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ELL796: Signals and Systems in Biology

Course outline

If you are doing the course, please join the Piazza forum (the access code has been announced in class).

Instructors: Kushal K. Shah and Sumeet Agarwal
3 credits (3-0-0)
I Semester 2015–16
M Th 9:30–10:50, LH 619

Evaluation components

Planned schedule

Serial no. Lecture nos. Topics Instructor Slides
1 1–2 Introduction to Cellular and Molecular Biology SA & KKS Overview; Introduction to Biology
2 3–4 Introduction to Evolution; Modelling Evolution SA & KKS Introduction; Genetic Algorithms; Quasispecies
3 5 Discussion session on evolution
4 6–7 The Data Revolution: Genomics/Transcriptomics/Proteomics SA DNA sequencing; Gene/Protein expression & interactions
5 8–9 Introduction to Signal Processing and Random Processes KKS Fourier Analysis; Entropy and Correlation; Probability Distributions
6 10 Hidden Markov Models for Gene Identification SA
7 11–14 Genomic Signal Processing KKS DNA Periodicity; Gene Coding Regions: Fourier Analysis; Gene Coding Regions: Information Theory; Origin of Replication – I; DNA Phylogeny; DNA Randomness
8 15 Discussion session on genomic signal processing
9 16–18 Primer on networks; Protein interaction networks SA Date and Party hubs
10 19–21 Regulatory & signaling networks, motifs, and dynamics K. Sriram; SA Systems Biology – Signaling Motifs
11 22–23 Student presentations: Mini project 1
12 24 Evolvability and Learning SA Evolvability as Learnability
13 25–26 Large-scale network modelling and inference SA Dynamics and Inference on Biological Networks; Learning Predictive Models of Gene Dynamics
14 27 Discussion session on network biology
15 28 Student presentations: Mini project 2

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