| 01 |
07-31 (Wed) |
- Introduction to the course: Finding the faults in our DNA
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1 |
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All biology is computational biology |
| 01 |
08-02 (Fri) |
- Sequences: Probability and Statistics
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2U;2A |
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Code for GC content |
| 02 |
08-07 (Wed) |
- Sequence : Statistics II
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3U;3A |
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| 02 |
08-09 (Fri) |
- Sequences: Statistics III and Alignment
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4U;4A |
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| 03 |
08-14 (Wed) |
- Global and Local Alignment
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5 |
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| 03 |
08-16 (Fri) |
- Genome search engines and Sequencing by synthesis
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6A;6B |
- Assignment 01 due
- Assignment 02 released
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Genomes 5 Ch 4 |
| 04 |
08-21 (Wed) |
- DNA mapping algorithms
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7 |
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Bioinformatics Algorithms 2nd Ed Ch 7 |
| 04 |
08-23 (Fri) |
- Hands on DNA-seq and
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8 |
- Assignment 02 due
- Assignment 03 released
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HandsOn 02 |
| 05 |
08-28 (Wed) |
- RNA-seq: Quantification
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9 |
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Genomes 5 Ch 12
EM notes
Dempster1977
Splicing video
Translation video
Coin Toss Python |
| 05 |
08-30 (Fri) |
- Sequencing review
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10 |
- Assignment 03 due
- Assignment 04 released
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| 06 |
09-04 (Wed) |
- RNA-seq normalization
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11 |
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| 06 |
09-06 (Fri) |
- Models for counts and variance stabilization and dimensionality reduction (PCA/SVD)
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12 |
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| 07 |
09-11 (Wed) |
- Differential expression analysis (GLMs), batch correction and multiple hypothesis testing
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| 07 |
09-13 (Fri) |
- RNA-seq Handson
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- Assignment 05 due
- Assignment 06 released
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| 08 |
09-18 (Wed) |
Mid-semester Week |
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| 08 |
09-20 (Fri) |
Mid-semester Week (Exam on 21st September, Saturday 11 AM - 1 PM) |
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| 09 |
09-25 (Wed) |
- Single cell transcriptomics: technologies and analysis
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- Assignment 06 due
- Assignment 07 released
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| 09 |
09-27 (Fri) |
- Single cell normalizationd and clustering and Hands-on
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| 10 |
10-02 (Wed) |
No class (institute holiday) |
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| 10 |
10-04 (Fri) |
Epigenomics: Methylation and molecular clocks |
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| 11 |
10-09 (Wed) |
Deciphering gene regulation: footprinting assays and expectation maximization |
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| 11 |
10-11 (Fri) |
Deciphering gene regulation: motif discovery |
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- Assignment 08 due
- Assignment 09 released
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| 12 |
10-16 (Wed) |
Hidden markov models and gene finding |
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| 12 |
10-18 (Fri) |
Genome wide association studies |
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- Assignment 09 due
- Assignment 10 released
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| 13 |
10-23 (Wed) |
Introduction to CRISPR and CRISPR screens |
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| 13 |
10-25 (Fri) |
Statistical models for modeling CRISPR screens |
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- Assignment 10 due
- Assignment 11 released
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| 14 |
10-30 (Wed) |
Multi-omics for human diseases |
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| 14 |
11-01 (Fri) |
Invited Talk 1 |
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- Assignment 11 due
- Assignment 12 released
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| 15 |
11-06 (Wed) |
Invited Talk 2 |
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| 15 |
11-08 (Fri) |
Review |
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