Course Modules

Welcome to 6.8701

Welcome to 6.8701 Welcome to 6.8701

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Home Page Poster Home Page Poster 1

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Lecture Videos + Recitations + Notes / Book Chapters

Lecture Videos + Recitations + Notes / Book Chapters Lecture Videos + Recitations + Notes / Book Chapters

External Url

Lecture Videos Playlist Lecture Videos Playlist 1

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External Url

Recitation recordings playlist Recitation recordings playlist 2

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External Url

Lecture Notes / Book Chapters Lecture Notes / Book Chapters 3

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Class Syllabus and Schedule

Class Syllabus and Schedule Class Syllabus and Schedule

Attachment

MLCB24 Class topics.pdf MLCB24 Class topics.pdf 3

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Lecture slides - Fall 2024

Lecture slides - Fall 2024 Lecture slides - Fall 2024

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Lecture 1: Introduction (09/05/24) Lecture 1: Introduction (09/05/24) 1

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Lecture 2: Expression, Clustering, Classification (09/10/24) Lecture 2: Expression, Clustering, Classification (09/10/24) 2

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Lecture 3: Single Cell Genomics (09/12/24) Lecture 3: Single Cell Genomics (09/12/24) 3

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Lecture 4: Sequential Pattern Matching, Alignment, DP, Hashing (09/17/24) Lecture 4: Sequential Pattern Matching, Alignment, DP, Hashing (09/17/24) 4

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Lecture 5: Epigenomics and HMMs (09/19/24) Lecture 5: Epigenomics and HMMs (09/19/24) 5

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Lecture 6: Regulatory Genomics (9/24/24) Lecture 6: Regulatory Genomics (9/24/24) 6

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Lecture 7: Regulatory Networks (09/26/2024) Lecture 7: Regulatory Networks (09/26/2024) 7

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Lecture 8: Intro. Structural Biology (10/01/24) Lecture 8: Intro. Structural Biology (10/01/24) 8

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Lecture 9: Protein Folding (10/03/24) Lecture 9: Protein Folding (10/03/24) 9

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Lecture 10: Transformers and LLMs (10/08/24) Lecture 10: Transformers and LLMs (10/08/24) 10

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Lecture 11: PLMs and Transfer Learning (10/10/24) Lecture 11: PLMs and Transfer Learning (10/10/24) 11

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Lecture 12: DNA Language Models (10/17/24) Lecture 12: DNA Language Models (10/17/24) 12

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Lecture 13: Drug Development (10/22/24) Lecture 13: Drug Development (10/22/24) 13

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Lecture 14: Intro. Small Molecules (10/24/24) Lecture 14: Intro. Small Molecules (10/24/24) 14

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Lecture 15: Generating Small Molecules (10/29/24) Lecture 15: Generating Small Molecules (10/29/24) 15

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Lecture 16: Training Deep Networks (10/31/24) Lecture 16: Training Deep Networks (10/31/24) 16

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Lecture 17: Disease Association Mapping (11/05/24) Lecture 17: Disease Association Mapping (11/05/24) 17

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Lecture 18: Quantitative Trait Mapping (11/07/24) Lecture 18: Quantitative Trait Mapping (11/07/24) 18

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Lecture 19: Electronic Health Records (11/12/24) Lecture 19: Electronic Health Records (11/12/24) 19

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Lecture 20: In-Class Quiz (11/14/24) Lecture 20: In-Class Quiz (11/14/24) 20

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Lecture 21: Imaging Methods (11/19/24) Lecture 21: Imaging Methods (11/19/24) 21

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Lecture 22: Comparative Genomics (11/21/24) Lecture 22: Comparative Genomics (11/21/24) 22

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Lecture 23: Evolution (11/26/24) Lecture 23: Evolution (11/26/24) 23

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Lecture 24: Modeling Metabolism (12/03/24) Lecture 24: Modeling Metabolism (12/03/24) 24

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Lecture 25: Measuring Metabolism (12/05/24) Lecture 25: Measuring Metabolism (12/05/24) 25

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Lecture 26: Project Presentations (12/10/24) Lecture 26: Project Presentations (12/10/24) 26

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Book Chapters / Lecture Notes - Fall 2024

Book Chapters / Lecture Notes - Fall 2024 Book Chapters / Lecture Notes - Fall 2024

Attachment

Lecture01_Introduction_FA24.pdf Lecture01_Introduction_FA24.pdf 1

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Attachment

Lecture02_ExpressionClusteringClassificationChap.pdf Lecture02_ExpressionClusteringClassificationChap.pdf 2

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Attachment

Lecture03_SingleCellGenomics.pdf Lecture03_SingleCellGenomics.pdf 3

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Attachment

Lecture04_DynamicProgramming+BLAST.pdf Lecture04_DynamicProgramming+BLAST.pdf 4

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Attachment

Lecture05_Epigenomics_HMMs.pdf Lecture05_Epigenomics_HMMs.pdf 5

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Attachment

Lecture06_RegulatoryGenomics.pdf Lecture06_RegulatoryGenomics.pdf 6

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Attachment

Lecture07_RegulatoryNetworks.pdf Lecture07_RegulatoryNetworks.pdf 7

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Attachment

Lecture08_IntroToProteinStructure.pdf Lecture08_IntroToProteinStructure.pdf 8

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Attachment

Lecture09_AlgorithmsForProteinStructure.pdf Lecture09_AlgorithmsForProteinStructure.pdf 9

