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    
2/10 MINING - Seq. Comparison (con’t) + Multi-seq Alignment + Fast Alignment 25m3, 25m4, 25m5 23m3, 23m4, 23m5    
2/12 MINING - Variant Calling (incl. a focused section on SVs)+ Basic Multi-Omics 25m6a,23m6b, 23m7-pt1 23m6a, 23m6b,23m7    
2/17 Quiz on 1st Half quiz1 study guide      
2/19 MINING - Supervised Mining #2 + Deep Learning Fundamentals #1   23m8b,23m8c    
2/24 MINING - Deep Learning Fundamentals #2 + Unsupervised Mining #1   23m9a,23m9c    
2/26 MINING - Unsupervised Mining #2 + Single-Cell Analysis #1   23m9d, 23m9e    
3/3 MINING - Single-Cell Analysis #2 + Biomedical Image Analysis   23t1    
3/5 MINING - Network Analysis   23m10a, 23m10b, 23m10c, 23m10d, 23m10e    
           
           
3/7 Spring break begins        
           
3/24 MINING - Privacy   23m11a, 23m11b    
3/26 MINING/MODELING - Deep Learning Advanced I   23m12a    
3/31 MINING/MODELING - Deep Learning Advanced II   23m12b    
4/2 SIMULATION - Protein Simulation I   23s1    
4/7 SIMULATION - Protein Simulation II   23s2    
4/9 SIMULATION - Protein Simulation III   23s3    
4/14 SIMULATION - Protein Simulation IV   23s4    
4/16 SIMULATION - Protein Simulation V   23s5    
4/21 Quiz on 2nd Half        
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 unless indicated otherwise)
MPEG (2021)
25i1 Introduction to Biomedical Data Science x x I1 I1
25i2a Introduction to Personal Genomes     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 part1 part1 M7 M7
           
25m8a Supervised Data Mining - Decision Trees     M8a M8a
25m8b Supervised Data Mining - ROC & Cross-validation     M8b M8b
25m8c Supervised Data Mining - SVMs     M8c M8c
           
25t3 Deep Learning Fundamentals I        
25t4 Deep Learning Fundamentals II        
           
25m9a Unsupervised Data Mining - Clustering     M9a M9a
25m9c Unsupervised Data Mining - SVD     M9c M9c
25m9d Unsupervised Data Mining - SVD extensions     M9d M9d
           
25m9e Single Cell Analysis       23m9e
25t1 Single Cell part 2 (mabye should renumber this!!)       23t1
           
25m10a Networks - Intro     M10a M10a
25m10b Networks - Network Quantities     M10b M10b
25m10c Networks - Network Generation Models     M10c M10c
25m10d Networks - Network Toplogy Analysis     M10d M10d
25m10e Networks - Network Prediction       23m10e
           
25i3 Transition - Mining to Modeling       23i3
           
25m11a Privacy in Biomedical Data Science (esp. Genomic Privacy)        
25m11b Privacy in Biomedical Data Science (esp. Genomic Privacy)        
           
25t2 Image Analysis       22m11
           
25m12a Deep Learning III     M12a M12a
25m12b Deep Learning IV     M12b M12b
           
25s1 Protein Folding     S1 S1
25s2 Core Repacking     S2 S2
25s3 NMR Structures     S3 S3
25s4 Intrinsically Disordered Proteins     S4 S4
25s5 Simulation        

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