2011; 108(10):4258-63.
-
Fraiberger SP et al.
Quantifying reputation and success in art.
Science. 2018; 362(6416):825-9.
|
SS |
Monday, April 20
Cell-to-Cell Variability
|
Required:
|
PK |
Wednesday, April 22
Genetic Interactions
|
Required:
|
SS |
Monday, April 27
Signaling Dynamics
|
Signaling Dynamics Mini-Lecture
Required:
-
Li C et al.
Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation.
Cell Syst. 2018;6(4):409-423.
-
Christodoulou D et al.
Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli's Rapid Response to Oxidative Stress.
Cell Syst. 2018;6(5):569-578.
Resources:
-
Roussel MR and Zhu R.
Stochastic kinetics description of a simple transcription model.
Bull Math Biol. 2006; 68(7):1681-1713.
-
Chen WW et al.
Classic and contemporary approaches to modeling biochemical reactions.
Genes Dev. 2010; 24(17):1861-1875.
|
PS |
Wednesday, April 29
Chemical Genomics and Drug Discovery
|
Required:
Resources:
-
Overington JP et al.
How many drug targets are there?
Nat Rev Drug Discov. 2006; 5(12):993-996.
-
Lyu J et al.
Ultra-large library docking for discovering new chemotypes.
Nature. 2019; 566(7743):224-229
|
PS |
Friday, May 1 |
DUE @ 11:59PM: written proposal (5 pages, single-spaced, including figures but not references)
|
|
Monday, May 4 |
Proposal Presentations
2:30 - 4:45 PM
|
MB, SS |
Wednesday, May 6 |
Proposal Presentations
1:00 - 4:30 PM
|
MB, SS |