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Lecture10_AlgorithmsForProteinStructure.pdf Lecture10_AlgorithmsForProteinStructure.pdf 10

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Attachment

Lecture11_ProteinLanguageModels.pdf Lecture11_ProteinLanguageModels.pdf 12

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Attachment

Lecture12_DNALanguageModels.pdf Lecture12_DNALanguageModels.pdf 13

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Lecture13_IntroDrugDevelopment.pdf Lecture13_IntroDrugDevelopment.pdf 14

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Lecture14_Intro_Small_Molecules.pdf Lecture14_Intro_Small_Molecules.pdf 15

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Attachment

Lecture15_GeneratingSmallMolecules.pdf Lecture15_GeneratingSmallMolecules.pdf 16

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Attachment

Lecture16_TrainingDeepNetworks.pdf Lecture16_TrainingDeepNetworks.pdf 17

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Lecture17_Genetics_GWAS_PRS_Mechanism.pdf Lecture17_Genetics_GWAS_PRS_Mechanism.pdf 18

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Attachment

Lecture18_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf Lecture18_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf 19

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PSETs

PSETs PSETs

Assignment

PSET 0 PSET 0 3 1

assignment 1174589 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

PSET 1 PSET 1 9 2

assignment 1155191 1

Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Assignment

PSET 2 PSET 2 28 3

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Assignment

PSET 3 PSET 3 44 4

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Previous Papers & Projects Proposal Description

Previous Papers & Projects Proposal Description Previous Papers & Projects Proposal Description

Attachment

PreviousPaperDescription_Template.docx PreviousPaperDescription_Template.docx 1

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Attachment

MLCB23.suggested_papers_list.xlsx MLCB23.suggested_papers_list.xlsx 2

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Attachment

paper_summary_example1.pdf paper_summary_example1.pdf 3

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Attachment

paper_summary_example2.pdf paper_summary_example2.pdf 4

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Attachment

paper_summary_example3.pdf paper_summary_example3.pdf 5

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Attachment

ProjectProposal_Template.docx ProjectProposal_Template.docx 6

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Quiz Resources

Quiz Resources Quiz Resources

Attachment

Past_quiz_2021.pdf Past_quiz_2021.pdf 1

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Attachment

Past_quiz_2021_solutions.pdf Past_quiz_2021_solutions.pdf 3

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Attachment

MLCB_2023_Quiz5.pdf MLCB_2023_Quiz5.pdf 4

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Attachment

MLCB_2023_Quiz5_solution.pdf MLCB_2023_Quiz5_solution.pdf 5

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Page

Lecture Transcript Study Guide Lecture Transcript Study Guide 6

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Attachment

quiz22_solutions.pdf quiz22_solutions.pdf 7

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Quiz2022.pdf Quiz2022.pdf 8

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Lecture Slides - Fall 2023

Lecture Slides - Fall 2023 Lecture Slides - Fall 2023

Attachment

Lecture01_Introduction.pdf Lecture01_Introduction.pdf 3

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Attachment

Lecture02_ExpressionClusteringClassification.pdf Lecture02_ExpressionClusteringClassification.pdf 4

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Attachment

Lecture03_DynamicProgramming+BLAST.pdf Lecture03_DynamicProgramming+BLAST.pdf 5

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Attachment

Lecture04_Epigenomics_HMMs.pdf Lecture04_Epigenomics_HMMs.pdf 6

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Attachment

Lecture05a_RegulatoryGenomics_TRIM.pdf Lecture05a_RegulatoryGenomics_TRIM.pdf 7

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Attachment

Lecture06_MolecularModeling.pdf Lecture06_MolecularModeling.pdf 8

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Attachment

Lecture07_MolecularModeling+GenerativeModels.pdf Lecture07_MolecularModeling+GenerativeModels.pdf 9

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Attachment

Lecture08_ProteinLanguageModels.pdf Lecture08_ProteinLanguageModels.pdf 10

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Attachment

Lecture09_ProteinFolding.pdf Lecture09_ProteinFolding.pdf 11

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Lecture10_Docking.pdf Lecture10_Docking.pdf 12

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Attachment

Lecture11_Genetics_GWAS_PRS_Mechanism.pdf Lecture11_Genetics_GWAS_PRS_Mechanism.pdf 13

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Attachment

Lecture12_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf Lecture12_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf 14

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Attachment

Lecture13_SingleCellGenomics2b.pdf Lecture13_SingleCellGenomics2b.pdf 15

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Attachment

Lecture14_Networks1_InferenceAnalysis-v2.pdf Lecture14_Networks1_InferenceAnalysis-v2.pdf 16

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Attachment

Lecture15_EHR_Biobanks.pdf Lecture15_EHR_Biobanks.pdf 17

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Attachment

Lecture16_ComputerVision_Biology.pdf Lecture16_ComputerVision_Biology.pdf 18

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Attachment

Lecture17_ComparativeGenomics.pdf Lecture17_ComparativeGenomics.pdf 19

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Attachment

Lecture18a_Phylogenetics.pdf Lecture18a_Phylogenetics.pdf 20

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Attachment

Lecture19_Evolution_part3.pdf Lecture19_Evolution_part3.pdf 21

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Lecture20_Immunology.pdf Lecture20_Immunology.pdf 22

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Lecture21_Metabolism.pdf Lecture21_Metabolism.pdf 23

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Attachment

Lecture23_ProteinDesign.pdf Lecture23_ProteinDesign.pdf 24

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Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete