Syllabus

Below is the syllabus from Spring 2026.

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 last year, 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 2026 Spring’s Lecture 2025 Spring’s Lecture Comment
1/12 *YALE* Spring term classes begin, 8.20 a.m.      
         
1/12 Introduction 26i1-26i2a 25i1-25i2a  
1/14 DATA 3 - Proteomics I 26d3 25d3  
1/19 Martin Luther King Jr. Day; classes do not meet      
1/21 DATA 4 - Proteomics II 26d4 25d4  
1/26 DATA 1 - Genomics I 26d1 25d1  
1/28 DATA 2 - Genomics II 26d2 25d2  
2/2 DATA 5 - Knowledge Representation & Databases   25d5  
2/4 MINING - ELSI issues + Seq. Comparison + Multi-seq Alignment 26d6,26m3,26m4 23m3,25m4  
2/9 MINING - Fast Alignment + Variant Calling + Basic Multi-Omics 26m5,26m6a,26m6b,26m7-part1 25m5,25m6a,25m6b,25m7-part1  
2/11 MINING - Basic Multi-Omics, GWAS/QTL + Supervised Mining (DT+ SVM) 26m7p2, 26m7p3, 26m8a+b, 26m8c 25m7,25m8a, 25m8b  
2/16 Quiz on 1st Half     study guide
2/18 MINING - Personal Genome, Supervised Mining (DT+ SVM) (con’t) 26i2b, 26m8c 25i2b, 25m8c  
2/23 MINING - Supervised Mining #2 + Network Prediction+ Unsupervised Mining 26m9a, 26m9c, 26m10a, 26m10e 25m9a, 25m9c, 25m10a, 25m10e  
2/25 MINING - Deep Learning Fundamentals #1 + #2 26t3, 26t4 25t3, 25t4  
3/2 MINING - Biomed. Image Processing + RNN + GNN 26t2, 26t5 25t2  
3/4 MINING - Gen AI + Network Quantities + Network Generation 26t6, 26m10b, 26m10c 25m10b, 25m10c  
         
3/6 Spring break begins      
         
3/23 Class Resume, 8:20AM      
3/23 Deep Learning Advanced 26m12 25m12a, 25m12b  
3/25 Single cell 26h1 25m9e, 25t1  
3/30 Privacy 26h2 25m11a,25m11b  
4/1 MODELING 1 - Protein Simulation I   25s1  
4/6 MODELING 2 - Protein Simulation II   25s2  
4/8 Quiz on 2nd Half      
4/13 MODELING 3 - Protein Simulation III   25s3  
4/15 MODELING 4 - Protein Simulation IV   25s4  
4/20 MODELING 5 - Protein Simulation V   25s5  
4/22 Final Presentations      
4/24 *YALE* Classes end; Reading period begins      
4/29 *YALE* Final examinations begin      
5/6 *YALE* Final examinations end      

Lecture Slide Pack

# Topic PDF PPT Youtube (‘21) MPEG Lecture Summary
26i1-26i2a Introduction to Biomedical Data Science & Introduction to Personal Genomes x x i1,i2a 25i1-i2a 26i1-26i2a
26i2b An Individual’s Perspective on Personal Genomes x       26i2b
             
26d3 DATA - Proteomics I - Proteins x,Study Guide   D3   26d3
26d4 DATA - Proteomics II - Structure x   D4   26d4
             
26d1 DATA - Genomics I x   D1   26d1
26d2 DATA - Genomics II x   D2   26d2
             
26d5 Knowledge Representation & Databases x     26d5 26d5
             
26d6 ELSI issues x x   26d6 26d6
             
26m3 Sequence Comparison x x   26m3 26m3
26m4 Multiple Sequence Comparison x x   26m4 26m4
26m5 Fast Alignment x x     26m5
26m6a Variant Identification x x     26m6a
26m6b 1000 Genome + PCAWG summary x x     26m6b
             
26m7-part1 Multi-omic Analyses & Endophenotypes (RNA-seq & ChIP-seq) x x     26m7p1
26m7-part2 Multi-omic Analyses & Endophenotypes (AS, GWAS & eQTL) x x     26m7p2
26m7-part3 Multi-omic Analyses & Endophenotypes (Biosensors) x x     26m7p3
             
26m8a+b Supervised Mining: Preliminaries + Decision Trees x x     26m8a+b
26m9a Unsupervised Data Mining - Clustering x x     26m9a
26m9c Unsupervised Data Mining - SVD x x     26m9c
             
26m10a Networks - Intro x x     26m10a
26m10b Networks - Quantities x x     26m10b+c
26m10c Networks - Generation x x      
26m10e Networks - Network Prediction x x     26m10e
             
26t3 Deep Learning Fundamentals #1 x x     26t3
26t4 Deep Learning Fundamentals #2 x       26t4
             
26t2 Biomedical Image Analysis x       26t2
26t5 RNN+GNN x x     26t5
26t6 Gen AI x x     26t6
             
26m12 Deep Learning Advanced x        
26h1 Single Cell x        
26h2 Privacy x