Please see last year’s syllabus (with slide packs & videos 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 ‘21, an updated video will also be posted.)

Date Topic This year’s lecture Last year’s lecture Comment
1/25 *YALE* Spring term classes begin, 8.20 a.m.      
1/26 Introduction 22i1 I1 l1 took ~45’. Rest going over syllabus
1/31 DATA - Genomics I 22d1 D1  
2/2 DATA - Genomics II 22d2 D2  
2/7 DATA - Proteomics I 22d3 D3  
2/9 DATA - Proteomics II 22d3, 22d4 D4  
2/14 DATA - Personal Genomes Intro. + Starting Seq. Comparison 22i2a, 22m3, 22m4 I2a,M3,M4  
2/16 MINING - More Personal Genomes (now with an individual’s perspective) + more Seq. Comparison 22i2b, 22m4 I2b,M4  
2/21 MINING - Fast Alignment + Variant Calling & Stats (incl. a focused section on SVs) 22m5,22m6a,22m6b M5,M6a Stopped in 22m6b before PCAWG section
2/23 MINING - Knowledge Representation & Databases 22d5 D5  
2/28 MINING - Basic Multi-Omics + Supervised Mining 22m6b,22m7,22m8a M6b, M7,M8a Stopped in 22m8a before decision trees
3/2 MINING - Supervised Mining 22m8a,22m8b,22m8c,22m9a M8a,M8b,M8c,M9a Stopped in 22m9a, almost at end
3/7 MINING - Unsupervised Mining 22m9a,22m9b,22m9c,22m9d M9a,M9b,M9c,M9d  
3/9 MINING - Network Analysis + Textmining [MG + TF] 22t1,22m10a,22m10b,22m10c M10a,M10b,M10c  
3/14 MINING - Biosensor analysis & Privacy [MG + TF] 22t2,22m11    
3/16 Quiz on 1st Half     quiz 1 study guide
3/18 Spring break begins      
3/28 MINING/MODELLING - Deep Learning I 22m12a M12a  
3/30 MINING/MODELLING - Deep Learning II 22m12b M12b  
4/4 MINING/MODELLING - Deep Learning III 22m12c M12c  
4/11 MODELLING - Protein Simulation I 22s1 S1  
4/13 MODELLING - Protein Simulation II 22s1, 22s2 S2a  
4/18 MODELLING - Protein Simulation III 22s2, 22s3 S2b  
4/20 MODELLING - Protein Simulation IV 22s4 S3  
4/22 MODELLING - Protein Simulation V 22s5   Happening in place of morning section on Fri 4/22
4/25 Quiz on 2nd Half     quiz 2 study guide
4/27 Final Presentations      
4/29 *YALE* Classes end; Reading period begins      
5/6 *YALE* Final examinations begin      
5/11 *YALE* Final examinations end      

Lecture Slide Pack

# Topic PDF PPT
22i1 Introduction to Biomedical Data Science x x
22i2a Introduction to Personal Genomes x x
22i2b An Individual’s Perspective on Personal Genomes x  
22d1 DATA - Genomics I x  
22d2 DATA - Genomics II x  
22d3 DATA - Proteomics I - Proteins x  
22d4 DATA - Proteomics II - Structure x  
22d5 Knowledge Representation & Databases x x
22m3 Sequence Comparison x x
22m4 Multiple Sequence Comparison x x
22m5 Fast Alignment x x
22m6a Variant Identification, Focusing on SVs x x
22m6b 1000 Genome + PCAWG summary x x
22m7 Basic Multi-omics (pipeline processing) x x
22m8a Supervised Data Mining - Decision Trees x x
22m8b Supervised Data Mining - ROC & Cross-validation x x
22m8c Supervised Data Mining - SVMs x x
22m9a Unsupervised Data Mining - Clustering x x
22m9b Unsupervised Data Mining - Community Detection x x
22m9c Unsupervised Data Mining - SVD x x
22m9d Unsupervised Data Mining - RCA & CCA x x
22m10a Networks - Intro x x
22m10b Networks - Network Quantities x x
22m10c Networks - Network Generation Models x x
22t1 Biomedical Text Mining Intro x x
22m11 Biosensor Analysis [mp4] x x
22t2 Privacy in Biomedical Data Science (esp. Genomic Privacy) x x
22m12a Deep Learning I x x
22m12b Deep Learning II x x
22m12c Deep Learning III x x
22s1 Protein Folding x x
22s2 Core Repacking x x
22s3 NMR Structures x x
22s4 Intrinsically Disordered Proteins x x
22s5 Simulation    

See lab permissions statement in relation to resusing any of the above material.