Course Modules

Welcome to 6.8701

Welcome to 6.8701 Welcome to 6.8701

Page

Home Page Poster Home Page Poster 1
wiki_page 1168955 0

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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
external_url 1210939 0

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External Url

Recitation recordings playlist Recitation recordings playlist 2
external_url 1210941 0

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External Url

Lecture Notes / Book Chapters Lecture Notes / Book Chapters 3
external_url 1210942 0

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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
attachment 1174582 0

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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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Attachment

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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Attachment

Lecture13_IntroDrugDevelopment.pdf Lecture13_IntroDrugDevelopment.pdf 14
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Attachment

Lecture14_Intro_Small_Molecules.pdf Lecture14_Intro_Small_Molecules.pdf 15
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Attachment

Lecture15_GeneratingSmallMolecules.pdf Lecture15_GeneratingSmallMolecules.pdf 16
attachment 1209990 0

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Attachment

Lecture16_TrainingDeepNetworks.pdf Lecture16_TrainingDeepNetworks.pdf 17
attachment 1209991 0

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Attachment

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
assignment 1155192 1

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Assignment

PSET 3 PSET 3 44 4
assignment 1155193 1

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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
attachment 1155198 0

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Attachment

MLCB23.suggested_papers_list.xlsx MLCB23.suggested_papers_list.xlsx 2
attachment 1155199 0

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Attachment

paper_summary_example1.pdf paper_summary_example1.pdf 3
attachment 1155200 0

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Attachment

paper_summary_example2.pdf paper_summary_example2.pdf 4
attachment 1155201 0

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Attachment

paper_summary_example3.pdf paper_summary_example3.pdf 5
attachment 1155202 0

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Attachment

ProjectProposal_Template.docx ProjectProposal_Template.docx 6
attachment 1155203 0

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Quiz Resources

Quiz Resources Quiz Resources

Attachment

Past_quiz_2021.pdf Past_quiz_2021.pdf 1
attachment 1155210 0

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Attachment

Past_quiz_2021_solutions.pdf Past_quiz_2021_solutions.pdf 3
attachment 1155212 0

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Attachment

MLCB_2023_Quiz5.pdf MLCB_2023_Quiz5.pdf 4
attachment 1206627 0

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Attachment

MLCB_2023_Quiz5_solution.pdf MLCB_2023_Quiz5_solution.pdf 5
attachment 1209434 0

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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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Attachment

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
attachment 1155169 0

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Attachment

Lecture02_ExpressionClusteringClassification.pdf Lecture02_ExpressionClusteringClassification.pdf 4
attachment 1155170 0

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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
attachment 1155176 0

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Attachment

Lecture09_ProteinFolding.pdf Lecture09_ProteinFolding.pdf 11
attachment 1155177 0

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Attachment

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
attachment 1155179 0

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Attachment

Lecture12_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf Lecture12_DiseaseMechanism_Circuitry_eQTLs_Heritability.pdf 14
attachment 1155180 0

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Attachment

Lecture13_SingleCellGenomics2b.pdf Lecture13_SingleCellGenomics2b.pdf 15
attachment 1155181 0

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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
attachment 1155183 0

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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
attachment 1155185 0

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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
attachment 1155187 0

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Attachment

Lecture20_Immunology.pdf Lecture20_Immunology.pdf 22
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Attachment

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