Syllabus

Please see last year’s syllabus (with slide packs at the bottom) for previews for this year’s lectures, which will be slightly different. For this year, an updated slide pack will be posted after the lecture. (If it is substantially different from ‘22, an updated video will also be posted.) Video recordings for this year’s lectures can be found in the Media Library tab in Canvas.

  Topic 2025 Spring’s Lecture 2023 Spring’s Lecture Comment Lecture Summary
1/13 *YALE* Spring term classes begin, 8.20 a.m.        
           
1/13 Introduction 25i1-25i2a 23i1, 23i2a    
1/15 DATA - Proteomics I 25d3 23d3 Suggested Reading 25d3
1/22 DATA - Proteomics II 25d4 23d4 Suggested Reading 25d4
1/27 DATA - Genomics I 25d1 23d1   25d1
1/29 DATA - Genomics II 25d2 23d2   25d2
2/3 DATA - Knowledge Representation & Databases 25d5 23d5   25d5
2/5 MINING - Personal Genomes + Seq. Comparison 25i2b,25m3 23i2b,23m3   25i2b, 25m3-part1
2/10 MINING - Seq. Comparison (con’t) + Multi-seq Alignment + Fast Alignment 25m3, 25m4, 25m5 23m3, 23m4, 23m5   25m3-part2,25m4,25m5
2/12 MINING - Variant Calling (incl. a focused section on SVs)+ Basic Multi-Omics 25m6a，25m6b, 25m7-pt1 23m6a, 23m6b,23m7   25m6a,25m6b,25m7-part1
2/17 Quiz on 1st Half     quiz1 study guide, quiz1 key  
2/19 MINING - Basic Multi-Omics(con’t) + Supervised Mining #1 25m7-pt2, 25m8a, 25m8b 23m7,23m8a,23m8b   25m7-part2, 25m8a+b
2/24 MINING - Supervised Mining #2 + Deep Learning Fundamentals #1 + Deep Learning Fundamentals #2 25m8c, 25t3, 25t4-pt1 23m8c   25m8c, 25t3
2/26 MINING - Deep Learning Fundamentals #2 (con’t)+ Unsupervised Mining #1 25t4-pt2, 25m9a, 25m9c 23m9a, 23m9c   25t4-pt2, 25m9a, 25m9c
3/3 MINING - Single-Cell Analysis #1 + Single-Cell Analysis #2 + Network Analysis #1 25m9e, 25t1, 25m10a, 25m10b 23m9e, 23m10a, 23m10b   25m9e,25t1,25m10a, 25m10b
3/5 MINING - Network Analysis #2 + Biomedical Image Analysis 25m10e, 25t2, 25m10c 23m10c, 23m10d, 23m10e   25m10e, 25t2, 25m10c
           
           
3/7 Spring break begins        
           
3/24 MINING - Privacy 25m11a,25m11b 23m11a, 23m11b    
3/26 MINING/MODELING - Deep Learning Advanced I 25m12a 23m12a   25m12a
3/31 MINING/MODELING - Deep Learning Advanced II 25m12b 23m12b   25m12b
4/2 SIMULATION - Protein Simulation I 25s1 23s1   25s1
4/7 SIMULATION - Protein Simulation II 25s2 23s2   25s2
4/9 SIMULATION - Protein Simulation III 25s3 23s3   25s3
4/14 SIMULATION - Protein Simulation IV 25s4 23s4   25s4
4/16 SIMULATION - Protein Simulation V 25s5 23s5   25s5
4/21 Quiz on 2nd Half     quiz2 study guide, Quiz2 Key  
4/23 Final Presentations        
4/25 *YALE* Classes end; Reading period begins        
5/1 *YALE* Final examinations begin        
5/7 *YALE* Final examinations end        

Lecture Slide Pack

Lecture Slide Pack and Video          
# Topic PDF PPT Youtube (‘21) MPEG
25i1-i2a Introduction to Biomedical Data Science & Introduction to Personal Genomes x x I1，I2a 25i1-i2a
25i2b An Individual’s Perspective on Personal Genomes x x I2b i2b
           
23d3 DATA - Proteomics I - Proteins x   D3  
23d4 DATA - Proteomics II - Structure x   D4  
           
25d1 DATA - Genomics I x   D1 D1
25d2 DATA - Genomics II x   D2 D2
           
25d5 Knowledge Representation & Databases x   D5 D5
           
25m3 Sequence Comparison x x M3 M3
25m4 Multiple Sequence Comparison x x M4 M4
25m5 Fast Alignment x x M5 M5
25m6a Variant Identification x x M6a M6a
25m6b 1000 Genome + PCAWG summary x x M6b M6b
           
25m7 Basic Pipeline Processing for Genomics & Multi-omics pt1,pt2 p1,pt2 M7 M7, 25m7-pt2
           
25m8a8b Supervised Data Mining - Decision Trees x x 25m8a8b
25m8c Supervised Data Mining - SVMs x x M8c M8c
           
25t3 Deep Learning Fundamentals I x x    
25t4 Deep Learning Fundamentals II x x    
           
25m9a Unsupervised Data Mining - Clustering x x 25m9a
25m9c Unsupervised Data Mining - SVD x x 25m9c
           
25m9e Single Cell Analysis x x   23m9e
25t1 Single Cell part 2 x x   23t1
           
25t2 Image Analysis x x    
           
25m10a Networks - Intro x x M10a M10a
25m10b Networks - Network Quantities x x M10b M10b
25m10c Networks - Network Generation Models x x M10c M10c
25m10e Networks - Network Prediction x x   25m10e
           
25m11a Privacy in Biomedical Data Science (esp. Genomic Privacy) x x   25m11a
25m11b Privacy in Biomedical Data Science (esp. Genomic Privacy) x x   25m11b
           
25m12a Deep Learning Advanced I x   25m12a
25m12b Deep Learning Advanced II x     25m12b
          25m12b
25s1 Protein Folding x x 25s1
25s2 Core Repacking x x S2 S2
25s3 Protein-Protein Interactions x x
25s4 Molecular Dynamics    
25s5 Simulation x x    

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