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.

Date Topic This year’s lecture Last year’s lecture Comment
1/17 *YALE* Spring term classes begin, 8.20 a.m.      
         
1/18 Introduction 23i1 22i1  
1/23 DATA 1 - Genomics I 23d1 22d1  
1/25 DATA 2 - Genomics II 23d2 22d2  
1/30 DATA 3 - Proteomics I 23d3 22d3  
2/1 DATA 4 - Proteomics II 23d4 22d4  
2/6 MINING 1 - Personal Genomes + Seq. Comparison + Multi-seq Alignment 23i2a, 23m3, 23m4 22i2a, 22m3, 22m4  
2/8 MINING 2 - Fast Alignment + Variant Calling (incl. a focused section on SVs) 23m5,23m6a 22m5,22m6a,22m6b  
2/13 MINING 3 - Basic Multi-Omics Supervised Mining #1 23m6b,23m7,23m8a 22m6b,22m7,22m8a  
2/15 MINING 4 - Supervised Mining #2 + Unsupervised Mining #1 23m8b,23m8c,23m9a,23m9c 22m8a,22m8b,22m8c,22m9a  
2/20 DATA 5 - Knowledge Representation & Databases 23d5 22d5  
2/22 MINING 5 - Unsupervised Mining #2 + Single-Cell Analysis 23m9d, 23m9e 22m9d  
2/27 Quiz on 1st Half quiz 1 study guide   quiz 1 answer key
3/1 TOPICS 1 - Single-Cell Analysis (continues) + Privacy 23t1, 23t2 22t2  
3/6 TOPICS 2 - Network Analysis 23m10a, 23m10b, 23m10c, 23m10d, 23m10e 22m10a,22m10b,22m10c,M10d  
3/8 TOPICS 3 - Personal Genomes (from an individual’s perspective) 23i2b 22i2b  
         
         
3/10 Spring break begins      
         
3/27 TOPICS 4 - Deep Learning Fundamentals 23m12a 22m12a  
3/29 TOPICS 5 - Deep Learning Fundamentals (continues) 23m12b 22m12b  
4/3 TOPICS 6 - Deep Learning for Biology + Biosensor Data Analysis 22t3, 22t4    
4/5 MODELING 1 - Protein Simulation I 23s1 22s1  
4/10 MODELING 2 - Protein Simulation II 23s2 22s1, 22s2  
4/12 MODELING 3 - Protein Simulation III 23s3 22s2, 22s3  
4/17 MODELING 4 - Protein Simulation IV 23s4 22s4  
4/19 MODELING 5 - Protein Simulation V   22s5  
4/24 Quiz on 2nd Half quiz 2 study guide   quiz 2 answer key
4/26 Final Presentations      
4/28 *YALE* Classes end; Reading period begins      
5/4 *YALE* Final examinations begin      
5/10 *YALE* Final examinations end      

Lecture Slide Pack

See also additional readings for each topic: Additional Readings

# Topic PDF PPT Youtube
(‘21 unless indicated otherwise)		 MPEG (2021)
23i1 Introduction to Biomedical Data Science x x I1 I1
23i2a Introduction to Personal Genomes x x I2a  
23i2b An Individual’s Perspective on Personal Genomes x x I2b i2b
           
23d1 DATA - Genomics I x   D1 D1
23d2 DATA - Genomics II x   D2 D2
           
23d3 DATA - Proteomics I - Proteins x   D3  
23d4 DATA - Proteomics II - Structure x   D4  
           
23d5 Knowledge Representation & Databases x x D5 D5
           
23m3 Sequence Comparison x x M3 M3
23m4 Multiple Sequence Comparison x x M4 M4
23m5 Fast Alignment x x M5 M5
23m6a Variant Identification, Focusing on SVs x x M6a M6a
23m6b 1000 Genome + PCAWG summary x x M6b M6b
           
23m7 Basic Multi-omics (pipeline processing) x x M7 M7
           
23m8a Supervised Data Mining - Decision Trees x x M8a M8a
23m8b Supervised Data Mining - ROC & Cross-validation x x M8b M8b
23m8c Supervised Data Mining - SVMs x x M8c M8c
           
23m9a Unsupervised Data Mining - Clustering x x M9a M9a
23m9c Unsupervised Data Mining - SVD x x M9c M9c
23m9d Unsupervised Data Mining - SVD extensions x x M9d M9d
           
23m9e Single Cell Analysis x x   23m9e
23t1 Single Cell part 2 x x   23t1
           
23m10a Networks - Intro x x M10a M10a
23m10b Networks - Network Quantities x x M10b M10b
23m10c Networks - Network Generation Models x x M10c M10c
23m10d Networks - Network Toplogy Analysis x x M10d M10d
23m10e Networks - Network Prediction x x   23m10e
           
23i3 Transition - Mining to Modeling x x   23i3
           
23t2 Privacy in Biomedical Data Science (esp. Genomic Privacy) x x    
23t3 Biosensor Analysis x x   22m11
           
23m12a Deep Learning I x   M12a M12a
23m12b Deep Learning II x   M12b M12b
23t4 Deep Learning for Biology x     23t4
           
23s1 Protein Folding x x S1 S1
23s2 Core Repacking x x S2 S2
23s3 NMR Structures x x S3 S3
23s4 Intrinsically Disordered Proteins x x S4 S4
23s5 Simulation        

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